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https://f1000research.com/articles/10-86/v1
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09 Feb 21
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{
"type": "Research Article",
"title": "Clustering of childhood cancer in Colombia: a nationwide study",
"authors": [
"Edgar F. Manrique-Hernández",
"Marcela Pilar Rojas Díaz",
"Laura Andrea Rodriguez-Villamizar",
"Edgar F. Manrique-Hernández",
"Marcela Pilar Rojas Díaz"
],
"abstract": "Background: Childhood cancer is considered one the most important causes of death in children and adolescents, despite having a low incidence in this population. Spatial analysis has been previously used for the study of childhood cancer to study the geographical distribution of leukemias. This study aimed to identify the presence of space-time clusters of childhood of cancer excluding leukemia in Colombia between 2014 and 2017. Methods: All incident cancer cases (excluding leukemia) in children under the age of 15 years that had been confirmed by the National Surveillance System of Childhood Cancer between 2014 and 2017 were included. Kulldorf’s circular scan test was used to identify clusters using the municipality of residence as the spatial unit of analysis and the year of diagnosis as the temporal unit of analysis. A sensitivity analysis was conducted with different upper limit parameters for the at-risk population. Results: A total of 2006 cases of non-leukemia childhood cancer were analyzed, distributed in 432 municipalities with a mean annual incidence rate of 44 cases per million children under the age of 15. Central nervous system (CNS) tumors were the most frequent type. Four spatial clusters and two space-time clusters were identified in the central and southwest regions of the country. In the analysis for CNS tumors, a spatial cluster was identified in the central region of the country. Conclusions: The distribution of non-leukemia childhood cancer seems to have a clustered distribution in some Colombian regions that may suggest infectious or environmental factors associated with its incidence.",
"keywords": [
"Cluster Analysis",
"Neoplasms",
"Childhood",
"Epidemiology",
"Colombia"
],
"content": "Introduction\n\nChildhood cancer (CC) is considered one the most important causes of death in children and adolescents, despite having a low incidence in this population. The mean annual incidence of CC was estimated at 140.6 cases per million children between the age 0–14 years in the period of 2001 to 20101. The world health organization (WHO) estimates that nearly 300,000 new cases of CC are diagnosed every year in children between 0 and 19 years of age2. In the Americas it has been estimated that every year there are approximately 27,000 new cases of cancer in children under the age of 14 years, with an estimated mortality rate of 10,000 deaths/year3. The majority of the incident cases in the Americas belong to the Latin American and Caribbean region making up nearly 65% of the diagnosed cases3.\n\nCC is a set of diseases that does not have a clear etiology yet. There are several conditions that have been identified as risk factors which include genetic factors, some infectious diseases, exposure to pesticides, benzene and radiation, alcohol consumption during pregnancy, smoking, and the socioeconomic condition of the family4,5. Some of these factors are more specific than others, as was found with Burkitt´s and Hodgkin´s lymphoma, where the Epstein-Barr virus plays a relevant role. However, there are still controversies surrounding the etiology of these diseases5.\n\nSpatial analysis allows the identification of geographical patterns of health and disease related events that point out variations between populations contributing to the generation of hypotheses about possible etiologies6. Spatial analysis has been previously used for the study of CC, mainly for studying the geographical distribution of leukemias4,7, since this type of analysis allows for the identification of space and time variations in a geographical area that generate clusters that indicate an increase in the tendency of the cases4. Clusters of acute childhood leukemia have been identified in Colombia8, but analyses for CC other than leukemia are scarce5. The objective of this study was to perform an exploratory study with space-time aggrupation to identify clusters of incident cases of CC other than leukemia in Colombian municipalities between 2014 and 2017.\n\n\nMethods\n\nColombia is a country located in the north of South America, which limits with Venezuela and Brazil to the east, Panama to the Northwest, Peru and Ecuador to the south; it limits to the Caribbean sea with Panama, Costa Rica, Nicaragua, Honduras, Jamaica, Haiti, Dominican Republic, Venezuela and to the Pacific ocean with Panama, Costa Rica and Ecuador. The Colombian population for 2018 was approximately 48 million people9. Women make up 51.2% of the population, and children under the age of 15 years make up 22.6% compared to adults over the age of 65 years which represent 9.1%. Most of the Colombian population live in urban areas (77.1%)9.\n\nAll incident cases of non-leukemia CC diagnosed in children under 15 years of age between 2014 and 2017 were included. The data source was the National Surveillance System for Public Health (SIVIGILA, for its name in Spanish)10, which registers the newly confirmed and probable cases of CC in a systematic and mandatory manner. Surveillance for CC started in Colombia in 2008 with the registry of childhood leukemia cases and starting in 2013 the system registers all types of CC11. SIVIGILA verifies the confirmation of reported cases according to the results of diagnostic tests such as myelograms, immunotyping, histopathology or cytogenetic tests; adjusting the real number of confirmed cases and the diagnosis date. De-identified non-leukemia CC data were provided by the National Health Institute (INS for its name in Spanish), allowing access to the following variables: municipality of residence, date of birth, diagnosis date and type of CC according to the International Classification of Childhood Cancer, Third Edition (ICCC-3). Cases were assigned a consecutive number which cannot be used to identify cases. SIVIGILA is the most complete registry of CC in Colombia, taking into account that it has a nationwide coverage and the reports are updated weekly8.\n\nData from CNS and miscellaneous intracranial and intraspinal neoplasms (Group III) cases according to the ICCC-312 was extracted for a sub-analysis. This group is the second with the highest incidence after leukemias5,13.\n\nData for the at-risk population in the 1122 municipalities of Colombia was provided by the National Department of Statistics (DANE for its name in Spanish)10 which performed its last national census in 2018. For the calculation of the population between the years 2014 and 2017 the dynamics of DANE projections of population was used, and an interpolation of the population was conducted for each one of the municipalities for previous years14. The calculation of the coordinates (longitude and latitude) of the centroid of each municipality was done in QGIS version 3.16.3 using free cartographic information from the DANE Geoportal15.\n\nWe performed a descriptive analysis calculating frequencies and central tendency measurements. The incidence of CC was calculated for each municipality and a direct standardization by age and sex of the incidence rates was conducted using as reference the structure of children population for Colombia in 2017. Standardized rates and their respective confidence interval were obtained through STATA® version 14. The global Moran index was calculated to estimate the spatial autocorrelation. Choroplethic maps were built in order to visualize the standardized rates using the WGS84 projection for Colombia and the cartographic archives available for each municipality in the DANE cartography site using QGIS version 3.16.315.\n\nKuldorff’s circular scan test was used to identify spatial and spatio-temporal clusters16, using the SaTScan® software version 9.6. This is a spatial hypothesis test that runs consecutive scans in the study area with different circumference radii that increase in size; the null hypothesis of the test is that the risk of the event (in this case risk of non-leukemia CC) within the circle is the same as outside the scanned area. Space and space-time exploratory analysis were run using a Poisson distribution and scanning for high rates; the space analysis unit was the municipality of residence and the time analysis unit was the year of diagnosis. We used an upper limit of the population at risk of 25% and for a sensitivity analysis we assess the results using upper limits of 50% and 10%.\n\nThis research received ethical approval from the ethics committee of scientific research at the Universidad Industrial de Santander (CEINCI UIS), on October 27, 2017 (approval number 24-2017).\n\n\nResults\n\nSIVIGILA reported 2737 cases of non-leukemia CC between January 1st 2014 and December 31st 2017. A total of 731 cases were excluded for different reasons (Figure 1). Therefore, a total of 2006 cases were included for the analysis, which were reported in 432 of the 1122 municipalities of Colombia (38.5%). Subsequently, for the analysis of CNS tumors those who were included in the ICCC-3 classification group III were selected, obtaining 603 cases reported in 201 municipalities (17.9%).\n\nA slight majority of reported cases corresponded to males (54.74%) and 70.49% were reported in children under 9 years of age (0–4 years 33.5%, 5–9 years 36.99%, 10–14 years 29.51%). The mean annual incidence rate of non-leukemia CC was of 44 cases per million children under 15 years of age between 2014 and 2017 in Colombia. The highest incidence rates were reported in Meta (Villavicencio), Bogota D.C., Santander (Bucaramanga, Floridablanca), Bolivar (Cartagena), Valle del Cauca (Cali), Antioquia (Medellin), Cundinamarca (Soacha), Nariño (Pasto). The standardized rates by age and sex varied between 0 and 198 cases per million inhabitants under 15 years of age (Figure 2). The Moran index was of 0.0023 (p=0.211) which indicates a low spatial autocorrelation of the incidence rates across Colombian municipalities.\n\nFor CNS tumors, again the slight majority of cases were reported in the male population (55.39%) and the 71.97% of the cases were reported in children under the age of 9 (0–4 years, 30.35%; 5–9 years, 41.63%; 10–14 years, 28.03%). The departments with the highest number of cases were Bogota D.C, Valle del Cauca (Cali and Palmira), Antioquia (Medellin), Bolivar (Cartagena), Meta (Villavicencio), Santander (Bucaramanga), Cundinamarca (Soacha) and Nariño (Pasto).\n\nWe identified four clusters in the spatial analysis for non-leukemia CC (Figure 3). The first cluster in the central region of the country included 327 municipalities distributed in the following departments: Cundinamarca (95), Meta (6), Boyaca (122), Santander (76), Antioquia (7), Caldas (4), Casanare (13), Tolima (3) and Bogota D.C\n\nThis cluster has a radius of 172.11 Km and 798 cases, with an expected number of cases of 497.88 with a relative risk (RR)=2 and p value <0.0001. The second cluster was identified in the departments of Cundinamarca (57), Meta (7) and Bogota D.C. with a radius of 72.04 km, and superposition with the first cluster; in this cluster 623 cases were identified for a total of 358.29 expected cases with RR = 2.07 and p value <0.0001. The third cluster was identified in the southwest region of Colombia, corresponding to the city of Cali (Valle del Cauca) and without superposition with any other cluster. In this third cluster 152 cases were identified where 87.95 cases were expected, with a RR = 1.79 and a p value <0.0001. The fourth cluster was identified in 23 municipalities of the Santander (Northeast region) department, with a 58.50 km radius, super positioning with some municipalities from the first cluster; in this cluster there were 106 cases with 55.15 as the expected number of cases, obtaining a RR = 1.97 and a p value <0.0001.\n\nTwo clusters were identified in the space-time analysis for non-leukemia CC. The first cluster was located in the central region of the country corresponding to the following departments: Boyaca (122), Santander (76), Cundinamarca (95), Casanare (13), Meta (6), Caldas (4), Antioquia (7), Tolima (3), Bogota D.C. This cluster was identified between 2015 and 2016 with a radius of 172.11 Km, 491 cases reported with 249 expected obtaining a RR = 2.29 and p value <0.0001. The second cluster was identified in the city of Cali between 2016 and 2017, with 97 cases reported and 43.7 expected obtaining a RR = 2.28 and p value <0.0001.\n\nThe spatial analysis for CNS tumors identified one cluster in the following departments: Meta (27), Cundinamarca (86), Casanare (8), Huila (1), Tolima (8) and Bogota D.C. (Figure 4). This cluster has a radius of 177.43 km, with 237 cases reported and 122 expected for a RR = 2.55 and a p value <0.0001. The space-time analysis for CNS identified the same cluster in the central region corresponding to the following municipalities: Meta (16), Cundinamarca (95), Boyaca (30), Casanare (3), Tolima (1) and Bogota D.C. This cluster was identified between 2015 and 2016 with a radius of 112.53 km, with 143 cases reported and 58.9 expected obtaining a RR = 2.87 and p values <0.0001\n\nIn the sensitivity analysis for non-leukemia CC circular scan tests were run using values of the at-risk population of 10% and 50%. There were 304 identified municipalities in the central region of the country that showed consistency in the three analysis (using 10%, 25% and 50% upper limit of at-risk population) (Figure 5).\n\n\nDiscussion\n\nThis study identified the presence of non-leukemia CC clusters between 2014 and 2017 in Colombia, using information with nationwide coverage available in SIVIGILA. To our knowledge, this is the first nation-wide study in South America using spatial analysis to describe the distribution and clustering of non-leukemia CC.\n\nSpatial and spatio-temporal analysis have been previously used in this area, mainly in the study of the geographic pattern of leukemias7,17. A recent systematic review of space-time analysis identified 70 studies published up to 2016 of which 47 reported results for leukemias, 26 for lymphomas, 13 for CNS tumors and 12 for other types of tumors18. All 32 analyses used for the meta-analysis were from Europe and United States; this analysis showed evidence of leukemia clustering in children between 0 and 5 years of age. However, the evidence was not conclusive for lymphomas and CNS tumors.\n\nStudies of clustering for non-leukemia CC have been conducted in different continents showing some heterogeneity in their results. In Europe, Ortega et al.19 used elliptic analysis to identify clusters of CC in children under 15 years of age in Murcia, Spain between 1998 and 2009. This analysis identified a space-time cluster of lymphomas between 2011 and 2013. Also in Spain, a spatial case-control analysis between 1985 and 2015 including data from five autonomous regions explored the clustering of non-leukemia CC by site of residence and date of diagnosis; the authors found spatial clusters for all CC combined and for lymphomas at date of diagnosis, and for CNS embryonal tumors clustering at birth and diagnosis. The results, however, did not reach statistical significance for evidence of clustering when adjusted for multiple testing5.\n\nIn the Asian continent, a study in Palestine performed an analysis of CC clusters between 1998 and 2007 using the circular scan method; a greater clustering effect was found in metropolitan districts and one cluster of lymphomas was identified in an agricultural city between 1998 and 200220. In North America, Torabi and Rosychuk explored the presence of clusters of CC between 1983 and 2004 in the province of Alberta, Canada, using five different methods to analyze clustering, including circular scan tests. The study showed evidence of clustering to the south of the province but did not showed results by type of cancer21. In South America, in the province of Cordoba, Argentina, Agost reported one of the first studies in the region using the circular scan test to detect clusters of CC. Spatial clusters were found for leukemias, lymphoid neoplasms, CNS tumors and in the space-time analysis clusters of neuroblastoma and other peripheral tumors were also identified22.\n\nOverall, the European studies tend to report lack of evidence for CC clusters, whereas other continents (such as in this study) tend to show some clustering evidence. The heterogeneous nature of the findings could be related to different factors, primarily environmental conditions and the methods used. In classic epidemiology, the consistency of the results of association between exposure and events is core when assessing causality23. Nonetheless, in the spatial analysis the focus is on the description of the patterns and not the causality; this is why the heterogeneity of the results is important in these exploratory studies, since it can reflect conditions or exposures that may vary between and within populations.\n\nThe results of the studies can also differ due to the diversity of methods used. The spatial studies based on the analysis of areas (ecological approach) such as this study, and the studies in Canada and in Palestine20–22, seem to be more sensitive to the detection of clusters compared to the results of the studies based on point analysis (case-control studies) conducted in Europe5,13. We used an ecological approach for this first exploratory study because of the quality of information available in the country at municipality level and the absence of official data sources for selecting comparable controls. Kulldorf’s circular scan tests was chosen because it is optimal to detect clusters in a regular way, it has excellent performance detecting rare diseases in large populations such as CC24, and for its easy use through specific software that makes it standardized and reproducible.\n\nNon-leukemia CC clusters identified in Colombia are located mainly in the central region of the country near the mountain ranges that blend with large zones of agriculture and mining. These combined zones can generate special environments that allow the interaction of infectious agents, environmental, and occupational conditions that may have a space and time effect in the incidence of events such as CC. There is evidence that exposure to arsenic25 and pesticides26–28 is related to a greater risk of developing CC, especially leukemias, lymphomas and CNS tumors.\n\nOne of the main strengths of the study is the use of available information in the SIVIGILA that counts with nationwide coverage, a high-quality follow-up process, and the permanent adjustment of data by the National Health Institute. The inclusion of other types of CC, different to leukemia, in SIVIGILA was done in 2013; this is the reason we excluded this year from the study, in order to avoid bias in the reports during the transition period. Despite its systematic processes, SIVIGILA does not correspond to a specific population-based cancer registry, which operates in four Colombian cities29. For this reason, we recognize as a limitation that in the SNCCC could exist some level of sub-registry caused by the limitation of the access to the health care services, especially in rural and isolated areas. Additionally, the limited number of reported cases for group IV and subsequent groups of the ICCC-3 did not allow for the analysis of other groups different to group III (CNS).\n\n\nConclusion\n\nThe spatial distribution of non-leukemia CC seem to have clustered patterns in some regions of the country that suggest possible infectious, environmental or occupational factors related to its incidence. Future studies should assess the effect of these factors related to non-leukemia CC.\n\n\nData availability\n\nWe declare that we have permission for the free use of this data.\n\nZenodo: Clustering of childhood cancer in Colombia: a nationwide study. http://doi.org/10.5281/zenodo.448808010.\n\nThis project contains the following source data:\n\n- Database SIVIGILA by municipality (database of cases by type of cancer and municipality (geographic location) taken from SIVIGILA data)\n\n- Database DANE population (database of populations by municipality (geographic location) taken from DANE data)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "References\n\nSteliarova-Foucher E, Colombet M, Ries LAG, et al.: International incidence of childhood cancer, 2001-10: a population-based registry study. Lancet Oncol. 2017; 18(6): 719–31. PubMed Abstract | Publisher Full Text | Free Full Text\n\nEl cáncer infantil. [cited 2020 Jun 11]. Reference Source\n\nBravo CP, Cuadrado C, Gónzales I: Cáncer Infantil en Latinoamérica: Un Análisis Comparativo de la Respuesta de los Sistemas de Salud. Medwave. 2019; 19(Suppl 1): SP95. Publisher Full Text\n\nWheeler DC: A comparison of spatial clustering and cluster detection techniques for childhood leukemia incidence in Ohio, 1996-2003. Int J Health Geogr. 2007; 6: 13. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKonstantinoudis G, Kreis C, Ammann RA, et al.: Spatial clustering of childhood cancers in Switzerland: a nationwide study. Cancer Causes Control. 2018; 29(3): 353–62. PubMed Abstract | Publisher Full Text\n\nValbuena-García AM, Rodríguez-Villamizar LA: Análisis espacial en epidemiología: revisión de métodos. Rev Uni Ind Santander Salud. 2018; 50(4): 358–65. Publisher Full Text\n\nKnox EG, Gilman EA: Spatial clustering of childhood cancers in Great Britain. J Epidemiol Community Health. 1996; 50(3): 313–9. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRodriguez-Villamizar LA, Díaz MPR, Merchán LAA, et al.: Space-time clustering of childhood leukemia in Colombia: A nationwide study. BMC Cancer. 2020; 20(1): 48. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDANE: Censo Nacional de Población y censo nacional de vivienda Vivienda. DANE, Publ para todos. 2018. Reference Source\n\nManrique Hernández EF, Rojas Diaz MP, Rodriguez-Villamizar LA: Clustering of childhood cancer in Colombia: a nationwide study. 2021. http://www.doi.org/10.5281/zenodo.4488080\n\nFichas y Protocolos. [cited 2020 Jun 11].\n\nSteliarova-Foucher E, Stiller C, Lacour B, et al.: International classification of childhood cancer, third edition. Cancer. 2005; 103(7): 1457–67. PubMed Abstract | Publisher Full Text\n\nRamis R, Gómez-Barroso D, Tamayo I, et al.: Spatial analysis of childhood cancer: A case/control study. PLoS One. 2015; 10(5): e0127273. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCalidad de los datos en los registros de cáncer de base de población en Colombia. Biomedica. 2012; 32(4). [cited 2020 Jun 11]. Publisher Full Text\n\nGeoportal DANE - Inicio. [cited 2020 Jun 11].\n\nKulldorff M: A spatial scan statistic. Commun Stat - Theory Methods. 1997; 26(6): 1481–96. Publisher Full Text\n\nKreis C, Grotzer M, Hengartner H, et al.: Space-time clustering of childhood cancers in Switzerland: A nationwide study. Int J Cancer. 2016; 138(9): 2127–35. PubMed Abstract | Publisher Full Text\n\nKreis C, Doessegger E, Lupatsch JE, et al.: Space-time clustering of childhood cancers: a systematic review and pooled analysis. Eur J Epidemiol. 2019; 34(1): 9–21. PubMed Abstract | Publisher Full Text | Free Full Text\n\nOrtega-garcía JA, López-hernández FA, Cárceles-álvarez A: Analysis of small areas of pediatric cancer in the municipality of Murcia. An Pediatr (Barc). 2016; 84(3): 154–62. PubMed Abstract | Publisher Full Text\n\nBailony MR, Hararah MK, Salhab AR, et al.: Cancer registration and healthcare access in West Bank, Palestine: A GIS analysis of childhood cancer, 1998-2007. Int J Cancer. 2011; 129(5): 1180–9. PubMed Abstract | Publisher Full Text\n\nTorabi M, Rosychuk RJ: An examination of five spatial disease clustering methodologies for the identification of childhood cancer clusters in Alberta, Canada. Spat Spatiotemporal Epidemiol. 2011; 2(4): 321–30. PubMed Abstract | Publisher Full Text\n\nAgost L: Analysis of spatial-temporal clusters of childhood cancer incidence in the province of Córdoba, Argentina (2004-2013). Arch Argent Pediatr. 2016; 114(6): 534–543. PubMed Abstract | Publisher Full Text\n\nHill AB: The Environment and Disease: Association or causation? Proc R Soc Med. 1965; 58(5): 295–300. PubMed Abstract | Free Full Text\n\nGoujon-Bellec S, Demoury C, Guyot-Goubin A, et al.: Detection of clusters of a rare disease over a large territory: Performance of cluster detection methods. Int J Health Geogr. 2011; 10: 53. PubMed Abstract | Publisher Full Text | Free Full Text\n\nEngel A, Lamm SH: Arsenic exposure and childhood cancer--A systematic review of the literature. J Environ Health. 2008; 71(3): 12–6. PubMed Abstract\n\nChen M, Chang CH, Tao L, et al.: Residential exposure to pesticide during childhood and childhood cancers: A meta-analysis. Pediatrics. 2015; 136(4): 719–29. PubMed Abstract | Publisher Full Text\n\nvan Maele-Fabry G, Lantin AC, Hoet P, et al.: Residential exposure to pesticides and childhood leukaemia: A systematic review and meta-analysis. Environ Int. 2011; 37(1): 280–91. PubMed Abstract | Publisher Full Text\n\nCarles C, Bouvier G, Esquirol Y, et al.: Residential proximity to agricultural land and risk of brain tumor in the general population. Environ Res. 2017; 159: 321–30. PubMed Abstract | Publisher Full Text\n\nCendales R, Pardo C, Uribe C, et al.: Calidad de los datos en los registros de cáncer de base de población en Colombia. Biomedica. 2012; 32(4): 536–44. Publisher Full Text"
}
|
[
{
"id": "79234",
"date": "04 Mar 2021",
"name": "Lisandro Agost",
"expertise": [
"Reviewer Expertise Ecology - Epidemiology - Childhood Cancer - Pesticide Risk Indicators"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 attempts to identify non-leukemia childhood cancer clusters (population under 15 years of age), across Colombia between 2014 and 2017. It uses data from official government sources, both disease and population, at the municipal level.\nOverall the article is clear and concise, perhaps too concise on some points. It is important research but I would consider the following changes and suggestions before indexing:\nThe title is omitting information as it is not a study of all types of cancers. It should clarify that it is about non-leukemia childhood cancer.\n\nIntroduction section:\nThe mean annual incidence of CC was estimated at 140.6 cases per million children between the age 0–14 years in the period of 2001 to 2010. A geographical reference is missing - worldwide or what?\n\nThe world health organization (WHO) estimates that nearly 300,000 new cases of CC are diagnosed every year in children between 0 and 19 years of age. Although the data is important, perhaps it would be better to obtain it for the 0-15 age group in order to be more coherent in the text.\n\nMethods section:\nColombia is a country located in the north of South America... Description is too long, make a map of the study area or use the standardized rate map (Figure 2).\n\nWomen make up 51.2% of the population, and children under the age of 15 years make up 22.6% compared to adults over the age of 65 years which represent 9.1%. It is not clear why the data is divided in this way. Why don't the authors put the total female - male population and then only the population under 15 (divided into female and male if want)?\n\nThe global Moran index was calculated to estimate the spatial autocorrelation. It is not clear whether they do this statistical analysis in STATA or with what software.\n\nWe used an upper limit of the population at risk of 25% and for a sensitivity analysis we assess the results using upper limits of 50% and 10%. I would explain in a little more detail what this analysis is for and why it is done.\n\nResults section:\nIt would be interesting to show in this section (or in the annexes) a table with the distribution of cases per year, percentage of each group, crude and standardized rate, divided by ICCC 3 group (including leukaemias). Another interesting table, if it is not too big, would be to show the results of the distribution of cases per department, per year.\n\nIn general, none of the graphs or maps show the data sources. I don't know if this is a journal rule or if the authors omitted them.\n\nFigures 3 and 4 are not useful. They should be redrawn showing more clearly the units of analysis (municipalities), and the clusters individually. For figure 3, for example, I suggest making four enlarged maps (from the general map of Colombia) showing the departments with the number of municipalities that include each cluster. Or simply show the municipalities included in the cluster. Why not use a map similar to the one in figure 2 or 5?\n\nDiscussion section:\nIn general, I feel that the discussion of the results is not enough. The authors should expand it, taking into account that they found numerous clusters, with important associated indicators. At no point is there an in-depth discussion of the results of this research in relation to the findings of previous research on leukaemia clusters (Space-time clustering of childhood leukemia in Colombia: A nationwide study, 2020). It would be very interesting to complement these studies and discuss what they have in common.\n\nThe spatial studies based on the analysis of areas (ecological approach) such as this study, and the studies in Canada and in Palestine20–22,... There seems to be an error in the text or in the citation.\n\nIt should be made explicit or discussed why the authors used only this cluster analysis method (Kulldorf’s) and not others. Also, what other statistical methods the authors believe could complement, in future research, the results obtained.\n\nNon-leukemia CC clusters identified in Colombia are located mainly in the central region of the country near the mountain ranges... In this paragraph, I believe that the discussion of possible risk factors or associated risk factors for this disease should be expanded a little further and supported by literature from other research, reports or reviews. While the research does not set out to study causality, it can provide new lines of research by collecting and discussing possible risk factors. The bibliography of the risk factors mentioned above should be expanded.\n\nI did not find the definition of SNCCC.\n\nThe discussion of limitations is poor. They should be expanded, better explaining the limitations and scope of the methodologies used and the results obtained.\n\nConclusion section:\nSince the conclusion focuses on the possible factors associated with the results obtained, it seems important to me to develop these topics further in the Discussion section.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": [
{
"c_id": "6708",
"date": "25 Jun 2021",
"name": "Edgar F. Manrique-Hernández",
"role": "Author Response",
"response": "Clustering of childhood cancer in Colombia: a nationwide study Reviewer #1: Lisandro Agost. Centro de Ecología y Recursos Naturales Renovables (CERNAR) – IIByT CONICET-UNC, Córdoba, Argentina. The article attempts to identify non-leukemia childhood cancer clusters (population under 15 years of age), across Colombia between 2014 and 2017. It uses data from official government sources, both disease and population, at the municipal level. Overall the article is clear and concise, perhaps too concise on some points. It is important research but I would consider the following changes and suggestions before indexing: The title is omitting information as it is not a study of all types of cancers. It should clarify that it is about non-leukemia childhood cancer. Author's response to reviewer: Thank you for your detailed review and comments. We have edited the title. Clustering of non-leukemia childhood cancer in Colombia: a nationwide study. Introduction section: The mean annual incidence of CC was estimated at 140.6 cases per million children between the age 0–14 years in the period of 2001 to 2010. A geographical reference is missing - worldwide or what? Author's response to reviewer: Thank you for your detailed review and comments. We have added the clarification to worldwide reference in the manuscript. The world health organization (WHO) estimates that nearly 300,000 new cases of CC are diagnosed every year in children between 0 and 19 years of age. Although the data is important, perhaps it would be better to obtain it for the 0-15 age group in order to be more coherent in the text. Author's response to reviewer: Thank you for suggestion. The data is given by WHO for that range of age in the reference material. However, attending your comment on age range we modified the order of this sentence and it is now presented first and following information is related only to age range 0-14 years. Methods section: Colombia is a country located in the north of South America... Description is too long, make a map of the study area or use the standardized rate map (Figure 2). Author's response to reviewer: Thank you for your suggestion. We have edited the population paragraph eliminating the details of geographical limits. Women make up 51.2% of the population, and children under the age of 15 years make up 22.6% compared to adults over the age of 65 years which represent 9.1%. It is not clear why the data is divided in this way. Why don't the authors put the total female - male population and then only the population under 15 (divided into female and male if want)? Author's response to reviewer: Thank you for your detailed review and comments. We have edited the sentence in the manuscript. The global Moran index was calculated to estimate the spatial autocorrelation. It is not clear whether they do this statistical analysis in STATA or with what software. Author's response to reviewer: Thank you for your detailed review and comments. We have added the clarification or ArcGIS use in the manuscript. We used an upper limit of the population at risk of 25% and for a sensitivity analysis we assess the results using upper limits of 50% and 10%. I would explain in a little more detail what this analysis is for and why it is done. Author's response to reviewer: Thank you for your suggestion. We have edited the sentence clarifying the it was conducted to identify consistency of clustering results across different upper limits. Results section: It would be interesting to show in this section (or in the annexes) a table with the distribution of cases per year, percentage of each group, crude and standardized rate, divided by ICCC 3 group (including leukaemias). Another interesting table, if it is not too big, would be to show the results of the distribution of cases per department, per year. In general, none of the graphs or maps show the data sources. I don't know if this is a journal rule or if the authors omitted them. Author's response to reviewer: Thank you for your comments and suggestions. We have added Table 1 with the distribution of cases by sex, age group, year of diagnosis, and department or residence. Data source for childhood cancer is mentioned in the methods section (National Surveillance System for Public Health SIVIGILA, for its name in Spanish) but usually not included in maps as they are part of the manuscript. Figures 3 and 4 are not useful. They should be redrawn showing more clearly the units of analysis (municipalities), and the clusters individually. For figure 3, for example, I suggest making four enlarged maps (from the general map of Colombia) showing the departments with the number of municipalities that include each cluster. Or simply show the municipalities included in the cluster. Why not use a map similar to the one in figure 2 or 5? Author's response to reviewer: Thank you for your comment. We agree with your comment and have eliminated figures 3 and 4 as they show similar information in figure 5. Discussion section: In general, I feel that the discussion of the results is not enough. The authors should expand it, taking into account that they found numerous clusters, with important associated indicators. At no point is there an in-depth discussion of the results of this research in relation to the findings of previous research on leukaemia clusters (Space-time clustering of childhood leukemia in Colombia: A nationwide study, 2020). It would be very interesting to complement these studies and discuss what they have in common. Author's response to reviewer: Thank you for your comment. We have expanded the discussion section pointing out the potential meaning of the results and their relation with findings of clusters of leukemia in Colombia. The spatial studies based on the analysis of areas (ecological approach) such as this study, and the studies in Canada and in Palestine20–22,... There seems to be an error in the text or in the citation. Author's response to reviewer: Thank you for your detailed review. We have edited the sentence in the manuscript. It should be made explicit or discussed why the authors used only this cluster analysis method (Kulldorf’s) and not others. Also, what other statistical methods the authors believe could complement, in future research, the results obtained. Author's response to reviewer: Thank you for your comment. We have added a mention about the selection of method for cluster detection, its limitations and future analysis to complement data. Non-leukemia CC clusters identified in Colombia are located mainly in the central region of the country near the mountain ranges... In this paragraph, I believe that the discussion of possible risk factors or associated risk factors for this disease should be expanded a little further and supported by literature from other research, reports or reviews. While the research does not set out to study causality, it can provide new lines of research by collecting and discussing possible risk factors. The bibliography of the risk factors mentioned above should be expanded. Author's response to reviewer: Thank you for your comment. We have expanded the discussion of the potential factors that might be related to the clustering of non-leukemia childhood cancers in the center of the country, including infections, pesticides use, and other occupational and environmental risk factors for parents. I did not find the definition of SNCCC. Author's response to reviewer: Thank you for your detailed review and comments. We have corrected the acronym for SIVIGILA in the manuscript. The discussion of limitations is poor. They should be expanded, better explaining the limitations and scope of the methodologies used and the results obtained. Author's response to reviewer: Thank you for your comment. We have expanded the discussion of the limitations of the data sources and methodologies and the potential effects on the reported results. Conclusion section: Since the conclusion focuses on the possible factors associated with the results obtained, it seems important to me to develop these topics further in the Discussion section. Author's response to reviewer: Thank you for your comment. The topics mentioned in the conclusion section are now better explained in the discussion section."
}
]
},
{
"id": "81741",
"date": "15 Apr 2021",
"name": "Smita Asthana",
"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\nIt’s a well written paper, a nationwide summarization of non-leukemia childhood cancer cases clustering in Colombia from 2014 to 2017. The topic is important. I recommend indexing with minor changes. My suggestions as given below.\nSince it’s a study on non-leukemia cases this should be reflected in title of the manuscript also. Instead of 'childhood cancer' add 'non-leukemia childhood cancer'.\n\nIntroduction section second line, first paragraph “Childhood cancer (CC) …….. in this population.” Define the population instead of 'this population'.\n\nReference 2 can be given in English.\n\nIntroduction section, paragraph 1 line 5, for reference 2 please check the statement \"The world health organization (WHO) estimates that nearly 300,000 new cases of CC are diagnosed every year in children between 0 and 19 years of age”. The article that the authors are referring to is giving the incidence as 400,000 and not 300,000, and age group is also given different in this WHO fact sheet.\n\nMethod section - Its better to give reference for International childhood cancer third edition.\n\nIt would be better if the authors discuss in a few lines the implications of the study.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "6709",
"date": "25 Jun 2021",
"name": "Edgar F. Manrique-Hernández",
"role": "Author Response",
"response": "Clustering of childhood cancer in Colombia: a nationwide study Reviewer #2: Smita Asthana. Division of Epidemiology and Biostatistics, Institute of Cytology and Preventive Oncology, NOIDA, New Delhi, Delhi, India Since it’s a study on non-leukemia cases this should be reflected in title of the manuscript lso. Instead of 'childhood cancer' add 'non-leukemia childhood cancer'. Author's response to reviewer: Thank you for your detailed review and comments. We have edited the title Clustering of non-leukemia childhood cancer in Colombia: a nationwide study. Introduction section second line, first paragraph “Childhood cancer (CC) …….. in this population.” Define the population instead of 'this population'. Author's response to reviewer: Thank you for your detailed review and comments. This sentence uses the term \"this population\" since we previously referred to \"children and adolescents\" in the first line. We consider removing \"in this population\" from the sentence to avoid confusion for readers. Reference 2 can be given in English Author's response to reviewer: Thank you for your detailed review and comments. We have eliminated reference 2 (WHO fact sheet) as the source of data is the study reference 1. Introduction section, paragraph 1 line 5, for reference 2 please check the statement \"The world health organization (WHO) estimates that nearly 300,000 new cases of CC are diagnosed every year in children between 0 and 19 years of age”. The article that the authors are referring to is giving the incidence as 400,000 and not 300,000, and age group is also given different in this WHO fact sheet. Author's response to reviewer: Thank you for your detailed review. We have corrected the number (400,000 new cases) and checked the age range is correct according to the WHO fact sheet and reference 1. Method section - Its better to give reference for International childhood cancer third edition. Author's response to reviewer: Thank you for your comment. We have added the suggested reference in the manuscript. It would be better if the authors discuss in a few lines the implications of the study. Author's response to reviewer: Thank you for your comment. We have added the implications of the study and limitations of data and methods in the discussion section."
}
]
},
{
"id": "81740",
"date": "21 Apr 2021",
"name": "Stéphanie Goujon",
"expertise": [
"Reviewer Expertise epidemiology",
"biostatistics",
"childhood cancer",
"space-time variations",
"environmental 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 nationwide study conducted by Manrique-Hernández and colleagues described the space-time distribution of non-leukemia childhood cancers in Colombia. Based on data from the national health surveillance system, the study aimed at detecting spatial and spatio-temporal localised excesses of cases over the period 2014-2017, on the municipality scale. Describing spatial and temporal variations is of a great importance for childhood cancer surveillance. The authors used registry based data and the scan method developed by M. Kulldorff, which is appropriate for such a study. In a purely spatial analysis, they detected four widespread overlapping clusters of non-leukemia cases in two different areas, in which the number of observed cases were about twice the numbers expected under the hypothesis of homogeneous incidence rates over the whole study period. Space-time analyses identified clusters in the same areas, with excesses observed during shorter time periods.\n\nMajor comments:\nThere is a major issue concerning the interpretation of the results.\nThe authors concluded that the detected clusters \"may suggest infectious or environmental factors associated with its incidence\" (abstract and main text). The presence of localized clusters might actually suggest that a risk factor is present with a higher prevalence in these places than elsewhere in Colombia, but spatial heterogeneity might also be due to differences in case registration. I consider this point is of a primary importance and should be discussed further in the paper and in the abstract (it was discussed rapidly at the end of the discussion section).\nTo discuss that point, it would be useful to describe (at least briefly) in the paper the surveillance system in Colombia and to provide information on how the cases are identified nationwide. Are the data provided automatically to the NHS by hospital centers? Or do SIVIGILA members visit the hospital centers to collect data actively? Which hospital centers are visited or contacted? What are the main care pathways in Colombia? The authors cited several interesting papers that were written in Spanish and therefore not easily understandable.\nSpatial differences in case registration might be observed because of under-diagnoses or difficulties for the registry to identify cases in some regions. In the paper by Rodriguez-Villamizaron et al. on childhood leukemia (2020), the authors indicated that childhood cancer became a priority in Colombia since 2010. Do the authors consider that the new regulation was adopted homogeneously in Colombia since that date, or is it possible that access to diagnosis was different over the study period 2014-2017 depending on the place of residence? Besides, were all medical reports available nationwide during the study period?\nIn Rodriguez-Villamizaron et al. 2020, under-registration was also discussed and it was estimated that 17% of AL cases were not captured by the registry in 2016 (\"During this year [2016] 1394 incident cases of childhood cancer were identified and 1206 (86.5%) of them were reported to the NSSCC […] the NSSCC captured and registered 83% of all incident cases of childhood cancer in Colombia during 2016\"). If the missing cases were not homogeneously distributed in the municipalities, this could lead to clusters in areas where registration was more exhaustive. Do the authors have similar information for non-leukemia cases?\nA large cluster of childhood leukemia was detected in the center of Colombia. Can it be related to the large cluster of non-leukemia cases reported in the present study?\nThe four spatial clusters detected in the study were located in two distinct regions, as three clusters overlapped. The space-time clusters corresponded to the same spatial areas. In all, as a conclusion, I would say that only two clusters were detected (maybe over 2 years only) and I suggest to discuss the fact that the cluster frontiers were difficult to delineate (a well-known limit of the cluster detection methods). The size of the largest detected cluster, in the central region, and the magnitude o the relative risk should also be discussed. A relative risk of about 2 in such a large area is quite surprising and unexpected. If an infectious or environmental factor was responsible for such an excess, it would have to be strongly associated to the risk of non-leukemia cancer and highly prevalent in the cluster area (in comparison to the remaining part of Colombia).\n\nThe statistical methods used in this study, Moran’s test for spatial autocorrelation and the Kulldorff’s scan method for cluster detection, were appropriate. However, some details on the methodology and the parameters used could be added. In particular, the authors could add a reference for the Moran’s test for spatial autocorrelation, and explain how the neighborhood was defined in the study. Were two municipalities considered neighboring areas if the distance between their centroids was below a given threshold or if they shared a common border?\n\nIt would also be useful to provide further details on the scan method (estimation of a likelihood ratio for each window and selection of the most likely cluster, i.e. the window associated to the maximum ratio), and the simulations that were conducted to evaluate the significance thresholds (how many simulations were done?).\n\nSeveral other studies should be referred to in the introduction and discussion sections to provide more accurate information on childhood cancer etiology and the literature on childhood cancer clusters.\n(Suggested publications):\nEtiology:\n'Genetic and nongenetic risk factors for childhood cancer' by Spector et al. (20151). 'Environmental Exposure and Risk of Childhood Leukemia: An Overview' by Schüz et al. (20162).\n\nClustering:\n'Childhood cancer trends in a western Canadian province: a population-based 22-year retrospective study' by Rosychuk et al. (20103). 'Spatial clustering and space-time clusters of leukemia among children in Germany, 1987-2007' by Schmiedel et al. (20074). 'Leukemia and lymphoma incidence in children in Alberta, Canada: a population-based 22-year retrospective study by Kulkarni et al. (20115). 'A cluster analysis of Pediatric Cancer Incidence Rates in Florida: 2000-2010' by Amin et al. (20146). 'Spatial and temporal variations of childhood cancers: Literature review and contribution of the French national registry' by Goujon et al. (20187).\n\nMinor comments:\nAbstract:\n\"A sensitivity analysis was conducted with different upper limit parameters for the at-risk population.\" The upper limit was for the at-risk population included in the cluster.\n\nThere are 1122 municipalities nationwide. Several municipalities had no observed cases, so that the cases were actually distributed in 432 different municipalities. However, all the municipalities were included in the analyses (if the at-risk population was not null). I suggest therefore to report that \"2006 cases were distributed in 1122 municipalities\".\n\nRegarding CNS tumors, it would be informative to specify whether non malignant cases were included.\n\nConclusion: differences in case registration should also be considered as a possible explanation.\n\nIntroduction:\nBased on reference 1, \"The mean annual incidence of CC was estimated at 140.6 cases per million children\". This incidence rate was estimated worldwide, which could be specified.\n\n\"There are several conditions that have been identified as risk factors\". The factors cited in this sentence were associated with childhood cancer with different degree of evidence. Some factors are considered as known (high dose ionising radiation, chemotherapy, certain genetic syndromes and some genetic polymorphisms, some viruses in lymphomas) or highly suspected (domestic and occupational parental exposure, socioeconomic conditions, infections and immune system stimulation for leukemia, birth weight, benzene exposure, air pollution) risk factors, while for other factors the literature is more heterogeneous and no firm conclusion can be drawn to date (tobacco and alcohol consumption). It is important to consider that point when discussing the etiology.\n\nThe following sentence is quite long and difficult to understand: \"contributing to the generation of hypotheses about possible etiologies. Spatial analysis has been previously used for the study of CC, mainly for studying the geographical distribution of leukemias, since this type of analysis allows for the identification of space and time variations in a geographical area that generate clusters that indicate an increase in the tendency of the cases\".\n\nAt the end of the introduction, several studies on childhood cancer cluster detection are cited, but only one reference (ref 5) is provided for non-leukemia cancers. Maybe some of the references I reported above could be added here.\n\nMethods:\nCC cases were identified by the National Surveillance System for Public Health, which registers \"the newly confirmed and probable cases of CC\". It is unclear to me what \"probable cases\" means? It seems that CC diagnoses are confirmed on the basis of diagnostic exams and coded according to the ICCC-3, so could the authors explain what are the probable cases that are registered (if not confirmed why are they registered?).\n\nAre non-malignant CNS tumors registered in SIVIGILIA, and included in the study? Based on the number of CNS tumor cases reported in the result section (17.9% of non-leukemia cases), I assume that only malignant CNS tumors were included in the study. This information should be added in the main text and the abstract.\n\nStatistical analysis:\n\"We performed a descriptive analysis calculating frequencies and central tendency measurements.\" I don’t understand what \"central tendency measurements\" refers to?\n\nI understand that standardized rates were considered to account for potential differences in the age distribution of the pediatric population between municipalities. Were those potential differences also accounted for in the SaTScan analyses?\n\nResults:\n731 cases were excluded from the analyses, of which 57 had an unknown municipality of residence. It would be interesting to describe those cases in terms of type of diagnosis, year of diagnosis. Could the authors get other geographic information related to the area of residence? Were those cases grouped in a particular region?\n\nIt would be useful to describe the distribution of the pediatric population in the 1122 municipalities to illustrate the potential heterogeneity.\n\nThe annual incidence rate for non leukemia cancer (44 cases/million) seems to be quite low compared to the overall incidence rate reported in Stealiarova-Foucher et al. 2017 for South America (133.9 cases/million, table S3), even if leukemia were excluded, and compared to the range reported in figure 2 legend (\"more than 349 cases/million in the highest category\"). This point needs clarification.\n\nThe scan method selects the most likely cluster on the basis of a likelihood ratio that is calculated for each spatial window (from one municipality to the maximum size defined by the user). Likelihood ratios are very similar between two consecutive windows (as only one municipality or a small number of municipalities is added to the window at each step) that’s why overlapping significant clusters can be detected (as in this study). Wouldn’t it be interesting to run the scan method to detect non-overlapping cluster (this is an option in SaTScan)?\n\nFigure 2 is not as clear as figure 5. The four clusters can’t be identified precisely. Presenting one map for each cluster may be useful (or just 3 overlapping circles around the detected cluster areas in the central area and another circle centered on Cali).\n\nDiscussion:\nThe study cited in reference 18 focused on space-time clustering not on cluster detection. The authors reviewed the studies which tested for a space-time interaction, i.e. a general tendency of childhood cancer cases to occur more closely in space and time than expected under independent spatial and temporal patterns. This issue is really different from the question of detecting localized excesses of cases. The difference between space-time interaction and cluster detection (and even spatial clustering) should be clearly stated when presenting the results from reference 18.\n\nRegarding the heterogeneity of the previous study results on CC cluster detection, I agree with the authors that considering count data in geographical units or individual point data to detect localized clusters may lead to different conclusions, and may explained some differences between study results (end of page 7). However, I wouldn't say that the ecological approach is more sensitive than the point analysis on the basis of a small number of studies. It may be that some excesses actually existed in some countries in some particular time periods (not necessarily related to an environmental factor), while cases were more homogeneously distributed in other countries. Sensitivity refers to situations of true excesses.\n\nAt the end of the discussion, the authors noted \"that in the SNCCC could exist some level of sub-registry caused by the limitation of the access to the health care services, especially in rural and isolated areas. \"Again, this point is really important for the interpretation of the results (already noted as a major comment).\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": [
{
"c_id": "6710",
"date": "25 Jun 2021",
"name": "Edgar F. Manrique-Hernández",
"role": "Author Response",
"response": "Clustering of childhood cancer in Colombia: a nationwide study Reviewer #3 Stéphanie Goujon, Childhood and adolescent cancer team (EPICEA), UMR 1153 Centre of Research in Epidemiology and StatisticS (CRESS), Villejuif, France 21 Apr 2021 | for Version 1 The nationwide study conducted by Manrique-Hernández and colleagues described the spacetime distribution of non-leukemia childhood cancers in Colombia. Based on data from the national health surveillance system, the study aimed at detecting spatial and spatio-temporal localised excesses of cases over the period 2014-2017, on the municipality scale. Describing spatial and temporal variations is of a great importance for childhood cancer surveillance. The authors used registry based data and the scan method developed by M. Kulldorff, which is appropriate for such a study. In a purely spatial analysis, they detected four widespread overlapping clusters of nonleukemia cases in two different areas, in which the number of observed cases were about twice the numbers expected under the hypothesis of homogeneous incidence rates over the whole study period. Space-time analyses identified clusters in the same areas, with excesses observed during shorter time periods. Major comments: ○ There is a major issue concerning the interpretation of the results. The authors concluded that the detected clusters \"may suggest infectious or environmental factors associated with its incidence\" (abstract and main text). The presence of localized clusters might actually suggest that a risk factor is present with a higher prevalence in these places than elsewhere in Colombia, but spatial heterogeneity might also be due to differences in case registration. I consider this point is of a primary importance and should be discussed further in the paper and in the abstract (it was discussed rapidly at the end of the discussion section). To discuss that point, it would be useful to describe (at least briefly) in the paper the surveillance system in Colombia and to provide information on how the cases are identified nationwide. Are the data provided automatically to the NHS by hospital centers? Or do SIVIGILA members visit the hospital centers to collect data actively? Which hospital centers are visited or contacted? What are the main care pathways in Colombia? The authors cited several interesting papers that were written in Spanish and therefore not easily understandable. Spatial differences in case registration might be observed because of under-diagnoses or difficulties for the registry to identify cases in some regions. In the paper by RodriguezVillamizaron et al. on childhood leukemia (2020), the authors indicated that childhood cancer became a priority in Colombia since 2010. Do the authors consider that the new regulation was adopted homogeneously in Colombia since that date, or is it possible that access to diagnosis was different over the study period 2014-2017 depending on the place of residence? Besides, were all medical reports available nationwide during the study period? In Rodriguez-Villamizaron et al. 2020, under-registration was also discussed and it was estimated that 17% of AL cases were not captured by the registry in 2016 (\"During this year [2016] 1394 incident cases of childhood cancer were identified and 1206 (86.5%) of them were reported to the NSSCC […] the NSSCC captured and registered 83% of all incident cases of childhood cancer in Colombia during 2016\"). If the missing cases were not homogeneously distributed in the municipalities, this could lead to clusters in areas where registration was more exhaustive. Do the authors have similar information for non-leukemia cases? Author's response to reviewer: Thank you for your detailed review and comments. Certainly, spatial heterogeneity in this type of ecological spatial analysis can be observed due to diagnosis or reporting heterogeneity. For this study we selected as source of cancer cases the report to the national surveillance system for childhood cancer (NSSCC) from SIVIGILA because this is the strongest and more complete health information system that is operating in all 1,122 municipalities in Colombia. Unfortunately, the cancer population-based registries in Colombia are limited to four regions in the country which are representative of specific urban areas but do not represent the full spectrum of municipalities and regions in Colombia. The national surveillance system (SIVIGILA) is operated by the National Institute of Health (INS for Spanish) as a mandatory, systematic, and continuous registry with standardized protocols for more than 100 events of interest in public health. The system operates permanently in all municipalities based on immediate report for selected health events and weekly report for all events, including childhood cancer. The system is administrated and regulated by INS and operational support and training for municipalities is provided by the health secretary of each state (departments in Colombia). Childhood cancer surveillance began in 2008 when acute leukemia was included as a mandatory health notification event. In 2013 the system was extended to all types of childhood cancer. The system preserved the core formats and software for reporting acute childhood leukemia and therefore the extension to other cancer types had a shorter learning curve for the surveillance system´s personnel in municipalities. During the study period, notification of non-leukemia cancer were reported for 432 municipalities in almost all departments and districts (including municipalities with predominantly rural remote areas), which support the wide coverage of the surveillance system. For a previous study, we conducted a comparison between national high-cost account registry and SIVIGILA report during 2016 and found that 1394 incident cases of childhood cancer were identified and 1206 (86.5%) of them were reported to SIVIGILA, indicating that the systems captured 83% of all incident cases of childhood cancer in Colombia, which included non-leukemia cases. The 188 cases missing in SIVIGILA corresponded to different cancer diagnosis and municipalities distributed in 28 departments across the country. Therefore, we assumed that the presence of underreporting it is not concentrated in specific areas of the country and underreporting although is present, might not be the main explanation for the spatial heterogeneity in our results. However, health care access to cancer diagnosis is limited to specific regions in the country located in the main capital cities in Colombia and therefore delay in diagnosis (and derived delayed in reporting) might be present in remote semirural and rural municipalities. The analysis was conducted for 2014-2017 and databases were consolidated in 2019, therefore cases with delayed diagnosis had the opportunity to be included in the last two years as SIVIGILA required the reporting of incident and prevalent cases since 2014 for non-leukemia cases. However, the cases with missing diagnosis due to limitations in access to health care might be still present in the study but cannot be quantified. We have summarized and added these points or potential underreporting and underdiagnosis in the discussion section. A large cluster of childhood leukemia was detected in the center of Colombia. Can it be related to the large cluster of non-leukemia cases reported in the present study? Author's response to reviewer: Thank you for your comment. One cluster for childhood leukemia was also identified in the center of the country. Clusters for both leukemia and non-leukemia cases might be related to each other, however the non-leukemia cluster is larger (327 municipalities compared with 109 identified in the leukemia cluster), more expanded to the North of the leukemia cluster, and with higher incidence rates located in municipalities with predominant rural areas. We have added this comment in the discussion section. The four spatial clusters detected in the study were located in two distinct regions, as three clusters overlapped. The space-time clusters corresponded to the same spatial areas. In all, as a conclusion, I would say that only two clusters were detected (maybe over 2 years only) and I suggest to discuss the fact that the cluster frontiers were difficult to delineate (a wellknown limit of the cluster detection methods). The size of the largest detected cluster, in the central region, and the magnitude o the relative risk should also be discussed. A relative risk of about 2 in such a large area is quite surprising and unexpected. If an infectious or environmental factor was responsible for such an excess, it would have to be strongly associated to the risk of non-leukemia cancer and highly prevalent in the cluster area (in comparison to the remaining part of Colombia). Author's response to reviewer: Thank you for your comment. We agree with your comment about the overlapping of clusters and concentration of cases in two clusters (rather than four) with the first expanded in a large are in the central region with a high relative risk. We have corrected this aspect in the abstract and conclusion and added a more detailed comment on the limitation to delimited clusters in the central region in the discussion section. ○ The statistical methods used in this study, Moran’s test for spatial autocorrelation and the Kulldorff’s scan method for cluster detection, were appropriate. However, some details on the methodology and the paramete,rs used could be added. In particular, the authors could add a reference for the Moran’s test for spatial autocorrelation, and explain how the neighborhood was defined in the study. Were two municipalities considered neighboring areas if the distance between their centroids was below a given threshold or if they shared a common border? Author's response to reviewer: Thank you for your comment. The analysis considered neighboring based on the distance between the municipality´s centroids based on the Euclidean distance measured between two centroids of municipalities (with no threshold specification). We have added this comment in the methods section. ○ It would also be useful to provide further details on the scan method (estimation of a likelihood ratio for each window and selection of the most likely cluster, i.e. the window associated to the maximum ratio), and the simulations that were conducted to evaluate the significance thresholds (how many simulations were done?). Author's response to reviewer: Thank you for your comment. The selection of the most likely cluster was selected based on the p-value of the log likelihood ratio (p>0,05 was considered statistically significant) and 999 replications were used in the simulation to evaluate the significance of the inference. We have added this comment in the methods section. Several other studies should be referred to in the introduction and discussion sections to provide more accurate information on childhood cancer etiology and the literature on childhood cancer clusters. ○ (Suggested publications): Etiology: 'Genetic and nongenetic risk factors for childhood cancer' by Spector et al. (20151 ○ ). 'Environmental Exposure and Risk of Childhood Leukemia: An Overview' by Schüz et al. (20162). ○ Clustering: 'Childhood cancer trends in a western Canadian province: a population-based 22-year retrospective study' by Rosychuk et al. (20103). ○ 'Spatial clustering and space-time clusters of leukemia among children in Germany, 1987- 2007' by Schmiedel et al. (20074). ○ 'Leukemia and lymphoma incidence in children in Alberta, Canada: a population-based 22- year retrospective study by Kulkarni et al. (20115). ○ 'A cluster analysis of Pediatric Cancer Incidence Rates in Florida: 2000-2010' by Amin et al. (20146). ○ 'Spatial and temporal variations of childhood cancers: Literature review and contribution of the French national registry' by Goujon et al. (20187). Author's response to reviewer: Thank you for your suggestions. We have added the suggested references in the manuscript. Minor comments: Abstract: \"A sensitivity analysis was conducted with different upper limit parameters for the at-risk population.\" The upper limit was for the at-risk population included in the cluster. Author's response to reviewer: Thank you for your correction. We have edited the sentence. ○ There are 1122 municipalities nationwide. Several municipalities had no observed cases, so that the cases were actually distributed in 432 different municipalities. However, all the municipalities were included in the analyses (if the at-risk population was not null). I suggest therefore to report that \"2006 cases were distributed in 1122 municipalities\". Author's response to reviewer: Thank you for your comment. We have edited the sentence specifying the 1122 municipalities in the methods and the identification of cases in 432. ○ Regarding CNS tumors, it would be informative to specify whether non malignant cases were included. Author's response to reviewer: Thank you for your comment. According to SIVIGILA protocol, CNS tumors include malignant and non-malignant cases. We have added this specification in the methods section. ○ Conclusion: differences in case registration should also be considered as a possible explanation. Author's response to reviewer: Thank you for your suggestion. We have added that differences in case diagnosis in remote rural areas should also be considered as a possible explanation. Introduction: Based on reference 1, \"The mean annual incidence of CC was estimated at 140.6 cases per million children\". This incidence rate was estimated worldwide, which could be specified. Author's response to reviewer: Thank you for your suggestion. We have edited the sentence. ○ \"There are several conditions that have been identified as risk factors\". The factors cited in this sentence were associated with childhood cancer with different degree of evidence. Some factors are considered as known (high dose ionising radiation, chemotherapy, certain genetic syndromes and some genetic polymorphisms, some viruses in lymphomas) or highly suspected (domestic and occupational parental exposure, socioeconomic conditions, infections and immune system stimulation for leukemia, birth weight, benzene exposure, air pollution) risk factors, while for other factors the literature is more heterogeneous and no firm conclusion can be drawn to date (tobacco and alcohol consumption). It is important to consider that point when discussing the etiology. Author's response to reviewer: Thank you for your suggestion. We have added this comment in the introduction section for possible etiology for clusters. The following sentence is quite long and difficult to understand: \"contributing to the generation of hypotheses about possible etiologies. Spatial analysis has been previously used for the study of CC, mainly for studying the geographical distribution of leukemias, since this type of analysis allows for the identification of space and time variations in a geographical area that generate clusters that indicate an increase in the tendency of the cases\". Author's response to reviewer: Thank you for your comment. We have edited the sentence. ○ At the end of the introduction, several studies on childhood cancer cluster detection are cited, but only one reference (ref 5) is provided for non-leukemia cancers. Maybe some of the references I reported above could be added here. Author's response to reviewer: Thank you for your comment and suggested references. We have added some of the suggested references for non-leukemia cancers Methods: CC cases were identified by the National Surveillance System for Public Health, which registers \"the newly confirmed and probable cases of CC\". It is unclear to me what \"probable cases\" means? It seems that CC diagnoses are confirmed on the basis of diagnostic exams and coded according to the ICCC-3, so could the authors explain what are the probable cases that are registered (if not confirmed why are they registered?). Author's response to reviewer: The SIVIGILA protocol for childhood cancer includes the case definition of “probable” when first clinical diagnosis is given and the confirmation of cases should be reported in a maximum of four weeks. All included cases in the analysis are confirmed cases. We have added a clarification in this sentence. ○ Are non-malignant CNS tumors registered in SIVIGILIA, and included in the study? Based on the number of CNS tumor cases reported in the result section (17.9% of non-leukemia cases), I assume that only malignant CNS tumors were included in the study. This information should be added in the main text and the abstract Author's response to reviewer: Thank you for your comment. According to SIVIGILA protocol, CNS tumors include malignant and non-malignant cases. We have added this specification in this section. Statistical analysis: \"We performed a descriptive analysis calculating frequencies and central tendency measurements.\" I don’t understand what \"central tendency measurements\" refers to? Author's response to reviewer: Thank you for your comment. We refer to summary and dispersion measurements (i.e. mean and standard deviation), however in reported results we are providing only percentages so we agree on eliminating the word. We have edited the sentence specifying frequencies and percentages. ○ I understand that standardized rates were considered to account for potential differences in the age distribution of the pediatric population between municipalities. Were those potential differences also accounted for in the SaTScan analyses? Author's response to reviewer: No, the cluster analyses were conducted with total population by municipality and year. Results: 731 cases were excluded from the analyses, of which 57 had an unknown municipality of residence. It would be interesting to describe those cases in terms of type of diagnosis, year of diagnosis. Could the authors get other geographic information related to the area of residence? Were those cases grouped in a particular region? Author's response to reviewer: Thank you for your comment. The cases were reported with codification for department with no specification of municipality. The 57 cases belonged to 20 departments distributed across the country (Atlántico, Magdalena, Meta, Cesar, La Guajira, Valle, Tolima, Antioquia, Cundinamarca, Huila, Caquetá, Casanare, Amazonas, Chocó, Putumayo, Cauca, Santander, Bolívar, Norte de Santander y Córdoba). We have added this information in the results section. ○ It would be useful to describe the distribution of the pediatric population in the 1122 municipalities to illustrate the potential heterogeneity. Author's response to reviewer: Thank you for your comment. We have added a sentence describing the childhood population by municipaliy. (mean 9,880, median 3,336, minimum 149 in La Guadalupe municipality of Guainía and maximum 1,381,081 in Bogotá, the capital district) ○ The annual incidence rate for non leukemia cancer (44 cases/million) seems to be quite low compared to the overall incidence rate reported in Stealiarova-Foucher et al. 2017 for South America (133.9 cases/million, table S3), even if leukemia were excluded, and compared to the range reported in figure 2 legend (\"more than 349 cases/million in the highest category\"). This point needs clarification ○ The scan method selects the most likely cluster on the basis of a likelihood ratio that is calculated for each spatial window (from one municipality to the maximum size defined by the user). Likelihood ratios are very similar between two consecutive windows (as only one municipality or a small number of municipalities is added to the window at each step) that’s why overlapping significant clusters can be detected (as in this study). Wouldn’t it be interesting to run the scan method to detect non-overlapping cluster (this is an option in SaTScan)? Author's response to reviewer: Thank you for your comment. We have run the analysis with no overlap and found two spatial clusters. Therefore, results are presented for both analysis concluding the presence of two clusters. Figure 2 is not as clear as figure 5. The four clusters can’t be identified precisely. Presenting one map for each cluster may be useful (or just 3 overlapping circles around the detected cluster areas in the central area and another circle centered on Cali). Author's response to reviewer: Thank you for your comment. Figure 2 is showing rates by municipality and therefore the clusters are not identified and they are shown in figure 3 (previous figure 5). Discussion: The study cited in reference 18 focused on space-time clustering not on cluster detection. The authors reviewed the studies which tested for a space-time interaction, i.e. a general tendency of childhood cancer cases to occur more closely in space and time than expected under independent spatial and temporal patterns. This issue is really different from the question of detecting localized excesses of cases. The difference between space-time interaction and cluster detection (and even spatial clustering) should be clearly stated when presenting the results from reference 18. Author's response to reviewer: Thank you for your comment. We have complemented the paragraph and made this clarification. ○ Regarding the heterogeneity of the previous study results on CC cluster detection, I agree with the authors that considering count data in geographical units or individual point data to detect localized clusters may lead to different conclusions, and may explained some differences between study results (end of page 7). However, I wouldn't say that the ecological approach is more sensitive than the point analysis on the basis of a small number of studies. It may be that some excesses actually existed in some countries in some particular time periods (not necessarily related to an environmental factor), while cases were more homogeneously distributed in other countries. Sensitivity refers to situations of true excesses. Author's response to reviewer: Thank you. We agree with your comment. We have edited the sentence. ○ At the end of the discussion, the authors noted \"that in the SNCCC could exist some level of sub-registry caused by the limitation of the access to the health care services, especially in rural and isolated areas. \"Again, this point is really important for the interpretation of the results (already noted as a major comment). Author's response to reviewer: Thank you. We have added this aspect in abstract and conclusions and it is better explained in the discussion section. References 1. Spector LG, Pankratz N, Marcotte EL: Genetic and nongenetic risk factors for childhood cancer. Pediatr Clin North Am. 2015; 62 (1): 11-25 PubMed Abstract | Publisher Full Text 2. Schüz J, Erdmann F: Environmental Exposure and Risk of Childhood Leukemia: An Overview.Arch Med Res. 47 (8): 607-614 PubMed Abstract | Publisher Full Text 3. Rosychuk RJ, Witol A, Stobart K: Childhood cancer trends in a western Canadian province: a population-based 22-year retrospective study.Pediatr Blood Cancer. 2010; 55 (7): 1348-55 PubMed Abstract | Publisher Full Text 4. Schmiedel S, Blettner M, Kaatsch P, Schüz J: Spatial clustering and space-time clusters of leukemia among children in Germany, 1987-2007.Eur J Epidemiol. 2010; 25 (9): 627-33 PubMed Abstract | Publisher Full Text 5. Kulkarni K, Stobart K, Witol A, Rosychuk RJ: Leukemia and lymphoma incidence in children in Alberta, Canada: a population-based 22-year retrospective study.Pediatr Hematol Oncol. 2011; 28 (8): 649-60 PubMed Abstract | Publisher Full Text 6. Amin R, Hendryx M, Shull M, Bohnert A: A Cluster Analysis of Pediatric Cancer Incidence Rates in Florida: 2000–2010. Statistics and Public Policy. 2014; 1 (1): 69-77 Publisher Full Text 7. Goujon S, Kyrimi E, Faure L, Guissou S, et al.: Spatial and temporal variations of childhood cancers: Literature review and contribution of the French national registry.Cancer Med. 7 (10): 5299-5314 PubMed Abstract | Publisher Full Text."
}
]
},
{
"id": "81746",
"date": "07 May 2021",
"name": "Richard J.Q. McNally",
"expertise": [
"Reviewer Expertise Epidemiology"
],
"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 an interesting paper reporting clustering of childhood cancer in Colombia. However, there are a number of specific issues and these are listed below:\nThere needs to be more justification for choice of methods used.\n\nIs the interest only in the identification of specific spatial or space-time clusters, rather than more generalised spatial or space-time clustering?\n\nThe presence of specific clusters is more consistent with some localised environmental sources of exposure, rather than general exposures (such as infections). Could these clusters be linked with data on more specific localised exposures?\n\nI suggest that the authors also consider other methods for looking at generalised spatial clustering of space-time clustering. These include methods of Cuzick, Besag, Knox, Jacquez and Diggle.\n\nThe English language needs improving throughout.\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": "6711",
"date": "25 Jun 2021",
"name": "Edgar F. Manrique-Hernández",
"role": "Author Response",
"response": "Reviewer #4 Richard J.Q. McNally, Institute of Health and Society, Newcastle University, Newcastle, UK This is an interesting paper reporting clustering of childhood cancer in Colombia. Author's response to reviewer: Thank you for your comment. However, there are a number of specific issues and these are listed below: There needs to be more justification for choice of methods used. Author's response to reviewer: Thank you for your comment. We have added a comment on methods section for the selection of the circular scan test. We used Kulldorff’s spatio-temporal scan statistics because it is commonly used to detect spatial and/or temporal disease clusters in epidemiological studies and are appropriated for detecting regularly shaped clusters which we expect to find if clusters are related to localized environmental exposures at municipality level; this method have very good performance to detect large compact clusters of rare diseases in large territories compared to other scan methods, and it has a open software to implement the analysis which make it highly reproducible. Is the interest only in the identification of specific spatial or space-time clusters, rather than more generalised spatial or space-time clustering? Author's response to reviewer: Thank you for your comment. We were interested in overall clustering but specifically in the identification of localized spatial or space-time clusters. That is the reason we used a scan clustering method. The presence of specific clusters is more consistent with some localised environmental sources of exposure, rather than general exposures (such as infections). Could these clusters be linked with data on more specific localised exposures? Author's response to reviewer: Thank you for your comment. We conducted this exploratory study to assess the presence of localized clusters and as commented in the discussion sections, the localized central cluster open the door to further studies assessing specific localized exposures mainly related to environmental and occupational exposures related to pesticide’s uses and mining operations in the localized area identified. I suggest that the authors also consider other methods for looking at generalised spatial clustering of space-time clustering. These include methods of Cuzick, Besag, Knox, Jacquez and Diggle. Author's response to reviewer: Thank you for your suggestion. We have added the Besag and Newell´s statistic as an additional method for assessing spatial clustering and we found similar results at different cluster sizes. The English language needs improving throughout. Author's response to reviewer: Thank you for your comment. We have reviewed and improved the language style."
}
]
}
] | 1
|
https://f1000research.com/articles/10-86
|
https://f1000research.com/articles/10-502/v1
|
25 Jun 21
|
{
"type": "Research Article",
"title": "Ehlers-Danlos syndrome kyphoscoliotic type 2 caused by mutations in the FKBP14 gene: an analysis of five cases",
"authors": [
"Alla Nikolaevna Semyachkina",
"Ekaterina Alexandrovna Nikolaeva",
"Nailya Mansurovna Galeeva",
"Alexander Vladimirovich Polyakov",
"Maria Andreevna Kurnikova",
"Vera Аlexandrovna Belova",
"Irina Valerievna Shulyakova",
"Ilya Sergeevich Dantsev",
"Goar Vladimirovna Dzhivanshiryan",
"Ekaterina Alexandrovna Nikolaeva",
"Nailya Mansurovna Galeeva",
"Alexander Vladimirovich Polyakov",
"Maria Andreevna Kurnikova",
"Vera Аlexandrovna Belova",
"Irina Valerievna Shulyakova",
"Ilya Sergeevich Dantsev",
"Goar Vladimirovna Dzhivanshiryan"
],
"abstract": "Background. This study deals with a rare (orphan) monogenic connective tissue disorder - Ehlers-Danlos syndrome kyphoscoliotic type 2 (EDSKS2). Kyphoscoliotic type 2 Ehlers-Danlos syndrome is an autosomal recessive disorder caused by mutations in the FKBP14 gene (7p14.3), which encodes the FKBP22 protein. According to the 2017 classification, this type is in group seven - collagen spatial structure and cross-linking defects. We present results of clinical examination and molecular genetic analysis for five patients with age varying from two to fifteen years. Methods. Five patients were examined using clinical and laboratory methods. DNA samples used for the analysis were extracted from whole blood samples using a Wizard® Genomic DNA Purification Kit (Promega, USA) according to the manufacturer's protocol. Results. The major clinical findings were kyphoscoliosis, early motor development delay, muscular weakness, hypotonia and hearing loss. Molecular genetic analysis detected a homozygous c.362dupC duplication in exon 3 of the FKBP14 gene in all five patients. This mutation is common in various countries. Differential diagnostics were carried out to exclude other Ehlers-Danlos syndrome types and myopathies. Conclusions. Literature analysis and examination of five EDSKS2 patients demonstrated the involvement of major organs and systems, such as joints, spine, muscles, cardiovascular system, respiratory system, hearing, and vision, into the pathological process. Kidney mobility increases and nephroptosis seems to be secondary caused by muscular weakness. During molecular genetic analysis, to verify EDSKS2 it is recommended to initially search for the c.362dupC duplication, which appears to be common in European countries, including Russia.",
"keywords": [
"children",
"rare (orphan) disorders",
"monogenic connective tissue disorders",
"clinical findings",
"FKBP14 gene",
"c.362dupC duplication"
],
"content": "Introduction\n\nEhlers-Danlos syndrome (EDS) is commonly encountered by various medical specialists. It is mainly characterized by skin hyperelasticity, joint hypermobility, easy bruising, and hypertrophic scarring. The disorder is genetically heterogeneous: according to the 2017 classification, there are 13 clinical genetic types,1 divided into seven groups depending on the pathogenesis. The kyphoscoliotic type belongs to the B group – disorders of collagen folding and collagen cross-linking – or type VI in the 1997 classification. Patients with kyphoscoliotic type come to the attention of pediatricians, neurologists, and orthopaedists.\n\nEDS kyphoscoliotic type is an autosomal recessive disorder with estimated prevalence of one per 100,000 newborns.2 Its main symptoms (major clinical diagnostics criteria) are severe muscle hypotonia at birth (“floppiness”), early-onset kyphoscoliosis (usually progressive), hypermobility of joints, dislocations/subluxations (especially of knee joints).1 Additional (minor) diagnostic criteria include skin hyperelasticity, easy bruising, arterial ruptures/aneurisms, osteopenia/osteoporosis, bluish sclerae, umbilical/inguinal hernia, thorax deformations, marfanoid habitus, equinovarus feet deformities, myopia.\n\nEDS kyphoscoliotic type is currently subdivided into two subtypes. EDS kyphoscoliotic type 1 (EDSKS1) is caused by mutations in the PLOD1 gene (1p36.22), which encodes lysyl hydroxylase, a catalyst essential for the stability of the intermolecular collagen crosslinks.3,4 EDS kyphoscoliotic type 2 (EDSKS2) is caused by mutations in the FKBP14 gene (7p14.3), which encodes the FKBP22 protein. FKBP22 is a highly conservative peptidyl-prolyl cis-trans isomerase (PPIase), which catalyzes collagen folding and acts as a chaperone to collagen types III, VI, X.5 Thus, both genes are tied to collagen spatial structure formation.\n\nThese two subtypes are clinically similar, but slightly different. Mutations in the PLOD1 gene lead to moderate scarring and bruisability, microcornea, scleral and ocular ruptures, and facial abnormalities (low set ears, epicanthal folds, downslanting eyes, synophrys, high-arched palate). EDSKS2 is less explored because of its recent discovery and lower frequency. Some patients show signs of hearing loss (sensorineural, conductive or mixed) that were not present at birth, as well as follicular hyperkeratosis, muscular atrophy, and bladder diverticulum.\n\nBecause this EDS type is less frequent and not fully explored, in this study we present the clinical data of five patients with EDSKS2.\n\n\nMethods\n\nFive patients were examined using clinical and laboratory methods in the clinical genetics department of Veltischev Research and Clinical Institute for Pediatrics, Moscow, Russia. Molecular genetic analysis was carried out in the DNA diagnostics laboratory of Research Centre for Medical Genetics, Moscow, Russia.\n\nDNA samples used for the analysis were extracted from whole blood samples using a Wizard® Genomic DNA Purification Kit (Promega, USA) according to the manufacturer's protocol.\n\nThe sequence of the FKBP14 gene ((Accession number NG_032173.1 (genomic), Accession number NM_017946.4 (mRNA)) was analyzed for possible mutations via direct automated Sanger sequencing. Primer sequences, МgCl2 concentrations and primer annealing temperatures are presented in Table 1. PCR products were sequenced using the ABI PRISM Big Dye Terminator (v 3.1) Cycle Sequencing Kit (Applied Biosystems, Foster City, CA, USA) on an ABI3130xl Genetic Analyzer (Applied Biosystems, Foster City, CA, USA).\n\nSequencing results were analyzed using BLAST (Basic Local Alignment Search Tool) (http://www.ncbi.nlm.nih.gov/blast) to compare a subject nucleotide sequence with the database. In our research we worked with search database Human genomic plus transcript (Human G+T) using blastn (https://www.ncbi.nlm.nih.gov/Class/MLACourse/Modules/BLAST/nucleotide_blast.html) (Optimized for somewhat similar sequences).\n\n\nCase descriptions\n\nWe examined five patients with EDSKS2: three boys and two girls with age ranging from two to fifteen years (Table 2). In four families, the marriage did not appear to be consanguineous. However, in family number (no.) 3 (girl, 11 years) both parents had distant relatives originating from the same small village, which could potentially mean kinship.\n\n\nEthical approval\n\nThe study was approved by the Ethics committee of the Research and Clinical Institute of Pediatrics (approval number #2, 2021) named after Yuri Veltischev of the Pirogov Russian National Research Medical University of the Ministry of Health of the Russian Federation. A written informed consent was obtained from the participants and parents of participants under the age of 18 to take part in the study. The study was done in accordance with the principles outlined in the Helsinki Declaration (1964).\n\n\nResults\n\nAll patients had moderate to severe kyphoscoliosis, early motor development delay, muscular weakness, hypotonia, and hearing impairment (Table 2). Figure 1 and Figure 2 (a, b) show main phenotypic characteristics of patients no. 3 and 5 with EDSKS2. Physical development of the children at the time of examination varied. Probands no. 1 and 4 (three and fifteen years respectively) had very low, harmonic development (all values below third percentile). Patients no. 3 and 5 (eleven and two years respectively) had disharmonic physical development (no. 3 - average body length 25–50 percentile and very high mass >97 percentile; no. 5 - above average body length 50–75 percentile and below average mass 10–25 percentile). Patient no. 2 had high, harmonic physical development: all values above 90–97 percentile.\n\nThe age of kyphoscoliosis formation varied from eight to twenty-four months. Clinical examination and X-ray showed thoracolumbar kyphoscoliosis in all five cases. Three children (aged two, three, eight years) had kyphoscoliosis of the 2nd degree, while the older patients (11 and 15 years) had kyphoscoliosis of the 3rd and 4th degree respectively. Probands no. 2 and 4 (eight and fifteen years), aside from kyphoscoliosis, had pectus excavatum of the 2nd degree. Patients no. 1, 3, 4, and 5 had pes planovalgus. X-ray showed signs of osteoporosis in patients no. 1, 3, and 5. In addition to this, patient 1 had spina bifida sacralis dorsalis S3–S5.\n\nJoint hypermobility was evaluated as eight on the Beighton scale for four patients and as six for one patient (Patient no. 5). Four patients did not reach the maximum score of nine because of the rigid spine with restricted flexibility.\n\nHistory analysis for all five probands showed early motor development delay, decrease of tendon reflexes, “floppiness”, and positive Gowers' sign. Myopathy did not progress with age. Intellectual development was normal in four children, and patient no. 3 (girl, 11 years) had a slight developmental delay – her IQ was 80 (normal values 85–115).\n\nApprehensive analysis of internal organs showed pathological alterations, the most notable were cardiovascular and bronchopulmonary problems. ECG detected sinus arrhythmia of varying degree in three patients (no. 1, 3, and 4). Echocardiography results revealed open ductus arteriosus in two patients (no. 1 and 2), and borderline (17mm) narrowed aorta at sinotubular junction (Patient no. 3). According to spirometry results, combined respiratory pulmonary function impairments were found in three probands. It was impossible to carry out spirometry for two patients due to their age (two and three years). Bilateral nephroptosis was detected in two children (Patient no. 1 and 2), left side nephroptosis was noted in one patient (no. 5) as well as midshaft hypospadia.\n\nHearing loss, another main feature of EDSKS2, was diagnosed in three patients (three, eleven, and fifteen years). Mild to moderate bilateral sensorineural hearing loss was revealed in the 11-year-old girl (Patient no. 3) and 15-year-old boy (Patient no. 4), mild bilateral mixed hearing loss was detected in a three-year-old boy (Patient no. 5). Ophthalmologic problems were diagnosed in three children, and the most severe alterations were in the 15-year-old boy (Patient no. 4). He had progressive high myopia with astigmatism and right side chorioretinitis without signs of inflammation. Patient no. 1 (three-year-old boy) had mild bilateral hypermetropia and Patient no. 5 (two-year-old boy) had mixed bilateral astigmatism.\n\nBlood and urine tests, as well as biochemical analysis indicating basic metabolism levels, were normal in all five patients.\n\nA homozygous c.362dupC pathogenic variant in exon 3 of the FKBP14 gene was detected in all five patients (Accession number VCV000279809.13) (Figure 3).6\n\nWe present a brief highlight of a child’s clinical history (no. 4).\n\nZ., a 15-year-old boy, was admitted to a clinic with complaints of progressive thoracolumbar kyphoscoliosis, pectus excavatum, muscular weakness, fatigue impairing his ability to engage in physical activities and to walk independently for a moderate period of time, vision and hearing impairments.\n\nThe proband was born to young healthy non-related parents (Figure 4). His mother is currently 45-years-old, and his father is 41-years-old. The proband was from the third pregnancy, second delivery. It was established that the firstborn child was also male with the same clinical picture. He underwent multiple surgical operations to correct stage 4 kyphoscoliosis, but the last operation at the age of nine years was fatal.\n\nRoman numerals - generation number, Arabic numerals - family member number, numbers inside figures - family member's age, crossed out figures - deceased family member.\n\nThe second pregnancy was aborted medically on the mother’s request. The third pregnancy was complicated by gestosis with risk of termination in trimesters I and II, but resulted in timely physiological delivery. The newborn’s mass was 3000 g, body length 51 cm, APGAR score 6/7. Neonatologists stated the child’s limbs were in the position of adduction. Early motor development was delayed: he started holding his head around the age of six months, sitting up at 12 months, walking independently at three years. At the age of two years progressive thoracolumbar kyphoscoliosis and pectus excavatum were noted. The child was under medical observation at the place of residence, received symptomatic therapy, including sanatorial treatment. However, the disorder kept progressing, and its origin was unclear to specialists. Some form of progressive muscular dystrophy was suggested; in order to obtain a clearer diagnosis, the patient was referred to the clinical genetics department of Veltischev Research and Clinical Institute for Pediatrics, Moscow, Russia.\n\nUpon admission, the proband’s condition was evaluated to be moderate to severe, in accordance with his main disorder. His physical development was very low, harmonic: body length - 140 cm, mass - 31 kg respectively (below third percentile). The following phenotypic features were the most notable (Figure 5): thoracolumbar kyphoscoliosis of the 4th degree, pectus excavatum of the 2nd degree, pes planovalgus, joint hypermobility (eight on the Beighton scale), fatigue, muscular weakness resulting in Gowers’ maneuvers. Tendon reflexes were absent. Intellectual development corresponded to age.\n\na) Proband no. 4: very low height and body mass (<3 percentile), thoracolumbar kyphoscoliosis of the 4th degree, pectus excavatum of the 2nd degree; b) Proband no. 4: thoracolumbar kyphoscoliosis of the 4th degree, long thin limbs, pes planovalgus.\n\nCardiac functional examination showed moderate sinus arrhythmia with periods of tachycardia, heart rate was 115–88 bpm. Echocardiography showed no heart defects: the chambers were not enlarged, the valves were intact, the contractory function of the myocardium was satisfactory, the diastolic function was normal, false chordae was detected in the left ventricle.\n\nExternal ventilation function analysis showed profound combined respiratory pulmonary function impairment. Ultrasound examination of abdominal organs and kidneys did not reveal any pathology.\n\nX-ray examination of the thoracolumbar spine region (dorsal-plantar and lateral) confirmed the presence of S-shaped stage 4 thoracolumbar scoliosis.\n\nThe electroneuromyography data indicated the muscular type of lesion: a slight decrease in the amplitudes of M-waves, a decrease in the amplitudes and duration of the motor unit action potentials (MUAPs), accelerated recruitment of the MUAPs; interference pattern analysis (IPA) indicators were below the standard limits.\n\nPure tone threshold audiometry showed mild to moderate bilateral sensorineural hearing loss. An ophtalmologist’s examination showed progressive high myopia with astigmatism, as well as OD chorioretinitis without signs of inflammation.\n\nBlood and urine tests, as well as biochemical analysis indicating basic metabolism levels, were normal. Creatine kinase level was 167 upl, reference values 15–190 upl.\n\nClinical data suggested kyphoscoliotic type Ehlers-Danlos syndrome; it was also necessary to exclude congenital muscular dystrophy. The latter was suggested based on the congenital nature of the disorder, motor development delay, absence of tendon reflexes, muscular strength decrease, Gowers’ maneuvers, and electroneuromyography results. However, the slow muscular pathology progression with fast kyphoscoliosis progression (stage 4), normal CK levels, severe hypermobility syndrome (eight on the Beighton scale), and mild to moderate hearing loss called the diagnosis of primary muscular pathology into question. Molecular genetic analysis results showed a c.362dupC mutation in a homozygous state in exon 3 of the FKBP14 gene. The boy’s parents had this mutation in a heterozygous state. These acquired results allowed us to confirm the EDSKS2 diagnosis.\n\nThe proband’s family was given medical genetic counselling, according to which the risk of an affected child was 25%. The couple was inclined towards preimplantation diagnostics.\n\n\nDiscussion\n\nIn 2012, Baumann et al.5 used genetic mapping to describe the FKBP14 gene as a cause of Ehlers-Danlos syndrome kyphoscoliotic type. Since that moment, less than 30 such patients have been described in the medical literature.5,7–10 To date, according to The Human Gene Mutation Database (HGMD), eight pathogenic variants are described in the FKBP14 gene. The most common variant is the c.362dupC duplication, detected in 11 out of 17 patients by Giunta et al. (2018).9 The majority of patients with this variant are Caucasian from various countries: UK, Austria, Croatia, Poland, etc. One Columbian patient has been reported.10 The c.362dupC duplication was detected in a homozygous state in all five of our non-related patients from different regions of Russia. Baumann et al. (2012)5 suggested the presence of a founder effect. However, a recurrent mutation caused by replication slippage in the polycytidine tract cannot be excluded.\n\nThe FKBP14 gene encodes the FKBP22 protein, which is endoplasmic reticulum (ER) resident and controls post-translational modification of polypeptide chains containing hydroxyproline. FKBP22, a peptidyl-prolyl cis-trans isomerase, is a collagen folding catalyst and interacts with collagen types III, VI, and X.5,11 FKBP14-deficient skin fibroblast examination showed normal proportion and electrophoretic mobility of type I, III, and V collagen α-chains. Immunofluorescence revealed disorganisation of extracellular matrix proteins – collagen types I, III, VI, fibronectin, tenascins. Electronic microphotography of skin fibroblasts showed ER cisternae enlargement, fragmentation of elastic fibers. Symptoms of EDSKS1 and EDSKS2 are very similar: progressive kyphoscoliosis, severe congenital muscular hypotonia, hypermobility syndrome, skin hyperelasticity, medium arterial ruptures, osteopenia/osteoporosis. Diagnostic differentiation criteria: PLOD1-associated kyphoscoliotic type 1 - marfanoid phenotype, profound skin bruisability, scleral and ocular ruptures; FKBP14-associated kyphoscoliotic type 2 - hearing loss, follicular hyperkeratosis, muscular atrophy, bladder diverticulum. In addition, lysyl pyridinoline (LP) and hydroxylysyl pyridinoline (HP) excretion analysis may be useful - LP/HP ratio is increased in the case of kyphoscoliotic type 1.\n\nClinical findings in our patients corresponded to those described in the literature.2,5 The main symptom was progressive kyphoscoliosis in varying stages depending on the age. Three out of five patients had hearing loss, which is described in 73% of kyphoscoliotic type 2 cases.4 The exact pathogenesis of this impairment is unclear. Three patients had osteoporosis; according to the literature, it is one of the minor diagnostic criteria, leading to fractures in 13% of cases.4,9 Three children had congenital malformations affecting three systems: cardiovascular (open ductus arteriosus, borderline narrowed aorta), skeleto-muscular (spina bifida sacralis dorsalis S3-S5), and genital (midshaft hypospadia). Karyotype analysis and chromosomal microarray analysis did not show any abnormalities.\n\nAs shown in the literature, there are various types of Ehlers-Danlos syndrome with vascular complications (vascular, classic, classic-like, musculocontractural), which should be considered in differential diagnostics.1,7,12 These complications in kyphoscoliotic type 2 patients could be caused by a pathogenetic link of the FKBP14 gene with type III collagen, which is a significant component of vascular structure.13\n\nKyphoscoliotic type 2 with symptoms of severe muscular atrophy has to be differentiated from Ullrich and Bethlem myopathy, which is caused by type VI collagen defects. The latter does not cause skin hyperelasticity, ecchymoses, hearing loss, but does cause striae, atrophic scars, respiratory abnormalities, and major joint contractures, uncharacteristic of EDSKS2.\n\nWithout any doubt, with such similarities in clinical pictures of EDSKS2 and the above-mentioned disorders, the final diagnosis has to be verified by molecular genetic analysis.\n\n\nConclusion\n\nLiterature analysis and examination of five EDSKS2 patients demonstrated the involvement of major organs and systems, such as joints, spine, muscles, cardiovascular system, respiratory system, hearing, and vision, into the pathological process. Kidney mobility increases and nephroptosis seems to be secondary, caused by muscular weakness. During molecular genetic analysis, to verify EDSKS2 it is recommended to initially search for the c.362dupC duplication, which appears to be common in European countries, including Russia.\n\nMany questions regarding the disorder's clinical polymorphism and progressive course remain unanswered. Some of them might be solved by a more detailed analysis of the FKBP14 gene functions. The obtained information would improve our understanding of the disorder's pathogenetic mechanisms and aid in target therapy development.\n\n\nData availability\n\nClinVar: NM_017946.4(FKBP14):c.362dup (p.Glu122fs). Accession number VCV000279809.13; variation ID 279809; https://identifiers.org/clinvar:279809.\n\nNCBI Nucleotide: Homo sapiens FKBP prolyl isomerase 14 (FKBP14), RefSeqGene (LRG_454) on chromosome 7. Accession number NG_032173.1; https://identifiers.org/ncbiprotein:NG_032173.1.\n\nNCBI Nucleotide: Homo sapiens FKBP prolyl isomerase 14 (FKBP14), transcript variant 1, mRNA. Accession number NM_017946.4; https://identifiers.org/ncbiprotein:NM_017946.4.\n\n4TU.ResearchData: Underlying data for: Ehlers-Danlos syndrome kyphoscoliotic type 2 caused by mutations in the FKBP14 gene: an analysis of five cases. https://doi.org/10.4121/14705859.v1.6\n\nThis project contains the following underlying data:\n\n• Picture file 1. Gel of PCR fragments from patient no. 3. FKBP14 gene, exons 1–4.\n\n• Picture file 2. Electropherogram of the exon 3 of the FKBP14 gene. A homozygous c.362dupC pathogenic variant in exon 3 of the FKBP14 gene.\n\n• Data file 1. Readme.pdf.\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\n\nConsent\n\nA written informed consent for the publication of this manuscript including identifying images and other personal and clinical details was obtained from the participants and parents or legal guardians of all participants under the age of 18.",
"appendix": "References\n\nMalfait F, Francomano C, Byers P, et al.: The 2017 international classification of the Ehlers-Danlos syndromes. Am J Med Genet C Semin Med Genet. 2017; 175(1): 8–26. PubMed Abstract | Publisher Full Text\n\nRohrbach M, Vandersteen A, Yiş U, et al.: Phenotypic variability of the kyphoscoliotic type of Ehlers-Danlos syndrome (EDS VIA): clinical, molecular and biochemical delineation. Orphanet J Rare Dis. 2011; 6: 46. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKivirikko KI, Myllylä R: Posttranslational Enzymes in the Biosynthesis of Collagen: Intracellular Enzymes. Methods Enzymol. 1982; 82: 245–304. PubMed Abstract | Publisher Full Text\n\nLim PJ, Lindert U, Opitz L, et al.: Transcriptome Profiling of Primary Skin Fibroblasts Reveal Distinct Molecular Features Between PLOD1- and FKBP14-Kyphoscoliotic Ehlers–Danlos Syndrome. Genes. 2019; 10(7): 517. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBaumann M, Giunta C, Krabichler B, et al.: Mutations in FKBP14 Cause a Variant of Ehlers-Danlos Syndrome with Progressive Kyphoscoliosis, Myopathy, and Hearing Loss. Am J Hum Genet. 2012; 90(2): 201–216. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSemyachkina AN, Nikolaeva EA, Galeeva NM, et al.: Underlying data for ‘Ehlers-Danlos syndrome kyphoscoliotic type 2 caused by mutations in the FKBP14 gene: an analysis of five cases. 4TU.ResearchData. 2021. Publisher Full Text\n\nDordoni C, Ciaccio C, Venturini M, et al.: Further delineation of FKBP14-related Ehlers-Danlos syndrome: A patient with early vascular complications and non-progressive kyphoscoliosis, and literature review. Am J Med Genet A. 2016; 170(8): 2031–2038. PubMed Abstract | Publisher Full Text\n\nBursztejn AC, Baumann M, Lipsker D: Ehlers-Danlos syndrome related to FKBP14 mutations: detailed cutaneous phenotype. Clin Exp Dermatol. 2017; 42(1): 64–67. PubMed Abstract | Publisher Full Text\n\nGiunta C, Baumann M, Fauth C, et al.: A cohort of 17 patients with kyphoscoliotic Ehlers–Danlos syndrome caused by biallelic mutations in FKBP14: expansion of the clinical and mutational spectrum and description of the natural history. Genet Med. 2018; 20(1): 42–54. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRuiz-Botero F, Ramírez-Montaño D, Pachajoa H: FKBP14 kyphoscoliotic Ehlers-Danlos Syndrome in adolescent patient: the first Colombian report. Arch Argent Pediatr. 2019; 117(3): e274–e278. PubMed Abstract | Publisher Full Text\n\nIshikawa Y, Mizuno N, Holden P, et al.: The novel missense mutation Met48Lys in FKBP22 changes its structure and functions. Sci Rep. 2020; 10(1): 497. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMurray ML, Yang M, Fauth C, et al.: FKBP14-related Ehlers-Danlos syndrome: Expansion of the phenotype to include vascular complications. Am J Med Genet Part A. 2014; 164: 1750–1755. PubMed Abstract | Publisher Full Text\n\nGermain DP: Ehlers-Danlos syndrome type IV. Orphanet J Rare Dis. 2007; 2: 32. PubMed Abstract | Publisher Full Text | Free Full Text"
}
|
[
{
"id": "88243",
"date": "12 Jul 2021",
"name": "Matthias Baumann",
"expertise": [
"Reviewer Expertise Neuromuscular disorders",
"Ehlers-Danlos-Syndrome"
],
"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 in detail the findings in five additional patients with the rare kyphoscoliotic Ehlers-Danlos syndrome type 2 caused by mutations in the FKBP14 gene. They carried the most common c362dupC duplication. The patients of different age illustrate very well the spectrum of clinical symptoms. An interesting aspect, not well described so far, is the increased kidney mobility and nephroptosis.\nThe paper helps to increase the awareness for this rare connective tissue disease, which is probably still underdiagnosed.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
},
{
"id": "90354",
"date": "31 Aug 2021",
"name": "Tomoki Kosho",
"expertise": [
"Reviewer Expertise Clinical 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\nThe reviewer has evaluated a paper by Dr. Semyachkina, describing five patients with EDSKS2 caused by the same common variant in FKBP14. The disorder is very rare, and detailed clinical information would be valuable to understand the whole picture of the disorder including the natural history. Several issues have been found to be considered as follows:\nX-ray images of the spine, hands, and feet had better be considered to be included.\n\nHow about the intellectual status of these patients, normal or subnormal?\n\nHow about craniofacial features of these patients, some similarities among the series?\n\nHow about skin involvement, hyperextensibility, fragility, and bruisability?\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-502
|
https://f1000research.com/articles/10-501/v1
|
25 Jun 21
|
{
"type": "Research Article",
"title": "Hyperbaric oxygen therapy ameliorates the symptoms of post-concussion syndrome by inhibiting MMP-9 activity: a randomized controlled trial in Indonesia",
"authors": [
"Maximillian Christian Oley",
"Mendy Hatibie Oley",
"Eko Prasetyo",
"Billy Johnson Kepel",
"Mardoni Setiawan",
"Andi Asadul Islam",
"Mochammad Hatta",
"Deanette Michelle Aling",
"Marcella Tirza Tulong",
"Muhammad Faruk",
"Mendy Hatibie Oley",
"Eko Prasetyo",
"Billy Johnson Kepel",
"Mardoni Setiawan",
"Andi Asadul Islam",
"Mochammad Hatta",
"Deanette Michelle Aling",
"Marcella Tirza Tulong",
"Muhammad Faruk"
],
"abstract": "Introduction: Post-concussion syndrome is common in young adults and can greatly interfere with the quality of daily life. It has a wide range of symptoms that require prompt and well-targeted treatment to avoid further brain impairment. Hyperbaric oxygen therapy (HBOT) is a promising regenerative treatment option for these patients to help prevent the progression of post-concussion syndrome. This study aims to determine whether HBOT accelerates the healing process and reduces symptoms in patients with post-concussion syndrome. Methods: 20 patients with post-concussion syndrome participated in this randomized controlled trial study. After receiving standard mild traumatic brain injury treatment in accordance with the Advanced Trauma Life Support guidelines, the patients were divided into HBOT and control groups. Matrix metallopeptidase 9 (MMP-9) levels and Rivermead Post-Concussion Symptoms Questionnaire (RPQ) scores were used to compare the two groups (before HBOT & after 1st, 3rd, and 5th week). Results: The study sample was predominantly male (65%) with an average age of 60 years old. HBOT reduced serum MMP-9 levels by nearly 20 ng/mL (p < 0.001) compared with the control treatment. The efficacy of HBOT was also reflected in the RPQ scores, which were significantly lower in the HBOT group than the control group (before HBOT & after 1st, 3rd, 5th week) (-3.80 on RPQ-3, p = p<0.001; -16.20 on RPQ-13, p = p<0.001). Conclusion: HBOT ameliorated the symptoms associated with post-concussion syndrome through a mechanism that involves MMP-9 activity. The accelerated recovery observed in the present study supports the use of HBOT to treat post-concussion syndrome and potentially other forms of traumatic brain injury.",
"keywords": [
"Hyperbaric oxygen therapy",
"Traumatic brain injury",
"Post-concussion syndrome",
"Rivermead Post-Concussion Symptoms Questionnaire",
"Matrix metallopeptidase 9",
"Randomized controlled trial."
],
"content": "Introduction\n\nHead injury is the leading cause of death and disability among young adults.1 In Indonesia, head injuries account for almost half of all deaths caused by trauma.2–4 The symptoms of head injury range from mild to severe depending on the extent of brain damage.5 Patients with head injuries often experience considerable cognitive, behavioral, and communication impairment.6 These patients deserve prompt, effective treatments that are not only lifesaving but also preserve their brain function.\n\nHyperbaric oxygen therapy (HBOT) involves the inhalation of 100% oxygen at a higher pressure than the atmospheric standard. Patients inhale 100% oxygen, and pressure increases gradually to 2-3 absolute atmosphere (ATA).7–10 HBOT has become popular in the field of neurology because it inhibits apoptosis, suppresses inflammation, and protects the integrity of the blood-brain barrier (BBB), in addition to stimulating angiogenesis and neurogenesis. The neuroprotective effects of HBOT are most effective during the acute phase, which is the first 24 hours post-head injury.11\n\nThe anti-neuroinflammatory properties of HBOT are at least partially exerted by suppressing matrix metallopeptidase 9 (MMP-9) expression.12 MMP-9 is a Zn-dependent endopeptidase enzyme that maintains and remodels the extracellular matrix (ECM). MMP-9 is produced by microglia, neurons, oligodendrocytes, astrocytes, and the vascular endothelium.13 In chronic brain injury, HBOT increases cerebral blood flow, improves any related neuropsychological disorders, and promotes neurophysiological and electrophysiological recovery.14 As such, this therapy improves the quality of life in patients with post-concussion syndrome and prevents its progression to more advanced stages.15 Taken together, these data suggest that HBOT represents a promising therapeutic modality for various forms of head injury.\n\nThe persistence of symptoms associated with mild traumatic brain injury (TBI) is referred to as post-concussion syndrome. The majority of patients with post-concussion syndrome recover within three to six months.16 In most clinical trials on the survey-based, patient progress was evaluated by neuropsychological examination such as the Rivermead Post-Concussion Symptoms Questionnaire (RPQ). The RPQ is one of the most commonly used instruments for determining the severity of the symptoms caused by mild to moderate TBI. Individual item scores reflect the presence and severity of post-concussion symptoms that overlap with a wide range of conditions (e.g., pain, fatigue, and mental health conditions including depression). The RPQ is divided into two groups; RPQ-3 and RPQ-13. RPQ-3 consists of three initial symptoms, such as headaches, feelings of dizziness, nausea and/or vomiting. The RPQ-13 is a progression of these initial symptoms, such as noise sensitivity, sleep disturbance, fatigue, feeling irritable, feeling depressed or impatient, forgetfulness, poor concentration, taking longer to think, blurred vision, light sensitivity, double vision, and restlessness.17\n\nQuestionnaires are repeatedly administered to monitor the patient's progress over time and promptly identify changes in the severity of symptoms. The recovery process usually requires three to six months of conservative treatment to resolve the symptoms.18\n\nHowever, these conservative treatments are slow and sometimes ineffective, leaving patients with life-long symptoms ranging from headaches to impaired cognitive function. Therefore, the present study aims to determine whether and how HBOT accelerates post-concussion syndrome recovery by analyzing RPQ scores and MMP-9 levels, respectively. We hypothesize that HBOT can improve post-concussion symptoms by decreasing MMP-9 levels in patients with TBI undergoing HBOT compared with traditional therapeutic approaches.\n\n\nMethods\n\nThis study used a randomized controlled trial design to assess levels of MMP-9 and Rivermead Post-Concussion Symptoms Questionnaire (RPQ) scores at pre-treatment (baseline) and post-treatment at weeks one, three, and five.\n\nThe study was conducted after obtaining approval from the research ethics committee of Prof. Dr. R. D. Kandou Hospital, Manado (Code number: 125/EC/KEPK-KANDOU/XII/2020). This study was registered with the Research Registry with a registration number no. 6465 on January 17, 2021. Written informed consent was obtained from all the participants. The work was carried out in line with the Consolidated Standards of Reporting Trials (CONSORT) guidelines.19,20\n\nThis study included 20 patients with mild TBI. The patients were randomly divided according to treatment into a control group and an experimental group. The experimental group received HBOT in addition to the Advanced Trauma Life Support (ATLS) protocol while the control group only received the latter. In accordance with randomized controlled trial design, the patients in the control group were so selected because they refused to receive HBOT. The study was carried out at Dr. R. D. Kandou Hospital, Manado, North Sulawesi, Indonesia.\n\nAll patients received standard mild TBI treatment according to the ATLS protocol including head CT scans using computed tomography SOMATOM Scope (Siemens Healthineers AG, Erlangen, Germany) to identify any brain abnormalities. The HBOT group also received 60-minute HBOT sessions, breathing in 100% oxygen at 2-3 ATA, three times during this study at weeks one, three, and five.21\n\nItems in the questionnaires are divided into two groups. The first group (RPQ-3) consists of three items and the second group (RPQ-13) consists of 13 subsequent items.17,18,22 The total score for the RPQ-3 items range from 0-12 and reflect the baseline symptom pool of post-concussion symptoms. A higher RPQ-3 score requires reassessment and close monitoring.23\n\nPrior to initiating treatment in both groups, the RPQ was administered, blood samples were collected for serum MMP-9 assays, and head CT scans were performed to identify any brain abnormalities such as subarachnoid hemorrhage (SAH), epidural hematoma (EDH), subdural hemorrhage (SDH), and intracerebral hemorrhage (ICH). MMP-9 levels were measured in the Biomolecular and Immunology Laboratory of the Faculty of Medicine at Sam Ratulangi University in Manado, Indonesia after every HBOT session for both the HBOT and control groups. At the end of week 1, 3, and 5, all patients were reevaluated for serum MMP-9 levels and RPQ scores. An enzyme-linked immunosorbent assay (ELISA) was used to quantify MMP-9 levels in ng/mL, as described in the MMP9 Human ELISA Kit protocol (Invitrogen Corporation, Carlsbad, CA, USA), catalog number BMS2016-2.9,21,24\n\nMicrosoft Excel was used for data entry and R Statistical Software version 3.6.325 was used for all statistical analyses. For the categorical variables, frequency tables were used to assess distributions. Both center and dispersion values were calculated according to the type of variable as was the normality of the distribution for numeric variables. Normally distributed numeric variables are presented as means and standard deviations (SD). If the distribution is abnormal, median values and interquartile ranges (IQR) are given. Differences for each variable according to the treatment group (HBOT vs control) were analyzed using the t-test for numerical variables and the chi-square or Fisher's exact test for categorical variables. Changes in serum MMP-9 levels in the treatment group according to the time of examination were visually evaluated using graphs and linear mixed model analysis with random intercept; these analysis measurements were repeated for each study subject. The effects of HBOT on serum MMP-9 levels and RPQ scores were evaluated using linear regression models. The modeling results are reported as changes in the outcome value for each unit increase in the independent variable, lower and upper limits of the 95% confidence interval (CI), and p-values, which were considered statistically significant below 0.05.\n\n\nResults\n\nPatient characteristics including age, sex, and the presence of intracranial bleeding are presented in Table 1. The average patient age was 39 years and this was not significantly different between the HBOT and control groups. The male-to-female ratio was approximately 6.5: 3.5. Intracranial bleeding was found in over half of the cases and these were equally distributed between the HBOT and control groups. No patient dropped out during the 6-week study period.\n\na t-test for numeric variables, Fisher’s exact test for categorical variables.\n\nTable 2 displays the MMP-9 levels and RPQ scores at different measurement time points. The two patient groups had different MMP-9 serum levels even before treatment was initiated; however, this difference was not statistically significant. While both groups experienced decreases in MMP-9 levels during the course of this study, the reduction in the HBOT group was significantly greater than in the control group (40.6 ng/mL vs 21.7 ng/mL; p < 0.001). Therefore, even though the control group had higher MMP-9 levels at baseline, this was compensated for by the highly significant endpoint difference (the difference between both scores (delta) after five weeks).\n\na t-test for numeric variables, Fisher’s exact test for categorical variables.\n\nb Delta is the difference between pre-treatment and week 5.\n\nRPQ scores did not differ between the two study groups at baseline. However, by the end of week five, patients receiving HBOT had marked improvements in their RPQ scores compared with controls (mean 3.1 vs 6.5 for RPQ-3, 14.2 vs 29.6 for RPQ-13; both p-values < 0.001). As a result, the delta scores from baseline to week five in the HBOT group were higher compared with the control group (-8.0 vs -4.2 for RPQ-3, -23.4 vs -7.2 for RPQ-13; both p-values < 0.001).\n\nFigure 1 illustrates the changes in serum MMP-9 levels in both groups at four different time points. MMP-9 levels in the HBOT group are consistently lower and decline notably after two weeks compared with the control group. Figure 2 shows that the patients receiving HBOT had overall lower MMP-9 levels than those in the control group. Similarly, Figure 3 depicts the declining MMP-9 concentration in both groups over time and highlights that HBOT causes MMP-9 values to plummet within four weeks of initiating post-injury treatment compared with controls.\n\nRegression analysis using a linear mixed model revealed that changes in MMP-9 level depended on the interaction between both groups (HBOT vs control) and time (Figure 4). The p-values for the group, time, and the interaction of both variables were highly statistically significant (p < 0.001). There was a decrease in MMP-9 concentration in both groups over time, however, this decline was accelerated in the HBOT group compared with controls.\n\nTable 3 presents the regression analysis of the relationship between the outcome variables (MMP-9 concentration and RPQ scores) and HBOT administration. Scores for the individual variables were marked as “delta” and represent the difference between the results at week five and baseline. Compared with controls, the HBOT group exhibited significant declines in MMP-9 concentration (127.91 vs -9.76; p < 0.001), RPQ-3 (-4.78 vs -2.82; p < 0.001) and RPQ-13 scores (-19.62 vs 12.78; p < 0.001).\n\n\nDiscussion\n\nBased on their timing and different distinctive underlying pathomechanisms, head traumas are categorized as primary or secondary brain injury.26 Secondary brain injury occurs in the weeks following, and in response to, the primary brain injury, which occurs at the time of and is directly caused by the trauma itself. Patients with secondary brain injury experience biochemical, metabolic, and cellular changes that are orchestrated by a complex biochemical cascade that causes increased intracranial pressure, BBB damage, neuroinflammation, brain edema, brain hypoxia, ischemia, and neurodegeneration.27 The outcome of TBI is dependent on the secondary brain injury process.28 The starting point of our study is based on this secondary pathomechanism and its reversible, dynamic nature.\n\nThe ECM and BBB both play important roles in neuroplasticity.29 An imperative factor in the damage of the BBB is MMP-9, which is produced by microglia, the first line of defense against brain injury. As the sensors and effectors of the brain’s immune system, microglial activity is the primary marker of neuroinflammation.30,31\n\nEnzymes such as occludin and claudin cause the basal degradation of endothelial lamina by targeting laminin, fibronectin, collagen, proteoglycan, and tight junction proteins (degradation of ZO-1), which are also the two main functional elements of the BBB.32 The downstream outcomes of the enzymatic digestion of these structural proteins include cytoskeletal damage, the disruption of cellular homeostasis, ischemia, inflammation, tissue necrosis, and apoptosis.33\n\nThe stability of the microenvironment surrounding neurons, including the ECM, is necessary for healthy brain function. This stability is sustained by the BBB to maintain brain homeostasis and prevent cell death and dysfunction.32 The integrity of the BBB is the key to the restoration of brain homeostasis after physical injury. The BBB plays a pertinent role in this process because its integrity is influenced by MMP-9 activity, a major effector in secondary brain injury. Therefore, MMP-9 represents a reliable, relevant biological marker for predicting TBI outcome.34\n\nIn the present study, HBOT was administered to prevent or inhibit MMP-9 production. HBOT acts on the neutrophil adhesion mechanism in endothelial cells. More specifically, HBOT reduces the expression of endothelial adhesion molecules and inhibits neutrophil adhesion molecule clustering, thus reducing the number of neutrophils adhered to endothelial cells. Decreasing the number of neutrophils activates pro-inflammatory processes including the release of pro-inflammatory cytokines (e.g., IL1B, IL-6, IL8, and TNFa) and decreases the expression of MMP-9.35\n\nThe results of this study demonstrate HBOT’s ability to inhibit the production of MMP-9. Similarly, a study in Canada found improved cognitive function, quality of life, and elevated brain activity in patients with mild TBI and prolonged post-concussion syndrome after 40 HBOT sessions over two months.36\n\nIn another study, 40 rats were subjected to dynamic cortical deformation (DCD) and then divided into three treatment groups three hours after the initial trauma. 20 rats received HBOT with 100% oxygen at 2.8 ATA for 45 minutes, 10 received 100% oxygen for 45 minutes under normobaric conditions (1 ATA), and 10 were untreated (controls). Neuroinflammatory markers (TIMP-1 and TIMP-2) and MMP-9 levels were measured 96 hours after treatment. MMP-9 levels were found to be significantly lower in the HBOT group relative to controls. Inflammatory infiltration around the focus of necrotic brain tissue was prominent in most untreated animals and was composed predominantly of myeloperoxidase-positive neutrophils. Both normobaric and hyperbaric hyperoxia resulted in a significant decrease of neutrophil infiltration (GLM ANOVA main effect of treatment group: P < 0.0001; This reduction in the neuroinflammatory response was more extended with HBOT in comparison with normobaric hyperoxia (Tukey-Kramer P < 0.05).12\n\nHBOT decreases intracranial pressure (ICP), reduces cerebrospinal fluid (CSF) pressure in patients with acute brain injury, restores the metabolic activity of the substance grisea in a single-photon emission computerized tomography scans of the closed head injury, and to restore glucose metabolism after brain injury.37,38 HBOT decreases mortality rates and improves the functional outcome of patients with severe head injuries. In such chronic brain injuries, HBOT increases cerebral blood flow, improves neuropsychological disorders, and promotes neurophysiological and electrophysiological recovery.39\n\nSeveral studies have reported that multiple HBOT sessions can improve neurological deficits and cognitive impairment in both acute and advanced chronic phases of head injury in rats.40–42 The long-term therapeutic effects of HBOT are derived from the induction of angiogenesis, neuroplasticity, and proliferation and differentiation of nerve stem cells. When HBOT was administered within three hours post-injury in a fluid percussion mouse model of TBI, there was a significant increase in the number of endothelial cells, neurons, and new glial cells four days after the initial injury.40 Ten daily HBOT sessions at 2.5 ATA for 60 minutes enhances neuroplasticity by increasing axonal sprouting and synapse remodeling, contributing to the restoration of locomotor function in rats with TBI.42 Harch et al. study on the blood vessel density was measured bilaterally in the hippocampus using diaminobenzidine staining and correlated with MWT performance (Morris Water Task). They found increased vascular density in the bruised hippocampus and improved cognitive function in these rats after consecutive HBOT sessions (7 days/week, 1.5 ATA, 90-minute sessions/HBOT) over 40 days.43 Several signaling pathways and transcription factors have been implicated in HBOT-induced neurogenesis including, wingless-related integration site, hypoxia-inducible factors, and cAMP response element-binding.44\n\nThe outcome of this study was evaluated by the RPQ. RPQ-13 scores range from zero to 52, with higher scores reflecting more severe post-concussion syndrome. The RPQ-13 items encompass a group of advanced symptoms while the RPQ-3 symptoms include headaches, dizziness, and nausea. All those symptoms included in RPQ highly impact patient participation in social activities, psychosocial functioning, and lifestyle.17 During the three to six months typically required to resolve these symptoms patients are advised to gradually resume their routine activities. If symptoms do not resolve within this period, patients are usually often referred to a specialist for further assessment and treatment services.45\n\nThe data collected in the present study showed a notable decrease in the RPQ-3 and RPQ-13 scores. There was no significant difference in the baseline RPQs of the groups at the beginning of the study. However, by the end of the five weeks of treatment, the patients receiving HBOT had much better RPQ scores (mean 3.1 vs 6.5 for RPQ-3, and 14.2 vs 29.6 for RPQ-13; both p-values < 0.001). As a result, the delta score from baseline to the end of week five in the HBOT group was significantly lower than the control group [-8.0 vs -4.2 for RPQ-3 (p < 0.001), -23.4 vs -7.2 for RPQ-13 (p < 0.001)].\n\nThe decline in RPQ scores over time was significant. RPQ-3 (-3.80 (p < 0.001)) and RPQ-13 (16.20 (p < 0.001)). HBOT administration in patients with mild TBI contributed to this improvement RPQ scores. Based on the findings described here, HBOT confers great benefits by improving the quality of life of patients with mild TBI and likely prevents further brain damage by increasing cerebral blood flow, improving neuropsychological disorders, and promoting neurophysiological and electrophysiological recovery. Given that repeated HBOT sessions restored neurological deficits and cognitive impairment, HBOT should be incorporated as a therapeutic modality for the treatment of patients with head injuries. Although there are many benefits of HBOT, there are also several drawbacks such as seizures, oxygen poisoning, pneumothorax, and middle ear injuries.\n\nAlthough this study supports the efficacy of HBOT in treating post-concussion syndrome, the small sample population and single biomarker are limitations that must be addressed in future studies. The kinetics and underlying mechanisms of HBOT also warrant further investigation to maximize the many beneficial effects of HBOT.\n\n\nConclusions\n\nHBOT effectively relieves the symptoms associated with post-concussion syndrome through a mechanism that involves repressing MMP-9 activity.\n\n\nConsent statement\n\nWritten informed consent for publication of the patients’ details was obtained from the patients/a guardian of the patient.\n\n\nData availability\n\nZenodo: Hyperbaric oxygen therapy ameliorates the symptoms of post-concussion syndrome by inhibiting MMP-9 activity: A Randomized Controlled Trial in Indonesia. http://doi.org/10.5281/zenodo.4785703.46\n\nThis project contains the following underlying data.\n\n• Maximilian Data Post-Concussion Syndrome 2.docx (Patient characteristics)\n\n• Maximilian Data Post-Concussion Syndrome.xlsx (Human Matrix Metalloproteinase 9 (MMP-9) VALUE)\n\nThis project also contains the following reporting guidelines.\n\n• CONSORT checklist\n\n• CONSORT flowchart\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "References\n\nJalali R, Rezaei M: A Comparison of the Glasgow Coma Scale Score with Full Outline of Unresponsiveness Scale to Predict Patients’ Traumatic Brain Injury Outcomes in Intensive Care Units. Crit. Care Res. Pract. 2014; 2014: 1–4. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSamma L, Widodo D: A case evaluation of traumatic brain injury in Wahidin Sudirohusodo Hospital, Makassar during January 2016 - December 2017. Bali Med. J. 2019; 8: 542. Publisher Full Text\n\nWardoyo MS, Widodo D, Ihwan A, et al.: The relationship between different dosages of mannitol 20% and osmolarity, blood sugar serum, and coagulation factors in moderate brain injury patients with increased intracranial pressure. Med. Clínica Práctica. 2021; 4: 100235. Publisher Full Text\n\nPrasetyo E: The primary, secondary, and tertiary brain injury, Crit. Care Shock. 2020; 23: 4–13.\n\nNASEM: Evaluation of the Disability Determination Process for Traumatic Brain Injury in Veterans. In: Veterans Diagnosis Assess. Trauma. Brain Inj. Washington, D.C: National Academies Press; 2019. PubMed Abstract | Publisher Full Text\n\nSepahvand E, Jalali R, Mirzaei M, et al.: Glasgow coma scale versus full outline of unresponsiveness scale for prediction of outcomes in patients with traumatic brain injury in intensive care unit. Turk. Neurosurg. 2015; PubMed Abstract | Publisher Full Text\n\nShinomiya N: Molecular Mechanisms of Hyperbaric Oxygen Therapy. In: Hyperb. Oxyg. Ther. Singapore: Springer Singapore; 2020; 3–20. Publisher Full Text\n\nRaveenthiraraja T, Manoharan S: Hyperbaric oxygen therapy: A review. Int. J. Pharm. Pharm. Sci. 2013; 5: 52–54.\n\nOley MH, Oley MC, Tjandra DE, et al.: Hyperbaric oxygen therapy in the healing process of foot ulcers in diabetic type 2 patients marked by interleukin 6, vascular endothelial growth factor, and PEDIS score: A randomized controlled trial study. Int. J. Surg. Open. 2020; 27: 154–161. Publisher Full Text\n\nOley MH, Oley MC, Aling DMR, et al.: Effects of hyperbaric oxygen therapy on the healing of thermal burns and its relationship with ICAM-1: A case-control study. Ann. Med. Surg. 2021; 61: 104–109. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSánchez EC: Mechanisms of Action of Hyperbaric Oxygenation in Stroke. Crit. Care Nurs. Q. 2013; 36: 290–298. PubMed Abstract | Publisher Full Text\n\nVlodavsky E, Palzur E, Soustiel JF: Hyperbaric oxygen therapy reduces neuroinflammation and expression of matrix metalloproteinase-9 in the rat model of traumatic brain injury. Neuropathol. Appl. Neurobiol. 2006; 32: 40–50. PubMed Abstract | Publisher Full Text\n\nRempe RG, Hartz AM, Bauer B: Matrix metalloproteinases in the brain and blood–brain barrier: Versatile breakers and makers. J. Cereb. Blood Flow Metab. 2016; 36: 1481–1507. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWolf G, Cifu D, Baugh L, et al.: The Effect of Hyperbaric Oxygen on Symptoms after Mild Traumatic Brain Injury. J. Neurotrauma. 2012; 29: 2606–2612. PubMed Abstract | Publisher Full Text\n\nCifu DX, Hart BB, West SL, et al.: The Effect of Hyperbaric Oxygen on Persistent Postconcussion Symptoms. J. Head Trauma Rehabil. 2014; 29: 11–20. PubMed Abstract | Publisher Full Text\n\nD’Souza M, Trivedi R, Singh K, et al.: Traumatic brain injury and the post-concussion syndrome: A diffusion tensor tractography study. Indian J. Radiol. Imaging. 2015; 25: 404. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPotter S, Leigh E, Wade D, et al.: The Rivermead Post Concussion Symptoms Questionnaire. J. Neurol. 2006; 253: 1603–1614. Publisher Full Text\n\nAsselstine J, Kristman VL, Armstrong JJ, et al.: The Rivermead Post-Concussion Questionnaire score is associated with disability and self-reported recovery six months after mild traumatic brain injury in older adults. Brain Inj. 2020; 34: 195–202. PubMed Abstract | Publisher Full Text\n\nAgha RA, Borrelli MR, Vella-Baldacchino M, et al.: The STROCSS statement: Strengthening the Reporting of Cohort Studies in Surgery. Int. J. Surg. 2017; 46: 198–202. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSchulz KF, Altman DG, Moher D: CONSORT 2010 Statement: updated guidelines for reporting parallel group randomised trials. BMJ. 2010; 340: c332–c332. PubMed Abstract | Publisher Full Text | Free Full Text\n\nOley MH, Oley MC, Islam AA, et al.: Hyperbaric oxygen therapy in managing systemic inflammatory response syndrome caused by ischemia-reperfusion injury following hand replantation and long-term outcomes: A report of two cases. Ann. Med. Surg. 2020; 60: 155–161. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKing NS, Crawford S, Wenden FJ, et al.: The Rivermead Post Concussion Symptoms Questionnaire: a measure of symptoms commonly experienced after head injury and its reliability. J. Neurol. 1995; 242: 587–592. PubMed Abstract | Publisher Full Text\n\nEyres S, Carey A, Gilworth G, et al.: Construct validity and reliability of the Rivermead Post-Concussion Symptoms Questionnaire. Clin. Rehabil. 2005; 19: 878–887. PubMed Abstract | Publisher Full Text\n\nNasution RA, Islam AA, Hatta M, et al.: Role of CAPE in reducing oxidative stress in animal models with traumatic brain injury. Ann. Med. Surg. 2020; 57: 118–122. PubMed Abstract | Publisher Full Text | Free Full Text\n\nR Core Team: R: A Language and Environment for Statistical Computing.2018. Reference Source\n\nWerner C, Engelhard K: Pathophysiology of traumatic brain injury. Br. J. Anaesth. 2007; 99: 4–9. PubMed Abstract | Publisher Full Text\n\nFrattalone AR, Ling GSF: Moderate and Severe Traumatic Brain Injury. Neurosurg. Clin. N. Am. 2013; 24: 309–319. PubMed Abstract | Publisher Full Text\n\nAlves JL: Blood–brain barrier and traumatic brain injury. J. Neurosci. Res. 2014; 92: 141–147. Publisher Full Text\n\nThomsen MS, Routhe LJ, Moos T: The vascular basement membrane in the healthy and pathological brain. J. Cereb. Blood Flow Metab. 2017; 37: 3300–3317. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLoane DJ, Faden AI: Neuroprotection for traumatic brain injury: translational challenges and emerging therapeutic strategies. Trends Pharmacol. Sci. 2010; 31: 596–604. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLoane DJ, Byrnes KR: Role of microglia in neurotrauma. Neurotherapeutics. 2010; 7: 366–377. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDaneman R, Prat A: The Blood–Brain Barrier. Cold Spring Harb. Perspect. Biol. 2015; 7: a020412. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMittal M, Siddiqui MR, Tran K, et al.: Reactive Oxygen Species in Inflammation and Tissue Injury. Antioxid. Redox Signal. 2014; 20: 1126–1167. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGuilfoyle MR, Carpenter KLH, Helmy A, et al.: Matrix Metalloproteinase Expression in Contusional Traumatic Brain Injury: A Paired Microdialysis Study. J. Neurotrauma. 2015; 32: 1553–1559. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPekovic S, Dacic S, Krstic D, et al.: Hyperbaric Oxygen Therapy in Traumatic Brain Injury: Cellular and Molecular Mechanisms. In: Hyperb. Oxyg. Treat. Res. Clin. Pract. - Mech. Action Focus. InTech; 2018; Publisher Full Text\n\nBoussi-Gross R, Golan H, Fishlev G, et al.: Hyperbaric Oxygen Therapy Can Improve Post Concussion Syndrome Years after Mild Traumatic Brain Injury - Randomized Prospective Trial. PLoS One. 2013; 8: e79995. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHu Q, Manaenko A, Xu T, et al.: Hyperbaric oxygen therapy for traumatic brain injury: bench-to-bedside. Med. Gas Res. 2016; 6: 102. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHayakawa T, Kanai N, Kuroda R, et al.: Response of cerebrospinal fluid pressure to hyperbaric oxygenation. J. Neurol. Neurosurg. Psychiatry. 1971; 34: 580–586. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGolden ZL, Neubauer R, Golden CJ, et al.: Improvement in Cerebral Metabolism in Chronic Brain Injury after Hyperbaric Oxygen Therapy. Int. J. Neurosci. 2002; 112: 119–131. PubMed Abstract | Publisher Full Text\n\nLin K-C, Niu K-C, Tsai K-J, et al.: Attenuating inflammation but stimulating both angiogenesis and neurogenesis using hyperbaric oxygen in rats with traumatic brain injury. J. Trauma Acute Care Surg. 2012; 72: 650–659. PubMed Abstract | Publisher Full Text\n\nDaugherty WP, Levasseur JE, Sun D, et al.: Effects of hyperbaric oxygen therapy on cerebral oxygenation and mitochondrial function following moderate lateral fluid-percussion injury in rats. J. Neurosurg. 2004; 101: 499–504. PubMed Abstract | Publisher Full Text\n\nBrkic P, Stojiljkovic M, Jovanovic T, et al.: Hyperbaric oxygenation improves locomotor ability by enhancing neuroplastic responses after cortical ablation in rats. Brain Inj. 2012; 26: 1273–1284. PubMed Abstract | Publisher Full Text\n\nHarch PG, Kriedt C, Van Meter KW, et al.: Hyperbaric oxygen therapy improves spatial learning and memory in a rat model of chronic traumatic brain injury. Brain Res. 2007; 1174: 120–129. PubMed Abstract | Publisher Full Text\n\nMu J, Krafft PR, Zhang JH: Hyperbaric oxygen therapy promotes neurogenesis: where do we stand? Med. Gas Res. 2011; 1: 14. PubMed Abstract | Publisher Full Text | Free Full Text\n\nVoormolen DC, Haagsma JA, Polinder S, et al.: Post-Concussion Symptoms in Complicated vs. Uncomplicated Mild Traumatic Brain Injury Patients at Three and Six Months Post-Injury: Results from the CENTER-TBI Study. J. Clin. Med. 2019; 8: 1921. PubMed Abstract | Publisher Full Text | Free Full Text\n\nOley MC, Oley MH, Prasetyo E, et al.: Hyperbaric Oxygen Therapy Ameliorates the Symptoms of Post-Concussion Syndrome by Inhibiting MMP-9 Activity: A Randomized Controlled Trial in Indonesia. F1000res. 2021. Publisher Full Text"
}
|
[
{
"id": "88241",
"date": "28 Jun 2021",
"name": "David X. Cifu",
"expertise": [
"Reviewer Expertise TBI",
"HBOT",
"mild TBI",
"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\nThis is a small (n=20), unblinded RCT of low dose HBOT (three 60 minute sessions at b/n 2-3 ATA over 5 weeks) in middle-aged (mean 39 years old) people with (what were labeled) as mild TBI. The researchers identified reductions in serum MMP-9 and symptoms (RPQ) after 6 weeks.\nUnfortunately, this study is significantly underpowered, flawed in its diagnosis of mTBI (70% had intracranial bleeding, including SDH, EDH and IPH - the diagnosis of mTBI precludes these conditions), does not provide the specific time post-injury, the dosing of HBOT is atypical for mTBI trials, the controls refused to be in the HBOT arm (apparently that was by design?) and thus were negatively biased, and there was no HBOT sham so the treatment subjects were positively biased toward improvement.\nAdditionally, the authors have misquoted the mTBI/HBOT literature (e.g., references #14 and 15 do not support the efficacy of HBOT for mTBI) and do not seem to be aware of the HBOT literature. Of note, the abstract records the average age of participants as 60 years old, but the results section and tables identify it as 39 years old.\nThis study has too significant methodological limitations and inconsistencies to warrant 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? 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? No",
"responses": [
{
"c_id": "6908",
"date": "12 Jul 2021",
"name": "Maximillian Christian Oley",
"role": "Author Response",
"response": "The severity of TBI is assessed according to the GCS grading of the level of consciousness. Mild TBI can also be associated with intracranial lesions such as ICH, EDH, SDH, depressed fractures, etc. The space in the subarachnoid, interhemispheric, and cistern create room for compensation, thus mitigating the severity of the injury. Therefore, regardless of the size of the lesion, there is still tolerance so that symptoms will not be as severe. This is in accordance with the Monroe-Kelly law. This study was conducted on actual patients, not on animals, therefore it is difficult to reach homogeneity on our test subjects. We were unable to control the exact post-injury time as the time of injury and hospital transfer varies between patients, however, most patients received HBOT approximately one-week post-injury. In addition, to our knowledge, there is no guideline for HBOT dosing in brain injuries. The optimal oxygen dose and duration vary among several studies which makes the comparison process complicated and biased interpretations. Lastly, apologies for the difference in the results on the abstract from the results section. The average age of patients was 39 years."
}
]
},
{
"id": "88242",
"date": "26 Jul 2021",
"name": "Shai Efrati",
"expertise": [
"Reviewer Expertise Hyperbaric oxygen therapy",
"brain",
"traumatic brain injuries"
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe article entitled “Hyperbaric oxygen therapy ameliorates the symptoms of post-concussion syndrome by inhibiting MMP-9 activity: a randomized controlled trial in Indonesia” evaluated whether HBOT can accelerates the healing process, by measuring MMP, and reduces symptoms in patients with post-concussion syndrome by RPQ scores.\nThe study included 20 patients with post-concussion syndrome who were randomized into HBOT and control groups. HBOT reduced serum MMP-9 levels and improved the the RPQ scores.\nThe study suffers from major issues that needs to be address.\nWhat was the exact HBOT protocol? What does it mean 2-3 ATA? Was it 2 or 3? Based on what it was decided?\n\nWere only 3 sessions of HBOT given?\n\nIf somebody refused to receive HBOT, it is problematic to have them as a control since it is selection bias. It is higher significant since the sample size was relatively small.\n\nThe different in the baseline MMP mark the different between treatment and control groups.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? No\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? No\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "7339",
"date": "22 Oct 2021",
"name": "Maximillian Christian Oley",
"role": "Author Response",
"response": "Although several studies have shown favorable outcomes from incorporating HBOT at 1.5-2.4 ATA in the management of post-concussion syndrome, there isn’t an established protocol for the use of HBOT in this field.1-3 It is difficult homogenize our subjects since the level of tolerance is different in each patient. Also, patients did not receive HBOT simultaneously, this was an accumulation of our patients treated in the surgery department over a period of 6 months. Yes, 3 HBOT session were given. Even though the control group had higher MMP-9 levels at baseline, this was compensated for by the highly significant endpoint difference (the difference between both scores (delta) after five weeks). Moreover, to increase the validity of our study, we used another method of evaluation, which was the RPQ scores. Hu Q, Manaenko A, Guo Z, Huang L, Tang J, Zhang JH. Hyperbaric oxygen therapy for post concussion symptoms: issues may affect the results. Med Gas Res. 2015;5:10. Published 2015 Aug 25. doi:10.1186/s13618-015-0033-3 Harch PG, Andrews SR, Fogarty EF, Lucarini J, Van Meter KW. Case control study: hyperbaric oxygen treatment of mild traumatic brain injury persistent post-concussion syndrome and post-traumatic stress disorder. Med Gas Res. 2017;7(3):156-174. Published 2017 Oct 17. doi:10.4103/2045-9912.215745 Harch PG, Andrews SR, Rowe CJ, et al. Hyperbaric oxygen therapy for mild traumatic brain injury persistent postconcussion syndrome: a randomized controlled trial. Med Gas Res. 2020;10(1):8-20. doi:10.4103/2045-9912.279978"
}
]
}
] | 1
|
https://f1000research.com/articles/10-501
|
https://f1000research.com/articles/10-435/v1
|
02 Jun 21
|
{
"type": "Research Article",
"title": "Medication adherence in type 2 diabetes mellitus patients during Covid-19 pandemic: a cross-sectional study from the United Arab Emirates",
"authors": [
"Ameena Asheq",
"Akram Ashames",
"Moawia Al-Tabakha",
"Nageeb Hassan",
"Ammar Jairoun",
"Ameena Asheq",
"Moawia Al-Tabakha",
"Nageeb Hassan",
"Ammar Jairoun"
],
"abstract": "Background: Patients with chronic diseases often experience difficulty adhering to recommended treatments as instructed by their healthcare professionals. Recently, diabetes has been associated with the severity of the novel coronavirus disease (Covid-19), which raises the importance of improving medication adherence for diabetic patients to enhance the right use of antidiabetics amid the Covid-19 pandemic. Methods: This work assesses medication adherence among type 2 diabetes mellitus patients in the United Arab Emirates (UAE) and identifies the set of key demographic and health factors significantly associated with medication adherence. A descriptive cross-sectional study was conducted on an appropriate sample of type 2 diabetic patients in the UAE, with 180 patients of both genders and various social levels. A validated version of the eight-item Morisky Medication Adherence Scale (MMAS) was used for data collection. Results: The average MMAS score was 4.88, with 95% confidence intervals (CI) 4.6 and 5.2. 61.67% (n=111), 28.89% (n=52), and 9.44% (n=17) of patients were categorized into low, medium, and high adherent groups, respectively. These findings indicate that a high level of non-compliance to antidiabetic regimens among the population in the UAE. Conclusions: Patients demonstrated low level of compliance to antidiabetic regimens. Therefore, they must receive up-to-date knowledge about the disease and the treatment and enable easy access to their health care providers to enhance medication adherence.",
"keywords": [
"Type 2 Diabetes mellitus",
"Chronic diseases",
"Medication adherence",
"Coronavirus"
],
"content": "Introduction\n\nMedication adherence is the extent to which an individual takes medication as instructed by a healthcare professional. According to the World Health Organization (WHO), medication adherence is defined as “the degree to which the patient's behavior complies to the prescribed recommendations and instructions from the health care provider”.1 In this context, the concept aims to integrate the professional medical opinion and the patient's preferences and lifestyle where there is mutual cooperation between the physician and the patient to improve the outcome of the treatment and enhance the prescribed regimen's efficacy. Although adherence to medications guarantees a maximum benefit from the treatment plan, many patients do not comply with the instructions and the issue of non-adherence to medications is progressively increasing nowadays.2 There are several types of non-adherence described in the literature. The first type is called ‘primary non-adherence', in which the physician prescribes the treatment plan, but the patient does not follow the instructions from the beginning and does not initiate the plan itself. The second type of non-adherence is ‘non-persistence non-adherence', where the patients start the treatment regimen but do not complete it and stop the regimen without consulting their physicians. Several factors contribute to the development of this type. For example, lack of frequent communication between the patient and the physician, the patient feeling initial improvement after taking the primary doses of the prescribed drugs, the patient cannot afford the price of the completely prescribed regimen, or difficulty in the accessibility of the drug, especially in rare diseases that requires certain drugs. The third type of non-adherence is ‘non-confirming non-adherence' in which the patient does not strictly stick to the prescribed regimen. Instead, the patient changes the plan by altering doses or time, or even skipping some of them.3\n\nAssessing the patient's adherence is quite a challenging issue. However, there are several approaches adopted to fulfill this target. The first approach is the subjective method in which the patient, a family member, or caregiver is asked about the patient's commitment and the number of the doses taken with a specified time interval. The second method is the objective measurement, and it is achieved by counting the doses using electronic records for the medications or checking the pharmacy refill. A third method is the biochemical approach in which a non-harmful marker is added to the medication and then assessed in the organs where the drug is present or excreted, like assessing the serum or the drug's urine levels. The patient is considered compliant if compliance exceeds 80% of the prescribed plan of treatment.4\n\nRecently, diabetes has been associated with the severity of the novel coronavirus disease (Covid-19), which raises the importance of improving medication adherence for diabetic patients to enhance the right use of antidiabetics amid Covid-19 pandemic.5 As far as the authors of this work are aware, no published studies in the literature have studied medication adherence among diabetic patients during the Covid-19 pandemic in the United Arab Emirates (UAE). This work assesses medication adherence among type 2 diabetes mellitus patients in the UAE and identifies the set of key demographic and health factors significantly associated with medication adherence during the year of 2020.\n\n\nMethods\n\nInstitutional ethical approvals were obtained from Ajman University by the Research Ethics committee (Approval number P-F-H-2019-Nov-28) and the Saudi German Hospital in Ajman.\n\nSigned/verbal consent was obtained from the patients before data collection. Informed consent was given to all patients who participated in the study before answering the questionnaire and their personal information was kept in a closed closet for a certain period with full privacy was obtained from all subjects involved in the study.\n\nVerbal consent was for patients who were not willing to complete the questionnaire in the presence of the interviewer and was completed by five senior Pharmacy graduate students as trained interviewers/data collectors. Please, note that the presence of the interviewer can cause bias, and this should be avoided.\n\nThis work is a descriptive cross-sectional study conducted among a convenience sample of type 2 diabetic patients in the UAE. A validated version of the eight-item Morisky Medication Adherence Scale (MMAS-8) was used for data collection.6\n\nThe criteria used to collect data for the research were composed of inclusion/exclusion criteria. For inclusion, the data collected was from randomly selected diabetic patients, who must be above the age of 18 years old and must understand Arabic or English. Questionnaires were available for participants at the reception of the hospital and clinics in envelopes for patients waiting to see their doctors and they were invited to take part in the study while waiting. Exclusion criteria included pregnant women, people with mental illness, and/or those who refused to participate.\n\nIn a systematic review published in 2015, an average of 65.8 percent (ranging from 38.5 to 93.1%) were found to be adherent to their diabetic medication. As such, we need to find if in our study there is a significant difference from 65.8%.\n\nThe sample size of 384 was determined by the use of Survey Monkey sample size calculator. The proportion of the targeted characteristics in the Northern UAE could not be estimated. Therefore, we used a calculation formula to yield the maximum number of required sample size. The following formula was used based on the sample required to estimate a proportion with an approximate 95% confidence level\n\nwhere\n\nn: the desired sample size\n\nz: the standard normal deviation, set at 1.96 (corresponding to the 95% confidence level)\n\np: the proportion of the targeted characteristics in the region of Northern United Arab Emirates. Since there was no estimate available, it was set at 50% (or 0.50)\n\nq: 1-p\n\nd: absolute precision or accuracy, set at 0.05\n\nTherefore, the research sample size is\n\nDue to the current Covid-19 pandemic situation and lockdown, it was challenging to reach the targeted sample of 384. A total number of 180 participants was achieved.\n\nThe data was collected manually in the Saudi German Hospital in Ajman, six different clinics in Ajman and Sharjah, and via an online survey for other Northern Emirates. Physical questionnaires were available at the receptions of the hospital and clinics for participants who agreed to take part. Data collection took place from March 2020 to August 2020.\n\nThe self-reported eight-item MMAS was used to evaluate medication adherence among type 2 diabetes mellitus patients.23 Questions 1 through 7 have categorical responses (yes/no). Item 8 has five-points Likert scale. All the questions except question 5 are reverse coded to avoid participants responding in the same manner to a series of questions irrespective of their content; each “No” is coded “1” and each “yes” is coded “0”. For question 8, if the participant selects “0”, the given score is “1”, while if they select response “4”, the given score is “0”. Categorical responses “1, 2, 3” are respectively coded “0.25, 0.75, 0.75”. The total MMAS-8 scores range from 0-8. The adherence level is considered low if the MMAS-8 score is less than 6 (score < 6), medium if in the range of 6-7 and high if equal to 8.\n\nMissing total scores on multi-item instruments are equivalent to missing scores on a single-item instrument. Commonly used methods to deal with such missingness are complete-case analysis, mean imputation, or single-regression imputation. More advanced techniques that account for missing data uncertainty are multiple imputation or maximum likelihood estimation. Specific methods have also been developed for missing item scores in multi-item instruments, for example, person mean imputation, two-way imputation, response-function imputation, and multivariate normal imputation.\n\nThe data were analyzed by International Business Machines Corporation-Statistical Package for the Social Science (IBM-SPSS) version 25 (Chicago, USA). Before statistical analysis, all the dependent and independent variables were checked for any data entry errors or missing data. The number of responses and percentages were used to describe categorical variables and means ± relative standard deviation (RSD) was used to describe continuous variables. For instance, to identify outliers the distance between data point and the center of all data points to ensure data points do not fall within three SD of the mean. The normality of variables was tested using the Kolmogorov-Smirnov and Shapiro-Wilk test. Non-normally distributed data were stated using medians, interquartile ranges (IQR) and mean ranks. Qualitative variables were summarized using frequencies and percentages. The Chi-square and Fischer Exact tests were used to compare differences in proportions of qualitative variables. Univariate and multivariate logistic regression analysis was used to determine the significant factors associated with medication adherence. The stepwise method was used for variable selection and model building. A p-value < 0.05 was chosen to make statistical significance decisions.\n\nFour sources of error have been described that can threaten the precision and accuracy (i.e., reliability) of survey results and must be evaluated by readers. The first type of error, coverage error (sampling bias), occurs when there is a discrepancy between the target population and the population from which the sample was derived. This type of error can compromise the ability to generalize study results.\n\nSampling error (or random error) occurs when the researcher surveys only a subset (sample) of all possible subjects within the population of interest. Sample error is reported usually as the mean ±1 standard error from the mean (SEM).\n\nMeasurement error (response bias) occurs when the collection of data is influenced by the interviewer or when the survey item itself is unclear from the respondent's point of view. Parallel forms (usually consisting of alternatively worded items placed throughout the survey) of either specific survey items or the entire survey instrument have been used to increase reliability of mail survey research.\n\nAccurate assessment of measurement error relies on the provision of the questionnaire or tool used to collect data so that readers may analyze wording. Unfortunately, however, many articles relating to the results of survey research do not include the actual questionnaire used in the survey due to space and ownership issues.\n\nFinally, nonresponse error (nonresponse bias) occurs when a significant number of subjects in a sample do not respond to the survey when responders differ from non-responders in a way that influences, or could influence, the results. Since the lower response rate may increase the potential for higher nonresponse bias, and in order to minimize the possibility of nonresponse error we could manage to increase the number of participants by including more patients from different clinics in more geographical areas in UAE. To minimize bias from the interviewers, five pharmacy graduate students were recruited and trained to conduct the interviews.\n\n\nResults\n\nThe demographic data of patients are as shown in Table 1. A total of 180 patients participated in the study due to restrictions with Covid-19. Among the 180 participants, 47.2% (n = 85) were female and 52.8% (n = 95) were male. Of the total participants, 38 (21.1%) were aged 20-29 years, 36 (20.0%) were aged 30-39 years, 30 (16.7%) were aged 40-49 years, 39 (21.7%) were aged 50-59 years, and 37 (20.6%) were aged ≥ 60 years. The study participants were predominantly married (n = 147, 81.7%). Nearly half of the participants (n = 81, 45%) hold bachelor certificates. The emirates of residence reported were: 23 (12.8%) from Dubai, 78 (43.3%) from Sharjah, 60 (33.3%) from Ajman and 19 (10.6%) from other Emirates. The majority of the participants were non-Emirati (n = 155, 86.1%). Among the participants 114 (63.3%) had health insurance coverage and 73 (40.6%) had an income in the range of < 5,000 Arab Emirates Dirhams (AED), 54 (30%) earned between 5,000-14,000 AED, 34 (18.9%) had an income between 15,000-24,000 AED and 19 (10.6%) had an income higher than 25,000 AED.\n\nThe results of statistical modeling showed that patient's age, marital status, type of antidiabetic medications, and being confident about taking diabetes medication were strong determinants of medication adherence among patients with type 2 diabetes mellitus. Significantly decreased medication adherence was observed in those with single marital status (OR 0.366; 95%, CI 0.139–0.962), patients aged 50-59 years (OR 0.238; 95%, CI 0.058–0.983), patients aged 40-49 years (OR 0.195; 95%, CI 0.044–0.857) and patients aged 30-39 years (OR 0.195; 95%, CI 0.035–0.648). On the other hand, significantly increased medication adherence was observed in the patients who had non-insulin antidiabetic medication therapy (OR 3.085; 95%, CI 1.125–8.457) and those who were confident about taking diabetes medication (OR 8.200; 95%, CI 1.036–64.908).\n\nTable 2 shows the lifestyle and health information of the participants. Most of the participants exercise two times/week or less (n = 145, 80.6%) and 115 (63.9%) were nonsmokers.\n\nOf the total participants, 112 (62.2%) had one chronic disease, 35 (19.4%) had two chronic diseases, and 33 (18.3%) had ≥ three chronic diseases. The years since diagnosis as diabetic were as follows: 44 (24.4%) diagnosed as diabetic under one year ago, 55 (30.6%) within two to five years, and 81 (45%) diagnosed more than five years ago. Among the participants, 122 (67.8%) had a diabetic family history. Half of the study participants (n = 90, 50.0%) had one antidiabetic medication. The frequency of taking antidiabetic medications was as follows: 68 (37.8%) took the medication once, 83 (46.1%) twice, and 29 (16.1%) ≥ 3 times. The type of antidiabetic medication was detailed as follows: 38 (21.1%) had insulin therapy, 114 (63.3%) had non-insulin therapy, and 28 (15.6%) had both insulin and non-insulin therapy. The majority of the participants (n = 164, 91.1%) were confident about taking diabetes medications, and 120 (66.7%) believed that it is possible to develop complications if they do not take diabetes medication as instructed.\n\nThe average MMAS score was 4.88, with 95% confidence intervals of 4.6 and 5.2. Using the grading system mentioned in the Methods section, it can be claimed that the overall level of medication adherence was poor. Of the total 180 diabetic patients, (n = 111, 61.7%), (n = 52, 28.9%), and (n = 17, 9.4%) were low, medium, and high adherent groups, respectively. Table 3 presents the results of each item related to the MMAS-8.\n\nTable 4 shows the distribution of medication adherent groups according to demographic information. There was a statistically significant association between participants’ age and medication adherence, with low medication adherence scores among patients aged below 40 years compared to older patients (P = 0.020). Married patients were more likely to have better medication adherence scores than single participants (P = 0.018). Emirati patients were more likely to have better medication adherence scores than non-Emirati patients (P = 0.025).\n\nTable 5 shows the distribution of medication adherent groups according to lifestyle and health information. Patients who were confident about taking diabetes medication were more likely to have better medication adherence scores than those who weren’t confident about taking diabetes medication patients (P = 0.021).\n\nTable 6 displays univariate and multivariate logistic regression analysis results for the factors influencing medication adherence among patients with type 2 diabetes mellitus. The odds ratio in this table show the magnitude of the association, and their corresponding p-values indicate whether the association is statistically significant or not by using the cut-off values of 0.05, as mentioned in the Methods section.\n\nTo select the set of factors that jointly influence the medication adherence, we used the stepwise procedure applied to the multivariate logistic regression model. The results of this procedure showed that patient's age, marital status, type of antidiabetic medications, and being confident about taking diabetes medication were strong determents of medication adherence among patients with type 2 diabetes mellitus.\n\nSignificantly decreased medication adherence was observed in those with single marital status (OR 0.366; 95%, CI 0.139–0.962), patients aged 50-59 years (OR 0.238; 95%, CI 0.058–0.983), patients aged 40-49 years (OR 0.195; 95%, CI 0.044–0.857), and patients aged 30-39 years (OR 0.195; 95%, CI 0.035–0.648).\n\nOn the other hand, significantly increased medication adherence was observed in the patients who had non-insulin antidiabetic medication therapy (OR 3.085; 95%, CI 1.125–8.457), and those who were confident about taking diabetes medication (OR 8.200; 95%, CI 1.036–64.908).\n\n\nDiscussion\n\nAccording to the MMAS, our study showed that the prevalence of low adherence to antidiabetic medication was 61.67%, medium adherence was 28.89%, and high adherence was 9.44%. These findings reveal a high level of non-compliance to antidiabetic regimens among the UAE people. Our results were consistent with the findings reported by Al Haj et al., who interviewed 446 UAE patients from February 2015 to November 2015, and concluded that 64.6% of the UAE population were non-adherent to antidiabetic medications.7 They were also similar to the findings reported by Al Mazroui et al. about the non-compliance of UAE individuals to antidiabetic regimens, which reached almost 50% of the enrolled participants.8 Furthermore, it is evident that the percentage of non-adherence to antidiabetic medication in the UAE is quite similar to the other neighboring Gulf Cooperation Council (GCC) countries. For example, several studies reported a similar level of non-adherence among Saudi population, ranging from 50% to 70% of the enrolled participants.7,9–11 The similar results between the two countries are unsurprising, as they share many similar behavioral, cultural, and individual factors that may have contributed to the development of such a level of non-compliance. While the literature about adherence to antidiabetic medications among Arab individuals is quite minimal, several studies have discussed the same point worldwide. Kirkman et al., identified the level of non-adherence among the American population as 31%.12 Kalyango et al., reported similar levels among Ugandan individuals (28.9%)9. Other studies reported that the level of non-adherence in Malaysia ranges from 40% to 50%.13,14 In India, there were contradicting results that ranged from 30% to 60% of non-compliance.15,16 It can be seen from these results that the level of non-adherence is higher amongst the Arab population compared to Asian or American populations. One possible reason for the increased level of medication non-compliance among Arabs is that the level of diabetes, hypertension, and other chronic diseases is higher among Arab citizens, which increases the number of individuals diagnosed with these diseases and increases the probability of non-adherent individuals. Furthermore, the Arab people share other factors that directly contribute to higher levels of non-compliance among them. This may require more investigations to determine the contributing factors such as socioeconomic and lifestyle factors.\n\nStudies have shown that several factors are associated with the increased level of non-compliance to antidiabetic medications. Our study showed that age is a significant determinant of the level of adherence. We report that the level of adherence significantly decreased with increased age up to the age of 60 years old. There was no statistically significant decrease in the level of adherence among patients older than 60 years old. These results were slightly different to Al Haj and their coworkers’ findings, who concluded that the level of adherence is increased with age.17 Aloudah et al., also reported a lower level of adherence among the younger population compared to the older population.10 However, Mukherjee et al., reported similar results to our findings and concluded that the level of compliance significantly decreases with increased age.15 In addition, Ahmad et al., reported similar results about the impact of age on the level of adherence.14 A possible explanation for the decreased level of adherence with increased age of patients is that patients can forget about their medications and several studies have reported that forgetfulness is one of the leading causes behind non-adherence.15,18 Another factor that influences the level of non-compliance is marital status. Our study showed low adherence to antidiabetic medication among unmarried patients compared to married ones. These findings were consistent with Ahmed et al.,8 who reported similar findings of the significant effect of marital status on adherence level. Gelaw et al.,19 and Thakrar et al., concluded that married persons are more adherent to medications than single ones.16 The possible reason behind this relationship is that married individuals are more supported by their families to adhere to their regimens. In addition, forgetfulness is less likely when the family reminds the patient of his/her schedule and medication time. However, the effect of marital status was not proven in all the literature that studied the topic. Several studies reported no significant relationship between marital status and drug adherence.9,11,15,20 These contradicting results signify that further investigations need to be conducted in order to find out the real relationship between the variables.\n\nThe regimen of antidiabetic medications was thoroughly analyzed in several publications. Studies discussed the types and number of prescribed antidiabetic agents and their effect on the level of adherence. In our study, we found out that the level of adherence is increased with non-insulin antidiabetic medications compared to the insulin group. Our results were consistent with most of the previous literature. Mukhurjee et al., reported that a low adherence level is found among the patient group who were prescribed insulin only or insulin combined with oral hypoglycemic agents (OHAs) compared to people who use OHAs only.15 The same findings were reported by Khan et al.,11 Chua et al.,13 Ahmad et al.,14 Al Haj et al.,17 Aminde et al.,21 and Bali et al.22 Each of the previously mentioned studies confirmed that insulin only, or in combination with OHAs, is a significant factor in decreasing adherence and patients are more adherent when only OHAs are prescribed. A possible explanation for this finding is that people prefer to take their drugs via oral routes rather than injections. Hence, they are more adherent when taking oral pills. In addition, a combination of insulin and pills means that the patient must take two different drugs at different times; this increases non-adherence, as they have to stick to two (or more) drugs rather than only one. The previous hypothesis is supported by most of the previously mentioned papers, which reported a lower adherence level with increased numbers of medications.11,14 Despite several literature reports that supported our results, some authors reported different findings. Ahmed et al., reported no significant difference between the number of prescribed drugs and adherence level (P = 0.224).8 Kalyango et al., also reported no significant effect of either the number of administrated drugs or the administration route on the level of patient's adherence to the medications.8 The mainstay of literature is consistent with our findings, which supports our hypothesis that the number of drugs and the administration route do affect patients' compliance with antidiabetic medications.\n\nWe also found that the patient's knowledge and persuasion to take the medication were significantly associated with higher adherence to the medication. These results were consistent with other literature which supported our findings and reported a higher level of adherence associated with increased patient knowledge of the drugs and the complications of the disease.14,15 The reason behind this finding is quite obvious. It is expected that patients’ adherence increases when they realize the importance of the drug on the prognosis of their condition, complications of the diseases, and the burden of their pathology on the family, community, and themselves in the first place.\n\nInterestingly, we found no significant relationship between the level of adherence to antidiabetic medications and factors such as sex, educational level, monthly income, exercise, smoking, and the duration of diabetes. Each of these factors was discussed in one of the previously mentioned literature and one paper discussed a significant effect between each of these factors and the level of adherence11. In this study, low level of adherence is associated with young and male people, and that people with high education and monthly are more adherent to their medication. It was also found that the duration of diabetes when exceeding 10 years is also associated with low levels of adherence.\n\nA possible limitation to our findings is the low number of participants enrolled in the study. Due to the current pandemic situation, we only managed to enroll 180 patients while most of the previous studies used the data of more than our number. Further investigations need to be conducted to reassess the effect of these factors on the level of patient's adherence to antidiabetic medications.\n\n\nConclusions\n\nPatient adherence to antidiabetic medications is crucial in maintaining low blood sugar levels. With the recent findings that link diabetes with the severity of Covid-19, it is essential to test the willingness of patients to improve adherence to their antidiabetic regimens during the pandemic. Our study showed that the prevalence of low adherence to antidiabetic medication is 61.67%, medium adherence is 28.89%, and high adherence is 9.44%. These results revealed a high degree of non-compliance to antidiabetic regimens among UAE individuals. Non-adherence can occur as a result of the patient intentionally disregarding their treatment schedule, or as a result of carelessness and/or forgetfulness, whereby patients often omit their medication from their daily routine or take the medication later than necessary. We should ensure that patients receive up-to-date knowledge about the disease and drugs, apply prescription treatment activities, provide written and oral information to the patient, and enable patients to contact their health care providers regularly to enhance medication adherence.\n\n\nData availability\n\nThe questionnaire responses and interviews for those not willing to complete the questionnaire themselves that were collected/conducted from/with the participants are not openly available to protect the confidentiality and privacy of the participants. All document files were eradicated after data analysis. De-identified questionnaire responses are available in English and Arabic. The data can be obtained by applying to the Ajman University Ethical Committee through rec@ajman.ac.ae. Alternatively, please contact the corresponding author Dr. Akram Ashames at a.ashames@ajman.ac.ae who can facilitate this process. The ethical committee will study data requests on a case-by-case basis to ensure integrity, objectivity, confidentiality, and professional behavior.\n\nMendeley data: ‘Questionnaire on medication adherence UAE’. http://dx.doi.org/10.17632/prvft3d63z.1.23\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "References\n\nDobbels F, Van Damme-Lombaert R, Vanhaecke J, et al.: Growing pains: Non-adherence with the immunosuppressive regimen in adolescent transplant recipients. Pediatr Transplant. 2005; 9(3): 381–90. PubMed Abstract | Publisher Full Text\n\nJimmy B, Jose J: Patient medication adherence: Measures in daily practice. Oman Med J. 2011; 26(3): 155–9. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHorne R, Weinman J, Barber N, et al.: Concordance, adherence and compliance in medicine taking. Mult Scler. 2005.\n\nWinkler A, Teuscher AU, Mueller B, et al.: Monitoring adherence to prescribed medication in type 2 diabetic patients treated with sulfonylureas. Swiss Med Wkly. 2002. PubMed Abstract\n\nBanerjeea M, Chakraborty S, Pal R: Diabetes self-management amid COVID-19 pandemic. Diabetes Metab Syndr. Clin Res Rev. 2020; 14: 351–4. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMorisky DE, Ang A, Krousel-Wood M, et al.: Predictive validity of a medication adherence measure in an outpatient setting. J Clin Hypertens. 2008; 10: 348–54. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAl Mazroui NR, Kamal MM, Ghabash NM, et al.: Influence of pharmaceutical care on health outcomes in patients with Type 2 diabetes mellitus. Br J Clin Pharmacol. 2009; 67(5): 547–57. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAhmed NO, Abugalambo S, Almethen GH: Adherence to oral hypoglycemic medication among patients with diabetes in Saudi Arabia. Int J Health Sci (Qassim). 2017; 11(3): 45–9. PubMed Abstract | Free Full Text\n\nKalyango JN, Owino E, Nambuya AP: Non-adherence to diabetes treatment at mulago hospital in Uganda: Prevalence and associated factors. Afr Health Sci. 2008; 8(2): 67–73. PubMed Abstract | Free Full Text\n\nAloudah NM, Scott NW, Aljadhey HS, et al.: Medication adherence among patients with type 2 diabetes: A mixed methods study. PLoS One. 2018; 13(12): 1–18. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKhan AR, Lateef ZNA, Aithan MAA, et al.: Original Article Factors contributing to non-compliance among diabetics attending primary health centers in the Al Hasa district of Saudi Arabia.2012; 19(1). PubMed Abstract | Publisher Full Text | Free Full Text\n\nKirkman MS, Rowan-Martin MT, Levin R, et al.: Determinants of adherence to diabetes medications: Findings from a large pharmacy claims database. Diabetes Care. 2015; 38(4): 604–9. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChua SS, Chan SP: Medication adherence and achievement of glycaemic targets in ambulatory type 2 diabetic patients. J Appl Pharm Sci. 2011; 1(4): 55–9.\n\nSufiza Ahmad N, Ramli A, Islahudin F, et al.: Medication adherence in patients with type 2 diabetes mellitus treated at primary health clinics in Malaysia. Patient Prefer Adherence. 2013; 7: 525–30. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMukherjee S, Sarkar BS, Das KK, et al.: Original articlecompliance to antidiabetic drugs: Observations from the diabetic clinic of a medical college in Kolkata, India. J Clin Diagnostic Res. 2013; 7(4): 661–5. Publisher Full Text\n\nThakrar DV, Tundia MN, Vyas BL, et al.: A Cross Sectional Study on Medication Adherence and Factors Associated With Non-Compliance among Type-II Diabetic Patients From Udaipur, Rajasthan, India.2020; 11(1): 48–54.\n\nAl-Haj Mohd MMM, Phung H, Sun J, et al.: Improving adherence to medication in adults with diabetes in the United Arab Emirates. BMC Public Health. 2016; 16(1): 1–11. PubMed Abstract | Publisher Full Text | Free Full Text\n\nOdegard PS, Carpinito G, Christensen DB: Medication adherence program: Adherence challenges and interventions in type 2 diabetes. J Am Pharm Assoc. 2013; 53(3): 267–72. PubMed Abstract | Publisher Full Text\n\nGelaw BK, Mohammed A, Tegegne GT, et al.: Nonadherence and contributing factors among ambulatory patients with antidiabetic medications in Adama Referral Hospital. J Diabetes Res. 2014; 2014. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSaad AMJ, Younes ZMH, Ahmed H, et al.: Self-efficacy, self-care and glycemic control in Saudi Arabian patients with type 2 diabetes mellitus: A cross-sectional survey. Diabetes Res Clin Pract . PubMed Abstract | Publisher Full Text\n\nAminde LN, Tindong M, Ngwasiri CA, et al.: adherence to antidiabetic medication and factors associated with non-adherence among patients with type-2 diabetes mellitus in two regional hospitals in Cameroon. BMC Endocr Disord. 2019; 19(1): 1–9. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBali H, Ekhmimi Y, Khan M, et al.: Level of Compliance Among Diabetic and Hypertensive Patients and Affecting Factors in Al-Madina, Kingdom of Saudi Arabia. Int J Adv Res. 2016; 4(10): 1125–33. Publisher Full Text\n\nAshames A: Questionnaire on medication adherence UAE. Mendeley Data. 2021: V1. Publisher Full Text"
}
|
[
{
"id": "86528",
"date": "09 Jun 2021",
"name": "Khairi Mustafa Salem Fahelelbom",
"expertise": [
"Reviewer Expertise Pharmaceutical analysis"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nTotally, the present article is well-established, the results are presented in very clear manner, and the subject is very interesting, but some minor revision should be considered.\n\nIntroduction:\n\nKindly add up-to-date references to support your discussion. More references to previous related works can be added (Eg. Roncon et al. (20201), Alromaihi et al. (20202), Fang et al. (20203))\n\nMethods: For the online survey design, kindly mention:\n\nwhich platform did you use for the data collection.\n\nwhich tools did you use to distribute the online survey among the participants?\n\nResults:\n\nResults section is clearly and well-presented.\n\nDiscussion:\n\nPlease draw a concise conclusion from this study and present the limitations and future research and provide further information about study implications 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? 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/10-435
|
https://f1000research.com/articles/10-500/v1
|
25 Jun 21
|
{
"type": "Research Article",
"title": "Home hazard assessment and environmental modification to prevent falls in older people: the OTIS trial",
"authors": [
"Sarah Cockayne",
"Alison Pighills",
"Caroline Fairhurst",
"Joy Adamson",
"Shelley Crossland",
"Avril Drummond",
"Catherine Hewitt",
"Sara Rodgers",
"Sarah Ronaldson",
"Jenny McCaffery",
"Katie Whiteside",
"Arabella Scantlebury",
"Lyn Robinson-Smith",
"Ann Cochrane",
"Sarah E Lamb",
"Sophie Boyes",
"Simon Gilbody",
"Clare Relton",
"David Torgerson",
"The OTIS study",
"Alison Pighills",
"Caroline Fairhurst",
"Joy Adamson",
"Shelley Crossland",
"Avril Drummond",
"Catherine Hewitt",
"Sara Rodgers",
"Sarah Ronaldson",
"Jenny McCaffery",
"Katie Whiteside",
"Arabella Scantlebury",
"Lyn Robinson-Smith",
"Ann Cochrane",
"Sarah E Lamb",
"Sophie Boyes",
"Simon Gilbody",
"Clare Relton",
"David Torgerson"
],
"abstract": "Background: Falls in older people are a major cause of morbidity and mortality. There is some evidence to suggest that home hazard assessment and environmental modification delivered by an occupational therapist may reduce falls. The objective of this study was to evaluate the effectiveness of this intervention, relative to usual care.\nMethods: A pragmatic, two-arm modified cohort randomised controlled trial in eight NHS trusts in primary and secondary care in England. In total, 1331 community-dwelling adults aged 65 years and over with a history of falls or fear of falling were randomised in a 2:1 allocation to either usual care plus a falls prevention leaflet (n=901) or to receive the home hazard assessment and environmental modification intervention, plus usual care and a falls prevention leaflet (n=430). The primary outcome was the number of falls per participant over the 12 months from randomisation. Secondary outcomes included: proportion of fallers and multiple fallers, time to fall, and fear of falling.\nResults: All 1331 randomised participants (mean age 80 years, 872 [65.5%] female) were included in the primary analysis. There was a small increase in the rate of falls in the intervention group relative to usual care (adjusted incidence rate ratio 1.17, 95% CI 0.99 to 1.38; p=0.07). A similar proportion of participants in the intervention (57.0%) and usual care group (56.2%) reported at least one fall over 12 months. There were no differences in any of the other secondary outcomes and no serious, related adverse events were reported.\n\nConclusions: Home hazard assessment and environmental modification delivered by an occupational therapist did not reduce falls in community-dwelling older people deemed at higher risk of falling recruited to this trial.",
"keywords": [
"Home hazard assessment and environmental modification",
"falls prevention",
"older adults",
"modified cohort randomized controlled trial"
],
"content": "Introduction\n\nFalls in community-dwelling older people are a major source of morbidity and cost to society.1,2 A third of people over the age of 65 years fall each year, and those over 75 years are more likely to experience repeated falls. This issue will increase, given the ageing population. For some, the consequences of falling are serious; approximately 20% of falls require medical attention, costing the NHS approximately £2 billion per year, due mainly to the cost of treating hip fractures.3\n\nOlder people often attribute environmental factors, such as uneven surfaces, as the cause of their falls.4,5 Occupational therapists (OTs) routinely undertake environmental assessments of older peoples’ homes and recommend fall-prevention strategies. At the time of designing the trial, there is some evidence from a Cochrane review to suggest that home hazard assessment and environmental modification is effective at reducing falls particularly in those at higher risk of falling and when delivered by an occupational therapist.6 Guidance from the National Institute for Health and Care Excellence recommends that people who require hospital treatment following a fall should receive a home hazard assessment and environmental modification intervention by a suitably trained healthcare professional; however, no specific recommendations are provided for people at increased risk of falling but who have not required hospital treatment following a fall. A previous trial reported a reduction in falls as a secondary outcome following an OT-led home hazard assessment and environmental modification in this population.7 However, this was a pilot trial that did not include a cost-effectiveness analysis. Therefore, in order to find out if these preliminary findings could be confirmed and if home hazard assessment and environmental modification is cost-effective, we undertook OTIS (the Occupational Therapist Intervention Study).8,9\n\n\nMethods\n\nWe conducted OTIS,9 a pragmatic, multicentre, two-arm, parallel-group, modified cohort randomised controlled trial, (cRCT)10 between October 2016 and August 2019. The protocol was approved by West of Scotland Research Ethics Committee 3 (REC reference 16/WS/0154) and has been published.8\n\nWe recruited participants from eight NHS trusts in England based in primary and secondary care. Participants were initially recruited into an observational cohort, after being informed about the embedded trial and the possibility of being offered an OT home assessment visit. Potential participants were identified using: (i) cohorts held at the Yorkshire Health Study11 and York Trials Unit (YTU);12-14 (ii) a database search of General Practitioner (GP) patients; (iii) advertising (e.g. in faith magazines and GP surgeries); and (iv) opportunistic screening by podiatrists and GPs. Once identified, potential participants were sent trial information including a screening questionnaire and consent form to complete and return to YTU if they wished to take part.\n\nParticipants were eligible for the cohort if they: (i) were aged 65 years or over; (ii) were community dwelling, i.e. not living in a nursing/residential home; and (iii) reported a fear of falling or a fall in the previous 12 months. Participants were excluded if they were unable to: (i) give informed consent (e.g. due to dementia or Alzheimer’s disease); (ii) speak English and had no relative or friend to translate/interpret for them; (iii) walk 10 feet even using a walking aid; or (iv) if they had had an OT assessment for falls prevention in the past 12 months or were waiting for an assessment.\n\nEligible participants were sent a baseline questionnaire and monthly falls calendars to record when they fell and the number of times, to post back to YTU. Participants were eligible to be randomised once they had returned a completed baseline questionnaire and at least one falls calendar in the preceding three months.\n\nParticipants were randomised using the YTU’s secure, remote, web-based randomisation service, stratified by centre. When OTs had capacity to deliver the intervention visits, a member of the trial team at YTU randomised a batch of eligible participants from that centre in a single block. The size was determined by the number of participants available to randomise and the number the centre had capacity to deliver the intervention to within a reasonable timeframe. The allocation sequence was generated by an independent data systems manager, who was not involved in recruitment. To reduce costs, unequal allocation was used in favour of the usual care group, usually 2:1; however, on occasion, other allocation ratios were used. For example, towards the end of recruitment, some centres had capacity to see more, or fewer, than a third of the remaining eligible participants who were pending randomisation, so ratios ranging from 1:1 to 9.7:1 (usual care:intervention) were used to allow as many eligible participants to be randomised as possible. It was not possible to blind trial participants, the research team actively involved in the day-to-day running of the study or the statistician to treatment group, due to the unequal allocation ratio. However, data entry staff were blinded.\n\nBoth groups were sent a falls prevention leaflet produced by Age UK (‘Staying Steady’, published in June 2015) and continued to receive their usual healthcare from their GP or other healthcare professionals irrespective of the trial. In addition, the intervention group were offered one OT home hazard assessment and environmental modification. The intervention was delivered by Health and Care Professions Council registered OTs, who were trained by the study team to use the Westmead Home Safety Assessment Form (WeHSA).\n\nThe assessment was guided by the validated WeHSA form.15 This validated tool, consisting of 57 items, split into 15 domains was developed in Australia for older people. The OTs used this assessment tool to help identify potential falls hazards and risk-taking behaviours when walking through the participant’s home. A list of recommendations was agreed and a record of any suggested equipment made. This included: steps; outdoor lights; external rails to the outside of the property; ramp; wheelchair; grab rails/bannister; mobility aids; furniture raisers; shower rails/bath safety bars; bath lift; removable bath board; raised toilet seat; toilet frame; step; safety aids; sensor-operated or remove control lights; emergency alarms; assistive technology devices; light bulbs; bed hoist; bed; key safe; ferrules; walking aid parking devices; ladders; carpet glue/reflective anti-slip tape; alterations to house; or other miscellaneous items. The visits lasted approximately one hour during which recommendations on appropriate home modifications such as improving lighting were made.\n\nTreatment fidelity was explored by observations of the home visits, audits of training methods and case report forms completed by OTs, and semi-structured interviews.\n\nThe primary outcome was the rate of falls sustained per participant over the 12 months from randomisation. A fall was defined as an unexpected event in which the participant comes to rest on the ground, floor or lower level.16 Falls were reported via the monthly falls calendars and we also asked about number of falls in the past four months on questionnaires posted to participants at four, eight and 12 months post-randomisation. Participants who indicated on their falls calendar that they had fallen were telephoned to complete a Falls Data Collection Sheet (FDCS) to ascertain cause, location and consequences of the fall (e.g. superficial injury, fracture, hospital admission). Secondary outcomes:\n\n• fear of falling (participant questionnaires at four, eight and 12 months, via the question, “During the past 4 weeks have you worried about having a fall?”. Response categories were: All of the time; Most of the time; A good bit of the time; Some of the time; A little of the time; and None of the time. These were scored 1 to 6 and treated as continuous in the analysis. This measure has not been validated but was used by some of the authors in the earlier REFORM trial,12 where it correlated moderately well (r=0.6) with the validated Short Falls Efficacy Scale (Short FES-I),17 and it is quicker to complete;\n\n• fracture rate (via self-reported FDCS);\n\n• time to each fall (falls calendars);\n\n• proportion of participants reporting at least one fall or multiple (two or more) falls over 12 months; and\n\n• adverse events (collected via follow-up questionnaires or during phone calls).\n\nParticipants who did not return falls calendars or questionnaires were telephoned for data and/or posted reminders. The primary source of falls data was the post-randomisation monthly falls calendars, but where none were returned, falls data from the follow-up questionnaires were used, if provided. The economic analysis will be published separately.\n\nWe proposed to randomise 1299 participants 2:1 to usual care (n = 866) or intervention (n = 433). This allowed for 10% attrition and provided 90% power (two-sided, α = 0.05) to show a difference in the percentage of participants who fall at least once in the 12 months following randomisation from 60% in the usual care group to 50% in the intervention group. The sample size is based on a binary outcome rather that the primary outcome as power calculations for count data require greater assumptions and parameter estimates and, at the start of this trial, we felt there was insufficient data on which to reliably base this calculation.\n\nStatistical analyses were performed using Stata v1518 on an intention-to-treat (ITT) basis, using two-sided tests at the 5% significance level. Stata (RRID: SCR_012763) is a proprietary software; an open-access alternative that can perform an equivalent function to Stata for analysis is R, a free software environment for statistical computing and graphics (RRID: SCR_001905).\n\nFor the primary analysis, mixed-effects negative binomial regression was used adjusting for sex, age at randomisation, history of falling (number of falls in 12 months prior to recruitment: <2/≥2) and allocation ratio as fixed effects, and centre as a random effect. The model included an exposure variable for the number of months that the participant provided falls data. Where no falls data were provided at all, we assumed zero falls over a negligible follow-up time of 0.1 months to achieve a strict ITT analysis. The adjusted incidence rate ratio (IRR), 95% confidence interval (CI) and p-value are presented.\n\nA Complier Average Causal Effect (CACE) analysis19-21 to assess the impact of receiving the OT home assessment visit within 12 months of randomisation on the primary estimate was undertaken, using a two-stage instrumental variable (IV) regression approach with randomised group as the IV.\n\nA post hoc sensitivity analysis, including Parkinson’s disease as a covariate in the primary model, was undertaken due to a chance baseline imbalance in the proportion of participants in the two groups with this disease. Further sensitivity analyses considered the impact of missing data and clustering by OT. Pre-specified subgroup analyses assessed differential effects of the intervention based on whether a participant received hospital care as a result of a fall in the four months before baseline.\n\nFear of falling was analysed using a mixed effects, covariance pattern model incorporating all post-randomisation time points and adjusting for baseline fear of falling, sex, age, history of falling, allocation ratio, treatment group, time and a treatment-by-time interaction, with participant and centre as random effects. Logistic regression models explored the likelihood of reporting at least one fall, more than one fall, and a fear of falling (at least “some of the time”) at 12 months. Time between falls was analysed using the Andersen and Gill method for repeated events, via a Cox Proportional Hazards regression model with robust standard errors to account for dependent observations by participant. These models adjusted as for the primary outcome.\n\n\nResults\n\nBetween October 2016 and August 2018, we mailed out to 19308 potential participants (Figure 1); a total of 3100 screening forms were returned and reviewed for eligibility. We randomised 1331 participants to the intervention (n = 430) or usual care group (n = 901), with 381 (88.6%) intervention participants receiving an OTIS intervention visit within 12 months of randomisation (Figure 2).\n\nBaseline characteristics were comparable between the groups (Tables 1 and 2), apart from a chance imbalance in the proportion of participants with Parkinson’s disease (intervention n = 14, 3.3%; usual care n = 9, 1.0%).\n\na Note more than one option can be chosen.\n\na Balance problems whilst walking or dressing, or at least moderate problems doing usual activities, or one or more fall in previous 12 months.\n\nOverall, 1303 (97.9%) participants returned at least one falls calendar following randomisation (intervention n = 419, 97.4%; usual care n = 884, 98.1%); a further five (four usual care, one intervention) provided falls data via a participant questionnaire. Questionnaire data were used for analysis for these participants. In total, 2260 falls were reported: 826 in the intervention group (mean 1.9 per participant, SD 5.5, median 1, range 0 to 94) over a mean of 338 days (median 365), and 1434 in the usual care group (mean 1.6, SD 3.0, median 1, range 0 to 41) over a mean of 345 days (median 365). The adjusted negative binomial model indicated an increase in fall rate in the intervention group relative to usual care (IRR 1.17, 95% CI 0.99 to 1.38; p = 0.07); this was not statistically significant. This result was robust to sensitivity analyses (Table 3).\n\na Over 12 months.\n\nb At 12 months post-randomisation.\n\nc Logistic regression was used to assess whether any baseline factors were associated with missing falls outcome data. Participants who had had at least one previous fall were more likely to have missing outcome data (OR 5.84, 95% CI 1.13 to 30.21; p = 0.04). This was added as a covariate in the primary analysis.\n\nAbout a tenth of participants (intervention group n = 41, 9.5%; usual care group n = 83, 9.2%) reported that they attended hospital for a fall in the four months before baseline. There appeared to be a qualitative interaction between this factor and treatment group, with those in this subgroup benefiting from the intervention (IRR 0.86, 95% CI 0.50 to 1.47) compared with those who did not attend hospital for a fall in the four months before baseline (IRR 1.21, 95% CI 1.01 to 1.44); however, the interaction term between this factor and treatment group included in the primary model was not statistically significant (p = 0.24).\n\nThere was no evidence of a difference in any of the secondary outcomes or other data (Table 3 and Table 4) and no serious related adverse events reported.\n\nThe data suggested that the OTs received adequate training and delivered the intervention, mainly as intended. OTs commented that some trial participants did not reflect those seen in their usual clinical care as they were higher functioning. Recommendations were followed to varying degrees and depended on whether they were provided by health or social care services. A full account of the assessment of treatment fidelity will be published separately.\n\n\nDiscussion\n\nWe found no evidence that OT-delivered home hazard assessment and environmental modification reduced falls in community-dwelling older people. A 17% increase in fall rate was observed in the intervention group compared with usual care, but this was not statistically significant, nor were there any statistically significant differences in any secondary outcome. The number of control participants receiving a home visit or attending a falls clinic was low (9.2% and 4.6%, respectively) and unlikely to account for the lack of difference in falls rate. Whilst the OTs delivered the intervention mainly as intended, the recommendations were followed in varying degrees by participants.\n\nIntervention participants may have reported more falls due to reporting bias, if they were more mindful of the need to report falls following their assessment. This may have a positive impact in practice if fallers are more likely to acknowledge their falls and seek further assistance. Alternatively, following the OT visit, intervention participants may have felt more confident and less concerned about falling, leading them to undertake more risk-taking behaviours and falling more.\n\nOne participant, in the intervention group, reported 94 falls, which was substantially higher than the next largest number of falls of 41 (usual care group). This high value is likely to have influenced the magnitude of the treatment effect. The participant had Parkinson’s disease and we observed a difference in the proportion of participants with Parkinson’s disease between the two groups. In the post hoc sensitivity analysis adjusting for Parkinson’s disease, the treatment effect was reduced.\n\nOTIS results were not consistent with a previous pilot RCT, which found a statistically significant reduction in falls among participants receiving a home assessment.7 This may be due to OTIS participants having a lower risk of falls, as fewer fell during the 12-month follow-up than in the pilot trial (56% versus 66%).\n\nThe strength of OTIS lies in its robust methodology. The modified cRCT design allowed us to maximise recruitment as we were able to rescreen participants who were initially ineligible for the trial. Post-randomisation attrition rates were minimised by the use of a pre-randomisation run-in period, during which time participants engaged in returning falls calendars. Resentful demoralisation in the control group was minimised as only those in the intervention group were notified of group allocation. Collecting falls data by monthly calendar, and the ability to report falls by telephone, minimised participant recall bias. The main limitation was that outcome data relating to falls were self-reported, which could have led to inaccuracies. In addition, despite the fact that over 90% of participants returned outcome data, a post hoc power calculation for the primary outcome, based on negative binomial regression and using parameters estimated from this and our previous REFORM trial,12 indicated we were only powered at about 70% to detect the 17% increase in falls we observed.\n\nIn conclusion, this large, high-quality trial did not find any benefit of an OT-led home environmental assessment on self-reported falls among a population of older, community-dwelling people who had an elevated falls risk due to a previous recent fall or a fear of falling.\n\n\nData availability\n\nFull underlying (non-aggregated) data cannot be made publicly available since the ethics approval of this study does not cover openly publishing non-aggregated data.\n\nIn order to access this data, it must be requested from the corresponding author. Data requestors will have to provide: i) written description and legally binding confirmation that their data use is within the scope of the study; ii) detailed written description and legally binding confirmation of their actions to be taken to protect the data (e.g. with regard to transfer, storage, back-up, destruction, misuse, and use by other parties), as legally required and to current national and international standards (data protection concept); and iii) legally binding and written confirmation and description that their use of this data is in line with all applicable national and international laws (e.g. the General Data Protection Regulation of the EU).\n\nOpen Science Framework: CONSORT checklist for ‘Home hazard assessment and environmental modification to prevent falls in older people: the OTIS trial’, https://doi.org/10.17605/OSF.IO/P8AU2.22\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nAll participants will give written informed consent prior to entry to the study.",
"appendix": "Acknowledgements\n\nThe authors would like to acknowledge the participants who generously gave up their time to be part of the trial and to the Occupational Therapists who delivered the intervention and other staff from participating sites for their help with recruitment. We also thank our Patient Public Involvement group who provided valuable input throughout the study. We would also like to thank our Trial Steering/Data Monitoring and Ethics Committee for their support and guidance throughout the trial.\n\n\nReferences\n\nIglesias CP, Manca A, Torgerson DJ: The health-related quality of life and cost implications of falls in elderly women. Osteoporo Int. 2009; 20: 869–878. PubMed Abstract | Publisher Full Text\n\nBurns ER, Stevens JA, Lee R: The direct costs of fatal and non-fatal falls among older adults - United States. J Safety Res. 2016; 58: 99–103. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBritish Orthopaedic Association: The Care of Patients with Fragility Fracture. London: British Orthopaedic Association; 2007.\n\nRubenstein LZ: Falls in older people: epidemiology, risk factors and strategies for prevention. Age Ageing. 2006; 35: ii37–ii41. PubMed Abstract | Publisher Full Text\n\nTalbot LA, Musiol RJ, Witham EK, et al.: Falls in young, middle-aged and older community dwelling adults: perceived cause, environmental factors and injury. BMC Public Health. 2005; 5: 86. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGillespie LD, Robertson MC, Gillespie WJ, et al.: Interventions for preventing falls in older people living in the community. Cochrane Database of Syst Rev. 2012; 10.1002/14651858.CD007146.pub3: 1465–858. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPighills AC, Torgerson DJ, Sheldon TA, et al.: Environmental assessment and modification to prevent falls in older people. J. Am. Geriat. Soc. 2011; 59: 26–33. PubMed Abstract | Publisher Full Text\n\nCockayne S, Pighills A, Adamson J, et al.: Can occupational therapist-led home environmental assessment prevent falls in older people? A modified cohort randomised controlled trial protocol. BMJ Open. 2018; 8: e022488. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCockayne, Pighills S, Adamson J, et al.: Does occupational therapist-led home environmental assessment and modification reduce falls among high risk older people: A multicentre cohort randomised controlled trial (OTIS) with embedded qualitative and economic evaluations. Health Technol Assess. 2020; in press.\n\nRelton C, Torgerson D, O’Cathain A, et al.: Rethinking pragmatic randomised controlled trials: introducing the “cohort multiple randomised controlled trial” design. BMJ. 2010; 340: c1066. PubMed Abstract | Publisher Full Text\n\nRelton C, Bissell P, Smith C, et al.: South Yorkshire Cohort: a cohort trials facility study of health and weight-Protocol for the recruitment phase. BMC Public Health. 2011; 11: 640. Publisher Full Text\n\nCockayne S, Rodgers S, Green L, et al.: Clinical effectiveness and cost-effectiveness of a multifaceted podiatry intervention for falls prevention in older people: a multicentre cohort randomised controlled trial (the REducing Falls with ORthoses and a Multifaceted podiatry intervention trial). Health Technol Assess. 2017; 21: 1–198. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMitchell N, Hewitt C, Adamson J, et al.: A randomised evaluation of CollAborative care and active surveillance for Screen-Positive EldeRs with sub-threshold depression (CASPER): study protocol for a randomised controlled trial. Trials. 2011; 12: 225. PubMed Abstract | Publisher Full Text | Free Full Text\n\nShepstone L, Fordham R, Lenaghan E, et al.: A pragmatic randomised controlled trial of the effectiveness and cost-effectiveness of screening older women for the prevention of fractures: rationale, design and methods for the SCOOP study. Osteoporo Int. 2012; 23: 2507–2515. PubMed Abstract | Publisher Full Text\n\nClemson L, Fitzgerald MH, Heard R, et al.: Inter-rater reliability of a home fall hazards assessment tool. OTJR. 1999; 19: 83–98. Publisher Full Text\n\nLamb SE, Jørstad-Stein EC, Hauer K, et al.: Prevention of Falls Network Europe Outcomes Consensus Group. Development of a common outcome data set for fall injury prevention trials: the Prevention of Falls Network Europe consensus. J. Am. Geriat. Soc. 2005; 53: 1618–1622.\n\nKempen GI, Yardley L, van Haastregt JC, et al.: The Short FES-I: a shortened version of the falls efficacy scale-international to assess fear of falling. Age Ageing. 2008; 37: 45–50. PubMed Abstract | Publisher Full Text\n\nStataCorp: Stata Statistical Software: Release 15. In. College Station, TX: StataCorp LP; 2017.\n\nSussman JB, Hayward RA: An IV for the RCT: using instrumental variables to adjust for treatment contamination in randomised controlled trials. BMJ. 2010; 340: c2073. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDunn G: Instrumental Variables. Chichester: John Wiley & Sons; 2005.\n\nHewitt CE, Torgerson DJ, Miles JNV: Is there another way to take account of noncompliance in randomized controlled trials? Can Medl Assoc J. 2006; 175: 347. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCockayne S, Fairhurst C: OTIS main clinical results.2021, June 18. Publisher Full Text"
}
|
[
{
"id": "88201",
"date": "08 Jul 2021",
"name": "Carina U. Persson",
"expertise": [
"Reviewer Expertise My expertise is within research concerning fall/falls",
"rehabilitation medicine and psychometric properties."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe aim of the study was to evaluate the effectiveness of home hazard assessment and environmental modification delivered by an occupational therapist. The primary outcome was the number of falls per participant over the 12 months from randomization. The secondary outcomes were fear of falling, fracture rate, time to each fall, the proportion of fallers, and adverse events.\nThis two-arm modified cohort randomized trial included 1,331 community-dwelling adults aged 65 years or older deemed at higher risk of falling (with fear of falling or a history of falls). By using a web-based randomization service and an unequal allocation (2:1 in favour of the usual care group), the participants were randomized to either an intervention group or a usual care/control group. The intervention group was given a home hazard assessment and an environmental modification beyond usual care and a falls prevention leaflet to prevent falls compared with usual care and a falls prevention leaflet.\nStatistical methods used were mixed-effects negative binomial regression, Complier Average Causal Effect analysis, mixed-effects, covariance pattern model, and Cox proportional hazards regression model. The compliance with the recommendations was followed in varying degrees by participants. The authors did not find any evidence that OT-delivered home hazard assessment and environmental modification reduced falls in community-dwelling older people, nor did they find any difference between the groups regarding any of the secondary outcomes.\nThank you for showing me confidence in reviewing your interesting paper: Home hazard assessment and environmental modification to prevent falls in older people: the OTIS trial.\nI can see that you have spent many hours on your research project and the current article. Although it is well-written, I have some suggestions which I hope and believe can contribute to improvement:\nAbstract\nI understand that for reasons of space, it can be difficult to fit everything within given words. However, not all readers are familiar with the abbreviation of NHS as National Health Service.\n\nSecondary outcomes and adverse events are described in the Methods and Results, but they are not mentioned as objectives as expected.\n\nThe keywords used are definitely informative. However, they are not MeSH terms. Please consider whether you should use MeSH terms (for example “Safety”, “Accidental falls” and “Adult”).\n\nIntroduction\nPlease clarify the aim of the current study. The last sentence is somewhat confusing since it seems to involve both the aim of the current study and the primary drivers to undertake OTIS from the original beginning.\n\nMethods\nStudy design: Please inform the readers what the modification refers to.\n\nSetting and participants, third paragraph: Please clarify what the baseline questionnaire involves (self-reporting of the number of prescribed medications, comorbidities, fall in last 12 months, and so on).\n\nRandomisation and blinding, line 4: “…to deliver the intervention within a reasonable timeframe”. Please clarify the definition of “reasonable”.\n\nConcerning Outcome measures and the secondary outcomes: Adjust/mention the adverse events in the Abstract and clarify the objectives in the Introduction accordingly.\n\nConcerning Outcome measures and the secondary outcome fear of falling: The six response categories described for fear of falling seem to be ordinal data. For ordinal data, the distances between the scale steps are unknown. Consequently, ordinal data should not be analyzed as continuous data.\n\nWas fracture data using the FDCS validated by a review of the medical records?\n\nConcerning Outcome measures and the secondary outcome, adverse events: Please define “adverse events”.\n\nLast paragraph: I suggest the authors be stringent and add HR, 95% CI, and p-value where you write about the Cox Proportional Hazards regression model.\nNote: For the statistical analyses used, at least those first described, I suggest a review by a qualified statistician.\nResults\nPlease consider if the initial part of the first sentence should be moved to the Methods.\n\nCurrently, a presentation of the environmental modifications, the intervention in question, is missing and requested. Now it is unclear how many and what kind of modifications were completed.\n\nOutcomes, first paragraph: Please consider referring to Table 3. At present, there is some duplication of data (also in other paragraphs).\n\nPlease extend the data commentary for Table 4. At present, I think it is far too vague.\n\nTable 2: I am curious about how many had not experienced a fall in the previous 12 months.\n\nTable 2 and the characteristic risk of falling: Please consider to, in the footnote, give the definition of “balance problems” and of “moderate problems” beyond at least one fall in the previous 12 months. Was it a subjectively based need of supervision or tactile support and/or experience of protective reactions whilst walking, dressing, and performing usual activities? Or was “balance problems” and “moderate problems” based entirely on the individual's own interpretation of balance problems, without a given definition (with the exception related to experienced falls)?\n\nTable 3, first line “Number of falls per person”: Please delete “per person”. Please consider whether you instead should write “Total number of falls”.\n\nTable 3, second line “Mean (SD)”: Please add “Number of falls per person” in front of “mean (SD)”.\n\nTable 3, under the heading sensitivity analyses: Explain the abbreviation CACE in the footnote.\n\nRegarding “mean resource use” in Table 4: Mean resource use is not included in the aim or as a primary or secondary outcome. Please adjust the Introduction and Methods accordingly. Is mean resource use a description of actual usual care? If so, the title should be changed so that it is clear.\n\nTable 4: Give the number of participants (i.e. n= ) for the “Intervention” and “Usual care” in the heading.\n\nTable 4: Enter the units for the two mean (SD) columns (namely, number of visits and overnight stays). Adjust the first column accordingly, i.e. keep just the professions (GP, Nurse, Occupational Therapist, and so on) and the place for care. Finally, explain the abbreviation A&E.\n\nWhat about missing data in Table 5?\n\nUnfortunate and a weakness is that a full account of the compliance with the recommendations, the intervention under investigation, is not reported in the current publication. The data is needed in this publication for the reader to be able to interpret the results correctly.\n\nLast paragraph, first sentence: Please clarify the reasoning/data presentation related to the data commentary on adequate training.\n\nDiscussion\n\nPlease consider using your second sentence also in the Abstract since this sentence is more straightforward.\n\nPlease clarify any circumstances concerning or reflect about the 41 who “withdrew from treatment”.\n\nPlease add a paragraph in which you discuss your results in relation to previous research in the field.\n\nPlease consider commenting on any significance of the method used (advertising) to identify potential participants.\n\nPlease consider commenting on any cultural/environmental differences between England and Australia, about the fact that the WeHSA form was developed in Australia.\n\nPlease consider discussing any similarities between the items/domains included in the WeHSA form and “Staying Steady”, respectively, and how this may have affected the outcome/s.\n\nPlease consider including a reflection on the expected impact on recommendations obtained from a professional versus a leaflet.\n\nPlease consider discussing the low response rate, that the majority were women, and the generalizability of the results.\n\nGeneral\nPlease use the radix character (comma) to separate groups of thousands, as you do in Figure 1 and Figure 2.\n\nOnce again, thank you, and good luck with the current and future research projects. Best wishes.\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": "129185",
"date": "21 Apr 2022",
"name": "Alex McConnachie",
"expertise": [
"Reviewer Expertise Biostatistics",
"Clinical Trials"
],
"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\nCockayne et al present the results of a cohort randomised controlled trial of a falls prevention intervention. No evidence is found that the intervention is beneficial. This review focuses mainly on the statistical aspects of the paper.\nOverall this is a good write-up of a very good study. My comments are fairly minor.\nThere is a statement that the statistician could not be blind during the study due to the unequal allocation ratio. I think this is a little weak – if the statistician was blind to the randomisation, they will not know who is in each group, regardless of the allocation ratio. Still, there are many practical reasons for being unable to keep the statisticians blind in a trial such as this, and it is unlikely to have adversely affected the study, so this is not a major issue.\nThe fear of falling question, collected on a 6-point scale, is analysed as if it were continuous. This might be OK, depending on whether the modelling assumptions are met. Otherwise, an ordinal regression might be better for this outcome.\nThe main sample size calculation checks out OK, but I do not see what the post-hoc calculation adds to the paper. If the intervention effect observed is not statistically significant, then it seems obvious that the study was not powered to detect it. I would leave it out.\nFor the primary analysis, the allocation ratio is included as a fixed effect. Maybe I am missing something, but I cannot see why the outcome should vary systematically in relation to the allocation ratio. The problem with varying allocation ratios (as I understand it) is that the population, or the intervention, might vary over time, or from place to place, and populations randomised with different allocation ratios should be treated as separate subpopulations. One option might be to treat each randomisation “batch” as a separate group (i.e. include random effects for batches within centres). I doubt it will have a major impact on the intervention effect estimate, but I do not think the current analysis model makes sense.\nPersonally, I do not feel that including those with no outcome data by imputing no events in almost no time is worth doing. At best, this has no effect on the analysis. In my opinion, ITT is about the intention to treat, not the intention to follow up, and missing outcome data should be dealt with separately in sensitivity analyses. However, I accept that there are differing views on this.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-500
|
https://f1000research.com/articles/10-499/v1
|
25 Jun 21
|
{
"type": "Research Article",
"title": "Risk and protective factors of relapse in patients with first-episode schizophrenia from perspectives of health professionals: a qualitative study in northeastern Thailand",
"authors": [
"Jarunee Intharit",
"Khanogwan Kittiwattanagul",
"Wisit Chaveepojnkamjorn",
"Kukiat Tudpor",
"Jarunee Intharit",
"Khanogwan Kittiwattanagul",
"Wisit Chaveepojnkamjorn"
],
"abstract": "Background: Schizophrenia is a serious mental illness that can relapse after treatments. Risk and protective factors for relapse are dependent on multicultural contexts. Objective: To identify risk and protective factors related to relapse in first-episode schizophrenia (FES) in northeastern Thailand from perspectives of health professionals. Methods: This qualitative research collected data from 21 health professional staff members (psychiatric nurses, psychiatrists, psychologists, social workers, occupational therapists and nutritionist) of a tertiary psychiatric hospital of northeastern Thailand who had been involved in mental health care for schizophrenia for at least 5 years by in-depth interviews and group interview using semi-structured interview schedule. Content analyses was used to identify staff perception of factors that put patients at risk of relapse. Results: Data analyses demonstrated that factors related to relapse in FES patients were drug adherence (drug discontinuation, limited access to new generation drugs, self-dose reduction and skipping medication, and poor insight), family factors (stressful circumstances and family supports), substance abuses (narcotics, addictive substances, caffeinated drinks), concurrent medical illness (insomnia, thyroid diseases, and pregnancy-related hormonal changes), and natural course of disease. Conclusion: Factors affecting relapse in FES was not only drug adherence. Family factors, drug abuses, and concurrent health status should be also taken into account. A comprehensive mental health care program should be developed for FES patients in the region.",
"keywords": [
"first-episode schizophrenia",
"qualitative research",
"relapse",
"substance abuse",
"caregivers"
],
"content": "Introduction\n\nSchizophrenia is a chronic mental health disorder manifested by positive symptoms (suspiciousness, hallucinations, delusions, impaired cognitive ability, and disorganized speech or behavior) and negative symptoms (impairments in attention, loss of volition, social withdrawal, poverty of speech, and affective flattening)1,2. The prevalence of the disease varies between sites with median of approximately 15/100,000 persons3. The initial treatments of inpatient schizophrenia patients are antipsychotic drugs and other complementary interventions such as psychosocial therapy (social skill training and cognitive behavior therapy) and medical nutrition therapy4–6. Even though schizophrenic patients with first-episode psychosis (FEP) can be completely recovered by treatment programs, relapse can still occur. Relapse during the first few years after onset of the FEP is an important determinant for long-term clinical and functional outcome7. Rate of relapse in the first two years after the FEP is 28–43%8. The FEP constitutes a substantial burden for families, society, and health-care systems around the world9–11. Risk and protective factors in symptom severity of schizophrenia are different among countries and cultures12. Hence, identification of modifiable risk factors that could influence relapse is a crucial for planning treatment strategies. Therefore, the present qualitative study was aimed to investigate risk and protective factors in patients with first-episode schizophrenia in northeastern Thailand from perspectives of health professionals.\n\n\nMethods\n\nThis descriptive qualitative study based on Caelli’s generic principles using in-depth semi-structured interviews and focus group of health professionals to identify the risk and protective factors for relapse in patients with first-episode schizophrenia13. The health professionals participating in the study were purposively sampled from Khon Kaen Rajanagarindra Psychiatric Hospital (n = 21; male = 4, female = 17; aged between 34 and 52 years old) based on their qualification of at least three-year work experiences in the psychiatric hospital and informed consent. The study was carried out between January and July 2018. The research report complies with consensus-based minimum reporting guidelines for qualitative research (COREQ) (a copy of the checklist can be found in the Reporting guidelines). Data can be found at https://osf.io/4fhe5/?view_only=11d3b735eee44c61ac8e77b8bc15986a.\n\nResearcher study profiles and information about prior relationship/contact with research participants can be found in the Extended data14.\n\nAll procedures have been approved by the Ethical Review Committee for Human Research, Faculty of Public Health, Mahasarakham University (PH010/2560) and were carried out in accordance with the ethical principles in the Declaration of Helsinki. Clinical research methodology has been approved by the Thai Clinical Trials Registry (TCTR) TCTR20190923001. Pseudonyms were used to protect identity. Written informed consent forms were obtained from all participants and a copy of the form can be found in the Extended data14.\n\nAn experienced interviewer (J.I.), unknown to the participants and not involved in their work processes, conducted face-to-face and group semi-structured interviews allowing them reflecting points of view on the risk and protective factors. The interviews consisted of two parts – demographic data and 16 items of interviews on problems and causes of mental health status, severity of problems, perceived impact of problems, and needs for mental health care. The content validity of all the items has been confirmed by index of item-objective congruence (IOC). Only the items with IOC scores ≥ 0.75 were qualified and used. The interviews were undertaken and audio-recorded in Khon Kaen Rajanagarindra Psychiatric Hospital consulting rooms for approximately 90 minutes; and transcribed verbatim by the interviewer. Field notes were also made.\n\nData analysis was ongoing during the data collection. Transcripts were translated to English and coded using an agreed scheme by three independent coders (authors J.I., K.K. and K.T.). The transcripts were then sorted and organized using NVivo® 11 software package for managing and analyzing qualitative research data (QSR International, Melbourne, Australia). The data were coded and categorized to conceptualize emerging themes highlighted by the patients. All the answers from the participants were transported to the software, and the relevant sections from each questionnaire were coded and put into different categories. Using concept maps, the coded categories were further grouped to derive a particular theme from each group. Most representative quotations from the patients were used to bolster the themes. The transcripts were returned to the participants for correction proof. Coding tree analysis can be found in the Extended data14.\n\n\nResults\n\nTwenty-one health professionals (four males and seventeen females) were psychiatrists (5), psychiatric nurses (10), psychologists (2) social workers (2), a nutritionist, and an occupational therapist with mean age of 44.5±6 years old and average duration of services of 22.4±8.7 years. Fifteen staff work in the outpatient department and six persons serviced in the inpatient department. All details are shown in Table 1.\n\nBased on an analysis with the software, risk and protective factors were categorized into five main themes: drug adherence, family factors, substance abuses, concurrent medical illness, and natural course of disease as summarized in Table 2.\n\nAdherence is not limited to patient’s compliance to the treatment plan, but also their proper behavioral changes after diagnosis and life style adaptation in accordance with the treatment plan of the medical staff. Failure to follow medical prescription was attribute to various reasons, which could be further subdivided into four subthemes as follows.\n\nSubtheme 1.1: Drug discontinuation\n\nPatients took antipsychotic drugs until they felt better. They thought that they were fully recovered and hence skipped or discontinued taking drugs. Other reasons were unawareness of importance of the drugs, forgetfulness, and fear of side effects. Medical staff’s opinions are quoted as follows.\n\nPsychiatrist 2: “From my experience, relapse can be due to skipping drugs. The symptoms used to be controllable recur. In some cases, the relapse lasts for 1 week, some may last for 6–12 months.”\n\nPsychiatrist 3: “After we’ve sent them back home, some patients do not take drugs, causing relapse.”\n\nPsychiatrist 6: “Drug discontinuation, yes, many cases.”\n\nCommunity psychiatric nurse 1: “I used to follow up cases by phone. Some patients said that they had been completely recovered. No more drugs needed. This is one reason why they had to return to the hospital.”\n\nSome health professional provided reasons for discontinuation.\n\nPsychiatric nurse 1: “The patient said the drugs made him drooling and difficult speaking.”\n\nPsychiatric nurse 2: “Some antipsychotic drugs have side effects like poor or rigid walking.”\n\nPsychiatric nurse 3: “Refraining from taking drugs during the day since it made him drowsy and unable to teach (the patient was a teacher). Office workers tended to adjust dose of the drug themselves and didn’t want to take it due to the side effects like bad image and personality.”\n\nSubtheme 1.2: Limited access to new generation drugs\n\nHigh-quality and costly new-generation antipsychotic drugs were not prescribed for patients under basic healthcare coverage scheme. Therefore, these drugs were not accessible for economically poor people.\n\nPsychiatrist 4: “It’s about side effects. Some drugs have many side effects. Patients can’t tolerate and have to quit. For example, intramuscular injection of first-generation long-acting drugs, which are on the list (of the drugs for basic healthcare coverage scheme) can cause EPS (extrapyramidal side effects) more easily…rigid and stiff body. Meanwhile, less side effects can be seen in the patients using drugs like Paliperidone palmitate. But this drug is not covered by the scheme, very expensive, and so not accessible by most of the patients. Because of the side effects, patients were lost from follow-up or even from the whole treatment program and finally relapsed.”\n\nPsychiatrist 3: “Drugs play a big role. There’s big difference between typical and atypical drugs. The atypical ones prevent relapse better. So, patients who cannot access atypical drugs lose opportunities for better treatments.”\n\nPsychiatrist 2: “Patients have no access to atypical drugs according to their healthcare scheme…limited only to two atypical drugs. Another atypical drug is very expensive and not in the list (the National List of Essential Medicines of Thailand), so we cannot prescribe.”\n\nPsychiatrist 3: “At one point, when patients don’t respond to drugs, not so many choices left for us. Only typical drugs are in the list, so we lose control…no other choices. This makes it more complicated and more expensive for treatment cost. In some hospitals, they have just only first-generation antipsychotic drugs for newly diagnosed schizophrenia patients.”\n\nSubtheme 1.3: Self-dose reduction and skipping medication\n\nPatients took drugs until symptoms subsided and thought they fully had recovered. In some patients, they were worried about side effects. Then they arbitrarily decided to reduce drug dosage as stated below.\n\nPsychiatrist 6: “Patients think they get better, so they adjust drug dosage. They’re worried if they have taken them too much.”\n\nCommunity psychiatric nurse 1: “In some cases, they always skip drugs due to side effects. Instead of coming back for dose adjustment, they do it themselves or simply quit it. So, recurrence is so severe that they have to be re-admitted.”\n\nSubtheme 1.4: Poor insight\n\nSome patients lacked ability to recognize psychotic symptoms as illness. Thus, they did not need any treatments as mentioned below.\n\nCommunity psychiatric nurse 2: “In my point of view, a frequently found barrier to mental health care was that majority of patients denied their presence of illness…this was very clear. Then we forced them to come for treatment until they recovered. But they discontinued drugs when they were back home.”\n\nOccupational therapist: “First thing, they denied their illness. Then, yes, they received drugs, but not taking them.”\n\nPsychologist 2: “It’s a consequence from their denial of illness and kind of not understanding. They got home, not taking drugs, becoming relapsed, and coming back here again.”\n\nIn contrast, patients who well cooperated with care team would have better health in long term, being more peaceful or recovered from schizophrenia symptoms. They knew their needs for continuous treatments, managed to take drugs on their own. So, they came to receive medication for continuous treatments.\n\nPsychologist 1: “It’s compliance with treatments. For schizophrenia, drug adherence is important anyway. Continuous use of drugs has a huge effect. We have been seeing some cases routinely come for checkup, years past and still coming to receive new drugs.”\n\nCommunity psychiatric nurse 2: “From my experience, patients wouldn’t get relapse if they found jobs and had enough income. Meanwhile, medical staff took care of providing drugs, both oral and injection drugs. Community health staff gave mental support.”\n\nCommunity psychiatric nurse 2: “This case had first-episode schizophrenia with a problem of illness denial. So, we had to motivate his recognition of illness. This would guide him how he should take care for himself.”\n\nFamily factors in schizophrenia patients including stressful circumstances and family supports were addressed as causes of pressure as stated below.\n\nSubtheme 2.1: Stressful circumstances\n\nPersons with schizophrenia might not be able to appropriately cope with stressful circumstances such as losing their important persons, poor relationships, aggressive expressions, and poor communication.\n\nPsychiatrist 2: “From my experience, there are 4–5 reasons for relapse…the fourth one is stress. They might encounter life crisis like family loss and couldn’t cope with it. As a consequence, relapse happened despite they were taking drugs.”\n\nPsychiatrist 2: “Stress is one of relapse aggravating factors, especially the stress from critical lost events in their lives. When they lost, they failed to conform to the situation. Even though medications were continued, relapse could still occur.”\n\nCommunity nurse 2: “The factor that leads to severe first-episode and relapse, from my experience, is not alcohol, but principally is family pressure. When patients had family problems, they resorted to using alcohol and tobacco. Good friends would support their mind, but bad friends would ask them for drinking to release pressure. The drinking party is a talking panel for pressure.”\n\nPsychologist 1: “Well, a high expressed emotion has a high impact no matter how smart patients are. It can be very hostile as a cause of accumulative stress. The high expressed emotion is the variable that worsens psychotic symptoms in most cases.”\n\nPsychiatric nurse 1: “Some patients had been spoiled since their childhood, not accepting any rational talks. If they failed to control themselves, then the problems resumed. In some cases; on the other hand, if their parents were overly critical, psychotic symptoms might relapse. The patients could feel annoyed and lose self-control.”\n\nSocial worker 2: “Family problems like finance and debt can cause relapse and hospitalization. Particularly, poor communication among family members on financial topics can be stressful and aggravate the symptoms. In many cases, patients mentioned mother’s complaints of their laziness. Then they responded with ironic drinking of alcohol and smoking.”\n\nSubtheme 2.2: Family supports\n\nMost of schizophrenia patients receive family caring and supports15. These caregivers have been involved from the beginning – observing changed behaviors, bringing them to the hospitals, and supporting their routine cares in accordance with treatment plan until the patients can live their lives in society16. Therefore, competency of the caregivers is importance for them. In this present study, five subtopics related to family supports were found i.e., absenteeism of caregivers, unskilled caregivers, caregiver’s illiteracy on schizophrenia, family’s attitude, and poverty. When patients live alone or live with ever-busy family members, they have to confront with absenteeism of a primary caregiver. They lack continuous support, making it difficult to follow treatment plans as stated below.\n\nCommunity psychiatric nurse 1: “In community, some family members were so overloaded that they lost contact with the hospital. Well, it’s a matter of family income. In this case, a patient had to live alone and discontinued medications as he thought he had been fully recovered.”\n\nPsychiatric nurse 1: “The major problem was that patients lived with old grandparents. Other family members were tied up. The patients didn’t know when they should take antipsychotic drugs or when they had to come back for prescription refill. In some families, primary caregiver never showed up.”\n\nEducated caregivers play important roles in supporting and encouraging patients to follow treatment plans until they fully recover, having no relapse, and live their normal lives in society17. In this present study, it was found that some caregivers had inadequate skills to be in charge of drug adherence, hospital appointment, narcotic drug avoidance as well as guidance for patient’s self-improvement. Examples of the statements are presented as follows.\n\nCommunity psychiatric nurse 2: “Look, what has actually brought them to alcohol and other substances? Really, it’s their families. Lack of family support and caring can cause relapse. This is the key factor.”\n\nCommunity psychiatric nurse 2: “It’s just like a chain reaction. If they received good family supports, they would have stopped thinking about alcohol, ending a triggering process. In contrast, if their families were unsupportive, they would lose their spiritual anchors. This would eventually worsen their symptoms.”\n\nCommunity psychiatric nurse 1: “In fact, there’s problem in community. Most of caregivers for psychiatric patients are older persons.”\n\nPsychiatric nurse 1: “The primary caregiver was old. When she was busy, a neighbor would bring a patient to the hospital and back home. Then the neighbor went back to work. At home, the patient denied taking medicines. Then the caregiver couldn’t control the patient, not competent to give a care.”\n\nPsychologist 2: “For the first-episode patients, their family members still wouldn’t know how to take care of them. We might educate them on mental health issues. At first, it might not be clear for them. When the patient was calm and able to sleep well, symptoms seemed to be improving. The caregivers tended not to strictly instruct the patients. Even they instructed, the patients might not obey. Then the caregivers couldn’t do anything. On occasion, they were just powerless to control their mentally ill children.”\n\nLack of knowledge on etiology, symptoms, treatments, healthcare, and relapse prevention among family members and caregivers was another important risk factor as mentioned here.\n\nPsychiatric nurse 1: “In the first-episode patients, family members tended not to understand and didn’t believe that it’s schizophrenia. They thought it’s all about superstition.”\n\nPsychologist 1: “Family’s understanding of treatment process and related factors was important. Weak parents wouldn’t be able to control their children and lacked confidence to take care. If patients drank, the parents dared not dissuade them and had no idea what to do. Sometimes the parents were stress factors themselves – blaming of laziness without understanding the symptoms.”\n\nSocial worker 2: “In their point of view, family’s members didn’t realize that alcohols could aggravate the symptoms.”\n\nSocial worker 2: “Family’s members didn’t know how to manage patient’s behaviors. So, they were afraid that they might too strictly control the patient and situation would be getting worse. When they realized that the patients were mentally ill, the parents tended to treat them like physically ill persons. Some parents wouldn’t let their mentally ill children help with any housework, worrying about imposing too much stress on them. They still had to learn how to take care for the patients. Let them do some activities.”\n\nIn contrast, if caregivers were well-informed and adequately knowledgeable about schizophrenia, they would be able to support patients as addressed below.\n\nPsychologist 1: “If family members understood, it would reduce a lot of risk factors. They should understand process of treatments and had emotional maturity.”\n\nCommunity psychiatric nurse 2: “These factors were interrelated. If the family support was good, the patient would stop drinking alcohols and think about the family. Contrarily, if the family was bad, the patient would be without someone to lean on; and in turn the symptoms could be worsened.”\n\nIn the beginning, family members tended to have negative feeling toward mental illness such as disgrace and denial. The patients would not collaborate and the family didn’t not bring them to treatments as exemplified below.\n\nPsychiatric nurse 1: “Most of the patients never said they were ill.”\n\nSocial worker 1: “Some patients and their families didn’t accept an illness. They thought the patients were just normal and it’s too late when they arrived at the hospital. There’re two types of the families – protecting and denying. They tried to protect the patients or deny their illness as they’re afraid of social stigma.\n\nPsychologist 1: “In some cases, their families had negative attitude. They considered the patients as the weak persons. This attitude diminished the self-worth of persons. So, we had to support the patients, not only blaming them.”\n\nPsychiatric nurse 2: “In some community, people stigmatized patients. They tried to relegate the patients from the community.”\n\nIn contrast, if patient’s family members had positive attitude and accepted the illness, they would escort the patients to the hospital as well as encourage and support them as stated below.\n\nPsychiatrist 4: “As of lately, attitude of families toward psychiatric patients was better than in the past. Mental illness was previously seen as stigma, but it’s now more accepted as illness. In the past, some patients were confined and enchained, but not anymore. They are now allowed to live together with other family members and provided with medicines. They are not blamed as troubles, but considered as the ill persons, who need treatments and cares.”\n\nPsychiatrist 2: “I think that nowadays society has been wider open. In the past, psychiatric patients were chained and secretly kept in a storeroom. Lately, people in community accept and collaborate to help prevent them from relapse and let them be parts of the community. In some community, the patients have a chance to participate in charity or work for a little extra money. This reflects societal appreciation of the patients. As members of the community, they can get some money from a village fund to pay for taxi cabs, which bring them here to the hospital.”\n\nSome of patients and their families were poor, lived in a distance from the city, and lacked facilities, making it difficult for them to come for continuous follow up as shown in the following statements.\n\nPsychiatrist 3: “Psychosocial factor was that they lived so far away in the backcountry with limited basic needs and living costs; thus, coming to the hospital was difficult for them.”\n\nPsychiatric nurse 1: “Some family members said they couldn’t come, no money. Some had to wait for monthly subsistence allowance from the government fund to pay for a traveling cost. So, we asked them for an appointment only once. Then our doctors would prescribe drugs they could take at a local primary care center.”\n\nPsychiatric nurse 2: “Economic status could indirectly affect the patient’s symptoms. Most of the cases were poor and ill, having no money to come when the symptoms became worse. Caregivers were worried about work and had no time to bring the patients to the hospital.”\n\nPsychiatric nurse 1: “Most of the caregivers were old and poor. For example, they didn’t even have telephones. Then they gave us neighbor’s phone numbers, but turned out to be the wrong ones. It’s difficult for them to access online communication.”\n\nSome patients used narcotic drugs such as methamphetamines (meth pills and crystal meth), alcohols, cigarettes, energy drinks, coffee, and weight loss medications unwarily of their psychotic effects. The health professionals shared their experiences as narrated below.\n\nPsychiatrist 2: “From my experience, there were 4–5 reasons of relapse. One of these was substance use. It was an important cause of changing psychotic symptoms. The most frequently found were psychoactive substances like energy drinks, alcohols, or narcotics. Rice whisky and beer were mainly used by men. Meanwhile, diet pills were used by women to counteract weight gain, a side effect of antipsychotic drugs. Frequently, they quit the antipsychotic drugs and used diet pills and diet coffee drinks, especially in female teenagers.”\n\nPsychiatric nurse 1: “We had problem with readmission due to intractable factors. For example, liquor stores were easily accessed, patients were unaware of their own symptoms, and how they could manage the symptoms.”\n\nSocial worker 2: “Relapse in some cases resulted from alcohol drinking regardless of meth pill use. Alcohol is the psychoactive substance. Some patients said they didn’t drink whisky, but only energy drink. In fact, the one they talked about was an alcoholic energy drink. In some female patients, they believed that herbal liqueurs were good for health, which was not true. Actually, the herbal liqueurs could cause relapse. Other issues were cigarette smoking, and coffee.”\n\nPsychiatric nurse 5: “Some first-episode schizophrenia cases had been treated for 3–4 months until fully recovered. Then they got back to work for a couple of years, drinking alcohols. Then it became a long story of relapse afterwards.”\n\nPsychiatric nurse 1: “The thing was they quit medications, resorting to alcohol and drugs. As a result, relapse happened so severely like self-destruction and assaulting others. Some used energy drinks, coffee powder (not the drinking one), white whisky, and meth pills.”\n\nPsychiatric nurse 2: “Beside antipsychotic drugs, a second problems were addictive substances, most frequently alcohol or even underestimated substances like coffee and energy drinks. These were considered as triggering factors of relapse.”\n\nThe patients could have relapse due to other health problems, for example, sleeplessness, illness, pregnancy, and other conditions with medications as stated below.\n\nPsychiatrist 2: “Sleeplessness. If patients did not sleep well for several days in a roll such as going for boy scout camping, it could cause relapse.”\n\nPsychiatrist 5: “Physical conditions like hyperthyroid, pregnancy, and other concurrent drugs for medical illness could trigger relapse.”\n\nEven though patients followed all treatment plans and lived their normal lives, there was still a chance of relapse due to a natural pattern of schizophrenia as addressed below.\n\nPsychiatrist 2: “It’s about a natural course of disease. In some cases, relapses just happened even the patients adhered to treatment. Good or poor treatment outcome also depend on several factors.”\n\nPsychiatric nurse 1: “Some patients took antipsychotic drugs regularly, but it still relapsed.\n\nPsychologist 2: “Some patients had got relapse due to their uncooperativeness, but for some patients, relapse occurred in spite of good drug adherence.”\n\n\nDiscussion\n\nThailand is a developing country with an upper-middle income level and a population of approximately 70 million in 2021. Healthcare for psychiatric patients in Thailand is mainly provided by government-owned hospitals. Khon Kaen Rajanagarindra Psychiatric Hospital is one of five psychiatric hospitals in Northeast Thailand responsible for four provincial health areas (Roi-Et, Khon Kaen, Maha Sarakham, and Kalasin). This qualitative study revealed multiple important factors associated with relapse in FES from perspectives of health professionals working at the Khon Kaen Rajanagarindra Psychiatric Hospital. These factors were grouped into five themes: drug adherence, family factors, substance abuse, concurrent health problems, and natural course of schizophrenia.\n\nDrug adherence problems were further categorized into drug discontinuation, limited access to new generation drugs, self-dose reduction and skipping medication, and poor insight. Treatment guidelines for FES recommend at least one-year of antipsychotic drugs must be used following remission18. The patients who discontinued antipsychotic drugs expressed more positive symptoms, relapses, alcohol and cannabis use, reduced insight; and poorer quality of life19. These patients were more likely to live alone or live without family members involved in treatments. In this present study, the health professionals reported that their patients discontinued antipsychotic drugs without consultation. A major reason for discontinuation were intolerable side effects including extrapyramidal motor symptoms (difficult speaking and walking), drooling, and drowsiness20. These side effects usually result from first-generation drugs (FGAs, typical antipsychotics), which predominantly block dopaminergic neurotransmission by inhibiting dopamine 2 and 3 receptors (D2R and D3R) in the brain21. However, Liu-Seifert and colleagues reported different side effects i.e., weight gain, vomiting, dizziness, and fatigue in the patients using the second-generation antipsychotics (SGAs, atypical antipsychotics)22. These drugs are dopamine-serotonin antagonists with a high affinity for serotonin 2A (5HT-2AR) and lesser affinity to 2C, 6, and 7 receptors (5HT-2CR, 5HT-6R, and 5HT-7R). The 5HT-2C antagonism contributes to the weight gain produced by some SGAs23. Drug choice should be based on the patient’s clinical status and history of response to medication.\n\nSome patients still followed a medication plan, but arbitrarily reduced the dose or skipped some medications. Novak and Švab conducted a semi-structured focus group qualitative study in schizophrenia patients and found that they skipped medication because of intolerable side effects24. These side effects were reported to cause treatment-related stigma in the patients25. In worse cases, patients had poor insight from deficits of metacognition (ability to think about thinking)26. These patients lack insight into their own mental illness. As a result, they have poor adherence to treatment, subsequent illness relapse and rehospitalization. Verdoux and colleagues reported that over a period of first two years of FES, patients with poor medication adherence presented more frequently with an episodic course of illness and more readmission27. Therapeutic programs that can improve medication adherence should be implemented early in the course of psychosis to reduce the deleterious consequences of poor medication adherence on clinical outcomes27.\n\nIt has been reported that relapse rate in schizophrenia remains considerable even when prescribed medication adherence is well monitored28. Therefore, it is intriguing to clarify what other factors influence this relapse. Family factors related to FES in the present study were stressful circumstances and family supports. Family is a key supporting unit for schizophrenia patients by encouraging them to find the way of coping with psychotic symptoms29. In fact, family supports are important determinants for quality of life of schizophrenia patients30. Loss of family members are related to functional changes in the brain. Previous study demonstrated reduction of rostral anterior cingulate cortex (rACC) activity in the brain of patients with complicated grief after loss events31. It is known that the rACC is a region of the limbic system that is hypoactive during emotion processing in schizophrenia32. This might explain why the loss event-induced stress can trigger relapse in FES.\n\nAs depicted in the interview summary, high expressed emotion (high EE) coincides with intense and negative verbal exchanges. This commonly results in oppositional and conflictual consequences33. It has been revealed that living with family members with high EE doubled relapse risk34. The high EE consists of five components: critical comments, hostility, emotional overinvolvement (EOI), positive remarks, and warmth35. Critical comments are most common and exemplified by criticizing for being selfish or lazy, which are potential characteristics of negative symptoms36. Hostility is manifested by general criticisms or attitudes that are rejecting of the patient35. For example, caregivers state that patients are causes of problems and prefer to living away from them. Verma and colleagues found that applying psychoeducation program on problem-solving and communication skills in caregivers improved treatment outcomes in schizophrenia37. In Bangkok, Thailand, Imkome and Waraassawapati reported that caregivers learned from their experiences how to control patient’s psychotic symptoms as well as recognizing warning signs of the symptoms38. However, there are still no psychoeducational intervention or other methods applied to enhance their knowledge on mental health. In some countries, caregivers still believed that schizophrenia resulted from supernatural elements39. From literature, improving the mental health literacy even among primary health care professionals is required in developing countries40. These reports indicate that caregiver’s health literacy and attitude towards patients are still to be developed. Lastly, family’s poverty hinders psychotic symptom recovery and also limits resource allocation to family members, especially in low- and middle-income countries41,42. This present study indicated a positive influence of family supports on adaptation mechanisms of outpatients with schizophrenia. Hence, there is a need for relatives to provide support in order to facilitate adaptability.\n\nSubstance abuses are the third most frequently reported factors associated with relapse in schizophrenia43. Alvarez-Jimenez and colleagues showed a three-fold increase in risk of relapse in FES patients with persistent substance uses8. In this present study, illicit drugs such as amphetamine and methamphetamine; and psychoactive substances such as alcohol, energy drinks, coffee, and weight loss medications were reported as factors of psychotic relapse. Associated with higher frequency of relapse, several studies reported high comorbidity of substance abuse and schizophrenia44. Almost 75% of the FES patients reported the use of at least one substance in their lifetime45. Most frequently used substances are cannabis or alcohol alone and in combinations with opioids, stimulants, or cocaine46. In addition, a qualitative study showed that individuals with schizophrenia used caffeine at higher rates than the general population47. They consumed different types of caffeinated drinks the whole day including: cola, instant coffee, brewed coffee, tea, iced coffee, and energy drinks. In the same study, some participants also reported consumption of three or more different types of caffeinated drinks. In the present study, instant coffee drinks and energy drinks were major sources of caffeine. Most common reasons of substance use were for social recreation, for fun, and imitation of family members48.\n\nExacerbation of psychotic symptoms in patients with schizophrenia is caused by the multi determinants (biology factors, psychological and social factors). Previous studies showed that various concurrent physical health conditions including sleep disturbances, thyroid dysfunctions, and pregnancy can worsen psychotic symptoms. Schizophrenia patients with sleep disturbances were at a greater risk for worsening of positive symptoms after antipsychotic discontinuation49,50. These are linked to various forms of psychopathology of serotonin and dopamine systems51. Hyperthyroidism usually manifests with different psychiatric disorders such as anxiety, emotional psychosis, or depression52. Meanwhile, hypothyroidism is associated with negative symptoms of schizophrenia52. Sit and colleagues reported that postpartum psychosis occurred in 2/1,000 childbearing women within the first four weeks after delivery53. Etiology of the postpartum psychosis is hormonal shift after delivery in women with a history of mental illness54. Women with broadly defined affective psychoses were more likely to relapse earlier in the postpartum period55.\n\nSome patients experience relapse due to their uncooperativeness, but some patients still manifest relapse in spite of regular drug adherence. Hui and co-workers reported that relapse rates for the patients discontinuing and continuing medication were 79% and 41%, respectively56. In the discontinuation group, frontal dysfunction and dopamine hyperactivity predict relapse occurrence. Meanwhile in the continuation group, relapse is primed by signs of cognitive control deficits (cognitive disinhibition – inability to tune out stimuli that are irrelevant to the task/process)57. The proper cognitive control depends on coordination of various parts of the brain e.g., the medial frontal cortex, parietal regions, and dorsolateral prefrontal cortex (DLPFC)58. In schizophrenia patients with FES, it has been observed that levels of neurotransmitters (N-acetylaspartate and glutamate-glutamine-γ-aminobutyric acid complex) in the DLPFC are abnormal59. Altogether, abnormality of the brain per se is another potential cause of relapse in the FES.\n\n\nConclusion\n\nHealth care professionals perceived non-adherence to antipsychotic medication as a major together with family-related problems, substance abuses, concurrent health problems, and nature of schizophrenia. Adherence to antipsychotic medication, family support, and refraining from addictive substances were viewed as protective factors. The results also suggested that strengthening mental health psychoeducation by mental health professionals might help reduce relapse. This study calls for improvement in mental health care service delivery to individuals with schizophrenia. Establishing a program in mental health care that aims to produce competent mental health caregivers and professionals would improve clinical outcomes in mental health care service delivery.\n\n\nData availability\n\nOSF: Risk and protective factors of relapse in patients with first-episode schizophrenia from perspectives of health professionals: a qualitative study in northeastern Thailand. https://doi.org/10.17605/OSF.IO/4FHE514.\n\nThis project includes the following underlying data.\n\n- Raw data-Bilingual transcripts of interviews.rar\n\nOSF: Risk and protective factors of relapse in patients with first-episode schizophrenia from perspectives of health professionals: a qualitative study in northeastern Thailand. https://doi.org/10.17605/OSF.IO/4FHE514.\n\nThis project includes the following extended data.\n\n- Appendix 1 (Qualitative research study profiles)\n\n- Appendix 2 (Qualitative research study prior relationship/contact with research participants)\n\n- Bilingual interview guide\n\n- Coding tree analysis\n\n- A copy of written informed consent form\n\nOSF: COREQ checklist for ‘Risk and protective factors of relapse in patients with first-episode schizophrenia from perspectives of health professionals: a qualitative study in northeastern Thailand’. https://doi.org/10.17605/OSF.IO/4FHE514.\n\nData are available under the terms of the Creative Commons Zero \"No rights reserved\" data waiver (CC0 1.0 Public domain dedication).",
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PubMed Abstract | Publisher Full Text\n\nOhaeri JU, Fido AA: The opinion of caregivers on aspects of schizophrenia and major affective disorders in a Nigerian setting. Soc Psychiatry Psychiatr Epidemiol. 2001; 36(10): 493–9. PubMed Abstract | Publisher Full Text\n\nGanasen KA, Parker S, Hugo CJ, et al.: Mental health literacy: focus on developing countries. Afr J Psychiatry (Johannesbg). 2008; 11(1): 23–8. PubMed Abstract | Publisher Full Text\n\nRan MS, Yang LH, Liu YJ, et al.: The family economic status and outcome of people with schizophrenia in Xinjin, Chengdu, China: 14-year follow-up study. Int J Soc Psychiatry. 2017; 63(3): 203–11. PubMed Abstract | Publisher Full Text\n\nLund C, De Silva M, Plagerson S, et al.: Poverty and mental disorders: breaking the cycle in low-income and middle-income countries. Lancet. 2011; 378(9801): 1502–14. PubMed Abstract | Publisher Full Text\n\nOlivares JM, Sermon J, Hemels M, et al.: Definitions and drivers of relapse in patients with schizophrenia: a systematic literature review. Ann Gen Psychiatry. 2013; 12(1): 32. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMauri MC, Volonteri LS, De Gaspari IF, et al.: Substance abuse in first-episode schizophrenic patients: a retrospective study. Clin Pract Epidemiol Ment Health. 2006; 2: 4. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBanyal N, Bhattacharyya D, Yadav P: Study to determine the prevalance of substance use and factors associated with it, in first-episode of psychosis. Ind Psychiatry J. 2018; 27(2): 264–70. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPetersen L, Jeppesen P, Thorup A, et al.: Substance abuse and first-episode schizophrenia-spectrum disorders. The Danish OPUS trial. Early Interv Psychiatry. 2007; 1(1): 88–96. PubMed Abstract | Publisher Full Text\n\nThompson L, Pennay A, Zimmermann A, et al.: \"Clozapine makes me quite drowsy, so when I wake up in the morning those first cups of coffee are really handy\": an exploratory qualitative study of excessive caffeine consumption among individuals with schizophrenia. BMC Psychiatry. 2014; 14: 116. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLaudet AB, Magura S, Vogel HS, et al.: Perceived reasons for substance misuse among persons with a psychiatric disorder. Am J Orthopsychiatry. 2004; 74(3): 365–75. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCohrs S: Sleep disturbances in patients with schizophrenia : impact and effect of antipsychotics. CNS Drugs. 2008; 22(11): 939–62. PubMed Abstract | Publisher Full Text\n\nChemerinski E, Ho BC, Flaum M, et al.: Insomnia as a predictor for symptom worsening following antipsychotic withdrawal in schizophrenia. Compr Psychiatry. 2002; 43(5): 393–6. PubMed Abstract | Publisher Full Text\n\nHarvey AG, Murray G, Chandler RA, et al.: Sleep disturbance as transdiagnostic: consideration of neurobiological mechanisms. Clin Psychol Rev. 2011; 31(2): 225–35. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSantos NC, Costa P, Ruano D, et al.: Revisiting thyroid hormones in schizophrenia. J Thyroid Res. 2012; 2012: 569147. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSit D, Rothschild AJ, Wisner KL: A review of postpartum psychosis. J Womens Health (Larchmt). 2006; 15(4): 352–68. PubMed Abstract | Publisher Full Text | Free Full Text\n\nVigod SN, Villegas L, Dennis CL, et al.: Prevalence and risk factors for postpartum depression among women with preterm and low-birth-weight infants: a systematic review. BJOG. 2010; 117(5): 540–50. PubMed Abstract | Publisher Full Text\n\nTaylor CL, Stewart RJ, Howard LM: Relapse in the first three months postpartum in women with history of serious mental illness. 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}
|
[
{
"id": "142224",
"date": "12 Jul 2022",
"name": "Soumitra Das",
"expertise": [
"Reviewer Expertise Psychiatry",
"ADHD",
"Youth mental health",
"ECT"
],
"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\nEven though it does not reflect anything new in psychiatry, the paper talks about Thai-specific issues. Understanding a doctor's perspective is more like knowing the clinical acumens instead of knowing the real issues. Such interviews can be replicated with the patients or family itself.\nThe study is pretty easy and nothing much to add from my side. It's a straightforward study to do. I would recommend accepting it for indexing only because it brings area-specific data which might be useful for doctors in Thailand or similar countries.\n\nOverall the whole study might not have any value for the other parts of the globe.\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": "145345",
"date": "15 Aug 2022",
"name": "Padmavati Ramachandran",
"expertise": [
"Reviewer Expertise Schizophrenia research",
"physical health pf persons with medical comorbidity"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis paper aimed to identify risk and protective factors related to relapse in first-episode schizophrenia (FES) in northeastern Thailand from the perspectives of health professionals. A qualitative research design has been used. Results indicate multiple factors affect relapse rates.\n\nA critical review indicates several observations:\nLanguage needs to be checked throughout the paper for grammatical errors and also use of appropriate terms (e.g. use of the term 'schizophrenic' is not acceptable).\n\nThe abstract mentions content analysis whereas the data analysis section seems to describe thematic analysis.\n\nIntroduction: Would impaired cognitive ability be a positive symptom?\n\nMethods: How many FGD and IDI?\n\nResults: a) Use one term to refer to participants - either 'medical staff' or 'health professionals'. b) Repetitive quotes which convey the same meaning can be avoided. Some themes appear to have too many verbatim quotes and this makes the paper too lengthy. c) It might be helpful to use the term 'medication' instead of 'drugs' in Theme 1. Subsequent themes involve substance use and use of the term 'medication' may avoid confusion. d) The sub theme family supports could be made more reader-friendly by having further sub-headings and highlighting the most relevant quotes only. There is too much information under the heading currently.\n\nDiscussion: a) The term 'expressed emotion' has been mentioned and this was not used in the results section. b) Sit and colleagues reported that postpartum psychosis occurred in 2/1,000 childbearing women within the first four weeks after delivery - This statement is not entirely accurate. Women with mental illness have a chance of relapsing within the first 4 weeks.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-499
|
https://f1000research.com/articles/10-498/v1
|
25 Jun 21
|
{
"type": "Research Article",
"title": "No Pyro, No Party: Social factors, deliberate choices, and shared fan culture determine the use of illegal fireworks in a soccer stadium",
"authors": [
"Inge Merkelbach",
"Malte Dewies",
"Gera Noordzij",
"Semiha Denktas",
"Malte Dewies",
"Gera Noordzij",
"Semiha Denktas"
],
"abstract": "Lighting illegal fireworks inside soccer stadiums is a worldwide and persistent problem. Despite rules and regulations as well as rigorous enforcement, the use of illegal fireworks in football stadium is increasing rather than decreasing. Little is yet known about the causes and predictors of this behavior, preventing the development of effective interventions or communication strategies. We therefore conducted a qualitative study, using semistructured interviews with both supporters of a large Dutch soccer club who participated in lighting fireworks, and with professionals who dealt with illegal fireworks in daily practice. Semi-structures interviews were based on hooliganism literature as well as the COM-B model. We concluded that hooliganism and lighting illegal are distinctly different phenomena, although they share some underlying constructs. From a behavioral perspective, using the COM-B model as a framework, reflective motivation was identified as the strongest facilitator of lighting fireworks, which appeared to be an important part of supporter life and shared culture. Quick interventions that target automatic behavior, such as nudges, will probably thus not be successful in changing this behavior. Supporters suggest compromise between supporters and professionals as preferred future direction. Reported feelings of stigmatization by and feeling unappreciated by professionals, could interfere with successful implementation of this direction. Professionals however contradict negative to have judgements of supporters. Building a bridge between supporters and professionals should be a first step towards a solution.",
"keywords": [
"Soccer",
"illegal fireworks",
"COM-B",
"hooliganism",
"fan culture"
],
"content": "Introduction\n\nIn many countries around the world, supporters lighting fireworks in soccer stadiums is considered a growing problem. This is also the case in The Netherlands where lightning fireworks is the most often observed punishable offense in soccer stadiums (Nohlen & Harreveld, 2017) and where the number of incidents related to fireworks in soccer stadiums keeps increasing (e.g., Jaarverslag Voetbal en Veiligheid 2017/2018, 2018). Yet, lighting fireworks in soccer stadiums is illegal in The Netherlands as fireworks can legally be lit only around new year (article 2.1.1 of the Dutch Fireworks Decree). In addition, lighting fireworks is against regulations of the national (Royal Dutch Football Association; KNVB), the European (Union of European Football Associations; UEFA) and the global soccer associations (Fédération Internationale de Football Association: FIFA). Lighting fireworks concerns the safety of those inside the stadium as it is often difficult to keep the European recommended safety distance from fireworks of 1 to 15 meters (Guideline 2007/23/EG). Apart from potential direct damage or injury, lighting fireworks in stadiums was shown to cause a release of large amounts of nanoparticles, among which heavy metals, affecting health and the environment (Pirker et al., 2020). Containing the lighting of fireworks is thus important.\n\nEfforts to contain the lighting of fireworks are ample and directed towards soccer clubs as well as supporters. The UEFA fines soccer clubs if a club’s supporters light fireworks. In addition, the UEFA and the KNVB can require clubs to ban supporters from specific stadium boxes or the whole stadium for one or multiple matches. Individual supporters who are caught carrying or lighting fireworks inside the stadium or the stadium area receive fines from the KNVB and the Dutch government adding up to approximately 900 euros. In addition to these fines, those supporters receive a stadium ban of minimum six months. To detect fireworks offenders, soccer clubs frisk supporters at the entrances to the stadium area and surveillance is used, namely cameras, stewards, and the police. In short, fireworks in soccer stadiums affects many people, involves high costs, and demands much effort from clubs, stewards, police, and prosecution.\n\nThe high number of fireworks related incidents shows that the behavior continues and that current repressive efforts are not effective (enough) (Football and Safety Audit Team, 2017). Increasing restrictive measures even further has multiple downsides because it may not be effective, it is expensive, and it is likely to make the atmosphere in the stadium less pleasant and welcoming especially for the majority of complying supporters. For instance, when waiting times at stadiums entrances are increased because of intensified frisking. Behavior change strategies grounded in a better understanding of the behavior of lighting fireworks are currently seldomly used, but may be effective, less restrictive, and cheaper. Therefore, we took a behavioral approach interviewing soccer supporters and professionals to understand the use of fireworks in the stadium. Specifically, we focused on social, individual, and contextual factors that could explain the behavior. Behavioral explanations are crucial for identifying effective behavior change strategies (e.g., Howlett et al., 2020; Michie, Van Stralen & West, 2011).\n\nThis research was initiated when the municipality of Rotterdam approached the Behavioral Insights Group Rotterdam (BIG’R) in aiming to design strategies to contain the use of fireworks in the stadium of Rotterdam’s largest soccer club, Feyenoord. Like other behavioral insights teams around the world (Afif et al., 2018), BIG’R enables institutionalized collaborations between behavioral scientists and public servants to pioneer the application of behavioral insights for public policy (John, 2014). Feyenoord is one of the major soccer clubs of the Netherlands with on average about 45.000 supporters visiting home matches in the Feyenoord stadium (KNVB Expertise, 2015). Feyenoord is renowned for the extensive use of fireworks by the club’s supporters (Hellinga, 2019).\n\nTo the best of our knowledge, (behavioral) scientific literature on lighting fireworks in stadiums is limited, leaving the phenomenon largely unexplained. When lighting fireworks, supporters however necessarily make planned efforts to not get caught and they risk adverse consequences (stadium bans, fines). This suggests that they perceive this behavior as important or valuable. Indeed, Brechbuhl and colleagues (2017) report that lighting fireworks is seen as important and likely part of a shared culture and identity for fanatical soccer supporters. However, the authors do not analyze the behavior of illegally lighting fireworks in depth since not fireworks, but markers of escalation are the prime focus of their research. The notion that fireworks are important to substantial groups of supporters is supported by the existence of several websites (e.g., In de Hekken), songs (e.g., “No Pyro No Party”), blogs, and YouTube profiles that are created and managed by supporters which discuss the subject in a positive manner.\n\nFireworks offenders may (in part) be the same social group as hooligans because fireworks tend to be lit by fanatic supporters and in stadium boxes that are also popular among hooligans. Based on a survey, Scholz and Hurych (2018) states that the majority of soccer hooligans indeed also engages in lighting fireworks, suggesting at least a partial overlap between supporters who light fireworks and hooligans. In the absence of a body of literature specifically on lighting fireworks by supporters, what is known about supporters and hooliganism is used to inform and contextualize our research. Soccer hooliganism, defined as violent and destructive behavior (Budim, 2018), is often explained by group identity and a shared culture (Zimniak, 2020) in which the ingroup is contrasted with the outgroup (Ward, 2002). Within the ingroup, strong social ties, social identity within the group, and the use of symbolism are of great importance (Dionisio et al., 2008). Spaaij (2008) identifies six fundamental features of the hooligan identity: excitement and pleasurable emotional arousal, hard masculinity, territorial identifications, individual and collective management of reputation, a sense of solidarity and belonging, and representations of sovereignty and autonomy. Therefore, ingroup and identity features are candidates for explaining the use of fireworks.\n\nScholz and Hurych (2018) however categorized less than 5% of fanatical supporters (i.e., supporters visiting the most fanatical box of boxes in the stadium) as hooligans, and it seems that for most coordinated fireworks events more than 5% of fanatical supporters is involved. This suggests that at least part of all fireworks lit inside the stadium cannot be attributed to hooligans. How large the overlap is between supporters who light fireworks and hooligans, is currently unknown. Hooligans are known to be supported in their behaviors by a group of other supporters who have a positive attitude towards hooligans, so called hoolifans (Rookwood & Pearson, 2012). Supporters that light fireworks may be supported in a similar way by other supporters who encourage and reward that behavior. For instance, fanatical female soccer supporters from Czech Republic indicate to almost never light fireworks but almost exclusively regard it as a positive act and sometimes even assist (Scholz, 2020). They may not do it because fanatical fandom in soccer stadium is still associated with traditional masculinity (Kossakowski et al., 2020).\n\nIn the current study, we chose a qualitative design and took an interview approach. Explorative in-depth interviews are suitable for collecting information on complex (and understudied) phenomena (Sofaer, 1999). In order to gain understanding of both the perceived barriers as well as motivations for and facilitators of the behavior, interviews were based on elements described in hooliganism literature and the COM-B model (Michie et al., 2011). This general behavioral model assumes that capability (physical and psychological), opportunity (social and physical), and motivation (automatic and reflective) are basic conditions for the occurrence of all human behavior. We chose this model because we considered it broad enough to accommodate the elements from the hooliganism literature (such as social environment and motivation) and because it could guide the exploration of other personal, social, and contextual factors affecting the behavior. Additionally, we investigated possible solutions and visions for the future. We interviewed supporters who frequently lit fireworks at the time of the interview or sometime in the past. Some had recently received a stadium ban for lightning fireworks. As a frame of reference, we also interviewed professionals who dealt with fireworks in the stadium as part of their work, e.g., employees of Feyenoord and police officers. Permission to conduct this research was obtained from the ethics review committee DPECS, ESSB, of the Erasmus University Rotterdam (19-045).\n\n\nMethods\n\nSupporters: 16 fanatical supporters of Feyenoord participated in this study (i.e. all participating supporters had, or recently had had a season ticket). Data collection stopped at this point because the first author conducting all interviews felt saturation was reached because no new information came up in the last interviews. Although sample size is small, we believe we gained a complete picture of the behavior, because the studied behavior was very specific, and the target group relatively homogenous. We used purposive sampling and interviewed both supporters who were lighting fireworks at the time of the interview and supporters who had stopped doing so (both making up half of our sample). All supporters had lit fireworks during matches and/or Feyenoord-related events such as training sessions. Additionally, we interviewed supporters who had and had not been caught (half of the supporters currently lighting fireworks were caught as were a third of the supporters not lightning fireworks any longer). Participants were recruited a) through the official supporters association of Feyenoord or b) were known by the club because they carried out chores in order to shorten a recently received stadium ban related to fireworks.\n\nAll participants were men with a Dutch background. Participants were between 20 to 49 years of age, with a mean of 30 years. Several supporters showed their fandom through their appearance, for example by wearing Feyenoord clothing and tattoos. Some of the supporters who were interviewed via video calling also used Feyenoord related items for their interior design.\n\nProfessionals: 10 professionals participated in this study to offer an expert frame of reference. We again made use of purposive sampling trying to include at least one representative of all major institutions dealing with the issue. Participants worked at the municipality of Rotterdam (n = 1), soccer club Feyenoord (n = 3), the supporters association (n = 1), the police and justice department (n = 4), or a professional fireworks company that had conducted several legal fireworks shows in the Feyenoord stadium (n = 1). Data collection stopped after these 10 interviews because all major professional groups dealing with the issue had participated, and information provided by professionals within the same institution was highly similar. Professionals at higher management levels (e.g., KNVB or UEFA) could not be reached.\n\nPreparation and start-up-phase: The municipality of Rotterdam contacted BIG’R to contain the use of illegal fireworks in the Feyenoord soccer stadium. Several exploratory conversations with the municipality, the club, and the police and justice department took place. Due to the complexity and persistence of the problem and the lack of scientific literature on the subject, it was decided to carry out a qualitative study aiming to increase understanding of the behavior.\n\nRecruitment, selection, and requirements: Professionals were recruited via the professional network of the contact person of the municipality of Rotterdam. In two instances colleagues of these professionals were interviewed after a professional had suggested to interview them because of their relevant knowledge.\n\nVia professional contacts of Feyenoord or the Feyenoord supporter association, supporters received an information letter about this research. They could then give written consent to be approached by the research team them. Supporters were approached in the name of research (rather than in the name of the municipality) in order to ensure they felt comfortable to take part in the study. Supporters were assured they would not experience any negative consequences if they participated in this research and talked openly about their behavior. They were informed that their participation was an opportunity to have a voice in the public debate as the outcomes of this research would be shared with various institutions in order to facilitate finding solutions. Participants who agreed to participate gave written consent before the interview. For their participation, supporters received a Feyenoord gift card worth 15 euros. Professionals did not receive any reimbursement for their participation.\n\nInterview: Because the topic was sensitive, we decided to conduct one-on-one interviews. Interviews with professionals took place at their work locations and interviews with supporters took place in the Feyenoord stadium, a room offered by the Feyenoord supporter association, or via video calling due to COVID-19 measures. Supporters generally came across as motivated and eloquent. On average, interviews lasted about 50 minutes (range 25 to 90 minutes). The interviews were audio recorded and upon request participants could receive the audio recording or a transcribed version of their interview. However, none of the participants used this opportunity. After the interview, supporters were asked via email to anonymously answer a short online questionnaire evaluating the interview experience. From 12 who could be contacted via email, 10 filled in the survey (83%). In general, supporters experienced the interview as pleasant, and as an opportunity to share their opinion (see Table 1).\n\nInterview guide: All participants were asked the same set of questions (interview guides for supporters and professionals can be found in the Extended data) which could be complemented with questions based on the answers of participants (i.e., semi structured interview). Questions were partly based on hooliganism literature, and partly on the COM-B model (Michie et al., 2011).\n\nEvaluation of the interview experience: To be able to assess to what extent supporters felt they had been able to speak freely during the interview, they filled out a five-item questionnaire (see Table 1). Professionals did not fill out an evaluation because socially desirable answering or reluctance to provide answers was not expected to be an issue in this group since they did not report on their own illegal behavior.\n\nAll interviews were literally transcribed and coded by two researchers, using thematic analysis (Braun & Clarke, 2008). Codes were obtained through inductive coding in Atlas.ti 8.4 and grouped into categories. If multiple codes were applicable to the same piece of text, codes sometimes could overlap. Differences of opinion between coders were solved through discussion and consensus. Interviews of supporters were double coded, meaning that each quote received both a category and a subcategory (i.e., code) label. Because professional interviews were not considered the prime focus of the current study and are used as a frame of reference, only categories were coded here.\n\n\nResults\n\nDuring analysis we identified five categories with each code belonging to one of them. The categories were: Ingroup/Feyenoord culture vs. Outgroup (27 codes), Context (18 codes), Motivation for lightening fireworks (13 codes), Appreciation of measures and perceived barriers (21 codes), and Solutions and future perspectives (8 codes). See supplementary Table - codes and quotes (can be found in the Extended data) for a complete overview of supporter codes and how often they appeared. Based on the five main categories, we present our findings. Professionals’ opinions are also shortly discussed, offering a frame of reference.\n\nIngroup/Feyenoord culture vs. Outgroup: All supporters report that they have been supporting Feyenoord from early age onwards. Most of them came in contact via their father, some via peers. Being a Feyenoord supporter is an important part of the own identity, in which not soccer but the social ties are appreciated as most important. For example, one of the supporters stated clearly that his social life is determined by connections with other supporters:\n\n“It really is the binding factor in my social life. All my friends have a season pass, it has always been the case that my entire life and social life is about soccer. In this phase of my life, we see each other at matches and at birthdays of our children. But back in the day, we did everything together. On Saturdays, Sundays, and by the time is was Thursday it was time to hit the pub again.”\n\nSupporters describe a sharp dividing line between ingroup and outgroup. The ingroup is experienced as fanatic, loyal, and committed. Within this group, there is an established hierarchy, social control, and consideration for each other. Ingroup members participate in creating the atmosphere via fireworks, singing and cheering, or other actions. They have at least a season ticket to certain boxes, are seen as fanatical, and share club culture and social ties. Outsiders on the other hand are less important than ingroup members, however with varying appreciation of different kinds of outsiders. Other, less fanatical supporters who also come to the stadium are seen as relatively positive.\n\nSupporters also believe that these outgroup supporters evaluate both the fanatical group as well as the fireworks actions as positive. Generally, fanatical supporters report not really thinking about or not having an opinion about people who watch games on television. The media, the KNVB, and most of the time the club (and its board) are negatively appreciated.\n\nProfessionals describe Feyenoord as a working-class club and believe that fireworks are seen by the supporters as part of the soccer experience. Some of them mention that fireworks are part of soccer culture.\n\nMost supporters have a strong historical awareness and a sense of shared culture. Even the youngest supporters show a sense of nostalgia. Supporters believe that the supporter experience is currently restricted by measures and regulation, making the current experience less attractive. One supporter for example stated that people are no longer as enthusiastic about visiting matches as when fireworks were still allowed:\n\n“Back in the day we were allowed to light fireworks, there even was a special box for it. And when the team trained at the public training facility outside, there was a crowd of 20.000 to 30.000 people, it was just one big conflagration. And they’ve killed that. We can’t do fireworks, we can’t do anything, and people just stopped coming.”\n\nRelatedly, a large part of supporters state that fanatical supporters are generally stigmatized, especially by people in positions of power. This aspect was often brought up by the supporters rather than being directly linked to the prepared interview questions. Supporters experience that they are in general unjustly portrayed negatively and valued by the media, Feyenoord, and the KNVB. They report that these institutions describe them overly negative with a heavy focus on small negative incidents. Additionally, supporters feel they are being actively thwarted. Supporters suspect that the club and the KNVB do not appreciate fanatical supporters and wish to ban them from the stadium. They are believed to employ unjust measures to reach their goal (such as handing out stadium bans for very small offences).\n\n“I really get the feeling they want to ban us; we are chased out of our stadium.”\n\nProfessionals do however not speak negatively or in a stigmatizing manner about supporters. They characterize supporters who light fireworks as fanatical and highly involved in the club, both in spirit and action. They are seen as clearly different and separate from other supporters. Sometimes professionals use appreciative phrases like “real supporters” to describe the fanatical subgroup.\n\nContext: The context category describes the context in which fireworks were lit. This concerns the physical context (e.g., certain boxes), but also other more socially determined contextual aspects, such as unwritten rules. When it comes to social economic status and educational level, all supporters report a varied group of offenders. Generally, offenders are described as men between 16 and 40 years. Lighting fireworks generally happens coordinated and together with other supporters. Most often, coordinators of firework actions are experienced group members who typically do not light fireworks inside the stadium themselves. Lighting generally happens by younger members of the group. Supporters chose to collectively light fireworks because of the visual effects of coordinated group/mass actions, but also to reduce chances of getting caught. Supporters indicate that they take their direct environment into consideration when lightning fireworks. They scan their surroundings, try not to hurt anyone, and take the presence of children and elderly into account. Additionally, a set of consistent unwritten rules are in place, such as “no throwing of fireworks”. Social control makes sure that these rules are generally respected and followed. The following statement illustrates that the lighting of fireworks is not used to cause any annoyance or inconvenience:\n\n“I don’t want other people to be bothered by my behavior. If someone close to me can’t stand the smoke, I would not do it, or at least I would give a warning.”\n\nSupporters mention that social pressure or ingroup reputation could stimulate young members of the fanatical group to feel pressure to light fireworks. However, none of the supporters indicate that they themselves ever felt pressure. Own responsibility and choice are important and are frequently mentioned.\n\nSupporters describe that fireworks should not be lit during each and every game but should be saved for special occasions. Especially evening matches (because of the stronger visual effect), matches against larger clubs or rivals, and matches of high stakes are mentioned. Fireworks are also used for other occasions with a large emotional component, such as weddings, funerals, and memorials of supporters. Fireworks thus seem to be a broad and important aspect of supporter culture, used during many different momentous situations and contexts, as is illustrated in the following comment:\n\n“I have been at a wedding of soccer friends where fireworks were lit, that really adds something extra. Or at funerals, when someone has died. The entire Erasmus bridge [iconic bridge in Rotterdam] lit up with torches, that really gives you goosebumps.”\n\nSupporters do not perceive fireworks as unsafe. They feel fireworks are safe because supporters take each other into account, experience, knowledge, and knowhow of offenders. Additionally, supporters report to never or hardly ever experience any fireworks related incidents or injuries.\n\nSupporters make a clear distinction between smoke pots and torches, and bangers. The use of smoke pots and torches is broadly supported, while using bangers inside the stadium is broadly condemned. Some supporters even feel that supporters who do light bangers inside the stadium should be punished more severely than is currently happening. Supporters also mention that the current restrictions and regulations make lighting fireworks less safe. For offenders to not get caught, they wear face covering clothing and pass burning torches. Because fireworks are forbidden, no safety measures (such as buckets of sand) can be implemented in the stadium.\n\n“You know, part of the danger is really only caused by forbidding it.”\n\nProfessionals describe the group of offenders as diverse, with a variety of backgrounds and educational levels. Professionals also see lighting fireworks mostly as a group activity and seem to be aware of the different methods supporters use to prevent identification and prosecution. They describe that sometimes supporters light fireworks individually (“lone wolves”). However, these offenders are caught easily with the major problem being coordinated group lightnings of fireworks or repeated offenders. Professionals agree that important matches are more likely to evoke firework actions. Moreover, they admit to sometimes being surprised by fireworks actions. Some professionals have the idea that supporters would want as many fireworks in the stadium as possible. While almost all professionals feel that supporters underestimate the risks that lighting fireworks inside the stadium encompasses, they do feel that supporters try to act safely and responsibly.\n\nSome professionals do state that indeed the number of incidents is very low, but that potential incidents could turn out to have severe consequences. None of the professionals believes supporters to be indifferent, or to cause dangerous situations on purpose. The differentiation between bangers on the one hand and smoke bombs and torches on the other that is frequently made by supporters, is barely discussed by professionals. They seem to perceive fireworks as one category of products that represents danger to visitors of the stadium.\n\nMotivation for lightening firework: All supporters unanimously indicate that enhancement of the atmosphere is the primary reason for lighting fireworks. Supporters feel fireworks to contribute to a positive and fanatical atmosphere, also whipping up less fanatical supporters to sing and cheer along. Through this enhancement of the atmosphere, fireworks are believed to have a positive effect on the performance of Feyenoord players and potentially, but less importantly, an intimidating effect on the opponent’s players, as is described by the following supporter:\n\n“The moment these torches start burning, you immediately start hearing reactions in the stadium. They become enthusiastic; they start to make a noise. Like three years ago, we played Napoli. During the entire game, there weren’t any torches, and we were on a draw, ready to be eliminated [from the competition]. So, we decided, five minutes before the match would end, to support our team one last time. So, in the 85th minute, we lit a sea of torches. Everyone reacted positively, the entire crowd. Everyone stood up, started singing and cheering, and eventually, in the last minute, we scored. The former trainer admitted, it was us that gave the final push.”\n\nOffenders also enjoy lighting fireworks in the stadium. Additionally, reputation of the fanatical supporters group and competition with other supporter groups is named as an important motivation for lighting fireworks. When it comes to fireworks, interviewed supporters believe their reputation to be the best of The Netherlands. Living up to this reputation is perceived as very important, which is attempted by organizing the most beautiful, biggest, most daring, and best coordinated fireworks actions. One supporter described it as:\n\n“When it comes to fireworks in the stadium, Feyenoord is the best of the Netherlands. Of course, you see it everywhere, but we are the best. Head and shoulders.”\n\nFireworks actions are shared on social media and several websites with both the own ingroup as well as with fanatical supporters of other teams. Re-watching a successful fireworks action gives a sense of pride and togetherness. Competition between different supporter groups is described as positive and almost friendly. Supporters indicate they welcome and applaud well-executed fireworks actions by other supporter groups. The following statement makes clear that no hostility but competition between supporter groups is experienced:\n\n“It is all very positive. Rivalry has always been associated with beating the living hell out of each other, but when it comes to fireworks, that is not the case at all. It is a positive rivalry, we are trying to outdo each other in a friendly manner, on the one hand with singing, on the other hand with fireworks.”\n\nLastly, also some rebellion was named as a reason for lighting fireworks. Some supporters feel that the fact that lighting fireworks is forbidden, makes doing so even more thrilling and challenging. Supporters also indicate that harsh execution of measures directed at containing fireworks or introducing new measures, increases motivation to light more fireworks. This way, supporters try to show that they will not be controlled by any authorities, but they are the ones in charge of shaping their own supporter culture.\n\nEntertaining other supporters, protest, peer pressure, and intimidation of the opponent are not seen as important motivations to light fireworks. Just like supporters, professionals also indicate they believe enhancing the atmosphere and revelry are the most important motivations for lighting fireworks. Most professionals indicate that they can understand these reasons and can empathize with the supporters.\n\nProfessionals are very positive about other supporter driven actions, like large banners or flags. They know that supporters believe that lighting fireworks will enhance the performance of players. Professionals also believe that intimidating the opponent is an important motivation for supporters. Most professionals state that they do not believe fireworks to affect players’ performances. Professionals also mention competition with other supporter groups and personal reputation within the ingroup as reasons for lightning fireworks. While supporters do not mention peer pressure as an important reason for lighting fireworks, professionals mention it often.\n\nProfessionals indicate that there is a strict hierarchy in which young group member have to proof themselves to established members by (among other things) lighting fireworks.\n\nAppreciation of measures and perceived barriers: Supporters who have stopped fireworks give reaching a certain age or stage of life as most important reason for stopping. They also mention that the use of fireworks is not matching work or family life. However, in general supporters indicate that they experience few real barriers when it comes to lighting fireworks inside the stadium. Measures are perceived as ineffective, especially because the chances of getting caught are slim. If chances of getting caught were higher, a stadium ban would by far be the greatest barrier. Not being able to attend matches while peers can, is or would be experienced as very aversive. One supporter describes a stadium ban as follows:\n\n“You don’t even want to think about it, every game you are forced to watch on TV, you’re reminded you’re not in the stadium.”\n\nSupporters perceive the measures as exaggerated and patronizing. The fact that fireworks are not seen as causing any harm, plays an important role and receiving two fines (one from the KNVB and one from the government) is perceived as unfair. Most resistance is felt towards collective punishment. Especially the collective stadium ban is seen as out of proportion. Such punishments, which are perceived as unfair are said to even evoke more lighting of fireworks as an act of protest, instead of preventing the use of fireworks. Other measures are also perceived as counterproductive. Supporters state that because there are measures in place, lighting fireworks becomes less safe, and that less fireworks would hurt the achievements and reputation of the club, and thus also the club’s earnings.\n\nProfessionals indicate that measures are generally not effective (enough). The stadium ban is perceived as potentially most effective since it is seen as the most adverse. However, because of low chances of getting caught, this measure is also perceived as ineffective. Professionals thus share the opinion of supporters on this matter. Some professionals indicate that some measures are not effective at all (like frisking or the occasional use of sniffer dogs) but are implemented to showcase efforts to the KNVB and other organizations.\n\nFuture perspectives and solutions: Supporters unanimously indicate that fireworks make up an essential part of the supporter culture and can never be replaced by other products. While fireworks organized by the club are appreciated, this is not seen as a replacement for supporter driven fireworks. Real fireworks should be organized by supporters and should be spontaneous, rough, and real.\n\n“Nothing is as beautiful as an action organized by supporters, because it produces a certain spontaneity, intensity, and effectiveness.”\n\nAs possible solutions, supporters suggest a box in which fireworks are allowed. In this box, safety measures could be installed, such as extinguishing facilities. Another solution frequently mentioned is a ticket premium used to pay fines Feyenoord receives from the KNVB and UEFA. All supporters mention that they are willing to collaborate, compromise, and make agreements with the club for preparing fireworks actions together. However, both parties should be willing to compromise, as illustrated by the following quote:\n\n“Have supporters tell their story, what they find important. Now they’re just ruling from an ivory tower. They’re afraid to get among the people. But if they would, they would know what happens inside the stadium.”\n\nProfessionals suggest an even broader range of solutions. They, for example, suggest more replacements products, like confetti and laser shows. Some professionals mention that an outspoken disapproval of fireworks from other supporters or players might result in less fireworks actions. However, those professionals who communicate with fanatical supporters more often feel otherwise. Some professionals advocate stricter measures (like prohibiting wearing hoodies inside the stadium, or conducting a house search in case of a caught offender).\n\nMost professionals, however, state that they would prefer to see forms of legal and organized fireworks inside the stadium. Almost all professionals say that they would prefer to work together with supporters, would like to start a conversation, and are willing to aim for some form of compromise.\n\n\nDiscussion\n\nThe illegal lighting of fireworks by supporters inside soccer stadiums is an understudied and a therefore little understood phenomenon. To gain insights in this behavior and potential solutions, we conducted an interview study with both supporters showing this behavior and professionals who deal with this behavior.\n\nWe chose the COM-B model (Michie et al., 2011) to accommodate our findings (see the Extended data for an overview table). Starting with capability, supporters are convinced that they have the physical as well as psychological means to use fireworks safely and they are mostly unaware of any incidents. When it comes to physical opportunities, supporters take their environment into account to avoid hurting others. However, the absence of any physical safety measures makes lightning fireworks less safe. Generally, supporters see no replacement for supporters-led fireworks, which is associated with specific stadium boxes and matches. Social opportunity aspects seem to play a major role for the use of fireworks. Relevant ingroup members often light fireworks as well, and generally other supporters are believed to welcome the use of fireworks. The social context also influences when (during which matches, at which moment) and which fireworks are used via unwritten rules and group hierarchies. An important aspect is that supporters with their firework actions stand in competition for reputation with supporters from other clubs. Social contexts outside the stadium (namely one’s family and work requirements) may discourage individual supporters from the use of fireworks. Turning to motivation, it is obvious that lightning fireworks is strongly rooted in reflective motivation. One does not simply walk into the stadium with a torch, somewhat coincidentally. Rather, supporters prepare and conduct their firework actions deliberately and in groups, often coordinating their behaviour via social media, as becomes also clear from the quote by one of the supporters indicating that shortly before the end of the match against Napoli a great number of Feyenoord supports lit fireworks together to support the team. In addition, they are required to take deliberate measures to avoid getting caught and receiving a stadium ban that is perceived as dreadful. In fact, lightning fireworks is considered one’s individual choice. Supporters do not report vast amounts of peer pressure. Sometimes using fireworks is a collective act of protest or revelry against authorities or the club and their decisions. While lightning fireworks has a strong component of automatic motivations as it possesses strong positive qualities in terms of emotions (e.g., collective cheering) and senses (e.g., appealing images), lighting fireworks seems mostly a deliberate and conscious choice. It thus follows that simple, one-off behaviour change techniques (e.g., nudging, communication campaigns) targeting individual supporters are unlikely to contain the use of fireworks and that more sustainable attempts targeting social groups (e.g., culture change) are more promising.\n\nIndeed, the behavior should not just be considered an individual’s behavior that can be understood from just a psychological or behavioral perspective but should also be contextualized within its social and cultural context. We do this by using insights from literature on hooliganism. When the six fundamental features of the shared hooligan identity as defined by Spaaij (2008) are considered, the identity features of fireworks offenders seem to be largely comparable. Excitement and pleasurable emotional arousal (1) are often reported as important motivations for lighting fireworks, as is the acquirement of a positive reputation, both individually and on a group level (2). When describing the ingroup (Russal & Ward, 2002), supporters often refer to strong social ties (3) and the need for being able to be their “own boss” or to do as they please in “their” stadium (4). However, although offenders are (almost) exclusively male, masculinity (5) is not reported as an important factor in explaining the illegal lighting of fireworks. Also, territorial identification (6), the felt need to defend the stadium and surrounding grounds and invade rival’s territory (Ham et al., 2020) is important to hooligans, but is not seen as important to supporters who light fireworks. Possibly because supporters of rival clubs who light fireworks are not perceived as hostile but as comparable and sometimes even respected groups, being part of the same culture and community. Rivalry between these groups is described as almost amicable. The aggressive component central to hooliganism (Budim, 2018), does not appear to play any role in explaining the illegal lighting of fireworks; supporters describe it as a positive behavior meant to enhance the atmosphere inside the stadium and to boost the performance of their team, making this behavior distinctly different. In short, it may be hooligans who light fireworks, but lightning fireworks does not make a supporter a hooligan. A conclusion that was confirmed by the views of professionals.\n\nLighting fireworks can thus not be seen as just another aspect of hooligan culture and it clearly represents substantial cultural value, being a distinct behavior that is shared, valued, and learned by a specific group of people (Birukou et al., 2013). Within the ingroup, fireworks have substantial symbolic value, as illustrated by their use not only during important matches but also during important life events such as weddings, funerals, and memorials. This symbolic appreciation of fireworks is not unique to soccer culture, but can be found in many cultures worldwide, often signaling new beginnings or festivities (e.g., Lynn, 2006). Supporters describe the lighting of fireworks not as a hobby or pastime, but rather as shared cultural heritage, eliciting a sense of nostalgia and shared identity, that is often even passed on within families, as is often the case with fandom and soccer passion in general (e.g., Gil, 2010). Appreciating fireworks as part of the cultural heritage of a distinct and close cultural group, could explain the importance supporters assign to this behavior. Most professionals do not describe the use of fireworks by supporters from this perspective. Most mention the cultural context and value of fireworks only briefly. This could indicate an underestimation of the experienced value of fireworks by supporters.\n\nThis gap between the appreciation of the (cultural) importance of fireworks by supporters and professionals could signal a lack of mutual understanding. These differences in perception, and mutual incomprehension, and lack of perspective taking could be the breeding ground for the stigmatization supporters frequently report (Chung & Slater, 2013). Observational studies have shown that enforcement by authorities that is seen as too strict or unjust, could lead to more aggressive of unwanted behavior (e.g. Stott & Adang, 2003). This could also be the case when it comes to fireworks, since supporters often reported that they felt that professionals did not understand or appreciate them, consciously tried to thwart them, or even wanted or tried to ban them from the stadium all together. Supporters do thus not feel that they are treated properly and justly and, in line with procedural justice theory (Nagin & Telep, 2017), are thus not motivated to comply with laws and regulations.\n\nHowever, professionals do not hold as negative views of the supporters as supporters themselves believe they do. Professionals do generally not approve of illegally lighting fireworks, but often express appreciation of the positive intentions motivating it, and many of them praise the visual qualities of fireworks actions. Professionals mostly do not oppose the spirit of the fireworks, but point to practical barriers such as fines and safety concerns. Also, when professionals talk about the group of fanatical supporters in general, they are mostly described positively. Previous research into the willingness to engage with hooligans suggests that the stimulation of mutual perspective taking can result in more willingness to establish and maintain contact (Wang et al., 2014).\n\nBridging the perceived opposition between supporters and professionals could be a first step in reaching a solution acceptable to both parties. Both professionals and supporters indicate that banning fireworks from the stadium entirely is not possible, nor desirable. They question thus, although only implicitly, the current legal situation that is prohibiting all fireworks. Both groups mention dialogue, compromise, and mutual agreements as preferred solutions. Also, alternative ways of lighting fireworks inside the stadium are proposed by both groups; professionals mostly suggest lighting fireworks in collaboration with professionals companies, while supporters would appreciate actively contributing to the fireworks, for example in a fireworks box. When mutual trust and understanding is established, reaching consensus does not seem impossible, however current national and international legislation and regulations could stand in the way of solutions preferred locally.\n\nThe current study is unique because it was able to recruit a normally hard to reach group (i.e., fanatical soccer supporters) to participate in research, asking them about a sensitive topic (i.e., illegal behavior). However, supporters unanimously indicated to feel safe to discuss this topic and their views matched the images painted by professionals, suggesting supporters provided reliable information. The combination of supporter interviews and interviews with professionals dealing with the (illegal) fireworks in the stadium, offered a broad and presumably valid picture of the behavior at hand. Lastly, the current study explored an understudied, though important, topic.\n\nUnavoidably, the current study also has certain limitations. Most supporters were recruited via the Feyenoord Supporters Association, an organization which is known to endorse the (safe) use of fireworks inside the stadium, and which could thus be inclined to get across a (too) positive image of supporters who light fireworks. Possibly, this led to recruitment of the most eloquent and nuanced supporters, leaving out those who light fireworks with aggressive intentions. However, supporters who were recruited via Feyenoord, officially opposed to the use of fireworks by supporters, did not contradict these supporters but painted a similar picture.\n\nAdditionally, it is not clear to what extend the current findings are generalizable to other clubs or countries. However, research suggests that ultra (highly fanatical supporters) culture is largely comparable and even interconnected across Europe (Kennedy, 2013), while also the use of pyrotechnics is widespread, and described as a big, and often growing, problem all across Europe (Council of Europe, 2011). Testimonials of a fanatical supporter visiting different clubs and matches across the world to experience fan culture, including the use of fireworks, also suggest shared culture and similar motivations (Hellinga, 2019). While this suggests at least some generalizability, of course, some differences cannot be ruled out, for example masculinity, which is considered a major element in the profile of the typical fanatical soccer fan (Ben-Porat, 2010), could be more important and pronounced in some cultures than in some others. Lastly, the current study focused only on the subjective experiences and opinions of supporters and professionals. While exploring the topic from a behavioral point of view is important, this focus shed little light on for example health consequences and financial damage resulting from illegal use of fireworks inside the stadium. A study investigating the English Premier League shows that at least at English League Clubs, there is no longer an adverse connection between number of arrests and soccer club revenues (Jewell, Simmons & Szymanski, 2014). Keeping in mind that hooliganism is often referred to as the English Disease (Green & Simmons, 2015), emphasizing the extent to which hooliganism and illegal fan behavior have been associated with English soccer, one might hence conclude that in the rest of the world financial consequences of illegal behavior inside the stadium are limited too. However, knowing that England took severe measures and invested heavily in enforcement of stadium rules, we cannot be sure if this lack of connection is applicable to clubs in other countries. However, even if soccer clubs do not suffer large financial strain due to firework offences, deployment of police officers alone costs many man-hours and a lot of money (Nohlen & Harreveld, 2017). When it comes to damage to health, studies in fireworks related incidents inside stadium are, to the best of our knowledge, yet to be performed. However, research shows that use of pyrotechnics inside the stadium resulted in large amount of nanoparticles in the air, potentially dangerous to the health of supporters, and even more so to the health of athletes (Pirker et al., 2020).\n\n\nConclusion\n\nThe current study aimed at gaining insight in the behavior of illegally lighting fireworks inside the soccer stadium by supporters. Qualitative interview data on the topic, provided by supporters and professionals, were contextualized using insights from the hooligan literature, uncovering that although hooliganism and lighting fireworks inside the stadium share some underlying components, lighting fireworks is a distinct phenomenon, lacking the aggressive component that is central to hooliganism. When assessed from a behavioral perspective, motivation (reflective as well as automatic), as compared to capability and opportunity, seems to be the strongest facilitator of the behavior This suggests that interventions directed at making mere changes in context are unlikely to have lasting effects on behavior. Supporters underline this notion by suggesting compromise and conversation as preferred future direction. Supporters feeling stigmatized by professionals could however be a barrier for this direction. However, since professionals contradict this view and talk mostly positively about fanatical supporters, building a bridge between supporters and professionals could be a promising starting point.",
"appendix": "Acknowledgements\n\nWe thank the municipality of Rotterdam and Feyenoord Rotterdam for this research opportunity. We thank all participating supporters and professionals for their participation, enthusiasm, and frankness.\n\n\nData availability\n\nThe data collected for this study (voice recorded interviews) cannot be made available to the public in an open repository due to privacy reasons. Voice recordings are always defined as personal data and can be linked to specific persons. Anonymized transcripts of interviews (or relevant parts) can be shared upon specific request to the first author (merkelbach@essb.eur.nl). Please indicate in your request why the data is needed and how data will be used by sharing your research proposal with us. Data availability will be dependent on ethical approval of the ethics committee of DPECS, ESSB, of the Erasmus University Rotterdam.\n\nThis project contains the following extended data:\n\nZenodo: No Pyro No Party: Social factors, deliberate choices, and shared fan culture determine the use of illegal fireworks in a soccer stadium. 10.5281/zenodo.4835766 (Merkelbach et al., 2021).\n\n- Interview No Pyro No Party professionals.docx\n\n- Interview No Pyro No Party supporters.docx\n\n- Table – codes and quotes.docx\n\n- Table – COM-B and supporters views of fireworks.docx\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nAfif Z, Islan WW, Calvo-Gonzalez O, et al.: Behavioral science around the world: Profiles of 10 countries . Washington, D.C.: eMBeD brief, World Bank: Mind, Behavior, and Development Unit; 2018. Reference Source\n\nBen-Porat A: Football fandom: A bounded identification. Soccer & Society . 2010; 11(3): 277–290. Publisher Full Text\n\nBirukou A, Blanzieri E, Giorgini P, et al.: A formal definition of culture. In: Sycara K, Gelfand M, Abbe A Models for Intercultural Collaboration and Negotiation: Advances in Group Decision and Negotiation . 2013: 1–26. Publisher Full Text\n\nBraun V, Clarke V: Using thematic analysis in psychology. Qualitative Res Psychol . 2006; 3(2): 77–101. Publisher Full Text\n\nBrechbühl A, Schumacher Dimech A, Schmid ON, et al.: Escalation vs. non-escalation of fan violence in football? Narratives from ultra fans, police officers and security employees. Sport in Society . 2017; 20(7): 861–879. Publisher Full Text\n\nBudim A: “Sport Matters: Hooliganism and Corruption in Football” (Undergraduate thesis). 2018. Reference Source\n\nChung AH, Slater MD: Reducing stigma and out-group distinctions through perspective-taking in narratives. J Communication . 2013; 63(5): 894–911. Publisher Full Text\n\nCouncil of Europe: European Convention on Spectator Violence and Misbehaviour at Sports Events and in particular Football Matches (T-RV). 2011.\n\nDionisio P, Leal C, Moutinho L: Fandom affiliation and tribal behaviour: A sports marketing application. Qualitative Market Research: Int J . 2008; 11: 17–39. Publisher Full Text\n\nFootball and Safety Audit Team: Vuurwerk tijdens en rond voetbalwedstrijden: no pyro, no party? Aanbevelingen op de aanpak van vuurwerk in het betaald voetbal te verbeteren . 2017.\n\nGil GJ: Soccer and kinship in Argentina: The mother's brother and the heritage of identity. Soccer & Society . 2002; 3(3): 11–25. Publisher Full Text\n\nGreen C, Simmons R: The English disease: has football hooliganism been eliminated or just displaced?. In: The Economics of Competitive Sports . 2015: (pp. 39–55). Publisher Full Text\n\nHellinga JDerby Days – De twaalfde man.Nederland (published in-house): Jilke Hellinga; 2019.\n\nHowlett M, Ramesh M, Capano G: Policy-makers, policy-takers and policy tools: Dealing with behaviourial issues in policy design. J Comparative Policy Analysis: Research and Practice . 2020; 22(6): 487–497. Publisher Full Text\n\nJewell RT, Simmons R, Szymanski S: Bad for business? The effects of hooliganism on English professional football clubs. J Sports Economics . 2014; 15(5): 429–450. Publisher Full Text\n\nJohn P: Policy entrepreneurship in UK central government: The behavioural insights team and the use of randomized controlled trials. Public Policy Admin . 2014; 29(3): 257–267. Publisher Full Text\n\nKennedy D: A contextual analysis of Europe’s ultra football supporters movement. Soccer & Society . 2013; 14(2): 132–153. Publisher Full Text\n\nKNVB Expertise: Fan Onderzoek Eredivisie 2014/’15. 2015.\n\nKossakowski R, Antonowicz D, Jakubowska H: The reproduction of hegemonic masculinity in football fandom: An analysis of the performance of Polish ultras. In: Magrath R, Cleland J, Anderson E The Palgrave Handbook of Masculinity and Sport. Palgrave Macmillan, Cham; 2020. Publisher Full Text\n\nLynn MR: Sparks for sale: The culture and commerce of fireworks in early modern France. Eigteenth-Century Life . 2006; 30(2): 74–97. Publisher Full Text\n\nMerkelbach I, Dewies M, Noordzij G, et al.: No Pyro No Party: Social factors, deliberate choices, and shared fan culture determine the use of illegal fireworks in a soccer stadium.2021. Publisher Full Text\n\nMichie S, van Stralen MM, West R: The behaviour change wheel: A new method for characterising and designing behaviour change interventions. Implementation Sci. 2011; 6, 1–12. Publisher Full Text\n\nNagin DS, Telep CW: Procedural justice and legal compliance. Annual Review of Law and Social Science . 2017; 13: 5–28. Publisher Full Text\n\nNohlen HU, van Harreveld F: Psychologische inzichten in maatschappelijk (on) wenselijk gedrag: Sexting, voetbalvandalisme, winkeldiefstal, digitale geschiloplossing, en woonoverlast nader beschouwd . Universiteit van Amsterdam; 2017; Reference Source\n\nPirker L, Gradišek A, Višič B, et al.: Nanoparticle exposure due to pyrotechnics during a football match. Atmospheric Environment . 2020; 233: 117567. Publisher Full Text\n\nPolitie: Jaarverslag voetbal en veiligheid 2017-2018. 2018. Reference Source\n\nRookwood J, Pearson G: The hoolifan: Positive fan attitudes to football ‘hooliganism’. Int Rev Sociol Sport . 2012; 47(2): 149–164. Publisher Full Text\n\nScholz P: Female visitors and their behavior at football stadiums: Czechia case study. J Physical Education Sport . 2020; 20(4): 1803–1808. Publisher Full Text\n\nScholz P, Hurych E: The ethical issue in the case of selected football supporters: Deontology or consequentialism? J Physical Education Sport . 2018; 18(3): 1678–1684. Publisher Full Text\n\nSofaer S: Qualitative methods: What are they and why use them? Health Services Res . 1999; 34: 1101–1118. Reference Source\n\nSpaaij R: Men like us, boys like them: Violence, masculinity, and collective identity in football hooliganism. J Sport Social Issues . 2008; 32(4): 369–392. Publisher Full Text\n\nStott CJ, Adang OMJ: Policing football matches with an international dimension in the European union: Understanding and managing risk. Unpublished report to the U.K. Home Office; 2003. Reference Source\n\nvan Ham T, Adang OMJ, Ferwerda HB, et al.: Planned hooligan fights: Contributing factors and significance for individuals who take part. European J Criminol. 2020. Publisher Full Text\n\nWang CS, Kenneth T, Ku G, et al.: Perspective-Taking Increases Willingness to Engage in Intergroup Contact. PLOS ONE . 2014; 9(1): e85681. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWard RE Jr: Fan violence: Social problem or moral panic? Aggression Violent Behav . 2002; 7(5): 453–475. Publisher Full Text\n\nZimniak R: The sociological and psychological aspect of football hooliganism. Teisė . 2020; 117: 138–151. Publisher Full Text"
}
|
[
{
"id": "164325",
"date": "13 Mar 2023",
"name": "Bernardo Buarque De Hollanda",
"expertise": [
"Reviewer Expertise Contemporary History",
"Social Sciences"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe article faces a current issue of engaged supporter’s environments all over Europe, as well as other continents, based on a case study in the Netherlands.\nThe manuscript states a clear argument, goes beyond the juridic or normative debate, covers a dialog with the appropriate academic literature and provides an original approach, since it includes not only the discourses of the fans that take part in the core of the groups but rather interviews with the professionals responsible for the interdiction of the pyro artifacts inside the stadiums.\nNevertheless, it seems the authors infer the category “hooligans” to the other world realities, not considering for instance that there is a considerable supporters culture recognized as “Ultra groups”, not attached to the same hooliganism principles. To ultra groups (Italy, France, Marroc), the pyrotechnics used are central demands of their world.\nLast but not least, it seems important to hear from the authors to which extent the sample and the results of the inquiry with Feyenoord supporters and its local professionals could be generalized to the other realities of ‘fanatic’ soccer fandom in Europe and abroad.\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? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
},
{
"id": "158318",
"date": "09 May 2023",
"name": "Mark Doidge",
"expertise": [
"Reviewer Expertise Football fandom",
"political mobilisaiton",
"ultras",
"fan engagement"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 important article on a topical issue within football fandom. The findings indicate an important way forward for football authorities to address the issue.\nMy only main comment is about the literature and the framing of this within literature around hooliganism. It makes an allusion that use of pyro is linked to hooligan behaviour, even though the authors say it doesn't. Unintentionally, the authors are inferring this which is problematic. (see Back et al. 1999 Beyond the racist/hooligan couplet)1.\n\nPart of this could be overcome with an engagement with literature that isn't focused purely on hooliganism. The authors indicate that there is something called fanatical soccer supporters without theorising or outlining what these are, and how they are similar or different to hooligans. There is literature on ultras, that could be engaged with (e.g. Doidge, Kossakowski and Mintert, Test and Armstrong), other forms of fan engagement (e.g. the work of Pete Millward, Stacey Pope, Radek Kossakowski and others). Anthony King's postmodernity of football hooliganism may also be useful here.\n\nThere also needs to be some clarification on what pyrotechnics are. Some are fireworks, but some are flares, which are subtly different. The authors uncritically assume that fireworks are illegal in the introduction, therefore any use of pyro is illegal and therefore deviant. However, the findings indicate a less confrontational approach where understanding the issues and engaging in dialogue with fans is a way to move forward.\nThere are two minor comments.\n\nThe COM-B model isn't explained for those who are unfamiliar with it.\n\nThere is a misspelling of 'lighting' with 'lightening'.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-498
|
https://f1000research.com/articles/10-496/v1
|
25 Jun 21
|
{
"type": "Research Article",
"title": "Analysing antecedence of an intelligent voice assistant use intention and behaviour",
"authors": [
"Rusen N Tanribilir"
],
"abstract": "Background: As the use of intelligent voice assistant applications becomes more prevalent, a growing body of studies are examining individuals' interactions with intelligent voice assistants. However, very limited research has focused on comparing the antecedents of both use and non-use behaviour of individuals, based on the technology acceptance models. To fill this gap, the present study investigated antecedents of intelligent voice assistance use and use intention in a cross-sectional setting. Additionally, to go one step beyond the existing literature on technology acceptance models and theories, a new construct termed perceived needs, as well as the moderating role of perceived privacy concerns and perceived awareness, are introduced. Method: A quantitative, cross-sectional research design was utilised using a nonprobability sampling strategy through the online networking platforms. Total of 277 (n = 155 users vs n = 122 non-users) international adults age between 20-74 years (79.6% female, 20.4 % male) contributed to the study. Ordinary least squares (OLS) linear regression and Bivariate logistic regression analyses for non-users and users were conducted, respectively. Results: Both analyses revealed that peer influence and perceived needs related to the intention to use intelligent voice assistants for non-users, which applied to the current intelligent voice assistance users where privacy concerns were considered. Surprisingly, the key determinants of technology acceptance and use theories, such as perceived ease of use and perceived usefulness, did not hold for intelligent voice assistance usage. Conclusion: The current research contributed to the field by validating new constructs of perceived needs and the moderation role of perceived privacy concerns. However, in order to build on an existing body of knowledge, future studies should further examine the moderation role of perceived privacy concerns, perceived ease of use, and perceived usefulness in the same domain.",
"keywords": [
"Intelligent voice assistant",
"technology acceptance models",
"use intention",
"use behaviour",
"personal voice assistance"
],
"content": "Introduction\n\nIntelligent voice assistants (IVAs) are software agents embedded into smart devices that recognise and interpret the user’s speech and respond accordingly (Hoy, 2018). Cortana, Alexa, Siri and Google Assistant are the most prevalent IVAs across the United States and Europe (Garcia, Lopez, & Donis, 2018; ‘Preferred voice assistant’, 2018). They are programmed to provide both indoor and on the go services; examples of these services include providing information, dialling, setting a meeting, playing music and even chatting for entertainment purposes (Kiseleva et al., 2016).\n\nPresently, the interest in IVAs is rapidly increasing due to advancements in the capabilities of these agents (Zhao, Lu, & Hu, 2018), such as their success in completing more complex tasks with human-like communication skills (Purington, Taft, Sannon, Bazarova, &, Taylor, 2017). Research has shown that over half of people use IVAs daily (Garcia, Lopez, & Donis, 2018), and that smartphone embedded IVA use increased by 31 % worldwide in 2017 (‘Frequency with smartphone’, 2017).\n\nA growing body of literature has focused on diverse issues related to IVAs; examples include user satisfaction (Kiseleva et al., 2016), concerns about utilising 24-hour listening systems (Moorthy & Vu, 2015) or predictors of use behaviour in focus group settings (Cowan et al., 2017). However, very limited research has used the technology acceptance models (Davis, 1986; Venkatesh, Thong, & Xu, 2016) in IVA domains to understand the factors influencing IVA usage. Additionally, many of the studies have examined only current usage of IVAs (e.g., Kiseleva et al., 2016; Moorthy & Vu, 2015); thus, there is a need for research to adopt technology acceptance models (TAMs) and compare the antecedents of non-users and current users of IVAs.\n\nTherefore, this study aims to examine antecedents of IVA use and non-use through a cross-sectional setting and uses TAMs as the theoretical foundation. Furthermore, the current study seeks to extend the TAMs by including three additional constructs—perceived privacy concerns, perceived needs and awareness of functionalities. In doing so, the study ultimately intends to answer the central question: What distinguishes IVA users from non-users?\n\nIVAs are software agents that are primarily embedded in smart devices and operated through available Internet networks. Lacking a precise definition, literature has referred to these applications as ‘mobile assistants’, ‘intelligent personal assistants’, or ‘voice assistants’ (Jiang et al., 2015; Cowan et al., 2017). For this paper, these applications are simply referred to as ‘intelligent voice assistants’.\n\nWell known IVA market leaders include Apple’s Siri, Microsoft’s Cortana and Amazon’s Alexa (Cowan et al., 2017). IVAs can interpret both written and verbal human commands and respond in these ways (Hoy, 2018); these are known as multi-modal conversational systems (Jiang et al., 2015). IVAs can be activated with key wake words such as ‘Hey Siri’ for Apple. Once activated, the command is streamed to cloud-based data centres to be converted to computer language (Brown, 2016). Then, the most suitable personalised response is determined, and suggestions are created for the user.\n\nRecently, more literature on the topic has emerged due to the advancements in IVAs and the widespread use of the applications in various areas. Given the highly personal information disclosure requirements of IVA services, most studies have investigated the direct relationship between perceived privacy concerns and current usage, and these results primarily supported the importance of these concerns (e.g., Cowan et al., 2017). However, little is known about their moderating role. King and He (2006) briefly discussed the possibilities of this when they indicated that more moderating roles should be examined further to clarify the relationships of technology acceptance models and theories, which will be covered by the current research. This will also correspond to the expectation of Venkatesh et al. (2016), who emphasised that very limited research considered IVA usage based on the Technology Acceptance Models.\n\nThe TAM explains user information systems and technology acceptance processes based on theories from social psychology (Davis, 1989), which further enhanced the Unified Theory of Acceptance and Use of Technology (UTAUT2; Venkatesh, Thong, & Xu, 2012).\n\nTo conclude, a key element of this research is the base formed from the TAM and UTAUT, which will help to answer the main question efficiently: What distinguishes IVA users from non-users? (see Figure 1 for non-user Model 1 and Figure 2 for current users Model 2). In order to answer the main question, the following constructs were discussed and hypothesised.\n\nOn the left, predictors (independent variables) are illustrated. Among these, ‘perceived privacy concerns’ functions as moderator and the main predictor. Another moderator variable, ‘perceived awareness of intelligent voice assistant use’, is displayed in the middle. On the right, the dependent variable of ‘use intention’ for non-users is illustrated. Each arrow addresses a hypothesis or research question formulated around the relationships between independent variables, moderators, and dependent variables. The wide arrows indicate expected moderator correlations between the variables, whereas narrow arrows illustrate the potential direct correlation between the main predictors and the dependent variable.The direction of the expected relationships demonstrated by signs ‘+’ and ‘-’ that refers to a positive and negative relationship, respectively. IVA: intelligent voice assistant.\n\nOn the left, the candidate predictors (independent variables) are demonstrated whereas on the right, the dependent variable of ‘use behaviour’ for current users is illustrated. Each arrow addresses a hypothesis or research question formulated around the relationships between independent variables, moderators, and dependent variables. The wide arrows indicate expected moderator correlations between the variables, whereas narrow arrows illustrate the potential direct correlation between the main predictors and the dependent variable.The direction of the expected relationships demonstrated by signs ‘+’ and ‘-’ that refers to a positive and negative relationship, respectively. IVA: intelligent voice assistant.\n\nPrevious literature has shown that users who interact with these external agents (IVAs) have serious concerns about their personal data privacy (Mihale-Wilson, Zibuschka, & Hinz, 2017; Wu, n.d.). The perceived privacy concerns were defined as the ‘perceived concerns about possible loss of privacy as a result of information disclosure to a specific external agent’ (Xu, Smith, & Hart, 2011, p. 800). This consideration can be attributed to the sharing of considerable amounts of personal information with IVAs, so users are better served and have their needs gratified (Stucke & Ezrachi, 2017). Moreover, as the current study took smartphone embedded IVAs into account, where a great deal of personal information is stored, remarkable privacy concerns in relation to IVAs could arise. Therefore, it is convincing that high perceived privacy concerns towards IVAs might be a reason for not utilising these technological applications. To answer this question, the following hypothesis was formulated.\n\nH1: High levels of perceived privacy concerns towards IVAs are positively correlated with a greater likelihood of non-use.\n\nIn line with Unified Theory of Acceptance and Use of Technology (UTAUT2) model of Venkatesh et al. (2012) and considering the individuals’ present smartphone mediated communication habits (Karapanos, Teixeira, & Gouveia, 2016), investigating online communication behaviour should, theoretically, strengthen the understanding of personal technology acceptance behaviour. Online communication behaviour refers to ‘an individual’s cumulative communication frequency with online applications via smart devices’ and lends itself in the following relationship.\n\nH2: Higher levels of online communication behaviour via smart device applications (e.g., WhatsApp or iMessage) are positively correlated with an individual’s (a) use intention and (b) use behaviour of IVAs.\n\nTAMs (Venkatesh, 2000; Venkatesh, Speier, & Morris, 2002) demonstrated the importance of the ‘ease of use’ as a strong predictor for adopting new technologies. In the scope of the current study, the perceived ease of use concept was adapted from Davis (1989) to be defined as ‘an individual’s perception of effortlessness to use addressed technology’. Previous studies have further shown that perceived ease of use can predict both individuals’ usage behaviour related to technology (e.g., Moore & Benbasat, 1991), as well as their use intentions (e.g., Shroff, Deneen, & Ng, 2011). Given that IVAs are also technologically advanced, it is convincing to investigate the following hypothesis.\n\nH3: Perceived ease of use is positively correlated with an individual’s (a) use intentions and (b) use behaviour of IVAs.\n\nThe studies that employed TAMs have long argued that perceived usefulness is a primary determinant of the intention to use or adopt technology (Davis, 1989; Venkatesh, 1999; Venkatesh & Bala, 2008; Venkatesh & Davis, 2000; Venkatesh et al., 2002). The definition was adapted from Davis (1989) as the ‘degree to which a person believes that using a particular system would enhance his or her [daily life practices]’ (p. 320). Essentially, people tend to use or adopt addressed technology if they perceive it to be useful. Considering IVAs relate closely to the types of technology discussed in previous findings, in the IVA context, the current research assumption is as follows.\n\nH4: Higher levels of perceived usefulness are positively correlated with a higher likelihood of (a) use intention and (b) use behaviour regarding IVAs.\n\nFurthermore, individuals who are hedonically motivated are expected to use products or services to potentially gain excitement or joy (Venkatesh et al., 2012, Brown & Venkatesh, 2005), as they are motivated by affective or sensory stimulation and gratification. Therefore, a positive correlation between hedonic motivation and IVA use is plausible because new advanced functionalities provide a wide variety of fun features (Hoy, 2018), such as making jokes or displaying funny videos. In previous UTAUT models, hedonic motivation and social influence were only related to usage intention (Venkatesh, Morris, Davis, B.,& Davis., D, 2003; Venkatesh et al., 2012). However, in the current study, hedonic motivation and peer influence (social influence) are expected to predict both possible outcomes of use intention and behaviour. This approach will answer the call of Han and Yang (2017), who suggested that future studies should inspect both potential and current user’s IVA usage behaviours.\n\nH5: Higher levels of hedonic motivation are positively correlated with a greater likelihood of (a) use intention and (b) use behaviour regarding IVAs.\n\nThe Expectancy-Value Theory of Palmgreen and Rayburm (1982) indicated that individual media use is based on perceived needs. This concept was defined as ‘what individuals think about their needs, which is different from the actual need’ (Zhu & He, 2002, pp. 472-473). This concept has long been considered a reliable determinant of use behaviours and attitude in technology studies (e.g., Shih, 2004). Expanding on the literature, Zhu and He (2002) proposed that perceived need is an important motivation to predict the individual use behaviour and intention of any new form of technology. Considering the nature of IVAs as a beneficial helping tool, it is appropriate to propose the following hypothesis.\n\nH6: Perceived needs regarding IVAs (functions) positively correlate with a greater likelihood of (a) usage intention and (b) use behaviour concerning IVAs.\n\nIn line with the UTAUT2 model (Venkatesh et al., 2012) in the current paper, social influence will be referred to as ‘peer influence’. The definition was adapted from Fulk (1993) and refers to a ‘person’s consideration of his/her social network that potentially influences the attitude or cognition toward the addressed technology’ (p. 926). Studies on technology use have long examined whether cognition relates to technology changes in accordance with sources of information (Fulk, 1993; Schmitz & Fulk, 1991). Martins et al. (2013) found that a greater peer influence correlated with higher adoption rates for e-bank technology. Given that IVAs also fit this technological mould, it is valuable to examine the following hypothesis.\n\nH7: Peer influence regarding IVA use positively correlates with a stronger likelihood of (a) use intention and (b) use behaviour for IVAs.\n\nStudies have further suggested that without awareness of the system functionalities, attitude or usage behaviour cannot be developed (Abubakar & Ahmad, 2013; Shareef et al., 2009; Lopatovska et al., 2018). Previous studies conceptualised awareness of functionalities as ‘having and acquiring knowledge as much as a user perceived to be sufficient to learn the characteristics of online system and interact through perception or by means of information about ICT’ (Shareef, Kumar, Kumar, & Hasin, 2009, pp. 544-562). The current study echoes this by defining awareness of functionalities as an ‘individual’s perceived awareness of main IVA functions’.\n\nTaking the next step forward, research has shown that awareness of IVA functionalities was linked to privacy concerns where people increase privacy concerns after shown IVAs constant listening function (Manikonda, Deotale, & Kambhampati, 2017). This study will thus examine the moderation role of perceived awareness of IVA functionalities with the following hypothesis.\n\nH8: For non-users, negative relationships between perceived privacy concerns and the intention to use IVAs will be stronger when there is a higher level of perceived awareness of IVA functionalities than when there is a lower level of perceived awareness.\n\nEarlier, a potential direct relationship between perceived usefulness and use intention was proposed. However, IVA functionalities such as organising agendas or setting alarms (Porcheron, Fischer, Reeves, & Sharples, 2018) may not be as relevant to non-users, due to a lack of direct interaction with the IVAs. This consequently might influence how non-users evaluate the usefulness of IVAs. This works alongside the previously mentioned direct relationship (H4a), which proposes that individuals who find IVAs useful show a higher likelihood to intend to use IVAs. This relationship is then expected to be analysed with the following hypothesis.\n\nH9: For non-users, positive relationships between perceived usefulness and the intention to use IVAs will be stronger when there is a higher level of perceived awareness of IVA functionalities than when there is a lower level of perceived awareness.\n\nAccording to King and He (2006), potential moderators should also be considered in order to investigate further nuances in individual technology acceptance. One such moderator is perceived privacy concerns. It is already known that users should disclose remarkable amounts of personal information while interacting with IVAs to access more uniquely tailored functions (Stucke & Ezrachi, 2017). The necessity of high disclosure with such an online external agent could, however, lead individuals to indicate privacy concerns (Mihale-Wilson, Zibuschka, & Hinz, 2017; Wu, n.d.). This is due to a partial awareness and concern that their personal information could be leaked to third parties without their consent. Therefore, there is a strong justification for investigating the potential role of perceived privacy concerns in relation to other predictors.\n\nBecause, presently, people are communicating more regularly via online networking applications, such as WhatsApp (Karapanos, Teixeira, & Gouveia, 2016), which are embedded in smart devices, it is likely that people hold low privacy concerns towards online-based applications like IVAs since they use these applications regularly. This is in line with the findings of the study of Fogel and Nehmad (2009), which indicated that people who show greater risk-taking attitudes have an online networking platform account. Given that networking applications and IVAs both functions based on the shared personal information on online domains, investigation of the link between perceived privacy concerns and online communication behaviour of individuals is worth consideration with the following hypothesis.\n\nH10: Relationships between online communication behaviour via smart device applications and both (a) the intention to use IVAs and (b) use behaviour of IVAs will be stronger when there is a lower level of perceived privacy concerns towards IVAs than when there is a higher level of perceived privacy concerns.\n\nAs outlined earlier, privacy concerns and ease of use are two of the most influential determinants of technology use (e.g., Shroff, Deneen, & Ng, 2011; Mihale-Wilson, Zibuschka, & Hinz, 2017). Moreover, studies of Lai (2017), Shen and Chiou (2010) focused on how privacy concerns determine the relationship between ease of use and intention to use technological systems relate to Internet systems. Given that IVAs also function using online services, the current hypothesis was posed.\n\nH11: Relationships between perceived ease of use and both (a) the intention to use IVAs and (b) use behaviour of IVAs will be stronger when there is a lower level of perceived privacy concerns towards IVAs than when there is a higher level of perceived privacy concerns.\n\nFindings by Featherman and Fuller (2003) showed that as the privacy risk increases, the influence of perceived usefulness on behavioural intention disappears. Moreover, a study on social networking websites showed that privacy concerns moderated the effects of perceived usefulness on behavioural intention (Lai, 2017; Tan et al., 2012). Since very limited research considered this relation for current users, and the literature is still unclear regarding mixed results for intended use, further examination is needed.\n\nH12: Relationships between perceived usefulness and both (a) the intention to use IVAs and (b) use behaviour of IVAs will be stronger when there is a lower level of perceived privacy concerns towards IVAs than when there is a higher level of perceived privacy concerns.\n\nFurthermore, a study on smart home technology implementation for elderly residents showed that more than half of the respondents refused to use some services due to privacy concerns, despite indicating they might need such a system (Demiris, Hensel, Skubic, & Rantz, 2008). The literature on this relationship is minimal, though, and so clarifying whether this relation holds for both current users and non-users in regards to IVAs is an interesting gap to explore. Subsequently, the following hypothesis was formulated.\n\nH13: Relationships between perceived needs and both (a) the intention to use IVAs and (b) use behaviour of IVAs will be stronger when there is a lower level of perceived privacy concerns towards IVAs than when there is a higher level of perceived privacy concerns.\n\nSince previous studies have primarily focused on the direct relationship between hedonic motivation and technology use behaviour (Venkatesh et al., 2012), little is known about external factors that may influence this correlation. One such factor is perceived privacy concerns. This concern could lead individuals to overcome hedonic motivations when considering using IVAs. Therefore, the following research question was posed to better understand this relationship.\n\nRQ1: To what extent do perceived privacy concerns moderate the relationship between hedonic motivation and both (a) use intention and (b) use behaviour?\n\nVenkatesh and Morris (2000) further indicated that peer influence has a direct effect on technology use. However, the existing literature does not provide a sufficient explanation of whether perceived privacy concerns also impact the relationships between peer influence and outcomes (i.e., use intention and use behaviour) in the IVA domain. Thus, to investigate this relationship, the final research question was posed.\n\nRQ2: To what extent do perceived privacy concerns moderate the relationship between peer influence and both (a) use intention and (b) use behaviour?\n\n\nMethods\n\nSince limited research exists in this specific area of interest and test TAM & UTAUT theories, a cross-sectional study was selected to investigate the antecedents of individuals’ use and non-use behaviour with IVAs.\n\nThe sampling frame consisted of international adults at least 18 years of age; this sample is believed to strengthen the generalisability of the study (Maruping, Bala, Venkatesh, & Brown, 2017). Both non-users and current users were recruited through Facebook simultaneously using a single questionnaire, where the link of the survey was shared via the researcher’s personal Facebook page to various networking groups. Using snowball sampling, people were asked to recruit their friends and family either on their Facebook timeline or via personal e-mails.\n\nThe data collection period lasted from November 26th to December 9th, 2018. In total, 315 individuals agreed to participate in the study; however, after data was inspected, 38 respondents were removed due to incomplete questionnaires. Thus, 277 respondents made up the final sample and were included in the analyses. This number consisted of 125 non-users and 152 current users.\n\nAs Table 1 demonstrates, the sample ranged between 20-74 years old (M = 36.92, SD = 8.59). The descriptive statistics showed that women, high- and middle-level educated individuals, were overrepresented compared to low-level educated respondents. Similarly, full-time employees were overrepresented compared to unemployed respondents and students.\n\nThe table shows the proportion of the demographic variables in data: Education level, occupation, sex, and sample population for both users and none-user.\n\nThe ethical approval of the current research was obtained through Communication Science Department of University of Amsterdam in 2019 through the supervisor of the research. The data for this study was gathered through a self-reported survey. The University of Amsterdam’s Qualtrics account was used to distribute the questionnaire. Prior to gathering the data, collection of respondents’ IP addresses was switched off to meet European Union privacy regulations.\n\nAfter a brief introduction, respondents gave their informed consent to participate in the study at the beginning of the questionnaire by ticking the box. Respondents were notified that they could withdraw at any time and were given the opportunity to retrieve their answers within 24 hours of completion. To do so, respondents were asked to create a unique identification code consisting of the last four digits of their mobile phone number, which would enable the researcher to retrieve the data. Upon not receiving any request, the codes were deleted from the data wherein ultimate privacy of the respondents is preserved.\n\nDependent variables\n\nIVA use behaviour\n\nThe IVA use behaviour measure was based on the question: ‘Which of the following voice assistants do you currently use?’ Respondents were provided a list of IVA options along with an ‘I don’t use a voice assistant’ option. People who chose the latter were considered non-users, whereas people who indicated that they are currently engaging with at least one of the IVA options were considered users. This variable was recoded into the dichotomous grouping of current users vs non-users.\n\nIVA use intention\n\nThe IVA use intention measure was adopted from Venkatesh, Morris, Davis and Davis (2003). The statements asked respondents for their level of agreement 1 (strongly disagree) to 5 (strongly agree) on planned IVA use in the next 1-3 months. The items showed good internal consistency (α = .97). A composite score was created based on the mean of the items to form the variable ‘use intention’ (M = 2.23, SD = 1.00). This scale was used for the 127 respondents who were classified as non-users. Higher scores indicate a greater intention to use IVAs.\n\nPredictors\n\nEight variables are used in this study to predict the use intention and behaviour of individuals regarding IVAs (Table 2 for factorial analyses and factor loadings).\n\nThe table demonstrates the factor loadings of the scaled set of items extracted for each variable listed based on the factorial analysis conducted.\n\nCronbach’s alpha values varying between.80 and.97, showing the reliability of the items used for each variable.\n\nThe Kaiser-Meyer-Olkin Measure of Sampling Adequacy and Bartlett’s test of sphericity values are displayed on the top row, indicating the validity of the factor analysis.\n\nOn the right column, each factor’s ‘total variance explained’ values are illustrated based on the Principal Component Analysis shifting between 55. 74 and 93. 89, which is expected to be higher than 50%.\n\nPerceived need\n\nThe perceived need of IVAs measure consisted of five dimensions adjusted from Zhu and He’s (2002) scale. Examples of these are searching for personal information and navigation assistance. For each dimension, respondents indicated how important the needs were on five-point scales that ranged from 1 (not at all) to 5 (very much). The items had a good Cronbach’s alpha of.80. The variable ‘perceived need for IVA’ was then formed based on the mean score of all five items (M = 2.97, SD = 0.94). Higher values indicated a higher perceived need for IVA functions.\n\nPerceived privacy concerns\n\nPerceived privacy concern was measured with a combined scale adapted from existing literature (Xu, Teo, & Tan, 2005; Yang, Lee, & Zo, 2017). An identical agreement scale was used for five statements; an example of such a statement is ‘Disclosing my personal information to a voice assistant would cause many unforeseen problems’. The items showed high reliable internal consistency (α = .91). The items were thus averaged to form the ‘perceived privacy concerns’ (M = 3.47, SD = .77) variable. Higher scores indicated a greater perceived privacy concern.\n\nAwareness of the IVA functionalities\n\nThis measure was adapted from Urquhart et al.(2017). The respondents were asked to indicate which provided tasks they think IVAs can perform based on what they have learned, heard or know about the program. To do so, respondents were provided with a series of functions from which to choose. Items were anchored 1 (not at all aware) to 5 (very much aware). Items had a reliable Cronbach’s alpha of .84. The mean score was used to establish the final ‘awareness of the IVA functionalities’ variable (M = 3.23, SD = 1.10). Higher values indicate a higher awareness of IVA functions.\n\nOnline communication behaviour\n\nThe online communication behaviour measure was created specifically for the current research. It was measured by two indicators namely whether they use these devices for communication purpose and frequency of using smart devices to communicate with others. Respondents were provided a list of smart device options (e.g., iPhone) as well as ‘other’ and ‘I don’t communicate through smart devices’ options. Then, respondents indicated their frequency of smart device use for each listed item on a 5-point scale that ranged from 1 (never) to 5 (very often). A sum score was applied to form the new variable ‘online communication behaviour’ (M = 14.40, SD = 3.02). Higher scores indicate a higher level of multiple device usage for online communication purpose.\n\nPerceived usefulness\n\nPerceived usefulness was adopted from Davis (1989) and comprised six statements evaluated with 5-point Likert agreement scales. Respondents indicated the degree to which they believe that utilising IVAs might increase their task performance. This variable was constructed for both current users and non-users. Examples of the items included ‘Using voice assistants would improve my daily task performance’ and ‘I find voice assistants useful in my daily tasks’. Based on the mean scores of the items, the variable ‘perceived usefulness for non-users’ (M = 2.94, SD = 0.75) was formed and used in linear regression with use intention as the dependent variable. Cronbach’s alpha was high (.94). Additionally, to form the variable ‘perceived usefulness for users’, composite scores were created based on the mean scores of the items (M = 3.37, SD = 0.77). Cronbach’s alpha was.93. To conduct a logistic regression test for use behaviour (e.g., current users vs non-users), based on the sum scores, cumulative ‘perceived usefulness’ variable was constructed (M = 3.17, SD = 0.79). Higher scores indicate that individuals (would) find IVAs useful.\n\nPerceived ease of use\n\nThe perceived ease of use scale was adapted from Lu, Yao, and Yu (2005). This construct will help evaluate the degree to which individuals believe that using IVAs would not cost them any extra effort (Davis, 1989). Likert scales with 5-points were used to gauge respondents’ agreement with the four statements. Some examples are ‘Learning to use the voice assistant was easy for me’ and ‘My interaction with the voice assistant would not require a lot of mental effort’. The mean score (M = 3.56, SD = 0.68) was used to create the ultimate variable ‘perceived ease of use for non-users’ that was later analysed in a logistic regression with use intention as the outcome. Cronbach’s alpha was.80. For users, the total explained variance was 66.57% with a reliable Cronbach’s alpha of.83. These items were also averaged to form the variable ‘perceived ease of use for users’ (M = 3.63, SD = 0.74). Finally, to conduct a logistic regression for use behaviour (e.g., current users vs non-users), based on the sum scores, cumulative ‘perceived ease of use’ variable was constructed (M = 3.60, SD = 0.71). Higher scores indicate a higher perception that using IVAs could be/is practical in daily life.\n\nHedonic motivation\n\nHedonic motivation was adapted from Vandecasteele and Geuens (2010); it indicates whether motivation is derived from pursuit of fun and pleasure. This concept was constructed for both current users and non-users and was measured on a 5-point Likert agreement scale for four enjoyment related statements. One example statement is ‘Using new information technology is fun’ (Cronbach’s alpha of.90). A mean score was used to create the ultimate ‘hedonic motivation’ (M = 3.91, SD = 0.74) variable, where higher scores indicate greater hedonic motivation of individuals towards IVA usage.\n\nPeer influence\n\nThe peer influence measure was adapted from Taylor and Todd (1995) and was used to capture the potential power of social networking on individual technology use. One example item is ‘People who are important to me use a voice assistant.’ Identical 5-point Likert agreement scales were used to evaluate each item. Cronbach’s alpha was reliable (α = .89). A composite score was created based on the mean scores of the items and formed the variable ‘peer influence’ (M = 2.73, SD = 0.80). Higher scores indicate greater peer influence on individuals’ IVA current use and non-use.\n\nControl variables and demographics\n\nFive controls were included in this study to suppress spurious relationships. These are perceived technology innovativeness, previous IVA use (pre-use), occupation, education and sex. The respondents indicated their current employment status, occupation, the highest level of completed education and their sex.\n\nModeration variables\n\nPerceived technology innovativeness\n\nThe perceived technology innovativeness measure was adopted from Agarwal and Prasad (1998). This concept indicated whether possible proposed relationships are influenced by an external variable. The 5-point Likert agreement scale was used to evaluate each of the four statements. An example item is ‘When I hear about new information technology, I would look for ways to experiment with it’. Cronbach’s alpha was reliable (α = .91). Based on the average score of the four items (M = 3.40, SD = 0.85), the variable ‘perceived technology innovativeness’ was formed. Higher scores indicated greater individual technology innovativeness towards new technology use in general.\n\nPrevious IVA use (pre-use)\n\nThe pre-use measure was established for the current study to identify whether previous experiences negatively influenced non-users’ current behaviour towards IVA use. Respondents were asked to indicate if they had ever used one of the provided IVA options in addition to an open answer option. Individuals could also select the ‘I have never used any IVA’ option. The concept was ultimately formed as a dichotomous grouping variable consisting of ‘pre-users’ and ‘non-pre-users’.\n\nTwo analyses were employed in the current study. OLS Linear regression analysis was used to address non-users’ behavioural intention, and logistic regression analysis was conducted to determine the antecedents of use behaviours (e.g., current users vs non-users). Both analyses were employed using a two-step approach. First, only main predictors and control variables were introduced into the model. Then, interaction terms were included. To test the moderation effects, two-way interactions were employed in all analyses. These analyses were evaluated in accordance with the standard 95% confidence intervals (CI) and p < .05 significance level.\n\nData was checked preceding the regression analyses in several ways. First, diagnostic collinearity statistics, residuals and outliers were checked. Data from one respondent was then excluded from the analysis due to the unrealistic questionnaire completion time. Moreover, although according to Myers (1990), the Variance Inflation Factor (VIF) < 10 does not indicate a major problem (as cited in Field, 2013, p. 325), as Bowerman and O'Connell (1990) suggested, to avoid possible bias the variables were centralised (M = 0.00, SD = 1.00; as cited in Field, 2013, p. 325). Z-values of each variable were additionally calculated in SPSS 24 to include interaction terms into moderation analyses. The following formula was used to compute the interaction terms.\n\nInteraction residuals = Predictor residuals * Moderator residuals\n\n\nResults\n\nThe overarching question for this research was ‘What distinguishes IVA users from non-users?’ To answer this, non-users’ use intention was first examined as a dependent variable. Then, the antecedents of use behaviour for both current users and non-users were examined (please see Tables 3 and 4 for correlations).\n\nThe table shows the correlations between dependent variables use behaviour, use intention and various control variables: Sex, occupation, age, education level, previous intelligent voice assistance use (Pre-IVA use), technology innovativeness (Tech inv.)\n\nValues ranged from -1 to +1, and close to +/- 1 indicate a high correlation.\n\n(‘-’ addresses a negative correlation, and ‘+’ addresses a positive correlation).\n\nSignificant correlations: age and occupation (.516**), use intention and age, sex, technology innovativeness (0.230**, 0.361**, 0.206* respectively) as well as use behaviour and technology innovativeness (.416**).\n\n** Correlation is significant at 0.01 level & * 0.05 (2-tailed).\n\nThe table shows the correlations between dependent variables ‘use behaviour’, ‘use intention’ and predictors (independent variables).\n\nValues ranged from −1 to +1, and close to +/− 1 indicate a high correlation.\n\n(‘−’ addresses a negative correlation, and ‘+’ addresses a positive correlation).\n\nSignificant correlations: Perceived technology innovativeness and peer influence, hedonic motivation, perceived need, perceived ease of use, use intention, use behaviour (0.206**, 0.185**, 0.184**, 0.206**, 0.354** respectively). Awareness of IVA functionalities and perceived technology innovativeness, hedonic motivation, perceived need, perceived ease of use, online communication behaviour, use intention (0.245**, 0.218**, 0.327**, 0.194**, 0.187**, −0. 178** respectively). Peer influence and hedonic motivation, perceived need, perceived usefulness, use intention, use behaviour (0.180**, 0.357**, 0.406**, 0. 407**, 0.317** respectively). Hedonic motivation and perceived need, perceived ease of use, online communication behaviour, use behaviour (0.130**, 0.292**, 0. 164**, 0. 165* respectively). Perceive need and perceived usefulness, online communication behaviour, use intention (0.480**, 0.186**, 0.380** respectively). Perceived usefulness and perceived ease of use, use behaviour (0. 187**, 0.270** respectively).\n\n** Correlation is significant at 0.01 level (2-tailed).\n\n* Correlation is significant at 0.05 level (2-tailed).\n\nThe hypotheses that addressed non-users’ intention were investigated using a two-step linear regression (OLS) analysis. First, the direct relationships between use intention and the main predictor variables (e.g., H1—perceived privacy concerns, H2a—online communication behaviour, H3a—perceived ease of use, H4a—perceived usefulness, H5a—hedonic motivation, H6a—perceived needs, and H7a—peer influence), along with the control variables (e.g., sex, occupation, education, perceived technology innovativeness and pre-use), were investigated (see Table 5 for analysis and tests).\n\nThe table shows the analyses run in two steps for both conceptual models of current users and non-user. T (t test) values, B (standardised coefficient), standard error, b* (unstandardised coefficient), p (significance values p <= 0.05), odds ratio (a measure of association between factors and an outcome) and 95 confidence intervals are displayed for significant results.\n\nOn the left section, in step one, OLS linear regression analysis, including the listed control variables and predictor (independent variables), revealed that hypotheses 6a, 7a: perceived needs and peer influence significantly correlates with the use intention for non-users.\n\nIn step two, moderator variables included in the analysis resulting in the opposite direction of hypothesis 10, which predicts the moderator role of perceived privacy concern on the relationship of online communication behaviour and use intention.\n\nOn the right section, a two-step analysis is displayed for the current users. The bivariate logistic regression analysis revealed that peer influence has a significant relationship with use behaviour (hypothesis 7b).\n\n* Low education was marginally significant (p = .053) for current users.\n\nIn regards to the main analysis, the multiple linear regression revealed that, overall, the model was significant, F(16, 107) = 5.33, p < .001, R2 = .44. The control variables were included in the performed tests.\n\nAs shown in Table 5, consistent with H6a, which posited that ‘Perceived needs regarding IVAs (functions) positively correlates with a greater likelihood of (a) use intention concerning IVAs’, the results of multiple OLS regression analysis revealed a positive correlation of perceived needs with use intention. Therefore, perceived needs significantly predicted the intention to use IVAs, providing support for H6a.\n\nH7a assumed that ‘Peer influence regarding IVA use positively correlates with a stronger likelihood of (a) use intention for IVAs’, and the analysis correspondingly revealed that (controlling for perceived privacy concerns, online communication behaviour, perceived ease of use, perceived usefulness, hedonic motivation, perceived needs and awareness of IVA functionalities) peer influence positively related to individuals’ use intention. As shown in Table 5, according to these results, peer influence predicted people’s use intention; therefore, H7a was supported.\n\nContrary to expectations, there were no significant direct relationships between the intention to use and perceived privacy concerns (H1), online communication behaviour (H2a), perceived ease of use (H3a), perceived usefulness (H4a), and hedonic motivation (H5a). Therefore, these hypotheses were not supported (see Table 5).\n\nAs Table 5 demonstrates, in the second step, the analysis examined the moderating role of perceived privacy concerns on the relationships between the dependent variable (e.g., use intention) and the various independent variables—perceived ease of use (H11a), perceived usefulness (H12a), perceived needs (H13a), hedonic motivation (RQ1a) and peer influence (RQ2a). Moreover, the moderating influence of awareness of IVA functionalities on the relationships between use intention and both perceived privacy concerns (H8) and perceived usefulness (H9) were analysed. Following the inclusion of these factors, the model overall showed a large effect size, F(8, 99) = 4.30, p < .001, R2 = .51. The model summary table demonstrated that the incremental increase between steps one and two regarding explained variance was significant, p < .001, ΔR2 = .07.\n\nAnalyses revealed that perceived privacy concerns had a positive and significant moderating effect on the relationship between online communication behaviour and use intention. Surprisingly, this relation was in the opposite direction of the hypothesis, as the current study proposed that (H10a) ‘Relationships between online communication behaviour via smart device applications and (a) the intention to use IVAs will be stronger when there is a lower level of perceived privacy concerns towards IVAs than when there is a higher level of perceived privacy concerns’. Rather, it was found that this relation was strong for people who held a high level of privacy concerns. Therefore, H10a was not supported.\n\nMoreover, the relationships between use intention as a dependent variable and the predictors—perceived ease of use (H11a), perceived usefulness (H12a), and perceived needs (H13a) were not moderated by perceived privacy concerns. Therefore, these hypotheses were not supported. In regards to remaining research questions, perceived privacy concerns did not moderate the relationships between the dependent variable use intention and either independent variables—hedonic motivation (RQ1a) or peer influence (RQ2a). Overview of the results can be seen in Table 5.\n\nTo analyse whether use of IVAs was directly (positively) correlated with online communication behaviour (H2b), perceived ease of use (H3b), perceived usefulness (H4b), hedonic motivation (H5b), perceived needs (H6b) and peer influence (H7b), a bivariate logistic regression was conducted. The analysis was run with a grouping variable where non-users served as the reference group (0; nnon-users = 122) and current users as the other group (1; nusers = 150).\n\nThe Omnibus Test of Model Coefficients showed that, overall, the model was significant (χ2 [14] = 76.61, p < .001). Additionally, the classification table revealed that the sample was 69.90% predictive.\n\nResults of the binary logistic regression analysis (controlling for, online communication behaviour, perceived ease of use, perceived usefulness, hedonic motivation, perceived needs and control variables: sex, occupation, education, perceived technology innovativeness) revealed a positive, significant, direct relationship between peer influence and current IVA usage. Therefore, H7b, which indicated that ‘Peer influence regarding IVA use positively correlates with a stronger likelihood of (b) use behaviour for IVAs’, was supported. However, direct correlations between IVA use as a dependent variable and the remaining predictors—online communication behaviour (H2b), perceived ease of use (H3b), perceived usefulness (H4b), hedonic motivation (H5b) and perceived needs (H6b)—were insignificant. Therefore, these hypotheses were not supported.\n\nIn regards to the second step (block 2), the Omnibus Test of Model Coefficients table for moderation analyses showed that, overall, the model was significant (χ2 [6] = 3.89, p < .001). Further, the classification table revealed that 71.% of the sample was predictive.\n\nResults of the binary logistic regression for two-way interaction effects revealed that perceived privacy concerns did not significantly moderate the relationships between IVA use behaviour as a dependent variable and the predictors—online communication behaviour (H10b), perceived ease of use (H11b), perceived usefulness (H12b) and perceived needs (H13b). Therefore, these hypotheses were not supported. Additionally, there were no significant moderation relationships regarding the research questions for hedonic motivation (RQ1b) and peer influence (RQ2b). Overview of the results can be seen in Table 5.\n\n\nDiscussion\n\nThe ultimate aim of this research was to determine key reasons for current IVA use and non-use behaviours and to understand the potential use intention of non-users. This was manifested in the research question: What distinguishes IVA users from non-users?\n\nThe current study investigated whether perceived needs predict the use intention and behaviours of IVA users and non-users. In line with previous technology studies (Zhu & He, 2002), this study showed that the perceived needs of the functionalities of IVA technology were positively related to the use intention of individuals. However, this relation did not hold for current users. Essentially, non-users indicated that they may need IVAs and therefore intend to use them. This finding provides partial support for one of the current study’s aims; it extends the existing technology acceptance literature on IVAs by considering new constructs. Therefore, perceived needs clearly explained some of the reasoning for individual’s IVA use intention.\n\nFurthermore, the insignificant perceived needs results regarding current use were in line with the respondents’ low (daily) IVA use frequency. The descriptive statistics showed that most (44.%) users utilised IVAs less than once per month, whereas daily usage was only 9.% thus, users of the current data showed that they do not feel needs for IVA functionalities; therefore, they do not use IVAs frequently which was in line with Garcia, Lopez, and Donis’ (2018) findings.\n\nMoreover, peer influence’s relationships with IVA current use and use intention was investigated. In line with expectations, both current users and non-users who intend to use IVAs indicated that they consider their friends or families’ point of view about IVA usage. The current users also considered themselves technologically innovative, which reflects the previous literature in similar domains. For instance, social influence impacted the adoption of wireless Internet services via mobile technology and internet banking (Lu, Yao, & Yu, 2005; Martins et al., 2013). Therefore, it was demonstrated that the main construct ‘social influence’ of UTAUT2 was also a strong predictor for the IVA domain.\n\nThe current study also examined whether hedonic motivation predicts use intention and current use of IVAs. Contrary to information provided by the TAM and UTAUT2, as well as studies on personal computer adoption in households (Brown & Venkatesh, 2005; Venkatesh et al., 2012), hedonic motivation did not predict current use or use intention for IVAs. Further investigation showed that more than half of the non-users indicated that they were ‘not aware at all’ or ‘slightly aware’ of (62.%) being able to ask voice assistants to entertain them. To clarify the proposed reasoning, future examination is needed with another data.\n\nSurprisingly, current results did not support the direct relationship between perceived ease of use and outcomes (e.g., use intention and current use of IVAs), which was contrary to TAMs and other Internet-related technology literature (Riffai, Grant & Edgar, 2012). The reason for insignificant results for current users could be related to user dissatisfaction of IVA task completion. As Kiseleva et al. (2016) indicated, the amount of effort respondents spend on a certain task was highly related to their satisfaction. For non-users, this absence is potentially due to a lack of experience with IVAs. These results also apply for the lacking support for perceived usefulness (e.g., Brill, 2018). Future studies should measure user satisfaction to clarify these assumptions.\n\nA similar explanation applies to perceived privacy concerns. Refuting much of the literature related to the topic (e.g., Cowan et al., 2017), the current study did not find support for the claim that low levels of privacy concerns related to IVA use intention contrary to the current users. Thus, individuals may not be aware of the extent to which they must disclose personal information in order to have their needs satisfied by IVA services, and thus, they may not ruminate on privacy concerns about IVAs. Future studies should better operationalise perceived privacy concerns, particularly for IVAs, to provide more information to the respondents about the consequences of a potential online data breach.\n\nThe key findings of the current examination were based only on the data that was gained through nonprobability sampling. Therefore, an overrepresentation of women and full-time employees could influence the generalisability of the current findings. Furthermore, since this study was cross-sectional, causality claims cannot be made with the current findings. Finally, this paper focused on smartphone embedded IVAs; therefore, the results found in this study may not reflect the use behaviour for IVAs on other platforms (Cowan et al., 2017).\n\nOverall, the results of the current research make a valuable contribution as it is a preceding step toward understanding the potential impact of interacting with smartphone embedded IVAs.",
"appendix": "Acknowledgements\n\nThis research was conducted under the care of the University of Amsterdam, Communication Science Department.\n\n\nData availability\n\nHarvard Dataverse: Voice Assistant Use, https://doi.org/10.7910/DVN/WON8RZ (Tanribilir 2021).\n\nHarvard Dataverse: Voice Assistant Use, https://doi.org/10.7910/DVN/WON8RZ (Tanribilir 2021).\n\nThis project contains the following extended data:\n\n- Survey: Instrument IVA Questionnaire\n\n- Coding key for data variables (Metadata)\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\nAbubakar FM, Ahmad HB: The moderating effect of technology awareness on the relationship between UTAUT constructs and behavioural intention to use technology: A conceptual paper. [PDF file]. Australian J Business Management Res. 2013, May; 3(2), 14–23. 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Publisher Full Text"
}
|
[
{
"id": "168195",
"date": "11 Apr 2023",
"name": "Pedro R. Palos-Sanchez",
"expertise": [
"Reviewer Expertise Technology acceptance models"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 focus of the paper Overall, this is an interesting research topic, closely related to analysis of antecedence of an intelligent voice assistant use intention and behaviour.\nTitle Use different words in title and keywords for a better positioning of the document in search engines and indexed databases.\nAbstract The abstract is appropriate, but author should include the word “survey” because this is the research method. Author must point out where the originality of this manuscript lies, in that it differs from other.\nIntroduction\nThe explanation of originality (research gap) uses too little evidence from previous studies. There is not much explanation for the research gap in the topic. This leads to the concern about the research novelty, especially in recent times.\n\nThe paper's structure is not shown in the introduction.\nTheoretical part and Background Literature\nThe author should add more recent research works related with the technology acceptance models, specially based in TAM and UTAUT. For example:\nPerceived privacy concerns\nPalos-Sanchez, P. R., Hernandez-Mogollon, J. M., & Campon-Cerro, A. M. (2017). The Behavioral Response to Location Based Services: An Examination of the Influence of Social and Environmental Benefits, and Privacy. Sustainability, 9(11), 1988. doi:10.3390/su9111988\n\nHedonic motivation\nPalos-Sanchez, P., Saura, J. R. & Velicia-Martin, F. (2022). A case study on a hedonic-motivation system adoption model in a game-based student response system. International Journal of Human-Computer Interaction. DOI: https://doi.org/10.1080/10447318.2022.2121801\n\nUse online 10.3389/fpsyg.2020.00429\nPlease summarize from the systematic literature review related with intelligent voice assistant.\nThe aim, Methodology, and Data\nThis section is well written. What software did you use for data analysis?\n\nWhat type of sampling was applied? Do you doing any pretest with the questionnaire? Can you describe? What is the reason for use OLS Linear regression analysis? Author must support this decision in other similar research works.\nResults\nOLS Linear regression analysis was used in this study for data analysis. The author should have reference to previous statistical articles and authors for understand the results.\nDiscussion\nThere is link between the result part (mainly based on data of survey) discussion part (mainly based on the literature review).\nConclusion\nConclusion section does not exist. A too general, failing to summarize the highlights of the results and discussion. What is the theoretical and practice implications of obtained results?\n\nThe authors should add the limitation of the research/results and directions for future research.\nReferences\nAdd DOI to some references\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
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https://f1000research.com/articles/10-496
|
https://f1000research.com/articles/10-203/v1
|
11 Mar 21
|
{
"type": "Research Article",
"title": "Zuotai (β-HgS)-containing 70 Wei Zhen-Zhu-Wan differs from mercury chloride and methylmercury on hepatic cytochrome P450 in mice",
"authors": [
"Yu Nie",
"Shang-Fu Xu",
"Yan-Liu Lu",
"Xiu-Rong Zhao",
"Cen Li",
"Li-Xin Wei",
"Jie Liu",
"Yu Nie",
"Shang-Fu Xu",
"Yan-Liu Lu",
"Xiu-Rong Zhao",
"Cen Li",
"Li-Xin Wei"
],
"abstract": "Background: Zuotai (mainly β-HgS)-containing 70 Wei-Zhen-Zhu-Wan (70W, Rannasangpei) is a famous Tibetan medicine for treating cardiovascular and gastrointestinal diseases. We have shown that 70W protected against CCl4 hepatotoxicity. CCl4 is metabolized via cytochrome P450 (CYP) to produce reactive metabolites. Whether 70W has any effect on CYPs is unknown and such effects should be compared with mercury compounds for safety evaluation.\n\nMethods: Mice were given clinical doses of 70W (0.15-1.5 g/kg, po), Zuotai (30 mg/kg, po), and compared to HgCl2 (33.6 mg/kg, po) and MeHg (3.1 mg/kg, po) for seven days. Liver RNA and protein were isolated for qPCR and Western-blot analysis. Results: 70W and Zuotai had no effects on hepatic mRNA expression of Cyp1a2, Cyp2b10, Cyp3a11, Cyp4a10 and Cyp7a1, and corresponding nuclear receptors [aryl hydrocarbon receptor (AhR), constitutive androstane receptor (CAR), pregnane X receptor (PXR), peroxisome proliferator-activated receptor-α (PPARα); farnesoid X receptor (FXR)]. In comparison, HgCl2 and MeHg increased mRNA expression of Cyp1a2, Cyp2b10, Cyp4a10 and Cyp7a1 except for Cyp3a11, and corresponding nuclear receptors except for PXR. Western-blot confirmed mRNA results, showing increases in CYP1A2, CYP2B1, CYP2E1, CYP4A and CYP7A1 by HgCl2 and MeHg only, and all treatments had no effects on CYP3A. Conclusions: Zuotai and Zuotai-containing 70W at clinical doses had minimal influence on hepatic CYPs and corresponding nuclear receptors, while HgCl2 and MeHg produced significant effects. Thus, the use of total Hg content to evaluate the safety of HgS-containing 70W is inappropriate.",
"keywords": [
"Zuotai",
"70 Wei-Zhen-Zhu-Wan (Rannasangpei",
"Qishiwei)",
"HgCl2",
"MeHg",
"Cytochrome P450",
"Nuclear receptors."
],
"content": "Introduction\n\nTibetan Medicine is one of the important medical heritages of the world1. Zuotai, a Tibetan medicine mixture containing β-HgS, has been included in many famous Tibetan medicines for the treatment of diseases2–4. A systematic review of available studies of Tibetan medicine, however, indicates that the literature in Western industrialized countries is scarce5. Traditional Tibetan medicines use polyherbo-metallic mixture recipes as opposed to a single ingredient in the treatment of diseases. For example, in a review of 193 herbo-metallic Tibetan medicine recipes for liver diseases, herbs/plants (181 kinds), animal products (7 kinds), and minerals (5 kinds) were frequently used6. Well-designed pharmacology and clinical studies are encouraged to elucidate the pharmacology, safety, and clinical efficacy of Tibetan medicines5,6.\n\nWe have recently indicated that chemical compositions of minerals (metals) are a major determinant of their therapeutic effects and toxicity in Tibetan medicines7. 70W Zhen-Zhu Wan (70W, also called Rannasangpei, Pamda-28, Qishiwei) is such an example 8. 70W was developed in the middle of fifteenth century and is composed of herbo-metallic mixtures, mainly from pearl, Hong-sik, Albergia odorifera, Nine stone, Saffron, Bezoar, Musk and Zuotai (a mineral mixture) in the treatment of cardiovascular, gastrointestinal, and neurodegenerative diseases8, and is listed in the 2015 edition of Pharmacopoeia of China9. 70W is effective experimentally against vascular dementia in rats10, and protects cerebral ischemia-reperfusion injury via blood-brain barrier and metabonomics with 18 identified active ingredients11. We have recently demonstrated that 70W is effective in protecting against LPS plus MPTP-induced chronic neuroinflammation and dopaminergic neuron loss8 and could modulate gut microbiota as a means of protection8,12. 70W dose-dependently protected against CCl4-induced liver injury, probably by activation of the Nrf2 antioxidant pathway13.\n\nCCl4 is metabolized via cytochrome P450 (CYP450), particularly CYP2E1, to produce reactive metabolites14. Whether the protective effects of 70W against CCl4 hepatotoxicity is related to CYP450 inhibition is not known. In addition, 70W might be used in combination with other medications since it has many beneficial effects because it contains many ingredients. It has the potential to cause herb-drug interactions, especially on the liver CYP450 gene, similar to other Chinese medicine formulae15. CYPs are the mixed function oxidase system mainly existing in the liver, and play roles in the metabolism of over 80% drugs16. Induction or inhibition of CYP450 is implicated in traditional medicine-induced hepatoprotection and/or hepatotoxicity15,17,18. CYP450 genes are regulated by corresponding nuclear receptors, their coordinated regulation affects hepatic phase I and phase II metabolisms19.\n\nThis study was therefore designed using 1–5 times clinical doses of 70W (0.15, 0.5 and 1.5 g/kg, po) for oral administration to mice for 7 days and comparing its effects with equivalent Hg contents of Zuotai, HgCl2, and 1/10 Hg contents of MeHg, in an attempt to obtain information for the safe use of Zuotai-containing 70W in the clinic.\n\n\nMethods\n\n70W and Zuotai was provided by Tibetan Medicine Manufacture Factory as described previously8, based on the 2015 edition of Pharmacopoeia of China for QA/QC control (Lot number Z20110561). 70W was prepared by grinding the pill into powder, adding distilled water to prepare the suspension for oral administration. Mercury chloride (HgCl2 Cat# M1136) and methylmercury (MeHgCl Cat# 442534) were from Sigma (St. Louis, MO, USA). All other chemicals were commercially available reagents.\n\nMale Kunming mice (20 ± 2 g) were purchased from Animal Experimental Center of theThird Military Medical University (Chongqing, China). Animals were maintained in the SPF-grade facilities at Zunyi Medical University, with a controlled environment (22 ± 1°C, 50 ± 2% humidity and a 12 h: 12 h light: dark cycle) and free access to purified water and standard laboratory feed. Efforts were made to ameliorate distress and harm to animals by daily monitoring and humane treatment of the animals. To reduce the use of animals, the minimal number of mice (n=5)/group according to the experiment requirement was used which are sufficient for statistical analysis. All animal care and experimental protocols are complied with the Animal Management Guidelines of the Chinese Ministry of Health and approved by Animal Use and Care Committee of Zunyi Medical University (2015-07).\n\nMice were randomly divided into seven groups of five mice each (Total number n=35), respectively as the control, 70W (0.15, 0.5, 1.5g/kg), Zuotai (30 mg/kg, the amount contained in 70W), HgCl2 (33.6 mg/kg, equivalent Hg as HgS) and MeHgCl (MeHg, 3.1 mg/kg, 1/10 of Hg). Mice were given oral administration for seven consecutive days. The dose regimen selection was based on our prior publications for 70W (at clinical dose)8 or for zuotai and mercury compounds20. Twenty-four hours after the last dose, the animals were euthanized and the livers were collected and stored at 80°C prior to analysis.\n\nThe activities of alanine aminotransferase (ALT) and aspartate aminotransferase (AST) were determined by commercial kits (Jaingcheng, Nanjing, China)21. Liver samples were fixed in 10% formalin prior to routine processing and paraffin embedding. Liver sections (4 µm) were dewaxed in xylene, rehydrated in different concentrations of alcohol (100%, 95%, 80%, 75%) and stained with hematoxylin, followed by counterstaining with eosin. After rinsing, the slides were rehydrated with series of alcohol (75%, 95%. 100%) and mounted with cover glass slip. The slides were examined in nine random fields under a light microscope (Leica Microsystems Ltd., Wetzlar, Germany)21,22．\n\nApproximately 50–100 mg of tissue was homogenized in 1 ml TRIzol (TakaRa Biotechnology, Dalian, China) and the total RNA was extracted according to manufacturer’s instructions. The quality and quantity of RNA were determined by the Nanodrop (Thermo Scientific, ND-2000, USA), with 260/280 ratio >1.8. Total RNA was reverse transcribed with a High Capacity Reverse Transcriptase Kit (Applied Biosystems, Foster City, CA, USA). The primers were designed with Primer3 software and listed in Table 1．\n\nThe 15 µL PCR reaction mix contained 3 µL of cDNA (10 ng/µL), 7.5 µL of iQTM SYBR Green Supermix (Bio-Rad Laboratories, Hercules, CA), 0.5 µL of primer mix (10 µM each), and 4 µL of ddH2O. After 5 min denature at 95°C, 40 cycles were performed: annealing and extension at 60°C for 45 seconds and denature at 95°C for 10 seconds. Dissociation curve was performed after finishing 40 cycles to verify the quality of primers and amplification. Relative expression of genes was calculated by the 2-ΔΔCt method and normalized to the house keeping gene β-actin or expressed as a percentage of controls8,21.\n\nApproximately 80 mg of liver tissue was homogenized with RIPA lysis buffer containing 1 mM PMSF and freshly prepared proteinase inhibitors. The homogenates were centrifuged at 12,000 g at 4⍛C for 10 min, and the protein concentration in the supernatants was determined by the BCA assay, and denatures at 90⍛C for 10 min with Nupage loading buffer. Approximately 30 µg proteins were separated in the 10% Nupage gel and transferred to the PVDF membrane. The membranes were blocked in 5% of the skim milk for 1 hour at room temperature, followed by incubation with primary antibodies (CYP1A2 (1:500), CYP2B1 (1:500), CYP2E1 (1:500), CYP3A4 (1:500), CYP4 (1:500), CYP7A1 (1:500), and GAPDH (1:2000)) at 4°C overnight. After washing the membranes with TBST four times, the secondary horseradish peroxidase (HRP) labelled anti-rabbit, or anti-mouse antibodies were added (1:5000) (Beyotime, Shanghai, China), and incubated at room temperature for 1 hour. The enhanced chemiluminescent reagents (ECL) were used to detect the intensity of protein-antibody complexes, and intensity was semi-quantified with Quantity One software (Bio-Rad, USA)18.\n\nData were expressed as mean and standard error. SPSS 19 was used for statistical analysis. Data were analyzed using a one-way analysis of variance (ANOVA), followed by Duncan’s multiple range test, and a p value < 0.05 was considered significant.\n\n\nResults\n\nAt the doses of 70W and Zuotai used in the present study, animals were healthy, without body weight loss and no mortality occurred. No significant elevations of serum ALT and AST were evident, and histology did not reveal overt lesions12,20–22. HgCl2 and MeHg groups showed body weight loss and mild histology lesions, consistent with prior publications12,21,22.\n\nFigure 1 illustrates mRNA expression of nuclear receptors (left side) and cytochrome P450 isozyme genes (right side). The aryl hydrocarbon receptor (AhR) mainly mediates the expression of CYP1A enzymes such Cyp1a2; Constitutive androstane receptor (CAR) mediates CYP2 enzymes such as Cyp2b10; Pregnane X receptor (PXR) plays an important role in the regulation of CYP3A enzymes such as Cyp3a11; Peroxisome proliferator-activated receptor α (PPARα) regulates induction of CYP4A enzymes such as Cyp4a1019. The Farnesoid X receptor (FXR) regulates cholesterol 7α hydroxylase (Cyp7a1) induction23. The results show that compared with the controls, 70W at 0.15, 0.5, and 1.5 g/kg doses and Zuotai (β-HgS, 30 mg/kg) had no effects on these nuclear receptor and CYP gene expressions. In contrast, HgCl2 (33.6 mg/kg) and MeHg (3.1 mg/kg) significantly increased AhR, Cyp1a2, CAR, Cyp2b10, PPARα, Cyp4a10, FXR, and Cyp7a1, while having no significant effects on PXR, Cyp3a11 (Figure 1).\n\nMice were given 70W 0.15, 0.5, and 1.5 g/kg, po. Zuotai (30 mg/kg, po), HgCl2 (33.6 mg/kg, po), and MeHg (3.1 mg/kg, po) daily for seven days, and hepatic RNA and protein were extracted for RT-PCR analysis. Data are mean ± SE, n = 5. *Significantly different from control, p< 0.05.\n\nFigure 2 illustrates protein expression of P450 isozymes. Figure 2A shows representative western-blots for CYP1A2, CYP2B1, CYP2E1, CYP3A, CYP4A, and CYP7A1; Figure 2B shows the statistical analysis of 3-5 replicates. Consistent with mRNA expression, 70W at 0.15, 0.5, and 1.5 g/kg doses and Zuotai (β-HgS, 30 mg/kg) had no apparent effects on cytochrome P450 isozyme protein expressions. In contrast, HgCl2 (33.6 mg/kg) and MeHg (3.1 mg/kg) significantly increased CYP1A2, CYP2B1, CYP4A, and CYP7A1, while having no effects on CYP3A (Figure 2).\n\nMice were given 70W 0.15, 0.5, and 1.5 g/kg, po. Zuotai (30 mg/kg, po), HgCl2 (33.6 mg/kg, po), and MeHg (3.1 mg/kg, po) daily for seven days, and hepatic proteins were extracted and pooled for Western-blot analysis. A, the representative western-blot; B, statistical analysis of P450 proteins. Data are mean ± SE of 3-5 replicates. *Significantly different from control, p< 0.05.\n\n\nDiscussion\n\nThe potential efficacy and toxicity of minerals (metals) in traditional medicines is currently a matter of debate7,24. In the present research, we examined the effects of β-HgS-containing Zuotai and Zuotai-containing 70W on hepatic CYP 1-4 and CYP-7 families, and their corresponding nuclear receptors, compared to HgCl2 and MeHg at both mRNA and protein levels. Briefly, 70W at 1 to 5-times clinical doses and Zuotai (β-HgS, 30 mg/kg, po) administered for seven days did not produce significant effects on the liver CYP450 gene and protein expressions in mice. HgCl2 and MeHg at 1/10 Hg dosing increased the expression of CYP1A, CYP2B, CYP2E1, and CYP7A at the mRNA and/or protein levels. These results further demonstrate that chemical forms of metals are a major determinant of their biological effects and that the use of HgCl2 or MeHg for risk assessment on minerals in traditional medicines is inappropriate7.\n\nTibetan medicine has thousands of years of history and is still used in the world today to treat a variety of diseases, including liver diseases1–4,6. Herbal-metallic preparations are believed to assist the delivery of drugs to the target, contribute to therapeutic effects, and reduce toxicity7. 70W is a famous Tibetan medicine listed in the 2015 Edition of Chinese Pharmacopoeia for the treatment of various diseases3,10. The major ingredients in 70W and the mode of the protection against cerebral ischemia-reperfusion injury has recently been demonstrated11. We have shown that 70W is effective against CCl4-induced liver injury, protected LPS plus MPTP-induced neurotoxicity8, and modulated gut microbiota8,12. The present study further demonstrated that the hepatoprotective effects of 70W is not due to the inhibition of CYP450 to reduce CCl4 bioactivation, rather the activation of the Nrf2 antioxidant pathway13.\n\nZuotai is a mineral mixture, with 54% of β-HgS25, and is included in a small amount to many valuable Tibetan medicines1–3. Mercury (Hg) is a toxic metal; the safety of Hg-containing traditional medicines is of concern24. The chemical speciation, spatial distribution of mercury from Zuotai are different from that of HgCl27,25, resulting in differential toxicity. A recent human study revealed that Zuotai-containing Tibetan medicines are safe at clinical doses26–28, including 70W29. Indeed, Zuotai differs from HgCl2 and MeHg in producing hepatotoxicity21, nephrotoxicity30, and intestinal toxicity with gut microbiome disruptions20. The present study demonstrated that Zuotai-containing 70W at clinical doses had minimal effects on hepatic CYP450, supporting the notion that Zuotai and 70W at clinical doses are safe26–29.\n\nCytochrome P450 1A1 (CYP1A1) is a hepatic and extrahepatic enzyme that is regulated by the AhR signaling pathway and is regarded as carcinogen activation CYP450 family31. CYP-1 family includes CYP1A1, CYP1A2, and CYP1B1，and CYP1A1/CYP1A2 has become a therapeutic tool for the bioactivation of prodrugs, particularly cytotoxic agents. Little is known about effects of 70W on CYP1A family. We have shown previously that oral Zuotai (β-HgS) and cinnabar (α-HgS) had minimal effects of hepatic P4501A family gene expression32. However, in rats, Zuotai at higher doses could decrease CYP1A2 activity33. In comparison, the effects of HgCl2 on CYP1A expression were more dramatic. In Zebra fish, a low dose (0.1 LC50) of HgCl2 increased CYP1A1, but at higher doses (0.4 and 0.8 LC50), the expression of CYP1A1 was suppressed34. In the mouse heart, kidney and lung, HgCl2 (2.5 mg/kg, ip) increased CYP1A1, along with other CYP450 isoforms35. In the present study, HgCl2 at 33.6 mg/kg increased CYP1A2 at mRNA and protein levels, largely in agreement with the above literature32–35 In another study, mice that chronically (6 weeks) received HgCl2 (32 mg/kg) and MeHg (2.6 mg/kg), had increased expressions of hepatic Cyp1a1 and Cyp1b1, while cinnabar (HgS, 300 mg/kg) and cinnabar-containing An-Gong-Niu-Huang Wan were ineffective36. Thus, the effects of mercury compounds on CYP1 family are dependent on the mercury forms, the dose, route, and duration of administration.\n\nThe CYP-2 family is easily induced by many xenobiotics such as phenobarbital. CAR is shown to play a crucial role in the activation of CYP2B genes by xenobiotics19. The CYP-2 family mainly includes the CYP2B subfamily and CYP2E1. CYP2E1 metabolizes an extensive array of pollutants, drugs, and other small molecules, often resulting in bioactivation to reactive metabolites, which in turn damage mitochondria37. HgCl2-induced hepatotoxicity and oxidative stress is partially mediated through its effects on CYP2E138. HgCl2 (2.5 mg/kg, ip) increased the expression of Cyp2b9 and Cyp2b10 in mice hearts39 and HgCl2 (33.6 mg/kg, po) increased Cyp2b10 expression in the livers of mice32. Under the present experimental conditions, Cyp2b10 mRNA and CYP2B protein expression were increased by HgCl2 and MeHg only.\n\nCYP3A is the most abundant subfamily of CYP450, with the highest content in the liver and intestines, and is involved in the metabolism of clinical drugs17,18. CYP3A can be induced or inhibited by a variety of substances. In the present study conditions, 70W and mercury compounds had minimal effects on Cyp3a11 mRNA and CYP3A protein expression. The length of Hg compound administration could make a difference as compared to the present study.\n\nCYP4A is involved in lipid metabolism and is regulated by PPARα, their dysregulations are implicated in xenobiotics induced adverse effects leading to various human diseases19. Researchers found that HgCl2 exposure is associated with increased risk of cardiovascular disease and profound cardiotoxicity, and their results show that mercury treatment caused a significant induction of the cardiac hypertrophy markers, along with CYP4A genes (Cyp4a10, Cyp4a12, Cyp4a14)35. In the present study, 70W and Zuotai at 1–5 times clinical doses do not have appreciable effects on PPARα and Cyp4a10 mRNA expression and CYP4A protein expression, while HgCl2 and MeHg increased PPARα and Cyp4a10 mRNA, as well as CYP4A protein, consistent with our prior observation that HgCl2 increased PPARα and Cyp4a10 in livers of mice after seven days of administration32. In mice chronically (6 weeks) dosed with HgCl2 (32 mg/kg) and MeHg (2.6 mg/kg), the expression of Cyp4a10 was increased, but cinnabar (HgS, 300 mg/kg) and cinnabar-containing An-Gong-Niu-Huang Wan was ineffective36. Increased expression of the CYP-4A family genes under the dose of HgCl2 and MeHg used in the present study could impact lipid metabolism.\n\nCYP7A1 is a rate-limiting enzyme for bile acid synthesis and is regulated by FXR23. Little is known on the effects of mercury compounds on FXR and CYP7A1 expression. The present study showed that 70W and Zuotai did not affect CYP7A1, while HgCl2 and MeHg increased Cyp7a1 mRNA and CYP7A1 protein. The biological effects of CYP7A1 induction by HgCl2 and MeHg warrant further investigation.\n\n\nConclusions\n\nThe present study showed β-HgS and β-HgS containing 70W (1–5-times of clinical dose) did not produce appreciable effects on hepatic CYP450 enzyme gene/protein expression compared to equal Hg content as HgCl2 or 1/10 of Hg content as MeHg, suggesting that (1) the protection of 70W against CCl4 hepatotoxicity is not due to inhibition of CYP450 (CYP2E1); (2) 70W appeared to be safe under recommended clinical doses; and (3) HgCl2 and MeHg had significant effects on CYP450 expression, correlated with their potential toxic effects to the liver.\n\n\nAbbreviations\n\n70 Wei-Zhen-Zhu-Wan (70W, also called Rannasangpei; Qishiwei); Cytochrome P450 (CYP450); Aryl hydrocarbon receptor (AhR); Constitutive androstane receptor (CAR); Pregnane X receptor (PXR); Peroxisome proliferator-activated receptors (PPARs); farnesoid X receptor (FXR).\n\n\nData availability\n\nZenodo: Zuotai (β-HgS)-containing 70 Wei Zhen-Zhu-Wan differs from mercury chloride and methylmercury on hepatic cytochrome P450, http://doi.org/10.5281/zenodo.440371740\n\nThis project contains the following underlying data:\n\n- PCR and WB figure data (PCR-WB)\n\n- Raw western-blot data (CYP-WB). Please note that full blot images are not available\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "Acknowledgements\n\nA previous version of this article is available on Research Square: https://doi.org/10.21203/rs.3.rs-32118/v1\n\n\nReferences\n\nSchwabl H, Vennos C: From medical tradition to traditional medicine: A Tibetan formula in the European framework. J Ethnopharmacol. 2015; 167: 108–114. PubMed Abstract | Publisher Full Text\n\nHuang HB, Wang QZ, Wang XW, et al.: [Overview of current researches on Tibetan medicine \"zuotai\"]. Zhongguo Zhong Yao Za Zhi. 2013; 38(17): 2886–2888. PubMed Abstract\n\nKan ZB: [An introduction of Zuotai in Tibetan patent medicine]. Zhongguo Zhong Yao Za Zhi. 2013; 38(10): 1621–1623. PubMed Abstract\n\nSchwabl A, Gämperle E: [Special aspects of quality of Tibetan medicines--insights from over 40 years of manufacturing experience in Switzerland]. Forsch Komplementmed. 2013; 20 Suppl 2: 14–16. PubMed Abstract | Publisher Full Text\n\nReuter KP, Weißhuhn TE, Witt CM: Tibetan medicine: a systematic review of the clinical research available in the west. Evid Based Complement Alternat Med. 2013; 2013: 213407. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLi Q, Li H J, Xu T, et al.: Natural Medicines Used in the Traditional Tibetan Medical System for the Treatment of Liver Diseases. Front Pharmacol. 2018; 9: 29. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLiu J, Zhang F, Ravikanth V, et al.: Chemical Compositions of Metals in Bhasmas and Tibetan Zuotai Are a Major Determinant of Their Therapeutic Effects and Toxicity. Evid Based Complement Alternat Med. 2019; 2019: 1697804. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHu AL, Song S, Li Y, et al.: Mercury sulfide-containing Hua-Feng-Dan and 70W (Rannasangpei) protect against LPS plus MPTP-induced neurotoxicity and disturbance of gut microbiota in mice. J Ethnopharmacol. 2020; 254: 112674. PubMed Abstract | Publisher Full Text\n\nChinese Pharmacopoeia: Pharmacopeia of the People's Republic of China. Chinese Medical Press. 2015; 1. Reference Source\n\nWu P, Luo Y, Zhen L, et al.: Rannasangpei Is a Therapeutic Agent in the Treatment of Vascular Dementia. Evid Based Complement Alternat Med. 2016; 2016: 2530105. PubMed Abstract | Publisher Full Text | Free Full Text\n\nXu M, Wu R, Liang Y, et al.: Protective effect and mechanism of Qishiwei Zhenzhu pills on cerebral ischemia-reperfusion injury via blood-brain barrier and metabonomics. Biomed Pharmacother. 2020; 131: 110723. PubMed Abstract | Publisher Full Text\n\nZhang BB, Nie, Y, Hu AL, et al.: Effect of Qishiwei pearl pills on intestinal microbiota in mice. Zhong Cheng Yao. 2020; 42(3): 626–631.\n\nNie Y, Zhang BB, Du YZ, et al.: Protective effects of 70 Wei Zhen-Zhu-Wan against carbon tetrachloride induced liver injury in mice. Zunyi Medical University. 2018; 40: 358–363.\n\nRaucy JL, Kraner JC, Lasker JM: Bioactivation of halogenated hydrocarbons by cytochrome P4502E1. Crit Rev Toxicol. 1993; 23(1): 1–20. PubMed Abstract | Publisher Full Text\n\nJin SE, Ha H, Shin HK: Effects of traditional herbal formulae on human CYP450 isozymes. Chin J Integr Med. 2017; 23(1): 62–69. PubMed Abstract | Publisher Full Text\n\nParvez MK, Rishi V: Herb-Drug Interactions and Hepatotoxicity. Curr Drug Metab. 2019; 20(4): 275–282. PubMed Abstract | Publisher Full Text\n\nLu Y, Xie T, Zhang Y, et al.: Triptolide Induces hepatotoxicity via inhibition of CYP450s in Rat liver microsomes. BMC Complement Altern Med. 2017; 17(1): 15. PubMed Abstract | Publisher Full Text | Free Full Text\n\nXu S, Liu J, Shi J, et al.: 2,3,4',5-tetrahydroxystilbene-2-O-β-D-glucoside exacerbates acetaminophen-induced hepatotoxicity by inducing hepatic expression of CYP2E1, CYP3A4 and CYP1A2. Sci Rep. 2017; 7(1): 16511. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAleksunes LM, Klaassen CD: Coordinated regulation of hepatic phase I and II drug-metabolizing genes and transporters using AhR-, CAR-, PXR-, PPARα-, and Nrf2-null mice. Drug Metab Dispos. 2012; 40(7): 1366–1379. PubMed Abstract | Publisher Full Text | Free Full Text\n\nZhang BB, Liu YM, Hu AL, et al.: HgS and Zuotai differ from HgCl(2) and methyl mercury in intestinal Hg absorption, transporter expression and gut microbiome in mice. Toxicol Appl Pharmacol. 2019; 379: 114615. PubMed Abstract | Publisher Full Text\n\nWu Q, Li WK, Zhou ZP, et al.: The Tibetan medicine Zuotai differs from HgCl2 and MeHg in producing liver injury in mice. Regul Toxicol Pharmacol. 2016; 78: 1–7. PubMed Abstract | Publisher Full Text\n\nZhang BB, Li WK, Hou WY, et al.: Zuotai and HgS differ from HgCl2 and methyl mercury in Hg accumulation and toxicity in weanling and aged rats. Toxicol Appl Pharmacol. 2017; 331: 76–84. PubMed Abstract | Publisher Full Text\n\nLiu J, Lu H, Lu YF, et al.: Potency of individual bile acids to regulate bile acid synthesis and transport genes in primary human hepatocyte cultures. Toxicol Sci. 2014; 141(2): 538–546. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLiu J, Wei LX, Wang Q, et al.: A review of cinnabar (HgS) and/or realgar (As4S4)-containing traditional medicines. J Ethnopharmacol. 2018; 210: 340–350. PubMed Abstract | Publisher Full Text\n\nLi C, Xu W, Chu S, et al.: The chemical speciation, spatial distribution and toxicity of mercury from Tibetan medicine Zuotai, β-HgS and HgCl2) in mouse kidney. J Trace Elem Med Biol. 2018; 45: 104–113. PubMed Abstract | Publisher Full Text\n\nLi C, Wang DP, Duo J, et al.: [Study on safety of Tibetan medicine zuotai and preliminary study on clinical safety of its compound dangzuo]. Zhongguo Zhong Yao Za Zhi. 2014; 39(13): 2573–2582. PubMed Abstract\n\nSallon S, Dory Y, Barghouthy Y, et al.: Is mercury in Tibetan Medicine toxic? Clinical, neurocognitive and biochemical results of an initial cross-sectional study. Exp Biol Med (Maywood). 2017; 242(3): 316–332. PubMed Abstract | Publisher Full Text | Free Full Text\n\nVickers AJ, van Haselen R, Heger M: Can homeopathically prepared mercury cause symptoms in healthy volunteers? A randomized, double-blind placebo-controlled trial. J Altern Complement Med. 2001; 7(2): 141–148. PubMed Abstract | Publisher Full Text\n\nYu YH, Li LS: Effect of Rannasangpei on human liver and kidney function and blood biochemistry. Shi-Zhen Guoyi Guoyao. 2014; 25: 2848–2851.\n\nLiu J, Lu YF, Li WK, et al.: Mercury sulfides are much less nephrotoxic than mercury chloride and methylmercury in mice. Toxicol Lett. 2016; 262: 153–160. PubMed Abstract | Publisher Full Text\n\nAnwar-Mohamed A, Elbekai RH, El-Kadi AO: Regulation of CYP1A1 by heavy metals and consequences for drug metabolism. Expert Opin Drug Metab Toxicol. 2009; 5(5): 501–521. PubMed Abstract | Publisher Full Text\n\nXu SF, Wu Q, Zhang BB, et al.: Comparison of mercury sulfides with mercury chloride and methylmercury on hepatic P450, phase-2 and transporter gene expression in mice. J Trace Elem Med Biol. 2016; 37: 37–43. PubMed Abstract | Publisher Full Text\n\nLi XY, Liu YN, Li YP, et al.: [Effect of Tibetan medicine zuotai on the activity, protein and mRNA expression of CYP1A2 and NAT2]. Yao Xue Xue Bao. 2014; 49(2): 267–272. PubMed Abstract\n\nZhen H, Wen M, Yang Y, et al.: Toxic effects of HgCl2 on activities of SOD, AchE and relative expression of SOD, AChE, CYP1A1 of zebrafish. Ecotoxicology. 2014; 23(10): 1842–1845. PubMed Abstract | Publisher Full Text\n\nAmara IE, Elshenawy OH, Abdelrady M, et al.: Acute mercury toxicity modulates cytochrome P450, soluble epoxide hydrolase and their associated arachidonic acid metabolites in C57Bl/6 mouse heart. Toxicol Lett. 2014; 226(1): 53–62. PubMed Abstract | Publisher Full Text\n\nLu YF, Wu Q, Liang SX, et al.: Evaluation of hepatotoxicity potential of cinnabar-containing An-Gong-Niu-Huang Wan, a patent traditional Chinese medicine. Regul Toxicol Pharmacol. 2011; 60(2): 206–211. PubMed Abstract | Publisher Full Text\n\nHartman JH, Miller GP, Meyer JN: Toxicological Implications of Mitochondrial Localization of CYP2E1. Toxicol Res (Camb). 2017; 6(3): 273–289. PubMed Abstract | Publisher Full Text | Free Full Text\n\nJoshi D, Mittal DK, Shukla S, et al.: Curcuma longa Linn. extract and curcumin protect CYP 2E1 enzymatic activity against mercuric chloride-induced hepatotoxicity and oxidative stress: A protective approach. Exp Toxicol Pathol. 2017; 69(6): 373–382. PubMed Abstract | Publisher Full Text\n\nAmara IE, Anwar-Mohamed A, Abdelhamid G, et al.: Mercury modulates the cytochrome P450 1a1, 1a2 and 1b1 in C57BL/6J mice: in vivo and in vitro studies. Toxicol Appl Pharmacol. 2013; 266(3): 419–429. PubMed Abstract | Publisher Full Text\n\nNie Y, Xu SF, Lu YL, et al.: Zuotai (β-HgS)-containing 70 Wei Zhen-Zhu-Wan differs from mercury chloride and methylmercury on hepatic cytochrome P450 (Version 1). 2020. http://www.doi.org/10.5281/zenodo.4403717"
}
|
[
{
"id": "81779",
"date": "30 Mar 2021",
"name": "Xingguo Cheng",
"expertise": [
"Reviewer Expertise 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\nBecause of their toxic components and potential drug-drug interaction, many traditional Asian Medicine, including Tibetan Medicine, have been raising health concerns. In this manuscript, Nie et al evaluated and compared the expression regulation of several P450s by Zuotai, mercury chloride and methylmercury, given the same mercury content level. The authors suggested that it is not appropriate to simply use total Hg content to evaluate the safety of HgS-containing Zuotai. Overall, the study is straight-forward.\n\nFigure legend of Figure 1: should be total RNA from mouse liver was extracted and processed for RT-PCR analysis.\n\nIn animal treatment section, the mice should be treated with Zuotai, mercury chloride and methylmercury by using the unit of mmole/kg or micromole/kg, but not mg/kg unit.\n\nThe authors have assessed Cyp7a1 and FXR expression. To make the studies more relevant, the authors may consider to measure total bile acids in mouse serum, a biomarker of liver injury.\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": "6636",
"date": "05 May 2021",
"name": "Jie Liu",
"role": "Author Response",
"response": "Thanks for the comments. Some of the inquiries could be found in listed references Nie et al., 2018."
},
{
"c_id": "6637",
"date": "05 May 2021",
"name": "Jie Liu",
"role": "Author Response",
"response": "Figure legend of Figure 1: should be total RNA from mouse liver was extracted and processed for RT-PCR analysis. Answer: Yes In animal treatment section, the mice should be treated with Zuotai, mercury chloride and methylmercury by using the unit of mmole/kg or micromole/kg, but not mg/kg unit. Answer: Since Zoutai is a mineral mixture, we can only use mg/kg. mercury chloride and MeHg were used based on mol basis as HgS The authors have assessed Cyp7a1 and FXR expression. To make the studies more relevant, the authors may consider to measure total bile acids in mouse serum, a biomarker of liver injury. Answer: Good suggestion for future consideration. ALT and histology in prior publications verified the toxicity"
}
]
},
{
"id": "81778",
"date": "30 Apr 2021",
"name": "Xian-Ju Huang",
"expertise": [
"Reviewer Expertise Pharmacology and toxicology"
],
"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 was well designed to discuss the hepatotoxicity of Zuotai-containing 70W and the data persuasive. However, some errors should be corrected.\nThe dose of 70W (0.15-1.5 g/kg) should be 1-10 times clinical doses. The author described as 1-5 times.\n\nThe data of ALT and AST as well as pathological changes were not shown in the results. However, the methods have mentioned. Please check them.\n\nThe introduction section, the second paragraph, line 2, \"Pamda-28\" may not be true, please check it.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-203
|
https://f1000research.com/articles/10-494/v1
|
24 Jun 21
|
{
"type": "Research Article",
"title": "A preliminary study of Japanese co-workers’ attitudes towards migrant workers’ Japanese language skills in blue-collar workplaces",
"authors": [
"Liang Morita"
],
"abstract": "Background: This is a preliminary study of Japanese co-workers’ attitudes towards migrant workers’ Japanese language skills in blue-collar workplaces. This is an important topic, seeing as Japanese co-workers’ attitudes can result in inequalities at the workplace, directly impacting migrant workers’ everyday lives. Understanding these attitudes and addressing them can improve migrant workers’ experiences. Methods: The study is based on content analysis of documents taken from English-language sources. Results: The author found that Japanese co-workers and employers assume ownership of the means of communication, expecting only Japanese to be used at the workplace. They also underrate migrant workers’ Japanese proficiency. Conclusions: Although the data has its limitations, the study provides some insight and can potentially serve as a base for further research.",
"keywords": [
"Japan",
"blue-collar",
"migrant workers",
"attitudes",
"workplace"
],
"content": "1. Introduction\n\nRecent research in blue-collar workplaces1 in Norway (Kraft, 2019a; Lonsmann and Kraft, 2018) have shown that Norwegian workers’ attitudes towards Polish migrant workers’ Norwegian language skills can result in inequalities at the workplace. Japan is a country known for its exclusionary attitudes towards foreigners (Doudou, 2006; Morita, 2015; Park, 2017), so it is reasonable to ask if Japanese co-workers have similar attitudes towards migrant workers’ Japanese proficiency. Since Japan amended its immigration law2 to formally accept blue-collar migrant workers in April 2019, there is some urgency for research looking into Japanese co-workers’ attitudes.\n\nThe April 2019 revision to the immigration law is ground-breaking in the sense that it officially accepts blue-collar migrant workers for the first time in Japanese history. Migrant workers were only accepted through ‘side doors’3 in the past. Two new visa categories were created in 2019: one for lower skilled workers and the other for higher skilled workers. These workers are employed in accommodation, agriculture, aviation, building-cleaning, car-maintenance, construction, electronics, food-manufacturing, fisheries, food services, forging technology, industrial machinery, nursing care, and shipbuilding. Both visas are referred to as ‘Specified Skilled Worker visas’ (MFA, 2019a, 2019b).\n\nThe conditions attached to the visas include applicants having to pass tests in trade skills and basic Japanese language. The lower skilled visa carries a limit of five years, while the higher skilled one can be renewed indefinitely as long as the applicant has a valid employment contract. Holders of the latter may bring their family to Japan and are eligible to apply for permanent residency (MFA, 2019a, 2019b).\n\nThe Japanese language requirement for the visas indicates the expectation that Japanese is to be used at the workplace. This is understandable since Japanese blue-collar workers are most likely to have secondary-level education and do not have command of foreign languages. It is a practical matter to ask migrant workers to learn some Japanese so that Japanese co-workers can communicate with them. The question which follows is whether migrant workers’ less-than-perfect Japanese will be accepted by their Japanese co-workers. This is a fair question to ask, since Japan is a country in which there is widespread interest in speaking correct Japanese (Miyo and Chung, 2006), resulting in a situation in which those who speak correct Japanese are considered as regular members of society, while those who do not are not accepted. Native speakers’ Japanese is also thought of more highly than the Japanese spoken by foreign learners (Miyo and Chung, 2006).\n\nKusunoki’s (2018) study is one of the very few which investigate Japanese co-workers’ attitudes towards their foreign colleagues’ Japanese language skills. The study takes place in hospital settings in which foreign nurse trainees are employed under the Economic Partnership Agreement (EPA). Japan signed EPAs with Indonesia, the Philippines and Vietnam to enable nurses and healthcare workers in these countries to work in Japan. The condition attached is that these professionals work as assistants or trainees until they pass the Japanese national licensing examination in Japanese. After they obtain their licenses they are employed as fully fledged professionals and as equals to their Japanese counterparts.\n\nKusunoki (2018) found that Japanese co-workers assumed ownership of the means of communication, meaning that they not only expect Japanese to be used when the EPA trainees communicate with them, they also expect Japanese to be used when the trainees are speaking among themselves. The reason given is that since the trainees are in Japan, they are learning Japanese, and Japanese co-workers understand Japanese only, therefore only Japanese should be used. Furthermore, Japanese co-workers underrate the Japanese proficiency of the trainees.\n\nDrawing on Kusunoki’s findings, the present paper is a preliminary study of Japanese co-workers’ attitudes towards migrant workers’ Japanese in blue-collar workplaces. It asks two questions: firstly, if Japanese co-workers assume ownership of the means of communication, expecting only Japanese to be used at the workplace, and secondly, if they underrate migrant workers’ Japanese.\n\nAfter the significance of the two attitudes is explained in the next section, the methodology and data are presented in Sections 3 and 4, respectively. The findings are discussed in Section 5, and the concluding remarks in Section 6 bring the paper to an end.\n\n\n2. Attitudes can become covert mechanisms of language policies\n\nAttitudes such as assumption of the means of communication and underrating of migrant workers’ language skills are significant. This section draws on research on language policy, especially Shohamy’s (2006) work, to demonstrate their importance.\n\nLanguage policy is often associated with overt mechanisms such as official documents, declarations, language standards, curricula, tests, and other types of documents, which are used to manipulate and control language practices. Lonsmann and Kraft (2018) focused on the official languages, which are overt mechanisms, in a warehouse in Denmark and on construction sites in Norway. More subtle and hidden, however, are the covert and hidden mechanisms of language policies. These mechanisms can be used in conversations and negotiations to exercise control over the language space, and can serve as major devices that affect and create de facto language policies (Shohamy, 2006).\n\nAttitudes such as assumption of the means of communication and underrating of migrant workers’ language proficiency can become covert mechanisms if made known frequently enough. Identifying them as potential covert mechanisms is consistent with Shohamy’s (2006) call for a broader perspective of language policy. Assumption of the means of communication, if made known often, can become a covert mechanism of a policy to use Japanese only in the workplace. Likewise, underrating of migrant workers’ Japanese can become a covert mechanism of a policy to raise their Japanese proficiency. The effects of these mechanisms can be as far-reaching as those of overt mechanisms such as the introduction of an official language or minimum standard of Japanese.\n\nThere are many reasons why covert mechanisms deserve attention and study. Shohamy (2006) emphasised that a real language policy should not be observed, understood and interpreted only through declared policy statements, but through a variety of devices that are used to perpetuate language policies, often in covert and implicit ways. These devices, which may not appear to be policy devices, have direct effects on language practice. Schiffman (1996), who also agrees with the distinction between overt and covert mechanisms, stressed that there is a need to study de facto policies, and that covert mechanisms are often overlooked.\n\n\n3. Methodology\n\nThis paper draws on the documentary research method (McCulloch, 2004) to study the attitudes of Japanese co-workers towards migrant workers’ Japanese language skills. Documentary research is built on the belief that analysing documents and understanding them help us develop a study. Documents include policy reports, committee papers, public treatises, works of fiction, diaries, autobiographies, newspapers, magazines, letters and electronic mail (McCulloch, 2004).\n\nThe author started with a search on the internet using various combinations of the keywords ‘migrant worker’, ‘blue-collar’, ‘Japan’ and ‘Japanese language’, and found few results which contained comments made by Japanese co-workers or employers on migrant workers’ Japanese proficiency. One of the results was a report by Builders and Wood Workers International (BWI), penned after they inspected the 2020 Tokyo Olympics construction sites (BWI, 2019), which contained remarks on the Japanese language abilities of migrant workers. Also among the results were a few newspaper articles, so the author took a closer look at newspapers by conducting keyword searches via online archives of the major English-language newspapers: The Japan Times, The Japan News, The Mainichi, and Nikkei Asia.\n\nShe attempted a few different keyword searches for articles published between January 2015 and December 2020, using ‘migrant workers’, ‘blue-collar workers’ and ‘foreign workers’. ‘Foreign workers’ retrieved the largest numbers of articles, which is 233 articles in The Japan Times, 1,928 articles in The Japan News, 375 articles in The Mainichi and 1,160 articles in Nikkei Asia. The author read through the articles and found that most of the search results for The Japan News and Nikkei Asia were barely related to foreign workers. Among those that were related to foreign workers in all four newspapers, many articles were written in the run-up to the introduction of the Specified Skilled visas, debating the issues involved and announcing the visas’ specifics. There were also many articles on abuses of the Technical Intern Training Program4 (TITP), detailing poor treatment and underpayment of the foreign interns.\n\nOnly two newspaper articles which contained comments on migrant workers’ Japanese were found.5 The first is a news story by Nikkei Asia about a TITP intern who was sent to do decontamination work in Fukushima (Lang, 2018). The second is by The Japan Times, and is about small firms taking on foreign employees (Nagata, 2019). Content analysis was performed on all three documents (the BWI report and two newspaper articles). In future research, the data must include Japanese-language sources in order to increase the size of the data as well as to provide a more balanced point of view.\n\nIn spite of the limitations of the data, and the fact that it is based on what is reported in documents rather than information recorded by the author, the study can still provide some insight. Its findings are also consistent with Kusunoki (2018), Kraft (2019a) and Lonsmann and Kraft (2018). Until the author gains access to blue-collar workplaces, this study can serve as a base for future research.\n\n\n4. Data\n\nIn sections 4.1, 4.2 and 4.3 below, background information and a summary of each of the three documents analysed in this paper are provided.\n\nBuilding and Wood Workers’ International (BWI) is a global federation of trade unions in the building, building materials, wood, forestry, and related industries. It is a non-profit organisation based in Geneva, and has regional offices and project offices scattered around the world. Its goals are to organise workers into trade unions, and more importantly, to improve standards in the construction industry in the long run. BWI appears to have significant experience in large-scale sports events, having been involved in the 2012 Euro Cup in Poland and Ukraine, the 2018 World Cup in Russia, and the 2018 Winter Olympics in PyeongChang.\n\nBWI seems to have no political agenda apart from seeking to improve workers’ rights. It claims to focus on supporting its affiliates to achieve better working conditions and ensure safety and health for workers in all projects related to large-scale sports events (BWI, 2019). It also aspires to leave behind a legacy of improved standards in the construction industry after the events.\n\nThe BWI report was penned after an international delegation visited the 2020 Tokyo Olympics construction sites in September 2018 (BWI, 2019). The gist of the report is that there was an acute labour shortage and the workers were overworked. More relevant to the present paper is the short section on migrant workers. At one site there were migrant workers, or strictly speaking, TITP interns, but the Japanese workers noted that these interns were given only menial tasks to perform, such as shifting raw materials. BWI pointed out that shifting raw materials is a task that should be carried out with forklifts or other equipment, and that the interns could more effectively contribute on the construction site if they were assigned work that would develop their skills (BWI, 2019). Some of the remarks made by the site management revealed their attitudes towards the interns’ Japanese language skills.\n\nNikkei Asia is a weekly publication owned by Nikkei Inc. Nikkei Inc’s flagship publication, The Nikkei, claims to be the world’s largest financial newspaper. Nikkei Asia targets business readers, and is slightly to the right on the political spectrum. Unlike left-leaning newspapers such as The Mainichi, which sympathises with migrant workers and frequently runs stories on the injustices they suffer (such as a recent series on the plight of Vietnamese TITP interns), Nikkei Asia features fewer stories on the misfortunes of individual migrant workers.\n\nIt is difficult to ascertain but it seems likely that the TITP intern approached Nikkei Asia with his story. After Nikkei Asia ran the article, it was taken up by other newspapers, which based their reporting on the original article in Nikkei Asia. The story appeared in March 2018, providing details on a TITP intern’s experience of being sent to Fukushima Prefecture to do decontamination work, even though it was not within the scope of his duties as he understood it (Lang, 2018). The 24-year-old Vietnamese male, who was hired by a construction company, said he had been sent to residential areas in Fukushima on numerous occasions to demolish contaminated structures. His Japanese employer was interviewed for the story, and his responses revealed his attitudes towards the intern’s Japanese language skills.\n\nThe Japan Times claims to be the most widely read English language newspaper in the country. It also boasts of being the largest and oldest English language daily newspaper. It appears to be in a neutral position politically, with no particular leanings. However, the article analysed in this paper is part of a series which claims to examine Japan’s immigration policy as the country opens its doors to an increasing number of migrant workers (Nagata, 2019). The article is dated 21st April 2019, the same month in which the Specified Skilled Worker visas were introduced. It wouldn’t be unreasonable to assume that the newspaper was trying to be supportive of the new visas, thereby adopting an optimistic tone, as well as providing a ‘happy ending’ to the story in which the featured companies’ efforts result in success.\n\nThe article mainly focuses on the experiences of Sakae Casting Co, a small aluminium manufacturer located in Tokyo. Two other firms with similar experiences are also mentioned towards the end of the article. Sakae’s CEO, Takahashi Suzuki, believes that foreign employees are necessary for overseas expansion of his business. After a difficult process of adaptation, the foreign employees are integrated and Suzuki successfully expands his business.\n\n\n5. Findings\n\nJapanese co-workers or employers assume ownership of the means of communication in all three documents analysed. Analyses of the documents are presented below, beginning with the BWI report.\n\nIn the report, the site management of one construction site reported that the TITP interns working there spoke no Japanese and communication was a challenge, especially on health and safety matters:\n\n‘The next day the BWI Mission visited the TMG (Tokyo Metropolitan Government)-managed Canoe Slalom Course, where site management reported that there were indeed a number of migrant workers on the site. At the same time, it was reported that they (the migrant workers) spoke no Japanese and communication was a challenge, particularly on OHS (Occupational Health and Safety) matters.’ (BWI 2019: 11)\n\nWhen the above extract is read in conjunction with the Japanese workers’ observation that the interns were given only menial tasks, such as shifting raw materials, it seems likely that it was because they did not speak Japanese that they were assigned such work. Although the management did not explicitly state that it was due to that, given the context that there was an acute labour shortage and the Japanese workers were overworked, it is the most likely explanation. It appears that the Japanese supervisors felt they lacked the means to communicate to the interns the complexity of more challenging tasks, as well as the health and safety issues involved. Although under Japanese law, employers must ensure that foreign employees can understand the health and safety procedures, the interns noted that there was no special provision to translate safety materials or procedures into other languages (BWI, 2019).\n\nReading between the lines, it seems that the management implicitly assumed that Japanese is the only means of communication, which suggests ownership of the means of communication. Their reasoning appears to be that since the interns did not speak Japanese, there was no way of communicating with them. This reasoning is made to appear to be common sense in that ‘it was reported that they (the migrant workers) spoke no Japanese and communication was a challenge’ (BWI 2019: 11); since the interns did not speak Japanese, and Japanese was the only means of communication, therefore communication was difficult. It is untrue that Japanese was the only means of communication. The management and Japanese workers could have been taught Vietnamese, Chinese or any other language.\n\nProficiency in the hegemonic6 language of the state is often used to classify people, and those who are not proficient are frequently said to be unable to function in society (Shohamy, 2006; Shohamy, 2009). In this case, the interns seem to have been classified or labelled as ‘non-speakers of Japanese’ and are seen as being capable of menial tasks such as moving raw materials only. This deprives the construction site of the contribution they are potentially capable of making as well as the interns of the opportunity to develop their skills. It echoes Kraft’s (2019b) finding, that Norwegians think that Polish workers on Norwegian construction sites need to be restricted to simple tasks because they do not speak Norwegian.\n\nIn the second document analysed (the Nikkei Asia story about a TITP intern who was sent to do decontamination work in Fukushima), the intern’s employer also assumes ownership of the means of communication. In order to provide adequate context, the analysis below includes what the employer said prior to the sentences indicating ownership of the means of communication.\n\nWhen Nikkei Asia interviewed the employer, who was also the president of the construction company, he defended his decision to send the intern to Fukushima:\n\n‘“The technical intern training program sounds nice, but in reality, for the foreigners in the program, it’s the money that matters.” The president of his (the intern’s) former company acknowledged that the man was given decontamination work but denied there was anything illegal about it. The foreign trainee, the president said, was doing “what the Japanese workers were doing.” “We do various kinds of work; decontamination is just one,” the president added. “The location was a residential area and wasn’t particularly dangerous.”’ (Lang, 2018)\n\nBased on the beginning of the extract, we can see that the employer perceives TITP interns as opportunistic individuals. He thinks that as long as the intern is assigned the same duties as his Japanese employees and therefore treated equally, the risks involved in decontamination work do not matter. He used the word ‘foreign’ before ‘intern’, even though it was obvious which intern the interview was about. He then referred to ‘the Japanese workers’ rather than ‘other workers’, so the contrast between the categories ‘foreign’ and ‘Japanese’ is accentuated. He then attempts to downplay the risks by pointing out that the work site was a residential area, as opposed to, presumably, the nuclear power plant.\n\nThe employer’s response continues below:\n\n‘He (the president) said the nature of the decontamination work was explained before going to the site. “We always give a training session before going to a site,” the president said. “In fact, we spent a day for training at the office on the site before we did the decontamination work. He (the intern) may not have understood it because he didn’t understand Japanese, but if he had asked, we would have given him a full explanation.”’ (Lang, 2018)\n\nThe employer’s reasoning appears to be that it was because the intern did not understand Japanese that he was not provided with an explanation on the decontamination work. However, if the intern were to be treated equally to the Japanese employees, the employer should have made sure he understood, with perhaps a mixture of Japanese, English, gestures and drawings. It is clear here that equality is a principle used at the employer’s convenience. It was convenient earlier when he cited equality with the Japanese employees as justification for assigning the intern decontamination work. When it is inconvenient, meaning the employer has to be willing to make an effort to be understood, he explains his lack of willingness and effort away by saying the intern did not understand Japanese. As in the BWI report, Japanese is assumed to be the only language of the workplace in as if this is common sense.\n\nIn the third document analysed (The Japan Times story on small firms taking on foreign employees), ownership of the means of communication was also found. The extract below is taken from the middle of the article, where Suzuki, the CEO of Sakae Casting Co, describes what happened after he hired foreign employees:\n\n‘But right away Suzuki realized the company wasn’t properly prepared to take in non-Japanese staff. Language limitations meant that many had trouble communicating, which frustrated their Japanese co-workers tasked with training. (1)\n\nThat frustration piled up among the Japanese workers until one day the following year, it exploded. They demanded that Suzuki stop hiring foreign employees, threatening a walkout. (2)\n\n“It was (choosing) either them or foreign workers,” Suzuki recalled. “Thinking of the company’s future, I couldn’t give up on the strategy to expand business overseas.” (3)\n\nAnd that was what he told the Japanese employees. In the end, the plant chief whom Suzuki worked with for many years walked away. But the rest stayed. (4)\n\nSuzuki believes his hard line – refusing to meet the workers’ demand to stop hiring foreign staff – made the Japanese workers realize he was serious. (5)\n\n“From there, I think their mindset changed a bit,” he said. (6)\n\nJapanese workers started making efforts to create a work environment more friendly for foreign employees, using English for some in-house communications and taking online English lessons that the company provided.’ (7) (Nagata, 2019)\n\nAlthough Suzuki did not explicitly state at the beginning of the extract what language was used when his employees experienced ‘language limitations’ which frustrated the Japanese employees, paragraph (7) implies that it was not English. English was only used later, after he asserted his position on keeping the foreign employees. The most logical interpretation is that the Japanese employees used Japanese with the foreign employees at the beginning, and failed to communicate. The use of Japanese again indicates ownership of the means of communication.\n\nParagraph (1) suggests that communication difficulties were the only cause of the Japanese employees’ frustration, and this frustration led them to threaten to leave. They appear to have been insistent about using Japanese. One of them, the plant chief, sacrificed his job of many years because of this attitude.\n\nThe turnaround in the Japanese employees’ attitudes, from insistence on the use of Japanese to willingness to use English, is significant. Suzuki’s firm position on foreign employees being necessary for overseas expansion seems to have led to the change. He practically coerced the Japanese employees into using English. This shows that firm leadership may be one way to persuade Japanese employees to relinquish ownership of the means of communication. This news story also suggests that the Japanese are capable of using English at work, in spite of the common belief that their English is only adequate for passing examinations.\n\nAs long as Japanese co-workers claim ownership of the means of communication, expecting Japanese to be used, they discount the possibility of using a mixture of Japanese, English, and gestures as a means of communication. Recent research (Blackledge and Creese, 2017; Creese and Blackledge, 2019; Creese, Blackledge and Hu, 2018) has in fact shown that effective communication can be achieved with fragments of various languages, signs, and gestures, also known as translanguaging. As this field of research grows, it challenges the more traditional understanding of language and communication, especially mastery of a language, as indispensable to successful communication. What we have observed in Japanese co-workers and employers in this section is adherence to the socially and politically defined boundary of a national language, namely, Japanese (Otheguy, Garcia and Reid, 2015). As more migrant workers arrive and blue-collar workplaces become more diverse, adherence to Japanese will stand in contrast to the reality that translanguaging is the norm when people from different backgrounds are brought together (Blackledge and Creese, 2017; Creese and Blackledge, 2019; Creese, Blackledge and Hu, 2018). Studies conducted in blue-collar workplaces (Dijkstra et al., 2020; Goncalves, 2020; Theodoropoulou, 2019) also attest to the effectiveness and prevalence of translanguaging.\n\nIn addition to the successful use of translanguaging, a hotel kitchen in Austria also shows how an inclusive work environment can be achieved when higher-level employees are willing to accommodate to the communication needs of lower-level employees. In this workplace, higher-level Austrian employees accommodate for lower-level Romanian employees by using online translation services, fragments of various languages, gestures, body language, and signs (Goncalves, 2020). This unusual bottom-up approach results in an inclusive and successful workplace, and serves as an example for Japanese co-workers and employers.\n\nJapanese co-workers and employers underrate migrant workers’ Japanese language skills in the first two documents analysed.\n\nIn the first document, the construction site management commented that the TITP interns spoke no Japanese. The extract below is the same as that cited in section 5.1:\n\n‘The next day the BWI Mission visited the TMG (Tokyo Metropolitan Government)-managed Canoe Slalom Course, where site management reported that there were indeed a number of migrant workers on the site. At the same time, it was reported that they (the migrant workers) spoke no Japanese and communication was a challenge, particularly on OHS (Occupational Health and Safety) matters.’ (BWI 2019: 11)\n\nTITP interns are usually taught Japanese for about six months before coming to Japan, and another month after arrival, usually in a language school (Obe and Funatsu, 2018). To say that ‘they spoke no Japanese’ underrates their Japanese.\n\nIt is unclear what qualifies as speaking Japanese to the management. In her study of communication on Norwegian construction sites, Kraft (2019a) noted that the level of competence required to pass as a speaker is opaque. One Polish worker in particular was competent in understanding Norwegian and his job, but was regarded by Norwegian and Swedish foremen as well as team leaders as ‘speaking no Norwegian at all’ (Kraft, 2019a; Lonsmann and Kraft, 2018). Kraft observes that Polish workers are often better at understanding other languages than their Norwegian and Swedish co-workers think. Having received seven months’ instruction in the Japanese language, the interns are likely to understand more Japanese than the management give them credit for. Polish lorry drivers are likewise thought of as being unable to communicate in the Netherlands, in spite of the fact that they successfully complete their assignments (Dijkstra et al., 2020).\n\n‘Svorsk’, which is a mixed language that results from inter-accommodation between Swedish and Norwegian speakers, is commonly used on Norwegian construction sites (Kraft, 2019a). Also prevalent is ‘construction site English’, which refers to grammatically imperfect and gesture-dependent English. Instead of grammatically correct sentences, central words carrying specific work-related meanings, combined with objects such as tools, technical drawings and models of the buildings, often serve as the means of communication (Lonsmann and Kraft, 2018). Having a shared professional knowledge eases communication. Although languages such as Vietnamese or Chinese are not commonly taught in Japan, English is. English is practically compulsory for all students in school. There is no reason why a mixture of Japanese, English, gestures, objects and drawings should not be used on construction sites, although it would require some measure of accommodation from both parties, or as Kubota (2013) and Canagarajah (2017a, 2017b) point out, the willingness to communicate.\n\nA good example of willingness to communicate or accommodate has been given in section 5.1, in the hotel kitchen in Austria where higher-level Austrian employees adapt to the language abilities of lower-level Romanian employees (Goncalves, 2020). This is partly motivated by the desire to have an inclusive workplace and partly due to the fact that there is a labour shortage. Japan is also in the grip of a labour shortage because of its rapidly aging and declining population (Green, 2017), which is the very reason why the Specified Skilled Worker visas were introduced. Unlike the Austrian kitchen, in which online translation services, fragments of various languages, gestures, body language, and signs are used by the Austrian staff (Goncalves, 2020), Japan’s labour shortage has not yet pushed Japanese co-workers and employers to look beyond the Japanese language.\n\nSimilarly, in the second document analysed, the employer underrates the intern’s Japanese language skills. The extract below is the same as that cited in section 5.1:\n\n‘He (the president) said the nature of the decontamination work was explained before going to the site. “We always give a training session before going to a site,” the president said. “In fact, we spent a day for training at the office on the site before we did the decontamination work. He (the intern) may not have understood it because he didn’t understand Japanese, but if he had asked, we would have given him a full explanation.”’ (Lang, 2018)\n\nTo say that ‘he didn’t understand Japanese’ underrates the intern’s Japanese proficiency. This statement is contradicted by the following:\n\n‘He (the intern) said he often saw Japanese colleagues holding what appeared to be radiation detectors close to the ground and saying to each other things like, “This spot seems dangerous.” The man complained to the company president about the unexpected work but was told, “If you’re scared, go home to Vietnam.”’ (Lang, 2018)\n\nThe intern clearly understands Japanese, or he would not have understood what the Japanese employees were saying about dangerous spots. In addition, he spoke sufficient Japanese to complain to the employer about his work. The employer was also aware that the intern understood Japanese, or he would not have suggested going home to Vietnam. In spite of all the above, the intern was thought of as ‘not understanding Japanese’ (Lang, 2018). The criteria for ‘understanding Japanese’ is again unclear here.\n\nUnderrating migrant workers’ Japanese can result in inequalities at the workplace and their exclusion. O’Rourke et al. (2015) argue that, to be more inclusive of immigrants, we should value their various linguistic resources, shifting from expectations of native-speaker mastery of a language to include partial and imperfect use. Recent research has also found that immigrants use and claim ownership of language as part of their repertoire in various ways and for different purposes (Garcia and Li, 2014).\n\nStereotypical images of foreign workers’ poor linguistic abilities can undermine the effectiveness and efficacy of their work (Dijkstra et al., 2020). We have seen in this section that underrating migrant workers’ language skills can also lead to exclusion from meaningful work and work briefings, as well as from permanent employment contracts (Kraft, 2019a; Lonsmann and Kraft, 2018).\n\n\n6. Concluding remarks\n\nTo answer the questions asked in the Introduction, the author has found that, firstly, Japanese co-workers do assume ownership of the means of communication, expecting only Japanese to be used at the workplace, and secondly, they do underrate migrant workers’ Japanese language skills.\n\nThe above findings cast doubt on the efficacy of the Japanese language test required by the Specified Skilled Worker visas. The test will provide further reason for Japanese co-workers to insist on the use of Japanese, thereby exacerbating current tendencies to assume ownership of the means of communication. In addition, Japanese co-workers who underrate migrant workers’ Japanese in spite of their seven months’ language training are likely to continue to do so to those who passed a test. It would be more effective to address Japanese co-workers’ attitudes than to have migrant workers invest significant amounts of time, effort and money in passing the test. Furthermore, language tests are typically centred on monolingual norms, and their contents are distant from the realities of communication in a diverse environment (Shohamy, 2006, 2009). This is confirmed by Niveria and Rojas-Lizana (2019), who found that the required test focuses on reading and listening skills.\n\nAlthough this is only a preliminary study based on limited data taken from English-language sources, it can serve as a base for further research. Japanese co-workers’ attitudes towards migrant workers’ Japanese can result in inequalities at the workplace, directly impacting migrant workers’ everyday lives. Understanding these attitudes and addressing them can help to improve migrant workers’ experiences.",
"appendix": "Footnotes\n\n1 Blue-collar workplaces are defined as workplaces in the production sector which usually require strength or physical skills. Blue-collar workers are those employed at production sites.\n\n2 A brief description of recent immigration to Japan provides a backdrop to what is happening at present. After the end of World War II, the first significant numbers of immigrants arrived in the late 1970s. They consisted of, firstly, women mostly from the Philippines, Korea, Taiwan and Thailand, who came on the ‘entertainer’ visa. The second category of immigrants were Indochinese refugees from Vietnam, Cambodia and Laos. The third were descendants of the Japanese left behind in China at the end of World War II. The final category is made up of business professionals from Europe and North America (Green, 2017; Oishi, 2012a, 2012b; Vogt, 2015). A large number of immigrants arrived in the 1980s, which was a period of rapid economic growth also known as the ‘bubble economy’. They were mostly Koreans and Taiwanese. The numbers of those from the US and other Asian countries also increased. In the 1990s and 2000s, Japanese-Brazilians and -Peruvians came to work, and their numbers increased dramatically before falling in the early 2010s (Green, 2017; Oishi, 2012a, 2012b; Vogt, 2015).\n\n3 The first side door is the Technical Intern Training Program (TITP), which has been permitting workers from less developed Asian countries and Peru to come to work in Japan as trainees since 1993. The second side door is for Japanese-Brazilian and -Peruvian workers who have Japanese ancestry. The official rationale for this visa is for Japanese-Brazilians and -Peruvians to acquaint themselves with Japan, although in reality they serve as much-needed blue-collar workers.\n\n4 The Technical Intern Training Program was established in 1993 to allow interns from less developed Asian countries and Peru to work in Japan and gain experience and technical know-how to take back to their home countries. The programme has been widely criticised and discredited as an excuse to bring in unskilled workers. Abuse of the programme as well as the interns is rampant.\n\n5 The reader may have concerns about the author selecting only articles which support her position. That is not the case at all. The only two articles which contained comments on migrant workers’ Japanese are presented in this paper.\n\n6 Hegemony (Gramsci, 1971) is the domination of one group over another, and this domination is often supported by legitimating norms and ideas, making it seem like common sense (Blommaert et al., 2003). In multilingual contexts, the more powerful group often assumes that the ‘local’ language, typically the official language of the nation state, is the one and only language to be used (Lonsmann and Kraft, 2018). Researchers (Blackledge, 2000; Piller, 2016) have pointed out that in spite of the multilingual realities we live in, these hegemonic and monolingual norms predominate.\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\nReferences\n\nBlackledge A: Monolingual ideologies in multilingual states: Language, hegemony and social justice in Western liberal democracies. 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Publisher Full Text\n\nPiller I: Linguistic Diversity and Social Justice: An Introduction to Applied Sociolinguistics . Oxford: Oxford University Press; 2016.\n\nSchiffman H: Linguistic Culture and Language Policy . London: Routledge; 1996.\n\nShohamy E: Language Policy: Hidden Agendas and New Approaches . London: Routledge; 2006.\n\nShohamy E: Language tests for immigrants: Why language? Why tests? Why citizenship? In: Hogan-Brun G, Mar-Molinero C, Stevenson P (Eds.), Discourses on Language and Integration: Critical Perspectives on Language Testing Regimes in Europe. Amsterdam: John Benjamins; 2009; (pp. 45–59).\n\nTheodoropoulou I: Blue-collar workplace communicative practices: A case study in construction sites in Qatar. Lang Policy . 2019: 1–25. Publisher Full Text\n\nVogt G: Foreign workers in Japan. In: Babb J (Ed.), The Sage Handbook of Modern Japanese Studies. London: Sage; 2015; (pp. 567–582)."
}
|
[
{
"id": "160049",
"date": "18 Jan 2023",
"name": "Peerayuth Charoensukmongkol",
"expertise": [
"Reviewer Expertise Organizational behavior",
"Cross-cultural 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 paper provides insightful evidence about Japanese co-workers’ attitudes towards migrant workers’ Japanese language skills. Overall, the results add meaningful contribution to literature. However, the paper is still weak in terms of the theoretical foundation that can be used to support the role of language skills in the cross-cultural work context. The authors will need to provide some theoretical foundation and related literature about the role of common language in a work context that can affect relationships among employees who speak different languages. In the point, the authors should add some extra content in the literature review section about the theory and some research evidence which can explain why language proficiency of expats can help them to get along well with coworkers in a foreign country. In particular, I recommend two relevant papers which provide information on this issue, which should be covered in the literature review.\n\nFu and Charoensukmongkol (20211).\n\nSeriwatana and Charoensukmongkol (20212).\n\nThe discussion of the findings also needs to be made related to the theoretical foundation. This can help strengthening the theoretical contribution of the research.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
},
{
"id": "164593",
"date": "07 Mar 2023",
"name": "Maria Grazia Monaci",
"expertise": [
"Reviewer Expertise social psychology"
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn this study the author uses content analysis to examine coworker’s attitude toward migrant workers in Japan. Although this is an interesting topic, my enthusiasm for the manuscript is severely diminished by not only the several methodological issues, but also by the general structure of the manuscript, in which I have identified major conceptual, methodological, and technical shortcomings. The author admits that the study is exploratory and with weaknesses, nevertheless some limiting choices need at least to be justified. Why has the research of relevant text and sources been restricted to English newspapers or sources? Also, 3 text seem a very scarce base. Please, add rationale underlying this choice.\nThe study aims at studying the attitudes of Japanese co-workers towards migrants coworkers, however it is not clear where the aim originates from a theoretical base. Only the concept of the relevance of language proficiency has been previously introduced, but not really in relation to the attitudes of coworkers. Besides, as a social psychologist, I have doubts that “attitudes” is the right term here. The first indagated construct (assumptions of the means of communication) seems more a behavior, a decision, or a language policy as actually stated at a certain point, and foremost not of the coworkers but of the managements, as emerged also from the analyzed text. A confusion in the terminology which appears in the paper, for instance calling the examined attitudes “covert mechanisms,” or even “devises”. Later in the paper, the attitude of the Japanese workers towards migrant coworkers proficiency in Japanese language is also referred to as a stereotypical image of foreign workers’ poor linguistic abilities, probably the most correct definition.\nNonetheless, the concepts mentioned are at very different levels, and indifferently considered as attitudes of the coworkers or of the employers. In the presentation of the findings, the order of the paragraphs should be improved. For example, the first sentence is already a strong statement of the expected results, before presenting them (“Japanese co-workers or employers – who between the two? – assume ownership of the means of communication in all three document analysed. Analyses of the documents are presented below…..). Same at the beginning of paragraph 5,2, again with no distinction between coworkers and employers. I would leave comments after the analyses. Several comments about the results (with related references) should be moved to the Concluding remarks section.\n\nThere are also redundancies; for example restating concepts as “having a shared professional knowledge eases communication”, or about the Romanian employees adapting language abilities at a lower level (repeated twice in a very similar manner). In my opinion, the hypotheses must be clarified, based on the previous literature, and it would be helpful to state what can confirm previous research and to clearly indicate the new research questions.\nIn sum, although this topic has great relevance, I am not sure that this study can make a significant contribution to the literature. The author admits limitations without however justifying such limitations; an example is the last sentence of the abstract which refers not to concrete conclusions of the study but it is really generic and mainly about limitations. From my point of view, it would be necessary to considerably modify the approach of the study to clear certain issues.\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? Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-494
|
https://f1000research.com/articles/10-117/v1
|
16 Feb 21
|
{
"type": "Research Article",
"title": "Comparative cross-sectional assessment of knowledge, attitude and practice among university students and employees towards the use of the microbiology laboratory equipment",
"authors": [
"Muzaheed Muzaheed",
"Omar S. El-Masry",
"Ali A. Rabaan",
"Faisal Alzahrani",
"Amer Alomar",
"Faraz Ahmed Farooqi",
"Omar S. El-Masry",
"Ali A. Rabaan",
"Faisal Alzahrani",
"Amer Alomar",
"Faraz Ahmed Farooqi"
],
"abstract": "Background: Continuous evaluation of students and employee’s knowledge and attitude in clinical laboratories is mandatory to ensure a high level of competency, proper practice and to assess the need for training, which shall be reflected on the quality of laboratory results. The aim of the present study was to evaluate the knowledge, attitude, and practice in microbiology laboratories among employees (at King Fahd Hospital of the University) and clinical laboratory students (at Imam Abdulrahman Bin Faisal University)\n\nMethods: This was a cross-sectional survey of 30 2nd year students, 26 3rd year students, 24 4th year students in the Clinical Laboratory Sciences department, and 30 employees. Participants completed a survey comprising 30 questions to assess their knowledge and attitude towards the use of equipment and practice in the microbiology laboratory. Results: The results indicated that there was no significant difference between the average scores of all levels of students regarding their knowledge (p = 0.85, 0.999, and 0.869), attitude (p = 0.883, 0.996, 0.853), and practice (p=0.633, 0.325, 0.858) in the microbiology laboratory. Employees scores (knowledge;5.03±2.646, attitude; 12.03±4.89, and practice; 7.7±6.11) were quite poor, as indicated by the lower average results than that of students (knowledge; 5.65±3.08, attitude; 13.25±5.33, and practice; 13.46±5.7). Conclusions: It is concluded that the knowledge, attitude, and practice of students and employees in the microbiology laboratory needs to be meticulously monitored and improved to ensure high achievement of learning outcomes and better overall performance in the laboratory. This may be achieved through using frequent quizzes and continuous education programs.",
"keywords": [
"Knowledge",
"Attitude",
"Practice",
"Assessment",
"Survey",
"Microbiology",
"Laboratory"
],
"content": "Introduction\n\nMicrobiology laboratories are unique work environments that exert potential health hazards, which requires focused knowledge and training for all users. The risk of exposure to pathogens and misuse of laboratory equipment are two important hazards related to microbiology laboratories. Throughout history, and due to the lack of safe practice and personal errors many laboratory workers have contracted infections1. Similarly, mishandling of laboratory equipment, especially those operating at high temperatures or speeds can pose considerable risks to the laboratory personnel2. In order to reduce these risks related to the use of equipment and practice in the microbiology laboratory, dedicated safety training and education should be in place for every laboratory2.\n\nMicrobiology laboratory equipment can be broadly classified as disposable or reusable. The most common reusable components include microscopes, autoclaves, colony counters, vortex mixers, hot air ovens, refrigerators, distilled water plants, Bunsen burners, and pipettes. Laboratory students and employees should follow the related standard operating procedures (SOPs) while using this equipment, and failure to do so can cause damage to the equipment and expose laboratory personnel to a possible hazard3. Likewise, the use of disposable equipment, including petri plates, pipetting tips and personal protective equipment (PPE) should be carried out in a proper manner and with care so that they do not become a cause of infection spread. This requires prior knowledge and training on how to use and dispose of these laboratory tools3.\n\nThe importance of practices and attitudes of personnel working in microbiology laboratories has been highlighted in various studies4. In this respect, workers should be professionally trained and participate in continuous training courses to ensure their correct and safe usage of laboratory equipment5. From our point of view, the accuracy of diagnostic test results and their reliability may depend on the laboratory technician’s knowledge, attitude and standardized practice in the laboratory. The aim of the present study was to evaluate the knowledge, attitude and practice (KAP) of the students (department of clinical laboratory sciences, Imam Abdulrahman Bin Faisal University) and staff (King Fahd Hospital of the University) towards the microbiology laboratory and the use of its equipment.\n\n\nMethods\n\nThis was a cross-sectional questionnaire-based study, conducted among the undergraduate students of the Clinical Laboratory Science Department at Imam Abdulrahman Bin Faisal university and the technical staff working in the teaching hospital of the university in Dammam, eastern province of Saudi Arabia.\n\nA structured self-administered questionnaire was designed by the authors and reviewed by subject experts (Dr. S. Acharya., Assistant professor of microbiology and Dr. Elfadil A, Assistant professor of microbiology and Immunology) for its content, relevance, readability, and comprehension. The questionnaire was distributed to 10 randomly selected participants as preliminary pilot testing of the target population. Minor modifications were recommended by the pilot study group and were done before dissemination of the survey to the sample population. The overall Cronbach alpha value was 0.79 suggesting acceptable consistency of the questionnaire. Those who participated in the pilot study were excluded from the final analysis.\n\nThe survey was written in English and consisted of 30 questions divided into four main sections12. The questionnaire started with a section asking for participants’ year of study, specialization, department, and college. Sections two to-four comprised 10 questions each to evaluate knowledge, attitudes and practice in the microbiology laboratory, respectively. All questions evaluating knowledge, attitude and practice were associated with categorical responses: yes/no/not sure.\n\nAll students in years 2, 3 and 4 who belonged to the department of clinical laboratory sciences at Imam Abdulrahman Bin Faisal University, were asked to participate in the study. Students from other departments as well as those who had recently changed their specialty to clinical laboratory sciences were excluded from participation. All the staff of the microbiology laboratory at King Fahd Hospital of the University were asked to participate. Staff members who recently joined were excluded; only staff members with at least five years’ experience were included in the study.\n\nThe survey was hosted on the online resource “Question Pro”. The college registrar provided the of email addresses of all pupils in each university year. The link for the survey was then sent to the students and completed in the period between February 2020 – September 2020. The objectives of the research were explained to the students on the very first page and students were proceeded to take the survey only after checking the consent box. Participation was voluntary, and no benefits or incentives were given to participants. There were no personal data collected during this study.\n\nData was initially exported to MS Excel 365 from the “QuestionPro” database. After cleaning the dataset was imported to Statistical Package for Social Science (SPSS version 22, Inc. USA) for further analysis. Data was presented as frequencies, percentage, mean and SD. The knowledge sections of the questionnaire contained 10 questions and response were collected as wrong answer (marked 0) and correct answer (marked 1). Attitude and practice scores were coded as yes, don’t know and no (3, 2, 1, respectively). Overall and for each section the items internal consistency was evaluated through Cronbach's Alpha. Comparison between student’s scores was conducted using one-way analysis of variance (ANOVA), while the student independent sample t-test was employed to compare between students’ and employees’ scores. The p-value of ≤0.05 was considered statistically significant.\n\n\nResults\n\nThe questionnaire was disseminated to a target sample comprising 30 students in each study level (2nd, 3rd and 4th year students) and 30 employees making the total number of target participants 120; among them 110 responded6. Out of 110, 30 were 2nd year students, 26 were 3rd year students, 24 were 4th year students and 30 were employees (microbiology laboratory personnel). All of participants belonged to the same university and its teaching hospital. The response rate was 73%, incomplete or denied participation were excluded. Overall, it was found that students’ percentages of correct answer were higher than the employees. In brief the average student scores (mean±S.D) in the knowledge domain were 5.80±2.49 (2nd year), 5.35±3.58, (3rd year), and 5.79±3.27 (4th year) out of a maximum of 10 points. The average scores in the attitude domain were 13.53±6.404 (2nd year), 12.85±5.409 (3rd year), and 13.67±3.691 (4th year) out of a maximum of 30 points. Regarding practice, student scores were 14.60±5.73 (2nd year), 13.16±6.34 (3rd year) and 12.33±5.001 (4th year) out of a maximum of 30 points. Whilst mean (SD) employees scores were 5.03±2.646 out of 10 for knowledge, 12.03±4.89 out of 30 for attitude, and 7.7±6.11 out of 30 for practice. Among the all knowledge related question the only one item (The UV-visible spectrophotometer uses light visible range) was answered correctly by the majority of the employees (Table 1), likewise the good practice response was also higher among the students whereas the “don’t know” response for several items was higher among the employees (Table 2). However, the attitude response of both groups was somehow similar almost for all items (Table 3).\n\nThe items (questions) used in the current study to assess the performance of students and employees in knowledge, attitude and practice domains are summarized in Table 1, Table 2, Table 3. The correct answer for each question was indicated in the tables along with the listed options for the participants. The reliability of the questionnaire items used to assess knowledge, attitude and practice was evaluated by assessing the internal consistency of each domain’s questions by calculating the Cronbach's Alpha (Table 4). The values of the Cronbach's Alpha coefficient for knowledge, attitude and practice were 0.888, 0.916, and 0.932, respectively, indicating that the items in each group are closely related as a set of questions.\n\nThe overall average scores of the three domains for the whole study sample are shown in Table 5 and the average performance scores for each group are shown in Table 6. Among the students, the 2nd year students who are the most junior students in this study had the highest level of knowledge (5.80±2.49), followed by the most senior 4th year (5.79±3.27) and 3rd year students (5.35±3.58). Faculty surprisingly had the lowest knowledge score among the participants (5.03±2.64). Likewise, the average scores of the 4th year and the 2nd year students in attitude-related questions were close (13.67±3.69 and 13.53±6.40, respectively). The lowest score in the attitude domain was reported for the 3rd year students followed by the employees (12.85±5.40 and 12.03±4.89). Regarding practice-related questions, the 2nd year students achieved the best scores (14.6±5.73), followed by the 3rd year (13.16±6.34) and the 4th year students (12.33±5.00). The employees score was the least, and surprisingly, low in this domain also (7.7±6.11).\n\nThe average scores of 2nd, 3rd, and 4th year students in the three domains were compared using one-way analysis of variance ANOVA (Table 7). The results indicated that there was no significant difference between the average knowledge scores of: the 2nd and 3rd year students (p = 0.85); the 2nd and 4th year students (p = 0.999); and the 3rd and 4th year students (p = 0.869). There was similarly a non-significant difference observed for the average attitude scores between the above-mentioned groups (p=0.883, 0.996, and 0.853, respectively), as well as for practice (p= 0.633, 0.325, and 0.858, respectively).\n\n*p<0.05 considered statistically significant\n\nThe independent sample t-test (Table 8) was used to compare the KAP scores between employees and students. The results indicated a non-significant difference between students and employees regarding knowledge or attitude (p=0.335 and 0.24, respectively). On the other hand, the difference between students and employees’ scores for practice-related questions was significantly different (13.46±5.7 and 7.70±6.11, respectively, p<0.0001).\n\n*p<0.05 considered statistically significant\n\n\nDiscussion\n\nThe present survey was carried out to evaluate and analyze three domains: knowledge, attitude and practice towards equipment used in the microbiology lab by university students and employees. The results of the current study revealed that there was no significant difference between students in different years regarding their KAP in the microbiology lab. Of note, employees had the lowest scores amongst the studied groups. In this respect, employee’s average scores for practice-related questions were significantly different from the average score of students in the same domain. Similar findings have been reported by Jairoun and colleagues7 who evaluated KAP of medical students (MS) and non-medical students (NS) towards the use of antibiotics in the United Arab Emirates (UAE). They reported that medical students had better knowledge of antibiotics and their side effects compared to the non-medical students; however, employees showed the least knowledge when compared to the students. Since employees mostly do routine work, they may not bother to get more awareness about laboratory equipment as noticed from the assessment of the employees’ KAP regarding health precautions in the laboratory. This is disappointing as they play a very important role in regulating daily tasks of the laboratory; this may compromise laboratory results and jeopardize health management outcomes in patients. In addition, employees play a significant role in students’ training.\n\nIn another context, Barikani8, stated that around 50% of the students surveyed had knowledge of 'hand washing before and after using gloves\", but only 40% developed the attitude to do that. Moreover, the number of students who practiced hand washing was reduced to 16.2%, which showed the non-serious behavior of the students. In our opinion, this behavior can be explained based on the fact that with seniority, students tend to ignore rules and instructions and become more careless towards the usage of equipment. Students’ attitudes were analyzed through a questionnaire and not based on observation and therefore reflect their subjective views. From the results, it can be stipulated that students disregard proper attitude protocols towards the use of laboratory.\n\nThe lab employees who participated in the current survey showed the lowest average in all three KAP domains. The results may be explained, from our own perspective, by the tendency of most employees to ignore laboratory-related instructions, and this might be reflected in their attitude and practice. Also, the low average scores of employees in the knowledge domain might be explained by the lack of continuous training and participation in educational programs. In this context, we understand that some employees might have forgotten about using different technique, and the reason behind it might be the low frequency of such procedures and/or the expansion in laboratory automation. Similar results were reported by Ejilemele and Ojulu2, who carried out a KAP survey in pathology laboratory staff. They reported gross insufficiencies in the KAP of safety protocols by the laboratory staff in different microbiology areas. It was found that laboratory employees lack the required KAP about safe specimen collection, standard use of PPE, and usage of centrifuge and first aid kits.\n\nThe current study was also designed to analyze the students’ approach and practice towards facilities/equipment they are provided with. It might be concluded from the results of the current study that knowledge and attitude affect the practice. Results showed that students’ achievement in all levels was comparative, though ideally, KAP should be higher in more senior students as skills-related learning outcomes and capacity of laboratory training are introduced in much higher weights in final years of study, which would be reflected in their knowledge and practical skills. This means that higher levels students might become irresponsible and less serious towards rules and concepts with time, though the difference was not statistically significant. These findings are in agreement with the findings of behavioral survey carried out by Askarian and colleagues9. They reported that the carelessness in behavior was observed in Iranian medical students towards practice of standard isolation precautions. When they were tested for precautionary measures taken, most of them did not know about the recommended disinfecting techniques. Another study also showed that knowledge and attitudes among medical students were acceptable but practices towards standard isolation precautions was poor10.\n\nIt was also observed in the current study that employees’ scores were markedly lower for practice than those for students, which means they have lesser knowledge of equipment and laboratory management. The result revealed their incompetence compared with students. Probably, the lack of dedication and problematic conduct directly affect employee’s own safety and health, as well as students. These findings are alarming, as employees should supposedly have better knowledge, attitude, and practice of correct laboratory procedures than students. Students may be careless as they are learning, but it should not be tolerated by supervisors. Our findings are in harmony with a survey carried out by Zaveri and Karia11 who analyzed the KAP of laboratory technicians regarding standard precautions using a cross-sectional study. They reported that health care workers (technicians directly involved with the work in the laboratories of selected hospitals) showed poor knowledge, attitude, and practices of universal work precautions that are defined, according to the center for disease control, as precautions to prevent blood borne infections to workers who provide first-aid or health services12.\n\n\nConclusion\n\nThese findings highlight the importance of this and similar surveys that help us to evaluate the status of knowledge, attitude and practice of laboratory students and employees in standard microbiology practice. Based on the results, it can be suggested that lab employees should be trained so that they are not only present to keep an eye on students, but are qualified to provide help and guidance to students regarding experiments, equipment usage, cleanliness and safety. This study also highlights the need for regular educational courses for lab employees to keep them updated about the latest equipment and any new practices. Moreover, we propose that students should be evaluated regularly on their learning and attitudes, as ensuring the right attitude and practice towards microbiology equipment is necessary for the safety of both users and equipment, especially in more senior students.\n\nTo this end, the authors may conclude that as university students progress through their degree, their knowledge and attitude may not necessarily improve; learning and good conduct cannot be proportional to passing classes. In this context, we may suggest that knowledge, attitude and practice develop by motivation and determination. The present study showed that commitment of students towards knowledge and practice is directly proportional to their attitude. From this study, we conclude that it is particularly important to evaluate the learning process of students and employees and they should be regularly assessed.\n\nThe conclusion from the current study was mainly based on questionnaire data, which may not reflect evidence-based practice of both studied groups (students and employees). Therefore, combining questionnaires with laboratory observations could reflect the better picture of KAP in the clinical laboratory. Also, the current study evaluated KAP domains in a single batch of clinical laboratory science students and focused on microbiology instruments, which means that the findings cannot be generalized to different students and employee populations.\n\n\nData availability\n\nHarvard Dataverse: Comparative cross-sectional assessment of knowledge, attitude and practice among university students and employees towards the use of the microbiology laboratory equipment. https://doi.org/10.7910/DVN/4JHK2W6.\n\nThis project contains the following underlying data:\n\n- Raw data excel file\n\nHarvard Dataverse: Comparative cross-sectional assessment of knowledge, attitude and practice among university students and employees towards the use of the microbiology laboratory equipment. https://doi.org/10.7910/DVN/4JHK2W6.\n\nThis project contains the following extended data:\n\n- Questionnaire\n\nData are available under the terms of the Creative Commons Zero \"No rights reserved\" data waiver (CC0 1.0 Public domain dedication).\n\n\nEthical approval\n\nUpon discussion with a review board representative, ethical approval for this study was not applied for since the data collected was all anonymous and did therefore not violate privacy or confidentiality of the participants.\n\n\nConsent\n\nParticipants were asked about their willingness to participate on the first-display page of the questionnaire which informed them that their participation was voluntary and presented a tick box to provide consent.",
"appendix": "References\n\nAppendix A, Biosafety in Microbiological and Biomedical Laboratories. (DC): National Academies Press (US). 1989. Reference Source\n\nEjilemele AA, Ojule AC: Knowledge, attitude and practice of aspects of laboratory safety in Pathology Laboratories at the University of Port Harcourt Teaching Hospital, Nigeria. Niger J Clin Pract. 2005; 8(2): 102–106. PubMed Abstract\n\nNayeem A: An Assignment of Microbiology Laboratory Use of Microbiology Lab, Chemical and Equipment. 2008. Reference Source\n\nSkinhöj P: Occupational risks in Danish clinical chemical laboratories. II. Infections. Scand J Clin Lab Invest. 1974; 33(1): 27–29. PubMed Abstract | Publisher Full Text\n\nRichmond JY, McKinney RW: Biosafety in microbiological and biomedical laboratories. US Department of Health and Human Services, Public Health Service, Centers for Disease Control and Prevention. 1999. Reference Source\n\nMuzaheed: Comparative cross-sectional assessment of knowledge, attitude and practice among university students and employees towards the use of the microbiology laboratory equipment. Harvard Dataverse, V2. 2021. http://www.doi.org/10.7910/DVN/4JHK2W\n\nJairoun A, Hassan N, Ali A, et al.: Knowledge, attitude and practice of antibiotic use among university students: a cross sectional study in UAE. BMC Public Health. 2019; 19(1): 518. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBarikani A, Afaghi A: Knowledge, attitude and practice towards standard isolation precautions among Iranian medical students. Glob J Health Sci. 2012; 4(2): 142–146. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAskarian M, Honarvar B, Tabatabaee HR, et al.: Knowledge, practice and attitude towards standard isolation precautions in Iranian medical students. J Hosp Infect. 2004; 58(4): 292–296. PubMed Abstract | Publisher Full Text\n\nAskarian M, Memish ZA, Khan AA: Knowledge, practice, and attitude among Iranian nurses, midwives, and students regarding standard isolation precautions. Infect Control Hosp Epidemiol. 2007; 28(2): 241–244. PubMed Abstract | Publisher Full Text\n\nZaveri JR: Knowledge, attitudes and practice of laboratory technicians regarding universal work precaution. Natl J Med Res. 2012; 2(1): 113–115. Reference Source\n\nJohnson and Johnson Medical Inc: Blood-borne infection. A practical guide to OSHA compliance Arlington. Johnson and Johnson Medical Inc. 1992."
}
|
[
{
"id": "81847",
"date": "30 Mar 2021",
"name": "Rama Bhat P",
"expertise": [
"Reviewer Expertise Microbiology",
"Immunomodulatory studies",
"Plant biotechnology",
"Biodiversity conservation. Herbal formulation",
"Anticancer and Antidiabetic studies with animal models",
"EBT"
],
"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 article well planned and executed nicely with experimental designs. The introduction was brief and relevant to the work. Sampling method in general with multicentric experiment has accurately taken individual groups. Statistical methods followed has made the analysis more accurate. The presentation of the results is also good with tables at appropriate places. Discussion compared the results with available reports made more close to research data with level of significance. Literature were cited at respective places.\nThere are few points to be noted before acceptance of the paper to be indexed:\nCorrections made were highlighted and changes required are given here. (e.g. \"Petri plates\" - here, Petri is the name of scientist, so it should be in capital.\n\nOther corrections like capital word or, \"et al.\" were also marked. In the tables remove the full stop at the end of title. Then % was there in all the numbers in the table 1-3 in the last column. Remove it from second line onwards as it is shown in headline.\nAfter the minor corrections the paper can be accepted to be indexed.\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": "86979",
"date": "14 Jun 2021",
"name": "Kavita Batra",
"expertise": [
"Reviewer Expertise Data analytics",
"behavioral research",
"infectious diseases",
"health promotion"
],
"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\nHere is a review of the manuscript entitled “Comparative cross-sectional assessment of knowledge, attitude, and practice among university students and employees towards the use of the microbiology laboratory equipment.” The findings of this study will serve as the baseline data to evaluate learning outcomes and performance of students and staff in the microbiology laboratory settings. Despite this contribution, we believe there are opportunities to further strengthen this manuscript. We will share these in a bulleted format in the order that they appear.\nAbstract\n\nAuthors have included study setting (name of the institution/lab) in the purpose, which should be moved under methods. In methods section of the abstract: Overall sample size has not been provided; however, authors have provided the year wise breakup. No mention about the statistical method used has been made. Inclusion and exclusion criteria of the participants are missing. Please indicate whether the survey was web-based or paper and pencil? We are not sure what measure authors intend to indicate by 0.999, 0.869, 0.996, 0.853). Are these 95% CIs? Overall, the abstract needs revisions to be able to stand alone.\n\nIntroduction\nIntroduction is concise and somewhat relevant. Authors have discussed the standard operating procedures (SOPs) and implications of not following them. However, it is very brief and includes only five references. There is a need for more substantial literature base to support the necessity for the study. The knowledge, attitudes, and practice (KAP) paradigm is an older version of health behavior research and the contemporary literature has moved to theory-based paradigms. Rationale for using the older KAP model needs to be explicated.\n\nMethods\n\nMethodology particularly statistical analysis needs to be strengthened. Authors did not provide sample justification. In the study design subsection: when this study was conducted? Please replace “study instrument” with “survey instrument” There is a no mention of the psychometric testing of the instrument, namely validity and reliability in the methods section. Cronbach’s alphas have been provided in the results which are only indicative of internal consistency. How the face, content, and construct validity of the instrument were assessed? In their absence the results cannot be trustworthy. Was test-retest reliability done? In its absence the results cannot be trustworthy. There is no mention of the type of sampling technique or justification of sample size by the researchers. The reviewers wonder the rationale behind not using the gender question in the survey. It will be intriguing to know if there were any differences across gender. Researchers could have formed two groups of students (Juniors vs. Seniors) to see if there are any differences? Why first year students were not included in the study? Please provide the rationale in the eligibility criteria. It will be interesting to conduct a correlation test among the constructs of the survey, which is missing in the study. How missing data were handled has not been mentioned? Please spell out abbreviations when first time used in the text. For example, SD\n\nResults\nWe would encourage authors to use CHAMP guidelines (https://pubmed.ncbi.nlm.nih.gov/33514558/) for reporting. In the headers of all the table, please indicate the sample size. Tables should be limited to only show correct response percentages instead of other answers. Please add one more table of the correlation as suggested in the methods section above.\n\nDiscussion\n\nWe think justification to the important results have not been provided adequately. For example, authors have discussed previous studies related to antibiotic use, which we think is out of context.\n\nThe discussion section is very weak and is not backed by sufficient literature review. Please add more on the potential value of this study. Several limitations remain unacknowledged, for instance generalizability, self-reporting bias etc. The authors write, “The conclusion from the current study was mainly based on questionnaire data, which may not reflect evidence-based practice of both studied groups (students and employees).” The words “evidence-based” are typically used for empirically tested interventions and their use in this context is somewhat confusing.\n\nOn, the whole, in our opinion, this manuscript is not suitable for indexing in its present form.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? No",
"responses": []
},
{
"id": "86974",
"date": "15 Jun 2021",
"name": "Pathiyil Ravi Shankar",
"expertise": [
"Reviewer Expertise Rational use of medicines Pharmacovigilance Questionnaire based research Health Professions Education"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe study is well-written, and the table is well presented.\nThe period of study was nearly seven months which is long for a cross-sectional study. Participants may have communicated with each other which can influence the results.\nI am confused about whether a sample of respondents was chosen or if all respondents were invited to participate?\nDoes the sample chosen represent the population of students and employees in terms of demographic characteristics?\nThe quality of written English is mostly good. However, corrections may be required in a few places.\nResults I wanted to confirm that the employees involved in the study were all faculty members for the clinical laboratory sciences course.\nWhat percentage of students from different years and employees participated in the study?\nThe authors should try to explain better why the knowledge of students did not improve as they progressed through the course.\nWhat were the qualifications of the employees? How are they selected? Is there no refresher training provided to them? Do they have annual appraisals conducted?\nCould the level of English proficiency of the employees affected their response and the scores obtained?\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": "6835",
"date": "23 Jun 2021",
"name": ". Muzaheed",
"role": "Author Response",
"response": "Firstly, we thank the reviewer for reviewing our article and providing constructive and positive comments. We have revised our manuscript to address all comments without compromising the writing integrity. Please, find below our responses to reviewer comments. Reviewers’ comment: The study is well-written, and the table is well presented. Author’s Response: Thank you for your admiration. Reviewers’ comment: The period of study was nearly seven months which is long for a cross-sectional study. Participants may have communicated with each other which can influence the results. Author’s Response: Thank you for your valuable comments we are aware that cross-sectional data should be collected in a short time as much as possible to avoid any bias as mentioned; however, we would like to indicate that the seven months’ time was the time taken for the whole study including data analysis and writing up of the manuscript. We have revised our manuscript to make it clearer to the readers. Also, all participants who were included in the pilot study were removed from participation. Reviewers’ comment: I am confused about whether a sample of respondents was chosen or if all respondents were invited to participate? Author’s Response: We conducted a pilot study by choosing a random sample to validate our survey then all the participants were invited and those who responded were included in the study without selection except those who participate in the pilot study. We hope that this is clear and addressed this comment. Reviewers’ comment: Does the sample chosen represent the population of students and employees in terms of demographic characteristics? Author’s Response: We tried to make the study sample as representative as possible by inviting all students in levels 2, 3, and 4 also all employees in the microbiology laboratory who met our inclusion criteria were given the chance to participate in our study as described in the method’s section. Reviewers’ comment: The quality of written English is mostly good. However, corrections may be required in a few places. Author’s Response: We revised our article to correct any potential technical error. Reviewers’ comment: I wanted to confirm that the employees involved in the study were all faculty members for the clinical laboratory sciences course. Author’s Response: Yes, they are graduates of the clinical laboratory sciences program. Reviewers’ comment: What percentage of students from different years and employees participated in the study? Author’s Response: Thank you for the comment. In response to this comment, we have mentioned the total numbers of students and employees who were invited to participate as well as the numbers who responded to the survey as indicated at the beginning of the results section. We will update the article by including the percentage also. Reviewers’ comment: The authors should try to explain better why the knowledge of students did not improve as they progressed through the course. Author’s Response: Thank you for the valuable comment; we have tried to elaborate on this, please check. Reviewers’ comment: What were the qualifications of the employees? How are they selected? Is there no refresher training provided to them? Do they have annual appraisals conducted? Author’s Response: The employees are graduates of the clinical laboratory sciences program. They have been selected according to the criteria mentioned in the methods section. As far as we are aware, There are “Continuous Education Programs” as well as the annual appraisal. Reviewers’ comment: Could the level of English proficiency of the employees affected their response and the scores obtained? Author’s Response: All clinical laboratory sciences graduates should provide an English proficiency testing certificate before joining the program. Also teaching is in English and instructions indicated that investigators are available to answer any questions and clarify any ambiguous information. In this respect, we think that this was not a concern during the survey."
}
]
}
] | 1
|
https://f1000research.com/articles/10-117
|
https://f1000research.com/articles/8-1687/v1
|
25 Sep 19
|
{
"type": "Research Article",
"title": "The effect of triple antibiotic paste as an intracanal medication with an anti-inflammatory drug on post-operative pain of asymptomatic uniradicular necrotic teeth: a double blind randomized clinical trial",
"authors": [
"Mohamed Omaia",
"Maged Negm",
"Yousra Nashaat",
"Nehal Nabil",
"Amal Othman",
"Maged Negm",
"Yousra Nashaat",
"Nehal Nabil",
"Amal Othman"
],
"abstract": "Background: Flare-ups may occur after root canal treatment which consist of acute exacerbation of asymptomatic pulpal and/or periradicular pathologic condition. The causative factors of interappointment pain include mechanical, chemical or microbial irritation to the pulp or periradicular tissues. The potential role of microorganisms in interappointment pain is why the success of endodontic treatment depends on complete eradication of microorganisms capable of causing an intraradicular or extraradicular infection. This can be achieved by mechanical cleaning and shaping, in conjunction with irrigation and antibacterial agents. The aim of this study was to assess the ability of triple antibiotic paste with the anti-inflammatory drug diclofenac potassium versus calcium hydroxide used as an intra-canal medication in reducing post-operative pain. Methods: 84 patients with asymptomatic uniradicular necrotic teeth were randomly assigned into two groups according to the intra-canal medication used: calcium hydroxide group (CH) and triple antibiotic paste with diclofenac potassium group (TAPC). In the first treatment session, intracoronal cavity preparation was performed after rubber dam isolation followed by chemo-mechanical preparation using rotary Protaper Universal files with saline irrigation followed by intra-canal medication placement then postoperative pain was assessed at 24, 48 and 72 hours postoperatively using Visual Analogue Scale (VAS). In the second treatment session, intracanal medications were removed by irrigation using saline followed by obturation. Results: Both intracanal medicaments resulted in a statistically significant decrease in mean pain value from 24 to 48 and 72 hours postoperatively. While when comparing both groups, TAPC intracanal medication showed less post-operative pain compared to that of the CH group at 24, 48 and 72 hours with a statistically significant difference at 48 hours only. Conclusion: Both intracanal medicaments were efficient in reducing post-operative pain in asymptomatic uniradicular necrotic teeth. Trial registration: Clinicaltrial.gov NCT02907489, 20/09/2016.",
"keywords": [
"TAP",
"diclofenac potassium",
"anti-inflammatory",
"calcium hydroxide",
"intracanal medication",
"necrotic",
"post-operative pain."
],
"content": "Introduction\n\nThe severity and incidence of post-operative pain are usually associated with specific dental treatments; the highest of which is root canal therapy1.\n\nPost-operative pain is a common finding after endodontic treatment, its incidence ranges from 3% to 58%. It may be due to microbial, mechanical or chemical injury to the periapical tissues2,3. It is the main reason why patients seek endodontic treatment, therefore it must be accompanied by efficient relief of pain to be considered successful by both patients and clinicians4.\n\nIndeed, acute periradicular inflammation such as acute periodontitis or acute periradicular abscess secondary to intracanal procedure is one of the causes of postoperative pain5,6. Infected debris from the root canal system may induce an acute inflammatory response of the tissues in response to the applied irritants7.\n\nMicroorganisms are the primary cause for pulp and periapical diseases. The failure to eliminate them and their by-products may result in persistent irritation and impaired healing8.\n\nPain is a subjective experience and difficult to quantify and standardize. Pain is influenced by many factors e.g. personality, behavior, physical and psychological factors; making it a challenge to measure. Several scales and methods have been used for the assessment of pain after endodontic therapy. Among them, numerical, verbal and visual analogue scales are used in most clinical studies9.\n\nA visual analogue scale was used to assess postoperative pain. This is a valid and reliable method which has been widely used in endodontic literature10,11.\n\nPost-endodontic pain, particularly after initial root canal treatment, should ideally be eliminated by the therapy; however, analgesics and/or anti-inflammatory drugs are frequently required to reduce post-operative pain9.\n\nEndodontic therapy is directed toward one specific aim: to cure or prevent periradicular periodontitis. Our challenge as endodontists is to implement methods to eliminate these microorganisms during and after root canal treatment.\n\nIt has been suggested that calcium hydroxide has pain preventive properties because of its antimicrobial and tissue altering effects12. Furtheremore studies have shown that calcium hydroxide has the ability to dissolve necrotic tissues alone or may increase the effect of other solvents. This suggests that calcium hydroxide would be an effective agent in cleaning and disinfecting infected root canals13.\n\nSystemic antibiotics appear to be clinically effective as an adjunct in certain surgical and nonsurgical endodontic procedures. Their administration is not without potential risk of adverse systemic effects, such as toxicity, allergic reactions and the development of resistant strains of microbes14. Furthermore, the systemic administration of antibiotics depends on patient’s compliance with the dosing regimens followed by absorption through the gastro-intestinal tract and distribution via the circulatory system to bring the drug to the infected site. Hence, the infected area requires a normal blood supply which is no longer the case for teeth with necrotic pulps and for teeth without pulp tissue. Therefore, local application of antibiotics within the root canal system may be a more effective mode for delivering the drug15.\n\nA successful endodontic treatment is therefore dependent on the initial eradication of all the bacteria, i.e. those present in the root canal as well as those already penetrated in depth16. The achievement of microbicidal doses becomes critical in the endodontic environment, because in such harsh conditions bacteria may aggregate to form a biofilm or enter a stationary phase, thus acquiring a resistant phenotype. Accordingly, in endodontic therapy the local use of antibiotics allows the use of the necessary very high concentrations17.\n\nBecause root canal infections are polymicrobial, consisting of both aerobic and anaerobic bacterial species, a single antibiotic may not be effective in root canal disinfection. Therefore, a combination of antibiotics, mainly consisting of ciprofloxacin, metronidazole and minocycline, referred to as triple antibiotic paste (TAP) has been suggested for root canal disinfection18,19.\n\n\nMethods\n\nThe study design is a parallel double blind randomized controlled clinical trial with a 1:1 allocation ratio and a Superiority Framework. The study was conducted between March 2017 and July 2018 in the Endodontic clinic of the Faculty of Dentistry, Cairo University. The protocol of this study was approved by the Ethics Committee of the Faculty of Oral and Dental Medicine, Cairo University, Egypt (approval number 16/10/28). The nature of this study, and potential risks were explained to the patients and informed consent forms were signed before treatment sessions. This trial was registered with ClinicalTrials.gov on 20th September 2016 (NCT02907489).\n\nThis article was written in concordance with the CONSORT checklist 2010 (see reporting guidelines).\n\nTo assess TAPC versus CH regarding the postoperative pain, an independent t test was done. It was estimated that a total of 75 patients would be required for the detection of a difference between groups using a two-tailed α of 0.05 and a power of 0.80 if the absolute difference in post-operative pain is 0.35 with SD 0.65 as reported in Johns et al., 201420. To compensate losses during the follow-up this number should be increased to 84 patients (10% more than the calculated). Sample size was calculated using G* power program (3.1.9.2/ 2014) (University of Düsseldorf, Düsseldorf, Germany).\n\nThe subjects were selected from the regular attendees of endodontic clinic, Faculty of Dentistry, Cairo University. A written announcement was published in the endodontic clinic to inform the attendees regarding the trial, the patients who indicated their interest to participate in the study were checked for eligibility and signed an informed consent.\n\nPatients were carefully diagnosed and checked for the eligibility criteria through careful clinical examination using a diagnostic mirror and probe, percussion with the back of a diagnostic mirror and palpation with the index finger to indicate the presence of any swelling or tenderness were done. An electric pulp tester (Denjoy DY310, Henan) that was positioned at the middle third of the labial/buccal surface of the tooth was used to check pulp vitality of the affected tooth, with the adjacent and contra-lateral teeth used as a control. All data was recorded in medical history charts, dental history charts and pain scale charts (Extended data21).\n\nPreoperative pain was recorded, with each patient given pain scale chart (visual analogue scale (VAS)) in order to record his/her pain level before any intervention. The pain scale (0–10 scale) consisted of a 100 mm horizontal ruler with no numbers except a 0 at the first part of the scale and a 10 in the last part of the scale. The patients were asked to mark the point that was equivalent to their pain perception. The pain levels were classified as no pain (0), mild pain (1-3), moderate pain (4-7) or severe pain (8-10) and postoperative pain was assessed at 24, 48 and 72 hours after intracanal medication placement.\n\nThe VAS is considered to be a valid and reliable scale for the measurement of pain. This method may have some limitations in terms of objectivity considering the heterogeneity of personal character22. However, previous studies argued that this method can be considered adequately reliable23. Therefore, VAS was used in this study to evaluate post-operative pain.\n\nIn total, 84 participants were included in the study with maxillary or mandibular asymptomatic necrotic single rooted teeth as studies have suggested that postoperative pain is more likely to occur in multirooted teeth because in multirooted tooth other variable exist which may affect our treatment outcome24. Non-vital teeth were selected because research has found that post-operative pain in teeth with non-vital pulp are more common than teeth with vital pulp due to the presence of high level of irritants and infectious agents in pulpal and periapical region25–27. Asymptomatic teeth were chosen because studies have shown that the presence of preoperative pain can significantly increase the possibility of postoperative pain27,28.\n\nInclusion criteria: Subjects aged between 18–50 years. Both male and female medically free (without any systemic diseases) and healthy subjects. Mandibular and maxillary single rooted asymptomatic non vital teeth were chosen.\n\nExclusion criteria: Teeth with acute dentoalveolar abscess, subjects having more than one tooth that require root canal treatment. Subjects that have taken analgesic, anti-inflammatory or antibiotic drugs during the 10 days prior to the start of treatment. Pregnant females. Subjects with systemic diseases such as endocrine diseases, infectious diseases or psychological disturbance. Subjects taking chronic pain medications. Teeth with periodontal disease or pulp calcification.\n\nPatients were randomly assigned into two groups (n=42/group) according to the intra-canal medication used, using computer generated randomization (www.random.org). The assistant supervisor (A.O.) generated the random sequence and assigned the participants to the intervention or control groups.\n\nExperimental group: triple antibiotic paste + Catafast (TAPC). Control group: calcium hydroxide paste (CH).\n\nPrimary outcome: Post-operative pain change.\n\nMeasuring device: Visual analogue scale.\n\nMeasuring unit: Ordinal.\n\n*All categories of pain considered success.\n\nSecondary outcome: Intracanal bacterial reduction of each strain of bacteria obtained from the root canals before (S1) and after instrumentation (S2) in the first treatment session. Subsequently, intra-canal medication was placed and bacterial reduction was assessed in the second session after 3 days (S3) using colony forming unit test.\n\nMeasuring device: Bacterial culture.\n\nMeasuring unit: Colony forming units per milliliter of blood agar medium.\n\n*Secondary outcome will be published in a separate manuscript.\n\nFirst visit: Preoperative intraoral periapical radiograph was taken (Kodak intraoral periapical films speed D, Size 2, KODAK). Teeth were anaesthetized by local anesthesia with a non-disposable metallic aspirating syringe using 1.8 ml Mepivacaine HCl 2% - Levonordefrin 1:20000 (Carpule Mepecaine-L, Alexandria Company for Pharmaceuticals and Chemical Industries, Egypt, #1423). An access cavity preparation was performed using round bur size 3 and endo-Z bur for deroofing under a continuous irrigation with sterile physiologic saline (El Nasr Pharmaceutical Chemicals CO., Abu Zaabal, Egypt). A rubber dam was placed. The patency of the canals was checked using size 15 K-files (MANI, INC., Tochigi, Japan). Working length was determined using an electronic apex locator (Root ZX, J.Morita USA, Irvine, CA) at the “0.5” mark then was confirmed with intraoral periapical radiograph, to be 0.5–1 mm, shorter than radiographic apex. The canals were instrumented to a size 25 K-type file (MANI, INC., Tochigi, Japan). Preparation of teeth was performed with rotary ProTaper Universal instruments (Dentsply Maillefer, TN, USA) in an endodontic motor and reducing hand piece (X-Smart, Dentsply Maillefer, USA), according to the manufacturer instructions. The canals were thoroughly irrigated using 2ml of sterile physiologic saline as an irrigant between each instrument and the next. At this stage the canals were dried and filled with intra-canal medication according to the randomly selected group (TAPC group- combination of 500 mg ciprofloxacin, 500 mg metronidazole, 55 mg minocycline and 50 mg diclofenac potassium ground and then mixed with saline to obtain creamy consistency and CH group #MB-302001) (Table 1). A cotton pellet was placed in the pulp chamber and the access cavity was sealed with a temporary filling Orafil-G (Prevest Denpro, Digiana, India #11002). Postoperative pain was assessed with a visual analog scale at 24, 48 and 72 hours after the procedures.\n\nThe recommended retention period for intracanal medication is no less than 14 days. However, recontamination of the canal may take place if the medicament is retained for 2 weeks29,30. That is why intracanal medicaments was placed for 72 hours in the present study.\n\nSecond visit: After 72 hours the patients returned and the intracanal medication was removed by irrigation with a sterile physiologic saline. Periapical radiograph was taken with the master gutta percha ProTaper cone (Dentsply Maillefer, TN, USA) for master cone verification. Obturation was done by modified single cone technique using ProTaper gutta percha points, ADseal resin sealer (META BIOMED Co, Chungbuk, Korea #DM-15-4) and auxiliaries gutta percha cones size 25 (META BIOMED Co, Chungbuk, Korea). A cotton pellet was placed in the pulp chamber and the access cavity was sealed with a temporary filling. Postoperative intraoral periapical radiograph was taken.\n\nThe study was double-blinded in which participants, the outcome assessor and data analyst were blinded in this trial. The operator couldn’t be blinded due to the nature of the study as the intracanal medicament must be exposed and can’t be masked.\n\nParticipants: Participants did not know which group they were treated with; Numbered papers indicating the intra-canal medicament to be used were packed in opaque closed envelopes by M.N., where the patient picked up an envelope. After mechanical preparation, operator M.O. opened the envelope and used the intra-canal medicament assigned to that patient according to the number present inside the envelope.\n\nOutcome Assessor: The assistant supervisor (Y.N.) who collected the VAS, did not know which group the participants were assigned to.\n\nData Analyst: The assistant supervisor (N.N.) performed the statistical analysis.\n\nIf any harm was seen in the participants either in intervention or control groups they were recorded and reported at the end of the trial. The treatment according to the harm:\n\n- Pain: administration of Anti-inflammatory analgesics. (Brufen 600 mg, 1 tablet when needed).\n\n- Swelling: hot fomentation, mouth rinse with salty warm water, antibiotic administration in-case of presence of fever or lymphadenopathy (Augmentin 1 gm, capsule every 12 hour for 5 days).\n\nData were presented as means and standard deviations (SD) when appropriate. Data explored for normality was performed using D’Agostino-Pearson test. Independent t-test was used to compare between tested groups in age and mean pain (VAS). Chi square test was used to compare between tested groups for gender, teeth position and distribution and VAS scores. The significance level was set at P ≤ 0.05 (α=0.05). Intention to treat was used to adjust analysis for loss of patients during follow up period.\n\nStatistical analysis was performed with IBM® SPSS® (IBM Corp. Released 2015. IBM SPSS Statistics for Windows, Version 23.0. Armonk, NY: IBM Corp.)\n\n\nResults\n\n93 patients were assessed for eligibility, 9 patients were excluded (5 were not meeting inclusion criteria while 4 declined to participate); in total 84 patients were randomly assigned, received intended treatment, and were analysed for the primary outcome (see underlying data21). 3 participants were lost during follow up period after the first treatment session (2 from CH group and 1 from TAPC group) as they refused to continue and their treated tooth was extracted, implants to replace the extracted tooth were offered but none of the participants elected to have one. A CONSORT flow diagram is available as part of the reporting guidelines. Demographic data; age and gender had no significant difference between the two groups (P=0.966 and 0.141 respectively; Table 2 and Table 3).\n\nNS=non-significant, *= Significant\n\n*: Significant at P ≤ 0.05\n\n1. CH: Calcium hydroxide group.\n\n2. TAPC: Triple antibiotic paste+catafast group\n\nNS=non-significant, *= Significant\n\n*: Significant at P ≤ 0.05\n\n1. CH: Calcium hydroxide group.\n\n2. TAPC: Triple antibiotic paste+catafast group.\n\nThe overall highest incidence of pain values in both groups was at 24 hours postoperatively. Whereas the lowest incidence of pain values was at 72 hours postoperatively with a statistically significant difference between them (P≤0.001). The TAPC group showed statistically significant lower postoperative pain values at 48 hours only compared with the CH group (P=0.041), while at 24 and 72 hours there was no statistical significance (P=0.083 and 0.063, respectively) (Figure 1 and Table 4).\n\nDifferent letters within each column indicates significant difference.\n\nNS=non-significant, *= Significant,\n\n*: Significant at P ≤ 0.05.\n\n1. CH: Calcium hydroxide group.\n\n2. TAPC: Triple antibiotic paste+catafast group.\n\n\nDiscussion\n\nPost-endodontic pain is one of the major problems for both patients and dentists32. Development of post-operative pain after root canal treatment frequently occurs. Several risk factors such as gender, age, type of intracanal medication used, presence of pre-operative pain, pulpal and periradicular diagnosis and apical extrusion of debris have been correlated with the occurrence of flare-ups33,34. Preoperative pain was recorded for each patient before starting treatment as it was considered a risk factor that can affect the postoperative pain35,36.\n\nIn this study, both groups were substantially homogeneous at diagnosis and had similar preoperative clinical conditions. Onay et al. (2015)34 found that age, gender and tooth type did not influence the incidence of flare-ups. However, Arias et al. (2013)37 and Sadaf et al. (2014)35 reported that age, gender, tooth type and pre-operative pain are factors that influence post-operative pain. In the present study, the results showed a non-significant correlation between mean post-operative pain with gender and age of the patients in both groups except for CH group (after 24 and 48 hours).\n\nIn this study, factors affecting post-operative pain were excluded such as patients taking drugs that alter pain perception’ such as analgesics and antibiotics; patients with systemic diseases that could affect treatment; or patients suffering from psychological disturbances.\n\nThe purpose of this randomized clinical trial was to compare post-operative pain intensity after local medication with triple antibiotic paste together with an anti-inflammatory drug with that of calcium hydroxide. The incidence and intensity of postoperative pain was recorded at 24, 48 and 72 hours after placement of intra-canal medication.\n\nAn observable drop in pain levels in different follow up periods of both groups were recorded. This was in accordance to Pak et al. (2011)38 who reported that post-treatment pain decreased substantially after 1–2 days of treatment and continued to drop to minimal levels after 7 days.\n\nAlthough the TAPC group showed lower mean pain score levels at 24 and 72 hours than CH group, there was no statistically significant difference in the pain levels between both groups. While after 48 hours the mean pain score was significantly lower in TAPC group than CH with a statistically significant difference. Diclofenac has shown a substantial reduction of postendodontic pain when administered preoperatively in a single oral dose39. Sharma et al. (1994) evaluated pain-relief post extraction in patients receiving oral ibuprofen. Pain-relief was attributed to the rapid absorption of granule formulation and/or a local action of ibuprofen in solution in the mouth40. Therefore, potential advantages that may be acquired by the use of NSAIDs as intracanal medicament are: anti-inflammatory action and local analgesia.\n\nAlthough calcium hydroxide is considered the gold standard for disinfecting root canals and has been widely used as an intra-canal medicament since 1920’s41, its role in eliminating bacteria associated with apical infections is controversial. Microorganism have the ability to invade the dentinal tubules and buffer the high pH produced by calcium hydroxide compromising its antimicrobial activity42. Calcium hydroxide release hydroxyl ions which increase alkalinity leading to death of bacteria and microorganisms inside the root canal42.\n\nAdditionally, some studies showed that calcium hydroxide is insufficient for the elimination of some symptoms, and thus, antibiotic pastes are used as an alternative43,44 due to their good antimicrobial and biocompatible properties45,46. This could be attributed to the combined spectrum of antimicrobial activity and synergetic or additive actions of antibiotics “ciprofloxacin, metronidazole, and minocycline” found in TAP. Individually, ciprofloxacin has a broad spectrum activity and acts against both Gram-positive and Gram-negative bacteria by inactivating enzymes and inhibiting cell division47. Metronidazole is effective against obligate anaerobes, which are common in the deep dentin of infected root canals and acts by disrupting bacterial DNA47. Minocycline is a broad-spectrum tetracycline antibiotic and acts by inhibiting protein synthesis and inhibiting matrix metalloproteinase enzyme47. Combination of these three antibiotics overcomes bacterial resistance and achieves higher antimicrobial action18. Previous studies have shown favorable results when antibiotic mixture of ciprofloxacin, metronidazole, and minocycline has been used as topical root canal agents18,19,48. The absence of inter-appointment flare-up with TAP can also be attributed to the anti-inflammatory property of minocycline49. Although antibiotic pastes have been successfully used in endodontic procedures, they should be completely removed before final root canal obturation to avoid their negative effects, such as tooth discoloration, cytotoxicity, and prevention of sealer or cement penetration into root dentin50,51. However, it is impossible to completely remove antibiotic pastes from the root canal using conventional irrigation protocol51–53.\n\nThis study is a randomized clinical trial conducted on a relatively large sample size male and female patients with age ranging between 18-50, in real clinical settings and was conducted efficiently so it may be reasonable to generalize the results. It proposes an alternative way for decreasing post-operative pain of asymptomatic uniradicular necrotic teeth.\n\nWithin the limitations of this study, it is recommended to use the TAPC intracanal medicaments in necrotic cases, which could lead to efficient pain relief post-operatively. It could also be recommended to modify the eligibility criteria to include teeth with irreversible pulpitis to evaluate the effect of the presence of inflamed vital pulpal tissues on the post-operative pain.\n\nFurther in vivo and immunological studies are needed to identify the exact mechanism by which the TAPC resulted in decreasing postoperative pain and to determine the cytotoxic effect of TAPC.\n\n\nConclusion\n\nThe use of triple antibiotic paste with diclofenac potassium anti-inflammatory drug as well as calcium hydroxide as intracanal medications proved to be efficient in reducing post-operative pain in asymptomatic uniradicular necrotic teeth.\n\n\nData availability\n\nFigshare: The effect of triple antibiotic paste as an intracanal medication with an anti-inflammatory drug on post-operative pain of asymptomatic uniradicular necrotic teeth: a double blind randomized clinical trial. https://doi.org/10.6084/m9.figshare.827698121\n\nThis project contains the following underlying data:\n\nResults.xlsx (Demographic and pain data for participants)\n\nFigshare: The effect of triple antibiotic paste as an intracanal medication with an anti-inflammatory drug on post-operative pain of asymptomatic uniradicular necrotic teeth: a double blind randomized clinical trial. https://doi.org/10.6084/m9.figshare.827698121\n\nThis project contains the following extended data:\n\nDIAGNOSTIC CHART.docx (Form used to collect patient data)\n\nPain scale chart english version.docx (Visual analogue pain scale, English)\n\nPain scale chart arabic version.docx (Visual analogue pain scale, Arabic)\n\nFigshare: CONSORT checklist and flowchart for article ‘The effect of triple antibiotic paste as an intracanal medication with an anti-inflammatory drug on post-operative pain of asymptomatic uniradicular necrotic teeth: a double blind randomized clinical trial.’ https://doi.org/10.6084/m9.figshare.827698121",
"appendix": "Grant information\n\nThe author(s) declared that no grants were involved in supporting this work.\n\n\nReferences\n\nKayaoglu G, Gurel M, Saricam E, et al.: Predictive Model of Intraoperative Pain during Endodontic Treatment: Prospective Observational Clinical Study. J Endod. 2016; 42(1): 36–41. PubMed Abstract | Publisher Full Text\n\nSathorn C, Parashos P, Messer H: The prevalence of postoperative pain and flare-up in single- and multiple-visit endodontic treatment: a systematic review. Int Endod J. 2008; 41(2): 91–9. PubMed Abstract | Publisher Full Text\n\nSiqueira JF, Barnett F: Interappointment pain: mechanisms, diagnosis and treatment. Endod Top. 2004; 7(1): 93–109. Publisher Full Text\n\nO’Keefe EM: Pain in endodontic therapy: preliminary study. J Endod. 1976; 2(10): 315–319. PubMed Abstract | Publisher Full Text\n\nNg YL, Glennon JP, Setchell DJ, et al.: Prevalence of and factors affecting post-obturation pain in patients undergoing root canal treatment. Int Endod J. 2004; 37(6): 381–91. PubMed Abstract | Publisher Full Text\n\nWalton R, Fouad A: Endodontic interappointment flare-ups: a prospective study of incidence and related factors. J Endod. 1992; 18(4): 172–7. PubMed Abstract | Publisher Full Text\n\nChávez de Paz Villanueva LE: Fusobacterium nucleatum in endodontic flare-ups. Oral Surg Oral Med Oral Pathol Oral Radiol Endod. 2002; 93(2): 179–83. PubMed Abstract | Publisher Full Text\n\nGoldman M, Rankin C, Mehlman R, et al.: The immunologic implications and clinical management of the endodontic flare-up. Compendium. 1988; 9(2): 126–30. PubMed Abstract\n\nElzaki WM, Abubakr NH, Ziada HM, et al.: Double-blind Randomized Placebo-controlled Clinical Trial of Efficiency of Nonsteroidal Anti-inflammatory Drugs in the Control of Post-endodontic Pain. J Endod. 2016; 42(6): 835–42. PubMed Abstract | Publisher Full Text\n\nHargreaves KM, Keiser K: Local anesthetic failure in endodontics: mechanisms and management. Endod Topics. 2002; 1(1): 26–39. Publisher Full Text\n\nPolycarpou N, Ng YL, Canavan D, et al.: Prevalence of persistent pain after endodontic treatment and factors affecting its occurrence in cases with complete radiographic healing. Int Endod J. 2005; 38(3): 169–78. PubMed Abstract | Publisher Full Text\n\nWalton RE, Holton IF Jr, Michelich R: Calcium hydroxide as an intracanal medication: effect on posttreatment pain. J Endod. 2003; 29(10): 627–9. PubMed Abstract | Publisher Full Text\n\nSafavi KE, Dowden WE, Introcaso JH, et al.: A comparison of antimicrobial effects of calcium hydroxide and iodine-potassium iodide. J Endod. 1985; 11(10): 454–6. PubMed Abstract | Publisher Full Text\n\nJagdale S, Bhargava K, Bhosale S, et al.: Comparative evaluation of coronal discoloration induced by two triple antibiotic revascularization protocols when used at varying depths of temporary sealing material at the end of varying time periods. J Conserv Dent. 2018; 21(4): 388–93. PubMed Abstract | Free Full Text\n\nGilad JZ, Teles R, Goodson M, et al.: Development of a clindamycin-impregnated fiber as an intracanal medication in endodontic therapy. J Endod. 1999; 25(11): 722–7. PubMed Abstract | Publisher Full Text\n\nRahimi S, Janani M, Lotfi M, et al.: A review of antibacterial agents in endodontic treatment. Iran Endod J. 2014; 9(3): 161–8. PubMed Abstract | Free Full Text\n\nKhademi AA, Mohammadi Z, Havaee A: Evaluation of the antibacterial substantivity of several intra-canal agents. Aust Endod J. 2006; 32(3): 112–5. PubMed Abstract | Publisher Full Text\n\nHoshino E, Kurihara-Ando N, Sato I, et al.: In-vitro antibacterial susceptibility of bacteria taken from infected root dentine to a mixture of ciprofloxacin, metronidazole and minocycline. Int Endod J. 1996; 29(2): 125–30. PubMed Abstract | Publisher Full Text\n\nWindley W 3rd, Teixeira F, Levin L, et al.: Disinfection of immature teeth with a triple antibiotic paste. J Endod. 2005; 31(6): 439–43. PubMed Abstract | Publisher Full Text\n\nJohns DA, Varughese JM, Thomas K, et al.: Clinical and radiographical evaluation of the healing of large periapical lesions using triple antibiotic paste, photo activated disinfection and calcium hydroxide when used as root canal disinfectant. J Clin Exp Dent. 2014; 6(3): 230–6. PubMed Abstract | Publisher Full Text | Free Full Text\n\nomaia m, negm m, nashaat y, et al.: The effect of triple antibiotic paste as an intracanal medication with an anti-inflammatory drug on post-operative pain of asymptomatic uniradicular necrotic teeth: a double blind randomized clinical trial. figshare. Dataset. 2019. http://www.doi.org/10.6084/m9.figshare.8276981.v8\n\nSoltanoff W: A comparative study of the single-visit and the multiple-visit endodontic procedure. J Endod. 1978; 4(9): 278–81. PubMed Abstract | Publisher Full Text\n\nGenet JM, Hart AA, Wesselink PR, et al.: Preoperative and operative factors associated with pain after the first endodontic visit. Int Endod J. 1987; 20(2): 53–64. PubMed Abstract | Publisher Full Text\n\nClem WH: Posttreatment endodontic pain. J Am Dent Assoc. 1970; 81(5): 1166–70. PubMed Abstract | Publisher Full Text\n\nAlbashaireh ZS, Alnegrish AS: Postobturation pain after single- and multiple-visit endodontic therapy. A prospective study. J Dent. 1998; 26(3): 227–32. PubMed Abstract | Publisher Full Text\n\nTorabinejad M, Kettering JD, McGraw JC, et al.: Factors associated with endodontic interappointment emergencies of teeth with necrotic pulps. J Endod. 1988; 14(5): 261–6. PubMed Abstract | Publisher Full Text\n\nLund I, Lundeberg T, Sandberg L, et al.: Lack of interchangeability between visual analogue and verbal rating pain scales: a cross sectional description of pain etiology groups. BMC Med Res Methodol. 2005; 5: 31. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBalto K: Single- or multiple-visit endodontics: which technique results in fewest postoperative problems? Evid Based Dent. 2009; 10(1): 16. PubMed Abstract | Publisher Full Text\n\nAbbott PV: Medicaments: aids to success in endodontics. Part 2. Clinical recommendations. Aust Dent J. 1990; 35(6): 491–6. PubMed Abstract | Publisher Full Text\n\nGomes BP, Sato E, Ferraz CC, et al.: Evaluation of time required for recontamination of coronally sealed canals medicated with calcium hydroxide and chlorhexidine. Int Endod J. 2003; 36(9): 604–9. PubMed Abstract | Publisher Full Text\n\nTakushige T, Cruz EV, Asgor Moral A, et al.: Endodontic treatment of primary teeth using a combination of antibacterial drugs. Int Endod J. 2004; 37(2): 132–8. PubMed Abstract | Publisher Full Text\n\nMokhtari F, Yazdi K, Mahabadi AM, et al.: Effect of Premedication with Indomethacin and Ibuprofen on Postoperative Endodontic Pain: A Clinical Trial. Iran Endod J. 2016; 11(1): 57–62. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPamboo J, Hans MK, Kumaraswamy BN, et al.: Incidence and factors associated with flare-ups in a post graduate programme in the indian population. J Clin Exp Dent. 2014; 6(5): e514–9. PubMed Abstract | Publisher Full Text | Free Full Text\n\nOnay EO, Ungor M, Yazici AC: The evaluation of endodontic flare-ups and their relationship to various risk factors. BMC Oral Health. 2015; 15(1): 142. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSadaf D, Ahmad MZ: Factors associated with postoperative pain in endodontic therapy. Int J Biomed Sci. 2014; 10(4): 243–7. PubMed Abstract | Free Full Text\n\nAlRahabi MK: Predictors, prevention, and management of postoperative pain associated with nonsurgical root canal treatment: A systematic review. J Taibah Univ Med Sci. 2017; 12(5): 376–84. Publisher Full Text\n\nArias A, de la Macorra JC, Hidalgo JJ, et al.: Predictive models of pain following root canal treatment: a prospective clinical study. Int Endod J. 2013; 46(8): 784–93. PubMed Abstract | Publisher Full Text\n\nPak JG, White SN: Pain prevalence and severity before, during, and after root canal treatment: a systematic review. J Endod. 2011; 37(4): 429–38. PubMed Abstract | Publisher Full Text\n\nMetri M, Hegde S, Bhandi S: Effect of pretreatment diclofenac sodium on postendodontic pain: A randomised controlled trial. J Conserv Dent. 2016; 19(1): 7–10. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSharma NK, Kindelan JD, Hutchinson D, et al.: A study to compare ibuprofen effervescent granules with ibuprofen tablets in the treatment of acute dental pain. Prim Dent Care. 1994; 1(1): 5–8. PubMed Abstract\n\nSiqueira JF Jr, Lopes HP: Mechanisms of antimicrobial activity of calcium hydroxide: a critical review. Int Endod J. 1999; 32(5): 361–9. PubMed Abstract | Publisher Full Text\n\nHaapasalo HK, Sirén EK, Waltimo TM, et al.: Inactivation of local root canal medicaments by dentine: an in vitro study. Int Endod J. 2000; 33(2): 126–131. PubMed Abstract | Publisher Full Text\n\nEr K, Kuştarci A, Ozan U, et al.: Nonsurgical endodontic treatment of dens invaginatus in a mandibular premolar with large periradicular lesion: a case report. J Endod. 2007; 33(3): 322–4. PubMed Abstract | Publisher Full Text\n\nTaneja S, Kumari M: Use of triple antibiotic paste in the treatment of large periradicular lesions. J Investig Clin Dent. 2012; 3(1): 72–6. PubMed Abstract | Publisher Full Text\n\nGomes-Filho JE, Duarte PC, de Oliveira CB, et al.: Tissue reaction to a triantibiotic paste used for endodontic tissue self-regeneration of nonvital immature permanent teeth. J Endod. 2012; 38(1): 91–4. PubMed Abstract | Publisher Full Text\n\nThibodeau B, Teixeira F, Yamauchi M, et al.: Pulp revascularization of immature dog teeth with apical periodontitis. J Endod. 2007; 33(6): 680–9. PubMed Abstract | Publisher Full Text\n\nBrunton LL, Lazo JS, Parker KL: Goodman and Gilman's the pharmacological basis of therapeutics. 11th ed. New York: McGraw Hill companies; 2006; 1111–26. (1049–72). 1182–7. Reference Source\n\nAlam T, Nakazawa F, Nakajo K, et al.: Susceptibility of Enterococcus faecalis to a combination of antibacterial drugs (3 mix) in vitro. J Oral Biosci. 2005; 47(4): 315–20. Publisher Full Text\n\nDunston CR, Griffiths HR, Lambert PA, et al.: Proteomic analysis of the anti-inflammatory action of minocycline. Proteomics. 2011; 11(1): 42–51. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAkcay M, Arslan H, Topcuoglu HS, et al.: Effect of calcium hydroxide and double and triple antibiotic pastes on the bond strength of epoxy resin-based sealer to root canal dentin. J Endod. 2014; 40(10): 1663–7. PubMed Abstract | Publisher Full Text\n\nAkcay M, Arslan H, Yasa B, et al.: Spectrophotometric analysis of crown discoloration induced by various antibiotic pastes used in revascularization. J Endod. 2014; 40(6): 845–8. PubMed Abstract | Publisher Full Text\n\nArslan H, Capar ID, Saygili G, et al.: Efficacy of various irrigation protocols on the removal of triple antibiotic paste. Int Endod J. 2014; 47(6): 594–9. PubMed Abstract | Publisher Full Text\n\nBerkhoff JA, Chen PB, Teixeira FB, et al.: Evaluation of triple antibiotic paste removal by different irrigation procedures. J Endod. 2014; 40(8): 1172–7. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "55604",
"date": "18 Nov 2019",
"name": "Maram E. Khallaf",
"expertise": [
"Reviewer Expertise Endodontics"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nArticle addresses an important point during endodontic treatment which is post operative pain. A sound and clear clinical trial is done representing the true clinical situation.\nThe use of triple antibiotic paste with the addition of an anti-inflammatory drug showed same results regarding the postoperative pain as calcium hydroxide.\nResults of the intracanal bacterial reduction are not clearly shown in the text or discussed. Article needs more recent citations.\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": "5673",
"date": "03 Jul 2020",
"name": "Mohamed Omaia",
"role": "Author Response",
"response": "Results of intracanal bacterial reduction as secondary outcome will be published in separate article."
}
]
},
{
"id": "64970",
"date": "01 Jul 2020",
"name": "Jyothi Mandava",
"expertise": [
"Reviewer Expertise Remineralization procedures in early carious lesions and in Regenarative procedures"
],
"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 acceptable scientific standard with some corrections:\nThe introduction part is not structured well and the flow of the written matter is missing.\n\nThe objectives and hypotheses of the study were not discussed.\n\nIn the discussion, it was reported that CH group has shown significant correlation between post-operative pain with gender and age of the patients but the statistical analysis was not provided.\n\nPreferable to place definitive conclusions from the outcome of the study.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
},
{
"id": "66350",
"date": "10 Aug 2020",
"name": "Mahalaxmi Sekar",
"expertise": [
"Reviewer Expertise Endodontics",
"dentin bonding",
"regeneration",
"remineralisation"
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis paper is aimed to comparatively evaluate the effectiveness of triple antibiotic paste with the anti-inflammatory drug diclofenac potassium and calcium hydroxide when used as an intra-canal medication in reducing post-operative pain.\nIntroduction: Should set the basis of the need for the study, with enough references to mitigate the study.\n\nPlease state the lacunae in the current literature as to necessitate your study.\n\nMention the drawbacks of CH and the rationale of adding Catafast to TAPC.\n\nMention the aim and objectives in the main text of the manuscript.\n\nFurther, the justification for choosing diclofenac over other anti-inflammatory drugs has not been highlighted.\n\nMethodology: The article describes a novel double-blind randomized clinical trial and the author has clearly explained the process of selection of the subjects. Though the methodology has been elaborately explained, literature evidence reveals the use of TAP in the concentration of 1:1:1 as intracanal medicament, whereas in this study the concentration used is 500mg ciprofloxacin, 500mg metronidazole, 55mg minocycline, and 50mg diclofenac potassium. The low concentration ofdiclofenac used might not justify the role of an anti-inflammatory agent since it may negatively influence the results of the study. In addition, the authors have used commercial calcium hydroxide (metapex) comprising of iodoform which is an antiseptic agent that could also contribute to reducing post-operative pain.\nResults: The pain was recorded at 24, 48, and 72 hours using VAS scale. During this period any participants suffering from pain or swelling both in the intervention and control groups were noted by the author as mentioned in the manuscript. However, the number of participants experiencing these symptoms and who received pharmacological therapy is not mentioned in the article, which might play a key role in influencing the overall results of the study. The author has analysed the age and gender comparison between the groups, however, the author could have subcategorised the wide age range of 18-50 years and denoted the number of participants falling under each category in the 2 groups, as it would be a major contributory factor.\nDiscussion: The intracanal medicaments are usually placed for about a week, the author could have discussed the reasons for choosing a short time interval of 24,48 and 72 hours. The author has substantiated with literature evidence on the use of ibuprofen for pain relief but has chosen diclofenac potassium. The author could have emphasized the use of diclofenac potassium with literature evidence, described the mechanism of action of the drug in improving the efficacy of TAP which would have added more value to the article. The author should have explained the purpose of using a lesser concentration of diclofenac potassium. The reasons for drawing the conclusions are also not clearly dealt with in the manuscript.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? 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?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? No\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": [
{
"c_id": "6814",
"date": "23 Jun 2021",
"name": "Mohamed Omaia",
"role": "Author Response",
"response": "Drawbacks of CH and the rationale of adding Catafast to TAPC. had been mentioned in the discussion. While the mechanism of action of diclofenac potassium had been added to the new version of manuscript."
}
]
}
] | 1
|
https://f1000research.com/articles/8-1687
|
https://f1000research.com/articles/10-236/v1
|
24 Mar 21
|
{
"type": "Research Article",
"title": "An exploratory study of social media users’ engagement with COVID-19 vaccine-related content",
"authors": [
"Md. Sayeed Al-Zaman"
],
"abstract": "Background: Facebook, as the world’s most popular social media platform, has been playing various important roles throughout the COVID-19 pandemic, allowing users to produce and share health-related information that both eases and complicates public health communication. However, the characteristics of vaccine-related Facebook content and users’ reaction to the vaccine issue has been an unexplored area to date. Methods: To fill the previous knowledge-gap, this exploratory study wants to understand the communication climate of Facebook on the COVID-19 vaccine issue, including the nature of dominant content and users’ engagement patterns with them. Therefore, the study analyzes the 10,000 most popular Facebook posts with the highest interactions on the vaccine issue. Results: The results show that Facebook users prioritize more vaccine-related news links (71.22%) over other content. The declining interactions on the issue suggests that interaction growth mainly depends on positive news on the vaccine. Finally, users’ reaction to the vaccine issue is dominantly positive, though they may show a highly negative attitude toward vaccine misinformation. Conclusions: A few limitations and strengths of this study are discussed along with values and implications. This study for the first time analyzes Bangla language-based Facebook content related to the COVID-19 vaccine issue, which is largely overlooked in global academic research.",
"keywords": [
"COVID-19 vaccine",
"Facebook",
"social media content",
"user engagement",
"medicine."
],
"content": "Introduction\n\nThis exploratory study seeks to understand the characteristics of coronavirus disease 2019 (COVID-19) vaccine-related social media content and how users engage with them. COVID-19 has already claimed 1.76 million lives worldwide, making the public health condition critical. Meanwhile, lockdown and social distancing interrupt face-to-face human communication (Limaye et al., 2020). Such a situation lets social media bridge the communication gap by delivering necessary information (Goel & Gupta, 2020; González-Padilla & Tortolero-Blanco, 2020). Researchers categorized COVID-19 online information into 11 types: valid information, comforting information, perplexing information, misinformation, disinformation, shocking information, contradictory information, doubtful information, progressive information, postponed information, and confidential information (Ashrafi-Rizi & Kazempour, 2020). Two broader categories may represent all of them: useful information that helps public health communication, and faulty information that interrupts public health communication. For example, social media was responsible for fake COVID-19 prescriptions and medications that claimed many human lives (Islam et al., 2020). On the contrary, infographics containing COVID-19 health information delivered through Twitter and WeChat helped rapid COVID-19 knowledge dissemination (Chan et al., 2020). Similarly, on the one hand, social media helps to run positive and effective virtual campaigns for the COVID-19 vaccine around the world, and, on the other hand, vaccine opposition and misinformation obstruct the vaccination process (Bonnevie et al., 2020). A report says 31 million Facebook users follow anti-vaccine groups with 17 million YouTube users subscribing to similar accounts (Burki, 2020). Therefore, it is imperative to understand social media users’ sentiments regarding the COVID-19 vaccine, and the nature of vaccine-related content that dominates social media platforms.\n\nPrevious studies from both the public health and communication domain dealt with different aspects of the COVID-19 vaccine, such as vaccine hesitancy (Bonnevie et al., 2020; Jamison et al., 2020; Puri et al., 2020), vaccine misinformation (Jamison et al., 2020; Loomba et al., 2020), media, and the COVID-19 vaccine (Olijo, 2020). However, no attention has been paid to social media users’ engagement with the COVID-19 vaccine issue. The present research attempts to fill this gap.\n\n\nMethods\n\nThis research attempts to understand the communication climate of Facebook surrounding the COVID-19 vaccine issue, the nature of dominant content and users’ engagement patterns with them.\n\nFacebook is the most popular social media platform in Bangladesh (94.46%), compared to YouTube (3.31%) and Twitter (0.3%), so I selected it as the source of data for this study. I collected the data from Facebook pages using CrowdTangle, a public insights tool owned and operated by Facebook. It can access public pages and groups to collect various types of data. However, I excluded group data in this research because Facebook groups and pages are different in terms of users’ interaction patterns, participation rates, and security issues. To collect the data from relevant Facebook posts, I conducted a keyword search. Most of the Facebook users in Bangladesh who write in the Bangla language use the Bangla alphabet. For that reason, I determined the following Bangla keywords: “corona vaccine,” “coronar vaccine,” “corona tika,” “coronar tika,” “corona oshudh,” “coronar oshudh,” “corona protishedhok,” and “coronar protishedhok.” All search terms can be translated as corona vaccine or vaccine of the corona.\n\nI set the timeline from 8 March to 2 December 2020. The first case of coronavirus in Bangladesh was identified on 8 March 2020. As Facebook is an interactive platform, so I collected the data on 17 December 2020 (15 days after the end date of the data collection period) after stabilizing the threads. The search result produced 37,460 Facebook posts relevant to the topic. Of them, I selected the top 10,000 posts for the final analysis based on their total interactions, which was 26.70% of the total search results: These posts were from 1,087 different Facebook pages, on average 9.20 posts from each page. I categorized the content into six types: link, live video, native video, photo, status, and YouTube video. In Facebook, each of the mentioned content can usually have the following definitions and modes: a link and a photo can be shared with or without any text; live video can be completed or scheduled; native video is video that is uploaded directly to Facebook; a status is mainly text-based, often contains other elements, such as tags; YouTube videos are often embedded/shared on Facebook. I measured the users’ engagement based on nine interaction parameters, including six Facebook reactions: comments (mean [M]=32.90, standard deviation [SD]=140.06), shares (M=145.17, SD=1345.86), like (M=1377.04, SD=4792.64), love (M=74.98, SD=788.35), wow (M=6.50, SD=40.33), haha (M=52.79, SD=408.28), sad (M=16, SD=372.76), angry (M=3.67, SD=55.05), and care (M=5.40, SD=51.67). The numbers and percentages are presented in tables, time-series data are presented in graphs.\n\nIn February 2016, Facebook introduced five basic reactions: love, sad, wow, haha, and angry, alongside like or thumbs-up. These reactions were influenced by the six universal reactions: fear, anger, joy, sadness, disgust, and surprise (Gu et al., 2019), proposed by Ekman (1992) based on human facial expressions (Keltner et al., 2019). However, studies found that disgust and anger, and fear and surprise share similar characteristics, meaning the four following emotions should be considered as the actual basic emotions: anger, joy, sadness, and surprise (Jack et al., 2014). Unlike basic emotions, Facebook reactions represent more varied and often contradictory expressions: like or thumbs-up usually expresses likeness, agreement, happiness, approval, and acceptance; love expresses positivity, affection, empathy, support, kindness, and liking something with feeling; sad expresses empathy, grief, tragedy, and support; haha expresses laughter, fun, mockery, and often rejection; wow expresses muted disdain, surprise, immediate shock, and skepticism; and angry expresses denial, aggressiveness, strong and overt disdain, and dislike (Al-Rawi, 2020).\n\nIn contrast to the idea of basic emotions, the circumplex model of affect proposes that human emotion is more complex and diverse than the basic emotion theory explains (Russell, 1980). At least 28 interconnected emotional states of humans can be defined with two variables: emotional valence or sentiment and emotional arousal or intensity (Citron et al., 2014; Freeman et al., 2020; Yang & Chen, 2012). This two-dimensional model of human emotions defines emotional valence as positive and negative and emotional arousal as high and low (Preoţiuc-Pietro et al., 2016). In this study, I tried to position Facebook reactions within this paradigm but with little modification. For valence, I defined like, love, wow, and care as positive, and angry, sad, and haha reactions as negative valence (Giuntini et al., 2019). As the number of Facebook emotions is limited, unlike the circumplex model that has 28 distinct but relative emotions, I defined the seven reactions as follows: love, care, angry, and wow as high arousal, and like and sad as low arousal. That means positive high includes love, care, and haha; positive low includes like; negative high includes angry and wow; negative low includes sad. Although like, according to its defined meanings, belong to the lower arousal dimension, its degree is moderate, which is closer to the high arousal dimension (see Russell, 1980). Again, Al-Rawi (2020) defined wow as positive, I defined it as negative based on the findings of Jack et al. (2014) (i.e., fear and surprise are the same, and wow expresses surprise or shock, which is negative). It is important to note that expressions through these reactions vary widely, and a reaction may express contradictory emotions: haha both expresses joy and refutation. It makes this reaction’s position in the paradigm uncertain: it can be positive high and negative high. For such ambiguous nature, previous studies excluded haha from their interpretations (e.g., Al-Rawi, 2020).\n\n\nResults\n\nOf the six content types, link (n=8,614; 86.14%) was dominant, followed by photos (n=491; 4.91%) and native videos (n=466; 4.66%); YouTube video (n=52; 0.52%) was on the bottom of the list (Table 1). During the time span, links were shared the most in July (n=1,696; 19.69%), followed by August (n=1,331; 15.45%); photos were shared the most in July (n=147; 29.94%) as well, followed by October (n=72; 14.66%). July (20.73%) had the highest percentage of content, followed by August (15.28%) and April (14.33%). Figure 1 shows that the percentage of the links content type was dropping gradually with a few fluctuations. On the other hand, the percentages of live video and status were slowly increasing with a few drops. However, except for the line of links, other lines do not show any significant changes.\n\nAll posts generated 17,144,403 interactions during the time span. The numbers of interactions were higher in the first half of the period, roughly from April to July 2020 (Figure 2). The interactions reached to the highest on 17 April 2020 (n=201,834), with a few more surges on 27 April (n=135,941), 9 May (n=176,936), 22 June (n=131,564), and 2 July (n=169,524). The average interactions dropped in the following months, and again increased slightly in the mid-October 2020 and late-November 2020. However, except 17 October (n=116,743) and 21 November (n=100,619), the interactions were dropping gradually after July 2020 till December 2020.\n\nOf all content types, links (71.22%) received the highest interactions, followed by native videos (16.52%), while YouTube videos (0.54%) received the lowest interactions. In all content types, like as a reaction had the highest percentages: in all except status, the second-highest was love; in status (11.16%), the second-highest was haha (Table 2). A comparison of interaction percentages among the content types shows that YouTube video (4.16% and 1.35%) received relatively higher percentages of comments and care in its interaction types, followed by native videos (4.05%); native videos (19%) were shared more often, followed by live video (8.33%). Of the six reactions, links received relatively higher percentages of likes (84.14%); photos received higher percentages of love (16.80%); statuses received higher percentages of wow (0.65%), haha (11.16%), and sad (5.58%).\n\nOf the total interactions during the period, 1.92% (n=328,976) were comments and 8.47% (n=1,451,726) were shares (Table 3). Of the six reactions, likes were the highest (80.32%), followed by love (4.37%) and haha (3.08%); angry (0.21%) had the lowest share. Within all interaction types, link had the highest percentages: 70.92% comments, 56.21% shares, 74.61% like, 47.85% love, 70.77% wow, 66.12% haha, 46.40% sad, 85.59% angry, and 51.60% care (Table 3). Within comments (11.23%) and love (25.04%), photo had the second-highest percentages; within haha (13.80%) and sad (22.78%), status had the second-highest percentages; within shares (37.07%), likes (15.01%), wow (13.88%), angry (6.41%), and care (20.84%), native video had the second-highest percentages.\n\n\nDiscussion\n\nThis study for the first time attempts to explore the nature of content and public engagement in the COVID-19 vaccine issue on Facebook. To provide some novel insights, the top 10,000 most interactive and relevant Facebook posts have been analyzed following a combination of three communication research techniques: time series analysis, network analysis, and sentiment analysis.\n\nThis exploratory research has a few main findings. Vaccine-related links were the highest in percentage (86.14%) of all Facebook content during the period and the highest shared content (56.21%) as well, which counters the result of Baresch et al. (2011) that showed Facebook users’ infrequently (49%) share news through links. Links shared in social media platforms are mostly news items primarily from different online news portals (Baresch et al., 2011), which infers that Bangladeshi Facebook users mostly consume news items related to the COVID-19 vaccine. However, the decline of links suggests that users are increasingly becoming less interested in vaccine-related news. Kleis Nielsen et al. (2020) also found a similar tendency that using Facebook for COVID-19 news and information is declining: from 10 April to 24 June 2020, the percentage declined from 24 to 12. Unlike the present study, however, the previous study considered all COVID-19 issues instead of only the vaccine issue and produced a similar result.\n\nThe interactions were higher during the first half of the period but decreased with time. Interactions surge mainly due to vaccine-related news irrespective of its valence (i.e. positive and negative). However, it seems positive news helps interactions to grow more than negative news. For example, two crucial vaccine-related positive news items from mainstream media influenced the interaction to reach its highest on 17 April: “The University of Oxford declared that the vaccine for COVID-19 would come in September,” and “The trial of COVID-19 vaccine would begin from the next week” (e.g. Daily Jugantor). The interaction reached its second-highest on 27 April due to a few more positive news events: “Corona vaccine production will start from May this year,” and “India’s Serum Institute will start producing COVID-19 vaccine soon” (e.g. Bangla Tribune, DW). Nevertheless, no significant positive follow-ups occurred in the consecutive months, so the interaction lines remained steady most of the time. Another surge on 17 October was for positive news articles: “Russia produced the first COVID-19 vaccine in the world,” and “Bangladesh’s Globe Biotech claimed the invention of COVID-19 vaccine” (e.g. BBC News, Prothom Alo).\n\nLike and love are the two leading reactions, meaning the valence of users’ reaction to vaccine-related content is positive and, to some extent, highly intense. On the other hand, the lowest instances of the angry reaction indicate users’ minimal negative emotion toward the issue. Both tendencies indicate a positive valence with from moderate to high arousal, suggesting Facebook users’ optimistic attitude toward the COVID-19 vaccine. But note that users’ sentiments can be different for different content types: link has more positive valence, whereas status has comparatively more negative valence. However, news links often produce discontent among users, perhaps due to presenting unsatisfactory and undesired information, such as the cancellation and failure of vaccine, and demystified fake news. In practice, the COVID-19 vaccine produced uncertainties among the public around the world, often allowing many to produce vaccine-related misinformation and fake prescriptions (Limaye et al., 2020). Also, during the pandemic period, COVID-19 misinformation is highly prevalent in social media platforms like Facebook (Al-Zaman et al., 2020; Islam et al., 2020).\n\nAnother finding shows that links about the vaccine generate more interactions than others. More specifically, links are shared more and generate more comments compared to the other content types. Previous studies revealed that the primary reason for Facebook users’ news link-sharing behavior is to share important news with others that might be helpful (Baek et al., 2011). It allows easier dissemination of news and sociality, the attachment to other users. In this regard, the present study expands on the previous knowledge, adding that users not only share links containing important information but also links allow more users to engage in discussion.\n\n\nConclusion: Limitations & strengths\n\nThis study has a few limitations. First, Facebook only introduced the care reaction in April 2020. It means interaction data before April could not include care responses, which may have impacts on the overall percentages. Second, Bangla is a complex language: diverse expressions and spellings of words can indicate the same thing. Therefore, though I searched for a single topic, my search terms were not likely to incorporate all posts. More search terms, such as “COVID-19 vaccine” and “COVID-19 medicine” could yield more search results that could have led to different findings. Third, although this study explored the content types, it failed to explain what these contents contain: vaccine news, instructions, or something else? Further research should explore what types of vaccine-related information Facebook users really consume. Fourth, previous studies found that, though links most likely contain additional text or status, they often contain photos as well (Baresch et al., 2011), often making the three content types (i.e. link, photo, and status) difficult to categorize separately. The data for this study were automated and collected using CrowdTangle, which left room for doubt regarding this issue. Finally, sentiment analysis based on only Facebook reactions and excluding textual analysis may not be representative, and, to some extent, could produce unreliable results. For example, the like reaction could be a result of the absence of any particular emotion (Giuntini et al., 2019).\n\nApart from these limitations, this study has strengths in a few areas. First, Bangla language-based Facebook content is largely overlooked in academic research, perhaps due to the absence of research interest or research efficiency among researchers. The present study filled this gap a little. Second, how Facebook users react to the issue of the COVID-19 vaccine is still an unexplored but necessary area of research. In this regard, the novel findings of this macro study may help psychology and communication researchers to understand the diverse reactions and emotional positions of Bangladeshi Facebook users on the COVID-19 vaccine issue. Third, this study provides new perspectives to rethink social media users’ views toward the COVID-19 vaccine. While previous studies emphasized vaccine hesitancy, negatively portrayed social media users’ sentiments toward the COVID-19 vaccine, and found that vaccine opposition was rising among social media users, the present study showed that social media users are more positive toward the vaccine issue, which the past studies could barely identify (Bonnevie et al., 2020; Puri et al., 2020). Finally, this research dealt with a larger dataset than the previous studies on the COVID-19 vaccine (Jamison et al., 2020; Rovetta & Bhagavathula, 2020), which makes the results more reliable. This is an exploratory study that may not provide conclusive findings in some cases. Therefore, further research is required to provide more insights in this regard.\n\n\nData availability\n\nHarvard Dataverse: An exploratory study of social media users’ engagement with COVID-19 vaccine-related contents\n\nhttps://doi.org/10.7910/DVN/RCWH9D (Al-Zaman, 2021)\n\nThis project contains the following underlying data:\n\nCOVID_medicine_posts_data.xlsx\n\nThe data in this dataset were collected using the CrowdTangle platform. The Excel dataset includes six sheets. The first sheet titled “COVID-19 vaccine” contains the raw data with 31 different variables, such as sources (e.g. FB pages) of data, date of the posts, content types, users’ engagement indicators (e.g. number of reactions, comments, and shares), and link descriptions. The remaining five sheets contain the analyses of the data for this study. For example, Main Data includes only the twelve variables analysed in the present study. Similarly, each of Types & Interactions, Interactions & Time, and Types & Time include data of two variables, and often their cross-tabulations as well. I would like to recommend the researchers who are interested in this dataset utilize the first sheet (i.e. COVID-19 vaccine) for their study or other purposes.\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\nAl-Rawi A: Networked Emotional News on Social Media. Journalism Practice. 2020; 14(9): 1125–1141. Publisher Full Text\n\nAl-Zaman MS, Sife SA, Sultana M, et al.: Social Media Rumors in Bangladesh. Journal of Information Science Theory and Practices. 2020; 8(3): 77–90. Publisher Full Text\n\nAl-Zaman MS: An exploratory study of social media users’ engagement with COVID-19 vaccine-related contents. Harvard Dataverse, V1. 2021. http://www.doi.org/10.7910/DVN/RCWH9D\n\nAshrafi-Rizi H, Kazempour Z: Information Typology in Coronavirus (COVID-19) Crisis; a Commentary. Arch Acad Emerg Med. 2020; 8(1): e19. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBaek K, Holton A, Harp D, et al.: The links that bind: Uncovering novel motivations for linking on Facebook. Comput Human Behav. 2011; 27(6): 2243–2248. Publisher Full Text\n\nBaresch B, Knight L, Harp D, et al.: Friends Who Choose Your News: An analysis of content links on Facebook. In 12th International Symposium on Online Journalism. Austin, Texas: ISOJ: The Official Research Journal, 2011; 1–24. Reference Source\n\nBonnevie E, Gallegos-Jeffrey A, Goldbarg J, et al.: Quantifying the rise of vaccine opposition on Twitter during the COVID-19 pandemic. J Commun Healthc. 2020; 14(1): 12–19. Publisher Full Text\n\nBurki T: The online anti-vaccine movement in the age of COVID-19. Lancet Digit Health. 2020; 2(10): e504–e505. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChan AKM, Nickson CP, Rudolph JW, et al.: Social media for rapid knowledge dissemination: early experience from the COVID-19 pandemic. Anaesthesia. 2020; 75(12): 1579–1582. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCitron FMM, Gray MA, Critchley HD, et al.: Emotional valence and arousal affect reading in an interactive way: Neuroimaging evidence for an approach-withdrawal framework. Neuropsychologia. 2014; 56(100): 79–89. PubMed Abstract | Publisher Full Text | Free Full Text\n\nEkman P: An Argument for Basic Emotions. Cogn Emot. 1992; 6(3–4): 169–200. Publisher Full Text\n\nFreeman C, Alhoori H, Shahzad M: Measuring the diversity of Facebook reactions to research. Proc ACM Hum Comput Interact. 2020; 4(GROUP, Article 12): 1–17. Publisher Full Text\n\nGiuntini FT, Ruiz LP, De Fátima Kirchner L, et al.: How do I feel? Identifying emotional expressions on Facebook reactions using clustering mechanism. IEEE Access. 2019; 7: 53909–53921. Publisher Full Text\n\nGoel A, Gupta L: Social Media in the Times of COVID-19. J Clin Rheumatol. 2020; 26(6): 220–223. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGonzález-Padilla DA, Tortolero-Blanco L: Social media influence in the COVID-19 pandemic. Int Braz J Urol. 2020; 46(suppl.1): 120–124. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGu S, Wang F, Patel NP, et al.: A Model for Basic Emotions Using Observations of Behavior in Drosophila. Front Psychol. 2019; 10: 1–13. PubMed Abstract | Publisher Full Text | Free Full Text\n\nIslam MS, Sarkar T, Khan SH, et al.: COVID-19-Related Infodemic and Its Impact on Public Health: A Global Social Media Analysis. Am J Trop Med Hyg. 2020; 103(4): 1621–1629. PubMed Abstract | Publisher Full Text | Free Full Text\n\nJack RE, Garrod OGB, Schyns PG: Dynamic facial expressions of emotion transmit an evolving hierarchy of signals over time. Curr Biol. 2014; 24(2): 187–192. PubMed Abstract | Publisher Full Text\n\nJamison AM, Broniatowski DA, Dredze M, et al.: Not just conspiracy theories: Vaccine opponents and proponents add to the COVID-19 ‘infodemic’ on Twitter. Harvard Kennedy School Misinformation Review. 2020; 1(3). Publisher Full Text\n\nKeltner D, Sauter D, Tracy J, et al.: Emotional Expression: Advances in Basic Emotion Theory. J Nonverbal Behav. Springer New York LLC, 2019; 43(2): 133–160. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKleis Nielsen R, Kalogeropoulos A, Fletcher R: Social Media Very Widely Used, but Use for News and Information about COVID-19 is Declining. London. 2020. (Accessed: 24 December 2020). Reference Source\n\nLimaye RJ, Sauer M, Ali J, et al.: Building trust while influencing online COVID-19 content in the social media world. Lancet Digit Health. Elsevier Ltd, 2020; 2(6): e277–e278. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLoomba S, de Figueiredo A, Piatek SJ, et al.: Measuring the Impact of Exposure to COVID-19 Vaccine Misinformation on Vaccine Intent in the UK and US. medRxiv. 2020. Publisher Full Text\n\nOlijo II: Nigerian media and the global race towards developing a COVID-19 vaccine. Ianna Journal of Interdisciplinary Studies. 2020; 2(1): 65–74. (Accessed: 25 December 2020). Reference Source\n\nPreoţiuc-Pietro D, Schwartz HA, Park G, et al.: Modelling Valence and Arousal in Facebook posts. In Proceedings of NAACL-HLT. San Diego, California: Association for Computational Linguistics, 2016; 9–15. Publisher Full Text\n\nPuri N, Coomes EA, Haghbayan H, et al.: Social media and vaccine hesitancy: new updates for the era of COVID-19 and globalized infectious diseases. Hum Vaccin Immunother. 2020; 16(11): 2586–2593. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRovetta A, Bhagavathula AS: COVID-19-Related Web Search Behaviors and Infodemic Attitudes in Italy: Infodemiological Study. JMIR Public Health Surveill. 2020; 6(2): e19374. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRussell JA: A circumplex model of affect. J Pers Soc Psychol. 1980; 39(6): 1161–1178. Publisher Full Text\n\nYang YH, Chen HH: Machine recognition of music emotion: A review. ACM Trans Intell Syst Technol. 2012; 3(3): 1–30. Publisher Full Text"
}
|
[
{
"id": "86107",
"date": "09 Jun 2021",
"name": "Jayaseelan Rathinaswamy",
"expertise": [
"Reviewer Expertise New Media Studies",
"Developmental Communication are my strong areas of research."
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe results of the study should be more focused towards implications, which is missing. The conclusion gives positive and negative aspects of Facebook on COVID-19 and but doesn't give a strong conclusion.\n\nThe Researcher/s have used time frame analysis but not mentioned which type of approach they have adopted.\n\nThe researcher used 1st person in some places as 'I' and it should be changed as 3rd person eg: \"the researcher/ 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?\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": "6778",
"date": "16 Jun 2021",
"name": "Md. Sayeed Al-Zaman",
"role": "Author Response",
"response": "Many thanks to the reviewer for such valuable comments on this manuscript. The following changes have been made using Track Change according to the suggestions: Thanks for pointing out the apparent limitation regarding the result interpretation. However, a glimpse of the intellectual implication of the results has already been included at the end of the conclusion (please, see from “Apart from these limitations, this study has strengths in a few areas…” to “Finally, this research dealt with a larger dataset than the previous studies on the COVID-19 vaccine…”). Also, the last sentence would inform the readers that this is an exploratory study, and such studies might have limitations from different aspects (e.g., reaching some certain and concrete conclusions), but it can guide future studies in this area. From this perspective, the inability to forecast very concise practical and policy-related significance could be difficult for this study. A one-sentence clarification regarding the data analysis has now been added to the methodology. The use of “I” is now replaced with “we”, which is an ideal practice in the scholarly arena."
}
]
}
] | 1
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https://f1000research.com/articles/10-236
|
https://f1000research.com/articles/9-1219/v1
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09 Oct 20
|
{
"type": "Study Protocol",
"title": "XENOBREAST Trial: A prospective study of xenografts establishment from surgical specimens of patients with triple negative or luminal b breast cancer",
"authors": [
"Hugo Veyssière",
"Judith Passildas",
"Angeline Ginzac",
"Sejdi Lusho",
"Yannick Bidet",
"Ioana Molnar",
"Maureen Bernadach",
"Mathias Cavaille",
"Nina Radosevic-Robin",
"Xavier Durando",
"Judith Passildas",
"Angeline Ginzac",
"Sejdi Lusho",
"Yannick Bidet",
"Ioana Molnar",
"Maureen Bernadach",
"Mathias Cavaille",
"Nina Radosevic-Robin",
"Xavier Durando"
],
"abstract": "Introduction: Patient-derived xenografts (PDX) can be used to explore tumour pathophysiology and could be useful to better understand therapeutic response in breast cancer. PDX from mammary tumours are usually made from metastatic tumours. Thus, PDX from primitive mammary tumours or after neoadjuvant treatment are still rare. This study aims to assess the feasibility to establish xenografts from tumour samples of patients with triple negative or luminal B breast cancer in neoadjuvant, adjuvant or metastatic setting. Methods: XENOBREAST is a single-centre and prospective study. This feasibility pilot trial aims to produce xenografts from tumour samples of patients with triple negative or luminal B breast cancer. Patient enrolment is expected to take 3 years: 85 patients will be enrolled and followed for 28 months. Additional blood samples will be taken as part of the study. Surgical specimens from post-NAC surgery, primary surgery or surgical excision of the metastases will be collected to establish PDX. Histomolecular characteristics of the established PDX will be investigated and compared with the initial histomolecular profile of the collected tumours to ensure that they are well-established. Ethics and dissemination: XENOBREAST belongs to category 2 interventional research on the human person. This study has been approved by the Sud Méditerranée IV – Montpellier ethics committee. It is conducted notably in accordance with the Declaration of Helsinki and General Data Protection Regulation (GDPR). Study data and findings will be published in peer-reviewed medical journals. We also plan to present the study and all data at national congresses and conferences. Registration: ClinicalTrials.gov ID NCT04133077; registered on October 21, 2019.",
"keywords": [
"Patient-Derived Xenografts",
"Triple negative breast cancer",
"Luminal B breast cancer",
"Interventional research"
],
"content": "Introduction\n\nBreast cancer can be classified into different molecular subtypes according to gene expression: luminal A (Hormone Receptor positive (HR+)/human epidermal growth factor receptor 2 negative (HER2-), with high HR expression), luminal B (HR+/HER2- or HR+/HER2+, with low HR expression), HER2-enriched (amplification of ERBB2 gene, regardless of HR status) and triple-negative (HR-/HER2-). Luminal B and triple-negative tumours account respectively for approximately 20% and 10–15% of all breast cancers1–3. Although rarer than luminal A breast cancers, luminal B and triple-negative tumours are often high-grade tumours with a poorer prognosis1.\n\nThe establishment of patient derived xenografts (PDX) could be useful to discover new treatments and strategies needed in the fight against these subtypes of breast cancer. PDX are derived from tumour tissue in which the tumour architecture and the proportion of cancer and stromal cells are both maintained: advantages not found in cell lines. Therefore, PDX effectively model intra- and inter-tumoural heterogeneity4,5.\n\nThus, PDX are used to answer questions such as the contribution of tumour heterogeneity to therapeutic response, patterns of tumour progression during metastatic progression and mechanisms of treatment resistance6.\n\nMost of the available PDX, derived from breast cancer, were generated from metastatic tumours. In particular, it may allow the identification of eventual molecular therapeutic targets in metastatic setting.\n\nIt is also necessary to have PDX models from primary breast lesions that are resistant to neoadjuvant therapies. Recent prospective studies show that PDX can be obtained from neoadjuvant breast tumours and demonstrate the feasibility of tumour sequencing in these situations7,8. Breast cancer patients with residual disease after neoadjuvant chemotherapy (NAC) have an increased risk of recurrence. Similarly, high-grade breast tumours treated by primary surgery are very rare, poorly known, and aggressive.\n\nThe production of PDX from post-NAC residual breast tumours or from high-grade breast tumours will provide data on the molecular characteristics of these tumours with a high risk of recurrence.\n\nIn this study, we want to establish PDX from tumour samples of patients with triple-negative and luminal B breast cancers in neoadjuvant, adjuvant or metastatic settings. In addition, to verify whether or not the PDX obtained is consistent with the original tumour, we will study the tumour exomes of both the PDX and the original tumour. The study of the patients’ constitutional exome will serve as the basis for this comparison and is an essential element in the overall somatic analysis.\n\n\nMethods\n\nThis is a single-centre prospective trial designed to establish xenografts from surgical specimens of patients with triple negative or luminal B breast cancer in neoadjuvant, adjuvant or metastatic setting. Patient enrolment is expected to take 3 years: 85 patients will be enrolled and followed during 28 months.\n\nStudy design is presented in Figure 1. The management of patients in the study may vary depending on the setting: neo-adjuvant, adjuvant or metastatic. In all the settings and as a part of their medical follow-up, patients will go through a pre-operative biological assessment. For patients in metastatic setting, this assessment will be performed before surgical excision of the metastases. Blood samples will be used to perform sequencing of the patient's constitutional exome. At the end of the surgery, one sample of the surgical specimen will be taken to generate PDX and another one to sequence the patient's tumour exome.\n\nAdult women with triple negative or luminal B breast cancer in neoadjuvant, adjuvant or metastatic setting will be included. In all the settings, patients will go through a pre-operative biological assessment. Blood samples will be used to perform sequencing of the patient's constitutional exome. At the end of the surgery (post-NAC surgery, primary surgery or surgical excision of the metastases), a sample of the surgical specimen will be taken to generate patient-derived xenografts (PDX) and another one to sequence the patient's tumour exome.\n\nParticipants can withdraw at any time. Data obtained will be retained with consent, and any reasons given for withdrawal will be recorded.\n\nThe patient-derived tumour xenograft platform called XenTech will generate the PDX. All PDX will be established as approved by the ethical authorisation #16569: « Développement d’une collection de modèles de tumeurs humaines greffés sur souris (PDX) ». The different steps of the development of an established xenograft model are summarized in Figure 2. Overall, fresh surgical tissue will be cut into small fragments and grafted into the inter-scapular region or into the renal capsule of 6- to 13-week-old female immunodeficient or severe-combined immuno-deficiency (SCID) or non-obese diabetic SCID mice. Mice should weigh 18g at 6 months. At the onset of tumour growth, a latency period of 1 to 9 months is expected. The mouse generation with the patient derived graft will be called F0 and the following generations will be numbered F1, F2, and F3. When the tumour volume reaches the ethical limit (10% of the total weight of the mouse), the tumour is removed and fragmented as follows: a part is grafted to a new set of mice; a second part is fixed in formalin and embedded in paraffin for histological studies; a third part is frozen in liquid nitrogen for molecular studies; and a last part is frozen in a 10% DMSO solution to generate a viable tissue stock. These steps are repeated for the F1, F2 and F3 generation. A xenograft will be considered as well-established in the third generation (F3). When it is necessary, the animal will be sacrificed by cervical dislocation. For the duration of the study, mice will be housed, by a maximum of 6, in individually ventilated cages. They will be housed in a light-dark cycle with temperature and hygrometry control. The mice will have throughout the duration of the project a complete diet and drinking water.\n\nFresh surgical tissue will be grafted into the inter-scapular region or into the renal capsule of immunodeficient or severe-combined immuno-deficiency mice. When the tumour volume reaches the ethical limit, the tumour is removed and fragmented as follows: a part is grafted to a new set of mice; a second part is fixed in formalin and embedded in paraffin for histological studies; a third part is frozen in liquid nitrogen for molecular studies; and a last part is frozen in a 10% DMSO solution to generate a viable tissue stock. These steps are repeated for the F1, F2 and F3 generation. A xenograft will be considered as well-established in the third generation (F3).\n\nInclusion and exclusion criteria are presented in Table 1. Briefly, adult women (18 years or older) with triple-negative or luminal B breast cancer in neoadjuvant, adjuvant or metastatic setting will be included.\n\nEligible patients will be offered the opportunity to participate in the study by their oncologist or their surgeon. Patients who agree to participate in this study will provide written informed consents (clinical consent and genetic consent) for enrolment.\n\nThis feasibility study aims to obtain xenografts from tumours that are either rare or tumours that are resistant to treatment and therefore difficult to establish. We consider that a minimum of five successful grafts would meet this objective. Under these conditions, knowing the graft success rate specific to each histological type and the proportion of luminal B (2/3) and triple-negative breast cancers (1/3), we calculate the number of subjects required so that the lower bound of the 95% confidence interval (CI) of the success rate multiplied by the number of subjects is ≥5.\n\nTo obtain a xenograft, the average rate is 30% from triple-negative tumours and 10% from luminal B tumours. Taking these data into account, we will include 2/3 luminal B tumours and 1/3 triple negative tumours: the expected rate of successful xenografts will be approximately 17%. The number of patients needed to be included is therefore at least 65: lower bound of the CI-95% of 17% for 65 subjects = 8% or 5 patients (8%×65=5.2).\n\nSince for some patients the tumour will be of sufficient size for imaging, but of insufficient size in the operating room, we consider that this number should be increased by 30%, to a total number of 85 patients.\n\nThe primary objective of the XENOBREAST trial is to establish xenografts from tumour samples of patients with triple negative or luminal B breast cancer in neoadjuvant, adjuvant or metastatic setting. Furthermore, the study aims to investigate histomolecular characteristics of the established PDX and to compare these characteristics with the initial histomolecular profile of the collected tumours.\n\nData collected are the patient's age (month and year of birth), pathology, treatments received, response to treatments, date and nature of surgery (primary tumour, metastasis), data concerning exomes (constitutional and tumour), as well as histomolecular profiles of the initial tumour and of the different xenograft generations. To define these histomolecular profiles we will quantify the expression of the oestrogen, progesterone and androgen receptors by immunohistochemistry, the amplification status of the ERBB2 gene, and the fraction of tumour cells expressing Ki67. Finally, tumours will be classified into molecular classes according to the above-mentioned data: luminal A, luminal B, HER2-enriched or triple negative.\n\nData collected and transmitted to the sponsor of the study by the investigators will be pseudonymized. Study data will not contain any names or other personal identifiers such as addresses. Patients included in the trial will be identified by a code specific to this trial. The investigator will have access to the correspondence table between the patient's last name, first name, date of birth and the code assigned in the trial.\n\nPrimary analysis. The main outcome of this feasibility trial is the number of successful xenografts obtained, a xenograft being considered successful when it reaches the F3 generation and its molecular subtype defined by immunohistochemistry has remained identical to the original tumour. The percentage of tumours yielding a successful xenograft will also be calculated, along with a 95% confidence interval. The feasibility will be considered acceptable if at least five successful transplants are obtained.\n\nSecondary analysis. A diversity analysis of genomic data from the tumour exomes and the constitutional exome will be performed. Differential analyses using bioinformatics tools adapted to these data could be envisaged if the number of patients allows it. We will describe in detail the collected tumours (description of the population, histomolecular profile, anatomopathological data, etc.). Qualitative characteristics will be described using their number and frequency, and quantitative characteristics (age at diagnosis, tumour size, etc.) using standard distribution parameters: mean, median, standard deviation, extremes, normality.\n\nThe characteristics of the tumours will also be described according to whether or not a xenograft was successful. These characteristics will also be compared, if the sample sizes allow it, using Fisher’s exact test, and Welch's t-test or the non-parametric Mann-Whitney U-test if needed. All tests will be two-sided and the statistical significance threshold will be generally set at 0.05 except in case of differential analyses on the exome data where multiple testing corrections will be applied.\n\nThe XENOBREAST trial has been approved by an ethics committee (Sud Méditerranée IV – Montpellier) on April 2020 (Reference: 20 03 02 and ID-RCB number: 2020-A00398-31). It is conducted notably in accordance with the Declaration of Helsinki and General Data Protection Regulation (GDPR).\n\nStudy data and finding will be published in peer-reviewed medical journals. We plan to present the study and all data at national congresses and conferences.\n\nParticipant recruitment is expected to begin in October 2020 and to finish in October 2023. The approved protocol is version 02, 24/03/2020.\n\n\nConclusion\n\nThe XENOBREAST study a feasibility pilot trial that will allow us to estimate the success rate of xenografts and to estimate PDX drift by comparing the histomolecular profile of the PDX to that of the tumour. In perspective, the generation of PDX from rare and chemo-resistant tumours would allow for testing new treatments before their administration in vivo. In the long term, the establishment of PDX from primary mammary tumours or after neoadjuvant treatment would allow a better understanding of the therapeutic response. Moreover, it could be a great model to explore tumour evolution patterns during metastatic progression and to observe tumour resistance mechanisms in non-metastatic tumours.\n\n\nData availability\n\nNo data are associated with this article.",
"appendix": "Acknowledgements\n\nThe authors thank the patient-derived xenografts platform XenTech for their help in the study design and in the PDX xenografts establishment. The authors also thank the Laboratoire d’Oncogénétique of the Jean PERRIN centre of Clermont-Ferrand.\n\n\nReferences\n\nDent R, Trudeau M, Pritchard KI, et al.: Triple-negative breast cancer: clinical features and patterns of recurrence. Clin Cancer Res. 2007; 13(15 Pt 1): 4429–4434. PubMed Abstract | Publisher Full Text\n\nPrat A, Pineda E, Adamo B, et al.: Clinical implications of the intrinsic molecular subtypes of breast cancer. Breast. 2015; 24 Suppl 2: S26–35. PubMed Abstract | Publisher Full Text\n\nVoduc KD, Cheang MCU, Tyldesley S, et al.: Breast cancer subtypes and the risk of local and regional relapse J Clin Oncol. 2010; 28(10): 1684–1691. PubMed Abstract | Publisher Full Text\n\nVarešlija D, Cocchiglia S, Byrne C, et al.: Patient-Derived Xenografts of Breast Cancer. In: Martin F, Stein T, Howlin J (eds). Methods Mol Biol. Springer, New York, NY. 2017; 1501: 327–336. PubMed Abstract | Publisher Full Text\n\nDeRose YS, Wang G, Lin YC, et al.: Tumor grafts derived from women with breast cancer authentically reflect tumor pathology, growth, metastasis and disease outcomes. Nat Med. 2011; 17(11): 1514–1520. PubMed Abstract | Publisher Full Text | Free Full Text\n\nByrne AT, Alférez DG, Amant F, et al.: Interrogating open issues in cancer precision medicine with patient-derived xenografts. Nat Rev Cancer. 2017; 17(4): 254–268. PubMed Abstract | Publisher Full Text\n\nGoetz MP, Kalari KR, Suman VJ, et al.: Tumor Sequencing and Patient-Derived Xenografts in the Neoadjuvant Treatment of Breast Cancer. J Natl Cancer Inst. 2017; 109(7): djw306. PubMed Abstract | Publisher Full Text | Free Full Text\n\nYu J, Qin B, Moyer AM, et al.: Establishing and characterizing patient-derived xenografts using pre-chemotherapy percutaneous biopsy and post-chemotherapy surgical samples from a prospective neoadjuvant breast cancer study. Breast Cancer Res. 2017; 19(1): 130. PubMed Abstract | Publisher Full Text | Free Full Text"
}
|
[
{
"id": "76613",
"date": "26 Jan 2021",
"name": "Jessica Finlay-Schultz",
"expertise": [
"Reviewer Expertise My expertise is in the establishment and propagation of breast cancer PDX models",
"primarily from hormone receptor positive tumors. My area of research includes estrogen and progesterone receptor signaling",
"crosstalk",
"and transcriptional regulation in breast cancer models",
"including PDX and cell lines derived from primary tissue and PDX models."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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, Veyssière et al. outline a study protocol for generation of PDX models from patient tumors of the triple negative or luminal B molecular subtypes. The overall study metrics and patient enrollment numbers appear sound, though the methods are light on experimental details. The writing is clear and concise, though the phrase “primitive mammary tumours” should be replaced with “primary mammary tumours” in the Abstract. While I understand that the authors will be using a private company to generate these PDX models, some details of their generation should be included, and the group would benefit from reviewing additional established PDX generation protocols.\nKabos et al. (PMID 22821401)1 have established that supplementation with 17β-estradiol is useful for the establishment of ER+ PDX models. Is there a plan for hormone supplementation for the Luminal B portion of this study?\n\nIn addition, breast cancer PDX models are often placed into the #4 mammary fat pad of these animals. Is there a specific reason behind avoiding this placement in this study?\n\nWill there be the use of an extracellular matrix for implantation of the primary tumor? While ECM use tends to increase xenograft take rates, there have been historical links between some ECM producers and the propagation of LDEV (Lactate Dehydrogenase Elevating Virus) with tumor tissues.\n\nReview and citation of Dobrolecki et al (PMID 28025748)2 will help answer some major questions in the breast tumor PDX field, and this should be referenced in your study, as it is a comprehensive review of the majority of well-established breast tumor PDX banks.\n\nPlease include that the primary molecule that differs between Luminal A and Luminal B tumors is Ki67. While Luminal B tumors may often exhibit lower HR expression, it is not the main factor used to classify these tumors.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Yes\n\nAre sufficient details of the methods provided to allow replication by others? No\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable",
"responses": [
{
"c_id": "6350",
"date": "10 Mar 2021",
"name": "Hugo Veyssière",
"role": "Author Response",
"response": "Thank you for taking the time to review our manuscript. We appreciate your helpful comments. 1) Kabos et al. (PMID 22821401)1 have established that supplementation with 17β-estradiol is useful for the establishment of ER+ PDX models. Is there a plan for hormone supplementation for the Luminal B portion of this study? All the ER+ PDX models are established in mice receiving 17β-estradiol supplementation in the drinking water. A sentence has been added in our manuscript. 2) In addition, breast cancer PDX models are often placed into the #4 mammary fat pad of these animals. Is there a specific reason behind avoiding this placement in this study? For breast cancer PDXs, the placement in the interscapular region is a choice made by Xentech when it began generating breast cancer PDXs. This implant site allows easy access to a well vascularized region with tissue that in female mice is in continuity with the mammary gland. 3) Will there be the use of an extracellular matrix for implantation of the primary tumor? While ECM use tends to increase xenograft take rates, there have been historical links between some ECM producers and the propagation of LDEV (Lactate Dehydrogenase Elevating Virus) with tumor tissues. We do not foresee the use of any matrix during the first implantation, only tumor fragments will be implanted. 4) Review and citation of Dobrolecki et al (PMID 28025748)2 will help answer some major questions in the breast tumor PDX field, and this should be referenced in your study, as it is a comprehensive review of the majority of well-established breast tumor PDX banks. Dobrolecki et al. has been added to references. 5) Please include that the primary molecule that differs between Luminal A and Luminal B tumors is Ki67. While Luminal B tumors may often exhibit lower HR expression, it is not the main factor used to classify these tumors. Precisions have been added in the article."
}
]
}
] | 1
|
https://f1000research.com/articles/9-1219
|
https://f1000research.com/articles/9-1320/v1
|
12 Nov 20
|
{
"type": "Data Note",
"title": "Extracting novel antimicrobial emergence events from scientific literature and medical reports",
"authors": [
"Emma Mendelsohn",
"Noam Ross",
"Allison M. White",
"Karissa Whiting",
"Cale Basaraba",
"Brooke Watson Madubuonwu",
"Erica Johnson",
"Mushtaq Dualeh",
"Zach Matson",
"Sonia Dattaray",
"Nchedochukwu Ezeokoli",
"Melanie Kirshenbaum Lieberman",
"Jacob Kotcher",
"Samantha Maher",
"Carlos Zambrana-Torrelio",
"Peter Daszak",
"Noam Ross",
"Allison M. White",
"Karissa Whiting",
"Cale Basaraba",
"Brooke Watson Madubuonwu",
"Erica Johnson",
"Mushtaq Dualeh",
"Zach Matson",
"Sonia Dattaray",
"Nchedochukwu Ezeokoli",
"Melanie Kirshenbaum Lieberman",
"Jacob Kotcher",
"Samantha Maher",
"Carlos Zambrana-Torrelio"
],
"abstract": "Despite considerable global surveillance of antimicrobial resistance (AMR), data on the global emergence of new resistance genotypes in bacteria has not been systematically compiled. We conducted a study of English-language scientific literature (2006-2017) and disease surveillance reports (1994-2017) to identify global events of novel AMR emergence (first clinical reports of unique drug-bacteria resistance combinations). We screened 24,966 abstracts and reports, ultimately identifying 1,773 novel AMR emergence events from 294 articles. Events were reported in 66 countries, with most events in the United States (152), India (129), and China (128). The most common bacteria demonstrating new resistance were Klebsiella pneumoniae (352) and Escherichia coli (218). Resistance was most common against antibiotic drugs imipenem (89 events), ciprofloxacin (85) and ceftazidime (82). We provide an open-access database of emergence events with standardized fields for bacterial species, drugs, location, and date, and we discuss guidelines and caveats for data analysis. This database may be broadly useful for understanding rates and patterns of AMR evolution, identifying global drivers and correlates, and targeting surveillance and interventions.",
"keywords": [
"Antimicrobial resistance",
"global health",
"open-access data"
],
"content": "Introduction\n\nAntimicrobial resistance (AMR) is a global health crisis that has compromised the effective treatment and prevention of a multitude of infections. The rise in AMR has been associated with increased mortality, longer hospitalizations, complications with medical procedures such as surgery and chemotherapy, and higher healthcare costs1–3. Resistance to antibiotics is a global public health issue and a particular concern in low- and middle-income countries, where many high-burden diseases such as malaria, respiratory infections, and tuberculosis can no longer be treated by common antimicrobial drugs1,4. Combating AMR requires a multidimensional global response to optimize antimicrobial drug use, improve awareness, increase traceability and usage reporting, and promote research1,5–7.\n\nAMR surveillance by researchers, hospital networks, and state governments is key to characterizing and responding to the crisis. Current global-scale datasets primarily focus on the presence or prevalence of known resistance genotypes and phenotypes in bacterial populations. In 2014, the World Health Organization (WHO) published surveillance data obtained from 129 member states on nine bacterial pathogen-antibacterial drug combinations of public health importance, finding high rates of resistance reported across the globe3. The ResistanceMap database, maintained by the Center of Disease Dynamics, Economics & Policy, provides nationally-aggregated data from 46 countries on the prevalence of resistance in 12 bacterial species against 17 classes of antibiotics8.\n\nTo our knowledge, however, there is no publicly available dataset that specifically identifies the spatial and temporal patterns of the emergence of novel bacterial pathogen resistance to antibiotic drugs in humans. Such data are critical to understanding macroecological patterns and drivers of AMR emergence and identifying geographic and phenotypic targets for surveillance, research, and interventions. Further, this database may support on-going agreements and programs developed by intergovernmental organizations such as the United Nations, World Health Organization, Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services, Convention on Biological Diversity, and development agencies such as the World Bank, the Global Environment Facility, and other regional banks.\n\nWe conducted a systematic review to identify novel AMR emergence events reported in English-language scientific literature from 2006–2017 and disease surveillance reports from 1994–2017. We focused specifically on human clinical cases and included any reported resistance of a bacterium to an antimicrobial drug (i.e., we did not limit the search to a subset of bacteria or drugs). We screened 24,966 abstracts and reports, identifying 1,791 articles potentially reporting novel emergence events, and ultimately, 294 relevant studies reporting 1,773 total novel events. We present an open-access database of these events with cleaned and standardized fields for location of emergence, bacterial species, antimicrobial drug, emergence date, and data source. We provide usage notes on systematic biases and ambiguities in the data. In addition, we provide data on all screened and processed articles from which data were harvested.\n\n\nMethods\n\nDevelopment of the AMR emergence database was a multi-step process consisting of a systematic literature search, abstract and report screening, article review and coding, and data cleaning and standardization (Figure 1).\n\nWe drew from PubMed and Embase scientific literature databases and ProMED-mail to develop our database of events. PubMed and Embase collectively encompass a large fraction of English-language biomedical scientific literature, while ProMED-mail consists of clinical reports and news alerts that may not ultimately be published in the scientific press and have a faster reporting speed. We selected a recent ten-year period for scientific literature (2006–2017). ProMED-mail reports were drawn from a longer time span (1994–2017), as we found scientific articles published 2006–2017 frequently described events occurring many years before.\n\nWe searched for peer-reviewed manuscripts in PubMed and Embase published using the following terms:\n\n'antibiotic resistance'/exp OR ('antibiotic' AND ('resistant' OR 'resistance')) OR 'antimicrobial resistance'/exp OR ('antimicrobial' AND ('resistant' OR 'resistance')) AND (first OR novel OR new OR emerging OR emergent) AND (case OR patient) AND [humans]/lim AND [2006–2017]/py\n\nThis search, completed August 2018, yielded 23,770 results.\n\nBecause ProMED-mail searches use partial word stem-based matching, we used only the search terms ‘antibiotic resistance’ and 'antimicrobial resistance’, which yielded 1,196 results. A total of 24,966 articles were compiled for screening.\n\nWe used the following inclusion criteria to screen the results of our literature search: the article must have described at least one clinical case (a) of infectious disease in a patient (b) caused by a novel (c) resistance (d) to a particular antimicrobial drug or drug combination (e) in bacteria (f). In this definition:\n\na) A “clinical case” is an individual who presents with symptoms to a medical professional and is determined by a medical professional to have been infected with the bacterium in question. Antimicrobial resistance in an asymptomatic individual’s commensal bacteria (as determined by a screening study, a “challenge” study, or a laboratory trial) does not meet the requirements of a clinical case.\n\nb) The “patient” from which the bacterium of interest is identified must be human and may be of any age or gender. More than one patient can be included in an emergence event if all patients fell ill and were confirmed to be infected with a resistant bacterium at the same time, for example in the early stages of an outbreak.\n\nc) “Novel” indicates that resistance to a given antimicrobial treatment in the bacterial species in question has not previously been detected or described in the country in question. In this definition, new mechanisms of resistance of a given bacteria to a given antimicrobial combination do not count as novel resistance (e.g. a novel plasmid carrying beta-lactamase in a bacterial species with previously described beta-lactam resistance).\n\nd) “Resistance” is the ability of the bacteria in question to survive standard antibacterial treatment against it. Survival is measured by the bacteria’s ability to continue to cause disease in its host or to spread to others for longer than the standard period following treatment. Standard treatments are determined by the WHO and by the countries in which the articles in the systematic review take place.\n\ne) An “antimicrobial drug or drug combination” is a drug, drug class, or specific combination of drugs used to treat bacterial infections in humans. We focused exclusively on antibiotic resistance rather than resistance to other antimicrobials due to better data availability and based on the hypothesis that drivers for other antimicrobials might be different than for antibiotics.\n\nf) “Bacteria” is a species or strain of pathogen in the domain Bacteria. This study does not assess the impact of resistance in viruses, fungi, or other pathogen types.\n\nFor results from the PubMed and Embase search, we programmatically downloaded abstracts and metadata. Article abstracts were manually reviewed by a team of screeners (all authors, see Author contributions, below) to determine whether they likely contained a report of a novel emergence event, according to the above criteria. To ensure uniformity in abstract evaluation, all reviewers received training on the inclusion criteria and were required to achieve 90% agreement with a practice set of 100 previously-screened abstracts. Abstracts were screened separately by two individuals. Reviewers classified articles as “yes”, “maybe”, or “no” for inclusion. If both reviewers classified an article as “yes” or “maybe”, the article was downloaded as full-text for further review and to be coded for the database. The inter-scorer agreement rate was 82%. In cases when an article was marked as “no” by one of the reviewers, and “yes” by the other reviewer, a third reviewer was assigned to determine if the article should be included. 1,583 articles from PubMed and Embase passed review criteria and were downloaded for further review. The R package metagear9 was used to screen articles and manage screening data.\n\nFull texts were downloaded for ProMED-mail search results, as ProMED-mail reports do not have abstracts. The first lines of each report were screened separately by two reviewers. If either reviewer classified a text as “yes” or “maybe”, it was selected for further review and to be coded for the database. 208 ProMED-mail texts passed this screening, contributing to a total of 1,791 total articles from PubMed, Embase, and ProMED-mail selected for review. Further details on the reproducible screening workflow are available in the data repository (see Data availability)10.\n\nArticles from PubMed, Embase and ProMED-mail that passed screening were selected for full-text analysis, each by one reviewer, unless quality assurance checks required follow-up review (see Data cleaning). Reviewers read full-text articles to determine whether they fully met the case criteria, above, and to extract data by coding the text. Articles were excluded at this stage if it was found that they referred to or were duplicate reports of a previous emergence of the same drug-bacteria resistance within the country, if they reported on a non-bacterial pathogen, or if they did not identify the drug or bacterial species. A total of 294 articles were retained after full-text screening.\n\nArticles were coded for four required fields: study country, drug name, bacteria, and event date. Drugs were coded to the lowest available taxonomic rank (i.e., specific drug rather than drug class, when available). Similarly, bacteria were coded at the species level when available. Where articles did not include an emergence location or date, location was inferred from the location of study authors’ institutions (often hospitals), and publication year was used for event date.\n\nIn addition to the required fields, articles were coded for the following secondary fields when available: patient attributes (age, gender, country of residence, recent travel locations, symptoms, comorbidities, and outcome), bacterial strains and markers, drug minimum inhibitory concentration (MIC) values, and hospital location (city, state/province). Screeners used MAXQDA11 software for article coding. To our knowledge, open-source equivalents to MAXQDA are not available; however, open-source software such as qcoder12 could be used to replicate MAXQDA if combined with suitable PDF pre-processing steps.\n\nWe matched free-form values coded in article text to standardized values and ontologies. All locations were matched to Google Place names and geocoded. Country names were maintained according to article reporting and were not standardized to official country recognitions (e.g., United Nations member states). Drug names and bacteria were matched and standardized against the Medical Subject Headings (MeSH)13 and National Center for Biotechnology Information (NCBI) Organismal Classification14 ontologies, respectively, as provided by the Bioportal platform15. Where reported names did not exactly match ontologies or had ambiguous matches, we manually reviewed and corrected names to match the ontologies, in some cases requiring review of the original study to confirm accuracy. Dates were converted to ISO 8601 format. In cases when studies reported a range of dates, only the start date was included in the database. Other, optional fields (patient demographics, etc.) were not standardized in the current database release.\n\nData cleaning and standardization was performed in R version 3.6.116, using the tidyverse framework17 for data manipulation. Geocoding used the Google Geocoding API via the ggmap R package18. Study dates were standardized using the lubridate R package19.\n\nWe implemented quality assurance checks throughout the data processing pipeline. We checked for errors in the MAXQDA article coding by confirming that all values were labeled and that links between values were properly assigned (e.g., links between drug names and MIC values). We checked for any studies missing study location, study date, drug, or bacteria, and manually revisited these articles to confirm missing fields. We also investigated any study reporting more than one location and/or date to confirm whether the study described multiple emergence events.\n\nAn earlier version of this article can be found on medRxiv (doi: https://doi.org/10.1101/2020.08.13.20165852).\n\n\nResults/Discussion\n\nWe present a database of 1,773 records of first clinical reports of unique bacterial-drug AMR detections by country, ranging from 1998 to 2017, drawn from 294 peer-reviewed articles and reports. (While the ProMED-mail search extended to 1994, the first reported event that met our study criteria occurred in 1998.) This database, serving as a complement to existing databases that track resistance and spread, will allow researchers to target efforts for surveillance and interventions and to analyze factors that contribute to AMR emergence.\n\nDatabase materials are available at DOI 10.5281/zenodo.3964895 (see Data availability)10. Field names and descriptions from the database (filename `events-db.csv`) are detailed in Table 1. The file `data-processed/articles-db.csv` contains metadata about each article in the database, including citation information and full abstracts. This file can be joined with `events-db.csv` by the `study_id` field.\n\nIn addition to the database, we present intermediate data used in the process of database development. All abstracts and ProMED-mail reports that were screened are in the `screening` directory. Raw exports from coded full-text articles are in .xlsx form in `data-raw/coded-segments`. (The coded full text articles themselves are not available in the data repository.) A pre-filtered, pre-transformed database that contains all fields (primary and secondary) and events (including some non-emergent events) is in `data-processed/segments.csv`. Further details on directory structure and usage are provided in the data repository documentation.\n\nWe identified AMR emergence events in 66 countries, with the most reported events in the United States (152), India (129), and China (128) (Figure 2). Events were reported from 1998 through 2017, with the most events occurring in 2011 (Figure 3). See Database usage notes for discussion on the effects of reporting bias on the spatial and temporal coverage of the database.\n\nPoints represent locations. Countries are shaded by event count.\n\nWe found that Klebsiella pneumoniae and Escherichia coli were the most common bacteria in emergence events (Figure 4), supporting results from other databases that have found high rates of AMR prevalence for these species3,8. Of concern, our database indicates that both bacteria species had the greatest number of reports of novel resistance to imipenem and meropenem (Figure 4), which are carbapenem antibiotics often considered last resort treatment options for infections acquired in health care settings3,20,21. Also concerning were 23 cases of emergent resistance to colistin in 23 countries and 14 distinct bacteria, including K. pneumoniae and E. coli. Colistin is critically important for treating infections when no other options are available21,22.\n\nGlobal antimicrobial resistance (AMR) emergence events for top 12 drugs (a) and bacteria (b), and for their combinations (c). Counts within bars represent distinct number of resistant bacteria (a) and drugs (b).\n\n\nDatabase usage notes\n\nThe database is developed using only English-language scientific literature and medical reporting events. It therefore represents events reported in this limited subset rather than truly representative clinical cases and strongly reflects reporting effort and practices. It is likely that AMR emergence events are systematically missing from the database for countries that are not English speaking and/or have less health care monitoring and reporting capacity, including those with lower GDP. Therefore, it is imperative that any analysis of the data account for the effects of reporting bias10.\n\nTemporal patterns of AMR emergence events in the database reflect potentially incomplete coverage prior to 2006, as only ProMED-mail (not PubMed or Embase) was searched for this period. Further, the decrease in emergence events from 2011–2017 reflects lags between event occurrence and reporting.\n\nThere are several sources of ambiguity in the dataset due to imprecise reporting in literature (Table 2). While most studies reported the exact city or hospital of the emergence event (n = 200), others reported only state/province (n = 21) or study country (n = 73). Differences in geographic scales would need to be considered if using this dataset for spatial analysis. In addition, there are inconsistencies in studies’ reporting of drug and bacteria names. While most studies reported specific drug names (n = 87), others reported broad classes of drugs (n = 35). Study authors that reported classes of drugs may have administered multiple drugs to the patient(s), but because the specific drugs were not reported, we were only able to count the drug as part of a single event. Similarly, bacteria were primarily reported to the species level (n = 106), but some were reported only to the genus or family level (n = 5). In these cases, it is possible that the species was novel or not identifiable. Many studies that reported bacterial species also reported strains, and it is possible that there are differences in resistance by strain. However, due to inconsistent reporting, we have not standardized reported strains.\n\nFinally, the database presents first AMR emergence events by country. Emergence events may be due to either mutation events or transport from other geographies. Analyses examining determinants of first emergence at a country level should consider import as a possible mechanism. Some studies reported locations of residence and recent travel of patients, and where available we have included this information, which may support such analysis. Analyses only examining first global emergence events should remove records of all but the earliest dates of each unique bacterial-drug combination.\n\n\nData availability\n\nZenodo: Extracting novel antimicrobial emergence events from scientific literature and medical reports. https://doi.org/10.5281/zenodo.396489510.\n\nThis project contains the following underlying data:\n\n`events-db.csv` (AMR emergence events database)\n\n`data-processed/articles-db.csv` (Metadata about each article in the database, including citation information and full abstracts. This file can be joined with `events-db.csv` by the `study_id` field.)\n\n`screening/` directory (All abstracts and ProMED-mail reports that were screened for potential inclusion in the database)\n\n`data-raw/coded-segments` (raw exports from coded full-text articles)\n\n`data-processed/segments.csv` (A pre-filtered, pre-transformed database that contains all fields ad events)\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\nCode availability\n\nSource code available from: https://github.com/ecohealthalliance/amr-db\n\nArchived source code at time of publication: https://doi.org/10.5281/zenodo.396489510\n\nLicense: MIT",
"appendix": "References\n\nWorld Health Organization: Global action plan on antimicrobial resistance. 2015. Reference Source\n\nCosgrove SE: The relationship between antimicrobial resistance and patient outcomes: mortality, length of hospital stay, and health care costs. Clin Infect Dis. 2006; 42 Suppl 2: S82–89. PubMed Abstract | Publisher Full Text\n\nWorld Health Organization: Antimicrobial resistance: global report on surveillance 2014. 2014. Reference Source\n\nByarugaba DK: A view on antimicrobial resistance in developing countries and responsible risk factors. Int J Antimicrob Agents. 2004; 24: 105–110. PubMed Abstract | Publisher Full Text\n\nMorgan DJ, Okeke IN, Laxminarayan R, et al.: Non-prescription antimicrobial use worldwide: a systematic review. Lancet Infect Dis. 2011; 11(9): 692–701. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCollignon P: The importance of a One Health approach to preventing the development and spread of antibiotic resistance. Curr Top Microbiol Immunol. 2013; 366: 19–36. PubMed Abstract | Publisher Full Text\n\nInteragency Coordination Group on Antimicrobial Resistance: No Time to Wait: Securing the Future from Drug-Resistant Infections. 2019. Reference Source\n\nResistanceMap: Center for Disease Dynamics, Economics & Policy. 2017. Reference Source\n\nLaJeunesse MJ: Facilitating systematic reviews, data extraction and meta-analysis with the metagear package for R. Methods in Ecology and Evolution. 2016; 7: 323–330. Publisher Full Text\n\nKonno K, et al.: Ignoring non-English-language studies may bias ecological meta-analyses. Ecol Evol. 2020; 10(13): 6373–6384. PubMed Abstract | Publisher Full Text | Free Full Text\n\nVERBI Software, MAXQDA 2018. 2017. Reference Source\n\nDuckles B, Sholler D, Draper J, et al.: qcoder: Lightweight Qualitative Coding. R package version 0.1.0. 2020. Reference Source\n\nNational Library of Medicine: Medical Subject Headings. 2020. Reference Source\n\nNational Library of Medicine: National Center for Biotechnology Information NCBI) Organismal Classification. 2012. Reference Source\n\nWhetzel PL, et al.: BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Nucleic Acids Res. 2011; 39(Web Server issue): W541–545. PubMed Abstract | Publisher Full Text | Free Full Text\n\nR Core Team: R Foundation for Statistical Computing, Vienna, Austria. 2019. Reference Source\n\nWickham HAM, Bryan J, Chang W, et al.: Welcome to the tidyverse. J Open Source Softw. 2019; 4: 1686. Publisher Full Text\n\nKahle D, Wickham H: ggmap: Spatial Visualization with ggplot2. The R Journal. 2013; 5: 144–161. Reference Source\n\nGrolemund G, Wickham H: Dates and Times Made Easy with {lubridate}. J Stat Softw. 2011; 40: 1–25. Reference Source\n\nCodjoe FS, Donkor ES: Carbapenem Resistance: A Review. Med Sci (Basel). 2017; 6(1): 1. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWorld Health Organization: Citically Important Antimicrobials for Human Medicine. 2016. Reference Source\n\nPaterson DL, Harris PNA: Colistin resistance: a major breach in our last line of defence. Lancet Infect Dis. 2016; 16(2): 132–133. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "75116",
"date": "07 Dec 2020",
"name": "Barbara Tornimbene",
"expertise": [
"Reviewer Expertise Surveillance of antimicrobial resistance."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 represents an impressive effort to fill in the gaps in our understanding of emergence and spread of antimicrobial resistance in bacterial pathogens and provides results of a systematic review of English-language scientific literature and surveillance reports to identify the spatial and temporal patterns of the emerging AMR.\nIs the rationale for creating the dataset(s) clearly described?\nAlthough the author rationale for generating a publicly available source of temporal and spatial data for emerging resistance is clear, it could be better explained in the title and the introduction that the creating of a database is the objective of the study. The authors could also go into more detail on how the database will support on-going agreements and programs, particularly by defining on-going agreements. It would be also important to clarify what will be the role of the government of countries that appear in the dataset, in terms of acknowledging and validating published data.\nAre the protocols appropriate and is the work technically sound?\nMerging of results originating from peer-reviewed literature, which undergoes a strict scientific scrutiny, and data generated by ProMED-mail, which does not follow the same rigour, can be exposed, particularly when reporting novel events, to high level of inconsistency. No distinction between study designs screened in the literature was applied and results adjusted accordingly. The exclusion criteria could be expanded. For example, no assessment of the quality and reliability of these studies was done before including them in the final pool of articles.\nThe search strategy may benefit from inclusion of terms related to “drug resistance”, the term used in quite a number of reports instead of “antibiotic resistance” or “antimicrobial resistance”, especially when reporting infections caused by MDR or XDR or PDR pathogens.\nFinally, the authors mentioned in the “Database usage notes” section that the reported events represent a limited subset of information and strongly reflect reporting effort and practices. Other limitations are also listed in this section. This should probably be part of the discussion and better reflected on the abstract when listing the most common bacteria demonstrating new resistance. Moreover, an in-depth discussion on the impact of these bias should be added, particularly the effect that variability in reporting effort and practices, and quality and reliability of the studies, have on obtained results.\nAre sufficient details of methods and materials provided to allow replication by others?\nSome definitions in the inclusion criteria are not sufficiently clear.\nA clinical case is defined as “an individual who presents with symptoms to a medical professional and is determined by a medical professional to have been infected with the bacterium in question”. This sounds rather vague and we believe that the authors could be more consistent when defining “bacterium in question” or “bacterium of interest”. This is important to understand how cases were included.\nThe definition of novel resistance seems to be uncertain. It has to be clearly explained in the paper why only phenotypic test results were chosen and why only specific drug-bug combinations are considered and not emergence of certain types of multidrug resistance. The authors might also want to clarify why detection of a novel gene responsible, using example given in the paper, for production of a new type of beta-lactamase or, specifically, carbapenemase, is not considered novel and should be ignored. Such an event has to be detected and followed as it may have a significant impact on treatment options and other public health implications. Again, more details should be given on how the “novelty” was identified when reviewing the papers. For example, the paper coded 15378 in the database describes both phenotypic and molecular resistance testing results obtained from 12 clinical isolates from 12 patients with infections caused by Enterococcus faecium and 11 supposedly novel resistance events were included in the database. But the only event that was defined by the authors of the report as novel was the first detection in the country of the clonal complex 17 VREF. Resistance to e.g. clindamycin, gentamicin, and several other antibiotics in all reported isolates could hardly be considered novel or emerging.\n\nThe authors should better explain the added value of including the “drug_parent_name” variable with the names of the taxonomic parent of antimicrobial drug, standardized to the MeSH ontology. While it may be reflecting the methodology of the database creation, using a classification more suited to the field of study, such as e.g. the Anatomical Therapeutic Chemical (ATC) classification system may be considered.\nFinally, as the main goal of the database is to present temporal and spatial data, a better definition of temporal data should be given. In the paper the authors mention “event date”, “start date”, “study date” and “end date”. Aside the lack of consistency it should be clearer if the authors are considering the date the patients started experiencing symptoms, the date the patients was diagnosed, the date the diagnosis results were obtained, or the date the study started. This is key to allow replication by others.\nAre the datasets clearly presented in a useable and accessible format?\nThe detailed dataset is easily accessible and could be downloaded but is not sufficiently user-friendly. Using it would require certain data management skills from the end-users and therefore might limit their number.\n\nIs the rationale for creating the dataset(s) clearly described? Partly\n\nAre the protocols appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and materials provided to allow replication by others? Partly\n\nAre the datasets clearly presented in a useable and accessible format? Partly",
"responses": [
{
"c_id": "6782",
"date": "21 Jun 2021",
"name": "Emma Mendelsohn",
"role": "Author Response",
"response": "Thank you for your thorough review. We appreciate your attention to detail and thoughtful comments, which we address below. Is the rationale for creating the dataset(s) clearly described? Although the author rationale for generating a publicly available source of temporal and spatial data for emerging resistance is clear, it could be better explained in the title and the introduction that the creating of a database is the objective of the study. The authors could also go into more detail on how the database will support on-going agreements and programs, particularly by defining on-going agreements. It would be also important to clarify what will be the role of the government of countries that appear in the dataset, in terms of acknowledging and validating published data. We agree and have emphasized the database as a study objective by changing the title to “A global repository of novel antimicrobial emergence events”. We also added details on the rationale and main goals of the paper in the introduction, highlighting the relevance of this dataset in supporting on-going international agreements and programs. Are the protocols appropriate and is the work technically sound? Merging of results originating from peer-reviewed literature, which undergoes a strict scientific scrutiny, and data generated by ProMED-mail, which does not follow the same rigour, can be exposed, particularly when reporting novel events, to high level of inconsistency. No distinction between study designs screened in the literature was applied and results adjusted accordingly. The exclusion criteria could be expanded. For example, no assessment of the quality and reliability of these studies was done before including them in the final pool of articles. Thank you for the relevant comment. This is an important point to be considered by the end-users. We have clarified in the manuscript that we did not conduct an assessment of study/report quality and have described this as a source of uncertainty. In addition, we have added a field to the database indicating whether an event is from a published study or from ProMED-mail, and we include in the text summarized counts of events by source type. The search strategy may benefit from inclusion of terms related to “drug resistance”, the term used in quite a number of reports instead of “antibiotic resistance” or “antimicrobial resistance”, especially when reporting infections caused by MDR or XDR or PDR pathogens. We agree that “drug resistance” may yield relevant results. Unfortunately we are unable to redo the existing literature search at this time due to the high level of effort required and additional human resources not available at this time. We will include this term in future iterations of the project. Finally, the authors mentioned in the “Database usage notes” section that the reported events represent a limited subset of information and strongly reflect reporting effort and practices. Other limitations are also listed in this section. This should probably be part of the discussion and better reflected on the abstract when listing the most common bacteria demonstrating new resistance. Moreover, an in-depth discussion on the impact of these bias should be added, particularly the effect that variability in reporting effort and practices, and quality and reliability of the studies, have on obtained results. We thank the reviewer for the suggestion. Bias in reporting effort is indeed a recurrent problem in surveillance. We have added mention of reporting biases to the abstract and discussion section (referring readers to Database usage notes for further detail). We also now address quality of studies as a source of uncertainty in the database. Are sufficient details of methods and materials provided to allow replication by others? Some definitions in the inclusion criteria are not sufficiently clear. A clinical case is defined as “an individual who presents with symptoms to a medical professional and is determined by a medical professional to have been infected with the bacterium in question”. This sounds rather vague and we believe that the authors could be more consistent when defining “bacterium in question” or “bacterium of interest”. This is important to understand how cases were included. We adjusted the wording to clarify that bacteria is any species of pathogen in the domain Bacteria, and have replaced the term “bacterium in question” with “bacterium species reported”. Due to inconsistencies in reporting, we were unable to consistently identify pathogens by strain. However, this data is available as an unstandardized field in the database and we added . The definition of novel resistance seems to be uncertain. It has to be clearly explained in the paper why only phenotypic test results were chosen and why only specific drug-bug combinations are considered and not emergence of certain types of multidrug resistance. The authors might also want to clarify why detection of a novel gene responsible, using example given in the paper, for production of a new type of beta-lactamase or, specifically, carbapenemase, is not considered novel and should be ignored. Such an event has to be detected and followed as it may have a significant impact on treatment options and other public health implications. Again, more details should be given on how the “novelty” was identified when reviewing the papers. For example, the paper coded 15378 in the database describes both phenotypic and molecular resistance testing results obtained from 12 clinical isolates from 12 patients with infections caused by Enterococcus faecium and 11 supposedly novel resistance events were included in the database. But the only event that was defined by the authors of the report as novel was the first detection in the country of the clonal complex 17 VREF. Resistance to e.g. clindamycin, gentamicin, and several other antibiotics in all reported isolates could hardly be considered novel or emerging. We agree this is a source of uncertainty in the database. In response to your comment, we have revisited the drug name standardization and disaggregated all drug combinations, as we had not been consistent in identifying combinations. We are now treating all drugs as being separately administered. Unfortunately, due to inconsistencies in reporting, we are not able to effectively characterize which drugs were administered independently and which were administered as part of a complex. We address this uncertainty in the Database usage notes. The authors should better explain the added value of including the “drug_parent_name” variable with the names of the taxonomic parent of antimicrobial drug, standardized to the MeSH ontology. While it may be reflecting the methodology of the database creation, using a classification more suited to the field of study, such as e.g. the Anatomical Therapeutic Chemical (ATC) classification system may be considered. Based on your comments we explored standardizing drug names to ATC. We found that results were very similar to MeSH (i.e., counts changed only slightly) . We discuss this in the manuscript and have added an alternate version of the database with ATC standardization to the project repository. Finally, as the main goal of the database is to present temporal and spatial data, a better definition of temporal data should be given. In the paper the authors mention “event date”, “start date”, “study date” and “end date”. Aside the lack of consistency it should be clearer if the authors are considering the date the patients started experiencing symptoms, the date the patients was diagnosed, the date the diagnosis results were obtained, or the date the study started. This is key to allow replication by others. We switched to consistent usage of “start date” and clarified that it refers to the date the patient presented to the hospital or clinic. Are the datasets clearly presented in a useable and accessible format? The detailed dataset is easily accessible and could be downloaded but is not sufficiently user-friendly. Using it would require certain data management skills from the end-users and therefore might limit their number. We added a sentence to clarify that the database is available for download as a single csv file (`events-db.csv`)"
}
]
},
{
"id": "78874",
"date": "15 Feb 2021",
"name": "Ellen Stobberingh",
"expertise": [
"Reviewer Expertise Antimicrobial resistance prevalence and spread",
"Bacteriology."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 analysed the prevalence of novel AMR in humans in the country. Several questions need to be clarified: - Inclusion criteria:\n\nAMR in asymptomatic commensals were not included as these do not meet the inclusion criteria of clinical cases. However, resistance in commensals is frequently the precursor of resistance in clincal isolates. Excluding the commensals might contribute to lower prevalence and later report of resistance.\n\nFocus on humans only did not address the One health approach which is especially relevant in AMR because of the spread from animals to humans. This should be added in the discussion.\n\nNovel: was defined as novel for that country. But the resistance might be described already in other countries. Transfer from these countries for instance via travel might contribute to spread of these AMR to other countries and is not a novel resistance. Pick up of AMR resistance during travel starts mostly as a commensal and later on possible as infection. Please comment.\n\nResistance: defined as to survive AMR treatment, i.e. the bacteria is able to continue to cause disease in the host or to spread to others for a longer than the standard period as determined by the WHO or the national guidelines. What to do in case of discrepancy between these two?\n\nInterscore 82% in case of discrepancy the decision of a third reviewer was decisive?\n\nWhat is the possible explanation for the highest prevalence in 2011?\n\nResistance to carbapenems as last resort, colistin when no other options are available. This suggests a discrepancy, please rephrase.\n\nIs the rationale for creating the dataset(s) clearly described? Partly\n\nAre the protocols appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and materials provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a useable and accessible format? Yes",
"responses": [
{
"c_id": "6783",
"date": "21 Jun 2021",
"name": "Emma Mendelsohn",
"role": "Author Response",
"response": "Thank you for your thorough review and comments (especially appreciate your thoughts on the One Health context and potential spread mechanisms). We address your comments below. AMR in asymptomatic commensals were not included as these do not meet the inclusion criteria of clinical cases. However, resistance in commensals is frequently the precursor of resistance in clincal isolates. Excluding the commensals might contribute to lower prevalence and later report of resistance. We agree that asymptomatic commensals are important to identifying resistance before clinical emergence. However, we did not include commensals in the database as we found there is high variability in study design among these studies (e.g., drugs tested). Clinical reports, while still subject to variability and bias, tend to be more consistent in design (reporting only on resistances observed with illness). We address this concern in the Abstract and report screening section of the manuscript. Focus on humans only did not address the One health approach which is especially relevant in AMR because of the spread from animals to humans. This should be added in the discussion. This is a good point and we have added text about potential risk factors (including livestock) for emergence and the relevance to One Health in the discussion section. Novel: was defined as novel for that country. But the resistance might be described already in other countries. Transfer from these countries for instance via travel might contribute to spread of these AMR to other countries and is not a novel resistance. Pick up of AMR resistance during travel starts mostly as a commensal and later on possible as infection. Please comment. We agree and note that emergence events within a country may be due to mutation or transport from other geographies. For first global emergence events, users of the database should filter to the first occurrence of each bacteria-drug combination. We have added discussion about travel and migration being potential risk factors for emergence in countries. Resistance: defined as to survive AMR treatment, i.e. the bacteria is able to continue to cause disease in the host or to spread to others for a longer than the standard period as determined by the WHO or the national guidelines. What to do in case of discrepancy between these two? As most authors did not report which guidelines they used, we deferred to the authors selection of protocols and did not evaluate any potential discrepancies. We have added text to clarify this. Interscore 82% in case of discrepancy the decision of a third reviewer was decisive? Yes; we have rephrased to clarify this. What is the possible explanation for the highest prevalence in 2011? We have rephrased the text in Data usage notes to clarify that the peak in 2011 is likely an effect of reporting lag for more recent events. Resistance to carbapenems as last resort, colistin when no other options are available. This suggests a discrepancy, please rephrase. Good catch. We have rephrased."
}
]
}
] | 1
|
https://f1000research.com/articles/9-1320
|
https://f1000research.com/articles/9-601/v1
|
12 Jun 20
|
{
"type": "Software Tool Article",
"title": "Interactive exploratory data analysis of Integrative Human Microbiome Project data using Metaviz",
"authors": [
"Justin Wagner",
"Jayaram Kancherla",
"Domenick Braccia",
"James Matsumara",
"Victor Felix",
"Jonathan Crabtree",
"Anup Mahurkar",
"Héctor Corrada Bravo",
"Justin Wagner",
"Jayaram Kancherla",
"Domenick Braccia",
"James Matsumara",
"Victor Felix",
"Jonathan Crabtree",
"Anup Mahurkar"
],
"abstract": "The rich data produced by the second phase of the Human Microbiome Project (iHMP) offers a unique opportunity to test hypotheses that interactions between microbial communities and a human host might impact an individual’s health or disease status. In this work we describe infrastructure that integrates Metaviz, an interactive microbiome data analysis and visualization tool, with the iHMP Data Coordination Center web portal and the HMP2Data R/Bioconductor package. We describe integrative statistical and visual analyses of two datasets from iHMP using Metaviz along with the metagenomeSeq R/Bioconductor package for statistical analysis of differential abundance analysis. These use cases demonstrate the utility of a combined approach to access and analyze data from this resource.",
"keywords": [
"metagenomics",
"visualization",
"R/Bioconductor",
"Intergrative Human Microbiome Project"
],
"content": "Introduction\n\nMetagenomics allows researchers to perform a microbial community census and investigate associations between host phenotype and community status. Metagenomics has been used successfully to track pathogen spread1 and identify intervention strategies in childhood malnutrition2. Integrative analysis of samples using multiple sequencing technologies allows for comparison at various levels of granularity. The second phase of the Human Microbiome Project (iHMP) offers a unique opportunity to test hypotheses of interactions between the microbial community and the human host. To examine the iHMP data resource, we use Metaviz3, an interactive microbiome exploratory data analysis and visualization tool, and metagenomeSeq4, an R/Bioconductor package for statistical analysis of differential abundance analysis, for combined visual and statistical analysis.\n\nThe second phase of the HMP, also called the Integrative Human Microbiome Project (iHMP), consisted of focused studies of three diseases – Inflammatory Bowel Disease (IBD), Type II Diabetes (T2D), and Multi-Omic Microbiome Study: Pregnancy Initiative (MOMS-PI)5. The overall goal of the project was to identify associations between human microbiome community census data and the three diseases. Each of the studies were structured for the specific disease and consisted of separate cohorts.\n\nMetaviz6 is a web-based interactive visualization tool for microbiome data analysis. The architecture consists of a JavaScript front-end suite of charts (based on D3.js and Canvas) and a navigation component that lets users select portions of taxonomic hierarchies to visualize and analyze. Metaviz supports two backend data stores – a graph database and the metavizr R/Bioconductor package. Metaviz is tightly integrated with the metagenomeSeq statistical testing package so differential abundance testing results can be viewed directly in a Metaviz session. We host an instance of Metaviz that we call the UMD Metagenome Browser (http://metaviz.cbcb.umd.edu).\n\nVisualization tools for large-scale sequencing consortium projects provide a mechanism to explore and interact with data from multiple studies. These applications help users analyze individual datasets and examine trends across the entire project. MAGI is a web-application that enables a user to examine data from TCGA data7. The Earth Microbiome Project provides an interactive visualization web-application to analyze its data8. EMPeror offers interactive 3D visualizations of PCA plots to show distances between microbiome samples9. QIIME packages a number of tools for static plotting of Principal Coordinate Analysis and stacked bar plots10. MetaPhlAn2 uses a visualization package called GraphPhlan to produce phylogenetic trees and other plots11. The HMP2Data R/Bioconductor provides processed 16S sequencing data from the iHMP project in Bioconductor data structures12. We implemented Metaviz using design patterns from Epiviz13, an interactive epigenetics visualization tool, that visualizes data from a variety of epigenetic sequencing projects. We show how we leverage the microbiome measurement-based design of Metaviz to implement interactive exploration and hypothesis-testing of the iHMP resource.\n\n\nImplementation\n\nThe HMP Data Access and Coordination Center maintains a data repository and web portal (https://ihmpdcc.org). From this web portal, users can browse metadata for datasets, raw sequencing files, and processed files including taxonomic community profile abundance matrices. We implemented several mechanisms to interact with the HMP data resources through Metaviz6.\n\nWe loaded the 16S community profile abundance matrices for the samples from the IBD, T2D, and MOMS-PI studies as provided by the HMP2Data Bioconductor package12 into the UMD Metagenome Browser. A user can select each dataset from the application start screen. Figure 1 details the number of samples, with metadata to the extent available as of May 2020 from the HMP2Data package, from each project currently available in the UMD Metagenome Browser.\n\nTop: iHMP data accessible through the UMD Metagenome Browser. Middle (A, B): Single sample link from data portal to UMD Metagenome Browser. Bottom (C, D): Multiple samples manifest file upload and selection to UMD Metagenome Browser. We provide several mechanisms to access the HMP dataset from Metaviz. First, we loaded the three datasets (IBD, T2D, and MOMS-PI) into the hosted instance of Metaviz directly. A user can choose any of these datasets from the data selections screen then samples can be chosen within each dataset. We also link to the HMP Data Portal for single samples as shown in the Middle panel (A, B). Finally, the HMP Data Portal provides a “cart” functionality where a user can select multiple samples and download a manifest listing those files (C). A user can upload a manifest file containing selections from the 16S community abundance profiles from the same dataset (IBD, T2D, or MOMS-PI) to the UMD Metagenome Browser and a new Metaviz workspace is created with those files (D).\n\nWhen browsing the samples available from the HMP Data Portal, a user can view an individual abundance matrix in Metaviz using the Metaviz tool link from the file description page. When the user clicks the link, a redirect occurs to the UMD Metagenome Browser with a new workspace containing a FacetZoom navigation utility and a heatmap for that sample. Figure 1A shows the direct link functionality for samples in the IBD dataset and resulting workspace in Metaviz (Figure 1B).\n\nIn the HMP data portal, a user can select files with a shopping cart utility and download the selections as a manifest file. In the UMD Metagenome Browser, the user can upload the manifest file to create a Metaviz workspace on the fly for those samples. Currently, only files from the same project can be viewed in one workspace. Resolving taxonomic hierarchies across datasets in Metaviz is future work that could use a utility such as the metagenomeFeatures R/Bioconductor package14. Figure 1C shows the manifest file workflow for samples from the IBD dataset and resulting workspace in Metaviz (Figure 1D).\n\n\nOperation\n\nThe HMP Data Portal and Metaviz are web applications that can run in any modern browser. We recommend using Firefox (version 65 or later) or Chrome (version 65 or later) for best performance. Metavizr is a Bioconductor package and general guidelines from Bioconductor for requirements and installation should be followed (https://bioconductor.org/install/).\n\n\nUse cases\n\nIn the IBD cohort of the iHMP dataset, investigators sequenced a subset of samples using whole metagenome and 16S sequencing. We developed functions in metavizr to compare 16S and whole metagenome data for individual samples. Using the taxonomic profiles of the IBD samples, we matched the taxonomic features discovered with both sequencing methods. With this subset of features, we generated a single taxonomic hierarchy then loaded the 16S and whole metagenome abundance measurements into a metavizr object. Figure 2 shows an example analysis with stacked plots and scatter plots that link to a single FacetZoom to compare the degree of consistency of the data across sequencing methods.\n\nWe identified taxa present in the taxonomic hierarchy for each method and created a merged dataset. A FacetZoom (bottom) shows the common taxonomic features, two Stacked Plots (middle) show the proportion of all features aggregated to the Order level, and a set of scatter plots (top) for samples with WGS abundance on the X-axis and 16S abundance on the Y-axis. For WGS, the relative proportion output from MetaPhlan for taxa at the order level were transformed to counts per 1000 reads. The scatter plots show the variability in taxonomic community census estimates between sequencing methods. A static similar stacked plot visualization is shown in the main HMP consortium manuscript at the genus and species level across samples for comparison15. Metaviz allows users to make specific selections of the FacetZoom to compare taxa at various levels. The scatter plot also allows comparison at single sample resolution. Code to create this Metaviz session is available at the following gist: https://gist.github.com/jkanche/9216d465d18ab106be7a43f5340eb38a.\n\nThe IBD study consisted of two phases: a pilot, which we refer to in this work as the IBD Stool Pilot, and a larger phase that we call IBD iHMP. We use the taxonomic profiles for each phase available from the HMP2Data package and use the same taxonomic classification identifiers in the package. To upload project data on to the UMD Metagenome Browser, we extracted 16S count table and taxonomic annotation using the otu_table() and tax_table() methods of HMP2Data package. We then use metagenomeSeq and metavizr to import the count data along with taxonomy and sample metadata into a neo4j graph database16 using the metavizr neo4j import functionality. We used Metaviz6 for exploratory analysis and metagenomeSeq for confirmatory statistical testing. We examined the IBD Stool Pilot and IBD iHMP dataset separately.\n\nThe IBD Stool Pilot dataset contains 16S and whole metagenome sequencing results of stool samples from 41 Crohn’s disease (CD) subjects and 10 ulcerative colitis (UC) subjects. We focused our analysis on 16S sequencing and used Metaviz to visually identify taxa that showed a difference in abundance between CD and UC subjects. Figure 3 shows a typical visualization.\n\nA Metaviz workspace with a FacetZoom taxonomic hierarchy, heatmap, and boxplot for the specific feature in this instance s__:369227. This identifier was from the community abundance profiles available from the HMP2Data package. We identified taxonomic features at each level of the hierarchy using this integrated view and the results for features with a potential differential abundance are listed in Supplementary Table 1. The workspace is available at: http://metaviz.cbcb.umd.edu/?ws=oLq2Fr9AwVc.\n\nWe also used metagenomeSeq to test the differential abundance of features aggregated to each level of the taxonomy using the fitFeatureModel method that is based on a zero-inflated log-normal linear model. As shown in Table 1, two species had an absolute log fold-change greater than 1 and adjusted (Benjamini-Hochberg) p-value less than 0.1. Visually inspecting the IBD Stool Pilot data by aggregating counts to each level of the taxonomy we found the following features appearing differentially abundant: c__Betaproteobacteria, o__Burkholderiales, f__Ruminococcaceae, g__Lachnospira, g__[Ruminococcus], g__Faecalibacterium, s__:589277, s__:333166, s__:564806, s__:369227, s__:358104, s__:369486, s__gnavus:360015, s__prausnitzii:851865. Comparing these results and the metagenomeSeq differential abundance testing results in Table 1 shows that the taxonomic feature s__:369227 (member of the Lachnospiraceae family which are strictly anaerobic17) was identified using both methods. Members of Lachnospiraceae are abundant in human intestinal tracts and have been linked specifically to production of butyric acid17. Also, colonization with a specific strain of Lachnospiraceae in obese mice has been linked to development of hyperglycemia18. The second taxon, s__:363232, is a member of the genus Dorea which has recently been shown to be associated with diarrhea predominant irritable bowel syndrome19.\n\nWe used the fitFeatureModel of metagenomeSeq and aggregated counts to each level of the taxonomic hierarchy. Our analysis identified s__:369227 under family Lachnospiracea and s__:363232 under genus Dorea as differentially abundant between samples from subjects diagnosed with Ulcerative Colitis and Crohn’s Disease.\n\nThe IBD iHMP dataset consists of samples from subjects with CD, UC, and those without IBD (nonIBD). For these samples, we analyzed the 16S sequencing data of an ileum biopsy from the first visit for each subject, which yielded 72 samples with 32 from CD, 18 from CD, and 22 from nonIBD. We used metagenomeSeq to compute an F-statistic to determine if any taxonomic feature is associated with at least one group using the fitZig method (based on a zero-inflated Normal linear model on log-transformed counts appropriate for multi-category experiment designs). Figure 4 shows an example using Metaviz to visualize abundance profiles for phylum Fusobacteria, which was found to be differentially abundant across the three groups. Differential abundance of members of this phylum has previously been reported in studies of IBD20. Analysis code and results are available as Extended data21.\n\nUsing statistical analysis we identified taxonomic features that showed a difference in abundance between the three subject diagnosis categories: UC, CD, or nonIBD in the Fusobacteria phylum. This Metaviz workspace is available at: http://metaviz.cbcb.umd.edu/?ws=wHsHT56U8Ru.\n\n\nConclusion\n\nIn this work we presented software infrastructure linking Metaviz to the iHMP data resources6. We detailed the 16S taxonomic community profile data from iHMP available in the UMD Metagenome Browser. We then described linking the UMD Metagenome Browser to the iHMP Data Portal for single files and the manifest file utility for multiple file selections. We also performed visual exploratory and confirmatory differential abundance analysis of data from the IBD study. We first visualize 16S and whole metagenome sequencing abundance measurements for the same samples in metavizr. Then we use Metaviz and metagenomeSeq to analyze two datasets, IBD Stool Pilot and iHMP IBD, to examine taxonomic feature abundances in samples from UC, CD, and those without IBD. These illustrative analyses demonstrate the utility of Metaviz for integrative analysis with the HMP data resources. Visual inspection of taxonomic features coupled with statistical testing provides an effective mechanism to explore and test associations between bacterial communities and their human hosts.\n\n\nData availability\n\nThe 16S abundance matrices for IBD, T2D and the MOMS-PI studies were downloaded from the HMP2Data Bioconductor package. These datasets are then loaded into the neo4j graph database using import methods available in the metavizr22 Bioconductor package. These import scripts are available at https://gist.github.com/jkanche/c57d8220a33b41e21c4f6769a7aef7e4.\n\nFigshare: Differential Abundance Analysis - IBD (Figure 4). https://doi.org/10.6084/m9.figshare.12404222.v221.\n\nThis file contains differential abundance analysis code and results.\n\nExtended data are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nSoftware availability\n\nMetaviz is available at: http://metaviz.cbcb.umd.edu.\n\nSource code available from: https://github.com/epiviz/Metaviz.\n\nArchived source code at time of publication: http://doi.org/10.5281/zenodo.38718696.\n\nLicense: Artistic License version 2.0.",
"appendix": "References\n\nMiller RR, Montoya V, Gardy JL, et al.: Metagenomics for pathogen detection in public health. Genome Med. 2013; 5(9): 81. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBlanton LV, Charbonneau MR, Salih T, et al.: Gut bacteria that prevent growth impairments transmitted by microbiota from malnourished children. Science. 2016; 351(6275). PubMed Abstract | Publisher Full Text | Free Full Text\n\nWagner J, Chelaru F, Kancherla J, et al.: Metaviz: interactive statistical and visual analysis of metagenomic data. Nucleic Acids Res. 2018; 46(6): 2777–2787. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPaulson JN, Colin Stine O, Bravo HC, et al.: Differential abundance analysis for microbial marker-gene surveys. Nat Methods. 2013; 10(12): 1200–1202. PubMed Abstract | Publisher Full Text | Free Full Text\n\nIntegrative HMP (iHMP) Research Network Consortium: The integrative human microbiome project: Dynamic analysis of microbiome-host omics profiles during periods of human health and disease corresponding author. Cell Host Microbe. 2014; 16: 276–289. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKancherla J, Chelaru F, Hcorrada J, et al.: epiviz/Metaviz: release for submission (Version 0.1.1). Zenodo. 2020. http://www.doi.org/10.5281/zenodo.3871869\n\nLeiserson MDM, Gramazio CC, Hu J, et al.: MAGI: Visualization and collaborative annotation of genomic aberrations. Nat Methods. 2015; 12: 483–484. PubMed Abstract | Publisher Full Text\n\nThompson LR, Sanders JG, McDonald D, et al.: A communal catalogue reveals Earth’s multiscale microbial diversity. Nature. 2017; 551(7681): 457–463. PubMed Abstract | Publisher Full Text | Free Full Text\n\nVázquez-Baeza Y, Pirrung M, Gonzalez A, et al.: EMPeror: a tool for visualizing high-throughput microbial community data. Gigascience. 2013; 2(1): 16. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCaporaso JG, Kuczynski J, Stombaugh J, et al.: QIIME allows analysis of high-throughput community sequencing data. Nat Methods. 2010; 7(5): 335–336. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTruong DT, Franzosa EA, Tickle TL, et al.: MetaPhlAn2 for enhanced metagenomic taxonomic profiling. Nat Methods. 2015; 12(10): 902–903. PubMed Abstract | Publisher Full Text\n\nStansfield J, Dozmorov D: HMP2Data: 16s rRNA sequencing data from the Human Microbiome Project 2. 2019. Publisher Full Text\n\nChelaru F, Smith L, Goldstein N, et al.: Epiviz: Interactive visual analytics for functional genomics data. Nat Methods. 2014; 11(9): 938–40. PubMed Abstract | Publisher Full Text | Free Full Text\n\nOlson ND, Shah N, Kancherla J, et al.: metagenomeFeatures: An R package for working with 16S rRNA reference databases and marker-gene survey feature data. bioRxiv. 2018. Publisher Full Text\n\nHuman Microbiome Project Consortium: Structure, function and diversity of the healthy human microbiome. Nature. 2012; 486(7402): 207–14. PubMed Abstract | Publisher Full Text | Free Full Text\n\nThe Neo4j Graph Database. Reference Source\n\nMeehan CJ, Beiko RG: A phylogenomic view of ecological specialization in the lachnospiraceae, a family of digestive tract-associated bacteria. Genome Biol Evol. 2014; 6(3): 703–713. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKameyama K, Itoh K: Intestinal Colonization by a Lachnospiraceae Bacterium Contributes to the Development of Diabetes in Obese Mice. Microbes Environ. 2014; 29(4): 427–430. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMaharshak N, Ringel Y, Katibian D, et al.: Fecal and Mucosa-Associated Intestinal Microbiota in Patients with Diarrhea-Predominant Irritable Bowel Syndrome. Dig Dis Sci. 2018; 63(7): 1890–1899. PubMed Abstract | Publisher Full Text\n\nStrauss J, Kaplan GG, Beck PL, et al.: Invasive potential of gut mucosa-derived fusobacterium nucleatum positively correlates with IBD status of the host. Inflamm Bowel Dis. 2011; 17(9): 1971–1978. PubMed Abstract | Publisher Full Text\n\nBravo HC: Differential Abundance Analysis - IBD (Figure 4). figshare. Online resource. 2020. http://www.doi.org/10.6084/m9.figshare.12404222.v2\n\nBravo HC, Chelaru F, Kancherla J, et al.: metavizr: R Interface to the metaviz web app for interactive metagenomics data analysis and visualization. Publisher Full Text"
}
|
[
{
"id": "64704",
"date": "06 Jul 2020",
"name": "Ekaterina Smirnova",
"expertise": [
"Reviewer Expertise Biostatistics (working on Human Microbiome Project data)"
],
"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\nManuscript “Interactive exploratory data analysis of Integrative Human Microbiome Project data using Metaviz” by Wagner et al. provides a novel interactive tool for visualization of interactive Human Microbiome Project (iHMP) Data. This tool encompasses both the HMP Data coordination center (DAC) portal as well as the Bioconductor HMP2Data package. Given the size and complexity of HMP data, this visualization tool allows users to explore major data summaries and patterns. As such, this work is very timely and is highly recommended for publication.\n\nMajor comments:\nHow does the tool handle HMP DAC and HMP2Data package data updates? There is discussion that user can upload additional data manifest from HMP DAC portal, but what if the data already available thought Metaviz tool is updated on the DAC or Bioconductor?\n\nIs there an option to download data summaries? Such as demographics table, number of samples by body site, etc.\n\nMOMS-PI and T2D studies have protected meta data available through dbGap. If users apply for dbGap and get access, id there an option to merge meta data by sample ids and visualize using this tool?\n\nIt would be helpful to provide instructions how to create diversity boxplots by disease status (as in Figure 3). I tried creating these but could not produce them on the same plot.\n\nI recommend making alpha diversity plots by disease status a default plot when the data is selected using visualization tool.\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": "6595",
"date": "21 Jun 2021",
"name": "Hector Corrada Bravo",
"role": "Author Response",
"response": "Reviewer Comment: How does the tool handle HMP DAC and HMP2Data package data updates? There is discussion that user can upload additional data manifest from HMP DAC portal, but what if the data already available thought Metaviz tool is updated on the DAC or Bioconductor? Author Response: We updated the manuscript with the following: “As a community resource, we plan to update the Metaviz database within a month of Bioconductor releases of HMP2Data. We maintain links to the HMP Data Portal through the update of HMP2Data package URLs and provide default workspaces for the HMP2 datasets as well as those in HMP16SData R/Bioconductor package (https://epiviz.github.io/metaviz-workspaces/)” Reviewer Comment: Is there an option to download data summaries? Such as demographics table, number of samples by body site, etc. Author Response: We updated the manuscript with the following: “For generating data summaries, we recommend using the HMP2Data package with appropriate R libraries to summarize sample information and the interactive HMP Data Portal for data summaries over different samples or study attributes. We provide instructions in the metavizr vignette to handle visualizing data that would be added to an analysis session like protected variables from dbGAP” Reviewer Comment: MOMS-PI and T2D studies have protected meta data available through dbGap. If users apply for dbGap and get access, id there an option to merge meta data by sample ids and visualize using this tool? Author Response: We added a vignette to the metavizR Bioconductor package (https://github.com/epiviz/metavizr/pull/2/commits/756cc049a2c9264355e15df42cfa64d71ee141ae#diff-46f4a8e59ff35c66f1220d9cdc6abf687d92771b424f4a6dfed1434c998cd500) for added a protected variable and then generate new plots with it. Reviewer Comment: It would be helpful to provide instructions how to create diversity boxplots by disease status (as in Figure 3). I tried creating these but could not produce them on the same plot. Author Response: We added a tutorial at metaviz.org for including a diversity plot (https://epiviz.github.io/tutorials/metaviz/diversity_plot/). Reviewer Comment: I recommend making alpha diversity plots by disease status a default plot when the data is selected using visualization tool. Author Response: We created default workspaces at https://epiviz.github.io/metaviz-workspaces/ with alpha diversity plots on either the disease or an interesting attribute."
}
]
},
{
"id": "64700",
"date": "16 Jul 2020",
"name": "Edoardo Pasolli",
"expertise": [
"Reviewer Expertise Microbiome and bioinformatics"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe manuscript by Justin Wagner et al. presents an infrastructure that integrates Metaviz, an interactive microbiome data analysis and visualization tool that was previously published by the same authors, with the iHMP Data Coordination Center web portal and the HMP2Data R/Bioconductor package. The authors give an overall overview of the infrastructure in addition to a couple of use cases.\nThis is a nice and timely contribution that helps in using the large and complex set of available HMP data. The manuscript is already well structured, I have just few comments:\nPlease check all the links reported in the text. For example, the link to the data repository and web portal (https://ihmpdcc.org) doesn't seem to work.\n\nHow will the proposed infrastructure deal with likely updates (in terms of new data) of the HMP web portal?\n\nWhich are the options available to save/export the results generated in the proposed infrastructure? Please comment more about this in the text.\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": "6596",
"date": "21 Jun 2021",
"name": "Hector Corrada Bravo",
"role": "Author Response",
"response": "Reviewer Comment: Please check all the links reported in the text. For example, the link to the data repository and web portal (https://ihmpdcc.org) doesn't seem to work. Author Response: We have updated the link to http://www.ihmpdcc.org and checked that it resolves. Reviewer Comment: How will the proposed infrastructure deal with likely updates (in terms of new data) of the HMP web portal? Author Response: We updated the manuscript with the following: “As a community resource, we plan to update the Metaviz database within a month of Bioconductor releases of HMP2Data. We maintain links to the HMP Data Portal through the update of HMP2Data package URLs and provide default workspaces for the HMP2 datasets as well as those in HMP16SData R/Bioconductor package (https://epiviz.github.io/metaviz-workspaces/)” Reviewer Comment: Which are the options available to save/export the results generated in the proposed infrastructure? Please comment more about this in the text. Author Response: We added the following tutorial to https://epiviz.github.io/tutorials/metaviz/save_plots/"
}
]
},
{
"id": "64702",
"date": "20 Jul 2020",
"name": "Levi Waldron",
"expertise": [
"Reviewer Expertise bioinformatics",
"bioonductor",
"metagenomics",
"human microbiome analysis."
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors present a web tool for exploratory analysis of iHMP data, based on their existing metaviz software. The figures from the manuscript were easy to reproduce using the links and code provided. It seems like a useful new way to view, explore, and download iHMP data. I have only a couple minor comments:\nThe figures are low-resolution and text is a bit blurry. The lightest yellow text in Figure 2 isn't readable.\n\nFrom http://metaviz.cbcb.umd.edu/ it's not immediately obvious how to find the iHMP (HMP2) data. IBD and T2D do appear a ways down a list of available datasets, but this list takes a very long time to load for me (\"loading datasets and sample annotations...\"). I didn't find MOMS-PI but I may not have waited long enough. It would be worth providing direct links in the manuscript to workspaces for each dataset, like is already done for Figure 3.\n\nPerhaps explain the feature variables like c__Betaproteobacteria, o__Burkholderiales, f__Ruminococcaceae, g__Lachnospira, g__[Ruminococcus], g__Faecalibacterium, s__:589277, s__:333166, s__:564806, s__:369227, s__:358104, s__:369486, s__gnavus:360015, s__prausnitzii:851865 for readers who are familiar with scientific taxonomy names but not this format.\n\nIs the rationale for developing the new software tool clearly explained? Yes\n\nIs the description of the software tool technically sound? Yes\n\nAre sufficient details of the code, methods and analysis (if applicable) provided to allow replication of the software development and its use by others? Yes\n\nIs sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool? Yes\n\nAre the conclusions about the tool and its performance adequately supported by the findings presented in the article? Yes",
"responses": [
{
"c_id": "6597",
"date": "21 Jun 2021",
"name": "Hector Corrada Bravo",
"role": "Author Response",
"response": "Reviewer Comment: The figures are low-resolution and text is a bit blurry. The lightest yellow text in Figure 2 isn't readable. Author Response: We updated the color scheme for Figure 2. We also updated figures with a higher resolution. Reviewer Comment: From http://metaviz.cbcb.umd.edu/ it's not immediately obvious how to find the iHMP (HMP2) data. IBD and T2D do appear a ways down a list of available datasets, but this list takes a very long time to load for me (\"loading datasets and sample annotations...\"). I didn't find MOMS-PI but I may not have waited long enough. It would be worth providing direct links in the manuscript to workspaces for each dataset, like is already done for Figure 3. Author Response: We developed default workspaces for IBD, T2D, and MOMS-PI as well as put them at https://epiviz.github.io/metaviz-workspaces/ Reviewer Comment: Perhaps explain the feature variables like c__Betaproteobacteria, o__Burkholderiales, f__Ruminococcaceae, g__Lachnospira, g__[Ruminococcus], g__Faecalibacterium, s__:589277, s__:333166, s__:564806, s__:369227, s__:358104, s__:369486, s__gnavus:360015, s__prausnitzii:851865 for readers who are familiar with scientific taxonomy names but not this format. Author Response: We added the following text to the manuscript: “These taxonomic features describe paths in the taxonomy of the Kingdom Bacteria that was derived from the SILVA16 database. The documentation (https://ibdmdb.org/tunnel/public/HMP2/16S/1806/products) for the abundance profiles used in this analysis denotes that this taxonomic string was generated using the sequence of an OTU derived with the UPARSE algorithm17 that was mapped to the SILVA database. Among these features, \"c__Betaproteobacteria\" refers to Class Betaproteobacteria, \"o__Burkholderiales\" to Order Burkholderiales, while values towards the leaves of the taxonomy refer to entries in the SILVA database that have an identifier and a sequence but have not been provided formal names in the binomial nomenclature system”"
}
]
}
] | 1
|
https://f1000research.com/articles/9-601
|
https://f1000research.com/articles/9-1097/v1
|
04 Sep 20
|
{
"type": "Systematic Review",
"title": "The impact of the COVID-19 pandemic on self-harm and suicidal behaviour: a living systematic review",
"authors": [
"Ann John",
"Chukwudi Okolie",
"Emily Eyles",
"Roger T. Webb",
"Lena Schmidt",
"Luke A. McGuinness",
"Babatunde K. Olorisade",
"Ella Arensman",
"Keith Hawton",
"Nav Kapur",
"Paul Moran",
"Rory C. O'Connor",
"Siobhan O'Neill",
"Julian P.T. Higgins",
"David Gunnell",
"Chukwudi Okolie",
"Emily Eyles",
"Roger T. Webb",
"Lena Schmidt",
"Luke A. McGuinness",
"Babatunde K. Olorisade",
"Ella Arensman",
"Keith Hawton",
"Nav Kapur",
"Paul Moran",
"Rory C. O'Connor",
"Siobhan O'Neill",
"Julian P.T. Higgins",
"David Gunnell"
],
"abstract": "Background: The COVID-19 pandemic has caused morbidity and mortality, as well as, widespread disruption to people’s lives and livelihoods around the world. Given the health and economic threats posed by the pandemic to the global community, there are concerns that rates of suicide and suicidal behaviour may rise during and in its aftermath. Our living systematic review (LSR) focuses on suicide prevention in relation to COVID-19, with this iteration synthesising relevant evidence up to June 7th 2020. Method: Automated daily searches feed into a web-based database with screening and data extraction functionalities. Eligibility criteria include incidence/prevalence of suicidal behaviour, exposure-outcome relationships and effects of interventions in relation to the COVID-19 pandemic. Outcomes of interest are suicide, self-harm or attempted suicide and suicidal thoughts. No restrictions are placed on language or study type, except for single-person case reports. Results: Searches identified 2070 articles, 29 (28 studies) met our inclusion criteria, of which 14 articles were research letters or pre-prints awaiting peer review. All articles reported observational data: 12 cross-sectional; eight case series; five modelling; and three service utilisation studies. No studies reported on changes in rates of suicidal behaviour. Case series were largely drawn from news reporting in low/middle income countries and factors associated with suicide included fear of infection, social isolation and economic concerns.\n\nConclusions: A marked improvement in the quality of design, methods, and reporting in future studies is needed. There is thus far no clear evidence of an increase in suicide, self-harm, suicidal behaviour, or suicidal thoughts associated with the pandemic. However, suicide data are challenging to collect in real time and economic effects are evolving. Our LSR will provide a regular synthesis of the most up-to-date research evidence to guide public health and clinical policy to mitigate the impact of COVID-19 on suicide.\n\nPROSPERO registration: CRD42020183326 01/05/2020",
"keywords": [
"COVID-19",
"Living systematic review",
"Suicide",
"Attempted suicide",
"Self-harm",
"Suicidal thoughts"
],
"content": "Introduction\n\nThe COVID-19 pandemic is causing widespread societal disruption and loss of life globally. By the end of June 2020 over 10 million people had been infected and over 500,000 had died (Worldometer, 2020). There are concerns about the impact of the pandemic on population mental health (Holmes et al., 2020). These stem from the impact of the virus itself on people infected, as well as front-line workers caring for them (Kisely et al., 2020), and on population mental health from the public health measures that have been implemented to minimise the spread of the virus – in particular physical distancing, leading to social isolation, disruption of businesses, services and education and threats to peoples’ livelihoods. Physical distancing measures have resulted in substantial rises in unemployment, falls in GDP and concerns that many nations will enter a prolonged period of deep economic recession.\n\nThere are concerns that suicide and self-harm rates may rise during and in the aftermath of the pandemic (Gunnell et al., 2020; Reger et al., 2020). Time-series modelling indicated that the 1918-20 Spanish Flu pandemic, which caused well over 20 million deaths worldwide, led to a modest rise in the national suicide rate in the USA (Johnson & Mueller, 2002; Wasserman, 1992). Likewise, there is evidence that suicide rates increased briefly amongst people aged over 65 years in Hong Kong during the 2003 SARS epidemic, predominantly amongst those with more severe physical illness and physical dependency (Cheung et al., 2008).\n\nThe current context is, however, very different from previous epidemics and pandemics. The 2003 SARS epidemic was restricted to relatively few countries. Furthermore, during the 100-year period since the 1918-20 influenza pandemic, global and national health systems have improved, international travel and the speed of communication of information (and disinformation) have increased, antibiotics are available to treat secondary infection, and national economies have become more inter-dependent. The availability of the internet and technological advancement has made it far easier for people to communicate and engage in home working and home schooling. However, there are marked social inequalities in relation to access to technology and ability to stay safe and continue to work, within and between countries. Public health policies and responses, and the degree of access to technology to facilitate online clinical assessments and treatments differ greatly between countries.\n\nKey concerns in relation to suicide prevention during the pandemic include: uncertainty regarding how best to assess and support people with suicidal thoughts and behaviours, whilst maintaining physical distancing; people who have attempted suicide may not attend hospitals because they are worried about contracting COVID-19 or being a burden on the healthcare system at this time; diminished access to community-based support; exposure to traumatic experiences; and an economic recession may have an adverse impact on suicide rates (Chang et al., 2013; Stuckler et al., 2009). There have been increases in bereavement (with many being unusually complicated during the crisis), sales of alcohol (Finlay & Gilmore, 2020) and domestic violence (Mahase, 2020) – all risk factors for suicide (Turecki et al., 2019); the insensitive or irresponsible media reporting of suicide deaths associated with COVID-19 may be harmful; and in some countries access to highly lethal suicide methods such as firearms and pesticides may rise (Gunnell et al., 2020).\n\nIn the context of the COVID-19 pandemic there is likely to be a rapidly expanding research evidence base on its impact on suicide rates, and how best to mitigate such effects. It is therefore important that the best available knowledge is made rapidly available to policymakers, public health specialists and clinicians. To facilitate this, we are conducting a living systematic review focusing on suicide prevention in relation to COVID-19. Living systematic reviews are high-quality, up-to-date online summaries of research that are regularly updated, using efficient, often semi-automated, systems of production (Elliott et al., 2014). This paper reports the first set of findings from the review, based on relevant articles identified up to June 7th 2020.\n\n\nAim\n\nThe overarching aim of the review is to identify and appraise any newly published evidence from around the world that assesses the impact of the COVID-19 pandemic on suicide deaths, suicidal behaviours, self-harm and suicidal thoughts, or that assesses the effectiveness of strategies to reduce the risk of suicide deaths, suicidal behaviours, self-harm and suicidal thoughts, resulting from the COVID-19 pandemic.\n\n\nMethods\n\nThis living systematic review (Figure 1) follows published guidance for such reviews and for how expedited ‘living’ recommendations should be formed where relevant (Akl et al., 2017; Elliott et al., 2017). The review was prospectively registered (PROSPERO ID CRD42020183326; registered on 1 May 2020). An overview of our living review process is provided in Figure 1. A protocol (John et al., 2020a) was published in line with the Preferred Reporting Items for Systematic Review and Meta-Analysis Protocols guideline (Moher et al., 2015). Since publication of our protocol we have amended our methodology to: 1) search additionally the PsyArXiv and SocArXiv open access paper repositories; 2) include modelling studies within the scope of our review (e.g. to predict the likely impact of the pandemic on suicide rates); and 3) update our research questions to include adult self-neglect and parental neglect and fear of losing livelihood.\n\nThe process will be supported using automation technology and at three-monthly intervals the team will update the published version of the review. The latest and previous versions of this figure are available as extended data (John & Schmidt, 2020).\n\n\nEligibility criteria\n\nStudy participants may be adults or children of any ethnicities living in any country. Outcomes of interest are:\n\n1. Deaths by suicide\n\n2. Self-harm (intentional self-injury or self-poisoning regardless of motivation and intent) or attempted suicide (including hospital attendance and/or admission for these reasons)\n\n3. Suicidal thoughts/ideation\n\nStudies must address one of the following research questions:\n\n(i) What is the prevalence/incidence?\n\nPrevalence/incidence of each outcome during pandemic (including modelling studies)\n\n(ii) What is the comparative prevalence/incidence?\n\nPrevalence/incidence of each outcome during pandemic vs not during pandemic\n\n(iii) What are the effects of interventions?\n\nEffects of public health measures to combat COVID-19 (including physical distancing, school closures, interventions to address loss of income, interventions to tackle domestic violence) on each outcome\n\nEffects of changed and new approaches to clinical management of (perceived) elevated risk of self-harm or suicide risk on each outcome (any type of intervention is relevant)\n\n(iv) What are the effects of other exposures?\n\nImpact of media portrayal of each outcome and misinformation attributed to the pandemic on each outcome\n\nImpact of bereavement from COVID-19 on each outcome\n\nImpact of any COVID-19 related behaviour changes (domestic violence, alcohol, adult self-neglect, parental neglect, cyberbullying, isolation) on each outcome\n\nImpact of COVID-19-related workload on crisis lines on each outcome\n\nImpact of infection with COVID-19 (self or family member) on each outcome\n\nImpact of changes in availability of analgesics, firearms and pesticides on each outcome (method-specific and overall suicide rates)\n\nImpact of COVID-19 related socio-economic exposures (changes in fiscal policy; recession/depression: unemployment, debt, fear of losing livelihood, deprivation at the person-, family- or small-area level) on each outcome\n\nImpact on health and social care professionals: the stigma of working with COVID-19 patients or the (perceived) risk of infection/being a ‘carrier’, as well as work-related stress on each outcome\n\nImpact of changes in/reduced intensity of treatment for patients with mental health conditions, in particular those with severe psychiatric disorders.\n\nImpact of any other relevant exposure on our outcomes of interest.\n\n\nQualitative research\n\nWe include any qualitative research addressing perceptions or experiences around each outcome in relation to the COVID-19 pandemic (e.g. stigma of infection, isolation measures, complicated bereavement, media reporting, experience of delivering or receiving remote methods of self-harm/suicide risk assessment or provision of treatment; experience of seeking help for individuals in suicidal crisis); narratives provided for precipitating factors for each outcome.\n\nNo restrictions were placed on the types of study design eligible for inclusion, except for the exclusion of single-person case reports. Pre-prints were re-assessed at the time of publication and most current version included. There was no restriction on language of publication. We will draw on a combination of internet-based translation systems and network of colleagues to translate evidence in a language other than English.\n\n\nIdentification of eligible studies\n\nWe searched the following electronic databases: PubMed; Scopus; medRxiv, bioRxiv; the COVID-19 Open Research Dataset (CORD-19) by Semantic Scholar and the Allen Institute for AI, which includes relevant records from Microsoft Academic, Elsevier, arXiv and PMC; and the WHO COVID-19 database. A sample search strategy (for PubMed) appears in Box 1 from 1st Jan 2020 to June 7th 2020. We have developed a workflow that automates daily searches of these databases, and the code supporting this process can be found at https://github.com/mcguinlu/COVID_suicide_living. Searches are conducted daily via PubMed and Scopus application programme interface and the bioRxiv and medRxiv RSS feeds. Conversion scripts for the daily updated WHO and the weekly updated CORD-19 corpus are used to collect information from the remaining sources. The software includes a systematic search function based on regular expressions to search results retrieved from the WHO, CORD-19 and preprint repositories (search strategy available in extended data (John & Schmidt, 2020)). Our review is ongoing and we continue to investigate the use of other databases and to capture articles made available prior to peer review and assess eligibility and review internally. We therefore included PsyArXiv and SocArXiv repositories in our search strategy via their own open access platforms as we developed our automated system. For this version of the living review, Psy- and SocArXiv searches were carried out retrospectively on the 12th of June, using a publication date filter for Jan 1st 2020 – June 7th 2020.\n\nA two-stage screening process was undertaken to identify studies meeting the eligibility criteria. First, two authors (either CO or EE) assessed citations from the searches and identified potentially relevant titles and abstracts. Second, either DG, AJ or RW assessed the full texts of potentially eligible studies to identify studies to be included in the review. This process was managed via a custom-built online platform (Shiny web app, supported by a MongoDB database). The platform allowed for data extraction via a built-in form.\n\n\n\n((selfharm*[TIAB] OR self-harm*[TIAB] OR selfinjur*[TIAB] OR self-injur*[TIAB] OR selfmutilat*[TIAB] OR self-mutilat*[TIAB] OR suicid*[TIAB] OR parasuicid*[TIAB) OR (suicide[TIAB] OR suicidal ideation[TIAB] OR attempted suicide[TIAB]) OR (drug overdose[TIAB] OR self?poisoning[TIAB]) OR (self-injurious behavio?r[TIAB] OR self?mutilation[TIAB] OR automutilation[TIAB] OR suicidal behavio?r[TIAB] OR self?destructive behavio?r[TIAB] OR self?immolation[TIAB])) OR (cutt*[TIAB] OR head?bang[TIAB] OR overdose[TIAB] OR self?immolat*[TIAB] OR self?inflict*[TIAB]))) AND ((coronavirus disease?19[TIAB] OR sars?cov?2[TIAB] OR mers?cov[TIAB]) OR (19?ncov[TIAB] OR 2019?ncov[TIAB] OR n?cov[TIAB]) OR (\"severe acute respiratory syndrome coronavirus 2\" [Supplementary Concept] OR \"COVID-19\" [Supplementary Concept] OR COVID-19 [tw] OR coronavirus [tw] OR nCoV[TIAB] OR HCoV[TIAB] OR ((virus*[Title] OR coronavirus[Title] OR nCoV[Title] OR infectious[Title] OR HCoV[Title] OR novel[Title])AND (Wuhan[Title] OR China[Title] OR Chinese[Title] OR 2019[Title] OR 19[Title] OR COVID*[Title] OR SARS-Cov-2[Title] OR NCP*[Title]) OR “Coronavirus”[MeSH]))))\n\n\nData collection and assessment of risk of bias\n\nOne author (DG, AJ or RW) extracted data from each included study using a piloted data extraction form (see extended data (John & Schmidt, 2020)), and the extracted data were checked by one other author (AJ, or EE where AJ extracted data). Disagreements were resolved through discussion, and where this failed, by referral to a third reviewer (KH, NK or PM). Irrespective of study design, data source and outcome measure examined, the following basic data were extracted: citation; study aims and objectives; country/setting; characteristics of participants; methods; outcome measures (related to self-harm / suicidal behaviour and COVID-19); key findings; strengths and limitations; reviewer’s notes. For articles where causal inferences are made - i.e. randomised or non-randomised studies examining the effects of interventions or aetiological epidemiological studies of the effects of exposures – we used a suitable version of the ROBINS-I or ROBINS-E tool to assess risk of bias as appropriate based on the research question and study design (Morgan et al., 2017; Sterne et al., 2016).\n\n\nData synthesis\n\nWe synthesised studies according to themes based on research questions and study design, using tables and narrative. Results were synthesised separately for studies in the general population, in health and social care staff and other at-risk occupations, and in vulnerable populations (e.g. people of older age or those with underlying conditions that predispose them to becoming severely ill or dying after contracting COVID-19). Where multiple studies addressed the same research questions, we assessed whether meta-analysis is appropriate and would conduct it where suitable, following standard guidance available in the Cochrane Handbook (Deeks et al., 2019). The current document is the first iteration of our review. We have not considered it appropriate to combine any results identified so far in a meta-analysis.\n\n\nLiving review method\n\nDetails of the living review method, justification for its use and our transition plan are provided in our protocol (John et al., 2020a). We plan to maintain the review in living mode for at least 12 months, from publication of the protocol (25th June 2020). We will undertake monthly screening and consider full updates at least every three months. We will extend the living mode at 6-monthly intervals if evidence is still being published regularly. We anticipate an end to the living phase of the review at most 24 months after initiation, at which point we plan to publish the cumulated evidence in the form of a standard systematic review. Any decision to update the review more or less frequently will depend on the likely impact of the new evidence on the conclusions of the review. Impactful evidence may be (i) evidence that affects policy and/ or (ii) substantial, high-quality research studies (e.g. a randomised trial or population-based observational cohort study). Since we have not as yet identified any new evidence that impacts on the conclusions of this review we next update will include studies up to the 7th of October 2020 after four months.\n\n\nResults\n\nIn total, 2070 citations were identified by 7 June 2020 from all electronic searches, after duplicates were removed (Figure 2). The cumulative numbers of articles over time that were identified by the search and included in the review are shown in Figure 3 and Figure 4.\n\nThe latest and previous versions of this figure are available as extended data (John & Schmidt, 2020).\n\nThe latest and previous versions of this figure are available as extended data (John & Schmidt, 2020).\n\nThe latest and previous versions of this figure are available as extended data (John & Schmidt, 2020).\n\nWe included 29 articles in the review, describing 28 independent studies. In total, six studies spanned several countries or were worldwide, including those using online Amazon Mechanical Turk survey samples; six were from the United States; four from China; two from India; one each from Australia, Bangladesh, Canada, Germany, Greece, Pakistan, Spain, France and Switzerland. All articles were based on observational studies: eight were case series with a sample of two or more; 13 were cross sectional surveys (12 independent populations); five were modelling studies; and three were service utilisation studies. Studies are summarised by these study types in Table 1, Table 2, Table 3 and Table 4. Roughly half (n=14) of the articles did not appear to have been peer reviewed. Ten articles were published as research letters to the Editor, four as pre-prints before peer review and in seven others there was a short time (<7 days) between submission and acceptance.\n\nThe latest and previous versions of this table are available as extended data (John & Schmidt, 2020).\n\nThe latest and previous versions of this table are available as extended data (John & Schmidt, 2020).\n\nThe latest and previous versions of this table are available as extended data (John & Schmidt, 2020).\n\nThe latest and previous versions of this table are available as extended data (John & Schmidt, 2020).\n\nTwo articles shared study populations (Killgore et al., 2020a; Killgore et al., 2020b). Excluding duplicate populations and modelling studies, the total number of unique participants was 33, 345. Most studies included both male and female participants except (Wu et al., 2020b) which was conducted in a population of pregnant women in their third trimester.\n\nTwo of the eight case series focused on suicide attempts and six on suicide deaths. Of the 12 independent cross-sectional surveys ten assessed suicidal thoughts of which two also assessed suicide attempts (Ammerman et al., 2020; Bryan et al., 2020), one thoughts of self-harm (Wu et al., 2020b) using a single item from the Edinburgh Postnatal Depression Scale (EPDS), one suicidality (Kaparounaki et al., 2020) using the Risk Assessment Suicidality Scale (RASS). A range of validated questionnairres were used to assess suicidal thoughts. Four used the question 9 single item from PHQ-9 ‘Have you had thoughts that you would be better off dead or of hurting yourself in some way’ with four levels of response ranging from ‘not at all’ to ‘nearly every day’ over the last 2 weeks. One each used: the Beck Depression Inventory-II (with one item where the participant choses one statement from among a group of four statements that best describes how they have been feeling during the past few days, ranging from ‘I don’t have thoughts of killing myself’ to ‘I would kill myself if I had the chance’); the WHO Self Reporting Questionnaire (with one item of 20 asking ‘Has the thought of ending your life been on your mind?’, response yes/no in the last 30 days); one used the question how many times over the last two weeks have you thought ‘I wished I was already dead so I did not have to deal with the coronavirus’ on a five point scale; and in two little detail was given regarding this outcome assessment.\n\nTwo studies used the Self-injurous Thoughts and Behaviours Interview (SITBI) to assess for presence (yes/no) of active suicidal thoughts (i.e., ‘Have you had thoughts of killing yourself?’) in the past month (Ammerman et al., 2020) and the other in the past month, year or over a year ago (Bryan et al., 2020). They also included the item for suicide attempts. Ammerman et al. (2020) used one adapted item from the SITBI ‘In the past month, have you attempted to kill yourself?’ (yes/no) and Bryan et al. (2020) ‘Have you ever made an actual attempt to kill yourself in which you had at least some intent to die?’ (yes/no) within the past month, year or more than a year ago.\n\nWe identified eight case series reports of suicide attempts and suicide deaths (Table 1). Five of these used news reports as their data source (Bhuiyan et al., 2020; Dsouza et al., 2020; Griffiths & Mamun, 2020; Mamun & Ullah, 2020; Thakur & Jain, 2020). Many reasons for COVID-19 related suicide or suicide attempts were suggested and usually this information was derived from a journalist’s report of the death. Contributory factors reported included fear of contracting the disease or of passing it on to others, reactive psychoses, financial or economic issues, loneliness and isolation due to quarantine, stress among health professionals, the uncertainty around when the pandemic would end, an inability for migrants to return home, frustration and the stigma of a (possibly perceived) positive result, which resulted in harassment or victimisation by others in the community. The largest case series (Dsouza et al., 2020) (n=72 suicide deaths) reported that the most commonly occurring antecedents to suicide were fear of infection (n=21) and financial crisis (n=19). One case series (Griffiths & Mamun, 2020), based on news reports, included suicide pacts by 6 couples (including one murder suicide and one double suicide attempt) from Bangladesh, India, Malaysia and the USA.\n\nThere were 13 articles describing cross-sectional surveys, reporting 12 independent studies (Table 2). Seven articles (6 independent studies) reported cross-sectional surveys in the general population. One study (Killgore et al., 2020a; Killgore et al., 2020b) was a nationally representative sample of English speaking participants aged 18-35 years from 50 US states; however, no details were given regarding how the participants were sampled. Bryan et al. (2020) used a panel quota sampling methodology and weighted their sample to match the USA general population by age, sex and ethnicity. Three studies used convenience sampling through Amazon Mechanical Turk crowdsourcing (Ammerman et al., 2020; Lee, 2020; Lee et al., 2020), which pays survey responders a small fee for participation and one (Plomecka et al., 2020) used online recruitment.\n\nParticipants were COVID-19 patients in three studies (Hao et al., 2020; Wu et al., 2020a; Zhao et al., 2020) and surveys were targeted at specific poulations in a further three: pregnant women (Wu et al., 2020b)), neurosurgeons (Sharif et al., 2020) and university students (Kaparounaki et al., 2020). The study by Wu et al. (2020b) was the only survey to report pre-pandemic/pre-illness data for comparison, although Killgore et al. (2020a) compared their findings to previous work (Morahan-Martin & Schumacher, 2003) and a number of studies compared their findings to estimates that were reported from earlier published studies.\n\nHigher levels of suicidal/self-harm thoughts were reported in individuals with: anxiety relating to COVID-19 (Lee, 2020); worry relating to COVID-19 mediated by insomnia (Killgore et al., 2020b); with loneliness (Killgore et al., 2020a); worsening of pre-existing mental illness during COVID-19 (Hao et al., 2020; Plomecka et al., 2020); and in students (Kaparounaki et al., 2020); people recovering from COVID-19 infection (Hao et al., 2020); as well as women who were in their third trimester of pregnancy during the pandemic, compared with measures taken amongst women at the same stage of pregnancy before the pandemic (Wu et al., 2020b). As these are cross-sectional studies the direction of association is not possible to determine and only one study used pre-pandemic measures recorded in the same population in a similar way (Wu et al., 2020b).\n\nOne study carried out in the USA exploited the natural experiment provided by states imposing physical distancing measures on different dates (Bryan et al., 2020). This study found no evidence of an increased risk of suicidal thoughts or attempts amongst those living in states with either stay-at-home orders or restrictions on large gatherings in place compared with states without these measures.\n\nWe identified five studies (Table 3) that have used modelling approaches to forecast the potential impact of the pandemic on future suicide rates (Bhatia, 2020; Kawohl & Nordt, 2020; McIntyre & Lee, 2020a; McIntyre & Lee, 2020b; Moser et al., 2020). Each was based on different assumptions, but models largely focused on the well-characterised impact on suicide rates of rises in unemployment (Chang et al., 2013; Stuckler et al., 2009). Unemployment rates are predicted to rise as a result of a post-pandemic recession, due to measures to control the spread of the virus on the wider economy and loss of work as many businesses have been forced to shut down.\n\nOnly one study modelled the effects of physical distancing measures on suicide rates (Moser et al., 2020); it did this by using suicide rates in prisoners in group or single cells as a model for lock-down in a group or in isolation. The prison population is exposed to multiple other risk factors for suicide (e.g. increased prevalence of mental illness, substance misuse and low socioeconomic position) (Humber et al., 2011; Rivlin et al., 2010), and this, coupled with the distinct differences between prison incarceration and the adoption of home quarantine procedures during the pandemic, this model is likely to over-estimate the potential impact of physical distancing measures on suicide.\n\nThe models suggest between a 1% rise (globally) (Kawohl & Nordt, 2020) and a 145% rise (in Switzerland) (Moser et al., 2020) in suicide deaths.\n\nWe identified three service utilisation studies (Pignon et al., 2020; Smalley et al., 2020; Titov et al., 2020) (Table 4). Smalley et al. (2020) reported a fall in ED visits for suicidal thoughts in Midwest USA, as well as a fall in the proportion of total visits that were for suicidal thoughts. In contrast Titov et al. (2020) found evidence of increased contact volume to a national digital mental health service in Australia. However, amongst contacts, while there was evidence of increased anxiety and levels of concerns about COVID-19, which increased with age, there was no evidence that the percentage of contacts with suicidal thoughts/plans increased. Pignon et al., 2020 reported that emergency psychiatric consultations for suicide attempts more than halved in a region of Paris in the first month of lockdown, compared to the same period in 2019.\n\n\nDiscussion\n\nIn total, 28 independent studies (29 articles) were included in this review covering a total of 33,345 studied individuals from around the world with a mix of low, middle and high income countries. Almost half of the articles were pre-prints published before peer review, or research letters that may not have been peer-reviewed. The majority of studies were case series or cross sectional surveys, almost all based on non-representative convenience samples. Only one study reported on the change in incidence of suicide or suicidal behaviour before versus after the onset of the pandemic (Pignon et al., 2020); this analysis was based on emergency psychiatric consultations for suicide attempt – and reported a decline, although levels of consultation could have been influenced by fears about using services or ideas of not burdening the health service rather than changes in incidence. A further study from China reported heightened levels of self-harm thoughts in pregnant women surveyed in the period after the onset of the pandemic, compared with levels reported amongst women surveyed at the same stage of pregnancy just before the pandemic (Wu et al., 2020b). No studies reported potentially harmful effects of lockdown/physical distancing measures in relation to our outcomes, although one study comparing the prevalence of suicidal thoughts and attempts in people living in USA states with varying timing and strigency of state-specific lockdowns found no evidence for such an ecological association (Bryan et al., 2020). Modelling studies that aimed to predict the impact of the pandemic on national or global suicide rates produced widely differing estimates of the likely impact and most focused on predictions based on previous studies of the impact of changes in unemployment levels on suicide. Three studies investgated service use patterns – one found a decline in ED visits for suicidal thoughts, one a decline in psychiatric emergency consultation for suicide attempt and the other reported an increase in contacts to a mental health digital platform but no changes in contacts for suicidal thoughts.\n\nWe identified eight case series reports of suicide attempts and suicide deaths, five based on news stories in India, Bangladesh and Pakistan. Given the relatively low quality of case series in the hierarchy of evidence, often reflecting small numbers and selection bias, but more importantly the lack of comparator data, drawing any reliable inferences from these studies is challenging. Furthermore, news reports report a non-representative sample of suicide deaths and often derive their information from bystanders and witnesses who are unlikely to know the full circumstances of the death (Khan et al., 2009). Nevertheless, these studies highlight circumstances surrounding apparently COVID-19-related suicides and flag the potential importance of factors such as economic difficulties, fear of the disease, and social isolation. Indeed in parts of the world without reliable suicide incidence data they may be the only source of information (Khan & Hyder, 2006).\n\nThe 12 cross-sectional studies investigated a range of issues. Findings indicated worries about COVID-19 and recent COVID-19 infection were associated with suicidal thoughts (Hao et al., 2020; Killgore et al., 2020a; Killgore et al., 2020b; Lee, 2020; Lee et al., 2020; Zhao et al., 2020) and, amongst pregnant women surveyed during the pandemic, thoughts of self-harm were higher than amongst those surveyed pre-pandemic. The one study comparing suicidal thoughts and behaviours amongst people living in areas with versus without physical distancing measures found no adverse association (Bryan et al., 2020). Surprisingly survey by Ammerman et al. (2020) from the USA indicated that social distancing was associated with reduced instances of suicidal thoughts early in the period of lockdown. Only one survey suggested it was nationally representative but lacked sampling details (Killgore et al., 2020a). Non-probability sampling lacks a sound theoretical basis for statistical inference (Neyman, 1934). Consequently, basic descriptive analyses and explorations of potential associations are appropriate but measures of uncertainty (i.e., confidence intervals around estimates of prevalence) are generally not valid. One study (Bryan et al., 2020) used panel quota sampling, but these sorts of adjustments for age, sex and ethnicity may miss other elements of bias and cannot account for groups not included at all, particularly if the response rate is unknown (Pierce et al., 2020). Four studies used convenience sampling which tend to attract volunteers who have access to the internet, are already engaged in research and have an interest in the topic. Hence responses may be unrepresentative of the general population, and associations observed among these healthy volunteers may not reflect associations that would be observed in others. Similarly, when assessing suicidal thoughts and behaviours, those in most distress or with co-existing mental illness, as well as older people, are less likely to participate in these sorts of surveys. There is no way to assess non-response bias in a convenience sample as might be possible in a probability-sampled survey (Pierce et al., 2020).\n\nThere was a large range in modelling estimates of the effect of the pandemic on suicide rates, varying between a 1% and a 145% rise. These differences between model estimates were partly due to differences in modelling assumptions, which are associated with considerable uncertainty. Given the methodological limitations, the uncertainty of assumptions about how the economies of individual countries will be affected, as well as international differences in financial supports given to businesses and people out of work, these predictive exercises can at best only provide a guide as to where action should be directed.\n\nTo date, there is little literature exploring COVID-19 and suicide deaths, suicidal behaviours, self-harm and suicidal thoughts and most of the published evidence that we identified had important limitations. Importantly, much of the literature is not yet peer reviewed so the quality of reported studies may change. There were eight research letters, five pre-prints and for many others very short timeframes between submission and acceptance. All included studies were observational in design and prone to multiple sources of bias (eg, recall bias, selection bias, confounding). No conclusions can be drawn regarding causality and temporality from cross sectional studies. However, such study designs may be appropriate in current circumstances where timeliness of studies to inform policy and practice are important. However many were carried out too quickly and too early (one to two weeks post lockdown) in the outbreak to make meaningful contributions to the evidence base. The lack of baseline data in the majority of surveys included in the review and adjustments made to standardised measures to assess suicidal behaviours as well as the range of measures and timing asked made assessment of findings problematic.\n\nWe did not include Google Trends studies (Jacobson et al., 2020; Knipe et al., 2020; Rana, 2020; Sinyor et al., 2020) since search data constitute a proxy measure but findings are largely mixed. We also excluded grey literature (Fancourt & Steptoe, 2020).\n\nA marked improvement in the quality of design, methods, and reporting in future studies is needed. There is thus far no clear evidence of an increase in suicidal behaviour or self-harm associated with the pandemic nor with the measures taken to curb the spread of COVID-19. The current iteration of out living review highlights the methodological issues of early evidence from around the world that assesses the impact of the COVID-19 pandemic on suicide deaths, suicidal behaviours, self-harm and suicidal thoughts, or that assesses the effectiveness of strategies to reduce the risk of suicide deaths, suicidal behaviours, self-harm and suicidal thoughts, resulting from the COVID-19 pandemic. However, suicide data are challenging to collect in real time and the economic effects are evolving. Our living review will provide a regular synthesis of the most up-to-date research evidence to guide public health and clinical policy to mitigate the impact of COVID-19 on suicide.\n\n\nData availability\n\nHarvard Dataverse: Full review data for: \"The impact of the COVID-19 pandemic on self-harm and suicidal behaviour: update of living systematic review\". https://doi.org/10.7910/DVN/7WZXZK (John & Schmidt, 2020)\n\nThis project contains the following underlying data:\n\n- Screening_snapshot.csv (Screening progress for literature published before June 7th)\n\nHarvard Dataverse: Full review data for: \"The impact of the COVID-19 pandemic on self-harm and suicidal behaviour: update of living systematic review\". https://doi.org/10.7910/DVN/7WZXZK (John & Schmidt, 2020)\n\nThis project contains the following extended data:\n\nLSR update tables and figures.docx (Tables and figures from this publication)\n\nPRISMA.doc\n\nData regarding the Protocol are available via our Harvard Dataverse repository for the protocol\n\nHarvard Dataverse: Underlying data for: The impact of the Covid-19 pandemic on suicidal behaviour: a living systematic review protocol. https://doi.org/10.7910/DVN/9JYHLS (John et al., 2020b)\n\nThat project contains the following extended data:\n\nSearch.docx (additional information about the searches, including full search strategies)\n\nData extraction sheet/ study report\n\nFigure 1\n\nPrisma.pdf (the PRISMA-P statement)\n\nProspero registration\n\nHarvard Dataverse: PRISMA checklist for ‘The impact of the COVID-19 pandemic on self-harm and suicidal behaviour: a living systematic review’ https://doi.org/10.7910/DVN/7WZXZK (John & Schmidt, 2020)\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\nThe development version of the software for automated searching is available from Github: https://github.com/mcguinlu/COVID_suicide_living.\n\nArchived source code at time of publication: http://doi.org/10.5281/zenodo.3871366 (McGuinness & Schmidt, 2020)\n\nLicense: MIT",
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Cochrane handbook for systematic reviews of interventions. 2nd ed.: John Wiley & Sons. 2019. Reference Source\n\nDsouza DD, Quadros S, Hyderabadwala ZJ, et al.: Aggregated COVID-19 suicide incidences in India: Fear of COVID-19 infection is the prominent causative factor. Psychiatry Res. 2020; 290: 113145. PubMed Abstract | Publisher Full Text\n\nElliott JH, Synnot A, Turner T, et al.: Living systematic review: 1. Introduction—the why what, when, and how. J Clin Epidemiol. 2017; 91: 23–30. 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(2): e1001603. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFancourt D, Steptoe A: COVID-19 social study. Nuffield Foundation. 2020. Reference Source\n\nFinlay I, Gilmore I: Covid-19 and alcohol—a dangerous cocktail. BMJ. 2020; 369: m1987. PubMed Abstract | Publisher Full Text\n\nGriffiths MD, Mamun MA: COVID-19 suicidal behavior among couples and suicide pacts: Case study evidence from press reports. Psychiatry Res. 2020; 289: 113105. PubMed Abstract | Publisher Full Text\n\nGunnell D, Appleby L, Arensman E, et al.: Suicide risk and prevention during the COVID-19 pandemic. Lancet Psychiatry. 2020; 7(6): 468–471. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHao F, Tan W, Jiang L, et al.: Do psychiatric patients experience more psychiatric symptoms during COVID-19 pandemic and lockdown? A case-control study with service and research implications for immunopsychiatry. Brain Behav Immun. 2020; 87: 100–106. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHolmes EA, O'Connor RC, Perry VH, et al.: Multidisciplinary research priorities for the COVID-19 pandemic: a call for action for mental health science. Lancet Psychiatry. 2020; 7(6): 547–560. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHumber N, Piper M, Appleby L, et al.: Characteristics of and trends in subgroups of prisoner suicides in England and Wales. Psychol Med. 2011; 41(11): 2275–2285. PubMed Abstract | Publisher Full Text\n\nJacobson NC, Lekkas D, Price G, et al.: Flattening the Mental Health Curve: COVID-19 Stay-at-Home Orders Are Associated With Alterations in Mental Health Search Behavior in the United States. JMIR Ment Health. 2020; 7(6): e19347. PubMed Abstract | Publisher Full Text | Free Full Text\n\nJohn A, Eyles E, Mcguinness LA, et al.: The impact of the COVID-19 pandemic on self-harm and suicidal behaviour: protocol for a living systematic review [version 1; peer review: 1 approved, 1 approved with reservations] F1000Research. 2020a; 9: 644. Publisher Full Text\n\nJohn A, Eyles EC, McGuinness LA, et al.: Underlying data for: The impact of the Covid-19 pandemic on suicidal behaviour: a living systematic review protocol [Data set]. Harvard Dataverse. 2020b. http://www.doi.org/10.7910/DVN/9JYHLS\n\nJohn J, Schmidt L: \"Full review data for: \"The impact of the COVID-19 pandemic on self-harm and suicidal behaviour: update of living systematic review\"\". Harvard Dataverse, V3, 2020. http://www.doi.org/10.7910/DVN/7WZXZK\n\nJohnson NP, Mueller J: Updating the accounts: global mortality of the 1918-1920\" Spanish\" influenza pandemic. Bull Hist Med. 2002; 76(1): 105–115. PubMed Abstract | Publisher Full Text\n\nKaparounaki CK, Patsali ME, Mousa DPV, et al.: University students’ mental health amidst the COVID-19 quarantine in Greece. Psychiatry Res. 2020; 290: 113111. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKawohl W, Nordt C: COVID-19, unemployment, and suicide. Lancet Psychiatry. 2020; 7(5): 389–390. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKhan MM, Ahmed A, Khan SR: Female suicide rates in Ghizer, Pakistan. Suicide Life Threat Behav. 2009; 39(2): 227–230. PubMed Abstract | Publisher Full Text\n\nKhan MM, Hyder AA: Suicides in the developing world: Case study from Pakistan. Suicide Life Threat Behav. 2006; 36(1): 76–81. PubMed Abstract | Publisher Full Text\n\nKillgore WD, Cloonan SA, Taylor EC, et al.: Loneliness: A signature mental health concern in the era of COVID-19. Psychiatry Res. 2020a; 290: 113117. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKillgore WD, Cloonan SA, Taylor EC, et al.: Suicidal ideation during the COVID-19 pandemic: the role of insomnia. Psychiatry Res. 2020b; 290: 113134. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKisely S, Warren N, McMahon L, et al.: Occurrence, prevention, and management of the psychological effects of emerging virus outbreaks on healthcare workers: rapid review and meta-analysis. BMJ. 2020; 369. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKnipe D, Evans H, Marchant A, et al.: Mapping population mental health concerns related to COVID-19 and the consequences of physical distancing: a Google trends analysis [version 2; peer review: 2 approved] Wellcome Open Res. 2020; 5: 82. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLee SA: Coronavirus Anxiety Scale: A brief mental health screener for COVID-19 related anxiety. Death Stud. 2020; 44(7): 393–401. PubMed Abstract | Publisher Full Text\n\nLee SA, Mathis AA, Jobe MC, et al.: Clinically significant fear and anxiety of COVID-19: A psychometric examination of the Coronavirus Anxiety Scale. Psychiatry Res. 2020; 290: 113112. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMahase E: Covid-19: EU states report 60% rise in emergency calls about domestic violence. BMJ. 2020; 369: m1872. PubMed Abstract | Publisher Full Text\n\nMamun MA, Ullah I: COVID-19 suicides in Pakistan, dying off not COVID-19 fear but poverty?–The forthcoming economic challenges for a developing country. Brain Behav Immun. 2020; 87: 163–166. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMcGuinness LA, Schmidt L: mcguinlu/COVID_suicide_living: Initial Release (v1.0.0) [Computer software].Zenodo.2020. http://www.doi.org/10.5281/ZENODO.3871366\n\nMcintyre RS, Lee Y: Preventing suicide in the context of the COVID-19 pandemic. World Psychiatry. 2020a; 19(2): 250–251. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMcintyre RS, Lee Y: Projected increases in suicide in Canada as a consequence of COVID-19. Psychiatry Res. 2020b; 290: 113104. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMoher D, Shamseer L, Clarke M, et al.: Preferred reporting items for systematic review and meta-analysis protocols (PRISMA-P) 2015 statement. Syst Rev. 2015; 4(1): 1. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMorahan-martin J, Schumacher P: Loneliness and social uses of the Internet. Comput Hum Behav. 2003; 19(6): 659–671. Publisher Full Text\n\nMorgan R, Sterne JA, Higgins JP, et al.: A new instrument to assess Risk of Bias in Non-randomised Studies of Exposures (ROBINS-E): Application to studies of environmental exposure Global Evidence Summit. Cape Town. 2017. Reference Source\n\nMorin CM, Belleville G, Bélanger L, et al.: The Insomnia Severity Index: psychometric indicators to detect insomnia cases and evaluate treatment response. Sleep. 2011; 34(5): 601–608. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMoser DA, Glaus J, Frangou S, et al.: Years of life lost due to the psychosocial consequences of COVID19 mitigation strategies based on Swiss data. Eur Psychiatry. 2020; 63(1): e58. PubMed Abstract | Publisher Full Text | Free Full Text\n\nNeyman J: On the two different aspects of the representative method: the method of stratified sampling and the method of purposive selection. J R Stat Soc B. 1934; 97(4): 558–625. Publisher Full Text\n\nPierce M, Mcmanus S, Jessop C, et al.: Says who? The significance of sampling in mental health surveys during COVID-19. Lancet Psychiatry. 2020; 7(7): 567–568. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPignon B, Gourevitch R, Tebeka S, et al.: Dramatic reduction of psychiatric emergency consultations during lockdown linked to COVID-19 in Paris and suburbs. Psychiatry Clin Neurosci. 2020. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPlomecka MB, Gobbi S, Neckels R, et al.: Mental Health Impact of COVID-19: A global study of risk and resilience factors. medRxiv. 2020. Publisher Full Text\n\nRana U: Elderly Suicides in India: An Emerging Concern during COVID-19 Pandemic. Int Psychogeriatr. 2020; 1–2. PubMed Abstract | Publisher Full Text | Free Full Text\n\nReger MA, Stanley IH, Joiner TE: Suicide Mortality and Coronavirus Disease 2019—A Perfect Storm? JAMA Psychiatry. 2020. PubMed Abstract | Publisher Full Text\n\nRivlin A, Hawton K, Marzano L, et al.: Psychiatric disorders in male prisoners who made near-lethal suicide attempts: case–control study. Br J Psychiatry. 2010; 197(4): 313–319. PubMed Abstract | Publisher Full Text\n\nSahoo S, Bharadwaj S, Parveen S, et al.: Self-harm and COVID-19 Pandemic: An emerging concern–A report of 2 cases from India. Asian J Psychiatr. 2020; 51: 102104. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSharif S, Amin F, Hafiz M, et al.: COVID 19-Depression and Neurosurgeons. World Neurosurg. 2020; 140: e401–e410. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSinyor M, Spittal MJ, Niederkrotenthaler T: Changes in Suicide and Resilience-related Google Searches during the Early Stages of the COVID-19 Pandemic. Can J Psychiatry. 2020; 706743720933426. PubMed Abstract | Publisher Full Text\n\nSmalley CM, Malone DA, Meldon SW, et al.: The impact of COVID-19 on suicidal ideation and alcohol presentations to emergency departments in a large healthcare system. Am J Emerg Med. 2020; S0735-6757(20)30457-5. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSterne JA, HernÁn MA, Reeves BC, et al.: ROBINS-I: a tool for assessing risk of bias in non-randomised studies of interventions. BMJ. 2016; 355: i4919. PubMed Abstract | Publisher Full Text | Free Full Text\n\nStuckler D, Basu S, Suhrcke M, et al.: The public health effect of economic crises and alternative policy responses in Europe: an empirical analysis. Lancet. 2009; 374(9686): 315–323. PubMed Abstract | Publisher Full Text\n\nThakur V, Jain A: COVID 2019-suicides: A global psychological pandemic. Brain Behav Immun. 2020; 88: 952–953. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTitov N, Staples L, Kayrouz R, et al.: Rapid report: Early demand, profiles and concerns of mental health users during the coronavirus (COVID-19) pandemic. Internet Interv. 2020; 21: 100327. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTurecki G, Brent DA, Gunnell D, et al.: Suicide and suicide risk. Nat Rev Dis Primers. 2019; 5: 73. Publisher Full Text\n\nValdés-Florido MJ, López-Díaz A, Palermo-Zeballos FJ, et al.: Reactive psychoses in the context of the COVID-19 pandemic: clinical perspectives from a case series. Rev Psiquiatr Salud Ment. 2020; 13(2): 90–94. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWasserman IM: The impact of epidemic,war prohibition and media on suicide: United States, 1910– 1920. Suicide Life Threat Behav. 1992; 22(2): 240–254. PubMed Abstract\n\nWong TW, Gao Y, Tam WWS: Anxiety among university students during the SARS epidemic in Hong Kong. Stress Health. 2007; 23(1): 31–35. Publisher Full Text | Free Full Text\n\nWorldometer: Covid-19 Coronavirus Pandemic [Online]. 2020. [Accessed 07/06/2020]. Reference Source\n\nWu C, Hu X, Song J, et al.: Mental health status and related influencing factors of COVID-19 survivors in Wuhan, China. Clin Transl Med. 2020a; 10(2): e52. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWu Y, Zhang C, Liu H, et al.: Perinatal depressive and anxiety symptoms of pregnant women along with COVID-19 outbreak in China. Am J Obstet Gynecol. 2020b; 223(2): 240.e1–240.e9. PubMed Abstract | Publisher Full Text | Free Full Text\n\nZhao Q, Hu C, Feng R, et al.: Investigation of the mental health of patients with novel coronavirus pneumonia. Chinese Journal of Neurology. 2020."
}
|
[
{
"id": "71350",
"date": "22 Sep 2020",
"name": "Lakshmi Vijayakumar",
"expertise": [
"Reviewer Expertise suicide research"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is a much needed study during the pandemic which is constantly evolving with many ramifications.\n\nIn the category of what are the effects of other exposures, suicide by railways can be added. In fact there a likely reduction of railway suicides. The other addition could be the impact of working from home, change in workplace etc.\n\nThe authors have righty pointed out that the studies are from newspaper reports, non-representative samples and cross-sectional, hence the generalizability of these findings are limited.\n\nOne is not sure of when studies using proxy data like newspaper data are included, and why Google trend studies are not included.\n\nThe paper is a call for more robust well-designed studies to understand the association between the pandemic and suicidal behaviour.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? Yes\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes",
"responses": []
},
{
"id": "75857",
"date": "11 Jan 2021",
"name": "Kimberly A Van Orden",
"expertise": [
"Reviewer Expertise Suicide prevention"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 provides a review of empirical studies on suicide ideation, behavior, and deaths as related to the COVID-19 pandemic (up to June 2020). Given prior data linking disasters and crises more generally, and pandemics specifically, to changes in suicide rates, describing any changes in suicide rates (as well as suicide ideation and non-fatal behavior) due to the COVID-19 pandemic could contribute to suicide prevention science and promote public health efforts to save lives. A key strength of this paper is its design as a ‘living review’ that will be updated every six months as more data is available. Another strength is the transparent reporting on search methods and strategies.\nA limitation of the paper is inadequate attention to study quality in the analysis and interpretation of findings. I will give several examples. First, the authors report that they used a formal tool to assess the risk of bias for epidemiological or clinical trial design studies, but do not report findings from these assessments; given that many papers included in the review were not peer reviewed, it seems especially useful for the authors to use such assessments of study quality to guide their review and to ‘weight’ findings from these studies in their analysis. Second, the degree of methodological rigor could be assessed for all studies, not just those with epidemiology/clinical trial designs and the authors should consider doing so. Third, the authors indicate in the primary table that letters to the editor were ‘probably not peer reviewed.’ Given that this information could be verified by contacting the journals, this would be a useful strategy to bolster findings from this review. Fourth, when the authors describe the findings, they do not differentiate between findings that appear methodologically-sound versus those that may not be, thus negating one of the most useful features of review papers for readers.\nAnother limitation of the paper is that it provides relatively little synthesis or conclusions, which is a key function of review papers, as opposed to a database that contains a listing of available studies. The discussion section includes more of a summary of what studies examined (and did not examine) as opposed to a synthesis of findings. The authors do not provide a nuanced discussion of the fact that these studies come from numerous countries around the world and what addressing this issue could potentially tell us about possible variability in suicide rates around the world. They do not discuss limitations with sampling that appeared across studies (e.g., generalizability of online platforms like M-Turk). In the discussion section, the authors conclude that “a marked improvement in the quality of design, methods, and reporting in future studies is needed.” This may be accurate, but I do not think it is an especially useful statement to guide the field. A more useful set of statements might involve a synthesis of methodological strengths and weaknesses as well as a discussion on strategies that can be taken going forward to address these weaknesses. The authors do not posit further implications; this may be accurate—that nothing else can be concluded right now—but in that case, perhaps the paper is premature.\nThe authors should provide additional details on the methods used for the review process to construct Tables 1-4. In particular, for the column labeled ‘Conclusions,’ presumably, this refers to conclusions made by the authors of the original papers? This should be stated explicitly. Did the authors of this review include all conclusions made by the authors of the original studies in the table or did they select ones deemed most useful? How did the authors of this review select the limitations and comments included in the final column? Some of the comments included in that final column appear opinion-based and are not supported by data from the papers (e.g., prevalence is “surprisingly low” or these data “cannot be interpreted” and “usefully”).\nFor future updates, the authors should consider providing dates for data collection in their tables given that the timing of when studies are conducted may moderate findings, given the variability in length of physical distancing, amount of economic disruption, and the number of deaths due to COVID-19.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? No\n\nIs the statistical analysis and its interpretation appropriate? Not applicable\n\nAre the conclusions drawn adequately supported by the results presented in the review? Partly",
"responses": []
},
{
"id": "77902",
"date": "08 Feb 2021",
"name": "Gonzalo Martinez-Ales",
"expertise": [
"Reviewer Expertise Psychiatric 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\nThis manuscript is a great scientific contribution. The main strength of the manuscript (that it builds on a remarkable effort -- their living systematic review) goes hand in hand with the most important limitation (the period included in the particular iteration that is under consideration for publication). I would like to thank the authors for such a great addition to science (the living systematic review) and express my admiration. Next, I expand on these observations.\nThe introduction is right on target and reads well. A reference to recent increases in gun purchases in the US (e.g., https://www.businessinsider.com/gun-sales-boom-2020-background-checks-hit-record-highs-2021-1). Methods are sound. Results are concise and informative. The tables are particularly interesting and we congratulate the authors on the table including modelling studies as it conveys the most important information easily. The discussion also reads well and adjusts well to the findings.\nThere is, however, a major limitation to this study that authors may want to address: the limited period of time included. This iteration of the review stopped including papers by July 7th, roughly 4 months after the pandemic hit Western countries for the first time. Notably, this review would have been of great interest if published over the summer. Several research reports (and important grey literature) have become public in the meantime, some adding to the evidence reviewed here without notably changing the overarching results but enhancing their reliability (and probably creating the necessary ground for a quantitative summary or a meta-analysis) and, more importantly, some creating groundbreaking evidence that may change the conclusion of this review (such as the Nature Comms paper by Tanaka and Okamoto using data from Japan to show an initial dip and subsequent increase in suicide rates in Japan).\n\nSee some key recent key additions to the literature as an example:\nhttps://www.nature.com/articles/s41562-020-01042-z1\nhttps://www.medrxiv.org/content/10.1101/2020.11.13.20231571v12\nhttps://www.medrxiv.org/content/10.1101/2020.10.06.20207530v53\nhttps://www.medrxiv.org/content/10.1101/2020.10.21.20187419v14\nhttps://www.medrxiv.org/content/10.1101/2020.10.20.20215343v15\nThe impact of this profound and sound review is somewhat limited by the period included: readers should resort to the authors’ ongoing live 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? Not applicable\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/9-1097
|
https://f1000research.com/articles/9-1374/v1
|
26 Nov 20
|
{
"type": "Software Tool Article",
"title": "GeNePy3D: a quantitative geometry python toolbox for large scale bioimaging",
"authors": [
"Minh-Son Phan",
"Anatole Chessel",
"Minh-Son Phan"
],
"abstract": "The advent of large-scale fluorescence and electronic microscopy techniques along with maturing image analysis is giving life sciences a deluge of geometrical objects in 2D/3D(+t) to deal with. These objects take the form of large scale, localised, precise, single cell, quantitative data such as cells’ positions, shapes, trajectories or lineages, axon traces in whole brains atlases or varied intracellular protein localisations, often in multiple experimental conditions. The data mining of those geometrical objects requires a variety of mathematical and computational tools of diverse accessibility and complexity. Here we present a new Python library for quantitative 3D geometry called GeNePy3D which helps handle and mine information and knowledge from geometric data, providing a unified application programming interface (API) to methods from several domains including computational geometry, scale space methods or spatial statistics. By framing this library as generically as possible, and by linking it to as many state-of-the-art reference algorithms and projects as needed, we help render those often specialist methods accessible to a larger community. We exemplify the usefulness of the GeNePy3D toolbox by re-analysing a recently published whole-brain zebrafish neuronal atlas, with other applications and examples available online. Along with an open source, documented and exemplified code, we release reusable containers to allow for convenient and wide usability and increased reproducibility.",
"keywords": [
"bioimage informatics",
"quantitative geometry",
"computational geometry",
"workflow",
"python"
],
"content": "Introduction\n\nBioimage informatics aims at bringing microscopy into quantitative biology, associating higher level information to pixels to answer complex biological questions. In particular machine learning based techniques1 are easing the image analysis step, extracting geometrical objects from multidimensional images. But the next step, transforming that geometrical information into biological knowledge, involves a very diverse set of algorithmic tools in distinct communities, from spatial statistics2,3 to computational geometry4,5 or neuroinformatics6. Similarly, the software ecosystem around geometrical data analysis is very diverse and heterogeneous, with reference algorithm implementation spread across languages (Spatstat7 for spatial statistics in R, CGAL8 for computational geometry in C++) or across module in python (scipy9 for generic algorithms, anytree10 for trees, trimesh11 for meshes etc), a lack of generic geometric data exchange format and standard graphical tools like Fiji12 and Icy13 being limited in the flexibility of the analysis easily available. To address this problem, we propose GeNePy3D14,15, a python library meant as a ’middleware’ library to facilitate building data analysis workflows for geometrical objects by providing one convenient API for geometrical data I/O, conversion and interaction between geometrical objects and access to many common and less common algorithm. We will introduce below the architecture of the library and show one example workflow, re-analysing a published dataset of zebrafish brain neuronal traces by combining traces and brain region to extract quantitative metrics per region.\n\n\nMethods\n\nGeNePy3D14,15 was designed with any computational-minded life scientist as target user, to provide a simple and homogeneous API. GeNePy3D consists of four main objects (Figure 1) corresponding to four basic geometrical objects of interest: Points (cells or intracellular object positions...), Curve (particles tracks, neurite branches, microtubules...), Tree (neuronal traces, dividing cell tracks) and Surface (cell surface or other tissue level structure...). Each of them has its own attributes, functions and I/O. We provide ways to transform between them, (decomposing a Tree into sequences of Curve, or converting Points into the Surface that enclose them). Interaction between objects of the same/different classes are also available (alignment of Curves/Surface, optimal transport-based distance between two Points, intersection between Curve and Surface, etc.) Altogether, GeNePy3D offers a unified and seamless way to analyse complex geometrical biological data.\n\nThe library is structured around four main classes for four principal geometrical objects, and propose various functions acting on them or converting between them, either implemented anew or linking to recognized library.\n\nGeNePy3D is implemented in Python, taking advantage of a high-level programming language with simple syntax and many open-source packages. We reused algorithms and functions available from various recognised packages when possible, and developed our own implementation when needed, within a unique interface. Most of the packages we link to are available from the Python package Index (PyPi) and can be easily installed via Python package manager (pip). Figure 1 lists out some functions with colors denoting the package used. Standard ones includes Numpy, Scipy, or Matplotlib, more specific ones includes AnyTree for tree manipulation, TriMesh for surface manipulation or ScikitLearn for machine learning tasks. Other feature are listed as optional, as they come from harder to install or less recognized sources, including the C++ library CGAL, only partially available in Python, for generic object interaction in 3D, or the optimal transport method implemented in PyEMD. Some original development available in GeNePy3d include an algorithm to compute local 3D scale we recently published16. Many common input/output formats are supported including SWC for Tree, CSV, XYZ for Points/Curve and STL and OFF for Surface.\n\nGeNePy3D works with Python 3.6. Details of the specific software requirements, documentation including the installation instruction and Python notebooks examples can be accessed via https://genepy3d.gitlab.io. Example pipelines using GeNePy3D are run using Jupyter notebooks. To ease the use and deployment of GeNePy3D we provide ready to use docker containers at https://gitlab.com/genepy3d/genepy3d_dockers.\n\n\nUse case\n\nTo exemplify the use of GeNePy3D14,15, we reanalyzed a recently published dataset containing up to 2000 traced neurons across the whole brain of larval zebrafish17. The authors annotated 36 symmetric regions and established a connectivity atlas for the neurons within these regions. Figure 2A illustrates a possible workflow using GeNePy3D for reanalyzing the dataset. The inputs consist of neuronal traces in SWC formats and a 3D volume in NRRD format containing different annotated labels for the 36 brain regions. The traces are imported into GeNePy3D under Tree objects, while the regions are reconstructed into Surface objects using marching cube algorithm. Figure 2B top illustrates the outline of the Tectum along with all neuronal traces arriving to this brain region. We then extracted branching point positions from the neuronal traces (Tree→Points), decomposed them into sections (Tree→Curves) and checked whether the branching points or curve sections lies within or outside each region (interaction with Surface). Examples of decomposing the traces, computing sections inside and outside the Tectum region are shown in Figure 2B bottom. Finally, we measured within the brain regions neuronal lengths, number of branching points, tortuosities (proportion of length over distance between two end points of the curve), and local 3D scales16 (scale at which the curve transforms to 3D).\n\n(A) Workflow schema. (B) Example of intermediate data and operations from the workflow: outline surface of the Tectum and all neurons arriving to it (top), decomposition of a neuronal tree into sections (displayed with random colors) based on branching positions (bottom left), and computing of neuronal sections inside/outside the Tectum (bottom right). (C) Resulting quantifications: distribution of average neuronal lengths for groups of neurons arriving to/originating from/passing all brain regions (top), and heat map of averaged neuronal lengths over each brain region for group of neurons arriving to the brain regions (bottom). The regions with small number of arriving neurons (< 10 neurons) are excluded (in gray). The letters (i-iv) in (B) illustrate some steps in (A).\n\nPart of the resulting quantification obtained are shown Figure 2C. The top graph shows a longer neuronal length on averaged for groups of neurons arriving to and originating from the regions compared to ones passing through. Figure 2C bottom shows a map of the averaged neuronal length for each brain regions for arriving neurons showing that neurons coming from fore- and midbrain are much longer than those from hindbrain. Detail of all processing steps and additional quantified results can be found at https://gitlab.com/genepy3d/genepy3d_examples/-/tree/master/zebrafish_atlas.\n\n\nConclusions\n\nThe advent of machine learning and large scale imaging is leading to large geometrical datasets, and GeNePy3d14,15 aims at enabling complex analysis workflows based on those objects. But as in other aspects of bioimage informatics, the key will be for the community to work together and define common formats and structures for region of interests and geometric objects to ease the interactions between the various visualisation, data management or analysis tools, and convert raw images to biological knowledge. GeNePy3d is ready to become a component of that ecosystem.\n\n\nData availability\n\nThe data used for Figure 2 has been published in https://fishatlas.neuro.mpg.de. To download the traces, we choose ’single axons’, ’connect without logging in’, chose ’Kunst et al. 2019’ in publications; once all neurons are loaded the download option appears.\n\n\nSoftware availability\n\nGeNePy3D is hosted at: https://genepy3d.gitlab.io and easily installable through the PyPi tool.\n\nSource code available at: https://gitlab.com/genepy3d.\n\nArchived source code at time of publication:\n\nGeNePy3D: https://doi.org/10.5281/zenodo.426946614.\n\nGeNePy3D_GPL: https://doi.org/10.5281/zenodo.426948415.\n\nLicense: The library is distributed as two packages for licensing reasons. The main package GeNePy3D14 is under a BSD 3-Clause Licence, while features that necessitate linking to GPL-licensed code are distributed separately in GeNePy3D_GPL15, under the GNU General Public License v3.0.\n\nThe source code for the analysis of Figure 2 is available at https://gitlab.com/genepy3d/genepy3d_examples/-/tree/master/zebrafish_atlas.",
"appendix": "Acknowledgements\n\nThe authors wish to acknowledge Jean Livet, Emmanuel Beaurepaire and Katherine Matho for fruitful discussions and the collaboration that gave the incentive to develop this library, and Debora Keller-Olivier for reading the manuscript. This publication was supported by COST Action NEUBIAS (CA15124), funded by COST (European Cooperation in Science and Technology.\n\n\nReferences\n\nMoen E, Bannon D, Kudo T, et al.: Deep learning for cellular image analysis. Nat Methods. 2019; 16(12): 1233–1246. PubMed Abstract | Publisher Full Text\n\nChessel A, Dodgson J, Carazo-Salas RE: Spherical spatial statistics for 3D fluorescence video-microscopy. In Proceedings-International Symposiumon Biomedical Imaging. 2012. Publisher Full Text\n\nLagache T, Grassart A, Dallongeville S, et al.: Mapping molecular assemblies with fluorescence microscopy and object-based spatial statistics. Nat Commun. 2018; 9(1): 698. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChessel A, Cinquin B, Bardin S, et al.: ComputationalGeometry-BasedScale-SpaceandModalImageDecompositionApplicationtoLightVideo-MicroscopyImaging. volume 5567 of Lecture Notes in Computer Science. Springer Berlin Heidelberg, Berlin, Heidelberg, 2009. Reference Source\n\nKashiwagi Y, Higashi T, Obashi K, et al.: Computational geometry analysis of dendritic spines by structured illumination microscopy. Nat Commun. 2019; 10(1): 1285. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBates AS, Manton JD, Jagannathan SR, et al.: The natverse, a versatile toolbox for combining and analysing neuroanatomical data. eLife. 2020; 9: e53350. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBaddeley A, Turner R: spatstat: An R Package for Analyzing Spatial Point Patterns. J Stat Softw. 2005; 12(6). Reference Source\n\nThe CGAL Project: CGAL User and Reference Manual. CGAL Editorial Board, 5.1 edition, 2020. Reference Source\n\nVirtanen P, Gommers R, Oliphant TE, et al.: SciPy 1.0: fundamental algorithms for scientific computing in Python. Nat Methods. 2020; 17(3): 261–272. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAnytree.2016. Reference Source\n\nDawson-Haggerty, et al.: Trimesh. 2019. Reference Source\n\nSchindelin J, Arganda-Carreras I, Frise E, et al.: Fiji: An open-source platform for biological-image analysis. Nat Methods. 2012; 9(7): 676–682. PubMed Abstract | Publisher Full Text | Free Full Text\n\nde Chaumont F, Dallongeville S, Olivo-Marin JC: ICY: a new open-source community image processing software. In IEEE International Symposiumon Biomedical Imaging(ISBI). 2011. Publisher Full Text\n\nPhan MS, Chessel A: Genepy3d. October 2020. http://www.doi.org/10.5281/zenodo.4269466\n\nPhan MS, Chessel A: Genepy3d_gpl. October 2020. http://www.doi.org/10.5281/zenodo.4269484\n\nPhan MS, Matho K, Livet J: Emmanuel Beaurepaire, and Anatole Chessel. A scale-space approach for 3D neuronal traces analysis. bioRxiv. 2020. Publisher Full Text\n\nKunst M, Laurell E, Mokayes N, et al.: A Cellular-Resolution Atlas of the Larval Zebrafish Brain. Neuron. 2019; 103(1): 21–38.e5. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "75563",
"date": "15 Dec 2020",
"name": "Virginie Uhlmann",
"expertise": [
"Reviewer Expertise Bioimage 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 authors describe GeNePy3D, a Python toolbox that facilitates the processing and quantification of geometrical objects extracted from images. The goal is for this package to bring together the methods provided in various existing geometrical processing libraries such as PyEMD, Trimesh, or AnyTree. The provided example reanalyzing the larval zebrafish connectome dataset of Kunst et al. is well-chosen and convincing. Overall, GeNePy3D is an absolutely relevant software that is likely to be impactful in the bioimage analysis community.\nMajor comments:\nThe authors mention Fiji and Icy, which are indeed widely used to quantify geometry from bioimages. They however do not spell out clearly how they envision GeNePy3D to interact with these GUI-based (and Java-based!) alternatives. More details on this aspect should be provided.\n\nThe GitHub repo should be better documented, in particular when it comes to describing the methods used in functions such as a curve or surface alignment (hence the \"sufficient details of the code\" point above flagged as \"partly\").\n\nThe article's title emphasizes the \"large scale\" aspect of GeNePy3D. From the implementation's description, I am under the impression that the scaling ability of this package comes \"for free\" from the fact that numpy, scipy, pandas, etc all scale extremely well. If there is more and specific efforts have been put into developing methods in a specific manner so as to allow processing of large datasets, this aspect should be discussed in more detail in the implementation section. If not and if this really is simply a consequence of using well-developed Python libraries, I would suggest downplaying a bit the \"large scale\" aspect of the toolbox.\n\nMinor comments:\nThe package name, GeNePy3D, is poorly chosen for two reasons: 1) the meaning of the acronym is unclear, 2) there exists already at least 3 different Python packages called genepy, all containing entirely unrelated algorithms. I would strongly suggest coming up with a more self-descriptive and less overused name.\n\nI am no expert in software licensing, but I worry that the two-licenses solution adopted here may be unnecessarily confusing for the end-user. Wouldn't there be a way to package the entirety of the library under a single BSD3/GPL license, or license it all under the most restrictive of the two if applicable? If having two repos under two licenses really is the only possible solution, some clear explanation of why this is so should be provided in the article.\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": "6796",
"date": "17 Jun 2021",
"name": "Anatole Chessel",
"role": "Author Response",
"response": "The authors describe GeNePy3D, a Python toolbox that facilitates the processing and quantification of geometrical objects extracted from images. The goal is for this package to bring together the methods provided in various existing geometrical processing libraries such as PyEMD, Trimesh, or AnyTree. The provided example reanalyzing the larval zebrafish connectome dataset of Kunst et al. is well-chosen and convincing. Overall, GeNePy3D is an absolutely relevant software that is likely to be impactful in the bioimage analysis community. We thank the reviewer for this positive overall assessment. Major comments: The authors mention Fiji and Icy, which are indeed widely used to quantify geometry from bioimages. They however do not spell out clearly how they envision GeNePy3D to interact with these GUI-based (and Java-based!) alternatives. More details on this aspect should be provided. Indeed Fiji and icy, and more generally the java-based ecosystem of bioimage informatics tools is very important in the community. The python-based ecosystem is becoming very important as well, with developments around napari and scikit image for example. Linking those two ecosystems is very important to allow heterogeneous workflows, and various solutions have been proposed such as https://github.com/imagej/pyimagej; but we feel this question is generally beyond the scope of this work, which presents a new python library and thus is usable wherever python is usable. For geometrical objects specifically, the development of a common exchange format would go a long way into allowing interactions between genepy3d and the java world, and is definitely part of the roadmap of future development, in genepy3d or elsewhere. The GitHub repo should be better documented, in particular when it comes to describing the methods used in functions such as a curve or surface alignment (hence the \"sufficient details of the code\" point above flagged as \"partly\"). We improved and reformatted the documentation, to make it easier to access and follow. The main documentation, with tutorials and generic information is still at genepy3d.gitlab.io. The reference documentation of the API is now hosted on readthedocs, separately for the two packages: genepy3d.readthedocs.io and genepy3d_gpl.readthedocs.io. Specifically for the alignment functions: that aspect is still essentially lacking in the library as is it, mainly because we had no occasion to implement it. There is one ‘align’ function for curves, which is quite specific and is now better documented. There is a huge bibliography on those topics and many available implementations; it is something that would be very useful to have in the library and that we do plan to tackle in the future. We removed explicit mention of alignment algorithms in the text, to avoid misleading the reader. The article's title emphasizes the \"large scale\" aspect of GeNePy3D. From the implementation's description, I am under the impression that the scaling ability of this package comes \"for free\" from the fact that numpy, scipy, pandas, etc all scale extremely well. If there is more and specific efforts have been put into developing methods in a specific manner so as to allow processing of large datasets, this aspect should be discussed in more detail in the implementation section. If not and if this really is simply a consequence of using well-developed Python libraries, I would suggest downplaying a bit the \"large scale\" aspect of the toolbox. The original applications were on large scale images, hence the ‘large scale’ in the title, but it is true that the genepy3d library itself does not provide any specific development for large scale processing. We propose to drop ‘large scale’ from the title to reflect that point, if that is possible at this stage of the publication process. Minor comments: The package name, GeNePy3D, is poorly chosen for two reasons: 1) the meaning of the acronym is unclear, 2) there exists already at least 3 different Python packages called genepy, all containing entirely unrelated algorithms. I would strongly suggest coming up with a more self-descriptive and less overused name. Finding a name for a project is complicated and we agree that, in retrospect, better choices most likely exist. It originally stood for Geometry of Neuron in Python in 3D. It might be clearer when heard (something like ‘geeneepaï’). We may indeed change it in the future, if it gains traction and the user and developer base expands; when going out of alpha for example. I am no expert in software licensing, but I worry that the two-licenses solution adopted here may be unnecessarily confusing for the end-user. Wouldn't there be a way to package the entirety of the library under a single BSD3/GPL license, or license it all under the most restrictive of the two if applicable? If having two repos under two licenses really is the only possible solution, some clear explanation of why this is so should be provided in the article. We would have welcomed another solution but we do not know of a clean, legal way to mix, in a project under BSD, both GPL and BSD code. Since we want the bulk of the library to be under a BSD license for compatibility with the rest of the python ecosystem (see also this argument for BSD in scientific code: https://www.astrobetter.com/blog/2014/03/10/the-whys-and-hows-of-licensing-scientific-code/), this means corralling out GPL bits. We will try to make them as small as possible, and the added complexity is mitigated by modern python package management, which makes it trivial to install additional packages. We added a sentence to explain this reasoning in the text."
}
]
},
{
"id": "80682",
"date": "16 Mar 2021",
"name": "Yizhi Wang",
"expertise": [
"Reviewer Expertise Bioimage informatics",
"machine learning"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe author design a Python package to analyze the various geometric objects extracted from microscopy images of the brain. The package combines tools from computational geometry, spatial statistic, and other fields into a unified API. The usefulness of the package is demonstrated by an example of re-analyzing the zebrafish brain region and neuron traces.\n\nThe tool should be very useful in gaining insights from the microscopy imaging data. The package is adequately documented, and the Docker file makes it easier to use for many users.\n\nIs the rationale for developing the new software tool clearly explained? Yes\n\nIs the description of the software tool technically sound? Yes\n\nAre sufficient details of the code, methods and analysis (if applicable) provided to allow replication of the software development and its use by others? Yes\n\nIs sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool? Yes\n\nAre the conclusions about the tool and its performance adequately supported by the findings presented in the article? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/9-1374
|
https://f1000research.com/articles/10-483/v1
|
17 Jun 21
|
{
"type": "Research Article",
"title": "A new modified Lehmann type – II G class of distributions: exponential distribution with theory, simulation, and applications to engineering sector",
"authors": [
"Oluwafemi Samson Balogun",
"Muhammad Zeshan Arshad",
"Muhammad Zafar Iqbal",
"Madiha Ghamkhar",
"Oluwafemi Samson Balogun",
"Muhammad Zafar Iqbal",
"Madiha Ghamkhar"
],
"abstract": "Background: Modeling against non-normal data a challenge for theoretical and applied scientists to choose a lifetime model and expect to perform optimally against experimental, reliability engineering, hydrology, ecology, and agriculture sciences, phenomena. Method: We have introduced a new G class that generates relatively more flexible models to its baseline and we refer to it as the new modified Lehmann Type – II (ML–II) G class of distributions. A list of new members of ML–II-G class is developed and as a sub-model the exponential distribution, known as the ML-II-Exp distribution is considered for further discussion. Several mathematical and reliability characters along with explicit expressions for moments, quantile function, and order statistics are derived and discussed in detail. Furthermore, plots of density and hazard rate functions are sketched out over the certain choices of the parametric values. For the estimation of the model parameters, we utilized the method of maximum likelihood estimation. Results: The applicability of the ML–II–G class is evaluated via ML–II–Exp distribution. ML–II–Exp distribution is modeled to four suitable lifetime datasets and the results are compared with the well-known competing models. Some well recognized goodness–of–fit including -Log-likelihood (-LL), Anderson-Darling (A*), Cramer-Von Mises (W*), and Kolmogorov-Smirnov (K-S) test statistics are considered for the selection of a better fit model. Conclusion: The minimum value of the goodness–of–fit is the criteria of a better fit model that the ML–II–Exp distribution perfectly satisfies. Hence, we affirm that the ML–II–Exp distribution is a better fit model than its competitors.",
"keywords": [
"Lehmann Type – II Distribution",
"Exponential Distribution",
"Hazard Rate Function",
"Moments",
"Rényi Entropy",
"Maximum Likelihood Estimation",
"Simulation."
],
"content": "Introduction\n\nOver the past two decades, the growing attention of researchers towards the development of new G families has explored the remarkable characteristics of baseline models. New models open new horizons for theoretical and applied researchers to address real-world problems, to proficiently and adequately fit them to asymmetric and complex random phenomena. Accordingly, several classes of distributions have been developed and discussed in the literature. For more details, we encourage the reader to see the credible work of some notable scientists including Marshall and Olkin1 Gx/Gx+αG¯x, who developed a new technique to generate models; Eugene et al.,2 who proposed beta generated-G class Gbetax; the quadratic rank transmutation map technique introduced by Shaw and Buckley3 [1+λGx−λG2x]; the Kumaraswamy generalized-G class proposed by Cordeiro and Castro4 [1−1−Gαxβ]; the gamma-G class proposed by Ristic and Balakrishnan5 −logGx; the exponentiated generalized (EG) class proposed by Cordeiro et al.6 [1−1−Gxαβ]; the T–X family proposed by Alzaatreh et al.7 1−RWGx; the Weibull–G family proposed by Bourguignon et al.8 [1−exp(−αGx/G¯xβ)]; the beta Marshall–Olkin–G class proposed by Alizadeh et al.9 IMarshall–Olkinab; the logistic-X family proposed by Tahir et al.10 [1+−logG¯x−α−1]; Kumar et al.11 proposed DUS transformation eGx−1/e−1; Mahdavi and Kundu12 proposed Alpha transformation αGx−1/α−1; Elbatal et al.13 proposed a new Alpha power transformed family of distributions GxαGx/α; and recently, Ijaz et al.14 proposed a Gull alpha power Weibull family αGx/αGx; among others.\n\nThis paper is organised into the following sections. A new modified Lehmann Type–II (ML–II) G class of distributions accompanied by a table of some special models is proposed and developed in A new modified Lehmann Type – II–G Class of distributions. A special model of ML–II–G class, known as a modified Lehmann Type–II exponential (ML–II–Exp) distribution, along with its mathematical and reliability measures are derived and discussed in Mathematical properties. The method of maximum likelihood estimation is used to estimate the unknown model parameters and develop some simulation results to assess the performance of maximum likelihood estimations (MLEs) in Inference. Applications are discussed in four real data applications and finally, the conclusion is reported in Conclusions.\n\n\nA new modified Lehmann Type – II–G Class of distributions\n\nLehmann15 proposed the Lehmann Type–I (L - I) distribution, which was the simple exponentiated version of any arbitrary baseline model. Accordingly, the first credit goes to Gupta et al.16 because they applied L – I on exponential distribution. The associated cumulative distribution function (CDF) is given by\n\nCordeiro et al.4 deserves to be acknowledged as they use dual transformation that yielded the Lehmann Type – II (L–II) G class of distributions. The associated CDF is given by\n\nThe closed-form feature of the L–II distribution assists one to derive and study its numerous properties and in literature, both the approaches (L–I and L–II) have been extensively utilized to study the unexplored characteristics of the classical and modified models.\n\nWe develop a new G class, known as a modified Lehmann Type–II (ML–II) G class of distributions. The corresponding CDF is given by\n\nwhere Gxξϵ01 is a CDF of any arbitrary baseline model based on the parametric vector ξ, dependent on (r x 1) with −∞<α<1, and α,β>0 are the scale and shape parameters, respectively. Let gxξ=dGxξ/dx be the density function of any baseline model. The associated probability density function (PDF), hazard rate function (HRF), and quantile function of ML–II–G class of distributions are given by, respectively\n\nNow and onward, the modified Lehmann Type–II–G random variable X corresponding to fML–II−Gxαβξ will be denoted by X~ML– II–Gxαβξ.\n\nThis study aimed to propose a new G class of distributions that generates more flexible alternative continuous models relative to its parent distribution. From a computational point of view, new models are very simple to interpret. New models offer greater distributional flexibility and can provide a better fit over the complex random phenomena that exclusively arise in engineering sciences. However, to the best of our knowledge, no study has been conducted previously that discusses our new G class, deliberates the unexplained complex random phenomena so well and advances the fit to a diverse range of sophisticated lifetime data.\n\nLinear combination provides a much more informal approach to discuss the CDF and PDF than the conventional integral computation when determining the mathematical properties. For this, binomial expansion is given as follows:\n\nInfinite linear combinations of CDF (1) and PDF (2) of ML–II–G class are given by, respectively\n\nThe r-th ordinary moment (say μr/) of X is given by\n\nwhere coefficient ωij∗=−1i+jαjβi−βj, ωij=∑i,j=0∞−1i+jβ−1i−β−1j, and Ir,i+jxξ=∫−∞∞xrGi+jxξgxξdx.\n\nFurther, by (1), Lehmann Type–II–G class and baseline Gx model can be traced back at α=0, and α=0,β=1, respectively. The expansions of CDF (5) and PDF (6) provide us with the Exp-G class, which is quite useful for the generalization of models.\n\nIn reliability analysis and life testing of a component in quality control, order statistics (OS) and its moments are considered as a noteworthy measure. Let X1,X2,…,Xn be a random sample of size n that follows the Lehmann Type–II–G class and X1:n<X2:n<…<Xn:n be the corresponding OS. The random variables Xi,X1, and Xn be the i-th, minimum, and maximum OS of X.\n\nThe PDF of Xi is given by\n\nwhere =1,2,3,…,n,Fxξ, and fxξ are the associated CDF (5) with corresponding PDF (6) of the Lehmann Type–II–G family. Using the fact that\n\nBy placing the last expression in fi:nxξ, we get the most refined form of OS PDF and one may determine it by integrating (5–6) and the expression may be given as follows\n\nIn this section, we introduce a sub-model of ML–II–G class of distributions, known as a ML–II–Exp distribution. For this, we have the CDF and PDF of the exponential distribution GExpxθ=1−e−θx, and gExpxθ=θe−θx,forθ>0,0<x<∞, respectively. The associated CDF and corresponding PDF of the ML–II–Exp distribution are obtained by following (1–2) and its analytical expressions are given by respectively:\n\nwhere α is a scale and β,θ>0 are the shape parameters, respectively. By following (1–2), linear representation of CDF and PDF are given as follows, respectively\n\nwhere ζij=−1jθjβ+ij−βiαj1−α−β−ij!, ζij∗=−1j1−α−β−iαiθj+1−β−1ii+βjj!\n\nExpression in (11) is expected to be quite supportive in the forthcoming computations of various mathematical properties of the ML–II–Exp distribution.\n\n\nMathematical properties\n\nOne of the imperative roles of probability distribution in reliability engineering is to analyze and predict the life of a component. One may define the reliability function as the probability that a component survives until the time x and analytically it can be written as Rx=1−Fx.\n\nThe reliability function of X is given by\n\nIn reliability theory, the significant contribution of a function that measures the failure rate of a component in a particular time t is sometimes referred to as the HRF, failure rate function, or the force of mortality, and mathematically it can be written as hx=fx/Rx.\n\nThe HRF of X is given by\n\nNumerous notable reliability measures for the ML–II–Exp distribution can be discussed and derived, such as reverse HRF by hrxαβθ=fxαβθ/Rxαβθ, Mills ratio by Mxαβθ=Rxαβθ/fxαβθ, and Odd function by\n\nDifferent plots of PDF and HRFs of the ML–II–Exp distribution are sketched over the selected and fixed combinations of the model parameters, respectively. Figure 1 (a, b, c) presents the reversed-J, constant, unimodal, and right-skewed shapes of the PDF and Figure 2 (a, b, c) illustrates the decreasing and increasing HRF. However, an increasing HRF with some interesting facts are identified when suddenly spikes arise at the tail end of HRF is unexpectedly detected. Such kinds of trends are often observed in non-stationary time series lifetime phenomena.\n\nHere we study the limiting behavior of CDF, PDF, reliability, and HRFs of the ML–II–Exp distribution present in (8), (9), (13), and (14) at x→0 and x→∞.\n\nProposition-1: Limiting behavior of CDF, PDF, reliability, and HRFs of the ML–II–Exp distribution at x→0 is followed by\n\nProposition-2: Limiting behavior of CDF, PDF, reliability, and HRFs of the ML–II–Exp distribution at x→∞ is followed by\n\nLimiting behaviors developed in the above expressions may illustrate the effect of parameters on the tail of the ML–II–Exp distribution.\n\nMoments have a remarkable role in the discussion of the distribution theory, to study the significant characteristics of a probability distribution such as mean; variance; skewness, and kurtosis.\n\nTheorem 1: If X ∼ ML–II–Exp (x;α,β,θ), for x;β,θ>0, with −∞<α<1, then the r-th ordinary moment (say μr/) of X is given by\n\nwhere ηi=αi1−α−β−i−β−1i\n\nProof: μr/ can be written by following (11), as\n\nLet’s suppose θxβ+i=y;x=yθβ+i⟹dx=dyθβ+i\n\nlimits: as x⟶0⇒x⟶∞;y⟶0⇒y⟶∞.\n\nBy placing the above information in (15), we get\n\nby making simple computation on the last expression leads us to the r-th ordinary moment, in terms of the gamma function and it is given by\n\nwhere Γ. is a gamma function,Γx=∫0∞tx−1e−tdt,ηi=αi1−α−β−i−β−1i, and −∞<α<1.\n\nThe derived expression in (16) may serve a supportive and useful role in the development of several statistical measures. For instance: to deduce the mean of X, placer = 1 in (16). For the higher-order ordinary moments of X approximating to 2nd, 3rd, and 4th, and higher, these moments can be formulated by setting r = 2, 3, and 4 in (16), respectively. Additionally, to discuss the variability in X, the Fisher index (F. I = (VarX/EX)) may play a significant role in this scenario. To derive the negative moments of X, simply substitute r by –w in (16). One may perhaps further determine the well-established statistics such as skewness (τ1=μ32/μ23), and kurtosis (τ2=μ4/μ22), of X by integrating (16). A well-established relationship between the central moments μs and cumulants (Ks) of X may easily be defined by ordinary moments μs=∑k=0ssk−1kμ1/sμs−k/. Hence, the first four cumulants can be calculated by K1=μ1/,K2=μ2/−μ1/2 , K3=μ3/−3μ2/μ1/+2μ1/3, and K4=μ4/−4μ3/μ1/−3μ2/2+12μ2/μ1/2−6μ1/4, etc., respectively.\n\nIn Table 2, some numerical results of the first eight ordinary moments, ε2 = variance, τ1= skewness, and τ2= kurtosis for some chosen parameters are presented in S-I (α=0.9,θ=0.1,β=1.1), S-II (α=0.9,θ=0.5,β=1.5), S-III (α=0.8,θ=0.09,β=3.1), and S-IV (α=0.5,θ=0.009,β=5.1).\n\nThe residual life function/conditional survivor function of random variable Rt=X+t/X>t X is the probability that a component whose life says x, survives in an additional interval at t≥0. Analytically it can be written as\n\nThe residual life function of X is given by\n\nwith associated CDF\n\nPDF and HRF corresponding to (18) are given as follows, respectively\n\nMean residual life function is given by\n\nMoreover, the reverse residual life can be defined as: R¯t=t−X/X≤t.\n\nThe reverse residual life function of X is given by\n\nwith associated CDF\n\nPDF and HRF corresponding to (22) are given as follows, respectively\n\nMean reversed residual life function/mean waiting time is given by\n\nOne may derive the strong mean inactivity time of X by following\n\nwhere Φrt=∫0txrfxdx, is the r–th incomplete moment, μ1t/=∫0txfxdx=βθ∑i=0∞ηiβ+i2Γt2, and μ2t/=∫0tx2fxdx=βθ2∑i=0∞ηiβ+i3Γt3. By following (16), we may derive directly the μ1t/ and μ2t/ by holding “t=lθβ+i” as the upper bound. Furthermore, μ1t/ and μ2t/ are termed as the first and second lower incomplete moments of X, respectively, with ηi=αi1−α−β−i−β−1i, and −∞<α<1.\n\nWhen a system is quantified by disorderedness, randomness, diversity, or uncertainty, in general, it is known as entropy.\n\nRényi17 entropy of X is given by\n\nBy following (9), we simplify fx in terms of fζx, we get\n\nby placing the above expression in (25), we get\n\nhence, solving simple mathematics on the previous equation leads us to the most simplified form of the Rényi entropy of X and it is given by\n\nwhere vj=α1−αj−ζβ+1j,τζ=1θζβ+1,−∞<α<1.\n\nThe qth quantile function of ML–II–Exp distribution is obtained by inverting the CDF. Quantile function is defined as q=Fxq=PX≤xq,q∈01.\n\nThe quantile function of X is given by\n\nTo obtain the 1st quartile, median and 3rd quartile of X, place q = 0.25, 0.5, and 0.75 respectively in (26). Henceforth, to generate random numbers, one may assume that the CDF in (8) follows the uniform distribution u = U (0, 1).\n\nThe modal value of X is calculated by following the constraint f/xαβθ=dfxαβθdx=0. For convenience, fxαβθ can be rewritten as\n\nThe simplified form of f/xαβθ is given by\n\nHence, solving simple algebra on the previous equation may provide us with the most suitable form of the mode of X in support of f/xαβθ=0 and it is given by\n\nLet X1 and X2 be defined to discuss the strength and stress of a component, respectively, followed by the same uni-variate family of distributions, which will work in order if X2<X1. To discuss the reliability (say R) of X, it is given by R=PX2<X1.\n\nTheorem 2: Let X1∼ ML–II–Exp (x;α,β1,θ) and X2∼ ML–II–Exp (x;α,β2,θ) be independent random variables following the ML–II–Exp distribution; then the reliability is given by\n\nR=β1β1+β2\n\nProof: Reliability (R) is defined as\n\nR of X can be written by following (9), as\n\nLet’s suppose t=e−θx1−α+αe−θxβ1⇒−dt=1−αβ1θe−θβ1x1−α+αe−θxβ1+1dx;andtβ2β1=e−θx1−α+αe−θxβ2\n\nlimits: as x⟶0⇒t⟶1;x⟶∞⇒t⟶0.\n\nBy placing the above information in (27), we have\n\nHence, the simple computation of the above expression provides us with the reduced form of R in terms of β1 and β2, as we presume that the R is a function of β1 with increasing behavior and it is given by\n\nIn reliability analysis and life testing of a component in quality control, order statistics OS and its moments are considered as a noteworthy measure. Let X1,X2,…,Xn be a random sample of size n following the ML–II–Exp distribution and X1:n<X2:n<…<Xn:n be the corresponding OS. The random variables Xi,X1, and Xn be the i-th, minimum, and maximum OS of X.\n\nThe PDF of Xi is given by\n\nBy following (8) and (9), the PDF of Xi takes the form\n\nby utilizing some the techniques of binomial expansion (mentioned in the new modified Lehmann Type – II–G Class of distributions) to simplify (28), we get the reduced form of fi:nxαβθ and it is given as follows\n\nand we determine the linear representation of (29) and it can be written as\n\nIndeed, (29) has a supportive role in the calculation of r-th moment OS and hereafter, straightforward computation of (29) leads us to the r-th moment OS of X and it is given as follows\n\nwhere ηjk=−1ji−1jλkαk1−αλ−k,λ=−βn−i+j+1+1,v=βθn−i+j+1\n\nThe CDF of Xi is given by\n\nFurthermore, the minimum and maximum OS of X follows directly from (28) with i = 1 and i = n, respectively.\n\n\nInference\n\nIn this section, we estimate the parameters of the ML–II–Exp distribution by following the method of MLE, as this method provides the maximum information about the unknown model parameter. Let X1,X2,X3,…,Xn be a random sample of size n from the ML–II–Exp distribution, then the likelihood function LML-II-Expψ=αβθ=∏i=1nfML−II–Expxiψ of X is given by\n\nThe log-likelihood function, lψ is given by\n\nPartial derivatives of (33) w.r.t. α,θ, and β yield, respectively\n\nThe maximum likelihood estimates ( ψ̂i=α̂,β̂,θ̂) of the ML–II–Exp distribution can be obtained by maximizing (33) or by solving the above non-linear equations simultaneously. These non-linear equations, however, do not provide an analytical solution for the MLEs and the optimum value of α, β and θ. Consequently, iterative techniques such as the Newton-Raphson type algorithm are an appropriate choice in the support of MLEs.\n\nIn this sub-section, we discuss the performance of MLEs using the following algorithm.\n\nStep 1: A random sample x1, x2, x3 , ..., xn of sizes n = 25, 50, 100, 200, 300, 400, and 500 are generated from (26).\n\nStep 2: The required results are obtained based on the different combinations of the model parameters placed in S-V (α=0.9,θ=1.1,β=0.5), S-VI (α=0.5,θ=1.2,β=0.6), and S-VII (α=0.9,θ=0.2,β=0.06), S-VIII (α=0.5,θ=0.09,β=0.2), S-IX (α=0.1,θ=0.1,β=0.2) and S-X (α=0.9,θ=0.1,β=0.9).\n\nStep 3: Average MLEs and their corresponding standard errors (SEs) (in parenthesis) are presented in Table 4.\n\nStep 4: Estimated bias, root mean square error (RMSE), variance, and mean values are presented in Table 5.\n\nStep 5: Each sample is replicated N = 500 times.\n\nStep 6: A gradual decrease in SEs, biases, RMSE, variances, means, and MLEs pretty close to the true parameters are observed with increase in the sample sizes.\n\nStep 7: Finally, the estimates present in Tables 4 and 5 help us to specify that the method of maximum likelihood works consistently for the ML–II–Exp distribution.\n\nThe in-practice measures for the development of average estimate (AE), SE, bias, and RMSE are given as follows:\n\n\nFour real data applications\n\nIn this section, we explore four suitable lifetime datasets to model the ML–II–Exp distribution. These datasets are associated with the engineering sector. The first dataset relates to the study of failure times of 84 windshields for a particular model of aircraft (the unit for measurement is 1000 hours) that was first discussed by Ramos et al.18 The second dataset relates to the study of service times of 63 aircraft windshields (the unit for measurement is 1000 hours) that was discussed by Tahir et al.19 The third dataset follows the discussion of the breaking stress of carbon fibers (in Gba) that was initially developed by Nicholas and Padgett20 and finally the fourth one relates to the study of fatigue life of 6061 - T6 aluminum coupons cut parallel to the direction of rolling and oscillated at 18 cycles per second. The data set consists of 101 observations with maximum stress per cycle of 31,000 psi. This dataset was pioneered by Birnbaum and Saunders.21 Subsequently, this data was discussed by Shanker et al.,22 after subtracting 65 from each observation. The datasets are given in the underlying data.\n\nThe ML–II–Exp distribution is compared with the well-known models (CDF list is mentioned in Table 6). We follow some recognized selection criteria including -Log-likelihood (-LL), Anderson-Darling (A*), Cramer-Von Mises (W*), and Kolmogorov-Smirnov (K-S) test statistics. Some common results of descriptive statistics such as minimum value, 1st quartile, means, 3rd quartile, 95% confidence interval, and the maximum value, are tabulated in Table 3. The parameter estimates, standard errors (in parenthesis), and the goodness-of-fit are confirmed in Tables 7-10, respectively. The minimum value of the goodness-of-fit is the criteria of the better fit model that the ML–II–Exp distribution perfectly satisfies. Hence, we affirm that the ML–II–Exp distribution is a better fit than its competitors.\n\nFurthermore, for a visual comparison the fitted density and distribution functions, Kaplan-Meier survival and probability-probability (PP) plots, total time on test transform (TTT), and box plots, are presented in Figures 3–6 (a, b, c, d, e, f, g, h), respectively. These plots provide sufficient information about the closest fit to the data. All the numerical results in the subsequent tables are calculated with the assistance of statistical software RStudio-1.2.5033. with its package AdequacyModel. The explored datasets are given in the underlying data.\n\n\nConclusion\n\nIn this article, we introduced and studied a more flexible G class, called the modified Lehmann Type–II (ML–II) G class of distributions along with explicit expressions for the moments, quantile function, and OS. The exponential distribution was used as the baseline distribution for ML–II–G class, known as ML–II–Exp distribution. It was discussed comprehensively, which demonstrated the reversed-J, constant, unimodal, and right-skewed shapes of a density function. The method of MLE along with the simulation was carried out to investigate the performance of the proposed method. The efficiency of the ML–II–G class was evaluated when the most efficient and consistent results of ML–II–Exp distribution competed the well-known models and explored the dominance along with a better fit in four real-life datasets.\n\nWe hope that in the future, the proposed class and its sub-models will explore the wider range of applications in diverse areas of applied research and will be considered as a choice against the baseline models.\n\n\nData availability\n\nFigshare. four_dataset.csv. DOI: https://doi.org/10.6084/m9.figshare.14518383.v131\n\nThis project contains the following extended data:\n\n• Failure Time of 84 Windshield, Service Times of 63 Aircraft Windshield, Breaking Stress of Carbon Fibers and Fatigue Life of 6061 - T6 Aluminum Coupons used for the article titled “A New Modified Lehmann Type – II G Class of Distributions: Exponential Distribution with Theory, Simulation, and Applications to Engineering Sector”\n\n• Ramos et al. dataset\n\n• Tahir et al. dataset\n\n• Nicholas and Padgett dataset\n\n• Birnbaum and Saunders dataset\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC BY 4.0 Public domain dedication).",
"appendix": "Acknowledgments\n\nThe authors are grateful to the Editor-in-Chief and anonymous referrers for their constructive comments and valuable suggestions which certainly improved the quality of the paper. We dedicate this work to our mentor Professor Dr. Munir Ahmad (Late) who was the Founding President of the Islamic Society of Statistical Sciences (ISOSS), Editor-in-Chief of Pakistan Journal Statistics, and the paramedic staff that are scarifying their lives against the COVID-19 pandemic war.\n\n\nReferences\n\nMarshall AW, Olkin I: A New Method for Adding a Parameter to a Family of Distributions with Application to the Exponential and Weibull Families. Biometrika. 1997; 84: 641–652. Publisher Full Text\n\nEugene N, Lee C, Famoye F: Beta-normal distribution and its applications. Commun. Stat. Theory Methods. 2002; 31: 497–512. Publisher Full Text\n\nShaw WT, Buckley IRC: The alchemy of probability distributions: Beyond Gram-Charlier expansions, and a skew-kurtotic-normal distribution from a rank transmutation map. arXiv preprint arXiv:0901.0434. 2007.\n\nCordeiro GM, De Castro M: A new family of generalized distributions. J. Stat. Comput. Simul. 2011; 81: 883–893. Publisher Full Text\n\nRistic MM, Balakrishnan N: The gamma-exponentiated exponential distribution. J. Stat. Comput. Simul. 2012; 82: 1191–1206. Publisher Full Text\n\nCordeiro GM, Ortega EMM, da-Cunha DCC: The exponentiated generalized class of distributions. Data Sci. J. 2013; 11: 777–803. Publisher Full Text\n\nAlzaatreh A, Lee C, Famoye F: A new method for generating families of continuous distributions. Metron. 2013; 71: 63–79. Publisher Full Text\n\nBourguignon M, Silva RB, Cordeiro GM: The Weibull-G family of probability distributions. Data Sci. J. 2014; 12: 53–68. Publisher Full Text\n\nAlizadeh M, Cordeiro GM, de-Brito E, et al.: The beta Marshall-Olkin family of distributions. IJSDA. 2015; 2: Art 4. Publisher Full Text\n\nTahir MH, Cordeiro GM, Alzaatreh A, et al.: The Logistic-X family of distributions and its applications. Commun. Stat. Theory Methods. 2016; 45: 732–7349. Publisher Full Text\n\nKumar D, Singh U, Singh SK: A Method of Proposing New Distribution and its Application to Bladder Cancer Patients Data. JSAPL. 2015; 2: 235–245.\n\nMahdavi A, Kundu D: A new method for generating distributions with an application to exponential distribution. Commun. Stat. Theory Methods. 2017; 46: 6543–6557. Publisher Full Text\n\nElbatal I, Ahmad Z, Elgarhy M, et al.: A new alpha power transformed family of distributions: properties and applications to the Weibull model. J. Nonlinear Sci. Appl. 2019; 12: 1–20. Publisher Full Text\n\nIjaz M, Asim SM, Alamgir M, et al.: Gull Alpha Power Weibull distribution with applications to real and simulated data. PLoS ONE. 2020; 15: e0233080. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLehmann EL: The power of rank tests. Ann. Math. Stat. 1953: 23–43. Publisher Full Text\n\nGupta RC, Gupta PL, Gupta RD: Modeling failure time data by Lehman alternatives. Commun. Stat. Theory Methods. 1998; 4: 887–904. Publisher Full Text\n\nRényi A: On measures of entropy and information. In: Proceedings of the 4th Fourth Berkeley Symposium on Mathematical Statistics and Probability. Berkeley: University of California Press; 1961; 547–561.\n\nRamos MWA, Marinho PRD, Silva RV, et al.: The exponentiated Lomax Poisson distribution with an application to lifetime data. Adv Applications Statistics. 2013; 34: 107–135.\n\nTahir MH, Cordeiro GM, Mansoor M, et al.: The Weibull-Lomax Distribution: Properties and Applications. Hacet. J. Math. Stat. 2015; 44: 461–480. Publisher Full Text\n\nNicholas MD, Padgett WJ: A bootstrap control chart for Weibull percentiles. Qual. Reliab. Eng. Int. 2006; 22: 141–151. Publisher Full Text\n\nBirnbaum ZW, Saunders SC: Estimation for a family of life distributions with applications to fatigue. J. Appl. Probab. 1969; 6: 328–347. Publisher Full Text\n\nShanker R, Fesshaye H, Selvaraj S: On modeling of lifetimes data using exponential and lindley distributions. BBIJ. 2015; 2: 140–147. Publisher Full Text\n\nBalakrishnan N: Order statistics from the half logistic distribution. J. Stat. Comput. 1985; 20: 287–309. Publisher Full Text\n\nAhuja JC, Nash SW: The generalized Gompertz verhulst family of distributions. Sankhya. 1967; 29: 144–156. Publisher Full Text\n\nNadarajah S, Kotz S: The beta exponential distribution. Reliab. Eng. Syst. Saf. 2006; 91: 689–697. Publisher Full Text\n\nEl-Alosey AR: Random sum of new type of mixture of distribution. IJSS. 2007; 2: 49–57.\n\nLan Y, Leemis LM: The Logistic–Exponential Survival Distribution. Nav. Res. Logist. 2008; 55: 252–264. Publisher Full Text\n\nSalah MM, Raqab MZ, Ahsanullah M: Marshall-Olkin Exponential Distribution: Moments of Order Statistics. J. Appl. Stat. 2009; 17: 81–91.\n\nNadarajah S, Haghighi F: An extension of the exponential distribution. Stat. 2011; 45: 543–558. Publisher Full Text\n\nMerovci F, Puka L: Transmuted exponential distribution. Information Systems and Technology Innovation: their application in Economy.Albania; 2012.\n\nBalogun, Oluwafemi S, Arshad, et al.: four_dataset.csv. figshare. Dataset. 2021. Publisher Full Text"
}
|
[
{
"id": "102485",
"date": "22 Dec 2021",
"name": "Frank Gomes-Silva",
"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\nThe authors propose a new probabilistic class. Then, starting from this class, they propose a new distribution called ML-II-Exp. Present mathematical properties, simulation, and application for this new distribution. Here are some notes:\nThe introduction can be improved. More motivation is needed to introduce a new generator. More references should be added, for example:\nParameter induction in continuous univariate distributions: Well established G families, by Tahir and Nadarajah1; Compounding of distributions: a survey and new generalized classes, by Tahir and Cordeiro2, among others. These two references are important in giving readers an overview of the area.\n\nThe authors should have explored Lehmann's distributions - see, for example, My Musings on a Pioneering Work by Erich Lehmann and Its Rediscoveries on Some Families of Distributions, by Narayanaswamy Balakrishnan3. Professor Balakrishnan gives an explanation of Lehmann's contribution to the theory of distributions.\n\nAnother interesting article: Method for generating distributions and classes of probability distributions: the univariate case4, where authors generalize (and introduce new generators) to the vast majority of classes; class T-X is a particular case of this new method. It is worth noting that for the first time new generators are proposed from multiple baselines.\n\nWhat do you mean by DUS (in the introduction)?\n\nOn page 3 (just after Eq. 1), appears \\alpha <1 and then \\alpha > 0. What does that mean?\n\nIdentifiable problems are inconvenient when estimating the parameters of a model. A section to present proof of the model's (or even class') identifiability would be of interest. The following article presents an interesting section for identifiable issues: Normal-G Class of Probability Distributions: Properties and Applications5.\n\nEquation (22) appears in an unconventional form. The same goes for writing Equations (23) and (28). Writing in a conventional way!\n\nAt the end of the equations, put a period. Equations are part of the text.\n\nIn the simulation section, some discussions appear as steps. This can be confused with steps in an algorithm (which is usually placed in this type of section). The authors have presented an algorithm explaining a simulation. For example, what was done with the simulations that didn't converge?\n\nThe simulation can be improved. Note that the mean (for the \\theta parameter) is not close to the true value of the parameter.\n\nStandard errors play an important role in terms of accuracy. Standard errors are high in the first application for Alp-Exp and NH-Exp models. Where are the standard errors for the Etr-Exp model (in the first application)?\n\nThe W* and A* statistics are important measures of goodness-of-fit in distribution theory. But the proposed model (in the first application) loses to several others based on these indicators.\n\nIn Table 8, the standard error of the Etr-Exp model is too high.\n\nIn Table 9, the estimate for the parameter \\lambda is inconsistent since by definition \\lambda must be between -1 and 1.\n\nIn Table 9, where are the standard errors for the Etr-Exp model?\n\nTable 10 gives an estimate (for \\lambda) of -1.2479. This estimate is inconsistent since \\lambda must be between -1 and 1. For this same model (in this same line), the W* and A* statistics do not appear. Again, a very high standard error appears for the Etr-Exp model.\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": []
},
{
"id": "120000",
"date": "22 Feb 2022",
"name": "Nofiu Idowu Badmus",
"expertise": [
"Reviewer Expertise Inferential statistics",
"Computational Statistics",
"Distribution Theory"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nMy comments on the manuscript are as follows:\nGenerally, the paper is on non-normal data (i.e skewed data) as one of the challenges in Statistics in which several authors in literature have developed many suitable distributions/models to capture the excessive skewness and kurtosis of the data. Although, the authors of this paper based their work on a part/segment in parametric distribution using G-model as the basic. They discussed and explored numerous G-models in literature to support their research. Properties of the ML-II G model are presented. The model is tested using both simulation and real-life phenomena. The results show that their model supersedes other models considered.\nThe title should be “A new modified Lehmann type – II G class of distributions: Theory, Simulation, and Applications”.\n\nThe abstract contains the problem, methods used, findings, and result which is good and ok.\n\nIn the introduction, the CDFs of cited papers are not necessary to appear in the context except the CDF and PDF of the work they followed in their work. Therefore, the introduction should dwell more on the paper(s) they used. This implies that there is a need for them to upgrade/add more to the introduction.\n\nA new G class is developed which is known as a new modified Lehmann Type-II-(ML-II) G class of distributions. Why a new G class? Since we can see many G classes in the literature. What makes your G class better than others?\n\nUnder Order Statistics, after the second expression where you wrote “one may determine it by integrating (5–6)” – with respect to? This is missing.\n\nUnder limiting behavior, it should be: “Here, we obtain the limiting behavior of PDF, CDF…”.\n\nIn Table 2, it should be that some chosen parameters with several values are presented.\n\nIn the paper, it was discussed that lessing/setting one or two parameter(s) in the model led to some special cases emanating from the proposed model, One of those special cases is Lehmann Type II. Due to the fact that the author's work targeted Lehmann Type II they need to include/cite some Lehmann Type II research works from the literature review. The following articles can serve as a guide for authors:\n\nN. I. Badmus, T. A. Bamiduro and S. G. Ogunobi (2014). Lehmann Type II Weighted Weibull Distribution1.\n\nBadmus, N. Idowu and Bamiduro, T. Adebayo. (2015). Log-Lehmann Type II Weighted Weibull (LLWW) Regression Model: Theory and Method2.\n\nBadmus, N. I., Bamiduro, T. A., Akingbade, A. A and Rauf-Animasaun, M. A (2016). Estimation of Parameters in Generalized Modified Weighted Weibull Distribution3.\n\nBadmus, N. I., Alakija, T. O. and Olanrewaju, G. O. (2017). The Beta-Modified Weighted Rayleigh Distribution: Application to Virulent Tubercle Disease4.\n\nAuthors may source for other ones online.\nThe manuscript can be accepted subject to the corrections listed above. Thanks.\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": []
}
] | 1
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https://f1000research.com/articles/10-483
|
https://f1000research.com/articles/10-31/v1
|
18 Jan 21
|
{
"type": "Software Tool Article",
"title": "o2geosocial: Reconstructing who-infected-whom from routinely collected surveillance data",
"authors": [
"Alexis Robert",
"Sebastian Funk",
"Adam J Kucharski",
"Sebastian Funk",
"Adam J Kucharski"
],
"abstract": "Reconstructing the history of individual transmission events between cases is key to understanding what factors facilitate the spread of an infectious disease. Since conducting extended contact-tracing investigations can be logistically challenging and costly, statistical inference methods have been developed to reconstruct transmission trees from onset dates and genetic sequences. However, these methods are not as effective if the mutation rate of the virus is very slow, or if sequencing data is sparse. We developed the package o2geosocial to combine variables from routinely collected surveillance data with a simple transmission process model. The model reconstructs transmission trees when full genetic sequences are not available, or uninformative. Our model incorporates the reported age-group, onset date, location and genotype of infected cases to infer probabilistic transmission trees. The package also includes functions to summarise and visualise the inferred cluster size distribution. The results generated by o2geosocial can highlight regions where importations repeatedly caused large outbreaks, which may indicate a higher regional susceptibility to infections. It can also be used to generate the individual number of secondary transmissions, and show the features associated with individuals involved in high transmission events. The package is available for download from the Comprehensive R Archive Network (CRAN) and GitHub.",
"keywords": [
"Transmission tree reconstruction",
"Bayesian statistics",
"Monte Carlo Markov Chains",
"outbreaks",
"R"
],
"content": "Introduction\n\nThe identification of transmission trees and transmission events during infectious disease outbreaks can lead to identifying factors associated with subsequent transmissions1–3, describing the populations or the areas more vulnerable to importations and transmission4–7, and quantifying the impact of control measures8,9. The most straightforward approach to reconstruct who-infected-whom is to carry out patient interviews and establish the previous contacts to connect the reported cases. However, contact-tracing investigations are costly and can be challenging to implement. Statistical methods have therefore been developed to infer transmission trees from routinely collected epidemiological data9–14.\n\nThe Wallinga-Teunis method was first developed to infer probabilistic transmission trees from onset dates and serial intervals in a maximum likelihood framework9. Genetic sequencing of pathogens have since become more common, and new tools such as the R package outbreaker2 were created to combine the timing of infection and the genetic sequences in order to improve the accuracy of inferred transmission trees10,11,15–17. Nevertheless, the accuracy of these reconstruction methods relies on the proportion of sequenced cases, the quality of the sequences, and the characteristics of the pathogen18. For instance, the measles virus evolves very slowly, and sequences from unrelated cases can be very similar, which makes these methods ineffective for measles outbreaks19,20.\n\nThe package o2geosocial was designed to study outbreaks where sequences are uninformative, either because too few cases were sequenced or because the virus evolves too slowly. Building upon the framework presented in outbreaker2, o2geosocial was developed to infer who-infected-whom from variables routinely collected by surveillance systems, such as the onset date, age, location, and genotype of the cases4. Cases from different genotypes cannot be part of a similar transmission chain since differences in genotype illustrate major variations in their genetic sequences,21. Using age-stratified contact matrices and mobility models, we combined the different variables into a likelihood of connection between cases. In this paper, we first describe the structure of the package. From a use case based on simulated data, we then show how to run the model, evaluate the output, visualise the results of the inference, and customise the input functions to implement different mobility models.\n\n\nMethods\n\no2geosocial is implemented as an open-source R (version ≥ 3.5.0) package and can be run on all platforms (Windows, Mac, Linux). It incorporates C++ functions into a R framework using Rcpp22. Package dependencies and system requirements are documented in the o2geosocial CRAN repository. A stable version was released on Windows, Mac and Linux operating systems via a CRAN repository. The source code is available through Zenodo23 and the latest development version is available through a Github repository.\n\n\n\nThe main function of the package, called outbreaker(), uses Monte Carlo Markov Chains (MCMC) to sample from the posterior distribution of the underlying model24. For each case, it infers the infection date, the infector, and the number of missing generations between the case and their infector. It takes five lists as inputs: i) ‘moves’, ii) ‘likelihoods’, iii) ‘priors’, iv) ‘data’, and v) ‘config’. These five lists can be generated and modified using the functions custom_moves(), custom_likelihoods(), custom_priors(), create_config() and outbreaker_data().\n\nThe general implementation of o2geosocial follows the structure of outbreaker2 and builds upon it by adding the effect of the location and the age-stratified contact data to the reconstruction of transmission clusters. However, unlike outbreaker2, o2geosocial does not take genetic sequences as input. It uses genetic groups (e.g. genotype) to exclude connections between cases, i.e. two cases cannot be from the same cluster if they belong to different genetic groups25. Therefore, o2geosocial is adapted to reconstructing transmission clusters from large datasets where genetic sequences are not informative, either because the mutation rate of the virus is slow, or because sequencing is scarce.\n\nIn o2geosocial, the number of independent clusters in the dataset is inferred using two different processes (Figure 1). Firstly, the pre-clustering step aims to group cases before the MCMC runs following three criteria: Only cases reported in a radius of γ km, less than δ days before case i, and from similar or unreported genotype can be classified as potential infectors of i. Cases with overlapping potential infectors, and their potential infectors, are grouped together, and cases from different groups cannot be linked during the MCMC runs. The parameters γ and δ are defined as inputs of the function create_config(). Since surveillance datasets can include cases from unrelated outbreaks, the pre-clustering function was developed to remove impossible connections and speed up the MCMC runs.\n\nSecondly, as cases classified in the same group after the pre-clustering step may come from different clusters, we defined a likelihood threshold λ to spot and discard unlikely connections after the MCMC runs: if the likelihood of connection between cases from j to i is lower than λ, the connection is discarded and i is an import unrelated to j. In o2geosocial, the variable λ can either be an absolute (the log-likelihood threshold will be log(λ)) or a relative value (a quantile of the likelihood of all connections in all samples), and is defined by the variables ‘outlier_threshold’ and ‘outlier_relative’ in create_config().\n\nFinally, unlikely connections between cases can alter the inferred infection dates of cases and bias the transmission trees sampled form the MCMC runs. Therefore, we first run a short MCMC to remove these unlikely connections. From this run we compute n, the minimum number of connections with a likelihood lower than λ per sampled tree. We then add n imports to the starting tree and run a longer MCMC. Lastly, we remove the connections with likelihood lower than λ in the final samples and return the infector, infection date and probability of being an import for each case (Figure 1).\n\nIn the first step, cases are split in two groups that do not have overlapping potential infectors (i.e. they were reported in different places, or different times). In step 2, we estimate the minimum number of unlikely transmissions (n) in the samples (right panel). In step 3, we remove n transmissions from the initial tree, and generate samples. Finally, we remove the unlikely connections in each sample of Step 3 and compute the inferred cluster size distribution.\n\nThe functions custom_likelihoods() and custom_priors() can be used to edit each component of the likelihood and priors. By default, there are five components in the likelihood:\n\nGenotype component: There can be a maximum of one genotype reported per transmission tree. The genotype of a tree τ is the genotype reported for at least one of the cases belonging to τ. For each genotyped case igen and at every iteration, only cases from trees with the same genotype as igen, or without reported genotype can be listed as potential infectors.\n\nTherefore, the genetic component of the likelihood that a case i of genotype gi was infected by a case j belonging to the tree τj is defined as a binary value:\n\n\n\nConditional report ratio: As in the package outbreaker2, we allow for missing cases in transmission chains. The number of generations between cases i and j, denoted κji, is equal to 1 if j infected i. We define ρ as the conditional report ratio of the trees, which differs from the overall report ratio of an outbreak as only unreported cases within transmission chains impact the conditional report ratio. Entirely unreported clusters, or unreported cases infected earlier than the ancestor of a tree do not change the value of ρ. By default, the probability of observing κji missing generation between i and j from the conditional report ratio p(κji|ρ) follows an exponential distribution.\n\nThe conditional report ratio is estimated during the MCMC runs using a beta distribution prior. The two parameters of the beta prior can be changed using the variable prior_pi in create_config() (default to Beta(10,1)).\n\nTime component: The probability of ti being the infection date of the case i reported at time Ti depends on the distribution of the incubation period f. The incubation period is defined by the variable f_dens in the function outbreaker_data().\n\nThe probability that i was infected by j given their respective inferred dates of infection ti and tj is defined by the generation time of the disease wκji(ti – tj) (variable w_dens in outbreaker_data()), and the number of generations κji between i and j. The function wκji was defined as wκji = w * w * ...* w, where * is the convolution operator applied κji times.\n\nThis component of the likelihood follows the framework developed in the Wallinga-Teunis method, and in outbreaker2.\n\nSpatial component: The probability of connection between two regions k and l depends on the population sizes mk and ml, and the distance between regions dkl. Given spatial parameters a and b, s(k,l) is the probability that a case in the region k was infected by a case reported in l, and is defined using pkl, the connectivity between regions k and l:\n\n\n\nThe package comes with a built-in exponential gravity model: F(dkl,a)=e−b*dkl; or a power-law gravity model : F(dkl,a)=(1dkl)b. The exponential gravity model has been shown to be a better representation of short-distance mobility patterns26; it is therefore the default option since o2geosocial aims at reconstructing transmission in a community or a region. The type of gravity model can be changed by setting the parameter spatial_method to “power-law”: create_config(spatial_method = \"power_law\"). Other mobility models can be implemented by developing modules. In the use case, we give an example on how to replace the exponential gravity by Stouffer’s rank model27.\n\nThe parameters a and b are estimated during the MCMC run via posterior sampling. This requires re-computing the matrix of spatial connectivity between regions at each iteration and is time-consuming. Therefore, if either a or b is estimated, we allow for a maximum of 1 missing generation between cases (max(κji) = 2) and only compute s1(k,l) and s2(k,l) for regions that could potentially be connected. By default, the prior distribution of a and b are uniform.\n\nAge component: Given the age group of each case α(1,..,N) and the age-stratified social contact matrix, we introduced aκji(αi, αj), the probability that a case aged αj infected a case aged αi. This corresponds to the proportion of contacts to αi that came from individuals of age αj. Social contact matrices provided by large scale quantitative investigations such as the POLYMOD study quantify the probability of contact between infectors and infectees of different age groups28, and are imported using the R package socialmixr29. The contact matrix used in the MCMC run is defined by the variable a_dens in outbreaker_data().\n\nOverall likelihood: The overall likelihood that a case i was infected by the case j is equal to Li(ti,j,tj,θ) = log(f(ti – Ti)) + Lji(ti,tj,θ) where f(ti – Ti) is the likelihood that a case reported on Ti was infected on ti, and Lji(ti,tj,θ) is the log-likelihood of connection between i and j defined as:\n\n\n\nAt every iteration of the MCMC, a set of movements is used to propose an update of the transmission trees. This update is then accepted or rejected depending on the posterior density with the proposed trees. By default, eight movements are tested at each iteration. Three of them were already part of outbreaker2 and were not modified:\n\n(cpp_move_t_inf() changes the infection date of the cases; cpp_move_pi()changes the conditional report ratio; cpp_move_kappa() changes the number of generations between cases). Two movements were edited to scan each transmission tree in order to prevent different genotypes from being in the same tree: (cpp_move_alpha() changes the infector; cpp_move_swap_cases() swaps infector and infectee). The remaining three are new movements:\n\n• cpp_move_a() and cpp_move_b() change the spatial parameters a and b and update the probability of connection between regions.\n\n• cpp_move_ancestor() changes the ancestor of the tree. An ancestor is defined as the first case of a transmission tree. For each ancestor i, an index case is drawn from the pool of potential infectors, while another link is randomly picked and deleted.\n\n\nUse case\n\nTwo simulated datasets are included in o2geosocial: toy_outbreak_short and toy_outbreak_long. Both are lists describing simulated outbreaks and include three elements: i) cases: a data.table with the ID, location, onset date, genotype, age group, import status, cluster, generation and infector of each case; ii) dt_regions: a data table with the ID, population, longitude and latitude of each region; iii) age_contact: a numeric matrix of the proportion of contact between age groups. Both simulations were ran using distributions of the serial interval and the latent period typically associated with measles outbreaks: the incubation period followed a gamma distribution of mean 11.5 days (standard deviation 2.24 days)30; the serial interval followed a normal distribution of mean 11.7 days (standard deviation 2.0 days)31.\n\nIn this use case, we analyse toy_outbreak_short. The dataset contains 75 simulated cases from different census tracts of Ohio in 2014 (variable cens_tract). The census tracts represent areas established by the Bureau of Census for analyzing populations and generally contain between 2,500 to 8,000 inhabitants. The variable cluster describes the transmission tree each case belongs to, and \"generation\" is equal to the number of generations between the first case of the tree (generation = 1) and the case.\n\nIn this use case, we reconstruct the cluster size distribution of the simulated outbreaks using different models. We then evaluate the agreement between the inferred and the reference transmission clusters in each model, and compare the results obtained with each model. Finally, we assess the geographical heterogeneity of the reconstructed transmission dynamics. We use the package data.table for handling data throughout as it is optimised to deal with large datasets32. The methods defined in o2geosocial would work similarly if we had used the data.frame syntax and format.\n\n\n\nIn the simulated data, 95% of the clusters contain less than five cases, 47.6% of the clusters are isolated (also called singletons). One larger cluster includes 31 cases (Figure 2).\n\n\n\nWe set up the distributions the model will use to reconstruct the transmission trees. We define f_dens as the duration of the latent period, and w_dens as the serial interval. These distributions have previously been described for measles outbreaks30,31,33,34.\n\n\n\nThe age specific social contact patterns can be imported from the element age_contact of the list toy_outbreak_short. Alternatively, one can use the R package socialmixr to import a social contact matrix from the POLYMOD survey29.\n\n\n\nFinally, the distance matrix between regions is set up from the data table dt_regions, element of toy_outbreak_short. We use the column population to set up the population vector pop_vect. We compute the distance between each region into the distance matrix dist_mat using the package geosphere35.\n\n\n\nWe create the lists data, config, moves, likelihoods and priors to run the main function of the package. In this example, we use the default parameters to build moves, likelihoods and priors. The list data contains the distributions f_dens and w_dens, the population vector and the distance matrix, along with the onset dates, age group, location and genotype of the cases.\n\nRoutinely collected surveillance data can include information on the importation status of the cases. In order to investigate the impact of using prior information on the importation status of the cases on cluster reconstruction, we implement two different models: in out1 the import status is inferred by the model, whereas in out2 it is set as an input parameter of the model, which only estimates who infected whom.\n\nThe first short run in out1 is run with 10,000 iterations to find the minimum number of importations, and the main run lasts for 20,000 iterations in both models. As the import status of the cases is inferred in out1, we have to set a threshold to quantify what is an unlikely likelihood of transmission between cases. We use a relative outlier threshold at 0.9, which means that the threshold will be the 9th decile of the negative log-likelihoods Li(ti,j,tj,θ) in every sample.\n\n\n\nThe data frames out1 and out2 contain the posterior density, likelihood, and prior density of the trees generated at every iteration, along with the values of the spatial parameters a and b, the conditional report ratio pi, and the index, estimated infection date and number of generations for each case.\n\nThe function summary prints a summary of the data frame generated by outbreaker(). It contains a list with the number of steps, the distributions of the posterior, likelihood and priors, the parameter distributions, the most likely infector and the probability of being an import for each case, and the cluster size distribution.\n\n\n\nIn order to compare the reconstructed clusters to the data in each model, we plot the median inferred cluster size distribution in out1 and out2 and the credible intervals. First, we group together clusters of similar sizes by defining the breaks of each group in the vector group_cluster. In this example, we defined the size categories as 1; 2; 3 – 4; 5 – 9; 10 – 15; 15 – 40 and 40 + cases. The inferred cluster size distributions are shown in the element cluster from the output of summary(out1), and are aggregated using the input variable group_cluster.\n\n\n\nThe number of isolated cases in the inferred trees in out1 is lower than in the data (Figure 3). We can therefore conclude that when the import status of the cases was inferred, the model underestimated the number of clusters and tended to link together unrelated cases. The cluster size distribution when the import status of the cases is inferred depends on the likelihood threshold set in outlier_threshold and outlier_relative. Using different values of λ would impact the cluster size distribution in out1. Conversely, the cluster size distribution in out2 is very similar to the data (Figure 3).\n\n\n\nWe investigate the reconstructed transmission trees to ensure the index assigned to each case is in agreement with the reference dataset. To do so, we write two functions: in index_infer we compute the proportion of iterations where the inferred index of each case matches their actual index (perfect match); in index_clust we compute the proportion of iterations where the inferred index is from the same reference cluster as the actual index (close match).\n\n\n\n\n\nFigure 4 shows that the proportion of perfect and close match for most cases is lower in out1, which indicates that inferring the import status reduced the accuracy of the inference. Using previous investigations into the travel history of cases is key to improve the reconstruction of transmission history.\n\nPanel A: Proportion of iterations with the correct index for each case; Panel B: Proportion of iterations where the index is from the correct cluster.\n\n\n\nWe now investigate the geographical distribution of the importations, and the average number of secondary cases per region in out1 and out2. The maps are generated using the package ggplot236.\n\nFirst, we retrieve the boundary files of the census tracts in Ohio to generate the background of the maps using the package tigris37. We import them in a format compatible with the package sf and create one background map for each model.\n\n\n\nWe are interested in two outputs of the models: i) the number of imports per region, in order to highlight regions where importations of cases are most likely, and ii) the geographical distribution of the number of secondary cases per case, which gives insight into the areas most vulnerable to the spread of the disease.\n\nNumber of imports per region: The element tree of summary(out1) contains the most likely infector, the proportion of iterations where the index is the most likely infector and the median number of generations between the two cases, the most likely infection date and the chances of being an import for each case. We add two columns to dt_cases showing the probablity of being an import in out1 and out2 for each case. As the import status is not inferred in out2, prop_import2 is a binary value, and is equal to dt_cases$import.\n\n\n\nWe generate the number of imports per region in each model (vectors prop_reg1 and prop_reg2) and add it to the matrices describing the maps.\n\n\n\nWe plot the number of imports per region in each model (Figure 5). The right panel (out2) shows the geographical distribution of importations in the data. We observe discrepancies between the two panels. In out1, the inferred number of importations in the central areas is much lower than in the reference data. These maps highlight the uncertainty added when the import status of each case is inferred.\n\n\n\nAverage number of secondary cases per region: In this section, we map the number of secondary cases per case in each region to identify which regions were associated with higher levels of transmission. We define the function n_sec_per_reg to compute the average number of secondary cases per case and aggregate it per region. We then extract the median number of secondary cases per case in each region.\n\n\n\nWe now plot the geographical distribution of the median number of secondary cases in each region (Figure 6). Despite minor discrepancies, the maps generated by the two models are similar. Both show an important spatial heterogeneity. The eastern and central areas are associated with higher numbers of secondary cases. If we change the vectors n_sec1 and n_sec2 to plot different deciles, we show the dispersion of the number of secondary cases in the different iterations of the models.\n\n\n\nIn the previous example, we ran and evaluated two different models to reconstruct transmission clusters from simulated surveillance data, and highlighted the spatial heterogeneity of measles transmission in the region. These models were run using the default likelihood, prior and movement functions. Now we develop a third model, where the spatial connection between regions is based on the Stouffer’s rank method27.\n\nIn the Stouffer’s rank method, the absolute distance is not used to compute the probability of connection between regions. The connectivity between the regions k and l only depends on the summed population of all the regions closer to l than k. If we define this collection of regions Ωk,l = {i: 0 ≤ d(i,l) ≤ d(k,l)}, Stouffer’s distance is then pkl=mlc*(mk∑i∈Ωk,lmi)a. From this, we deduce the probability that a case from region l was infected by a case from region k.\n\n\n\nThis model is similar to the power-law gravity model with two main differences: i) each cell of the distance matrix should be equal to Σi∈Ωk,lmi, and ii) only one spatial parameter a is estimated. First, we create the distance matrix associated with Stouffer’s rank:\n\n\n\nSecondly, since the connectivity matrix in the Stouffer’s rank model is only computed from one spatial parameter, we write a new movement function cpp_stouffer to estimate it. The formula of the Stouffer’s rank connectivity matrix is similar to the power law gravity models. Therefore, cpp_stouffer is similar to the default movement cpp_move_a, and uses the same function to compute the probability matrix (cpp_log_like()). This function is written with the package Rcpp, and is sourced using the function Rcpp::sourceCpp22.\n\n\n\nWe modify the element a of the list of movements used in the last model. We set up the lists data and config using dist_mat_stouffer as the distance matrix. Since there is only one spatial parameter in this model, we set the parameter move_b to FALSE in create_config(), and we set the prior of b to the null function f_null.\n\n\n\nWe plot the inferred cluster size distribution and compare it to the reference data (Figure 7). We observe discrepancies between the inferred distribution and the data: the model over-estimates the number of clusters containing more than 15 cases and underestimates the number of small clusters and isolated individuals.\n\n\n\nFinally, we plot the proportion of perfect and close matches for each case (Figure 8). We observe that the fit obtained with the Stouffer’s rank method is consistently worse than the first two models. The Stouffer’s rank method did not improve the agreement between the inferred trees and the reference data.\n\nPanel A: Proportion of iterations with the correct index for each case; Panel B: Proportion of iterations where the index is from the correct cluster.\n\nThe simulated data used in the study were generated using an exponential gravity model, which explains why introducing the Stouffer’s rank method did not improve the inference. This is not representative of the performance of each mobility model at reconstructing actual transmission clusters.\n\n\n\n\nConclusion\n\nThe R package o2geosocial is a new tool for data analysis building upon the framework developed in outbreaker2. It uses routinely collected surveillance data to reconstruct transmission networks. It can be used on a broad range of diseases where genetic sequencing is not common, or informative. For instance, it has been applied on national measles surveillance data to reconstruct the cluster size distribution of outbreaks in the United States between 2001 and 20164. In this study, we presented an application on a simulated dataset using detailed geographic information on the location of cases.\n\nWe implemented several models to reconstruct the cluster size distribution of the simulated outbreak. Although each model was able to capture the overall dynamics of transmission, we observed discrepancies between the reference data and the reconstructed cluster size distribution for models where the importation status of the cases was inferred. These discrepancies are linked to the threshold set to define what is considered an unlikely connection. A looser threshold may lead to unrelated cases being connected and a lower number of inferred imports, whereas a stricter threshold increases the number of short transmission chains. Therefore, the use of epidemiological information describing importation status improves the accuracy of the transmission cluster reconstruction in o2geosocial. In case of incomplete epidemiological information, the user can set the importation status for some of the cases, and the others would be inferred. These results highlight that epidemiological investigations are crucial to improve our ability to reconstruct transmission events, particularly when unrelated importations happen concurrently.\n\nThe method described in this paper does not account for long-distance transmission, as transmission events are impossible in o2geosocial when the distance between regions is above the parameter gamma. In case of long-distance transmission, the infected case would be considered as a new importation. Nevertheless, this limitation is not critical since o2geosocial was designed to identify areas most susceptible to local transmission, i.e. regions where importations were likely to lead to local outbreaks.\n\nThe analyses presented in this paper were ran on simulated data, which partly explains the very close match between the inferred and reference cluster size distribution. Indeed, the distributions of the incubation period and serial interval used to generate the simulations were the same as the ones used for cluster inference. Using imprecise or inaccurate distributions can lead to biases in the reconstruction of the transmission trees.\n\nWe also showed how the model could be edited to implement different mobility models. Describing human mobility during infectious diseases outbreaks is challenging, and the performance of the models depends on the setting26,38–40. We encourage the development of extensions of o2geosocial to study a wide range of pathogens and settings where sequence data are not informative. We hope that wider use of o2geosocial can help maximise the information brought by routinely collected data and epidemiological investigations, in order to improve our understanding of outbreak dynamics.\n\n\nData availability\n\nZenodo: o2geosocial. https://doi.org/10.5281/zenodo.431744023.\n\nThis project contains the following underlying data:\n\n- alxsrobert/o2geosocial-v1.0.1.zip (data folder; simulated data generated from measles virus incubation period and serial interval)\n\nData are available under the terms of the Open Source Initiative MIT license.\n\n\nSoftware availability\n\nSoftware available from: https://CRAN.R-project.org/package=o2geosocial.\n\nSource code available from: https://github.com/alxsrobert/o2geosocial.\n\nArchived source code at time of publication: https://doi.org/10.5281/zenodo.431744023.\n\nLicense: MIT license.",
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Publisher Full Text\n\nMossong J, Hens N, Jit M, et al.: Social contacts and mixing patterns relevant to the spread of infectious diseases. PLoS Med. 2008; 5(3): e74. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFunk S: Socialmixr: social mixing matrices for infectious disease modelling. 2018. Reference Source\n\nKlinkenberg D, Nishiura H: The correlation between infectivity and incubation period of measles, estimated from households with two cases. J Theor Biol. 2011; 284(1): 52–60. PubMed Abstract | Publisher Full Text\n\nVink MA, Bootsma MCJ, Wallinga J: Serial intervals of respiratory infectious diseases: A systematic review and analysis. Am J Epidemiol. 2014; 180(9): 865–75. PubMed Abstract | Publisher Full Text\n\nDowle M, Srinivasan A, Goreck J: Package ‘data.table.’ Cran. 2016; Reference Source\n\nLessler J, Reich NG, Brookmeyer R, et al.: Incubation periods of acute respiratory viral infections: a systematic review. Lancet Infect Dis. 2009; 9(5): 291–300. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFine PEM: The Interval between Successive Cases of an Infectious Disease. Am J Epidemiol. 2003; 158(11): 1039–47. PubMed Abstract | Publisher Full Text\n\nHijmans RJ: Introduction to the geosphere package ( version 1 . 9-92 ). Cran. 2012; 1–26.\n\nWickham H: Ggplot2. Wiley Interdiscip Rev Comput Stat. 2011; 3: 180–5. Publisher Full Text\n\nTigris WK: An r package to access and work with geographic data from the us census bureau. The R Journal. 2016; 8(2): 231–242. Publisher Full Text\n\nTruscott J, Ferguson NM: Evaluating the Adequacy of Gravity Models as a Description of Human Mobility for Epidemic Modelling. PLoS Comput Biol. 2012; 8(10): e1002699. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBjørnstad ON, Grenfell BT, Viboud C, et al.: Comparison of alternative models of human movement and the spread of disease. BioRxiv. 2019; 1–15. Publisher Full Text\n\nMerler S, Ajelli M: The role of population heterogeneity and human mobility in the spread of pandemic influenza. Proc Biol Sci. 2010; 277(1681): 557–65. PubMed Abstract | Publisher Full Text | Free Full Text"
}
|
[
{
"id": "82935",
"date": "21 Apr 2021",
"name": "Paige B. Miller",
"expertise": [
"Reviewer Expertise Infectious disease modeling",
"transmission trees",
"social contact networks",
"tuberculosis"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors present the R package, o2geosocial, for reconstructing transmission trees of infectious diseases that have slow mutation rates or incomplete genetic sequencing data. The model description is technically strong and similar to other tree reconstruction papers. I was able to easily verify and implement examples described in the paper using o2geosocial. The limitations of the package are adequately discussed throughout. Overall, I think package and paper are good additions to transmission tree reconstruction tools and literature.\n\nI was wondering how flexible the package would be for including other types of data that researchers may want to include in the likelihood function, e.g., social groups, workplaces, shifts, etc. A brief discussion of these modifications in the \"Customize the likelihood section\" might help readers determine if this package would be helpful for them.\n\nIs the rationale for developing the new software tool clearly explained? Yes\n\nIs the description of the software tool technically sound? Yes\n\nAre sufficient details of the code, methods and analysis (if applicable) provided to allow replication of the software development and its use by others? Yes\n\nIs sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool? Yes\n\nAre the conclusions about the tool and its performance adequately supported by the findings presented in the article? Yes",
"responses": [
{
"c_id": "6728",
"date": "16 Jun 2021",
"name": "Alexis Robert",
"role": "Author Response",
"response": "Thank you very much for these positive comments. Indeed, we agree that making the package more flexible to integrate other data routinely-collected in certain settings is an important area of improvement. This is one of the things we want to facilitate in future versions of o2geosocial. We added the following sentences to the Conclusion to discuss this aspect: “Future developments in the package will focus on facilitating the integration of new variables in the likelihood of connection, such as cases’ workplace or school. Currently, such variables would have to be integrated within one of the components of the likelihood. We aim to simplify the addition of new parameters and components in the inference framework.”"
}
]
},
{
"id": "83247",
"date": "14 May 2021",
"name": "Eben Kenah",
"expertise": [
"Reviewer Expertise Statistical methods for infectious disease epidemiology",
"mathematical models of epidemics",
"epidemiologic methods",
"causal inference",
"survival 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\nWhile I appreciate the quality of the programming in o2geospatial and the detailed demonstration of its use, I think the interpretation of its results in infectious disease epidemiology is far from clear. The use of cluster size distributions to investigate the transmission of the disease is difficult because the apparent clusters are highly sensitive to the detection of cases, which is a particular problem if there are many subclinical cases as in influenza or COVID-19. The use of transmission tree reconstruction to understand risk factors for transmission is equally difficult because we are often lacking denominators (e.g., how many opportunities were there to transmit) and because a tree always has a mean outdegree just below one, which means that the censoring of secondary infections caused by infectious individuals in the later part of the observation period needs to be accounted for (e.g., see Fraser, PLOS One, 2007).\nThe use case centers around a simulated data set whose generation is not clearly described, and it is often difficult to compare the model results to the \"truth\" contained in the simulation. The analyses of the simulated data use the same incubation period and serial interval distributions, so the analyses do not give us any sense of how the results would be affected by the misspecification of these distributions. This is mentioned briefly in the Discussion (to the authors' credit), but it is a fundamental shortcoming of the use case because these distributions are never known in practice.\nComments:\n(page 4, paragraph second from bottom) \"sampled form\" should be \"sampled from\".\n\n(page 5, conditional report ratio) It would be more accurate to say that the number of missing generations follows a geometric distribution with mean (1 - \\rho) / \\rho, not an exponential distribution.\n\n(page 5, conditional report ratio) It is confusing to denote the conditional report ratio but then to refer to its prior distribution as prior_pi in the package. It would also be good to point out to readers that the prior distribution on the conditional report ratio is informative: It has a mean of 0.91 and a standard deviation of 0.08.\n\n(page 5, time component) The definition of f_dens given in the text does not seem to match its definition in outbreaker_data.R, where it is defined as the \"colonization time, i.e. the time interval during which the pathogen can be sampled from the patient\". The incubation period is usually defined as the time between infection and the onset of symptoms, so it would be helpful to specify whether T_i is meant to be the time of the report (as in the text) or the reported symptom onset date (as implied by calling T_i - t_i an incubation period).\n\n(page 5, time component) There are several problems that stem from the use of independent and identically distributed generation intervals as in the likelihood of Wallinga and Teunis (2004). First, generation intervals do not typically have the same distribution throughout an epidemic. They contract due to depletion of susceptibles and competing risks of infection from multiple sources. Thus, these likelihoods are only strictly correct in the very early stages of an epidemic (and only if there is negligible clustering of contacts). Second, it precludes an analysis of the effects of covariates on the risk of transmission between two individuals. Many critical questions in the response to an epidemic involve mechanisms of transmission and determinants of susceptibility and infectiousness. The proposed methods can address these questions only indirectly and on a coarse scale.\n\n(page 6, description of simulated data) The simulations used to generate the data need to be described in more detail, including how the clusters were defined. The simulations themselves appear to be branching processes, which have several important differences from true stochastic epidemic models that should be mentioned.\n\n(page 7, R code above Figure 2) The use of a normal distribution for a time-to-event distribution is surprising but not truly problematic. It might be good to call it something like a \"normal distribution truncated at zero\".\n\n(page 8, top box) The R code in this box is inconsistent in the use of spaces when setting argument values. I believe the standard is to put spaces around the equals signs, which is followed through most of the paper.\n\n(page 15, Figure 5) In Figure 4, the results from model 2 are the truth. In this figure, there is no obvious way of comparing the results of the models to any truth. The models produce very similar results, but do the estimated numbers of secondary cases correlate with an underlying true parameter such as a reproduction number?\n\n(page 19 and earlier) \"were ran\" should be \"were run\".\n\nIs the rationale for developing the new software tool clearly explained? Partly\n\nIs the description of the software tool technically sound? Yes\n\nAre sufficient details of the code, methods and analysis (if applicable) provided to allow replication of the software development and its use by others? Yes\n\nIs sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool? Partly\n\nAre the conclusions about the tool and its performance adequately supported by the findings presented in the article? Partly",
"responses": [
{
"c_id": "6729",
"date": "16 Jun 2021",
"name": "Alexis Robert",
"role": "Author Response",
"response": "Thank you for your thoughtful comments on this paper. Please find our responses below We agree that the limitations associated with the use of transmission trees should have been described in more detail. We have added a paragraph in the Discussion to list the main limitations associated with the use of cluster size distribution and transmission trees, and explain their value in infectious disease epidemiology. “The use of transmission trees and transmission clusters to assess current or future risk of outbreaks comes with various limitations. First, it relies upon the assumption that previous transmission patterns are representative of future outbreaks and requires previous incidence in the region of interest to be informative. Second, it requires past observed transmission events, and does not account for the number of opportunities of transmission per case. Where only sporadic isolated cases have been reported in the country, it is not possible to draw relevant conclusions on communities potentially most vulnerable to transmission. Third, partial detection of cases may bias the cluster size distribution, and under-estimate the number of secondary transmissions. Patterns of transmission, and characteristics associated with high-transmission events may still be observable but could introduce a bias if reporting is itself is affected by the same factors as is transmission. Finally, the use of transmission trees for real time modelling can be challenging, given the right-censoring of transmissions caused by recent infectious individuals (Fraser, 2007).” Despite these limitations we believe our package is an useful contribution to the field: As we outlined in the Introduction, transmission trees have repeatedly been used in the recent years to investigate various aspects of the transmission dynamics, such as superspreading events, determinants of transmission, or the impact of various policies, including for pathogens where part of the cases was not detected (Wang et al Nature 2020, Wang & Teunis Frontiers in Medicine, 2020, James et al, PLOS One 2021). The method we developed aims to improve the inference of transmission links between cases, so that information on outbreak dynamics can be deduced from transmission trees even in settings where they are not reconstructed through thorough contact tracing investigations. We agree that it is important to highlight the impact of potential misspecifications of the input distributions. The first section of the Extended Data document describes the impact of changing the mean or the standard deviation of both distributions on the accuracy of the reconstructed transmission trees. This is now also described in the Discussion; “We re-ran the inference procedure using different distributions (changing the mean or the standard deviation), the results can be seen in the Extended Data. When the distributions were set with lower standard deviations, several links were not observed in the inferred transmission trees anymore. Indeed, these connections had been made impossible since the range of likely values was narrower. In all other examples, the simulated and inferred clusters size distribution remained very close, we only observed a slight drop in the proportion of iterations that contain the right transmission links. Since the likelihood of connection is computed from several components, the discrepancies between the distributions used in the simulations and the model fits did not substantially changed the inferred trees.” This typo has been fixed, thank you for spotting it. We changed the distribution to a geometric distribution. We changed the definition of the conditional report ratio in the main text to Π , in order to match the commands defined in o2geosocial. We added the following to clarify that the default prior distribution was informative and could be edited before running the model: “By default, the prior distribution is parametrised as Beta(10,1), which is an informative prior of mean 0.9 and standard deviation 0.08.The two parameters of the beta prior distribution can be changed using the variable prior_pi in create_config().”” Thank you for noticing this. Indeed, f_dens represents the incubation period, i.e. the time between the reported symptom date and the infection date. Therefore, T_i is the reported symptom onset date. We clarified this in the Main Text, and changed the description of the variable in outbreaker_data.R. This will be updated on CRAN at the next submission. We agree that using independent and identically distributed generation intervals is a simplification, and does not represent the complexity observed throughout an epidemic. However, the temporal component of the likelihood function could be customised to generate different distributions of the generation intervals at different points of the outbreak. This would require implementing a new temporal likelihood function, which would use different values of w_dens depending on the time and regions , and adding it to the model using custom_likelihood(timing_infecttions = new_ll_timing()). We agree that in the current version of o2geosocial, the distributions used at different points would have to be defined prior to running the model, and could not be estimated as part of the fitting procedure. This will be an avenue for future development of the package, in order to seamlessly integrate new parameters to the models. We summarised these two points at the end of the “Customise the likelihood...” section: “In this use case, we only explored customising the spatial component. However, the other components of the likelihoods can also be edited, using the functions custom_priors(), custom_likelihoods(), or custom_moves(). For instance, to account for changes in the distribution of the generation time throughout an outbreak (Svensson 2007), one would have to change the element timing_infections of custom_likelihoods(). However, the distribution would need to be set prior to running the models.” In the Discussion we added “The default implementation of the method assumes that generation intervals are independent and identically distributed throughout an outbreak, whereas in reality, depletion of susceptibles and competing risk of infection through clustering of contacts would be expected to affect the generation interval. The method can be customised to integrate time varying generation intervals set prior to running the models. However, estimating the distribution of the generation interval during the inference procedure is more challenging to implement in the current framework, which may introduce a bias in our results.” We added the following paragraph to to the Use Case section to describe how the simulated data were generated: “In order to assess whether the method was able to reconstruct the transmission links between cases, we needed to simulate the transmission trees. Population-level compartmental models cannot be used to generate who-infected-whom. Therefore, we generated the dataset at an individual level, by simulating different transmission trees in the area of interest. The transmission trees were generated using the following process: 1. We created an imported case, with random onset date, region of origin, and age group. 2. We drew the number of secondary cases stemming from this case, using a random reproduction number. 3. If the number of secondary cases was greater than 0, the characteristics of the new cases were drawn using the distributions of the generation time, incubation periods, the spatial kernel, and the proportion of contacts between age groups. 4. We repeated steps 2 and 3, for each new case, until no more secondary cases were drawn (i.e. the random reproduction number in step 2 was 0 for all new case). 5. We repeated steps 1 to 4, until we reached a maximum number of cases, or maximum number of trees, defined before the simulation. Numerous factors influencing the transmission dynamics are not included in this simulation framework. However, we do not aim to generate transmission trees which describe the spread of a given pathogen (here measles) in a community with complete accuracy. The main aim of this simulated dataset is to highlight the inference capabilities of the reconstruction method, and to explore causes for discrepancies between the simulations and the model fits, in an ideal setting where all parameters are known and are accounted for in the model.” We changed how we refer to this distribution, we now use “normal distribution truncated at zero”. Thank you for this suggestion. We fixed the use of spaces in this box. Thank you for this suggestion. We have added a third panel to Figure 6, describing the average number of secondary cases per region in the simulations. Therefore, the results produced by both models can be compared to the data. We also added a comparison between the regional average number of secondary cases in the simulations and the 95% Credible Intervals of the models in the Extended data. We added the following sentences to describe Figure 6: “Similarly, we observe minor differences between the maps generated by the models and the simulated data. Most of the regions that repeatedly caused further transmissions in the simulations are identified by the models. In the Extended Data, we compared the regional number of secondary transmissions in the simulated data to the 95% Credible Intervals of both models, and found that the models were able to capture the input values in each region.” These typos have been modified, thank you for spotting them."
}
]
}
] | 1
|
https://f1000research.com/articles/10-31
|
https://f1000research.com/articles/10-480/v1
|
16 Jun 21
|
{
"type": "Research Article",
"title": "Characterization of SARS-CoV-2 East Java isolate, Indonesia",
"authors": [
"Fedik Abdul Rantam",
"Cita Rosita Sigit Prakoeswa",
"Damayanti Tinduh",
"Jusak Nugraha",
"Helen Susilowati",
"Andi Yasmin Wijaya",
"Ni Nyoman Tri Puspaningsih",
"Dwiyanti Puspitasari",
"Dominicus Husada",
"Neneng Dewi Kurniati",
"Aryati Aryati",
"Cita Rosita Sigit Prakoeswa",
"Damayanti Tinduh",
"Jusak Nugraha",
"Helen Susilowati",
"Andi Yasmin Wijaya",
"Ni Nyoman Tri Puspaningsih",
"Dwiyanti Puspitasari",
"Dominicus Husada",
"Neneng Dewi Kurniati",
"Aryati Aryati"
],
"abstract": "Background: Incidents of SARS-CoV-2 in East Java increased steadily, and it became the second epicenter in Indonesia. The COVID-19 pandemic caused a dire multisectoral crisis all around the world. This study investigates and characterizes local isolates from East Java, Indonesia.\n\nMethods: There were 54 patients suspected with SARS-COV-2 infection and 27 patients were COVID-19 positive. Virus isolates were obtained from COVID-19 inpatients’ nasopharyngeal swabs at the Dr Soetomo Teaching Hospital, Surabaya. There were only three isolates (#6, #11, #35) with good growth characteristics. Serial blind passage and cytopathic effect observation in the Vero E6 cell line were performed for virus isolation. Confirmation of the SARS-CoV-2 infection was proven by means of reverse transcriptase-polymerase chain reactions using SARS-CoV-2 specific primers, scanning electron microscopy, and scanning transmission electron microscopy examination. Whole genome sequencing was performed using ARTIC protocol. Furthermore, SARS-CoV-2 characterization was identified through a western blot using rabbit serum immunized with inactive SARS-CoV-2 vaccine and human natural COVID-19 infection serum.\n\nResults: Spike gene analysis of three samples (#6, #11, #35) found that the D614G mutation was detected in all isolates, although one isolate exhibited the D215Y and E484D mutation. Based on whole genome analysis, those three isolates were included in clade 20A, and two isolates were included in lineage B.1.6 with one isolate belongs to lineage B.1.4.7.\n\nConclusion: Based on molecular characterization and immunogenicity of SARS-CoV-2 East Java, Indonesia showed high titer and it has mutation in some regions.",
"keywords": [
"growth properties",
"COVID-19",
"SARS-CoV-2",
"virus isolation",
"infectious disease"
],
"content": "Introduction\n\nCoronaviruses are an enveloped positive single-stranded ribonucleic acid (RNA) virus that can infect several species via zoonotic transmission.1,2 The coronavirus viral particle is a heterogenous, spherical, crown shaped viral particle with a diameter ranging from 80–160 nm.2 Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) possesses several main structural proteins including envelope, membrane, nucleoprotein, and spike protein.3 Spike protein facilitates the SARS-CoV-2 infection interacting with the human angiotensin-converting enzyme-2 (ACE-2) protein, which acts as a receptor, and it is expressed in various tissues in the body.4 This abundant presence of a virus receptor could be responsible for its rapid spread of infection. In addition, spike protein as the main protein of interest such as envelope, membrane, and nucleoprotein could also have an immunogenic capability.3 Worldwide genomic surveillance has proven that the spike protein exhibits a tendency to have multiple sites of mutation.\n\nSeveral major mutations of concern in SARS-CoV-2 target the spike protein such as in the UK (lineage B.1.1.7), South Africa (B.1.351), and Brazil (lineage P.1), and caused concern as these mutations were responsible for enhancing SARS-CoV-2 infection morbidity and resistance of serum neutralization.5–7 However, these mutations were not proven to correlate with COVID-19 severity and mortality.\n\nThe SARS-CoV-2 infection caused the Coronavirus Disease 2019 (COVID-19) that was first reported in Wuhan, China, in December, 2019 and escalated quickly until it was declared a global pandemic by the World Health Organization (WHO) in March 2020.8,9 SARS-CoV-2 is spread through droplets and aerosol-mediated infection that relate to COVID-19 primary symptoms of respiratory complaints that vary from mild symptoms to dire acute respiratory distress syndrome (ARDS).10 However, in a recent development, it has been reported that the SARS-CoV-2 infection can spread from the respiratory tract port of entry to the whole human body, and can cause various clinical manifestations, from gastrointestinal symptoms (diarrhea, nausea, and vomiting), neurological symptoms (anosmia and decrease of taste senses), ophthalmological symptoms (conjunctivitis), nephrological symptoms (acute kidney injury), hypercoagulability state, and systemic viral sepsis.11,12\n\nIndonesia, one of the tropical countries in Southeast Asia, began to detect and report its patient zero on March 2, 2020, in Jakarta. After the first two confirmed cases were declared positive for infection of SARS-CoV-2, the infection began to spread across the Indonesian archipelago.13,14 In May, 2020, the incidence of SARS-CoV-2 increased steadily in Surabaya, making it the second epicenter in Indonesia after Jakarta.15\n\nIndonesia is the fourth most populated country in the world to be affected by the COVID-19 pandemic, and various areas of national concern have been impacted, including economics, politics, and human welfare.16,17 Researchers around the world are now racing against SARS-CoV-2, aiming to control its impact with a holistic approach.18 Development and evaluation of COVID-19 diagnostic tools, clinical management, and vaccine candidates are known to be global priorities, especially the protection of healthcare providers as frontline workers in pandemic management and mitigation, as they are more exposed to COVID-19.19,20 As SARS-CoV-2 spread around the globe, it was revealed that, based on the reported SARS-CoV-2 whole genome database, SARS-CoV-2 had already undergone several genetic mutations from its ancestor, generating evidence for distinct lineages by the summer of 2020.8 Therefore, it has been suggested that isolation and characterization of SARS-CoV-2 strains from various places is required to ensure a compatible tailor-made SARS-CoV-2 management plan for specific conditions.20,21 SARS-CoV-2 genomes that have been reported in Indonesia consist of predominantly lineage B.1 based on the GISAID SARS-CoV-2 genome database and they are divergent from the Wuhan isolate.21\n\nIt is reported that at the population level, there is relatively insufficient herd immunity to drive significant mutation, and there are several spike mutations that increase virus transmission without changes in clinical significance such as D614G. Moreover, an immune system exposed to a variant of SARS-CoV-2 can be active also on other variants, given the generation of polyclonal antibodies for multiple epitopes.22,23\n\nThis is the first report characterizing the SARS-CoV-2 East Java, Indonesia local isolates. This study collected SARS-CoV-2 material from three virus isolates and infected Vero E6 cells. Furthermore, this study aims to investigate the characterization of SARS-CoV-2 East Java, Indonesia local isolates.\n\n\nMethods\n\nSubject data was retrieved from Dr Soetomo General Hospital medical records. The first subject, (#35 subject), was a local transmission case of a 49-year-old man with a normal body mass index (22.9 kg/m2), who was discharged on the 15th day of hospital care. The second subject, (#6 subject), was a local transmission case of a 38-year-old woman with an overweight body mass index (25.2 kg/m2) and who rapidly tested positive for IgG with IgM antibodies. Subject #6 was admitted to inpatient care and deteriorated until being declared brain dead after six days of hospitalization due to respiratory failure. The third subject, (#11 subject), was a local transmission case of a 64-year-old woman with a normal body mass index (19.5 kg/m2) and a history of breast cancer, and was in remission. Subject #11 was discharged after 26 days of hospitalization.\n\nThere were 54 patients suspected with SARS-COV-2 infection and of these 27 patients were diagnosed COVID-19 positive during March to June 2020. A SARS-CoV-2 sample source was retrieved from COVID-19 confirmed inpatients in the Dr Soetomo General Hospital and three isolates originating from three individual subjects from Surabaya, Indonesia were obtained. Each subject was asked for informed consent. A nasopharyngeal swab was performed to obtain a SARS-CoV-2 sample using a sterile cotton swab. The sample cotton swab was then submerged in virus transport medium (VTM) containing a sterile filtered solution of Minimum Essential Media (MEM) (Gibco, USA), 1x penicillin-streptomycin (Gibco, USA), and 1x amphotericin B (Gibco, USA) as reported before.24 The sample was then immediately transferred, in a 4°C cool box containing an icepack, to the Research Center for Vaccine Technology and Development, Institute of Tropical Diseases Laboratory, Biosafety Level-3 (BSL-3) facility in Universitas Airlangga, Surabaya, East Java, Indonesia.25\n\nThere were only three samples from subjects #6, #11, #35 with good growth characteristics that provided isolates. Serial blind passage and cytopathic effect observation in the Vero E6 cell line were performed for virus isolation. The virus isolation that was performed in the Vero E6 cell line (ATCC, USA) was seeded on a T25 flask (Corning, USA) with a 2 × 106 cell count and cultured with a MEM (Gibco, USA), supplemented with 10% Fetal Bovine Serum (FBS) (Gibco, USA) until it reached 80% confluency (37°C and 5% CO2), (Figure 1), by introducing a 1 ml sample of VTM to the Vero E6 cell line culture for a one-hour incubation. After incubation, 4 ml of fresh MEM (Gibco, USA), supplemented with 10% FBS (Gibco, USA) were added. The cell was labeled as inoculation culture and observed daily through a phase contrast inverted microscope TMS (Nikon, Japan). After three days of inoculation, blind passage was performed to a fresh monolayer Vero E6 cell culture by introducing a 1 ml supernatant medium from infected cells with a one-hour incubation before adding 4 ml of fresh MEM supplemented with 10% FBS medium. Viral growth was analyzed using cytopathogenic effect (CPE) and plaque forming unit (PFU) assay. TCID50 evaluation of #35 isolate through plaque forming assay and Reed and Muench method was as follows: log10 50% end point dilution = log10 of dilution showing a mortality next above 50% - (difference of logarithms × logarithm of dilution factor). Generally, the following formula is used to calculate “difference of logarithms” (difference of logarithms is also known as “proportionate distance” or “interpolated value”): Difference of logarithms = [(mortality at dilution next above 50%)-50%] / [(mortality next above 50%) - (mortality next below 50%)].26\n\n(A) Cytopathic effect of infected Vero E6 cell in third blind passage on the eighth day post passage (40× magnification); (B) Cytopathic effect of infected Vero E6 cell in 15th blind passage on second day post passage (40× magnification); (C) Uninfected Vero E6 cell in 40× magnification; (D) Plaque-Forming Unit (PFU) evaluation (Nikon TMS inverted microscope, Japan).\n\nThe entire electron microscopy sample preparation was performed in a biosafety class II, type A2 biosafety cabinet (Nuaire, USA). SARS-CoV-2 morphology was assessed using a scanning electron microscope (SEM) and a scanning transmission electron microscope (STEM). Sample preparation for SEM was performed by collecting and filtering 1 ml of UV-inactivated infected medium from the virus culture during the occurrence of cytopathic effect through a 1 μm pore syringe nitrocellulose filter (Merck, USA) to trap the virus. Fixation, Periodic Acid-Schiff (PAS), was performed by filtering 2 ml of 2% glutaraldehyde (Serva, USA) through the virus-entrapped syringe filter and incubating at 4°C for four hours. The fixated syringe filter then went through a dehydration process with cold ethanol (Merck, USA), at a gradient of 50%, 70%, 85%, 95% ethanol, and absolute ethanol with 15 minutes of incubation for each sequential dehydration process. Glutaraldehyde fixation and 50–75% ethanol dehydration sequences were performed using a 4°C refrigerator in an airtight container. The 85% and absolute ethanol dehydration processes were carried out at room temperature. The nitrocellulose membrane filter was then extracted from the syringe filter using pliers and air-dried in a biosafety cabinet overnight. A FEI Quanta 650 FEG (FEI, USA) electron microscope in low vacuum SEM mode (80 Pa; 10 kV) at 80,000× magnification and Modular Automated Processing System (MAPS) software version 3.14.11 (ThermoFisher Scientific, Waltham, Massachusetts, United States) was used for sample observation.\n\nSTEM sample preparation was performed by collecting and pipetting 50μl UV-inactivated infected mediums from virus culture during the occurrence of cytopathic effect to parafilm. Immobilization of a SARS-CoV-2 viral particle was conducted on a formvar (SPI-chem, USA) coated copper electron microscope grid (EMS, USA). Formvar grid coating was performed according to UK standards for microbiology investigation protocols.27 The formvar-coated grid was pushed to an infected medium droplet on parafilm and incubated for 20 minutes. Excess infected medium was absorbed by filter paper, air-dried, and fixated with 2% glutaraldehyde in an airtight container (4°C, four hours). Excess glutaraldehyde was absorbed with filter paper and the virus-seeded grid was air-dried in a biosafety cabinet overnight. Negative staining was performed by utilizing 2% phosphotungstic acid (EMS, USA) with a one-minute incubation before observation. STEM sample observation was conducted using a FEI Quanta 650 FEG (FEI, USA) electron microscope through the STEM mode (1.5°C, 676 psi, 30kV) with MAPS software.28\n\nIdentification of SARS-CoV-2 virus culture was performed by total RNA extraction utilizing Trizol reagent (Thermo Fisher, USA) according to the manufacturer’s protocol. A Qubit™ RNA BR Assay Kit (Thermo Fisher Scientific, USA) with a Qubit™ fluorometer was used according to the kit manual.29 RT-PCR was performed from extracted RNA samples utilizing the Goscript® RT-PCR system (Promega, USA) with SARS-CoV-2 receptor-binding domain spike gene primers adopted from previous studies (forward: 5′-CCACAGACACTTGAGATTC-3′ and reverse: 5′-GCAACTGAATTTTCTGCACCA-3′) and according to supplied protocol by Lau et al.30\n\nConventional PCR was performed from RT-PCR cDNA using the previously described primer with GoTaq® green master mix (Promega, USA) in a Thermal Cycler XP machine (Bioer Technology, China). Conventional PCR conditions were conducted through initial denaturation (95°C, five minutes), amplification (45 cycles of ten seconds, 95°C), denaturation (ten seconds, 62°C) annealing, (ten seconds, 72°C) elongation, final elongation (72°C, five minutes), and PCR reaction termination (4°C, 30 minutes). PCR products were detected by performing agarose gel electrophoresis in 2% agarose gel (INTRON Biotechnology, South Korea) in 0.5x Tris-Boric-EDTA (TBE) Buffer (BIOWORLD, USA) with 110 volts for 60 minutes, the DNA band was stained with ethidium bromide (TCI, Japan), and visualized through the Gel Doc XR+ gel documentation system (Bio-Rad, USA). The PCR product length was confirmed with Image Lab software for PC version 6.1 (SOFT-LIT-170-9690-ILSPC-V-6-1, Bio-Rad Laboratories Inc, Hercules, California, US, https://www.bio-rad.com/en-id/product/image-lab-software?ID=KRE6P5E8Z) in alignment with a Thermal Cycler XP machine (Roche, USA).31,32\n\nWhole genome sequencing protocol was performed by targeted sequencing after gene amplification using ARTIC V3 primer sets RT-PCR before proceeding to PCR clean up, and processed with Nanopore sequencing kits in the GRIDION platform, according to provided protocols supplied with the kits.33 Whole-genome sequencing was performed by Genetika Science Indonesia Ltd through EPI2ME Labs software version 21.05 (https://labs.epi2me.io/wfindex) and trimming through Medaka software version 1.3.4 (https://nanoporetech.github.io/medaka/). Gene analysis was performed by RAMPART software version 1.7.1 (https://artic.network/ncov-2019/ncov2019-using-rampart.html) for mutation analysis and identification of the spike gene and the Wuhan Hu-1 as the reference sequence.34\n\nStaining of Vero E6 SARS-CoV-2 infected cells were performed with immunized rabbit antibody serum, and visualization with diaminobenzidine (DAB) was performed with horseradish peroxidase (HRP) conjugated anti-rabbit IgG. Unspecific binding blocking was performed with 0.5% bovine serum albumin. The positive infected cells that were stained brown were observed by an inverted light microscope (Nikon TMS, Japan).35\n\nViral protein was extracted from infected Vero E6 SARS-CoV-2 culture by RIPA buffer (ThermoFisher Scientific, US) and PMSF extraction (Sigma-Aldrich, US). The sample was centrifuged at 3000×g at 4°C for one hour, and the samples were subjected to polyacrylamide gel electrophoresis (PAGE).\n\nSamples were diluted and mixed with a Laemmli loading solution (Bio-Rad Laboratories Inc, US) and were denatured at 100°C for five minutes before loading on the polyacrylamide gel. Viral proteins were separated on 12% gradient polyacrylamide gels. The transfer of proteins to the PVDF membrane (Sigma-Aldrich, US) was performed with a Trans-Blot Turbo system (Bio-Rad Laboratories Inc, US) for seven minutes.36\n\nWestern blot was performed by using antibody serum from an immunized rabbit with visualization and with HRP-conjugated anti-rabbit IgG polyclonal antibody with 1:10.000 concentration (Cat. no. 611-103-122, Rockland, USA) and DAB (Rockland, USA). A comparison of the western blot was made with convalescent serum that was collected from a volunteer COVID-19 convalescent subject with visualization by HRP-conjugated anti-human IgG polyclonal antibody with 1:10.000 concentration (Cat. no. 611-103-123, Rockland, USA) and DAB with 1X concentration (DAB-10, Rockland, USA). This human serum was used to demonstrate human immune response to SARS-CoV-2.\n\nEthical clearance for this study was approved by the Institutional Review Board of the Dr Soetomo General Hospital, Surabaya (IRB Number IRB00008635), Ethical Clearance No. 0099/LOE/301.4.2/VIII/2020. During hospitalization, the subject or subject’s guardian was informed about the study and gave their written informed consent for participating in this study and use for publication.\n\n\nResults\n\nIn this study, we conducted the characterization of SARS-CoV-2 East Java isolate, Indonesia.37\n\nSARS-CoV-2 CPE appeared in the form of rounding, elevation, and detachment of Vero E6 monolayer cell culture as reported previously.38 Virus passage was performed periodically until stable cytopathic effect patterns were established (5–6 days’ interval) (see Figure 1).\n\nGrowth characteristics suggested a more adapted virus culture along with the blind passage progression and intervals with shorter CPE formation times. Moreover, TICD50 evaluation of #35 isolate through plaque forming assay and Reed and Muench method showed 1013.76 TICD50.\n\nFEI Quanta 650 FEG electron microscopy was performed in low vacuum SEM mode (80 Pa; 10 kV) at 80,000× magnification, and MAPS (Modular Automated Processing System) software observation was able to find several ovoid-shaped multilobulated viral particles that were observed in SEM, with an estimated diameter ranging from 125.8-199.1 nm between filter membrane fibers. Further analysis in STEM showed SARS-CoV-2 viral particles with its surface spike proteins and internal diameter ranging from 120–200 nm (see Figure 2).\n\nThe result of scanning transmission electron microscopy (STEM) (A, B) uninfected cells medium acted as a blank control; (C, D) the morphology of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infected patients under scanning electron microscopy (SEM) 80,000× and scanning transmission electron microscopy (STEM) (FEI Quanta 650 FEG (FEI, USA).\n\nThe visualization of a 398-base pair size band fragment of Receptor Binding Domain (RBD) sequences confirmed SARS-CoV-2 presence. (Roche, USA) (see Figure 3 and Raw RT-PCR Results of SARS-COV-239).\n\n(A) Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) S1/S2 cleavage site Receptor Binding Domain (RBD) detected by two-step reverse transcription-polymerase chain reaction (RT-PCR), DNA electrophoresis ethidium bromide staining, and visualized through the Gel Doc XR+ gel documentation system (Bio-Rad, USA).\n\nSpike gene analysis of three isolates from three patients found that only the D614G mutation was detected among the isolates, although in #35 isolates D215Y and E484D mutations were also present. Based on whole genome analysis, those three isolates were included in clade 20A, and two isolates were included in lineage B.1.6, with one isolate belonging to lineage B.1.4.7 (Table 1).\n\nImmunocytochemistry staining suggested that antibody serum from immunized rabbit and human natural infection serum could detect SARS-CoV-2 infected cells in virus culture, indicated by brown stained cells that were observed in light-inverted microscopy with 100x magnification (Nikon TMS, Tokyo, Japan) (see Figure 4).\n\nSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Vero E6 infected cells, immunocytochemistry using (A) uninfected Vero E6 cells as control; (B) rabbit antibody serum, (C) human antibody serum (100× magnification).\n\nComparison of western blot staining with antibody serum from immunized rabbit and human natural infection serum that was collected from a volunteer COVID-19 convalescent subject showed several main immunogenic proteins that were detected, including spike glycoprotein (S), nucleocapsid protein (N), membrane glycoprotein (M), accessory 3a protein, and envelope protein (E). Both western blot comparisons between rabbit antibody serum and human convalescent serum from the second wave of COVID-19 in Surabaya showed a relatively similar protein immunogenic capacity (see Figure 5).37,40\n\nSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) western blot staining with anti-SARS-CoV-2 Receptor Binding Domain (RBD) monoclonal antibody for detecting S1 protein (MAB10540, RnD System) (8% gel); (A): western blot staining with anti-SARS-CoV-2 S2 monoclonal antibody (MAB10557, RnD System) (8% gel); (B): western blot staining with rabbit antibody serum (12% gel); (C): western blot staining with human convalescent serum from the COVID-19 infection (8% gel); (D): (S) labeled for spike protein, (N) labeled for nucleoprotein protein, (M) labeled for membrane protein, (E) labeled for envelope protein.\n\n\nDiscussion\n\nIn this study, SARS-CoV-2 isolation was achieved by inoculation in Vero E6 cells and serial blind passages. Observation of phase contrast microscopy suggested CPE with a characteristic of rounding, syncytium formation, and cell detachment with plaque formation.26 Evaluation during virus passage exhibited a shorter time for developing CPE in line with increasing passage numbers that indicated a more adapted virus culture. The serial passage of virus in the culture exhibit with shorter CPE formation indicated increases in virus titers, adaptation, and more virus replication efficiency.41\n\nSARS-CoV-2 infection was confirmed by SEM, STEM, and RT-PCR examination. SEM observation showed a three-dimensional structure of viral particles without spike protein visualization with a viral particle diameter that was in line with previously reported cases. STEM observation showed cross-sectional images of viral particle structure, with spike protein visualization with a viral particle diameter relatively similar to a previous study that reported SARS-CoV-2 morphology using transmission electron microscope (TEM).26 However, interestingly, in this study, we found a rounded multilobulated SARS-CoV-2 viral particle structure (pleomorphic). SEM could detect a viral particle structure that was trapped in the filter fibers. However, the visualization was limited in the three-dimensional structure and could be biased. Fortunately, with STEM, the protein structure of the SARS-CoV-2 spike protein could be visualized more clearly than with SEM. In addition, adequate viral particle visualization enables viral particle internal diameter measurement. The confirmation of SARS-CoV-2 was done by a RT-PCR that detected the SARS-CoV-2 RBD that is located in the S1 subunit of the SARS-CoV-2 spike protein.23 Thus, the analysis of the SARS-CoV-2 spike gene shows the mutation of D614G that increases SARS-CoV-2 infectivity, whereas the E484D mutation was correlated with human immune serum neutralization resistance.21 Whole genome sequence analysis suggested that three isolates were included in clade 20A, and two isolates were included in lineage B.1.6, with one isolate belonging to lineage B.1.4.7. Lineage B.1 is the most abundant lineage that circulates in the environment. Evaluation of genetic stability could be evaluated during virus passage in the in vitro setting, as it is reported that genetic mutation may also occur besides natural infections and transmission.42\n\nSARS-CoV-2 infected Vero E6 cells showed a brown color as a positive marker, detected by means of immunized rabbit serum antibody and human natural infection serum antibody immunocytochemistry. Based on this result, evaluation of virus infectivity could be done.3 The comparison between the western blot analysis with immunized rabbit serum antibody and human natural infection serum may suggest that immune response towards SARS-CoV-2 infection tends to be relatively similar. Therefore, these results imply that SARS-CoV-2 immunogenic proteins may be suitable with a natural infection immune response.\n\nWestern blot examination suggested that the main protein of SARS-CoV-2, which consisted of S, N, M, accessory 3a, and E proteins, showed that these proteins possessed immunogenic capability.3 Yet, the main protein that plays an important role in SARS-CoV-2 infection, especially in the binding-to-host cells through ACE2 receptors, is spike protein.4 The binding of antibodies to this SARS-CoV-2 main protein could mediate a SARS-CoV-2 immune response and possibly provide immune protection towards COVID-19.\n\n\nConclusion\n\nBased on molecular characterization and immunogenicity of SARS-CoV-2 East Java, Indonesia showed high titer and it has mutation in some regions. Further study is still required to examine the genetic and immunogenic stability for seed vaccine exploration and it requires more investigation and clinical validation.\n\n\nData availability\n\nFigshare: Underlying data for ‘Characterization of SARS-CoV-2 East Java isolate, Indonesia’, https://doi.org/10.6084/m9.figshare.14703567.v1.37\n\nThis project contains the following underlying data:\n\n‘Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) western blot staining with anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Receptor Binding Domain (RBD) monoclonal antibody for detecting S1 protein’\n\n• Figure 5A. tiff\n\n• Figure 5B. tiff\n\n• Figure 5C. tiff\n\n• Figure 5D. tiff\n\nFigshare: https://doi.org/10.6084/m9.figshare.14703579.v1.39\n\nThis project contains the following underlying data:\n\n‘Raw RT-PCR Results of SARS-COV-2’\n\n• Raw PCR.tiff\n\nFigshare: https://doi.org/10.6084/m9.figshare.14703582.v1.40\n\nThis project contains the following underlying data:\n\n‘Gels for the Western blot (Raw) Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) western blot staining with anti-Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Receptor Binding Domain (RBD) monoclonal antibody for detecting S1 protein’\n\n• Raw WB A.tiff\n\n• Raw WB B.tiff\n\n• Raw WB C.tiff\n\n• Raw WB D.tiff\n\nData are available under the terms 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 was obtained from the patients.",
"appendix": "Acknowledgements\n\nThe authors thank the entire staff of Dr Soetomo General Hospital and Airlangga University for providing the access and facilities to perform this study. We thank Dr Rer. Nat. Setyawan Purnomo Sakti, M.Eng., and Nike as staff of Electron Microscopy Unit, Brawijaya University, Malang, Indonesia, for the assistance in electron microscopy. We thank Abdul Hadi Furqoni, M.Si. for the involvement in this study. We thank Suryo Kuncorojakti, Ph.D and Dr. Alexander Patera Nugraha for the discussion of this study. We thank the entire subject involved in this study for participating in research and development of COVID-19 management.\n\n\nReferences\n\nMacKenzie JS, Smith DW: COVID-19: A novel zoonotic disease caused by a coronavirus from China: What we know and what we don’t. Microbiol Aust. 2020; 41: 45–50. 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PubMed Abstract | Publisher Full Text | Free Full Text\n\nSon HA, Hang DTT, Thuan ND, et al.: A simple method for detection of a novel coronavirus (SARS-CoV-2) using one-step RT-PCR followed by restriction fragment length polymorphism. J Med Virol. 2020; 92: 2839–2846. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGonzález-González E, Trujillo-De Santiago G, Lara-Mayorga IM, et al.: Portable and accurate diagnostics for COVID-19: Combined use of the miniPCR thermocycler and a well-plate reader for SARS-CoV-2 virus detection. PLoS One. 2020; 15: 1–13. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLi J, Wang H, Mao L, et al.: Rapid genomic characterization of SARS-CoV-2 viruses from clinical specimens using nanopore sequencing. Sci Rep. 2020; 10: 1–10. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMapleson D, Drou N, Swarbreck D: RAMPART: a workflow management system for de novo genome assembly. Bioinformatics. 2015; 31: 1824–1826. PubMed Abstract | Publisher Full Text | Free Full Text\n\nZhang H, Zhou P, Wei Y, et al.: Histopathologic Changes and SARS-CoV-2 Immunostaining in the Lung of a Patient With COVID-19. Ann Intern Med. 2020; 172: 629–632. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSeenichamy A, Bahaman AR, Mutalib AR, et al.: Production and characterization of a polyclonal antibody of Anti-rLipL21-IgG against leptospira for early detection of acute leptospirosis. Biomed Res Int. 2014; 2014. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRantam: FA Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) western blot staining with anti-Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Receptor Binding Domain (RBD) monoclonal antibody for detecting S1 protein. Figshare. 2021. Publisher Full Text\n\nKim JM, Chung YS, Jo HJ, et al.: Identification of coronavirus isolated from a patient in Korea with covid-19. Osong Public Heal Res Perspect. 2020; 11: 3–7. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRantam: FA Raw RT-PCR Results of SARS-COV-2. Figshare. 2021. Publisher Full Text\n\nRantam: FA Gels for the Western blot (Raw) Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) western blot staining with anti-Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Receptor Binding Domain (RBD) monoclonal antibody for detecting S1 protein. Figshare. 2021. Publisher Full Text\n\nKumar N, Barua S, Riyesh T, et al.: Complexities in isolation and purification of multiple viruses from mixed viral infections: Viral interference, persistence and exclusion. PLoS One. 2016; 11: 1–24. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSasaki M, Uemura K, Sato A, et al.: SARS-CoV-2 variants with mutations at the S1/S2 cleavage site are generated in vitro during propagation in TMPRSS2-deficient cells. PLoS Pathog. 2021; 17: 1–17. PubMed Abstract | Publisher Full Text | Free Full Text"
}
|
[
{
"id": "87787",
"date": "16 Sep 2021",
"name": "Aulanni’am Aulanni'am",
"expertise": [
"Reviewer Expertise Biochemistry",
"Molecular diagnostic",
"medical devices development",
"Biomedics"
],
"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 showed the important result that can be studied by others. SARS-Cov2 isolate plays important roles for disease development so it will help for progressive effect prevention that lead to mortality. The technique applied in this work also reliable to follow in standard infectious laboratory. By identification of local isolates, it would be useful to identify disease transmission as well as the impact to disease progressive. They used standard method that can be followed by other researchers with the same objective\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? No source data required\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
},
{
"id": "93422",
"date": "20 Sep 2021",
"name": "Lidia Audrey Rocha Valadas",
"expertise": [
"Reviewer Expertise Dentistry",
"Saliva",
"Biofilms"
],
"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 interesting study that investigates and characterizes SARS-CoV-2 isolated from East Java, Indonesia. In general, the manuscript is well designed and and can be reproducible for others. The methods and results, specially, were very well conducted. Some of my suggestions below:\nI suggest a little change on the title, for example: Characterization of SARS-CoV-2 isolated in East Java-Indonesia.\n\nI suggest a flowchart on the Methods-Subject characteristics.\n\nIt's missing the ethical aspects (approval number of the project). It's cited just the consent signed.\n\nPlease provide the limitations.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
},
{
"id": "93419",
"date": "29 Sep 2021",
"name": "Marina Derkho",
"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 topic of the article is very relevant at the present time. Therefore, when describing the methods, it is desirable to give a scheme of research design.\n\nStatistical analysis may not be available in this article.\n\nIn Figure 4, you can more accurately indicate the presence of detected changes.\n\nThe conclusions do not reflect the presented data\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? No",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-480
|
https://f1000research.com/articles/10-71/v1
|
04 Feb 21
|
{
"type": "Research Article",
"title": "Worldviews of science teachers in educational-technological context as a key factor in digitalization of teaching practices",
"authors": [
"Dina Tsybulsky",
"Yulia Muchnik-Rozanov",
"Yulia Muchnik-Rozanov"
],
"abstract": "Background: This research deals with science teachers' worldviews in the educational-technological context. Obtaining a deeper insight into teachers' discourse regarding school digitalization and understanding teachers' worldviews in the educational-technological context may be viewed as crucially important since the latter tends to play a central role in the process of digitalization of teaching practices. Methods: This study addresses the following questions: (1) Was there a difference between the teachers regarding their foci of attention expressed via personal pronouns? (2) Was there a difference between the teachers in terms of the quality and degree of their emotional immersion in the discussed topic expressed through the use of emotion words? (3) What are the semantic fields of the word clusters that include the lexemes technology and digital, and do they implicitly convey differences in teachers' understanding of school digitalization? The data were extracted by means of in-depth interviews with 38 Israeli science teachers. The linguistic analysis was employed to examine teachers' language behavior. Results: The results point out the differences in teachers' worldviews, manifested through language behavior. In particular, the differences between the three groups of teachers (outside observers, circumspect participants, and conscientious participants) were found regarding their foci of attention, the level of emotional immersion, and their implicitly conveyed understanding of the digitalization of teaching practices. Conclusions: The teachers' worldviews are the key element for understanding what it means to be or not to be a teacher in a digital society. In addition, our study demonstrates that linguistic analysis in educational research is a promising methodological approach that can render an in-depth and comprehensive picture of the explored phenomenon.",
"keywords": [
"Educational-technological context",
"school digitalization",
"teachers’ worldviews",
"teachers’ beliefs",
"linguistic analysis"
],
"content": "Introduction\n\nThe digital age has brought profound changes in the global society. On the one hand, it made our lives easier, added new possibilities for humans while impacting human society (Ganascia, 2015). On the other hand, such transformation is naturally accompanied by challenges. Among the challenges that these enhancements inevitably created is the blurring of boundaries between personal and public (Oates, 2015), which implicate work-life balance, relationships, connections, and social interactions. Floridi (2015) describes the digital age as the era of hyper-connectivity, which adds another challenge to people who are connected to multiple spaces (online and offline) at the same time.\n\nChallenges that concern technology integration (Guzey & Roehrig, 2009), confidence in ICT literacy (Hsu et al., 2012), content knowledge (Schneider & Plasman, 2011), instruction (Herro et al., 2019), and pedagogical beliefs (Margot & Kettler, 2019) of teachers are well addressed in the literature (Davis et al., 2006). These and other challenges, as well as clear advantages brought by the digital age, tend to affect teachers’ worldviews regarding the process of digitalization in the educational-technological context. Obtaining a more in-depth insight into teachers’ discourse regarding school digitalization and understanding teachers’ worldviews in the educational-technological context may be viewed as crucially important since the latter tends to play a central role in the process of digitalization of teaching practices.\n\nTeachers’ worldviews. Worldviews – collections of beliefs relating to various aspects of our human experience – are often viewed as the foundation that influences the way we think about and responds to reality (deWitt, 2018; Hiebert, 2008; Naugle, 2002). Our worldview determines our fundamental ideas about the world, how we analyze our surroundings, and the actions we take.\n\nLately, the emergence of a digital society has been viewed as a change in people’s worldview (Ess, 2015; Floridi, 2014). Recently conducted studies in the educational context suggest that teachers’ worldviews are transformed in response to the profound change in the global society (Tsybulsky & Levin, 2017; Tsybulsky & Levin, 2019). Using content and structural analyses, the study of Tsybulsky and Levin (2019) found that science teachers’ worldviews could be classified into the following categories:\n\n1. The Outside Observer: These teachers are aware of the changes that occurred in the global society, yet they observed these phenomena from the outside. They are not consciously involved in the transformation accompanying the transition to a digital society. Only minor changes in their worldviews were observed.\n\n2. The Circumspect Participant: These teachers are aware of the digital transformation taking place in the global society. They are consciously involved in these changes but do not always support them either cognitively or emotionally. Apparent changes in their worldviews were observed.\n\n3. The Conscientious Participant: Are not only these teachers aware of the global developments, but they are also knowingly involved in making these changes take place. Their worldviews have been significantly transformed in response to school digitalization.\n\nFollowing the above study (Tsybulsky & Levin, 2019), the present work seeks to explore science teachers’ worldviews in the educational-technological context by observing their language behavior. We expected that the variations between the worldviews of teachers of the above-mentioned categories would be manifested in their language and, thus, could be revealed by analyzing the distinctive linguistic markers. To the best of our knowledge, only a few studies have addressed educational phenomena by exploring language behavior (Tsybulsky & Muchnik-Rozanov, 2019; Ursúa & Vasquez, 2008). However, our previous studies suggest that linguistic analysis is a promising method for understanding implicitly conveyed messages (in this context, implicitly conveyed messages in teachers’ narratives) (e.g., Muchnik-Rozanov & Tsybulsky, 2019; Muchnik-Rozanov & Tsybulsky, 2020).\n\nThe present study focuses on the theoretical frameworks and approaches addressed below.\n\nFirstly, Systemic Functional Linguistic (SFL) approach proposed by Halliday (1978) views language as a system of grammatical and lexical choices that a language user makes to convey certain meanings and thereby function in society (Halliday et al., 2014). In the process of communication, the focal point of the speakers’ attention can be placed on the external settings as well as on the interlocutors’ deep feelings (e.g., Pennebaker, 2011). Our study follows a beaten track within the SFL framework by analyzing the referential system of language (e.g., Fine, 2006; Rude et al., 2004; Smirnova et al., 2015). Specifically, this work examines how the participants’ foci of attention are realized through their choices of references (personal pronouns).\n\nSecondly, Tausczik & Pennebaker (2010), as well as Holmes et al. (2007), propose to analyze speakers’ or writers’ emotion words to understand the extent to which they are emotionally involved in the discussion on a specific topic. In addition, the analysis of the valence of emotion words pertains to understanding how the participants perceive various phenomena (e.g., ‘glad,’ ‘happy,’ ‘moving’ refer to positively perceived phenomena, whereas ‘cruel,’ ‘hard,’ ‘neglected’ are used to describe phenomena perceived as negative). In this study, emotion words were analyzed to explore the extent to which the participants are emotionally involved in the discourse in the educational-technological context.\n\nThe third linguistic theoretical framework of this study is based on Semantic Theory and focuses on the analysis of semantic fields, where a semantic field is defined as a set of interrelated lexemes that cover a particular aspect of reality (Brinton, 2000). The analysis of semantic fields can be employed to understand the worldviews among various communities as well as individuals. In the present study, the semantic fields of specific word sequences were analyzed to extract participants’ covertly expressed understanding of school digitalization.\n\nLinguistic analysis in education. Despite its wide utility in psychology (e.g., Freda et al., 2015; Weintraub, 1989) and psychiatry (e.g., Bersudsky et al., 2005; Fine, 2006; Nienow & Docherty, 2004; Smirnova et al., 2015), linguistic analysis has been relatively seldom employed in educational research. For example, linguistic analysis has been used to explore the notion of leadership in the context of educational administration (Anderson & Mungal, 2015; Crowhurst & Emslie, 2018). Another instance of applying linguistic analysis to educational research is researching interventions for children with disabilities in the context of special education (Imms et al., 2016). In addition, linguistic analysis of textbooks has been found to contribute to multicultural educational research by offering an insight into the role of textbooks in helping students find their own voice (Curdt-Christiansen & Weninger, 2015).\n\nA few studies have been dedicated to the analysis of associations between teaching, learning, and students’ identities across time and context (Tamatea et al., 2008; Sfard & Prusak, 2005) teachers’ ideological perspectives on their work (Llewellyn, 2005); inservice teachers’ identity (Heyd-Metzuyanim, 2019; Heyd-Metzuyanim & Shabtay, 2019), and preservice teachers’ identity (Tsybulsky & Muchnik-Rozanov, 2019; Ursúa & Vasquez, 2008).\n\nIn this study, a linguistic analysis was employed in educational research to explore inservice teachers’ worldviews in the educational-technological context, as expressed in their language behavior. It should be noted that, to the best of our knowledge, existing studies in the field have not utilized linguistic analysis to explore teachers’ worldviews in the realm of education.\n\n\nMethods\n\nThe present research addressed the following questions:\n\n1. Was there a difference between the teachers in terms of their foci of attention expressed via personal pronouns?\n\n2. Was there a difference between the teachers in terms of the quality and degree of their emotional immersion in the discussed topic expressed through emotion words?\n\n3. What are the semantic fields of the word clusters that include the lexemes technology and digital, and do they implicitly convey differences in teachers’ understanding of school digitalization?\n\nThis study’s participants were inservice high-school science teachers (n = 38) from a central metropolitan area of Israel. The participants were chosen with several concepts in mind. First, as the previous study aimed to identify teachers’ worldviews in the context of digitalization of teaching practices, science teachers constituted a group that was likely to be more open to and aware of technological developments. This led to the second assumption, namely, that a shift in the predominant sociocultural worldview would be detected first and foremost among those who teach a discipline that is continuously affected by technological progress. Third, students and teachers working and living in the central metropolitan area were likely to be the first to experience such a change, as they represent a high socioeconomic class compared to other parts of the country.\n\nWe used a voluntary group, which involved only those teachers who agreed to participate in the study. The participants were recruited by using a mailing list of the National Center of Science Teachers as well as by utilizing professional social networks. The teachers were informed about the research goals and procedure and indicated their willingness to participate by completing a written informed consent form (0% of dropout rate). The study was approved by the Behavioural Sciences Research Ethics Committee of the Technion (Approval number 2018-075).\n\nThe data collection tool selected for the study was the in-depth interview. The interviews took place at venues chosen by the interviewees, such as their schools, within the time slots the participants found convenient. Each interview lasted approximately 90 minutes. The focus of the interview protocol (Extended data: Appendix 1 (Tsybulsky, 2021)) was on participants’ feelings, thoughts, and emotions regarding digital technologies, as these were manifested in their personal and professional lives. The interviews were conducted by DT of this study. She is an expert in educational research, and in qualitative research in particular, with a PH.D. Degree in Science Education. All the interview data were audio-recorded and then transcribed in conventional orthographic local language by a Ph.D. student in science education, a native speaker, who is experienced in transcribing language data.\n\nAs it has been mentioned above (see Theoretical background), our analysis focuses on the three groups of teachers defined by the content structural analysis conducted in the earlier study (Tsybulsky & Levin, 2019): five teachers were assigned to the category of outside observers, 12 were assigned to the category of circumspect participants, and 21 teachers were assigned to the category of conscientious participants.\n\nThe linguistic analysis of the data focused on three markers: (1) personal pronouns as the indicators of the foci of attention; (2) emotion words as the indicators of teachers’ emotional involvement in the discussed topic; (3) semantic fields of the words that clustered with the lexemes technology and digital, as the indicators of participants’ implicit perceptions of school digitalization.\n\nTo explore teachers’ foci of attention (RQ1), we scrutinized the personal pronouns used by the participants. In an attempt to differentiate between the focus of attention placed on the external world versus inner feelings, the distinction between speech-role (SR) and non-speech-role (NSR) must be made (Halliday et al., 2014; Rochester & Martin, 1977). SR refers to the interlocutors (personal references of the first and the second person), whereas NSR refers to the external settings: places, people, and objects referred to by the speakers (third-person personal references).\n\nBased on Levenston (1970), we used a list of the personal pronouns mentioned above to code all personal references in the transcripts and then calculated the frequency of each type of pronoun. Then the frequencies of first- and second-person references were merged into the SR category. Similarly, the frequencies of all third-person references were merged into the NSR category. We converted the frequency totals into a rate per 1,000 words to control the length of the elicited and transcribed speech samples. The rates for SR references were compared to NSR references in the three groups of teachers: outside observers, circumspect participants, and conscientious participants.\n\nTo examine the degree and quality of participants’ emotional immersion into a topic discussed during the interview (RQ2), we analyzed two aspects of the emotion words employed by the participants. We considered the positive versus negative valence of the emotion words they employed, which indicate the speakers’ perceptions of their surrounding world, and also calculated the rate at which emotion words were used in one’s language performance has been associated with increased immersion in a described process or event (Holmes et al., 2007; Tausczik & Pennebaker, 2010). To this end, based on Tausczik & Pennebaker (2010), the lexemes and stems listed under the category of emotion words in the Linguistic Inquiry and Word Count (LIWC) software dictionary were translated into conventional Hebrew by a native speaker with a PH.D. Degree in Semitic Languages, who is also fluent in English. The transcripts were coded for all the lexemes and word stems in the list, and their frequencies were calculated. The frequency totals for emotion words of positive and negative valence were converted into rate per 1,000 words to control for the length of the elicited and transcribed speech samples. The rate of emotion words was compared among the three groups of teachers: outside observers, circumspect participants, and conscientious participants. In addition, we compared the frequencies of positive and negative emotion words in each of the three groups.\n\nTo explore participants’ implicitly conveyed understanding of school digitalization (RQ3), we looked for possible variations in the teachers’ word choices when discussing digital-age-related experiences in the context of their everyday professional teaching practices. To this end, the transcripts were coded for all the word clusters containing the two lexemes digital and technology. Word clusters with one of the required lexemes that, in addition, featured only prepositions, pronouns, and/or auxiliary and modal verbs were omitted from the semantic field analysis. Both the nature of the word clusters containing both the lexemes digital and technology and their distribution across semantic fields were compared across the three groups of teachers. The semantic distribution was measured as a percentage of the total number of word clusters in each teacher group. Overall, 95,409 words were analyzed throughout 38 transcribed interviews. Data analysis was conducted by YM. She is an expert in linguistic analysis with a PH.D. Degree in Linguistics. 30% of the data were also analyzed by DT using a coding protocol. Inter-coder reliability of 90% was achieved.\n\nDistinctive linguistic markers, subcategories, coding methods, and examples are summarised in Table 1.\n\n\nResults\n\nIt was found that there are some differences in the foci of attention between the three groups of teachers. Since the conscientious participants were predominantly focused on the situational context, they tended to use more non-speech-role references than the outside observers or the circumspect participants (57 vs. 39 and 45, respectively). These findings point out that those teachers who are consciously involved in the digital transformation of the global society refer to the external world more frequently than do other groups of teachers. The circumspect participants used fewer speech-role references than the outside observers or the conscientious participants (90 vs. 100 and 95). Such language behavior tends to signify a lack of personal involvement in the changes accompanying the process of digitalization. In this group and the outside observers, similar rates of non-speech-role references were found (45 and 39, respectively). These findings indicate that those teachers did not show more interest in the external world than outside observers, who felt alienated from the transition to a digital society.\n\nRegarding SR references, it was found that the outside observers used slightly more of this reference type than either the circumspect or the conscientious participants (100 vs. 90 and 95, respectively). The teachers in this group also used fewer NSR references than the circumspect participants or the conscientious participants (39 vs. 45 and 57, respectively). The above findings indicate that the outside observers were more focused on their own experiences and feelings than two other groups of teachers while discussing the transformations accompanying society’s digitalization in general and the digitalization of school in particular. Table 2 presents a summary of the findings regarding RQ1.\n\nIt was found that all teachers used emotion words (both positive and negative). However, there were some differences in the frequency rates of emotion words between the three observed groups. Firstly, our findings show that the conscientious participant group used the fewest number of emotion words compared to the teachers in the outside observer and circumspect participant groups (19 vs. 30 and 17). These findings suggest that the conscientious participant group was less immersed in the discussion on digitalization in an educational context than the teachers who were defined as the outside observers but more immersed than the teachers assigned to the circumspect participant group. Secondly, it was found that the language of the outside observers indicated that this group was more immersed in the phenomenon of a digital society than either of the other two groups (30), a finding that—although surprising— may be traced to their firm belief that the changes accompanying school digitalization are superficial and, perhaps, to a desire to conceal their real sense of alienation. Table 3 presents the summary of the findings regarding RQ2.\n\nIn regard to the analysis of negative and positive emotion words as two separate coding categories, our findings demonstrate the lowest rate of negative emotion words used by the teachers in the circumspect participant group (7). This finding reflects the teachers’ awareness of school digitalization as a necessary and inevitable process that, nevertheless, is accompanied by negative emotions. These negative emotions are associated with feeling external pressure to adjust to the digitalization process despite both affective and cognitive alienation.\n\nOur findings show that five semantic fields were associated with the lexemes digital and technology: pedagogical practices and the learning process, means and tools, emotional states, the rapid development of technology, and the younger generation. The semantic field of pedagogical practices and the learning process included such words as ‘teacher,’ ‘lesson,’ ‘understand,’ ‘learners,’ ‘struggling students,’ etc. The semantic field of means and tools referred to the words like ‘presentation,’ ‘virtual lab,’ ‘WhatsApp group,’ ‘computer,’ etc. The semantic field of emotional states comprised the words like ‘feel,’ ‘upset,’ ‘glad,’ ‘scared,’ etc. The semantic field of the rapid development of technology was associated with such words as ‘changes,’ ‘development,’ ‘progress,’ ‘technology,’ ‘ICT,’ etc. Finally, the semantic field of the younger generation incorporates words like ‘different generation,’ ‘future generation,’ ‘digital natives,’ ‘young people,’ ‘children,’ etc.\n\nWe found some differences between the three groups of teachers regarding the distribution across the semantic fields. The following semantic fields were observed among the conscientious participants: 1) pedagogical practices and the learning process; 2) means and tools; 3) emotional states. For this group of teachers, the most saturated semantic field was associated with pedagogical practices and the learning process (78%). By contrast, a significantly smaller number of clusters were produced by that group referred to the semantic field of means and tools (11%) and emotional states (6%). In addition, 5% of the clustering lexemes belonged to various semantic fields that could not be grouped.\n\nIn the circumspect participant group, the findings revealed the same three semantic fields (pedagogical practices and the learning process; means and tools; and emotional states), but a different distribution was observed (29%, 58%, and 7%, respectively.) A total of 6% of the words clustered with digital and technology belonged to various semantic fields and could not be categorized and analyzed in the present study.\n\nIn the outside observer group, we found the associations with all five semantic fields: emotional states (34%), rapid development (32%), the younger generation (18%), means and tools (8%), and pedagogical practices and the learning process (6%). Throughout the interviews with these teachers, only 2% of the clustering lexemes referred to diverse semantic fields that could not be grouped. Table 4 presents a summary of the findings regarding RQ3.\n\n* The total number of clusters with the lexemes digital and technology–88 (100%)\n\n** The total number of clusters with the lexemes digital and technology–311 (100%)\n\n*** The total number of clusters with the lexemes digital and technology–344 (100%)\n\nThese findings reflect the teachers’ implicitly conveyed understanding of school digitalization in the context of their everyday professional teaching practices. The teachers’ vision ranges from total acceptance and successful implementation to hostility and disagreement. High saturation of the semantic field associated with pedagogical practices and the learning process shows that the participants view digital technology as an integral part of their classroom experiences and perceive the digitalization process as natural and positive. The high saturation of the semantic field associated with emotional states indicates the teachers’ strong emotional involvement. Numerous clusters related to the semantic fields of the rapid development of technology and the younger generation (semantic fields that were found unique for the outside observer group) point at their awareness of the school digitalization process as well as understanding that the changes brought in by this process are inevitable but not necessarily beneficial for the new generation of students. The high saturation of the means and tools semantic field suggests that these teachers perceive the process of school digitalization only at the instrumental and practical level. At the same time, a few clusters associated with the field of means and tools reflect a deeper understanding of the digitalization process as a new reality that leads to redefining school practices.\n\n\nDiscussion\n\nTeachers reconstruct their identities and worldviews in the digital age, and these changes are conceptual (Avidov-Ungar & Forkosh-Baruch, 2018; Tsybulsky & Levin, 2019). Throughout this worldview reconstruction, teachers may be seen as belonging to one of three groups, based on their worldviews regarding school digitalization: the outside observer, the circumspect participant, or the conscientious participant (Tsybulsky & Levin, 2019). This study demonstrates that the worldview reconstruction is so profound that it manifests itself in the teachers’ language behavior.\n\nThe previous studies in the field employed a qualitative approach and the content analysis method. While content analysis deals with explicitly conveyed messages and views, the linguistic analysis performed in the current study aims to provide a deeper understanding of the teachers’ worldviews based on implicit aspects that are not related to the content of the conveyed message but rather to the way it is conveyed in terms of language use. In particular, our analysis sought to identify the foci of attention, the quality and degree of emotional immersion, and semantic fields of the word clusters containing the lexemes digital and technology as manifested in the language found in the transcripts of all three groups of teachers.\n\nThe results indicate that the conscientious participants, who are both affectively and cognitively involved in the school digitalization process, were more focused on and interested in the external world than the two other groups of teachers. The teachers in this group exhibited an intermediate level of emotional immersion. These findings indicate that teachers in this group perceived digital social and personal experiences, interactions, and artifacts, as well as the concomitant changes in the surrounding world, as an integral part of their daily lives and, consequently, as an intrinsic constituent of their personal and professional identities.\n\nThe observed distribution of semantic fields associated with word clusters containing the lexemes digital and technology indicates that the teachers who conscientiously participate in school digitalization viewed technology as an inseparable and integral part of this process. Expressions of emotion seldom accompanied descriptions of their digital pedagogical practices, and negative emotions were noticeably rare.\n\nThe circumspect participants were less focused on themselves than the two other groups of teachers, suggesting a more substantial differentiation between their personal and professional identities. They showed a relatively low level of emotional involvement when discussing the digitalization of society. As professionals, they were aware of the changes taking place in their realm, and they were willing to be involved in these changes to remain relevant and effective teachers. However, on a personal level, they did not consider themselves to be a part of a digital society and were emotionally distanced from it, which may be related to the paucity of experience in and interactions with the digital habitat. Besides, the findings regarding the semantic fields show that the teachers in this group perceive the process of school digitalization only at the instrumental and practical level. These teachers frequently claimed that ‘Technology is solely a tool.’ What matters is pedagogy’.\n\nMore than the two other groups of teachers, the outside observers were focused on themselves and less focused on the surrounding world. They also showed the highest level of emotional immersion. As they explicitly reported their awareness of the transformations taking place around them, these teachers’ language behavior reflects their emotional estrangement and distancing from a digital society (the world in which their students are immersed). The present linguistic analysis indicates that these teachers felt a contradiction between their values and what they observed regarding the transition to a digital society. Teachers’ language behavior in this group reflects their concerns about digital technology and its consequences for teaching and learning. Their worldview regarding ICT development and the accompanying transformations in the global society were manifested through powerful and mostly negative emotions.\n\nIn sum, the present study identified differences in the language of the three groups of teachers in terms of the interviewees’ foci of attention, the degree of their emotional immersion when discussing the digitalization of school, and the semantic fields evoked through word clusters containing the lexemes digital and technology. Moreover, findings of the current linguistic analysis made it possible to delve beneath the surface of explicit statements to reveal more than the teachers’ worldview, namely, their feelings, emotions, concerns, and attitudes. These results corroborate other studies, albeit limited in number, emphasizing the value of linguistic analysis for examining teachers’ perceptions and beliefs (Llewellyn, 2005; Muchnik-Rozanov & Tsybulsky, 2019; Muchnik-Rozanov & Tsybulsky, 2020; Tsybulsky & Muchnik-Rozanov, 2019).\n\nAlthough the number of the analyzed words was relatively large in linguistic analysis terms, it may be problematic because it features a certain degree of homogeneity in the selected population. Nonetheless, the methodological framework used herein, specifically examining worldviews by exploring three distinctive linguistic markers (personal pronouns, emotional words, semantic fields of specific word clusters), proved effective. Hence, it is recommended for use in future educational research conducted in a broader context as a way to shed additional light on inservice and preservice teachers’ values and beliefs.\n\nThe current study’s contribution is twofold. Firstly, our study contributes to the discourse on school digitalization. The teachers’ worldviews are the key element for understanding what it means to be or not to be a teacher in a digital society. Secondly, our study demonstrates the value of linguistic analysis in the realm of educational research. We believe that linguistic analysis in educational research is a highly promising methodological approach that can render a deep and comprehensive picture of the explored phenomenon.\n\n\nData availability\n\nThe transcripts underlying the results cannot be shared for the following reasons. Firstly, to meet the requirements of the Behavioural Sciences Research Ethics Committee of the Technion, researchers are forbidden to share recorded and/or transcribed interviews with anybody except the research team. An exception is made for publishing findings where anonymous interview quotes can be used. Second, the participants’ anonymity and data protection were insured in the written consent form signed by the participants prior to the commencement of the study. For interested researchers, please contact the Behavioral Sciences Research Ethics Committee of the Technion for access to the data (bs.ethics.technion@gmail.com).\n\nDANS: Appendix 1. Interview protocol, https://doi.org/10.17026/dans-27e-pmdu (Tsybulsky, 2021).\n\nThis project contains the following extended data:\n\n- Appendix 1. Interview Protocol\n\nData are under a DANS license (Open Access for Registered Users), which allows unrestricted access to the data, while stipulating that the user must comply with the Netherlands Code of Conduct for Research Integrity, the General Data Protection Regulation (GDPR) and other applicable laws and regulations.",
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Publisher Full Text\n\nPennebaker JW: The secret life of pronouns. New Scientist. 2011; 211(2828): 42–45. Reference Source\n\nRochester SR, Martin JR: The art of referring: The speaker’s use of noun phrases to instruct the listener. Discourse Process. 1977; 1: 137–181.\n\nRude S, Gortner EM, Pennebaker J: Language use of depressed and depression-vulnerable college students. Cognition & Emotion. 2004; 18(8): 1121–1133. Publisher Full Text\n\nSchneider RM, Plasman K: Science teacher learning progressions: A review of science teachers’ pedagogical content knowledge development. Review of Educational Research. 2011; 81(4): 530–565. Publisher Full Text\n\nSfard A, Prusak A: Telling identities: In search of an analytic tool for investigating learning as a culturally shaped activity. Educational Researcher. 2005; 34(4): 14–22. Publisher Full Text\n\nSmirnova D, Walters J, Fine J, et al.: Schizophrenia in Bilingual Immigrants: is Verbal Fluency Preserved in Second Language Acquisition? Eur Psychiatry. 2015; 30(S1): 28–31. Publisher Full Text\n\nTamatea L, Hardy J, Ninnes P: Paradoxical inscriptions of global subjects: critical discourse analysis of international schools’ websites in the Asia–Pacific Region. Critical Studies in Education. 2008; 49(2): 157–170. Publisher Full Text\n\nTausczik YR, Pennebaker JW: The psychological meaning of words: LIWC and computerized text analysis methods. J Lang Soc Psychol. 2010; 29(1): 24–54. Publisher Full Text\n\nTsybulsky Dr. DT (Technion): Appendix 1. Interview Protocol. DANS. 2021. http://www.doi.org/10.17026/dans-27e-pmdu\n\nTsybulsky D, Muchnik-Rozanov Y: The development of student-teachers’ professional identity while team-teaching science classes using a project-based learning approach: a multi-level analysis. Teaching and Teacher Education. 2019; 79: 48–59. Publisher Full Text\n\nTsybulsky D, Levin I: Science teachers’ worldviews in the age of the digital revolution: Structural and content analysis. Teaching and Teacher Education. 2019; 86. Publisher Full Text\n\nTsybulsky D, Levin I: Inquiry-based science education and the digital research triad. In: I. Levin & D. Tsybulsky (Eds.), Digital Tools and Solutions for Inquiry-Based STEM Learning.Hershey, PA: IGI Global. 2017; 140–165. Publisher Full Text\n\nUrsúa A, Vásquez C: Reflection and professional identity in teachers’ future-oriented discourse. Teaching and Teacher Education. 2008; 24: 1935–1946. Publisher Full Text\n\nWeintraub W: Verbal behavior in everyday life. New York: Springer. 1989. Reference Source"
}
|
[
{
"id": "78895",
"date": "02 Mar 2021",
"name": "Noemi Waight",
"expertise": [
"Reviewer Expertise Science education",
"technology design and implementation",
"nature of technology",
"teachers' practices with technological-supported",
"inquiry-based practices."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 focused on teachers’ discourse related to school digitization and understanding teachers’ worldviews in the educational-technology context. Specifically, this study explored science teachers’ worldviews in the educational-technological context by observing language behavior. While the focus on science teachers’ worldviews offered an alternative framework to examine teachers’ views, there were some important gaps in the narrative.\nImportantly, the manuscript attempted to map worldviews and language behavior, and while this was clearly articulated, what remained underdeveloped is the value of this connection for teaching and learning. In other words, it was not clear how this conceptualization was translated to inform practice. Here it would be important to engage the significance of this work and thus why the categorizations and linguistic patterns are important for science education.\nBased on my read, this manuscript was linked to a previous study that reported on worldviews and the categorization of teachers into three distinct groups. Yet, it was not clear how this designation occurred. What data sources were used to inform this categorization? The omission of this information is critical for understanding how linguistic patterns were related to the various types of teachers.\nGiven the above, the notion of world views as a theoretical framework was limited and was only superficially addressed. This needs to be expanded.\n\nAs noted above, the organization of the findings based on the categorization of worldviews was a bit confusing since the manuscript indicated that this occurred in a different study. Yet, as a reader this was needed in order to understand how the data informed this categorization and the language behavior.\nThe contributions of this work as reported in the manuscript requires more work. It was not clear how these contributions advance understanding of digitization in science teacher education? How did this work advance what we already know in this domain? In addition, I would suggest that the author(s) focus on the implications of their work for both practice and research.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? No source data required\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "6667",
"date": "21 May 2021",
"name": "Dina Tsybulsky",
"role": "Author Response",
"response": "Dear Prof. Noemi Waight, We are grateful for your valuable comments and suggestions that have contributed to improving our manuscript. The following are the detailed answers to your review. \"Importantly, the manuscript attempted to map worldviews and language behavior, and while this was clearly articulated, what remained underdeveloped is the value of this connection for teaching and learning. In other words, it was not clear how this conceptualization was translated to inform practice. Here it would be important to engage the significance of this work and thus why the categorizations and linguistic patterns are important for science education.\" Our study is not directly related to teaching and learning. However, since teachers are responsible for implementing the digitalization of today’s education by integrating ICT into education, their worldviews play a crucial role in this process (please see p.3). Our work contributes to understanding deep subconscious changes in teachers’ worldviews reflected in their language behaviour. Our linguistic analysis made it possible to delve beneath the surface of explicit statements to reveal implicit messages including their feelings, emotions, concerns, and attitudes. While content analysis (used in the previous study) deals with explicitly conveyed messages and views, the linguistic analysis performed in this study was aimed to provide a deeper understanding of the teachers’ worldviews based on implicit aspects related to the way a message is conveyed in terms of language use rather than to its content. Thus, we show the importance of linguistic analysis for examining teachers’ views and beliefs. On page 15, we have explained the study contribution. \"Based on my read, this manuscript was linked to a previous study that reported on worldviews and the categorization of teachers into three distinct groups. Yet, it was not clear how this designation occurred. What data sources were used to inform this categorization? The omission of this information is critical for understanding how linguistic patterns were related to the various types of teachers.\" We have explained how the designation into the three categories occurred referring to the data sources that were used (please see p. 3). \"Given the above, the notion of world views as a theoretical framework was limited and was only superficially addressed. This needs to be expanded.\" Thank you very much for this comment. We have expanded our theoretical framework regarding worldviews and added the definition of worldview construct by referring to the classic definition by Wilber (1995) (please see p. 3). \"As noted above, the organization of the findings based on the categorization of worldviews was a bit confusing since the manuscript indicated that this occurred in a different study. Yet, as a reader this was needed in order to understand how the data informed this categorization and the language behavior.\" Page 3 presents our explanation of the categorization of worldviews. \"The contributions of this work as reported in the manuscript requires more work. It was not clear how these contributions advance understanding of digitization in science teacher education? How did this work advance what we already know in this domain? In addition, I would suggest that the author(s) focus on the implications of their work for both practice and research.\" On page 15, we have explained the study contributions and implications. We thank you again for the effort you invested in improving our manuscript. We believe these efforts have resulted in a much stronger paper. It is very much appreciated. Sincerely, Authors"
}
]
},
{
"id": "82750",
"date": "20 Apr 2021",
"name": "Deniz Saribas",
"expertise": [
"Reviewer Expertise Science education"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe researchers interpreted the results based on the frequencies of the use of pronouns and words without providing any statistical analysis. Therefore, it is hard to decide whether the comparisions between the participants in different categories (outside observer, circumspect participant and conscientious participants) are statistically correct.\nFurthermore, it is not clear how the researchers classified these participants into three categories. Athough they declared that they are forbidden to share recorded and/or transcribed interviews with us, they could have shared the questions. The researchers also need to mention the implications of this study. Overall, it is an interesting research by giving insights of different teacher worldviews in a digital society. However, it needs the minor aforementioned revisions.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "6668",
"date": "21 May 2021",
"name": "Dina Tsybulsky",
"role": "Author Response",
"response": "Dear Prof. Deniz Sarıbaş, Thank you very much for reviewing our manuscript and offering valuable suggestions for its improvement. We really appreciate that you have invested time into our work in these challenging times. \"The researchers interpreted the results based on the frequencies of the use of pronouns and words without providing any statistical analysis. Therefore, it is hard to decide whether the comparisions between the participants in different categories (outside observer, circumspect participant and conscientious participants) are statistically correct.\" Thank you very much for this comment. Following your suggestion, we have checked for the statistical significance using the chi-square test (please see Results section). \"Furthermore, it is not clear how the researchers classified these participants into three categories.\" We have explained how the designation into the three categories occurred referring to the data sources that were used (please see p. 3). \"Although they declared that they are forbidden to share recorded and/or transcribed interviews with us, they could have shared the questions.\" Appendix 1 presents the interview questions (Tsybulsky, 2021). \"The researchers also need to mention the implications of this study.\" On page 15, we have explained the study implications. Sincerely, Authors"
}
]
}
] | 1
|
https://f1000research.com/articles/10-71
|
https://f1000research.com/articles/10-479/v1
|
16 Jun 21
|
{
"type": "Case Report",
"title": "Case Report: Postmortem bone histomorphometric analysis in a 38-year-old Japanese man with immobilization osteoporosis because of orthostatic hypotension related to amyloid light chain amyloidosis",
"authors": [
"Masaki Hatano",
"Izuru Kitajima",
"Masaki Nakamura",
"Kazuya Isawa",
"Tatsuya Suwabe",
"Junichi Hoshino",
"Keiichi Kinowaki",
"Kenichi Ohashi",
"Naoki Sawa",
"Seizo Yamamoto",
"Yoshifumi Ubara",
"Izuru Kitajima",
"Masaki Nakamura",
"Kazuya Isawa",
"Tatsuya Suwabe",
"Junichi Hoshino",
"Keiichi Kinowaki",
"Kenichi Ohashi",
"Naoki Sawa",
"Seizo Yamamoto",
"Yoshifumi Ubara"
],
"abstract": "We performed a postmortem bone histomorphometric analysis of iliac bone on a 38-year-old man who had been bedridden for the nine months before his death because of orthostatic hypotension and severe malnutrition related to amyloidκ-light-chain amyloidosis. Cancellous bone volume was greatly decreased, with a trabecular bone volume to total bone volume ratio of 6.77% (normal value, 19.56% ± 5.62%). Trabecular thinning was also apparent, with a trabecular thickness of 78.9 μm (normal value, 131.3 ± 28.1 μm), although the trabecula was still preserved. Cortical bone width was normal, although areas of porosity area were clear throughout the cortical bone. Our findings indicate that immobilization-related osteoporosis may be closely associated with loss of cancellous bone.",
"keywords": [
"amyloid light chain amyloidosis",
"bone histomorphometry",
"bed rest",
"disuse osteoporosis",
"immobilization osteoporosis"
],
"content": "Background\n\nImmobilization osteoporosis has been reported to occur after a stroke or spinal cord injury,1-3 spaceflight, and long-term bed rest.4,5 Long-term immobilization or unloading affect both bone formation and bone resorption and lead to bone loss and an increased risk of fracture.6,7 Despite decades of intense research, the effects of long-term bed rest on bone cells and the associated structural changes remain unclear. The effects are difficult to estimate because we cannot exclude factors associated with pre-existing disease and aging. Here, we present a postmortem bone histomorphometric analysis of a man who became bedridden approximately nine months before his death because of severe orthostatic hypotension related to amyloid light-chain (AL) amyloidosis.\n\n\nCase presentation\n\nAn autopsy was performed on a 38-year-old Japanese man with AL amyloidosis who died of interstitial pneumonia. The patient developed AL amyloidosis at the age of 37. At that time, he was otherwise healthy and had no family history of fracture.\n\nAt age 37, the patient developed abnormal bowel movements, consisting of alternating constipation and diarrhea, which gradually worsened. He also lost his appetite. He developed orthostatic hypotension and consequently had difficulties standing and sitting and became bedridden. Four months after becoming bedridden, he was admitted to our hospital for diagnosis and treatment.\n\nOn admission, the patient was 170.0 cm tall, but his weight had decreased from 90 kg to 62 kg over the previous four months. The laboratory data were as follows: serum albumin, 2.2 g/dL; total protein, 4.2 g/dL; urea nitrogen, 10 mg/dL; serum creatinine, 0.50 mg/dL; calcium, 8.3 mg/dL; phosphate, 3.8 mg/dL; alkaline phosphatase, 151 IU/L Japan Society of Clinical Chemistry (JSCC) method; normal range, 117 to 350), and C-reactive protein, 0.1 mg/dL. An immunologic evaluation found that serum immunoglobulin (Ig) G was 509 mg/dL (normal range, 870-1700 mg/dL); IgA, 98.0 mg/dL (normal range, 110-410 mg/dL); and IgM, 22.0 mg/dL (normal range, 35-220 mg/dL). Serum M-protein was not detectable by immunofixation. Urinalysis detected proteinuria (5.5 g/day), and immunofixation electrophoresis showed kappa (κ)-type Bence-Jones protein in the urine. Kidney biopsy and endoscopic examination of the colon biopsy both showedκ-positive AL-amyloidosis (Figure 1). Examination of the bone marrow revealed 2.8% monoclonal plasma cells (normal value < 10%); however, the patient did not fit the criteria for multiple myeloma because a full skeletal survey did not detect any osteolytic lesions. Thus, primaryκ-type AL amyloidosis was diagnosed.\n\n\n\n(a): Colon biopsy (PAS stain, light microscopy) (×100). Amorphous material was noted on small arteries and surrounding tissues in the subserosal layer.\n\n(b): Colon biopsy (Congo red stain, light microscopy) (×100). Congo red-material was positive for amorphous material.\n\n(c): Kidney biopsy (Congo red stain, light microscopy) (×400). Congo red material was noted in the glomeruli.\n\n(d): Kidney biopsy (κ-stain, immunofluorescence microscopy) (×400). κ-stain was positive for Congo red material).\n\n\nClinical course\n\nAt admission, the patient’s blood pressure was 100/60 mmHg in the sitting position but decreased to 60/30 mmHg in the standing position. Therefore, the patient remained in bed. Treatment was started with vincristine (0.4 mg/day for 4 days), adriamycin (14 mg/day for 4 days), and dexamethasone (40 mg/day for 12 days). However, five months after hospitalization, the patient suddenly died of interstitial pneumonia. At death, the patient had been bedridden for nine months.\n\nAfter obtaining consent from the patient’s family, we performed an autopsy. Bone histomorphometric analysis of the right iliac bone was performed at the Ito Bone Science Institute (Niigata, Japan); tetracycline double labeling was not performed.\n\n\nBone histomorphometric examination\n\nCancellous bone was assessed by bone histomorphometry (Table 1). All bone volume markers were decreased compared with the age-matched reference ranges presented in the report by Reccker et al.,8 as follows: trabecular bone volume to total volume, 6.77%; trabecular thickness, 78.9 μm; trabecular unit wall thickness, 21.0 μm.\n\nCancellous bone was assessed by bone histomorphometry. All bone volume markers were decreased compared with the age-matched reference ranges. All bone osteoid markers were also decreased compared with the age-matched reference range. The fibrous tissue volume to total volume could not be assessed, and the eroded surface to bone surface was increased to 16.2%.\n\nAll bone osteoid markers were also decreased compared with the age-matched reference range, as follows: osteoid volume to total volume ratio, 0.03%; osteoid volume to bone volume ratio, 0.51%; osteoid surface to bone surface ratio, 4.12%; and osteoid thickness, 6.91 μm. The fibrous tissue volume to total volume could not be assessed, and the eroded surface to bone surface was increased to 16.2%.\n\nThe cancellous bone volume was greatly decreased, and trabecular thinning was apparent; the trabecula was preserved, but the number of trabecular termini was increased to 52 points and the number of nodes (bifurcated trabecula) was decreased to 12 points (Figure 2a). Trabecula thinning indicated resorption by osteoclasts, and island bones and clubbing trabecula with bilateral termini were noted. We found more empty lacunae, which are characterized by the disappearance of osteocytes, than lacunae containing osteocytes (Figure 2b).\n\n\n\n(a) Low-power field of light microscopy (×20).\n\nThe cancellous bone volume was greatly decreased, and trabecular thinning was apparent; however, the trabecula was preserved, although the number of trabecular termini (N.Tm; red) was increased to 52 points and the number of nodes (bifurcated trabecula) (N.Nd; blue) was decreased to 12 points. Compared with the width of cancellous bone, the width of cortical bone was preserved with 1.65 mm and 0.78 mm. The number of cortical node structures connecting from the endocortical surface to the cancellous trabecula was decreased.\n\n(b) (A and B): Trabecula thinning indicated resorption by osteoclasts.\n\n(C) Island bones and clubbing trabecula with bilateral termini were noted.\n\n(D) More empty lacunae, characterized by the disappearance of osteocytes, were seen than lacunae containing osteocytes.\n\n(c) High-power field of cortical bone (×100, 200 or 400).\n\n(A, B and C) Large pores associated with enlargement of the bone marrow cavity due to resorption by osteoclasts.\n\n(D) More empty lacunae were seen than lacunae containing osteocytes.\n\nCortical bone was preserved with cortical bone width of 1.65 mm and 0.78 mm. However, the area of porosity to total cortical bone area ratio, which increases when large pores appear because of enlargement of the bone marrow cavity due to resorption by osteoclasts, was increased to 37.19% and 22.11% (Figure 2a, Table 1). The number of cortical node structure connecting from the endocortical surface to the cancellous trabecula was decreased (Figures 2a and 2c). More empty lacunae were seen than lacunae containing osteocytes (Figure 2c).\n\nSevere osteoporosis of cancellous bone closely associated with immobilization was diagnosed.\n\nPostmortem Iliac bone of a 46-year-old healthy man.\n\nThe standard values of cortical bone have not been reported. Therefore, to put the degree of osteoporosis in our patient into context, we determined the parameters of postmortem iliac bone of a 46-year-old healthy man. The control individual showed abundant cortical bone surrounding the cancellous bone. The cortical bone width was 1.45 mm and 0.67 mm, and the area of porosity area to total cortical bone area ratio was 3.2% and 8.45%.\n\n\nDiscussion\n\nImmobilization or skeletal unloading, which can occur during spaceflight, hindlimb suspension, and long-term bedrest, are well recognized as causes of loss of bone mass and strength. Both clinical and animal studies have reported on the mechanisms of bone loss in these situations.9-16 For example, previous research has examined the effects of tail suspension, tenotomy, or sciatic neurectomy in animal models and of bed rest with a head-down tilt in human studies.9,11,13-15\n\nIn animal models, unloading reduces the rate of bone formation because of changes in osteoblast progenitor cell recruitment and defective functioning of differentiated osteoblasts.9-11 On the other hand, the effect of immobilization or skeletal unloading has been reported to cause inconsistent changes in osteoclast surface and number.9-12\n\nIn a human study, 12 weeks of bed rest led to suppression of the osteoblastic surface in cancellous bone and an increase of bone resorption and eroded surface in both cancellous and cortical bone, although cortical and cancellous bone volume, as measured histomorphometrically, did not change.7 This study and another one found that mean cortical and trabecular thickness also did not change after long-term bed rest.7,13 Another study found that 120 days of bed rest led to loss of cancellous bone volume.14 However, mean trabecular separation and the node to terminus ratio did not change. The differences in the results of these studies were probably related to differences in their duration, the causes of immobilization, and the age and sex of the participants.15,16\n\nIn conclusion, we performed postmortem bone histomorphometric analysis of the iliac bone on a 39-year-old man who had been bedridden for nine months before his death because of severe orthostatic hypotension and severe malnutrition related to AL-amyloidosis. The cancellous bone volume was greatly decreased and trabecular thinning was apparent, although the trabecula was preserved. Cortical bone volume was also preserved. Our findings indicate that immobilization-related osteoporosis is associated mainly with bone loss in cancellous bone.\n\n\nLimitation\n\nThe significance of this report is limited to the presentation of pathological data showing that the long-term immobilization in the patient with AL amyloidosis leads to severe osteoporosis. However, the patient’s underlying low nutrient condition, which was caused by AL amyloidosis, may have contributed to the bone abnormalities.\n\n\nConsent\n\nThis investigation was conducted in accordance with the Declaration of Helsinki. Before his death, the patient provided written informed consent for publication of this case report.\n\nAfter his death, the patient’s wife provided written informed consent for publication of this case report and any accompanying images.\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 wish to thank Mrs. Akemi Ito (Ito Bone Science Institute, Niigata, Japan) for performing the bone histomorphometric analyses.\n\n\nReferences\n\nJørgensen L, Crabtree NJ, Reeve J, et al.: Ambulatory level and asymmetrical weight bearing after stroke affects bone loss in the upper and lower part of the femoral neck differently: bone adaptation after decreased mechanical loading. Bone. 2000; 27(5): 701–707. PubMed Abstract | Publisher Full Text\n\nDauty M, Perrouin Verbe B, Maugars Y, et al.: Supralesional and sublesional bone mineral density in spinal cord-injured patients. Bone. 2000; 27(2): 305–309. PubMed Abstract | Publisher Full Text\n\nCirnigliaro CM, Myslinski MJ, La Fountaine MF, et al.: Bone loss at the distal femur and proximal tibia in persons with spinal cord injury: imaging approaches, risk of fracture, and potential treatment options. Osteoporos Int. 2017; 28(3): 747–765. PubMed Abstract | Publisher Full Text\n\nLeblanc AD, Schneider VS, Evans HJ, et al.: Bone mineral loss and recovery after 17 weeks of bed rest. J Bone Miner Res. 1990; 5(8): 843–850. PubMed Abstract | Publisher Full Text\n\nRittweger J, Frost HM, Schiessl H, et al.: Muscle atrophy and bone loss after 90 days’ bed rest and the effects of flywheel resistive exercise and pamidronate: results from the LTBR study. Bone. 2005; 36(6): 1019–1029. PubMed Abstract | Publisher Full Text\n\nBikle DD, Sakata T, Halloran BP: The impact of skeletal unloading on bone formation. Gravit Space Biol Bull. 2003; 16(2): 45–54. PubMed Abstract\n\nZerwekh JE, Ruml LA, Gottschalk F, et al.: The effects of twelve weeks of bed rest on bone histology, biochemical markers of bone turnover, and calcium homeostasis in eleven normal subjects. J Bone Miner Res. 1998; 13(10): 1594–1601. PubMed Abstract | Publisher Full Text\n\nRecker RR, Kimmel DB, Parfitt MA, et al.: Static and tetracycline-based bone histomorphometric data from 34 normal postmenopausal females. J Bone Miner Res. 1988; 3(2): 133–144. PubMed Abstract | Publisher Full Text\n\nSakai A, Nakamura T: Changes in trabecular bone turnover and bone marrow cell development in tail-suspended mice. J Musculoskelet Neuronal Interact. 2001; 1(4): 387–392. PubMed Abstract\n\nMorey-Holton ER, Globus RK: Hindlimb unloading of growing rats: a model for predicting skeletal changes during space flight. Bone. 1998; 22(5 Suppl): 83S–88S. PubMed Abstract | Publisher Full Text\n\nMachwate M, Zerath E, Holy X, et al.: Systemic administration of transforming growth factor-beta 2 prevents the impaired bone formation and osteopenia induced by unloading in rats. J Clin Invest. 1995; 96(3): 1245–1253. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDamrongrungruang T, Kuroda S, Kondo H, et al.: A simple murine model for immobilization osteopenia. Clin Orthop Relat Res. 2004; 425: 244–251. PubMed Abstract | Publisher Full Text\n\nPalle S, Vico L, Bourrin S, et al.: Bone tissue response to four-month antiorthostatic bedrest: a bone histomorphometric study. Calcif Tissue Int. 1992; 51(3): 189–194. PubMed Abstract | Publisher Full Text\n\nThomsen JS, Morukov BV, Vico L, et al.: Cancellous bone structure of iliac crest biopsies following 370 days of head-down bed rest. Aviat Space Environ Med. 2005; 76(10): 915–922. PubMed Abstract\n\nThomsen JS, Ebbesen EN, Mosekilde L: Relationships between static histomorphometry and bone strength measurements in human iliac crest bone biopsies. Bone. 1998; 22(2): 153–163. PubMed Abstract | Publisher Full Text\n\nTeti A, Zallone A: Do osteocytes contribute to bone mineral homeostasis? Osteocytic osteolysis revisited. Bone. 2009; 44(1): 11–16. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "87757",
"date": "14 Jul 2021",
"name": "Naoki Kondo",
"expertise": [],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn this paper, the authors claim a post-mortem 38-year-old patient showed remarkable decreased parameter-related bone formation in both cancellous and cortical bones. Bone histomorphometric data itself is very relevant and well reported.\nMajor points\nI would like to know the significance of the increase of empty lacunae in the cortex for the case. For example, if osteocytes do not function as well, osteocytes cannot cause cortical bone damage and result in decreased cortical bone thickness.\n\nI think that bone metabolic marker data are deficient. Please add it if possible.\n\nHow can amyloidosis affect “immobilization osteoporosis”? In bone tissue, was amyloid protein detected? (Or was it possible technically?) If amyloid deposited in bone tissue and influenced bone turnover directly, this case report would be a more relevant one.\n\nI would like to know this case's bone mineral density if the authors measured it.\nMinor points\nI think that the age 39 is not correct in the last paragraph of the Discussion, please correct it.\n\nI also think \"postmortem Iliac bone of a 46-year-old healthy man\" at the 5th line from the end of the Case Presentation is very solitary and not natural. Please delete this sentence.\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": []
},
{
"id": "135350",
"date": "03 May 2022",
"name": "Matthew T. Drake",
"expertise": [
"Reviewer Expertise Human bone 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\nIn this manuscript, Hatano and colleagues report static bone histomorphometric analysis data from a 38-year-old Japanese male who died following nine months of bedrest in the context of light chain amyloidosis with associated severe orthostatic hypotension, proteinuria, and malnutrition. Overall, the clinical presentation is clear and the histomorphometry is very elegant.\nSpecific comments:\nDid the patient receive parenteral nutrition, or was chronic malnutrition continued over the entire nine months? If so, was there additional weight loss that occurred?\n\nMeasurement of markers of bone turnover (serum P1NP and CTX) would have been a nice addition to the data presented. Likewise, measurement of a 25(OH)D level would have been of value.\n\nTwo significant limitations to the data include:\na) the absence of dynamic data as would be allowed by tetracycline/doxycycline labeling to measure osteoblast and osteoclast function;\nb) comparison to a non-Japanese normative database that was composed only of postmenopausal female subjects, the youngest of whom was 45 years of age at time of inclusion.\nBoth should be listed in the discussion as significant limitations of the data as presented.\nMinor comments:\nChange Reccker to Recker (page 3).\n\nChange 39-year-old to 38-year-old (page 6).\n\nIs the background of the case’s history and progression described in sufficient detail? Yes\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Partly\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Yes\n\nIs the case presented with sufficient detail to be useful for other practitioners? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-479
|
https://f1000research.com/articles/9-823/v1
|
30 Jul 20
|
{
"type": "Research Article",
"title": "Who is making clinical trials for treatment or prevention of COVID-19? A review of Clinicaltrials.gov, May 2020",
"authors": [
"Martha Fors",
"Paloma González",
"Paloma González"
],
"abstract": "Background: Coronavirus disease 2019 (COVID-19) has rapidly progressed into the worst pandemic in recent years. There are currently no approved therapies to treat the disease. Several clinical trials are being conducted to evaluate therapeutic approaches. Methods: We conducted a cross-sectional descriptive study to examine the main characteristics of COVID-19-related clinical interventional trials registered with ClinicalTrials.gov until May 15th, 2020. Results: We included 519 trials, most of which were phase II or III, open-label and randomized trials. Disease treatment was evaluated in 75.5% of trials, while prevention was evaluated in 12.1%. A total of 243 trials were listed as recruiting, and 42.4% were not yet recruiting. Approximately 20% of the analyzed trials are investigating antimalarial agents, while 10.2% are studying the use of convalescent plasma to treat the disease. Antiretrovirals, monoclonal antibodies, the use of stem cells, nitric oxide gases and vaccines are the most commonly evaluated therapies. As of the publication of this review, none of the clinical trials had uploaded results. Conclusions: ClinicalTrials.gov is an important database that contains ongoing research trials on COVID-19, a disease that is of vital importance. This study quantifies the outcomes of COVID-19-related clinical trials. The safety and effectiveness of many therapeutic approaches are investigated to fight this disease.",
"keywords": [
"COVID-19",
"clinical trials",
"coronavirus",
"SARS-CoV2"
],
"content": "Introduction\n\nThe world is currently experiencing a general crisis regarding the healthcare system. SARS-CoV-2 has become a pandemic, and it has affected over 150 countries in a matter of weeks. The inability of many public health systems to address the spread of this disease has become notorious in many countries where the number of individuals with the disease and the number of deaths increase every day.\n\nCoronavirus disease 2019 (COVID-19) is caused by the SARS-CoV-2 betacoronavirus. COVID-19 shares 79% sequence identity with SARS-CoV, the virus that caused a major outbreak in 2002–20031.\n\nThe clinical characteristics of COVID-19 include pyrexia, radiological signs of acute respiratory distress, reduced or normal white blood cells, lymphopenia, and a failure to resolve complications (e.g., secondary bacterial infections such as bacterial pneumonia) after 3 to 5 days of antibiotic treatment2.\n\nThe presence of contradictory information on possible treatments for this disease, some of which lacks a scientific foundation, has generated irresponsible actions regarding approached to treat COVID-193.\n\nRandomized controlled trials (RCTs) are the gold standard design for evaluating the efficacy and safety of clinical interventions and are valued for their statistical rigor and low levels of bias4.\n\nRegulatory agencies are also contributing to the response to the coronavirus outbreak by providing general recommendations on how to use certain medicines that are still under investigation and guidance on measures that should be taken to stop the spread of the disease5.\n\nClinicalTrials.gov is a clinical trials registry that provides patients, family, health care professionals, investigators, and the general public with information about clinical studies on a wide range of diseases and conditions. This site is supported by the National Library of Medicine (NLM) at the National Institutes of Health (NIH) of the United States of America6.\n\nThis database provides a public list of initiated, ongoing, and completed clinical trials, and it is considered a source of summary result information to complement the medical literature. It is the world’s largest clinical trial registry, and it is publicly available and accessible to all citizens7.\n\nHow should COVID-19 be treated and what treatment options should be made available? Well-designed clinical trials are the answer to this question since they are the only type of study that is capable of assessing the efficacy and safety of new therapeutic approaches for any disease8,9.\n\nIn 2005, the International Committee of Medical Journal Editors (ICMJE) required that intervention trials be registered prior to the enrollment of the first subject as a prerequisite for publication in scientific journals. The registration of all clinical trials in any of the available public databases guarantees the transparency of research.\n\nThe numbers of cases and deaths caused by this pandemic are increasing continuously, demonstrating the need to identify therapeutic options for the disease. Drug repurposing may prove to be the best strategy for the quick development of novel therapeutic options10.\n\nThere are several drugs that are being evaluated, and some of the trials have yet to be initiated. Infected persons need to be treated with these drugs, but it is also necessary to determine the efficacy and safety profile of the therapies that are being used. There is a need to increase knowledge about the disease and enhance research efforts to find a cure for COVID-19, which will provide a scientific basis to make important decisions in health systems worldwide.\n\nIn this cross-sectional study, we aimed to examine the main characteristics of COVID-19-related clinical trials that were registered in ClinicalTrials.gov prior to March 27th, 2020.\n\n\nMethods\n\nThis is a cross-sectional analysis of all interventional studies that were registered on ClinicalTrials.gov. The database was downloaded on May 15th, 2020.\n\nA combination of search terms was used to retrieve interventional trials that examined COVID-19 (“coronavirus,” “SARS- CoV-2”, COVID-19). All trials were reviewed by two independent reviewers. Data on the design, masking, randomization, primary purpose, interventions, sample size grouping, type of therapeutic approaches and location of the included studies were extracted by the two reviewers manually, since the information extracted directly from the database was not suitable for statistical analysis and because it was necessary to create new variables with the extracted information. Information about recruitment status, phases of the trials, and funding sources were used the same way the database was established. Using this search strategy, 519 trials were identified. The search was restricted to interventional trials. Two reviewers (MF and PG) extracted data and checked each other’s work for accuracy. Disagreements between the two reviewers were settled by consensus.\n\n1. Trials investigating an intervention(s) on humans related to COVID-19\n\n2. Study in any phase\n\n3. Registered or published prior to the publication of this review\n\n1. None\n\nMost of the information regarding the design of the studies was in the same column in the original downloaded database; for the purposes of our analysis, elements of the design were separated into different variables within the database, and no additional form was used. We extracted the information in the same way as it is reflected in ClinicalTrials.gov: (see ClinicalTrials.gov data elements definitions):\n\nClinical trials were classified according phase (I, I/II, III, II/III, III, or IV), type of intervention models (single group assignment, parallel assignment, and sequential assignment), type of allocation (randomized allocation, nonrandomized and not applicable in case there was only one group of treatment), and type of masking (open label, single-blind masking, double-blind masking, triple-blind masking and quadruple-blind masking).\n\nOther characteristics of interest included primary purpose (basic science, treatment, supportive care, screening, diagnosis, prevention, health research services and others) and intervention type (drug, biological, behavioral, medical devices, diagnostic or other).\n\nRecruitment status was also recorded (not yet recruiting: the study has not started recruiting participants; recruiting: the study is currently recruiting participants; not recruiting: the study is ongoing, and participants are receiving an intervention or being examined, but potential participants are not currently being recruited or enrolled; terminated: the study has stopped early and will not start again; completed: the study has ended normally, and participants are no longer being examined or treated; withdrawn: the study stopped early, before enrolling its first participant; or unknown: a study on ClinicalTrials.gov whose last known status was recruiting, not yet recruiting, or active, not recruiting but that has passed its completion date and the status has not been verified within the past 2 years),\n\nWe included trials with participants of all ages and genders. We classified trials according to the estimated number of participants and categorized them as follows: up to 100, 101–500, 501–1000, + 1000 participants. We used the traditional development phases approach for the size of trials.\n\nWe also recorded the funding source for the trial. This describes the organization that provides funding or support for a clinical study. This support may include activities related to funding, design, implementation, data analysis, or reporting. Organizations listed as sponsors and collaborators for a study are considered the funders of the study.\n\nData were extracted directly from the ClinicalTrials.gov database, which contains information for all registry records, and we downloaded a file in comma-separated values (.csv) format (see underlying data11). We performed a descriptive analysis of COVID-19-related clinical trials registered in the database until May 15th, 2020.\n\nDescriptive statistics were used to summarize the trial characteristics: categorical variables are reported as frequencies and percentages, while continuous variables are reported as the mean and standard deviation. All the data were analyzed using SPSS 24.0.\n\n\nResults\n\nAmong the approximately 339,723 studies registered in the database, 829 were COVID-19-related trials, 519 of which were interventional studies (62.6%), making them eligible for inclusion in our study (Figure 1).\n\nPhase II and Phase III studies were the most common (30.1% and 18.1%, respectively). Parallel assignment design was the most common study design (77.8%). Most clinical trials were open-label (59.7%) and randomized (75.5%). Disease treatment trials accounted for 75.5% of the eligible trials. Approximately 60% of the studies were evaluating drugs (Table 111).\n\nThe funding characteristics for all interventional trials are displayed in Table 211. The most common source of funding was the pharmaceutical industry (12.3%).\n\nAs of May 2020, 243 of 519 trials were recruiting subjects, while 42.4% had their status as ‘‘not yet recruiting’’. Only ten of the trials were completed, and 25 were enrolling by invitation. A total of 0.6% were suspended trials, and 1.0% were withdrawn trials. Most of the studies (87.1%) included subjects who were 18 years and older (Table 211).\n\nThe median number of trials registered over time was 58 trials per month from January to April 2020. Figure 2 shows the increasing rate of trials posted on this website. During the first days of May, the number of trials registered was 128. Most of the trials found in this review are scheduled to end in 2020.\n\nTo assess the enrollment of participants in clinical trials, the authors recategorized this variable into four groups. It was observed that 42.6% of trials had up to 100 participants, and 39.5% had 101–500 participants (Figure 3). The median enrollment was 144 participants.\n\nAmong the included studies, 22.8% were investigating antimalarial agents, while 10.8% were investigating the use of convalescent plasma. Other therapeutics under evaluation included new vaccines (2.6%) as well as monoclonal antibodies, interferons and antiretrovirals (Table 311).\n\nAmong the included studies, 98.8% comprised both sexes, while 1.2% recruited only female participants.\n\nNone of the included trials have posted any results.\n\n\nDiscussion\n\nThis study provides a review of COVID-19-related clinical trials registered with ClinicalTrials.gov during the first five months of 2020. We examine the characteristics of the trials, including their design, location, funding characteristics, recruitment status, age of participants, gender of participants and study sample size. Another review has examined COVID-19-related trials registered in the WHO International Clinical Trials Registry Platform, and the first results have already been published12.\n\nPhase II and Phase III were the most common study phases. Almost all the included trials included participants of both sexes, and most of them included adults and older adults. Most of the infected subjects were aged between 18 and 99 years old.\n\nMore than 75% of the studies we analyzed were randomized trials, which are considered the gold standard for evaluating the efficacy and safety profile of any new treatment or for a new medical indication. The number of registered trials was high, most likely due to the efforts of many countries to combat this novel disease for which there is currently no treatment. The response to the COVID-19 pandemic from the community, particularly from researchers, has been excellent, but it is necessary to ensure the rights, safety and wellbeing of subjects. Well-designed clinical trials are important for guaranteeing these rights.\n\nA large proportion of studies (42.6%) enrolled 100 or fewer patients, but these studies are in the early phases of development, and thus, we are not concerned that these studies are underpowered or have a high risk of type II errors (signification level), which would lead to inappropriate conclusions regarding the effectiveness of a therapeutic approach.\n\nOverall, most trials focused on the treatment of the disease. This indicates that the possible therapeutic benefits of these interventions include reducing the number of fatal events due to the disease.\n\nAs indicated by the Centers for Disease Control and Prevention (CDC), the Food and Drug Administration (FDA) has not approved any drugs for treating COVID-19 that have demonstrated an adequate safety profile and adequate efficacy in randomized clinical trials with control groups13. According to the FDA, therapies that are under investigation to treat COVID-19 should only be examined in randomized controlled trials13.\n\nAmong the included studies, approximately 22% are evaluating antimalarial drugs such as chloroquine and hydroxychloroquine. Available evidence regarding the use of chloroquine in COVID-19 patients is limited, so there is still very low confidence in its efficacy for treating COVID-19. The use of chloroquine in the treatment of SARS-CoV-2 should be analyzed in light of both its promise and the potential adverse effects that have been observed in past endeavors to treat intense viral illnesses with chloroquine14.\n\nA systematic review of the use of chloroquine concluded that there is sufficient evidence of its effectiveness and safety for other indications, which justifies the clinical research on the use of chloroquine to treat patients with COVID-1915.\n\nCurrently, the use of the Monitored Emergency Use of Unregistered Interventions (MEURI) framework or the ethical approval of clinical trials are of vital importance, as stated by the World Health Organization15,16.\n\nWe found that the second most commonly used treatment was convalescent plasma, which is examined in 10.3% of the included studies. Using plasma for convalescent patients has been successfully used for the treatment of several viral diseases during different outbreaks, such as the 2003 SARS-CoV-1 epidemic, the 2009–2010 H1N1 influenza virus pandemic, and the 2012 MERS-CoV epidemic17. Patients accepting this treatment showed benefits approximately 1 week later, suggesting that high titer levels can be used to effectively neutralize the virus, avoid inflammatory responses and improve symptomatology without severe adverse events18. Information from China has shown that this therapy brings clinical and radiological improvement, decreases viral loads and increases survival times19.\n\nSeveral studies have evaluated multiple drugs with in vitro antiviral activity against SARS-CoV-2 and/or immunomodulatory effects that may have clinical benefit. We found that the use of lopinavir combined with ritonavir in the majority of cases was very frequent. The combination of these two drugs and other antiviral agents in the early stages of COVID-19 infection might hold promise for treating COVID-1915.\n\nFavipiravir was evaluated in 1.3% of the registered trials. This drug is considered a broad-spectrum antiviral that shows promise in the treatment of influenza virus infections, particularly due to the apparent lack resistant mutations against the drug in cell culture or animal studies20.\n\nRemdesivir has also demonstrated its efficacy in inhibiting coronaviruses such as SARS-CoV and MERS-CoV in vitro21. The use of remdesivir has been shown to limit the mortality rate of seriously ill patients needing invasive ventilation and patients who did not need invasive ventilation by 18% and 5%, respectively15.\n\nThe World Health Organization (WHO), the Surviving Sepsis Campaign Guide and the CDC have stated that there is no current evidence to recommend a specific antiviral treatment for patients with confirmed COVID-19, and such evidence can only derive from a controlled clinical trial16,22.\n\nIn a study of available scientific information, a group of scientists from Universidad Nacional de La Plata, Argentina, concluded that no studies have provided high-quality evidence for the use of hydroxychloroquine, chloroquine, or lopinavir/ritonavir to treat patients with COVID-1923.\n\nRegarding the use of nitric oxide, The Society of Critical Care Medicine recommends against the routine use of iNO in patients with COVID-19-induced pneumonia. Instead, they suggest the use of this treatment only in mechanically ventilated patients with severe ARDS and hypoxemia despite other rescue strategies22.\n\nThere are also a few studies that are evaluating vaccines (2.6%); additionally, there are many pharmaceutical companies developing new vaccines, but many of these evaluations are still in the preclinical stages24\n\nOur study shows that half of the trials are conducted in China, indicating that Chinese investigators or researchers are trying to find a cure as fast as possible. The number of trials in the United States is increasing, with the country conducting the second highest number of COVID-19-related clinical trials.\n\nThere are challenges in conducting clinical research on COVID-19, and these challenges are impacting the health systems around the world. There is good clinical guidance25 on how sponsors should adjust the management of clinical trials and participants during the COVID-19 pandemic. These guidelines must be followed to ensure that clinical trials are performed according national and international standards during this pandemic.\n\n\nConclusions\n\nThe efficacy and safety profile of many different therapeutic measures for patients infected by COVID-19 are being investigated. More than 500 studies have been registered within ClinicalTrials.gov. Most of these studies are interventional clinical trials evaluating drugs or biological agents.\n\nThese trials have already started and are evaluating different therapeutic approaches for COVID-19 treatment. It is necessary to discover new classes of medicines.\n\nThis is a descriptive assessment of the current information regarding COVID-19 clinical trials registered in the ClinicalTrials.gov registry until March 2020. This database is updated frequently, is very user-friendly and provides transparency regarding the type, design, distribution, and funding of clinical trials.\n\nThis study has some limitations. ClinicalTrials.gov does not include all the COVID-19 clinical trials registered and performed around the world. This study focuses on only one database; ClinicalTrials.gov is certainly one of the most important sources of information, but many others also provide valuable information.\n\n\nData availability\n\nOpen Science Framework: Clinical trials characteristics for treatment of COVID-19. https://doi.org/10.17605/OSF.IO/27QCP11\n\nThis project contains the following underlying data:\n\n- SearchResultsCOVID.csv (Extracted data from ClinicalTrials.gov)\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\nWe would like to thank the Universidad de Las Américas for its support for this work.\n\n\nReferences\n\nZhou P, Yang XL, Wang XG, et al.: Discovery of a novel coronavirus associated with the recent pneumonia outbreak in humans and its potential bat origin. bioRxiv. 2020. Publisher Full Text\n\nLake MA: What we know so far: COVID-19 current clinical knowledge and research. Clin Med (Lond). 2020; 20(2): 124–127. PubMed Abstract | Publisher Full Text | Free Full Text\n\nOsuchowski MF, Aletti F, Cavaillon JM, et al.: SARS-CoV-2/COVID-19: Evolving Reality, Global Response, Knowledge Gaps and Opportunities. Shock. 2020. PubMed Abstract | Publisher Full Text\n\nSaturni S, Bellini F, Braido F, et al.: Randomized Controlled Trials and real life studies. Approaches and methodologies: a clinical point of view. Pulm Pharmacol Ther. 2014; 27(2): 129–138. PubMed Abstract | Publisher Full Text\n\nKatz E: How Federal Agencies Are Responding to the New Coronavirus Outbreak. Retrieved. 2020. (2020, February 25). Reference Source\n\nClinicalTrials.gov. 2020. Reference Source\n\nZarin DA, Tse T: Medicine. Moving toward transparency of clinical trials. Science. 2008; 3(19): 1340–1342. PubMed Abstract | Publisher Full Text | Free Full Text\n\nhttps://www.ema.europa.eu/en/human-regulatory/overview/public-health-threats/coronavirus-disease-covid-19\n\nhttps://www.fda.gov/news-events/press-announcements/coronavirus-covid-19-update-daily-roundup-april-1-2020\n\nSenanayake SL: Drug repurposing strategies for COVID-19. Future Drug Discov. 2020; fdd-2020–0010. Publisher Full Text | Free Full Text\n\nFors M: Clinical trials characteristics for treatment of COVID-19. 2020. Reference Source\n\nMaguire BJ, Guérin PJ: A living systematic review protocol for COVID-19 clinical trial registrations [version 1; peer review: 2 approved]. Wellcome Open Res. 2020; 5: 60. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCDC: Interim Clinical Guidance for Management of Patients with Confirmed Coronavirus Disease (COVID-19).Reference Source\n\nTouret F, de Lamballerie X: Of chloroquine and COVID-19. Antiviral Res. 2020; 177: 104762. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCortegiani A, Ingoglia G, Ippolito M, et al.: A systematic review on the efficacy and safety of chloroquine for the treatment of COVID-19. J Crit Care. 2020; 57: 279–283. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWHO: Clinical management of severe acute respiratory infection (SARI) when COVID-19 disease is suspected: Interim guidance V 1.2. 2020. Reference Source\n\nZhang J, Xie B, Hashimoto K: Current status of potential therapeutic candidates for the COVID-19 crisis. Brain Behav Immun. 2020; 87: 59–73. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRoback JD, Guarner J: Convalescent plasma to treat COVID-19: possibilities and challenges. JAMA. 2020. PubMed Abstract | Publisher Full Text\n\nKai D, Liu B, Li C, et al.: Effectiveness of Convalescent Plasma Therapy in Severe COVID-19 Patients. Proc Natl Acad Sci U S A. 2020; 117(17): 9490–96. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGoldhill DH, Velthuis AJWT, Fletcher RA, et al.: The mechanism of resistance to favipiravir in influenza. Proc Natl Acad Sci U S A. 2018; 115(45): 11613–11618. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSheahan TP, Sims AC, Graham RL, et al.: Broad-spectrum antiviral GS-5734 inhibits both epidemic and zoonotic coronaviruses. Sci Transl Med. 2017; 9(396): eaal3653. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWalhazzani W, Møller Mh, Arabi YM, et al.: Surviving Sepsis Campaign: Guidelines on the Management of Critically Ill Adults with Coronavirus Disease 2019 (COVID-19). Intensive Care Med. 2020; 46(5): 854–887. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChloroquine, hydroxychloroquine, lopinavir / ritonavir, for the treatment of COVID-19 infection. CUFAR Rapid Review Report, March 29. Reference Source\n\nMarket watch. 2020. Reference Source\n\nEMA: Guidance on the management of clinical trials during the COVID-19 (coronavirus)pandemic. Reference Source"
}
|
[
{
"id": "68398",
"date": "05 Aug 2020",
"name": "Ana Marusic",
"expertise": [
"Reviewer Expertise Trial registration and transparency",
"research integrity"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 study describing clinical trials addressing COVID-19. It provides important data on activities undertaken to address the pandemic and it would be interesting to see the update of the study if that is possible in the next version. The study concluded with May 15, and I am sure that the situation with the registration and results changed. For example, there are now 2 studies with results and a total of 2890 registered studies on August 5, 2020 (using Covid19 as a search term). The authors describe the problem well in the Introduction and address well the methodological approach, which is sound and appropriate. Agreement between two assessors should be presented (e.g. kappa). Results are clearly presented and discussed. The discussion section mentions that half of the registered trials were from China, but the data on the geographical locations of the study was not presented. This needs to be corrected. Also, this issue needs to be addressed better in the Limitation section, as it is a pity that the authors did not search WHO's ICTRP portal, which includes CT.gov and many oSuch a search would give a better view of the global effort to combat CVOD-19 pandemic.\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": "5808",
"date": "19 Aug 2020",
"name": "Martha Fors",
"role": "Author Response",
"response": "Thank you very much for this report. We will try to keep this information updated and also look for other clinical trials registry as suggested by the reviewer. Martha Fors"
}
]
},
{
"id": "68401",
"date": "19 Aug 2020",
"name": "Andrea Cortegiani",
"expertise": [
"Reviewer Expertise 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\nThe authors submitted an interesting research article, reporting an analysis of the ongoing clinical trials on interventions for COVID-19. I have some concerns and some suggestions for the authors. Below, my specific comments by section.\n\nTitle:\nThe title is not clear in its current form. I suggest avoiding the use of questions and clearly expressing the design of the study. I see no need to add the date of the last update in the title and probably the phrase needs language editing.\n\nAbstract:\nI suggest avoiding the use of “most of”. The authors should report specific data.\n\nConclusions should focus on the key messages of the paper.\n\nMethods:\nWhen saying “All trials were reviewed by two independent reviewers”, please enter the initials of the reviewers in brackets.\n\nThe phrase “Using this search strategy, 519 trials were identified.” should be moved down to the results section.\n\nThe phrase “since the information extracted directly from the database was not suitable for statistical analysis and because it was necessary to create new variables with the extracted information” is not very clear. If not useful for the reproducibility of the methods, the authors may also consider to remove it.\n\nThe authors say that “Descriptive statistics were used to summarize the trial characteristics: categorical variables are reported as frequencies and percentages, while continuous variables are reported as the mean and standard deviation. All the data were analyzed using SPSS 24.0”. Was the normality of data distribution evaluated before selecting mean and SD as appropriate?\n\nThe timing of the study is unclear. The introduction says “we aimed to examine the main characteristics of COVID-19-related clinical trials that were registered in ClinicalTrials.gov prior to March 27th, 2020”. In the methods section, it is then said that “The database was downloaded on May 15th, 2020” and finally the results say “During the first days of May, the number of trials registered was 128”. Please clarify any timing restriction used as exclusion criteria and the exact date of data collection.\n\nResults:\nThe authors say “the approximately 339,723 studies”. Is the total number of registered studies available? If so, the exact number should be used, without approximations.\n\nAccording to Figure 1, the number 339,723 seems to be the result of the authors’ search query. This is in contrast with what stated in the main text. Please clarify.\n\nLooking at table 2, it is not clear what difference exists between “Industry”, “Industry/Other”, “Other/Industry”.\n\nPlease provide IQR when reporting medians (e.g. “The median enrollment was 144 participants”).\n\nDiscussion:\nThe authors say that “Another review has examined COVID-19-related trials registered in the WHO International Clinical Trials Registry Platform, and the first results have already been published” but the reference regards the protocol. I suggest to refer to the results, if available as said, and to discuss the similarity and the differences with the present study.\n\nThe authors say “A large proportion of studies (42.6%) enrolled 100 or fewer patients, but these studies are in the early phases of development, and thus, we are not concerned that these studies are underpowered or have a high risk of type II errors (signification level), which would lead to inappropriate conclusions regarding the effectiveness of a therapeutic approach”. This aspect has been largely debated and probably some references may be added to provide a more balanced discussion (e.g. https://doi.org/10.7326/M20-2959; https://doi.org/10.1001/jama.2020.8115).1,2\n\nIn the results section the authors say that “Among the included studies, 98.8% comprised both sexes, while 1.2% recruited only female participants”. Is this 1.2% related to specific populations (e.g. pregnant patients)? This may be eventually discussed and compared to recently published findings on this population (e.g. https://doi.org/10.1016/j.bja.2020.05.020; https://doi.org/10.1002/eahr.500060; https://doi.org/10.1016/S1473-3099(20)30638-1)3,4,5, that seems to be understudied.\n\nConclusions:\nConclusions should convey a key message for the readers.\n\nStrengths and limitations may be probably moved to the discussion section.\n\nGeneral and Minor Comments:\nLanguage editing is strongly suggested to improve the quality of the manuscript.\n\nThe osf registration (dated 24th June) says that “All studies from January to May 2020 were included”. As previously suggested, please verify that the correct timing is reported. The registration seems to be subsequent to data collection. If so, the authors should not refer to it as underlying data.\n\nThe reference to the .csv file should be added. The registered project contain a .csv file (https://osf.io/28jh7/). If it corresponds to the underlying data of this paper, please add it as a reference.\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": []
}
] | 1
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https://f1000research.com/articles/9-823
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https://f1000research.com/articles/9-171/v1
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09 Mar 20
|
{
"type": "Review",
"title": "The role of salivary contents and modern technologies in the remineralization of dental enamel: a review",
"authors": [
"Imran Farooq",
"Amr Bugshan",
"Amr Bugshan"
],
"abstract": "Human enamel once formed cannot be biologically repaired or replaced. Saliva has a significant role in remineralization of dental enamel. It not only has a buffering capacity to neutralize the oral cavity’s low pH generated after acidic encounters, but also acts as a carrier of essential ions, such as fluoride, calcium and phosphate, which have a positive role in enamel’s remineralization. This review discusses how salivary contents, like proteins and enzymes, have a natural role in enamel’s mineralization. In addition, the presence of ions, such as fluoride, calcium and phosphate, in saliva further enhances its capability to remineralize the demineralized enamel surface. The review further examines modern innovative technologies, based on biomimetic regeneration systems, including dentin phosphoproteins, aspartate-serine-serine, recombinant porcine amelogenin, leucine-rich amelogenin peptide and nano-hydroxyapatite, that promote enamel remineralization. Fluoride boosters like calcium phosphates, polyphosphates, and certain natural products can also play an important role in enamel remineralization.",
"keywords": [
"Saliva",
"Enamel",
"Remineralization",
"Fluoride",
"Calcium Phosphate"
],
"content": "Introduction\n\nDental enamel is a calcified tissue that forms the outer protective covering of the anatomical crown of a tooth1. Enamel once formed cannot be biologically repaired or replaced2. The oral cavity continuously goes through cycles of demineralization and remineralization3. Loosing minerals from the tooth after an acidic encounter is called demineralization, whereas restoration of these minerals back into the tooth structure is called remineralization4. During demineralization, the enamel surface becomes rough and rugged upon acidic encounter. Thus throughout the life of a tooth, there are enamel demineralization/remineralization cycles that dictate the extent of mineral balance and tissue integrity or degradation3. Human saliva has a buffering role and acts as a carrier of essential ions that can bring a constructive change in the structure of enamel, promoting remineralization5.\n\nThis review is aimed at providing an overview of enamel structure and an in-depth insight on its mineralization mechanism carried out by salivary contents. Literature published in the past 35 years (1985–2020) was explored on “Google Scholar” and “PubMed” search engine using the key words “saliva”, “enamel remineralization”, “salivary contents”, “fluoride and enamel”, and “calcium phosphate and enamel”. The search retrieved 1000+ hits and 500 relevant articles were then studied in detail. Conference abstracts, poster presentations, and all articles published in a language other than English were excluded from this review. A final selection of 65 pertinent articles was made and these were then included in this study for review.\n\n\nStructure of dental enamel\n\nDental enamel is composed of 96% inorganic material, 3% water, and 1% organic matrix6. The inorganic component of dental enamel is hydroxyapatite (HAP) crystal and human enamel is a hard, acellular, and avascular tissue1. Being acellular, it cannot be automatically replaced or repaired if damaged2. However, its very highly mineralized nature makes it extremely resistant to destruction7. Enamel’s high mineral content also makes it susceptible to demineralization by acids formed by bacteria in the mouth, which leads to dental caries3.\n\nTooth enamel is an intricate structure and requires a keen sense of three-dimensional geometry to appreciate it. Early micro-anatomical descriptions are incomplete and reflected the restrictions of light microscopy. Only after the advent of modern techniques using transmission and scanning electron microscopy, was the more complex structure of enamel revealed. Enamel’s composition includes fiber-like mineralized crystals and a small proportion of water and proteins that clamp the mineralized fibers with each other8. This arrangement of mineralized and non-mineralized components of enamel, disperses the forces passing through teeth and in this manner shields them from fractures4. Enamel is composed of discrete basic units called Enamel Rods (formerly enamel prisms), each surrounded by a rod sheath with these packed together and embedded in an inter-rod (inter-prismatic) substance9. Ameloblasts elaborate and secrete the enamel protein matrix that is subsequently mineralized by the addition of calcium phosphate crystallites10. When fully differentiated, ameloblasts are tall columnar cells fully equipped for protein synthesis11. The secretory end of the cell develops a projection (Tome’s process) through which the protein matrix and crystallites are laid down12. The appearance of the inter-rod (inter-prismatic) substance and rod sheath at a light microscope level is due to the changes in crystallite orientation as they are laid down by ameloblasts13. The main body of the enamel rod is ~5µm in diameter but towards the enamel surface, the diameter is greater14. The number of ameloblasts that form the enamel are thought to remain constant for each tooth15. At the beginning and end of amelogenesis, Tome’s process is absent at the secretory end of ameloblasts and unstructured enamel (rod-less/prism-less) is produced16. This prism-less enamel varies in thickness but there is a general agreement that prism-less enamel is composed of HAP crystals that are arranged parallel to one another and perpendicular to the enamel’s surface17.\n\nIt is quite a well-established fact that fluoride helps in the prevention of dental caries18. Fluoride has remained under extensive investigations because of its effects on the structure and properties of tooth minerals19. Ionic substitution is a common phenomenon in the oral cavity and two major stake holders are enamel and saliva20. The carbonate ion can replace hydroxyl or phosphate ions, magnesium can replace calcium, and fluoride can replace hydroxyl ions in the crystal lattice3. These ionic substitutions have a significant influence on the behavior of apatite including its solubility21. It is well-known that fluoride in the saliva (when it comes in contact with enamel) replaces the hydroxyl ion in the apatite crystal structure thus changing HAP into fluorapatite, which is more resistant to acidic attacks22. Therefore, understanding human body glands, particularly salivary glands, prior to going into details on the influence of salivary contents on remineralization of enamel becomes necessary.\n\n\nClassification of glands and types of salivary glands\n\nA gland is an organ that synthesizes a secretion for release and two major types of glands found in the human body are exocrine and endocrine glands23. Exocrine glands are those which lack a duct system and secrete their products through basal lamina into the bloodstream to regulate the body (for example, salivary and sweat glands)24. Endocrine glands possess a duct system and discharge their products into the ducts, which then lead them into the outer environment (for example, pituitary, thyroid and adrenal glands)24. A salivary gland is an organ that releases a secretion in the oral cavity, and it is further classified into major and minor types25. Major salivary glands are situated at a distance from the oral mucosa but are connected to it through extra glandular ducts26. Minor salivary glands reside in the mucosa or sub mucosa and can open directly inside the oral cavity27. The three major paired salivary glands in humans are parotid, submandibular, and sublingual glands28. Among the minor salivary glands, the important ones are von Ebner, Weber, buccal, labial, and palatal glands29.\n\n\nRole of saliva and its contents in remineralization of dental enamel\n\nHuman saliva is comprised of numerous contents and therefore has various functions. Saliva is a fluid that protects the mouth against harmful microorganisms and irritants30. It not only lubricates the oral tissues but also helps in various other functions, such as speech, mastication and swallowing, as well as protection of the teeth and oral tissues31. The ability of saliva to remineralize tooth enamel is dependent on various factors, discussed below.\n\nThe buffering capacity of saliva displays an imperative role in maintaining the level of pH in both saliva and plaque, therefore helping in neutralizing the effects of acid exposure5. The three buffer systems present in the saliva are carbonic acid/bicarbonate system (the most important), phosphate system, and protein system32. The breakdown of proteins by bacterial originated urease to urea and ammonia aids plays a role in maintaining a neutral pH in oral cavity33. The intake of certain supplemental hormones, like estrogen and progesterone, could also lead to an improvement in salivary buffering capacity in individuals33.\n\nProteins are part of the normal anatomy of human saliva and some salivary proteins, such as proline rich proteins, statherin and histatins, have an affinity for enamel surfaces and thus help remineralization by increasing local calcium concentration34. Other proteins, e.g. cathelicidin LL3, have an antimicrobial function; histatins are antibacterial, and alpha-defensin HNP1–3 are antiviral in function35. Certain proteins, like lactoferrin, can prevent Streptococcus mutans growth, as they can isolate iron from the oral environment, which is vital for bacterial metabolism33,36.\n\nLysozyme enzyme is found in humans in serum, amniotic fluid, and saliva37. Lysozyme found in saliva helps in the lysis of bacterial cells31 and is especially potent against gram-positive bacteria38. Lysozyme is also believed to have a part in prevention of bacterial aggregation and adherence, thus providing an opportunity for bacterial autolysins, which can then destroy cell walls of bacteria39. Salivary peroxidase enzyme preserves oral health by preventing build-up of hydrogen peroxide and deactivates carcinogenic compounds37.\n\nAt a normal pH, saliva is supersaturated with calcium and phosphate ions, therefore, demineralization does not take place40. Acids of bacterial origin and those coming from food or drinks tend to shift the equilibrium towards the mineral loss3. The phosphate concentration of saliva is reduced and at pH 5.5, saliva no longer remains supersaturated and demineralization initiates5. Saliva acts as a remineralizing agent and as a delivery vehicle of ions, like fluoride, which can then incorporate in the tissues41. It should be noted however, that complete substitution of fluoride with hydroxyl does not occur, but even a limited replacement is able to significantly reduce the incidence of dental caries and initiate remineralization33. The presence of partially demineralized crystallites is a pre-requisite for remineralization as these crystallites then act as nuclei for mineral deposition42. Fluoride in saliva could have three major roles; prevention of demineralization, promotion of remineralization, and interfering with growth of bacteria43. Dental caries starts with a white spot lesion (WSL) and these lesions can be reversed with appropriate fluoride therapy44. However recently, Dai et al. have reported that only fluoride therapy (FT) could be insufficient for reversal of WSLs and a combination of FT with fluoride varnish and FT with casein phosphopeptide-amorphous calcium phosphate (CPP-ACP) application could be more effective in remineralization45.\n\nBoth calcium and phosphate ions are required by fluoride to promote the natural remineralization process of enamel46. The water content present in enamel facilitates influx of acids and efflux of minerals thus causing demineralization20. It has been previously reported that during the demineralization process, calcium is released before phosphate ions; therefore using a calcium-based product could suppress the demineralization process effectively5. Due to the use of increased amounts of fluoride in dentifrices, concerns regarding its toxicity were raised and casein phosphopeptides (calcium and phosphate-based products) have been introduced47. For an equal rate of supersaturation, an ideal rate of enamel remineralization can be attained with a calcium/phosphate (Ca/P) ratio of 1.648. In the plaque, the Ca/P ratio is ~0.3, so supplemental calcium will enhance remineralization of enamel48. Salivary pellicle starts forming on the tooth surface almost immediately post-absorption of proteins and peptides onto the enamel’s surface49. Calcium binding peptides attract free calcium ions in the saliva and thus act as a pool for calcium ions in the pellicle50. In addition, diffusion of calcium ions through the pellicle inside the enamel’s surface takes place easily and this regulates the remineralization process51. Calcium phosphate embedded in salivary pellicle has a high solubility (almost ten times more than calcium phosphate in tooth mineral); therefore, it serves as a sacrificial mineral post-acidic challenge instead of calcium phosphate present in the tooth structure, preventing demineralization52.\n\n\nRecent advances in enamel remineralization therapies\n\nThere have been many recent innovative advances in systems that act through saliva to promote enamel remineralization, but that do not depend on fluoride therapies53. Philip divided these systems into two categories: (i) biomimetic regeneration technologies; and (ii) systems that boost fluoride effectiveness53. In the first category, the most important is tooth regeneration via dentin phosphoprotein (DPP). It has been shown previously that DPP has the ability to remineralize the tooth surface when it is present in a solution containing calcium and phosphate, just like saliva54. Many new systems have been derived based on DPP and among them the most active in promoting remineralization is aspartate-serine-serine (8DSS)55. Application of 8DSS to the enamel surface does not only prevent leaching of ions from the enamel surface, but also promotes binding of calcium and phosphate ions from the saliva53. Amelogenin is an important protein that regulates the growth and maturation of enamel crystals in newly formed enamel matrix15. This protein is absent in mature enamel, meaning it cannot regenerate56 . Modern systems, such as recombinant porcine amelogenin (rP172) and leucine-rich amelogenin peptide, stabilize calcium phosphate to enhance crystal formation and direct mineral growth respectively57,58. Nanohydroxyapatite is another bioactive material that can promote enamel remineralization53. As these particles are very small (nano-sized), they bind strongly to the enamel surface and fill up the gaps and holes in the enamel surface to repair it53,59.\n\nIn the second category, which are also known as fluoride promoters, many modern systems are available53. The most significant are calcium phosphate based systems and among them, the most important is CPP-ACP60. CPP-ACP particles are readily soluble in saliva and thus localize in plaque and act as a reservoir of calcium and phosphate ions61. Upon an acidic encounter, they release these ions to promote remineralization and inhibit demineralization61. Another material to boost enamel remineralization is bioactive glass, which is based on calcium sodium phosphosilicate composition62. It dissolves in aqueous solution to release sodium, calcium, and phosphate ions in the saliva, to which they interact, leading to deposition of a layer of HAP on the enamel’s surface63. Another major system in the second category is polyphosphate-based systems and among them the most essential is sodium trimetaphosphate (STMP)64. STMP not only promotes remineralization, but also inhibits its demineralization64. Some other natural products, such as thymoquinone, have shown good capability in promoting enamel remineralization in vitro65, but data on its in vivo effectiveness is still anticipated65.\n\n\nConclusion\n\nSaliva contains many important substances and also acts as a transporter of many important ions, such as calcium, phosphate and fluoride, which are essential for the promotion of remineralization. Pathogenicity of dental erosion and caries is directly influenced by the buffering capacity and contents of saliva. Saliva helps to maintain a constant reservoir of ions that help to neutralize the pH and prevent demineralization. Modern innovative technologies, for example biomimetic regeneration technologies, including dentin phosphoproteins, aspartate-serine-serine, recombinant porcine amelogenin, leucine-rich amelogenin peptide and nano-hydroxyapatite, promote enamel remineralization. Fluoride boosters, like calcium phosphates, polyphosphates and natural products, also play an important role in enamel remineralization.\n\n\nData availability\n\nNo data are associated with this article.",
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}
|
[
{
"id": "61101",
"date": "13 Mar 2020",
"name": "Rizwan Ullah",
"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\nI have the following comments and suggestions for the authors:\nWhat is the reason for choosing 35 years and two databases Google Scholar and PubMed? As some of the studies that may be some important papers published in journals indexed in other databases will be missing.\n\nPresent complete article search and selection process in a flow chart outlining the exclusion of articles at each stage. In methodology give a brief account how it was decided to include or exclude an article.\n\nKindly rephrase the sentence on Page 2. \" Only after the advent of modern techniques using transmission and scanning electron microscopy, was the more complex structure of enamel revealed\".\n\nKindly rephrase the students on Page 3 \"The breakdown of proteins by bacterial originated urease to urea and ammonia aids plays a role in maintaining a neutral pH in oral cavity\"\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": "5349",
"date": "01 Apr 2020",
"name": "Imran Farooq",
"role": "Author Response",
"response": "Thank you for your comments and accepting our article. We have revised the article as per your suggestions. 1) Many journals now consider references which are 10 years old outdated. We kept a bigger window for our article and this is the reason we did not include any reference which was published more than 35 years ago. To make sure we don't miss any important studies, we chose two databases instead of one. 2) A flow chart has now been added which depicts the search strategy involved in this study.3) This sentence has been rephrased.4) We believe the sentence is clear and unfortunately, rephrasing it would make it unclear."
}
]
},
{
"id": "61100",
"date": "16 Mar 2020",
"name": "A. Thirumal Raj",
"expertise": [
"Reviewer Expertise Oral pathology and microbiology"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIt is a well executed review. There are a few suggestions which could improve the overall impact of the review:\n\nAdding a schematic summarizing the de-mineralization and re-mineralization of dental enamel would improve the overall impact of the article.\n\nWas this a systematic review? If not mention that it is a narrative review based on published literature.\n\nA table summarizing the various recent techniques in re-mineralization along with each of their advantages and limitations would be vital for the article.\n\nThe article seems to end abruptly. Kindly add a couple of sentences on prospects of further research as the concluding sentence.\nThe above-mentioned corrections are just suggestions to improve the overall quality of the article. I recommend the authors consider implementing the recommendations.\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": "5350",
"date": "01 Apr 2020",
"name": "Imran Farooq",
"role": "Author Response",
"response": "Thank you for your comments and accepting our article. We have revised the article as per your suggestions. 1) We have added a micro-CT image which shows remineralization of enamel's surface. 2) We have now added the word \"narrative\" to the title.3) This would be part of our next paper which would be dealing with this point. 4) We have added few sentences to answer your concern."
}
]
},
{
"id": "61099",
"date": "25 Mar 2020",
"name": "Dr. Shakeel Abbas Kazmi",
"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\nIt is a well-written article. The role of salivary contents are comprehensively explained. I would like to suggest the following suggestions:\nThe inclusion criteria of the articles is a bit confusing. How the research started is well-written but later it is a bit confusing how 500 relevant articles were selected. It would be nice to know how these 500 articles were selected.\n\nSome flow charts, for the selection of the articles for research can be helpful.\n\nSimilarly, if there could be a chart, diagram or table before the conclusion, it would help in learning about the article summary.\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": "5351",
"date": "01 Apr 2020",
"name": "Imran Farooq",
"role": "Author Response",
"response": "Thank you for your comments and accepting our article. We have revised the article as per your suggestions. 1) We have added a flow chart depicting search strategy involved in this article. We hope this will answer your concern.2) A flow chart has been added as per your suggestion.3) Instead of a chart, we have added a micro-CT figure which shows remineralization of enamel surface."
}
]
}
] | 1
|
https://f1000research.com/articles/9-171
|
https://f1000research.com/articles/10-475/v1
|
15 Jun 21
|
{
"type": "Case Report",
"title": "Case Report: A rare case of renal-type clear cell carcinoma of the prostate",
"authors": [
"Muhammad Asykar Palinrungi",
"Rina Masadah",
"Khoirul Kholis",
"Syakri Syahrir",
"Syarif Syarif",
"Andhini L. R. Palinrungi",
"Eko Krahmadi",
"Muhammad Faruk",
"Rina Masadah",
"Khoirul Kholis",
"Syakri Syahrir",
"Syarif Syarif",
"Andhini L. R. Palinrungi",
"Eko Krahmadi",
"Muhammad Faruk"
],
"abstract": "Renal-type clear cell carcinoma (RTCCC) of the prostate is a rare form of kidney cancer that is infrequently reported in the literature. Here we describe the case of an 81-year-old male patient with a hard, immovable mass on his enlarged prostate, which was discovered through a digital rectal examination. His prostate-specific antigen (PSA) level was 23.01 ng/ml, and bone multi-slice computed tomography scans revealed several osteoblastic lesions on the inferior ramus of his bilateral pubic bone. Tissue recovered during the trans urethral resection of the prostate was indicative of RTCCC with typical prostatic adenocarcinoma (Gleason score 3 + 4 = 7). Concerning treatment course, bilateral subcapsular orchiectomy was chosen over medical hormonal therapy. Upon follow-up 12 months post-surgery, his lower urinary tract symptoms were nearly resolved and his serum PSA level had decreased to 3.2 ng/ml. Accurate RTCCC diagnosis remains a pressing concern that warrants further investigation to optimize treatment selection and patient outcome.",
"keywords": [
"Renal-type clear cell carcinoma",
"prostate",
"transurethral resection",
"PSA levels",
"prostate adenocarcinoma",
"Gleason score."
],
"content": "Introduction\n\nRenal-type clear cell carcinoma (RTCCC) of the prostate was first described by Singh et al. in 2003,1,2 and, therefore, the literature describing this new, rare form of kidney cancer is very limited.3 Differential diagnosis of clear cell lesions in the prostate is challenging due to the multitude of conditions that could potentially underly the presenting symptoms. This includes clear cell variants of the more common adenocarcinoma of the prostate and urothelial carcinoma, along with rare clear cell carcinoma of Mullerian origin, metastatic renal cell carcinoma, and clear cell carcinoma of the prostate.4 We report a very rare case of a male with RTCCC of the prostate, in line with the updated consensus-based surgical case report (CARE) guidelines.5\n\n\nCase report\n\nAn 81-year-old Buginese man who already underwent a cystostomy due to urine retention two weeks prior, was referred to our institution. The patient is a retired civil servant. His medical history included lower urinary tract symptoms and a trans urethral resection of the prostate (TURP) performed around eight months prior at a separate institution. Histopathological analysis indicated hyperplasia of the prostate and a digital rectal examination revealed that his enlarged prostate was hard in consistency and compressing the rectal wall. His serum markers and other biochemical parameters were all within the normal limits. Most importantly, his serum prostate-specific antigen (PSA) level was 23.01 ng/ml (normal value < 4 ng/ml). A hypoechoic lesion was found upon ultrasound examination, while both kidneys appeared healthy. Bone scans identified several osteoblast lesions on the inferior ramus of his bilateral pubic bone.\n\nThe patient underwent a urethrocystoscopy to evaluate his urethra and bladder followed by TURP. The resected tissue was histopathologically characterized as clear cell carcinoma and typical prostatic adenocarcinoma (Gleason score 3 + 4 = 7; Figure 1A). Immunohistochemistry showed areas immunoreactive to vimentin (VIM) (Figure 1B), epithelium membrane antigen (EMA) (Figure 1C), and membrane metalloendopeptidase, also known as cluster of differentiation 10 (CD-10) (Figure 1D).\n\nA. Clear cell adenocarcinoma of the prostate. Cuboidal/hobnail cells, enlarged nuclei with mild pleomorphism (black arrow) (hematoxylin and eosin stain, 400× magnification). B. Positive immunostaining for vimentin (IHC, 400×). C. Positive immunostaining for EMA (epithelial membrane antigen) (IHC, 400×). D. Positive immunostaining for CD10 (IHC, 400×).\n\nBilateral subcapsular orchiectomy was chosen over medical hormonal therapy as the best suited treatment course for this patient. At the 12-month post-surgery follow-up, he reported that his lower urinary tract symptoms were nearly resolved and his serum PSA level was within the normal range (3.2 ng/ml).\n\n\nDiscussion\n\nRTCCC is associated with specific cytological morphologies, including atypical, enlarged, protruding nuclei, as well as classic structural features, like tubules, solid nests, or sheets in vascular-rich stroma with interstitial inflammatory infiltration.1 The most likely differential diagnosis is metastatic renal cell carcinoma to the prostate, for which, to the best of our knowledge, only two cases have been described in the literature.4\n\nIn the case described here, ultrasound examination found no abnormalities in both kidneys. Therefore, we concluded that the primary possible RTCCC lesion comes from the prostate. The immunohistochemical expression profile indicated that positive expressions of vimentin, EMA, and CD10 and significantly elevated serum levels of PSA indicated prostate malignancy. A mere seven reports have been published describing cases of prostate RTCCC. Collectively, the patients included in these studies were 42 to 73 years old, had PSA levels between 0.18 and 82 ng/mL, and Gleason scores above 6. The immunohistochemical results include positive expression of vimentin, EMA, CD10, low-molecular-weight cytokeratin, pan-cytokeratin, cytokeratin 7, paired box 8 (PAX8), prostatic specific acid phosphatase, periodic acid-Schiff, and alpha-methylacyl-coA racemase. Of the seven patients described in published case-reports of RTCCC of the prostate, five underwent radical prostatectomy and the remaining two received TURP. Local recurrence in the pelvis was apparent 24 months after radical cystoprostatectomy in one patient and two patients died due to multi-organ failure (6 months after TURP and 29 months after radical cystoprostatectomy).3,4,6\n\nThe treatment of RTCCC of the prostate is similar to that used to combat the more common forms of prostate cancer.1–4,6 In the present case, bone scans revealed skeletal metastases at the inferior ramus of his bilateral pubic bone. After explaining the advantages and disadvantages of bilateral subcapsular orchiectomy and medical hormonal therapy, the patient chose the former, since the latter would require frequent trips to the outpatient department, which was problematic given how far he lives from the hospital and his limited access to transportation.\n\n\nConclusion\n\nThis case study of a patient with RTCCC of the prostate supports that this new, rare pathological entity is characterized by histological and immunohistochemical profiles similar to renal clear cell carcinoma. Accurate differential diagnosis, e.g., distinguishing RTCCC from clear cell urothelial carcinoma and metastatic clear cell renal cell carcinoma, remains a pressing concern that warrants further investigation to optimize treatment selection and patient outcome.\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/or clinical images was obtained from the patient.",
"appendix": "References\n\nWang Q, Xue Y: Renal-type clear cell carcinoma of the prostate: A case report. Oncol. Lett. 2015; 9: 2149–2152. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSingh H, Flores-Sandoval N, Abrams J: Renal-Type Clear Cell Carcinoma Occurring in the Prostate. Am. J. Surg. Pathol. 2003; 27. PubMed Abstract | Publisher Full Text Reference Source\n\nSato Y, Kataoka M, Hata J, et al.: Renal-type Clear Cell Carcinoma Occurring in the Prostate With Zinner Syndrome. Urol. Case Reports. 2016; 5: 9–12. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPatne SCU, Johri N, Katiyar R, et al.: Renal-type clear cell carcinoma of the prostate: a diagnostic challenge. Diagn. Pathol. 2015; 10: 193. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRiley DS, Barber MS, Kienle GS, et al.: CARE guidelines for case reports: explanation and elaboration document. J. Clin. Epidemiol. 2017; 89: 218–235. PubMed Abstract | Publisher Full Text\n\nKlaassen Z, Cleveland C, McCraw CO, et al.: Clear cell adenocarcinoma of the prostate: a rare oncologic entity in a 42-year-old African American man. Urology. 2014; 84: 997–1000. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "88829",
"date": "26 Jul 2021",
"name": "Prahara Yuri",
"expertise": [
"Reviewer Expertise Urology",
"pediatric urology",
"endourology",
"basic research",
"laparoscopy."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 nice manuscript. We read this with interest however we struggle to find new knowledge being presented here. This case was a rare case about Renal-type clear cell carcinoma (RTCCC) of the prostate and the suitable IHC examinations was performed to proof RTCCC.\nSounds precise and searchable.\nStructured abstract; summarizes the paper\nMy question are :\nWhy you choose surgical hormonal therapy either medical hormonal therapy in this patient?\n\nWould you perform radical cystoprostatectomy? When would you do it?\n\nIf you found any differences in your case compared to other cases. This would be a valuable addition at 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? 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": "7462",
"date": "01 Dec 2021",
"name": "Muhammad Asykar Palinrungi",
"role": "Author Response",
"response": "Dear reviewer, Thank you for your valuable comment. Our replies to the reviewer's inquiries and revised points are as follows. Reply to comment 1: Although the patient has been explained before, they still prefer surgery due to the long distance of his home from the closest health facility. Reply to comment 2: I will perform the procedure if the patient meets the criteria. Reply to comment 3: Thank you for your suggestions"
}
]
},
{
"id": "262433",
"date": "16 May 2024",
"name": "Athaya Febriantyo Purnomo",
"expertise": [
"Reviewer Expertise Urology",
"Immunology",
"Kidney Transplant",
"Oncology",
"Precision Medicine",
"Health Economic",
"Systematic Review",
"Surgery",
"Nephrology"
],
"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 presents a rare case of renal-type clear cell carcinoma (RTCCC) of the prostate in an 81-year-old male. It details his symptom history, diagnostic process, treatment choices, and outcomes with an emphasis on the uniqueness of the case due to its rarity and the diagnostic challenges it poses. The case is well documented according to the CARE guidelines and discusses the implications of the findings in the context of existing literature.\nThe background detailing the history and progression of the case is adequately described, giving a clear timeline of symptom development, diagnosis, and interventions leading up to the treatment.\nThe report provides an overview of physical examinations, diagnostic tests, and treatment. However, it lacks detailed quantitative data and images from diagnostic tests like bone scans and urethrocystoscopy results which would enhance the credibility and educational value of the case report. It would be beneficial to include these details to offer a comprehensive view of the diagnostic process.\nThe discussion effectively outlines the importance of the findings and their implications for understanding and managing RTCCC of the prostate. The relevance to future disease processes, diagnosis, and treatment is well articulated, establishing a clear link to the ongoing academic conversation about this rare cancer type.\nWhile the case is presented with basic details, it lacks depth in discussing the clinical decision-making process. More information on the rationale behind choosing bilateral subcapsular orchiectomy over medical hormonal therapy, based on the patient's specific conditions and prognosis, would be highly beneficial. Discussing alternative treatment options considered and why they were not selected could provide valuable insights for other practitioners.\nOverall, manuscript is scientifically robust with respect to its contributions to the literature on RTCCC of the prostate. However, to enhance its scientific soundness and utility to practitioners, certain areas require expansion and greater detail. Firstly, provide quantitative values and images from the diagnostic tests, especially the bone scans and urethrocystoscopy results, to substantiate the diagnosis and treatment decisions. Next, manuscript can be enhanced by elaborating on the treatment decision process, including a detailed discussion of alternative treatments considered and the specific reasons for choosing bilateral subcapsular orchiectomy over other options. Discuss potential complications and the management strategies considered for this patient, which would be valuable for practitioners handling similar cases.\n\nIs the background of the case’s history and progression described in sufficient detail? Yes\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Partly\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Yes\n\nIs the case presented with sufficient detail to be useful for other practitioners? Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-475
|
https://f1000research.com/articles/10-472/v1
|
15 Jun 21
|
{
"type": "Research Article",
"title": "Negative sentiment towards COVID-19 vaccines: A comparative study of USA and UK social media posts before vaccination rollout",
"authors": [
"James Lappeman",
"Keneilwe Munyai",
"Benjamin Mugo Kagina",
"James Lappeman",
"Keneilwe Munyai"
],
"abstract": "Abstract Introduction: The global spread of the COVID-19 pandemic was rapid and devastating to humanity. The public health response to the pandemic was rapid too. Completion of COVID-19 vaccine development was achieved in under a year. The USA and the UK were the first countries to rollout COVID-19 vaccines to contain the pandemic. Successful rollout of the vaccines hinges on many factors, among which is public trust.\n\nAim: To investigate the sentiments towards COVID-19 vaccines in the USA and UK prior to vaccination rollout. Methods: Neuro-linguistic programming with human validation was used to analyse a sample of 243,883 COVID-19 vaccine related social media posts from the USA and the UK in the period 28 July to 28 August 2020. The sentiment analysis measured polarity (positive, neutral, negative), and the themes present in negative comments.\n\nResults: In the sample of 243,883 social media posts, both the USA and the UK had a net sentiment profile of approximately 28% positive, 8% negative and 63% neutral sentiment. On further analysis, there were distinct differences between the two country’s social media sentiment towards COVID-19 vaccines. The differences were seen in the themes behind the negative sentiment. In the USA, the negative sentiments were mainly due to health and safety concerns, the fear of making a vaccine mandatory, and the role that pharmaceutical companies would play with the release of vaccines. In the UK the main driver of negative sentiment was the fear of making the vaccine mandatory (almost double the size of the sentiment in the USA). Conclusions: Negative sentiments towards COVID-19 vaccines were prevalent in the third quarter of 2020 in the USA and the UK. Reasons behind the negative sentiments can be used by authorities in the two countries to design evidence-based interventions to address the refusal of vaccination against COVID-19.",
"keywords": [
"COVID-19 pandemic",
"new vaccines",
"social media",
"sentiment analysis",
"USA and UK."
],
"content": "Introduction\n\nOn a global scale, Coronavirus disease 2019 (COVID-19) resulted in an unprecedented public health challenge, including disruption of social-economic and cultural systems1. The disease was declared a pandemic by the World Health Organisation (WHO) in March 20202. Public health interventions to contain the pandemic are guided by existing and emerging evidence on the epidemiology of the disease. To mitigate the impacts of the COVID-19 pandemic, tremendous and record-breaking efforts culminated in the development and subsequent rollout of novel vaccines3,4. In the first quarter of 2021, several vaccines were approved for emergency use by health regulatory authorities across the world. Against this background, a global survey on public acceptance of COVID-19 vaccines showed a wide-ranging acceptance rates of below 55% to a high of about 90%5.\n\nSuccessful rollout of COVID-19 vaccines to the communities will hinge on many key factors, among which is public trust and benefits of the vaccines6. Negative public sentiments and uncertainty towards COVID-19 vaccines can hinder high uptake during the rollout, resulting in less vaccination impact than expected. Therefore, characterising sentiments towards COVID-19 vaccines is an ongoing public health priority. Social media provides inexpensive access to large and global data that can be used for characterising vaccine sentiments, with the potential to identify priority areas for interventions to improve high uptake of vaccines.\n\nSocial media platforms are increasingly becoming frequent sources of vaccination misinformation7. Sentiment analysis of social media posts is an approach used for collecting and analysing posted information to gain detailed insights of people’s decision making process with regards to vaccination8,9. Research in the field of measuring vaccine sentiments from social media is advancing rapidly. Its applications are wide - from a gaining deeper understanding of sentiments towards specific vaccines, such as HPV, to understanding sentiments towards vaccination of vulnerable populations, such as pregnant women10,11. At a global scale, COVID-19 pandemic and the development of vaccines against the disease have generated unprecedented misinformation on social media12,13. We therefore conducted a social media sentiment analysis towards COVID-19 vaccines in the USA and the UK prior to the full-scale vaccination rollout. Both the USA and UK were among the first countries to rollout COVID-19 vaccines at scale and have the most pandemic-related deaths proportionally to their COVID-19 cases or population4. Leading pharma from both countries are front runners in the development and testing of new COVID-19 vaccines14.\n\n\n\nIn the planning phase of rolling out COVID-19 vaccines, Operation Warp Speed of the USA government committed significant resources to make available hundreds of millions of COVID-19 vaccine doses to the members of the public15. The USA has been a front runner in rolling out COVID-19 vaccines. However, experiences from the past, including recent pandemics, show that availability of vaccines does not necessarily translate to high vaccine uptake16,17. To address the potential low uptake, a Working Group on Readying Populations for COVID-19 Vaccine was formed18. The purpose of the group was “to develop and disseminate recommendations emanating from design thinking process and evidence from social, behavioural, and communication sciences, that would support realistic planning for a US COVID-19 vaccination campaign”18.\n\nIn December 2020, the UK Government authorised emergency use of a new COVID-19 vaccine19. The UK has past experience wherein misinformation on the safety of measles, mumps and rubella vaccination (The MMR vaccine) which resulted in a dramatic fall in uptake and subsequent outbreaks of measles20. Knowledge on the extent and nature of public trust on COVID-19 vaccines is useful for UK authorities. This understanding can be used to develop and implement strategies that will ensure high COVID-19 vaccine uptake.\n\nAgainst this background, we were interested in mining and analysing social media sentiments towards COVID-19 vaccines in the USA and the UK prior vaccination rollout. Social network analysis has been successfully used to understand COVID-19 pandemic sentiments in the USA21. In 2020, the USA and UK ranked first and fifth respectively with respect to leading countries based on number of Twitter users22. Although there are prior studies that have been conducted to characterise sentiment towards COVID-19 vaccines21, our study methodology has some unique aspects, including the broad scope of analysing unsolicited social media sentiment as opposed to survey methodologies that often involve subjective sampling.\n\n\nMethods\n\nFrom 28 July – 28 August 2020 (one month) of social media data were examined and allowed for unsolicited and noncoercive responses that captured the lived experiences of consumers commenting on the concept of a COVID-19 vaccine. The analysis was completed before a confirmed announcement of a vaccine was made by Pfizer in November 202023. Conversations about the COVID-19 vaccines were accessed via an application programming interface (API) called gnip: that enabled social media data to be gathered from Twitter. GNIP (an API aggregation company) was used to collect the social media data for the period and normalise the data24.\n\nThese posts were analysed for themes and sentiment with a computerised natural language processing (NLP) program provided by research company BrandsEye. This type of NLP is like that available on platforms like Amazon Lex, IBM Watson Assistant and DialogFlow. With the use of BrandsEye’s custom interface, a sub-sample of posts were sent for human topic analysis and sentiment validation25,26. This methodology of sub-sample validation improves the accuracy of net-sentiment measurement and topic analysis as NLP is still not accurate enough for precise interpretation of slang, sarcasm and emoji’s25. Mentions were analysed by the human raters (a large, distributed workforce who BrandsEye curate and pay to verify and mark-up raw social media data) and a set of themes were generated. Posts were then tagged according to these classified themes.\n\n\nResults\n\nIn total, 243,883 COVID-19 vaccine related posts were collected from both the USA and the UK for the sample period. A sub-sample of 8,392 posts were sent for human topic analysis and sentiment validation. Figure 1a and 1b provide examples of the kind of posts that were collected for analysis.\n\nAn example of raw data (tweets) by users from USA and UK are shown. Figure 1a: Sample of Tweets from the USA (Mentions anonymised to protect author privacy). Figure 1b: Sample of Tweets from the UK (Mentions anonymised to protect author privacy).\n\nThe sentiment margin of error was calculated by comparing how many percentage points this calculation’s result will differ from the real population value. For example, a 95% confidence interval with a 4% margin of error means that the statistic will be within 4 percentage points of the real population value 95% of the time. In the case of the data that verified for sentiment, the margin of error ranged from ±1.6% (overall sample) to ±2.3% (UK sample). The combined process of the machine learning algorithm and manual validation has created a confidence level of 95% and an overall 1.6% margin of error, showing a strong reliability of the data (Table 1).\n\nShows the total volume of twitter mentions BrandsEye identified about a COVID-19 vaccine from 28 July – 28 August 2020. BrandsEye’s Crowd of human contributors evaluated the sentiment contained in 8,392 mentions. Mentions were assigned sentiment scores of positive, negative or neutral. 1505 mentions were categorised into nine hesitancy themes. The resultant margin of error for COVID-19 vaccine sentiment is below 2.5% for both USA and UK, calculated at a 95% confidence interval.\n\nIn total, over 64% of the sampled posts had neutral sentiment relating to vaccines, whereas over 28% was expressed negative sentiment and less than 9% expressed positive sentiment (Figure 2). When isolating the two sampled countries’ specific sentiment profile, the sentiment was very similar in both the USA and UK.\n\nThe sentiment analysis measured by polarity (positive, neutral, negative). The polarity for the 2 countries is combined. Authors were most hesitant about a mandatory COVID-19 vaccine. Authors shared petitions to appeal restrictions that may be imposed on those who refuse the vaccine. Health and safety was the second most prevalent theme cited, as authors worried about adverse reactions and side effects. Authors hypothesised that the scientific process followed to produce the vaccine would be flawed due to institutions rushing to find an answer to the pandemic. Hesitancy mentions on average generated 4.8 engagements; 3.3 times higher than that seen in advocacy mentions. Authors mentioning developments in vaccine trials accounted for nearly a fifth of all advocacy conversation. These mentions also featured calls to action aimed at finding human volunteers in order to accelerate the research. Vaccine advocates expressed concern about the equitable distribution of the COVID-19 vaccine. This highlights a trend of institutional distrust that underlies vaccine-related conversation from both advocates and sceptics alike. Advocacy mentions generated an average of 1.4 engagements per mention.\n\nIn the USA, the majority of sentiment was neutral (63.2%) with negative being 28.7% and positive being 8.1%. In the UK, the majority was also neutral (63.8%) with negative being 27.5% and positive being 8.7% (Figure 3).\n\nThe sentiment analysis measured by polarity (advocacy, neutral and hesitancy). The polarity is shown for each country. The USA saw a lower ratio of advocacy mentions and a higher ratio of hesitancy mentions compared to the combined aggregate. Conversely, the UK saw a higher ratio of advocacy mentions and a lower ratio of hesitancy mentions.\n\nWhile the overall sentiment showed consistency between the two countries, the theme analysis did show that the distribution of drivers of negative sentiment were different in each country. In total, nine core themes were identified and quantified from the negative sentiment. These themes were coded as Conspiracy, No danger, Hoax, Health and safety, Mandatory, Pharmaceutical, Politics, Scientific process, and Vaccine efficacy. The themes were coded and defined based on the different sentiment profile in both the USA and the UK (Table 2).\n\nThemes on negative sentiments towards COVID-19 vaccine were identified, coded and a definition justifying the assigned code was provided. The % negative sentiments was then computed separately for tweets from the USA and UK. Mandatory vaccination was the dominant theme code in the UK while in both countries, health and safety concerns were dominant negative sentiments.\n\nIn the USA, the main drivers of negative sentiment for the sample period were health and safety concerns, the fear of making a vaccine mandatory and the role that pharmaceutical companies will play in the release of vaccines. In the UK, the main driver of negative sentiment was the fear of making the vaccine mandatory (almost double the size of the sentiment in the USA). The role of health and safety was second and slightly higher than in the USA (even though it was first in the USA, the USA sentiment was slightly more distributed among the six themes. Third was scientific process, which aligned closely in number to the USA, but was only fourth most prevalent theme there (Table 2).\n\n\nDiscussion\n\nThe impacts of the COVID-19 pandemic coupled with rapid vaccine development and rollout has demanded a rapid understanding of the public sentiment concerning the vaccines and how this may affect vaccination uptake. In this study, we tapped into huge volumes of opinionated social media data for analysis to gain insights on a topical issue about people’s potential to accept new COVID-19 vaccines in the USA and UK. Through sentiment mining and analysis, this study shows in both countries, negative public sentiments towards COVID-19 vaccines were nearly fourfold higher than positive sentiments before rollout. Interestingly, neutral public sentiments towards future COVID-19 vaccines dominated over negative and positive sentiments. Our findings agree with those reported by Loomba S et al., who used a randomized controlled trial in the USA and UK to quantify how exposure to online misinformation resulted to a large proportion not intending to get vaccinated against COVID-1927. Thematic analyses in both countries showed complexity and differential distribution of the reasons for the negative sentiments. Negative vaccine sentiments can translate to attitude, and then vaccine hesitancy. Our results indicate that, at the time the study was conducted, more than a quarter of the population in the USA and UK would not accept vaccination against COVID-19.\n\nSafety of rapidly developed COVID-19 vaccines was listed as the first and second main reasons of negative sentiment towards vaccination in the USA and UK respectively. This was not a surprising finding because, in general, vaccine safety ranks among the top reasons for lack of public vaccination confidence in most settings28. A poll conducted in the USA in June 2020 showed only about 50% of Americans were committed to receiving a COVID-19 vaccine, with acceptance commitment among some communities being as low as 40%29. One possible explanation for our findings is that the vaccines against COVID-19 were developed at a record speed and in the context of an infodemic, both these factors can exacerbate heightened negative safety sentiments30,31. As the vaccination rollout continues globally, and with millions of doses administered in the first quarter of 2021, preliminary safety reports from the USA show COVID-19 vaccination results to mild adverse events and in rare cases, allergic reactions32. The reports are in line with the expected safety profile. We propose widespread communication of up-to-date and accurate information on the observed effectiveness and safety profile of COVID-19 vaccines. Communication is at the core of any process to empower and change mindsets and perceptions. Understanding the audience and using language and methods that are accessible, reliable, and credible is critical to building public trust in COVID-19 vaccines and vaccination in general.\n\nBefore health regulatory approval for rollout to the public, vaccines are usually tested through a rigorous, well-established, and regulated processes33. Traditionally, vaccine development processes are often detached from political, media, and public attention. This did not happen with COVID-19 vaccine development due to the enormous attention the pandemic rightfully attracted. Therefore, it is not surprising that in our study, politics was a key theme identified as a driver of negative sentiment in both countries, albeit at moderate frequencies. Given that governments are major stakeholders for vaccinations, it is critical for leaders of government to not politicise the science of vaccine development as our results show this can be a driver of negative sentiments. Senior government leaders in the USA and the UK were among the first to publicly get vaccinated with new COVID-19 vaccines during the rollout. This is important in advancing positive sentiment of vaccines to the public. More must be done rapidly and openly to communicate accurate and up-to-date information on COVID-19 vaccines to improve public trust and positive sentiments.\n\nMandatory vaccination was listed as the first and second main reason of negative sentiment towards vaccination in the UK and USA respectively. With some degree of success, mandatory vaccination is legislated in some countries to address the resurgence of vaccine preventable diseases34,35. In the UK, discussions around mandatory vaccination featured in the mainstream media with senior health officials not completely ruling out such an option in mid-2020. Such discussions may have driven the high frequencies of negative sentiment observed in our study. Ethics on mandatory vaccination is a topic that generates a lot of controversies with individuals refusing to be vaccinated considered to cause harms to others36,37. Our findings suggest that careful considerations must be made by authorities prior developing legislation on mandatory COVID-19 vaccination as this can result in a backlash. Neither of these two countries have instituted a mandatory COVID-19 vaccination during the rollout. Other forms of legislation, such as incentivisation to be vaccinated can be considered in some settings36.\n\nIn the USA, lack of trust in the pharmaceutical industry was the third main reason cited for negative sentiment on COVID-19 vaccination. The same reason was ranked fourth in the UK. In general, mistrust by the public towards pharmaceutical industry is a key element driving vaccine hesitancy38. Further compounding the issue of the pharmaceutical industry in the context of COVID-19 vaccines is the relationship between governments and pharmaceutical companies, which may involve non-disclosure agreements39. Both the USA and the UK governments are key stakeholders in COVID-19 vaccine development through advanced market commitments as well as through regulatory processes39. The relationships between governments and the pharmaceutical industry remains under public scrutiny during the COVID-19 pandemic, hence the observed high rates of negative sentiments towards pharmaceutical industry was somewhat expected. Our results suggest that open and transparent communication from the pharmaceutical industry as well as the Governments has the potential to improve positive sentiment towards COVID-19 vaccines.\n\nScientific process was the third most frequently reported reason for negative sentiment in the UK and the same reason was ranked fourth in the USA. COVID-19 vaccines were developed at a rapid pace3. Mistrust in vaccine information is a key element of vaccine hesitancy38. Due to the rapid COVID-19 vaccine development process, public mistrust in the scientific process may have been driven by a lack of optimal communication as well as by misinformation. It is critical for researchers working in the field to continue communicating widely, openly and transparently on the reasons behind the remarkable success of COVID-19 vaccine development and how it was possible to achieve the success while maintaining expected standards of scientific rigour40.\n\nThere were other less frequent reasons for negative sentiments in both countries. The reasons were associated with vaccine efficacy, conspiracy, no danger and hoax. Taken together, our results show that reasons behind negative vaccine sentiments are many, complex, and can vary in scale across different countries.\n\nThere are limitations to this study. First, sentiments identified could be temporal and may have changed by the time COVID-19 vaccines are rolled out. There is a possibility of a shift in sentiment as more information such as safety, is made available to the public. This, however, provides further opportunity to extend this research to a longer time frame. A repeat mining and analysis of similar data will be needed to identify any changes in the sentiments. Second, it is hard to determine how representative the selected data was to make inference to the general population.\n\nIn conclusion, widespread access and use of safe, effective, and trusted vaccines will be crucial in the control of the COVID-19 pandemic. Our findings show that negative sentiments towards COVID-19 vaccines were prevalent in the third quarter of 2020 in the USA and the UK. Social media, such as twitter, has been an influential platform for information, disinformation and misinformation during the COVID-19 pandemic41. The findings of our study offer a snapshot of possible reasons that will make people to refuse COVID-19 vaccination. Tailor-made education and communication strategies addressing the identified and prevalent negative sentiments may result in higher uptake of future COVID-19 vaccines in the USA and UK.\n\n\nData availability\n\nThe raw data needed to replicate these analyses has not been made public by the data providers, meaning we are forbidden from sharing it in this paper. However, the reader can apply for access to the data through a direct application to BrandsEye for the purchase of this data. BrandsEye can be contacted on contact@brandseye.com. BrandsEye is a commercial research company that has had its data published in journals such as MethodsX (Elsivier) and the International Journal of Bank Marketing (Emerald). More details on how to apply to access these data can be found at https://www.brandseye.com.",
"appendix": "Authors contributions\n\nJL collected the data; JL and BMK conceived the study. KM reviewed the manuscript; BMK interpretated the data and wrote the first draft of the manuscript. All authors reviewed and approved the final manuscript for submission.\n\n\nAcknowledgement\n\nhttp://Brandseye.com\n\n\nReferences\n\nNoah S: Diffenbaugh CBF Gabrielle Wong-Parodi The COVID-19 lockdowns: a window into the Earth System. Nature reviews earth and environment. 2020; 1: 470–81.\n\nCucinotta D, Vanelli M: WHO Declares COVID-19 a Pandemic. Acta Biomed. 2020; 91(1): 157–60. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLurie N, Saville M, Hatchett R, et al.: Developing Covid-19 Vaccines at Pandemic Speed. N Engl J Med. 2020; 382(21): 1969–73. PubMed Abstract | Publisher Full Text\n\nOur World in Data: Coronavirus (COVID-19) Vaccinations. 2021; accessed on 3 March 2021. Reference Source\n\nLazarus JV, Ratzan SC, Palayew A, et al.: A global survey of potential acceptance of a COVID-19 vaccine. Nat Med. 2021; 27(2): 225–8. PubMed Abstract | Publisher Full Text | Free Full Text\n\nOzawa S, Stack ML: Public trust and vaccine acceptance-international perspectives. Hum Vaccin Immunother. 2013; 9(8): 1774–8. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBurki T: Vaccine misinformation and social media. The Lancet Digital Health. 2019; 1(6): E258–E9.\n\nSalathe M, Khandelwal S: Assessing vaccination sentiments with online social media: implications for infectious disease dynamics and control. PLoS Comput Biol. 2011; 7(10): e1002199. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWilson SL, Wiysonge C: Social media and vaccine hesitancy. BMJ Glob Health. 2020; 5(10). PubMed Abstract | Publisher Full Text | Free Full Text\n\nMartin S, Kilich E, Dada S, et al.: \"Vaccines for pregnant women…?! Absurd\" - Mapping maternal vaccination discourse and stance on social media over six months. Vaccine. 2020; 38(42): 6627–37. PubMed Abstract | Publisher Full Text\n\nDu J, Xu J, Song H, et al.: Optimization on machine learning based approaches for sentiment analysis on HPV vaccines related tweets. J Biomed Semantics. 2017; 8(1): 9. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCinelli M, Quattrociocchi W, Galeazzi A, et al.: The COVID-19 social media infodemic. Sci Rep. 2020; 10(1): 16598. PubMed Abstract | Publisher Full Text | Free Full Text\n\nIslam MS, Sarkar T, Khan SH, et al.: COVID-19-Related Infodemic and Its Impact on Public Health: A Global Social Media Analysis. Am J Trop Med Hyg. 2020; 103(4): 1621–9. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChung YH, Beiss V, Fiering SN, et al.: COVID-19 Vaccine Frontrunners and Their Nanotechnology Design. ACS Nano. 2020; 14(10): 12522–37. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHo RJY: Warp-Speed Covid-19 Vaccine Development: Beneficiaries of Maturation in Biopharmaceutical Technologies and Public-Private Partnerships. J Pharm Sci. 2021; 110(2): 615–8. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSteelFisher GK, Blendon RJ, Bekheit MM, et al.: The public's response to the 2009 H1N1 influenza pandemic. N Engl J Med. 2010; 362(22): e65. PubMed Abstract | Publisher Full Text\n\nPhadke VK, Bednarczyk RA, Salmon DA, et al.: Association Between Vaccine Refusal and Vaccine-Preventable Diseases in the United States A Review of Measles and Pertussis. JAMA. 2016; 315(11): 1149–58. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSchoch-Spana M, Brunson EK, Long R, et al.: The public's role in COVID-19 vaccination: Human-centered recommendations to enhance pandemic vaccine awareness, access, and acceptance in the United States. Vaccine. 2020; S0264-410X(20)31368-2. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMahase E: Vaccinating the UK: how the covid vaccine was approved, and other questions answered. BMJ. 2020; 371: m4759. PubMed Abstract | Publisher Full Text\n\nVivancos R, Keenan A, Farmer S, et al.: An ongoing large outbreak of measles in Merseyside, England, January to June 2012. Euro Surveill. 2012; 17(29): 20226. PubMed Abstract | Publisher Full Text\n\nHung M, Lauren E, Hon ES, et al.: Social Network Analysis of COVID-19 Sentiments: Application of Artificial Intelligence. J Med Internet Res. 2020; 22(8): e22590. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTankovska H: Social media - Statistics & Facts. (url accessed on 3 March 2021). 2021. Reference Source\n\nCohen J: Incredible milestone for science. Pfizer and BioNTech update their promising COVID-19 vaccine result. (url accessed on 3 March 2021). 2020. Reference Source\n\nWang DCH, Kazemzadeh A, Bar F, et al.: A system for real-time Twitter sentiment analysis of 2012 U.S. presidential election cycle. Proceedings of the ACL 2012 System Demonstrations. 2012; 12: 115–20. Reference Source\n\nLappeman J, Clark R, Evans J, et al.: Studying social media sentiment using human validated analysis. Methodsx. 2020; 7: 100867. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBrandsEye: Accurate opinion data through advanced sentiment analytics 2019. (url accessed on 3 March 2021). Reference Source\n\nLoomba S, de Figueiredo A, Piatek SJ, et al.: Measuring the impact of COVID-19 vaccine misinformation on vaccination intent in the UK and USA. Nat Hum Behav. 2021; 5(3): 337–348. PubMed Abstract | Publisher Full Text\n\nde Figueiredo A, Simas C, Karafillakis E, et al.: Mapping global trends in vaccine confidence and investigating barriers to vaccine uptake: a large-scale retrospective temporal modelling study. Lancet. 2020; 396(10255): 898–908. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCornwall W: Just 50% of Americans plan to get a COVID-19 vaccine. Here’s how to win over the rest. Science Magazine. (url accessed on 3 March 2021). 2020. Reference Source\n\nPetousis-Harris H: Assessing the Safety of COVID-19 Vaccines: A Primer. Drug Saf. 2020; 43(12): 1205–10. PubMed Abstract | Publisher Full Text | Free Full Text\n\nThe Lancet Infectious D: The COVID-19 infodemic. Lancet Infect Dis. 2020; 20(8): 875. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRemmel A: COVID vaccines and safety: what the research says. Nature. 2021; 590(7847): 538–540. PubMed Abstract | Publisher Full Text\n\nCunningham AL, Garcon N, Leo O, et al.: Vaccine development: From concept to early clinical testing. Vaccine. 2016; 34(52): 6655–64. PubMed Abstract | Publisher Full Text\n\nD'Ancona F, D'Amario C, Maraglino F, et al.: Introduction of new and reinforcement of existing compulsory vaccinations in Italy: first evaluation of the impact on vaccination coverage in 2017. Euro Surveill. 2018; 23(22): 1800238. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLevy-Bruhl D, Desenclos JC, Quelet S, et al.: Extension of French vaccination mandates: from the recommendation of the Steering Committee of the Citizen Consultation on Vaccination to the law. Euro Surveill. 2018; 23(17): 18–00048. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSavulescu J: Good reasons to vaccinate: mandatory or payment for risk? J Med Ethics. 2021; 47(2): 78–85. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFlanigan J: A defense of compulsory vaccination. HEC Forum. 2014; 26(1): 5–25. PubMed Abstract | Publisher Full Text\n\nCrescitelli MED, Ghirotto L, Sisson H, et al.: A meta-synthesis study of the key elements involved in childhood vaccine hesitancy. Public Health. 2020; 180: 38–45. PubMed Abstract | Publisher Full Text\n\nWouters OJ, Shadlen KC, Salcher-Konrad M, et al.: Challenges in ensuring global access to COVID-19 vaccines: production, affordability, allocation, and deployment. Lancet. 2021; 397(10278): 1023–1034. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDefendi HGT, da Silva Madeira L, Borschiver S: Analysis of the COVID-19 Vaccine Development Process: an Exploratory Study of Accelerating Factors and Innovative Environments. J Pharm Innov. 2021: 1–17. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKouzy R, Abi Jaoude J, Kraitem A, et al.: Coronavirus Goes Viral: Quantifying the COVID-19 Misinformation Epidemic on Twitter. Cureus. 2020; 12(3): e7255. PubMed Abstract | Publisher Full Text | Free Full Text"
}
|
[
{
"id": "89107",
"date": "26 Jul 2021",
"name": "Rakhi Tripathi",
"expertise": [
"Reviewer Expertise Social media analytics",
"Social listening",
"Digital technologies"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 well-written. It discusses the sentiments of citizens of the US and UK regarding COVID vaccination. The sentiments are extracted from social media and analyzed. The results are explained well especially the Table 2 where the themes related to negative sentiments are explained.\n\nFew suggestions would strengthen the paper:\nHow did the authors segment the data? How was the data cleaned; Any issues with sarcasm, multilingual posts, or posts consisting of slang? A paragraph on it would be useful.\n\nIt is unclear that the reach of each post is considered or not. For example, if an influencer tweets a negative sentiment and it engages millions then that post has a bigger impact as compared to the post with limited reach. It is important to discuss this factor.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
},
{
"id": "90462",
"date": "06 Sep 2021",
"name": "Daniel Thomas",
"expertise": [
"Reviewer Expertise Epidemiology",
"public health"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is a very interesting analysis of social media posts in two countries during Summer 2020 to assess public acceptability of COVID vaccination in advance of the rollout.\nIn terms of style it is well written and clear. The language is a bit dramatic at times, e.g. 'devastating to humanity', 'record-breaking' efforts' etc. and this could be toned down. The term 'pharma' should be specified in full. The titles of figures are very long, e.g. Figure 2, and the detailed explanation should go into the manuscript text.\nI have three main points on content:\nThere appears to be contradictory findings presented in the abstract (28% positive; 8% negative) compared to the results section (negative sentiment four fold higher than positive sentiment).\n\nThe results would have been more useful if some stratification by age, gender, socioeconomic status was presented. I presume this was not possible. If so, it should be recognized as a limitation and included in the discussion section. Also, it would have been useful to see some discussion about differential social media use in the UK and US by type of platform. In the UK for example younger people are more likely to use Instagram rather than Twitter or Facebook. Is that the case in the US?\n\nLastly, it would be helpful if the authors could expand on their discussion about the suitability of this approach for behavioral insight surveillance, to complement more traditional disease surveillance methods.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-472
|
https://f1000research.com/articles/10-281/v1
|
09 Apr 21
|
{
"type": "Data Note",
"title": "A draft sequence reference of the Psilocybe cubensis genome",
"authors": [
"Kevin McKernan",
"Liam T. Kane",
"Seth Crawford",
"Chen-Shan Chin",
"Aaron Trippe",
"Stephen McLaughlin",
"Liam T. Kane",
"Seth Crawford",
"Chen-Shan Chin",
"Aaron Trippe",
"Stephen McLaughlin"
],
"abstract": "We describe the use of high-fidelity single molecule sequencing to assemble the genome of the psychoactive Psilocybe cubensis mushroom. The genome is 46.6Mb, 46% GC, and in 32 contigs with an N50 of 3.3Mb. The BUSCO completeness scores are 97.6% with 1.2% duplicates. The Psilocybin synthesis cluster exists in a single 3.2Mb contig. The dataset is available from NCBI BioProject with accessions PRJNA687911 and PRJNA700437.",
"keywords": [
"Psilocybe cubensis",
"Genome",
"Single molecule sequencing",
"Psilocybin"
],
"content": "Introduction\n\nThere are several mushrooms capable of synthesizing the psychoactive compound psilocybin. This compound has been classified as a “breakthrough therapy” for depression by the FDA (Johnson and Griffiths 2017). The psilocybin pathway was identified by Fricke et al., but to date no public references exist in NCBI with N50s longer than 50kb (Fricke et al. 2017; Blei et al. 2018; Fricke et al. 2019a; Fricke et al. 2019b; Blei et al. 2020; Demmler et al. 2020; Fricke et al. 2020). A more contiguous genome assembly can assist in further resolution of the genetic diversity in the fungi’s secondary metabolite production.\n\n\nMethods\n\nDried stems from Psilocybe cubensis strain P.envy (strain name is anecdotal and obtained in Somerville, MA, USA) were used for isolation of high molecular weight (HMW) DNA using a modified CTAB/Chloroform and SPRI protocol. Briefly, 300mg of stem sample were ground to a fine powder using a -80C frozen mortar and pestle. 150 mg of powder was then aliquoted into 2 mL conical tubes (USA Scientific) with 1.5 mL cetrimonium bromide. These tubes were then incubated at room temperature on a tube rotator for 10 minutes. 6 uL of RNase A (Promega 4 mg/mL) was then added and both tubes were incubated at 37°C for one hour, vortexing every 15 minutes. Following this incubation, 7.5 uL Proteinase K (New England Biolabs 20 mg/mL) was added and the tubes were incubated at 60°C for 30 minutes, vortexing every 10 minutes. At the conclusion of the Proteinase K incubation, both tubes were incubated on ice for 10 minutes. The samples were then centrifuged for 5 minutes at 14000 rpm. 600 uL of supernatant was removed from each tube and added to 600 uL chloroform. The tubes were then vortexed until opaque and spun for 5 minutes at 14000 rpm. 400 uL of the aqueous layer was removed using a wide bore tip and added to a 1.5 mL Eppendorf tube. 400 uL MIP (marijuana infused products) Solution B and 400 uL DNA Binding Beads (Medicinal Genomics PN 420004) were added to the Eppendorf tube and inverted to homogenize. The tubes were then incubated at room temperature on the tube rotator for 15 minutes. The tubes were then removed from the rotator and placed on a magnetic tube rack for 3 minutes. The supernatant was removed, the beads were washed twice with 1 mL of 70% ethanol and allowed to dry for 5 minutes. The beads were then eluted in 100 uL of 56°C Elution Buffer (Medicinal Genomics PN 420004) using a wide bore tip and incubated at 56°C for 5 minutes. Following this incubation, the tubes were returned to the magnetic rack, the supernatant of both tubes were removed using a wide bore tip and pooled in a fresh Eppendorf tube. HMW DNA length was quantified on an Agilent TapeStation and produced a DIN of 8.1. Qubit Fluorometer (Thermo Fisher Scientific) quantified 55ng/ul. Nanodrop Spectrophotometer (Thermo Fisher Scientific) quantified 104ng/ul with 260/280nm ratio of 1.85 and 260/230nm of 0.95.\n\nSequencing libraries were constructed according to the manufacturer’s instructions for Pacific Biosciences Sequel II HiFi sequencing. 773,735 CCS reads were generated. Quast (Gurevich et al. 2013) was used to assess the quality of the input fasta sequence file (N50 = 13.9Kb) and the output assembly fasta file (3.33Mb N50).\n\nThe unfiltered CCS data was assembled using the Peregrine assembler (pg_asm 0.3.5,arm_config5e69f3d+) (Chin 2019). Reads were assembled into 32 contigs with lengths ranging from 32 kilobases to 4.6 megabases (Figure 1). BUSCO v3.0.2 completeness scores (97.6%) were measured using agaricales_odb10.2020-08-05 BUSCO lineage database (Table 1) (Simao et al. 2015; Waterhouse et al. 2018). FunAnnotate v1.8.4 was used to annotate the genome (Li and Wang 2021) resulting in 13,478 genes.\n\nThe final genome assembly was aligned to three other public Psilocybe cubensis datasets (Fricke et al. 2017; Torrens-Spence et al. 2018; Reynolds et al. 2018) and one different Psilocybe species (Psilocybe cyanescens) to verify taxonomic identification (Table 2). In total, 96-98.75% of these Psilocybe cubensis sequences align to the new HiFi generated Psilocybe cubensis P.envy reference using minimap2 and bwa-mem (Li and Durbin 2010; Li 2018). Mapping rates were determined using samtools flagstat on bam files (Li et al. 2009). Alignments were visualized with MUMmer V4.0.0beta2 and Integrative Genomics Viewer v2.4.16 (Delcher et al. 2003; Robinson et al. 2011; Thorvaldsdottir et al. 2013).\n\nA different Psilocybe species (Psilocybe cyanescens) genome was also mapped with much lower mapping efficiency.\n\nThree Illumina genome assemblies (Reynolds et al., McKernan et al., Fricke et al.) were additionally aligned using MUMmer for whole genome alignment plots (Figure 2).\n\nLeft is Psilocybe cyanescens from Reynolds et al. Middle is McKernan et al. (MGC) Illumina assembly. Right is Fricke et al. or JGI assembly.\n\n183,430 SNPs were identified with GATK v4.1.6.0 by comparing Illumina whole genome shotgun data (McKernan et al. NCBI Project: PRJNA687911) with the HiFi reference assembly. This equates to a SNP every 243 bases.\n\nThe N-methyltransferase gene responsible for Psilocybin production in P.envy contains a structural variation not seen in previous P. cubensis surveys (Figure 3). Illumina read mapping of the McKernan et al. P. cubensis assembly in NCBI (NCBI Project: PRJNA687911) demonstrates multiple read pairs spanning a 4.6kb insertion in the HiFi P. cubensis strain P.envy. This insertion extends the 3’ end of the P.envy N-methyltransferase gene. The 4.6kb insertion is also observed as a deletion in Psilocybe cyanescens and as a deletion in RNA-Seq data from Torrens-Spence et al. (NCBI Project: PRJNA450675) (Reynolds et al. 2018). Further work is required to understand the biological significance of this variation.\n\nTop track is Medicinal Genomics Illumina whole genome shotgun data of a different P. cubensis (strain name unknown: NCBI Project: PRJNA687911) mapped to the HiFi P. cubensis strain P.envy. Second track contains RNA-Seq data from a third P. cubensis genome (strain name also unknown: NCBI Project: PRJNA450675) hosted at JGI. Third track is Psilocybe cyanescens genome mapped to HiFi P. cubensis P.envy reference genome. Fourth track is FunAnnotate GFF3 annotation of the HiFi P. cubensis P.envy genome.\n\n\nConclusions\n\nA highly contiguous Psilocybe cubensis genome has been generated. The N50 contigs lengths are 75 fold more contiguous than the existing assembly available at JGI. This reference can aid in the identification of genetic variation that may impact psilocybin, psilocin, norpsilocin, baeocystin, norbaeocystin and aeruginascin production.\n\n\nData availability\n\nGenBank: Psilocybe cubensis strain MGC-MH-2018, whole genome shotgun sequencing project, Accession number JAFIQS000000000.1: https://www.ncbi.nlm.nih.gov/nuccore/JAFIQS000000000.1/.\n\nBioProject: Psilocybe cubensis, Accession number PRJNA687911: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA687911\n\nBioProject: Psilocybe cubensis strain: MGC-MH-2018, Accession number PRJNA700437: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA700437\n\nCoGe genome browser: Psilocybe cubensis (Psilocybe cubensis P.envy), https://genomevolution.org/coge/GenomeInfo.pl?gid=60487",
"appendix": "References\n\nBlei F, Baldeweg F, Fricke J, et al.: Biocatalytic Production of Psilocybin and Derivatives in Tryptophan Synthase-Enhanced Reactions. Chemistry. 2018. PubMed Abstract | Publisher Full Text\n\nBlei F, Dorner S, Fricke J, et al.: Simultaneous Production of Psilocybin and a Cocktail of beta-Carboline Monoamine Oxidase Inhibitors in “Magic” Mushrooms. Chemistry. 2020; 26: 729–734. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChin CS: Human Genome Assembly in 100 Minutes. bioRxiv. 2019. Publisher Full Text\n\nDelcher AL, Salzberg SL, Phillippy AM: Using MUMmer to identify similar regions in large sequence sets. Curr Protoc Bioinformatics. 2003; Chapter 10: Unit 10 13.\n\nDemmler R, Fricke J, Dorner S, et al.: S-Adenosyl-l-Methionine Salvage Impacts Psilocybin Formation in “Magic” Mushrooms. Chembiochem. 2020; 21: 1364–1371. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFricke J, Blei F, Hoffmeister D: Enzymatic Synthesis of Psilocybin. Angewandte Chemie. 2017; 56: 12352–12355. PubMed Abstract | Publisher Full Text\n\nFricke J, Kargbo R, Regestein L, et al.: Scalable Hybrid Synthetic/Biocatalytic Route to Psilocybin. Chemistry. 2020; 26: 8281–8285. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFricke J, Lenz C, Wick J, et al.: Production Options for Psilocybin: Making of the Magic. Chemistry. 2019a; 25: 897–903. PubMed Abstract | Publisher Full Text\n\nFricke J, Sherwood A, Kargbo R, et al.: Enzymatic Route toward 6-Methylated Baeocystin and Psilocybin. Chembiochem. 2019b; 20: 2824–2829. PubMed Abstract | Publisher Full Text\n\nGurevich A, Saveliev V, Vyahhi N, et al.: QUAST: quality assessment tool for genome assemblies. Bioinformatics. 2013; 29: 1072–1075. PubMed Abstract | Publisher Full Text | Free Full Text\n\nJohnson MW, Griffiths RR: Potential Therapeutic Effects of Psilocybin. Neurotherapeutics. 2017; 14: 734–740. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLi H: Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics. 2018; 34: 3094–3100. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLi H, Durbin R: Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics. 2010; 26: 589–595. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLi H, Handsaker B, Wysoker A, et al.: The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009; 25: 2078–2079. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLi WC, Wang TF: PacBio Long-Read Sequencing, Assembly, and Funannotate Reannotation of the Complete Genome of Trichoderma reesei QM6a. Methods Mol Biol. 2021; 2234: 311–329. PubMed Abstract | Publisher Full Text\n\nReynolds HT, Vijayakumar V, Gluck-Thaler E, et al.: Horizontal gene cluster transfer increased hallucinogenic mushroom diversity. Evol Lett. 2018; 2: 88–101. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRobinson JT, Thorvaldsdottir H, Winckler W, et al.: Integrative genomics viewer. Nat Biotechnol. 2011; 29: 24–26. PubMed Abstract | Publisher Full Text | Free 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\nThorvaldsdottir H, Robinson JT, Mesirov JP: Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform. 2013; 14: 178–192. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTorrens-Spence MP, Liu CT, Pluskal T, et al.: Monoamine Biosynthesis via a Noncanonical Calcium-Activatable Aromatic Amino Acid Decarboxylase in Psilocybin Mushroom. ACS Chem Biol. 2018; 13: 3343–3353. PubMed Abstract | Publisher Full Text\n\nWaterhouse RM, Seppey M, Simao FA, et al.: BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics. Mol Biol Evol. 2018; 35: 543–548. PubMed Abstract | Publisher Full Text | Free Full Text"
}
|
[
{
"id": "83396",
"date": "26 Apr 2021",
"name": "Jason C. Slot",
"expertise": [
"Reviewer Expertise Fungal ecology",
"microbial genomics",
"evolution",
"metabolism"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 presents a high quality assembly of the historically and medicinally important fungus, Psilocybe cubensis. Best practices were observed in sequencing, assembly, and annotation. The manuscript notes a potentially important structural variation present in the P. envy strain psilocybin N-methyltransferase gene, which resembles the variation in the more potent, by psilocybin content, Psilocybe cyanescens.\nIs the rationale for creating the dataset(s) clearly described?\nThe study was undertaken in order to provide a high quality reference genome for the species. To date, the genomes in the species and genus are fragmented more than is desirable for basic and applied comparative investigations of genome content and architecture.\nAre the protocols appropriate and is the work technically sound?\nThe Pacific Biosciences Sequel II HiFi methods used for sequencing are among the best for generating near-chromosome level assembly. Assembly was performed with cutting-edge Peregrine Assembler, and the annotation appropriately used the fungus-specific FunAnnotate pipeline. Single nucleotide polymorphisms (SNP) were called with appropriate software, but parameters were not detailed in the text. This and structural variation were not intended to be exhaustive, but provide intriguing statistics and examples to warrant follow-up investigations.\nAre sufficient details of methods and materials provided to allow replication by others?\nParameters for SNP calling would have to be further detailed in order to allow replication of raw SNP numbers between two isolates.\nAre the datasets clearly presented in a useable and accessible format?\nFigure 1 and both tables are clear and informative. Figure 2 readability would be improved by increasing the size of the axis titles. Figure 3 is not sufficiently informative or simple to acquire meaning as it is currently presented. This figure would benefit from marking the \"tracks\" clearly, but number and perhaps with additional labels for RNAseq, P. cyanescens, and annotation as the IGV display is too small to read as is. Is there significance to the locus that is presented in Figure 3? If not, then perhaps indicate it is a \"representative\" locus.\nOther comments:\nThe title might flow better as \"A draft reference assembly of...\".\n\nIn the introduction, \"several mushrooms\" might better be stated \"about 200 mushroom species\".\n\nIn the Introduction \" fungi's \" would be more syntactically correct as \"fungus' \"\n\nGiven that dried stems were used for genomic DNA isolation, it is expected that some additional microbial DNA might be present. Authors should note if the mushroom was produced axenically, or if contaminant reads were filtered to either prevent or address presence of additional species' genomes in the assembly.\n\nCitations are incomplete in the last sentence of \"Assembly and annotation\" section, and second sentence of \"Structural variation\" section.\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? Partly\n\nAre the datasets clearly presented in a useable and accessible format? Partly",
"responses": [
{
"c_id": "6701",
"date": "26 May 2021",
"name": "Kevin McKernan",
"role": "Author Response",
"response": "The reviewer makes excellent points. We will be making these suggested changes to the final manuscript."
}
]
},
{
"id": "83076",
"date": "21 May 2021",
"name": "Anders Goncalves da Silva",
"expertise": [
"Reviewer Expertise Population genetics",
"genotype-chemotype"
],
"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\nMcKernan and colleagues present on the first highly contiguous draft genome for the magic mushroom Psilocybe cubensis. We commend their use of High accuracy long read sequencing and an advanced bioinformatics pipeline to build a much more complete picture of the P. cubensis genome and for making it openly available to the public with the promise the genetic architecture of tryptamine expression in magic mushrooms.\n\nThe methods employed are state of the art and the authors provide sufficient access to the data to enable peers and the public to replicate the experiment. While they acknowledge that the HiFi sequencing approach comes with great advantages, in particular greatly improved contiguity and and BUSCO completeness scores compared to other P. cubensis genomes published to date, the authors did not acknowledge that fungi can have multiple nuclei in a cell, sometimes with completely different haplotypes. As such, we posit that their assembly could possibly be a metagenome assembly, rather than the assembly of a single genome, thus providing an alternative explanation to the large insertion detected in the norbaeocystin methyltranferase (psiM) gene.\nPerhaps a means to provide a remedy to this is to provide some additional background on the P. cubensis Penis Envy (PE) strain, in particular the alleged origin of the PE mutant and its probable clonal propagation. While anecdotal at best, the fabled “mutation” of PE appeared and was selected from a phenotype of an amazonian P. cubensis accession, as a towering fruiting body with a pale cap and missing partial veil, which was then preserved via clonal propagation. The mutant is also described as being more potent that most other P. cubensis strain, leading to the hypothesis that it had a skewed drug to prodrug ratio (psilocyn/psilocybin) which would hint to a mutation in the psiK gene as opposed to the large insertion in psiM.\nOther putative mechanisms could be polymorphisms at other loci involved in the psilocybin biosynthetic pathways as well as ancillary genes involved in the SAM salvage pathway (e.g. ref 1), a list of putative functional SNPs that may interact with the large insertion is shown here from an earlier version of the P.cubensis genome. Genotyping several strains at the 4.6kb insertion and ancillary SNPs may help shed light on the mechanism behind the higher perceived potency of PE compared to other P. cubensis strains and other species in the Psilocybe and Panaeolus genus, In that vein, the authors may gain additional insight by including the P. serbica var bohemica genome to their comparative analysis, provided that chemotypic information associated with each accessions is made available.\nNode Position Target gene Ontogeny NODE_599 19295 sahH S‐adenosyl‐l‐homocysteine hydrolase NODE_599 19304 sahH S‐adenosyl‐l‐homocysteine hydrolase NODE_599 19415 sahH S‐adenosyl‐l‐homocysteine hydrolase NODE_599 19421 sahH S‐adenosyl‐l‐homocysteine hydrolase NODE_599 19744 sahH S‐adenosyl‐l‐homocysteine hydrolase NODE_599 19746 sahH S‐adenosyl‐l‐homocysteine hydrolase NODE_599 20318 sahH S‐adenosyl‐l‐homocysteine hydrolase NODE_599 20779 sahH S‐adenosyl‐l‐homocysteine hydrolase NODE_599 20801 sahH S‐adenosyl‐l‐homocysteine hydrolase NODE_599 20840 sahH S‐adenosyl‐l‐homocysteine hydrolase NODE_6392 313322 samS S‐adenosyl‐l‐methionine synthetase NODE_6392 314122 samS S‐adenosyl‐l‐methionine synthetase NODE_6392 314300 samS S‐adenosyl‐l‐methionine synthetase NODE_712 1234504 metS l‐methionine synthetase NODE_755 63920 psiD tryptophan decarboxylase NODE_755 64575 psiD tryptophan decarboxylase NODE_755 64576 psiD tryptophan decarboxylase NODE_755 65088 psiD tryptophan decarboxylase NODE_755 65181 psiD tryptophan decarboxylase NODE_755 61250 psiM methyltransferase NODE_755 61711 psiM methyltransferase NODE_755 62335 psiM methyltransferase NODE_755 58208 psiT2 major-facilitator-type transporters NODE_755 58407 psiT2 major-facilitator-type transporters NODE_755 58772 psiT2 major-facilitator-type transporters NODE_755 58883 psiT2 major-facilitator-type transporters NODE_755 59054 psiT2 major-facilitator-type transporters NODE_755 59321 psiT2 major-facilitator-type transporters NODE_755 59372 psiT2 major-facilitator-type transporters NODE_755 59426 psiT2 major-facilitator-type transporters NODE_755 59484 psiT2 major-facilitator-type transporters NODE_755 59492 psiT2 major-facilitator-type transporters NODE_755 59504 psiT2 major-facilitator-type transporters NODE_755 59522 psiT2 major-facilitator-type transporters NODE_755 59537 psiT2 major-facilitator-type transporters NODE_755 59540 psiT2 major-facilitator-type transporters NODE_755 59566 psiT2 major-facilitator-type transporters NODE_755 59594 psiT2 major-facilitator-type transporters NODE_755 59648 psiT2 major-facilitator-type transporters NODE_755 59694 psiT2 major-facilitator-type transporters NODE_755 59771 psiT2 major-facilitator-type transporters NODE_755 59869 psiT2 major-facilitator-type transporters NODE_755 59875 psiT2 major-facilitator-type transporters NODE_755 56543 psiH P450 monooxygenase NODE_755 54126 psiK Kinase NODE_755 54132 psiK Kinase NODE_755 54136 psiK Kinase NODE_755 54159 psiK Kinase NODE_755 54213 psiK Kinase NODE_755 54223 psiK Kinase NODE_755 54311 psiK Kinase NODE_755 51932 psiT1 major-facilitator-type transporters NODE_755 52391 psiT1 major-facilitator-type transporters NODE_755 52473 psiT1 major-facilitator-type transporters NODE_755 52477 psiT1 major-facilitator-type transporters NODE_755 52491 psiT1 major-facilitator-type transporters NODE_755 52620 psiT1 major-facilitator-type transporters NODE_755 52688 psiT1 major-facilitator-type transporters NODE_755 52787 psiT1 major-facilitator-type transporters NODE_755 52793 psiT1 major-facilitator-type transporters\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/10-281
|
https://f1000research.com/articles/10-467/v1
|
14 Jun 21
|
{
"type": "Research Article",
"title": "Decaffeinated light-roasted green coffee and green tea extract combination improved metabolic parameters and modulated inflammatory genes in metabolic syndrome rats",
"authors": [
"Mohammad Saifur Rohman",
"Mifetika Lukitasari",
"Dwi Adi Nugroho",
"Risa Ramadhiani",
"Nashi Widodo",
"Inggita Kusumastuty",
"Nur Ida Panca Nugrahini",
"Mohammad Saifur Rohman",
"Dwi Adi Nugroho",
"Risa Ramadhiani",
"Nashi Widodo",
"Inggita Kusumastuty",
"Nur Ida Panca Nugrahini"
],
"abstract": "Background: Individually, green tea and green coffee have been extensively studied for mitigation of metabolic syndrome (MS) in both rats and humans; however, their combined effect requires further investigation. Thus, we compared the metabolic effect of combining green tea and decaffeinated light roasted green coffee on MS in rats. Methods: An MS animal model was constructed by feeding Sprague-Dawley rats with a high-fat-high-sucrose (HFHS) diet for eight weeks and a low dose of streptozotocin (STZ) injection at week 2. Rats fed with HFHS diets and injected with STZ successfully developed MS phenotypes, indicated by higher body weight, systolic blood pressure, plasma triglyceride level, plasma fasting blood glucose level, and lower plasma HDL-C level, compared to those fed with a normal chow diet. Subsequently, MS rats were continuously fed with HFHS and divided into four groups: MS rats, MS with 300 mg/bw.t green tea extract (GT), MS with 200 mg/bw.t green coffee extract (GC), and MS with combined green tea and green coffee extract (CM) for nine weeks. Results: Combining green tea and green coffee have synergistic effects on reducing plasma fasting blood glucose and triglyceride level. Inflammatory markers both in plasma and liver tissue robustly decreased in CM group rats. However, the reduction of systolic blood pressure was observed only in GT and CM groups. Moreover, all treatment resulted in an increase in plasma HDL-C level in MS rats. Conclusions: Our data highlighted that, in MS animal models, combined green tea and decaffeinated light roasted green coffee augment their several individual beneficial effects of improved metabolic parameters and modulated inflammatory genes.",
"keywords": [
"metabolic syndrome",
"green tea",
"green coffee",
"combined extracts"
],
"content": "Introduction\n\nMetabolic syndrome is a global public health concern. The prevalence of this disease is estimated to be about one-quarter of the world population. Metabolic syndrome is a condition that consists of risk factors such as abdominal obesity, increase triglycerides (TG), hyperglycemia, hypertension, and low high-density lipoprotein cholesterol (HDL-C) levels. Individuals with metabolic syndrome have a two to fivefold risk of developing diabetes, cardiovascular disease, stroke, and death from all causes1. The pathogenesis of metabolic syndrome involves the strong interaction of genetic and modifiable risk factors that constitute the metabolic syndrome. Previous studies have shown that nuclear factor-kappa B (NF-kB) signalling is a crucial pathway in chronic low-grade inflammation process and has been studied extensively in the context of obesity and the metabolic syndrome2,3. Management of this disease consists of a dual approach that combines lifestyle modification and pharmacological intervention on those risk factors. During the past decades, various natural compound derived from plant extracts showed a beneficial effect in the management of metabolic syndrome4.\n\nTea, dried leaves of Camellia sinensis, is classified into green, black, and Oolong tea according to its leaf treatment. It contains numerous catechins, mainly epicatechin, epicatechin-3-gallate, epigallocatechin, and epigallocatechin-3-gallate (EGCG)5,6. In recent years, green tea and its constituents have been massively studied for its beneficial health effects, including alleviation of metabolic syndrome. Most of these studies showed green tea extract and its isolated constituents lowered body weight, blood glucose levels, and increased insulin sensitivity in animal models with metabolic syndrome induced either by high-fat diets, insulin resistance, or genetic modification7. A meta-analysis by Zhong et al.8 also revealed that tea extract reduced body mass index (BMI) and body weight in metabolic syndrome patients. Comparable with green tea, green coffee has recently drawn attention due to its health benefit. Green coffee consists of phenolic compounds, such as chlorogenic acids (CGA), and cinnamic acids (caffeic, ferulic or coumaric acid) which are known as protective agents against metabolic syndrome and type 2 diabetes mellitus9. The meta-analysis by Roshan et al.10 and Nikpayam et al.11 showed green coffee administration had an ameliorating effect on metabolic syndrome parameters, such as systolic blood pressure, fasting blood glucose, and homeostatic model of assessment of insulin resistance (HOMA-IR). In addition, both green tea and green coffee have anti-inflammatory action and has been used as functional food for some metabolic disease protection12,13. However, some studies reported drawbacks of green coffee administration due to its caffeine content14–16. Hence, our study used decaffeinated coffee extracts to avoid the disadvantage of caffeine from coffee intake. Moreover, the CGA antioxidant activity is determined by the coffee’s roasting level17,18. Light roasted coffee beans possessed the highest CGA antioxidant activity. Our previous study showed that light roasted green coffee had a beneficial effect on adiponectin and insulin resistance amelioration in metabolic syndrome rat models19. While many studies reported the beneficial effect of green tea or green coffee extract on several diseases, few reported the impact of the combination of these two compounds. A study by Tulp et al.20 showed that natural compounds have shown greater activity when they are present in a mixture. Considering this, our study aimed to investigate the potential effects of green tea and decaffeinated light roasted green coffee combination in metabolic syndrome rats.\n\n\nMethods\n\nAll experimental procedures were approved by the ethical committee of Faculty of Medicine, Brawijaya University with registration number 405/EC/KEP/10/2016. All efforts were made to ameliorate harm to the animals by using the standard protocol from the Indonesian Ministry of Health ethical research guidelines for animal experimental research.\n\nA total of 25 male Sprague Dawley rats aged nine weeks old were obtained from the National Agency of Drug and Food Control, Indonesia. The number of animals was calculated using the Festing formulation21. The study was performed in the Animal Physiology Laboratory, Faculty of Mathematics and Natural Sciences, from March to July 2017. Rats were housed individually in a metabolic cage sized 50 cm x 30 cm x 15 cm at a temperature of 25°C and 40%–70% relative humidity. They were maintained with food and drink ad libitum with 12:12 hour light-dark cycle. After one week of acclimatization, the healthy rats were randomized using Excel (=RAND function) to determine their diet - either normal chow, high fat, or high sucrose (HFHS) diet - for the 17 weeks duration of the experimental protocol. On the 2nd week of the protocol, the HFHS fed rats were induced by a single intraperitoneal injection of streptozotocin (STZ) (bioWORLD cat.41910012-4) (30 mg/ kg B.W.). These procedures were performed in order to get experimental an animal model that represented the features of human metabolic syndrome. The experimental animals were not blinded during this study. The animals were fasted for 8-10 hours prior to blood drawing. The blood (0.5 ml) was obtained from the rats’ tail and then centrifuged with 4500 rpm for 15 minutes to get the serum. The fasting blood glucose, triglyceride, and HDL level were determined by GOD-PAP, GPO, and indirect methods, respectively (BIOLABO cat LP80209 for glucose level determination, cat 80019 for triglyceride level determination, cat 86536 and cat 80106 for HDL level determination). Animals with fasting blood glucose levels over 126 mg/dl, triglyceride level over 150 mg/dl, systolic blood pressure over 140 mmHg, and HDL cholesterol lower than 40 mg/dl were considered to have metabolic syndrome, based on NCEP-ATP III criteria22. Five rats were assigned to normal chow without STZ injection (NC). The metabolic syndrome rats were weight-matched distributed into four experimental groups (five rats/group) (i) HFHS and STZ injection (MS), (ii) HFHS, STZ injection, and green tea extract at 300 mg/kg B.W. (GT), (iii) HFHS, STZ injection, and green coffee extract at 200 mg/kg B.W. (GC), and (iv) HFHS, STZ injection, and combination extract of green tea and green coffee at 300 mg/kg and 200 mg/kg B.W, respectively23. The doses of the extract were obtained from our previous studies19,24,25. The dose of extract was given in millilitres based on weekly measured body weight and given via oral gavage daily. The food and water intake were recorded daily. The sacrifice procedures were explained as follows: (1) The rats were fasted for 12 hours; (2) After that, the rats were anesthetized by diethyl ether prior to the euthanasia in order to prevent painful euthanasia ; (3) After the rats being anesthetized, they were euthanised by cervical decapitation. (4) Immediately after the rats died the blood was drawn from the heart into a microcentrifuge tube; (5) The hepatic tissues were obtained from the right lobe. Serum samples were obtained by centrifugation at 4,000 x g for 15 minutes at 4°C.\n\nThe coffee bean was obtained from Dampit coffee plantation, Malang, Indonesia (800 MAMSL). An automatic coffee roaster (N500i) light roasted Coffea canephora var robusta at 180-200°C until the first crack. Furthermore, the coffee bean was mashed with a coffee grinder and then macerated by ethanol 95% to produce the crude extract. The ethanol solvent is used due to its polar feature that could attract the active compounds contained in the green coffee bean. Furthermore, the crude extract was filtered using a filter cloth to separate the liquid phase from the solid phase. Moreover, the liquid phase was concentrated using a rotary evaporator (RV10 autoV, IKA) at ±40°C. Finally, column chromatography completed using silica gel C18 17% (SiliaBond® C18, SiliCycle Inc) as a static phase to reduce the caffeine content, to attract more CGA, and to separate them from other substances, and then the filtered product was evaporated18,26.\n\nThe green tea was obtained from Sukawana green tea plantation, Bandung, Indonesia (1550 MAMSL). The second and third uppermost young green tea leaves were extracted. Green tea leaf weighing 500 grams was dried using a cabinet dryer (temperature of 50° C) for 8 hours to obtain green tea with 8 – 10% water content was measured using gravimetric analysis. The green tea was mashed with a blender and then boiled at 80°C for 30 minutes. The crude extract was filtered using a filter cloth to separate the liquid phase from the solid phase. The liquid phase was concentrated using a rotary evaporator at the temperature of ±40°C. Finally, column chromatography completed using silica gel C18 17% (SiliaBond® C18, SiliCycle Inc) as a static phase to attract bioactive compounds and to separate them from other substances, and then the filtered product was evaporated27,28.\n\nFor the determination of caffeine and chlorogenic acid levels in the coffee, and epigallocatechin gallat level in the green tea, 1 gram of extract was diluted with 100 mL of distilled water. The HPLC analysis was performed using a Shimadzu Brand chromatograph (model SCL10AVP, Japan) that set up with a C-18 reverse-phase column (Shim-pack VP ODS 5μm 150 x 4,6 mm). The HPLC was paired to a UV/visible spectrophotometric detector (SPD-20-A UV Vis Detector) then connected by an interface (CBM-101) to a microcomputer for data processing. The protocol for analysis were as follows: (1) flow (1 mL/ min for caffeine and chlorogenic acid and 0,45 ml/min for epigallocatechin); (2) mobile phase method using isocratic method with 25% methanol for caffeine and chlorogenic acid and 0,1% TFA in acetonitrile for epigallocatechin; (3) static phase silica C18 with column temperature 25°C; (4) 10 μL of injection volume for caffeine and chlorogenic acid and 1 μL for epigallocatechin ; (5) the wavelength detection at 272 nm for caffein, 324 nm for chlorogenic acid, and 280 nm for epigallocatechin; (6) run time 15 minutes for caffeine, 30 minutes for chlorogenic acid, and 20 minutes for epigallocatechin. The concentrations of the compounds were determined with standard concentration curves.\n\nDecaffeinated light roasted Green coffee extract and green tea extract doses were determined from the previous study in our laboratory. The optimum dose was 300 mg/bw.t for green tea extract and 200 mg/bw.t for green coffee extract19,24,25. Daily food intake and fluid intake was measured every day, and body weight was measured every week. The food and fluid intake for each rat was measured by subtracting the measured amount provided by the remaining amounts in the cage.\n\nThe serum concentrations of fasting glucose (BIOLABO, cat no. 80009), triglycerides (TG) (cat no. 80019), and HDL-Cholesterol (BIOLABO, cat no. 86516) were measured enzymatically using commercial kits. C-Reactive Protein (Elabscience cat no. E-EL-R0506) and TNF-a (Elabscience cat no. E-EL-R0019) were analyzed by enzyme-linked immunosorbent assay (ELISA).\n\nBlood pressure was measured using the tail-cuff method with a sphygmomanometer technique (Ugo Basile 58500) at the baseline and the end of the experiment. Three readings are taken consecutively, and the average was then calculated and taken as a final reading for SBP.\n\nTotal RNA of liver tissues was isolated using the Easy Blue (Intron Biotechnology, cat no. 17061) according to the manufacturer's protocol. Reverse transcription reaction was performed using a ReverTra Ace-α kit (Toyobo, FSK-101). Then the RNA expression levels were carried out using PCR Light Cycler 96 system (Takara, cat no. TP600) using a GoTaq Green Master PCR Kit (Promega, cat no, M7822) according to the manufacturer's protocols. Primer sequences were as follows: B-actin, forward:5´- TGA GAG GGA AAT CGT GCG TGA CAT-3´ and reverse: 5´-ACC GCT CAT TGC CGA TAG TGA TGA-3´; NF-KB, forward:5´-AAC GCA TCC CAA GGT GCT GGA A-3´ and reverse: 5´- GCA GCT GGA AAA GCT CAA GCC A-3´; TNF-α, forward:5´-CGT CAG CCG ATT TGC CAT TTC-3´ and reverse: 5´-TGG GCT CAT ACC AGG GCT TG-3´; IL-6, forward:5´- CCC AAC TTC CAA TGC TCT CCT AAT-3´ and reverse: 5´-GCA CAC TAG GTT TGC CGA GTA GA-3´. The PCR cycling conditions were as follows: 5 min at 95 °C; 35 cycles of 30 s at 95 °C, 30 s of annealing at 52.7°C, 52.7°C, 54.7°C, and 55 °C for NF-KB, TNF-α, IL-6 respectively, followed by extension for 30 s at 72 °C; and a final extension for 10 min at 72°C. The mRNA levels were quantified using spectrophotometer at 260 nm and 280 nm. of the target genes normalized to the expression level of β-actin.\n\nFor assessing TNF-α and CRP secretion, the blood of the rats collected and serum separated by centrifugation. Serum TNF-α and CRP concentrations were measured using an enzyme-linked immunosorbent assay according to the manufacturer's instructions (Elabscience E-EL-R0019 and E-EL-R0022 respectively). The optical density (OD) value was read by ELISA reader machine (Biotek ELx808) and the standard curve was generated to get the formula for TNF-α and CRP quantification. Measurements performed were in two replicates. The results presented are as ng/ml.\n\nThe experimental unit was a group of animals and the data obtained was presented in the form of the mean value and standard error of mean (SEM) calculated with GraphPad Prism 8.3.1 software. An independent t-test was used to analyze two of the tested group. Statistically significant differences were defined as p<0.05.\n\n\nResults\n\nAccording to HPLC analysis, the concentration of epigallocatechin-3-gallate in our green tea extract was 74,126 µg/g. While the concentration of chlorogenic acid and caffeine, and polyphenols in green coffee, was 27,134 and 43,473 µg/g green coffee extract, respectively29.\n\nAssessment of body weight, systolic blood pressure, fasting blood glucose level, triglyceride and HDL cholesterol plasma level of combination HFHS diet and a low dose of STZ injection revealed the presence of metabolic syndrome symptoms as classified by the NCEP-ATP III criteria. We observed higher body weight, systolic blood pressure, fasting blood glucose level, triglyceride plasma levels and lower plasma levels of HDL cholesterol in rats that received HFHS diet and STZ injection compared to control rats (Figure 1a and b), as expected.\n\n(a) Schematic diagram of study’s experimental design. (b) Body weight, systolic blood pressure, fasting blood glucose, triglyceride level and HDL cholesterol level at 8 weeks. (c) Body weight before extract administration (above) and after 9 weeks administration (above, below). (d) Food intake and food efficiency ratio after 9 weeks intervention. Data are expressed as mean ± SEM (N=4-5). *P<0.05, **P<0.01, ***P<0.001, ****P<0.0001 compared with NC.\n\nThen, during the nine following weeks, the rats that met NCEP-ATP III criteria were subjected to HFHS alone or HFHS with 300 mg/BW of green tea extract (GT), 200 mg/BW of decaffeinated light roasted green coffee extract (GC), and combination of those extracts (CM) (Figure 1a).\n\nAt the end of the intervention, all HFHS-fed- and STZ-injected rats had significantly lower body weight compared to normal chow-fed rats (Figure 1c). Additionally, all metabolic syndrome rats consumed more food (Figure 1d). These results indicate that the food efficiency ratio (weight gain/food intake) of all STZ-treated animals was significantly lower (***p<0.001, ****p<0.0001) compared to that of normal chow-fed rats (Figure 1d).\n\nAll supplemented metabolic syndrome rats presented reduced systolic blood pressure (Figure 2a). Green tea and combination of green tea and green coffee could significantly reduce the (*p<0.05) blood pressure after nine weeks of administration; however, the blood pressure of decaffeinated light roasted green coffee only-treated rats was not significantly different compared to their blood pressure before the intervention. Interestingly, compared to the metabolic syndrome rats (MS) group, the green tea extract (GT) group had the lowest systolic blood pressure. Moreover, the green tea treated rats' blood pressure was similar to those in normal chow-fed rats. These results suggest that green tea aloneor could significantly improve the systolic blood pressure of metabolic syndrome rats.\n\nSystolic blood pressure (a) and fasting blood glucose (b) before extract administration (left) and after 9 weeks extract administration (left, right). Data are expressed as mean ± SEM (N=4-5). *P<0.05, **P<0.01, ***P<0.001, ****P<0.0001 compared with NC. #P<0.05, ##P<0.01, ###P<0.001, ####P<0.0001 compared with MS. ††P<0.01 compared with GT. $$P<0.01 compared with GC.\n\nAll treatments successfully lowered the fasting blood glucose (FBG) levels in rats (Figure 2b). Compared to the blood glucose level before the intervention, only green tea-treated and combination-treated rats demonstrated a significant reduction in FBG. Although the FBG of every treated rat was significantly higher compared to its on normal chow group, combining green tea and green coffee could dramatically lower the fasting blood glucose among the treatment group. In general, green tea and decaffeinated light roasted green coffee combination could improve fasting blood glucose.\n\nCompared to levels before the intervention, all given extracts could significantly reduce triglyceride (TG) levels (*p<0,05) and improve HDL cholesterol levels (HDL-C) (*p<0.05, **p<0.01) (Figure 3a and 3b). After nine weeks of administration, only CM group rats had significantly reduced TG level compared to MS group rats, also, those rats had the lowest TG levels. In contrast, all treated rats had significantly higher HDL-C levels compared to metabolic syndrome rats. These data illustrated that the combined extract group had an improved the lipid profile.\n\nTriglyceride (a) and HDL cholesterol level (b) before extract administration (left) and after 9 weeks extract administration (left, right). Data are expressed as mean ± SEM (N=4-5). *P<0.05, **P<0.01, ***P<0.001, ****P<0.0001 compared with NC. #P<0.05, ##P<0.01, ###P<0.001, ####P<0.0001 compared with MS. ††P<0.01 compared with GT. $P<0.05 compared with GC.\n\nThe intervention rats showed a reduction of inflammatory markers in plasma and liver tissue compared to MS rats (Figure 4a and 4b). The combined extract-treated rats had the lowest plasma level of TNFα. Moreover, those rats also had the lowest relative mRNA expression of NF-kB, TNFα, and IL-6 in liver tissue, suggesting green tea and decaffeinated light roasted green coffee synergistically reduced inflammatory markers in both plasma and liver tissue\n\n(a) The plasma level of C-reactive protein (CRP) (above) and TNFα level (below). (b) Relative mRNA expression of NF-κB, TNFα, and IL-6 of liver tissue. Data are expressed as mean ± SEM (N=4-5). *P<0.05, **P<0.01, ***P<0.001, ****P<0.0001 compared with NC. #P<0.05, ##P<0.01, ###P<0.001, ####P<0.0001 compared with MS. †P<0.05, ††P<0.01 compared with GT. $P<0.05, $$P<0.01 compared with GC.\n\n\nDiscussion\n\nIn agreement with the previous literature30,31, we showed that the administration of green tea extract was sufficient to reduce blood pressure by 19%, which was similar to normal chow group. In contrast to green tea treatment, we did not find any differences in measured blood pressure before and after green coffee extract supplementation alone. Coffee contains many pharmacologically active components that inhibit the anti-hypertensive effect of antioxidative polyphenol, chlorogenic acid, such as hydroxy hydroquinone (HHQ)32. We did not fractionate the green coffee extract to eliminate HHQ, thus, this leads us to hypothesize that HHQ might inhibit the hypotensive effect of green coffee extract. Interestingly, the addition of green tea extract to light roasted green coffee extract was shown to help lower blood pressure compared to that of animals treated with decaffeinated light roasted green coffee extract only, suggesting that green tea extract exerts a more favourable influence on blood pressure.\n\nCompared to metabolic syndrome rats, our study showed either green tea or decaffeinated light roasted green coffee supplementation after nine weeks was sufficient to decrease fasting blood glucose and plasma triglyceride (TG) levels, and these results are supported by previous studies33,34. Unlike the plasma TG levels, findings on the potential effects of tea on HDL-C are mixed. Some studies reported null effects35,36, whereas some showed a significant increase5. However, few investigate the effect of green coffee on plasma HDL-C level. Here, our study presented green tea or green coffee extract alone after nine weeks of administration significantly increased plasma HDL-C level which was similar to normal chow-fed mice. Moreover, we showed that a synergistic effect was not found for the plasma HDL-C levels.\n\nMany studies reported that metabolic syndrome may induce and may be caused by low-grade chronic inflammation that can be detected systematically and within affected tissues, such as adipose tissue, liver, and vasculature37–39. As shown in the present study, both levels of systemic markers of inflammation, including C-reactive protein (CRP) and TNFα, and relative mRNA expression of NF-kB, TNFα, and IL-6 of liver tissue were increased in metabolic syndrome model rats. The liver plays a pivotal role in glucose and lipid homeostasis. Hepatic steatosis and its inflammatory state (steatohepatitis) are closely related to metabolic syndrome40. A recent review has established the critical role of NF-kB on the liver for the development of insulin resistance41. Chronic inflammation activation by NF-kB in the liver activates IKK-β in hepatocytes that exhibit hepatic and systemic insulin resistance, as expected, hepatic overexpression of IkBα, a repressor of NF-kB signalling, reverses the phenotype42.\n\nRecent reviews showed that targeting inflammation in chronic disease may be beneficial in metabolic disorders43,44. While only focusing on inflammation may be harmful to metabolic conditions due to potential immunosuppression, a review suggested anti-inflammatory nutritional intake as a new alternative in modulating metabolism and inflammation45. Several studies have revealed that green tea and green coffee reduced inflammatory markers in animal models12,46–48. Similar to those studies, we demonstrated that green tea or green coffee alone decreased plasma CRP and TNFα levels. Moreover, decreased mRNA expression level of inflammatory genes in the liver was found in rats treated with green tea or green coffee supplementation. Combining those compounds exacerbated the reduction of plasma TNFα and transcription of NF-kB, TNFα, and IL-6. Previous studies have shown that targeting hepatic inflammation by specific deletion of downstream NF-kB signalling, IKK-β and p65, shows an improvement in glucose homeostasis49,50. However, both studies showed that the improvement in insulin sensitivity is limited to the liver. Mice with IKK-β deletion in hepatocytes exhibited liver insulin sensitivity, but insulin resistance in muscle and fat in response to a high-fat diet49. Together these studies conclude that hepatic inflammation contributes to the development of the metabolic disorder, however, further detailed studies are needed to elucidate the beneficial effect of targeting inflammation in the liver.\n\nThere are some limitations to this study. First, we did not have data regarding inflammation profiles on other affected tissues, such as adipose tissue, which is directly associated with metabolic syndrome. Second, we could not establish a molecular mechanism for the beneficial effects of combined green tea and green coffee.\n\n\nConclusion\n\nIn our data highlight that, in metabolic syndrome rats, the combination of green tea and decaffeinated light roasted green coffee ameliorate hepatic inflammatory through suppression of NF-kB, TNFα, and IL-6 gene expression have synergistic metabolic and anti-inflammatory effects.\n\n\nData availability\n\nFigshare: Data for Combination Green Tea and Green Coffee Extract on Inflammatory in Metabolic Syndrome Rat Model. https://doi.org/10.6084/m9.figshare.13249163.v329.\n\nThis project contains the following underlying data:\n\n- Data of Metabolic Syndrome Rat Model.xlsx (This file contains the analysed data)\n\n- RAW data metabolic syndrome.xlsx (This file contains the actual observed values of the variables)\n\n- Chlorogenic acid Coffee HPLC.pdf (This file contains the value of coffee chlorogenic acid levels as measured by HPLC)\n\n- Caffeine coffee HPLC.pdf (This file contains the value of coffee caffeine levels as measured by HPLC)\n\n- Green Tea Cathecin HPLC.pdf (This file contains the value of the catechin levels in the tea)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "Acknowledgments\n\nThanks for Medical faculty of Brawijaya University, Molecular Biology Laboratory of Department of Biology Mathematics and Natural Sciences of Brawijaya University, and Ministry of Research, Technology, and Higher Education of the Republic of Indonesia.\n\n\nReferences\n\nAhsan F: JSM Human Nutrition and Food Science Metabolic Syndrome: Cluster of Diseases. JSM Human Nutri Food Sci. 2019; 5: 8. Reference Source\n\nCatrysse L, van Loo G: Inflammation and the Metabolic Syndrome - The Tissue-Specific Functions of NF-κB. Trends Cell Biol. 2017; 27(6): 417–29. PubMed Abstract | Publisher Full Text\n\nPatel H, Patel VH: Inflammation and Metabolic Syndrome: An Overview. Curr Res Nutr Food Sci. 2015; 3(3): 263–8. Publisher Full Text\n\nRochlani Y, Pothineni NV, Kovelamudi S, et al.: Metabolic syndrome: Pathophysiology, management, and modulation by natural compounds. Ther Adv Cardiovasc Dis. SAGE Publications Ltd; 2017; 11(8): 215–25. 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PubMed Abstract | Publisher Full Text\n\nShimoda H, Seki E, Aitani M: Inhibitory effect of green coffee bean extract on fat accumulation and body weight gain in mice. BMC Complement Altern Med. 2006; 6: 9. PubMed Abstract | Publisher Full Text | Free Full Text\n\nUeda-Wakagi M, Nagayasu H, Yamashita Y, et al.: Green tea ameliorates hyperglycemia by promoting the translocation of glucose transporter 4 in the skeletal muscle of diabetic rodents. Int J Mol Sci. 2019; 20(10): 2436. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAhmad RS, Butt MS, Sultan MT, et al.: Preventive role of green tea catechins from obesity and related disorders especially hypercholesterolemia and hyperglycemia. J Transl Med. 2015; 13: 79. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHamdaoui MH, Snoussi C, Dhaouadi K, et al.: Tea decoctions prevent body weight gain in rats fed high-fat diet; black tea being more efficient than green tea. J Nutr Intermed Metab. 2016; 6: 33–40. Publisher Full Text\n\nGuarner V, Rubio-Ruiz ME: Low-Grade Systemic Inflammation Connects Aging, Metabolic Syndrome and Cardiovascular Disease. Interdiscip Top Gerontol. 2015; 40: 99–106. PubMed Abstract | Publisher Full Text\n\nLumeng CN, Saltiel AR: Inflammatory links between obesity and metabolic disease. J Clin Invest. 2011; 121(6): 2111–7. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRomeo GR, Lee J, Shoelson SE: Metabolic Syndrome, Insulin Resistance, and Roles of Inflammation - Mechanisms and Therapeutic Targets. Arterioscler Thromb Vasc Biol. 2012; 32(8): 1771–6. PubMed Abstract | Publisher Full Text | Free Full Text\n\nYang KC, Hung HF, Lu CW, et al.: Association of Non-alcoholic Fatty Liver Disease with Metabolic Syndrome Independently of Central Obesity and Insulin Resistance. Sci Rep. 2016; 6: 27034. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCatrysse L, van Loo G: Inflammation and the Metabolic Syndrome: The Tissue-Specific Functions of NF-κB. Trends Cell Biol. 2017; 27(6): 417–29. PubMed Abstract | Publisher Full Text\n\nCai D, Yuan M, Frantz DF, et al.: Local and systemic insulin resistance resulting from hepatic activation of IKK-beta and NF-kappaB. Nat Med. 2005; 11(2): 183–90. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDonath MY: Targeting inflammation in the treatment of type 2 diabetes: Time to start. Nat Rev Drug Discov. 2014; 13(6): 465–76. PubMed Abstract | Publisher Full Text\n\nGoldfine AB, Shoelson SE: Therapeutic approaches targeting inflammation for diabetes and associated cardiovascular risk. J Clin Invest. 2017; 127(1): 83–93. PubMed Abstract | Publisher Full Text | Free Full Text\n\nvan den Brink W, van Bilsen J, Salic K, et al.: Current and Future Nutritional Strategies to Modulate Inflammatory Dynamics in Metabolic Disorders. Front Nutr. Frontiers Media S.A.; 2019; 6: 129. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCaro-Gómez E, Sierra JA, Escobar JS, et al.: Green coffee extract improves cardiometabolic parameters and modulates gut microbiota in high-fat-diet-fed ApoE -/- mice. Nutrients. 2019; 11(3): 497. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCialdella-Kam L, Ghosh S, Meaney MP, et al.: Quercetin and green tea extract supplementation downregulates genes related to tissue inflammatory responses to a 12-week high fat-diet in mice. Nutrients. 2017; 9(7): 773. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLu C, Zhu W, Shen CL, et al.: Green tea polyphenols reduce body weight in rats by modulating obesity-related genes. PLoS One. 2012; 7(6): e38332. PubMed Abstract | Publisher Full Text | Free Full Text\n\nArkan MC, Hevener AL, Greten FR, et al.: IKK-beta links inflammation to obesity-induced insulin resistance. Nat Med. 2005; 11(2): 191–8. 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}
|
[
{
"id": "92580",
"date": "06 Sep 2021",
"name": "Alex Boye",
"expertise": [
"Reviewer Expertise Pharmacology",
"natural product pharmacology",
"toxicology",
"cancer pharmacotherapy"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 authors investigated how a combination therapy comprising extracts of de-caffeinated light-roasted green coffee and green tea influence metabolic parameters and pro-inflammatory factors in a rat model of metabolic syndrome. I find the study to be interesting and relevant in the specific topic area. Nonetheless, the study will benefit from the following:\nThe title needs to capture the key metabolic factors as well as the name of the chemical used to induce metabolic syndrome in the rats.\n\nAuthors should avoid personalizing the study by limiting or better still avoid use of “we, our, us etc”.\n\nDose of STZ administered at week 2 should be mentioned in the abstract.\n\nLanguage should be improved throughout manuscript.\n\nAuthors should replace “constructed” with “established” in the abstract, line 6.\n\nThese factors (systolic blood pressure, plasma triglyceride level, plasma fasting blood glucose level) on their own do not represent phenotypes of MS, rather elevated levels of these factors.\n\nWhat was the dose of “combined green tea and green coffee extract (CM)“?\n\nLight roasted coffee should be hyphenated, i.e., light-roasted coffee. Use this throughout manuscript.\n\n“Drink” replace with “water”.\n\nImprove “…to get experimental an animal model that represented…“\n\n“with 4500 rpm “should be “at 4500 rpm“.\n\nHow was MS confirmed in rats?\n\nImprove “STZ injection, and combination extract of green tea and green coffee at 300 mg/kg and 200 mg/kg B.W, respectively“.\n\nState the dose of diethyl ether used to induce anesthesia.\n\nItalize Coffea canephora.\n\nCheck this “gallat“ should be “gallate”.\n\nThe organization of the “materials and method” section should reflect the order in which experiments were conducted. For example, collection, and preparation of extracts preceded animal studies.\n\nImprove the statistical analysis subsection. State how parameters measured were presented in figures and tables, mean ± s.e.m or SD. State the statistical software used in the analysis of data and its source (manufacturer, country of origin). State the specific statistic that were measured for comparison among groups (control and treatment groups). Follow convention by stating the P-value at which differences in mean was considered statistically significant.\n\nBoth language and results reporting under the results section need to be improved.\n\nProvide HPLC chromatogram for the two extracts as part of the results.\n\nPlease, avoid use of “we, our, us etc” throughout manuscript.\n\nImprove the discussion, e.g., “Coffee contains many pharmacologically active components that inhibit the anti-hypertensive effect of antioxidative polyphenol, chlorogenic acid, such as hydroxy hydroquinone (HHQ)32.“\n\nRewrite the conclusion by improving language. Also, it should advance future direction of the topic area while reflecting on the key findings of the current study.\n\nConsider replacing reference numbers 14 and 18, with a recent one if possible.\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": []
},
{
"id": "94464",
"date": "16 Sep 2021",
"name": "Nelly Mayulu",
"expertise": [
"Reviewer Expertise Functional Food",
"Natural Product",
"Non-communicable Diseases",
"Food and Nutrition",
"Antioxidants",
"Polyphenols"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 presents the results of Decaffeinated light-roasted green coffee and green tea extract combination to improve metabolic parameters and modulated inflammatory genes in metabolic syndrome rats. Interesting research, but the writing needs to be improved, as follows:\n1. In the abstract please state how many mice were used in total and in each group.\n2. In the abstract, state how many doses are used for STZ injection?\n3. In the abstract, the results for C-reactive protein (CRP), NF-κB, TNFα, and IL-6 have not been mentioned, please add them in the abstract.\n4. In the Methods: Biochemical analysis and ELISA section, the detailed kit of IL-6 and NF-κB has not been mentioned.\n5. High fat, or high sucrose (HFHS) diet needs to be clarified the percentage content of the feed (e.g. what percentage of fat and what percentage of sucrose, referring to which research HFHS is used?).\n6. The analysis of the levels of chlorogenic acid and caffeine, and polyphenols (epigallocatechin gallate) in green coffee using HPLC was carried out how many times it was repeated? Duplo? Triplicate? If there is please provide SD (Standard Deviation).\n7. Writing the Latin name of the species, please pay attention again (italics).\n8. Pay attention to the writing in the \"Isolation of total RNA and RT-PCR\" section, please correct the last sentence, (of the target genes normalized to the expression level of -actin).\n9. In the discussion, add references to the benefits of epigallocatechin-3-gallate and polyphenols in green coffee which are thought to contribute to having synergistic metabolic and anti-inflammatory effects.\n10. Why don't you test the levels on the combination of the two mixed extracts (Combination of Green Tea and Green Coffee Extract)?\nI recommend to be indexed after some improvements.\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": []
}
] | 1
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https://f1000research.com/articles/10-467
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https://f1000research.com/articles/10-233/v1
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24 Mar 21
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{
"type": "Systematic Review",
"title": "SARS-CoV-2 and the role of fomite 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 has been detected in fomites which suggests the virus could be transmitted via inanimate objects. However, there is uncertainty about the mechanistic pathway for such transmissions. Our objective was to identify, appraise and summarise the evidence from primary studies and systematic reviews assessing the role of fomites in 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, and Google Scholar; assess study quality based on five criteria and report important findings on an ongoing basis. Results: We found 64 studies: 63 primary studies and one systematic review (n=35). The settings for primary studies were predominantly in hospitals (69.8%) including general wards, ICU and SARS-CoV-2 isolation wards. There were variations in the study designs including timing of sample collection, hygiene procedures, ventilation settings and cycle threshold. The overall quality of reporting was low to moderate. The frequency of positive SARS-CoV-2 tests across 51 studies (using RT-PCR) ranged from 0.5% to 75%. Cycle threshold values ranged from 20.8 to 44.1. Viral concentrations were reported in 17 studies; however, discrepancies in the methods for estimation prevented comparison. Eleven studies (17.5%) attempted viral culture, but none found a cytopathic effect. Results of the systematic review showed that healthcare settings were most frequently tested (25/35, 71.4%), but laboratories reported the highest frequency of contaminated surfaces (20.5%, 17/83). Conclusions: The majority of studies report identification of SARS-CoV-2 RNA on inanimate surfaces; however, there is a lack of evidence demonstrating the recovery of viable virus. Lack of positive viral cultures and variation in cycle thresholds create uncertainty about fomites as a mode of transmission. Heterogeneity in study designs and methodology prevents comparisons of findings across studies. Standardized guidelines for conducting and reporting research on fomite transmission is warranted.",
"keywords": [
"Fomites",
"transmission",
"COVID-19",
"systematic review"
],
"content": "Introduction\n\nThe SARS-CoV-2 (COVID-19) pandemic is a major public health concern. According to WHO statistics, there have been over 90 million confirmed cases and over two million deaths globally as of 18th January 20211. Although many national governments have implemented control measures and vaccines are now being approved and administered, the rate of infection has not subsided as anticipated. Understanding the modes of transmission of SARS-CoV-2 is critical to developing effective public health and infection prevention measures to interrupt the chains of transmission2. Current evidence suggests SARS-CoV-2 is primarily transmitted via respiratory droplets and direct contact3, but other transmission routes have been suggested – aerosol and fomites.\n\nWhile the respiratory, airborne, and direct contact modes of transmission have been investigated in detail, the role of fomites in the transmission of SARS-CoV-2 is less clear. Findings from previous systematic reviews have shown that viruses from the respiratory tract, such as coronaviridae, can persist on inanimate surfaces for some days4, and it has been reported that SARS-CoV-2 can be transmitted indirectly through fomites or surfaces5. However, some authors have suggested that there is a low risk of transmission of SARS-CoV-2 through fomites6,7 and others have suggested that the risk of such transmission is exaggerated8.\n\nSeveral studies investigating the role of fomites in SARS-CoV-2 are now being published but the evidence from such studies has not been systematically evaluated. The objective of this review was to identify, appraise and summarize the evidence from primary studies and systematic reviews investigating the role of fomites in the transmission of SARS-CoV-2. Terminology for this article can be found in Box 1.\n\n\n\n1World Health Organization. Q&A: How is COVID-19 transmitted? https://www.who.int/vietnam/news/detail/14-07-2020-q-a-how-is-covid-19-transmitted\n\n2https://www.cebm.net/covid-19/sars-cov-2-viral-load-and-the-severity-of-covid-19/\n\n3https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7521909/\n\n\nMethods\n\nWe are undertaking an open evidence review investigating factors and circumstances that impact on the transmission of SARS-CoV-2, based on our published protocol last updated on the 1 December 2020 (archived protocol: Extended data: Appendix 19; original protocol: https://www.cebm.net/evidence-synthesis/transmission-dynamics-of-covid-19/). Briefly, this review aims to identify, appraise, and summarize the evidence (from studies peer-reviewed or awaiting peer review) relating to the role of fomites in the transmission of SARS-CoV-2 and the factors influencing transmissibility. We conducted an ongoing search in WHO Covid-19 Database, LitCovid, medRxiv, and Google Scholar for SARS-CoV-2 for keywords and associated synonyms. The searches for this update were conducted up to 20th December 2020. No language restrictions were imposed (see Extended data: Appendix 2 for the search strategies9).\n\nWe included studies of any design that investigated fomite transmission. Predictive or modelling studies were excluded. Results were reviewed for relevance and for articles that looked particularly relevant, forward citation matching was undertaken and relevant results were identified. We assessed the reporting quality of included studies using five domains from the QUADAS-2 criteria10; we adapted this tool because the included studies were not designed as diagnostic accuracy studies. We extracted the following information from included studies: study characteristics, 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 where reported. We also extracted information on viral cultures including the methods. One reviewer (IJO) assessed the risk of bias and extracted data from the included studies, and these were independently checked by a second reviewer (EAS). We presented the results in tabular format, and bar charts used to present the frequency of positive tests. Because of substantial heterogeneity across the included studies, we did not perform a meta-analysis.\n\n\nResults\n\nWe identified 709 non-duplicate citations of which 91 were considered eligible (Figure 1). We excluded 27 full-text studies because they did not meet our inclusion criteria (see Extended data: Appendix 39 for the list of excluded studies and reasons for exclusion). Finally, we included 64 studies: 63 primary studies and one systematic review (see Extended data: Appendix 4; characteristics of studies in Table 1 and Table 29).\n\nNone of the included studies were linked to or mentioned a published protocol. The risk of bias of the included studies is shown in Table 4. Less than half of the studies (47.6%) adequately reported the methods used, and none used methods to minimise bias. The overall quality of the studies was rated low to moderate (see Figure 2).\n\nWe found one “systematic review” investigating the role of fomites [Bedrosian 2020] (Table 2). The authors searched two electronic sources - articles were last downloaded on July 10, 2020. There was no published protocol, and the authors did not assess the quality of included studies. A total of 35 relevant studies were included. Over half of the studies (25/35, 75%) were conducted in healthcare settings, and four compared environmental contamination before and after standard disinfection procedures. No study assessed viral infectivity or viability, but all tested the presence or absence of SARS-CoV-2 RNA.\n\nWe found 63 primary studies (Table 1). In general, the studies did not report any hypothesis but investigated epidemiological or mechanistic evidence for fomite transmission. Forty-one studies (65.1%) were conducted in Asia, 15 (23.8%) in Europe, five (7.9%) in North America, and one each in Africa and South America (1.6% each). A total of 44 studies were conducted exclusively in hospital settings, two in hospital and quarantine facilities, three in the laboratory, and the remaining in other non-healthcare settings (public places, community, banknotes, workplace, cruise ship, quarantine rooms and hospital outdoors). Four studies were conducted exclusively in ICU and another three in ICU plus hospital wards. Five studies used before and after study design.\n\nIn 59 studies (96.7%), fomite transmission was examined in high-frequency touch surfaces (Table 1); the remaining four studies examined circulating banknotes (1), disposable chopsticks (1) hospital staff PPE (1), and unspecified (1). The timing and frequency of sample collection and disinfection procedures were heterogeneous across studies (see Table 3). Fourteen studies (23%) performed sample collection before disinfection procedures, five studies collected samples before and after disinfection procedures, while 11 studies collected samples after disinfection. In 33 studies, the timing of sampling in relation to disinfection was not specified. In one study [Ryu 2020], disinfection procedures were not performed as required because of a lack of PPE and staff being afraid of contracting SARS-CoV-2. The number of samples per study ranged from five [Jin 2020] to 5400 [Marshall 2020].\n\nEleven studies (17.5%) set out to perform viral cultures; nine of these utilised the Vero E6 cell lines method while two did not specify the method used (see Table 1). Thirteen studies (20.6%) reported cycle thresholds (Ct) for test positivity: ≤40 (8 studies); ≤43 (1 study); <35 (1 study); <36 (1 study); <37 (1 study) and <38 (1 study).\n\nAll studies reported data on the frequency of positive tests (Table 5). (Figure 3 shows the graphical representation of these frequencies.) The frequency of positive SARS-CoV-2 tests across 51 studies (via RT-PCR) ranged from 0.5% to 75%; 12 studies (19%) reported no positive tests. The highest frequency of positive tests was found in residential isolation rooms. Of the three studies conducted in ICU [Escudero 2000, Jin 2000, Ong 2000 and Seyedmehdi 2000], two reported positive test results (11.7% and 40%). All the four studies [Lei 2000, Ma 2000, Ge 2020, Jerry 2000] conducted in both ICU and general wards reported positive tests: 5%, 5.4%, 14.3% and 16.3%, respectively. One of the three laboratory studies [Bloise 2000] reported frequency of 18.2%; a second study [Lv 2020] reported no positive test with the conventional RT-PCR tests but reported 21.3% positivity with droplet digital PCR (ddPCR) tests; the third study [Zuckerman 2020] reported no positive tests. In a cross-sectional study of SARS-CoV-2 positive subjects confined to their cabins in a cruise ship [Suzuki 2020], the frequency of positive test was 9.7% (58/601); no positive test was detected in the non-case cabins. In one study of home quarantined subjects [Maestre 2020], 46.2% (12/26) of samples were positive for SARS-CoV-2 at two months (one month after the resolution of symptoms). In another study of two hospital patients who were SARS-CoV-2 positive [Shin 2020], no positive samples were detected after 41 days following weekly disinfection. One study conducted in a high-prevalence community setting [Döhla 2020] reported no significant association in the frequencies of positive tests between human and environmental samples (p=0.76). In all four before and after studies, there was a substantial reduction in the frequency of positive tests after surface disinfection.\n\nA total of 17 studies reported data on viral concentration (Table 5); the units of measure used to report this data varied across the studies and included genomic copies/swab (4 studies), genomic copies/cm2 (4 studies), genomic copies/mL (4 studies), and 1 study each for mean concentration, viruses/cm2, genomic units/m2, genomic copies/sample and RNA copies. We found it impossible to make any comparisons across the studies because of the heterogeneity in units of measurement.\n\nA total of 28 studies (44.4%) reported data in Ct with values ranging from 20.4 to 44.1 (Table 5). One study of ICU patients [Razzini 2020] reporting positive rates of 24.3% (9/34) had the lowest range of Ct (21.5-24), while another study of ICU and isolation ward patients [Lei 2020] reporting positive rates of 5% (9/182) had the highest range of Ct (38.6-44); in both studies, the Ct for positivity was ≤40.\n\nOf the 11 studies that planned to perform viral culture, only two (18.2%) reported Ct values that could act as prompts to undertake viral isolation (Table 6). Only two studies provided information on the timing of sample collection for viral culture but were missing key details with respect to collection related to the timing of the onset of symptoms of the patients with respect to the collection and timing. One study of subjects in a cruise ship [Suzuki 2020] reported collecting samples for viral culture from 1–17 days after the cabin was vacated on a cruise ship and at least 17 days after the quarantining to cabins was ordered and 8 days after the first cabin cleaning, while another study of patients in residential isolation [Santarpia 2020] reported collecting the samples on “days 5–9” or “day 10” of occupancy at a medical centre or quarantine unit, all of whom were evacuated from the same cruise ship reported previously and would have been at least 2 weeks from the last day of quarantine [Suzuki 2020]. The incubation period ranged from 4–7 days and there were subtle differences in the culture media used across the studies (Table 6). None of the studies reported success with viral culture despite positive RT-PCR detection tests. There were methodological issues with the techniques employed for viral culture across the studies (see Table 6).\n\n\nDiscussion\n\nWe found 63 primary studies investigating the role of fomites in SARS-CoV-2 transmission. The results of the majority of these studies show that SARS-CoV-2 RNA can be frequently detected on surfaces in both healthcare and non-healthcare settings. However, there were no positive culture results for studies that attempted to culture for viable virus. There is a wide variation in study setting and designs across studies, and the overall quality of published studies is low to moderate. The heterogeneity in study design and methodology makes it difficult to compare results across studies. The results of the systematic review (n=35) [Bedrosian 2020] showed that surface contamination was greatest in laboratories and least in households; however, none of the included studies addressed viral infectivity. The review authors did not assess the reporting quality of the primary studies and the search periods are now outdated.\n\nThe inability to culture the virus despite positive PCR detection tests may indicate either that surface contamination does not support viral growth and hence transmissibility or that the timing of collection was at a point of time where no viable virus would be likely to be found. The latter possibility is considered highly likely on the basis of culturing without the benefit of looking at the timing of the specimens with respect to symptom onset in the patients or evaluating Ct values to ensure they were very low to enhance the likelihood of finding viable virus or culturing attempts from samples with relatively high Ct values where it would be exceedingly difficult to culture viable virus. The substantial reduction in positive detection rates before and after studies (and in some ICU settings) suggests that good hygiene procedures can minimise the risk of surface contamination. The inconsistency in describing a priori Ct values across the studies, coupled with the wide range in actual Ct values, suggests that the reported positive SARS-CoV-2 RNA detection rates are markers of previous viral presence from non-viable virus.\n\nIn a systematic review assessing the role of fomites in virus transmission in the Middle East Respiratory Syndrome (MERS)11, the authors reported possible evidence of fomite contamination but the evidence for fomite transmission was anecdotal. Our review findings are consistent with these observations. In an observational study of four hospitalised patients with MERS12, there was positive viral culture from fomites including bed sheets, bed rails, intravenous fluid hangers, and radiograph devices. In contrast to that study, published research on SARS-CoV-2 shows no evidence of positive viral culture to date. Our review findings support several national and international guidelines recommending good hygiene practices to reduce the spread of SARS-CoV-213–15.\n\nWe identified one non-peer-reviewed (pre-print) systematic review that assessed fomite contamination in SARS-CoV-216. The authors concluded that the quality of measurements was poor, and the reliability of the data is uncertain. Our findings are consistent with these. Compared to that review, we searched more databases, included more than twice the number of included studies, and accounted for the reporting quality of included studies.\n\nAlthough there has been much research into fomite transmission of SARS-CoV-2, much uncertainty remains, and it is difficult to draw meaningful conclusions. Firstly, the variation in Ct across the studies suggests that there is no standardized threshold for detection of SARS-CoV-2 RNA. Some studies have shown that lower Ct correlates with higher genomic load17.\n\nThe studies included in this review used Ct of <35 to <43; these threshold values indicate that some of the positive tests reported in the studies may be misleading. Future research aimed at establishing internationally accepted Ct values should be considered a priority. The discrepancies in units of measurements for viral load and/or concentration also creates confusion. Therefore, standardized checklists for reporting of studies investigating SARS-CoV-2 transmission should be developed, including mandatory publishing of protocols, including the timing of the collection of any environmental specimens with respect to patient symptom onset. Looking for viable virus long after a patient has developed a significant innate and adaptive immunologic response will consistently yield negative results.\n\nThat all 11 culture studies failed to isolate the virus with significant fundamental methodological flaws indicates that the threshold for transmissibility from contaminated surfaces is unknown and more rigorous and carefully orchestrated studies are required before any conclusions may be drawn. One factor likely relates to the timing of sample collection after the onset of infection. Two studies reported the timeframe for sample collection but without precision while nine did not report any timelines. The mean incubation period of SARS-CoV-2 is 5–6 days2; therefore, sample collection within the first few days of infection onset is likely to yield greater viral RNA load and result in better infectivity and culture results. Future studies should endeavour to collect surface samples of likely contaminated surfaces and medical equipment within useful timeframes and should also report this variable with their results.\n\nAs reported in the results, findings from one study [Lv 2020] showed that detection rates were different when qRT-PCR was compared with ddPCR. Interestingly, the authors of another included study [Bloise 2020] concluded that qRT-PCR is unable to differentiate between infectious and non-infectious viruses. Therefore, the use of RT-PCR as the gold standard for detection of SARS-CoV-2 requires further research. The positive findings from the before and after studies show that good hygiene procedures should continue to be a cornerstone for the management of SARS-CoV-2 and other communicable diseases.\n\nTo our knowledge, this is the most comprehensive review to date that evaluates the role of fomites in SARS-CoV-2 transmission. We extensively searched the literature for published studies and included studies that are yet to undergo peer review. We also accounted for the quality of the studies and have presented summary data for some subgroups where possible. However, we recognize several limitations. We may not have identified all published studies investigating the role of fomites; indeed, several other studies may have been published after the last search date for this review. Heterogeneity due to variations in study designs and lack of uniformity in measurement metrics prevent us from statistically combining data across studies and limits the validity and applicability of the review results.\n\n\nConclusion\n\nThe evidence from published research suggests that SARS-CoV-2 RNA can be readily detected on surfaces and fomites. There is no evidence of viral infectivity or transmissibility via fomites to date but no studies to date have been found to be methodologically robust and of high enough quality to even adequately address the question. Good hygienic practices appear to reduce the incidence of surface contamination. Published studies are heterogeneous in design, methodology and viral reporting metrics and there are flaws in the reporting quality. Standardized guidelines for the design and reporting of research on fomite transmission should now be a priority.\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 Fomite Transmission: A Systematic Review, https://doi.org/10.6084/m9.figshare.14247113.v19.\n\nThis project contains the following extended data:\n\n- Appendix 1: Protocol\n\n- Appendix 2: Search Strategy\n\n- Appendix 3: List of excluded studies\n\n- Appendix 4: References to included studies\n\nFigshare: PRISMA checklist for ‘SARS-CoV-2 and the Role of Fomite Transmission: A Systematic Review’, https://doi.org/10.6084/m9.figshare.14247113.v19.\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. [Accessed 18/01/2021]. Reference Source\n\nWorld Health Organization: Transmission of SARS-CoV-2: implications for infection prevention precautions. [Accessed 16/01/2021]. 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\nKramer A, Schwebke I, Kampf G: How long do nosocomial pathogens persist on inanimate surfaces? A systematic review. BMC Infect Dis. 2006; 6: 130. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKaria R, Gupta I, Khandait H, et al.: COVID-19 and its Modes of Transmission. SN Compr Clin Med. 2020; 1–4. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMondelli MU, Colaneri M, Seminari EM, et al.: Low risk of SARS-CoV-2 transmission by fomites in real-life conditions. Lancet Infect Dis. 2020; S1473-3099(20)30678-2. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRahman HS, Aziz MS, Hussein RH, et al.: The transmission modes and sources of COVID-19: A systematic review. International Journal of Surgery Open. 2020; 26: 125–36. Publisher Full Text\n\nGoldman E: Exaggerated risk of transmission of COVID-19 by fomites. Lancet Infect Dis. 2020; 20(8): 892–893. PubMed Abstract | Publisher Full Text | Free Full Text\n\nOnakpoya I, Heneghan C, Spencer EA, et al.: Extended data: SARS-CoV-2 and the Role of Fomite Transmission: A Systematic Review. figshare. Journal contribution. 2021. http://www.doi.org/10.6084/m9.figshare.14247113.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\nDawson P, Malik MR, Parvez F, et al.: What Have We Learned About Middle East Respiratory Syndrome Coronavirus Emergence in Humans? A Systematic Literature Review. Vector Borne Zoonotic Dis. 2019; 19(3): 174–192. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBin SY, Heo JY, Song MS, et al.: Environmental Contamination and Viral Shedding in MERS Patients During MERS-CoV Outbreak in South Korea. Clin Infect Dis. 2016; 62(6): 755–60. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWorld Health Organization: Coronavirus disease (COVID-19) advice for the public. [Accessed 18th January, 2021]. Reference Source\n\nPublic Health England: Guidance COVID-19: cleaning in non-healthcare settings outside the home. Updated 16 October 2020. [Accessed 18th January, 2021]. Reference Source\n\nCenters for Disease Control and Prevention: COVID-19. How to Protect Yourself & Others. [Accessed 18th January, 2021]. Reference Source\n\nCherrie JW, Cherrie MPC, Davis A, et al.: Contamination of air and surfaces in workplaces with SARS-CoV-2 virus: a systematic review. Reference Source\n\nZacharioudakis IM, Prasad PJ, Zervou FN, et al.: Association of SARS-CoV-2 Genomic Load with COVID-19 Patient Outcomes. Ann Am Thorac Soc. 2020. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "82053",
"date": "06 Apr 2021",
"name": "Emanuel Goldman",
"expertise": [
"Reviewer Expertise Microbiology",
"Virology"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 have conducted an extensive comparison of many published studies attempting to assess the possibility of transmission of SARS-CoV-2 via fomites. Most of the studies reviewed involved samples from hospitals, although some studies were also from community settings. The authors report that none of the studies found infectious virus on fomites, and that viral RNA, while generally present to varying degrees, was likely of too poor quality in most instances to support infectivity anyway, based on relatively high cycle threshold (CT) values for the RNA samples.\nThis is a useful snapshot of where we are in the pandemic, and why thinking in the field has increasingly moved towards the view that fomite transmission is not a significant source of infection. This reviewer believes the authors are too timid in drawing that conclusion, only stating in the Abstract \"Lack of positive viral cultures and variation in cycle thresholds create uncertainty about fomites as a mode of transmission.\" I believe a more forceful statement about the insignificance of fomite transmission is warranted.\nIn the second paragraph of the Introduction, the authors do not adequately characterize the content of some of the references cited.\nThe authors write, \"it has been reported that SARS-CoV-2 can be transmitted indirectly through fomites or surfaces5.\" This is inaccurate; reference 5 is a review of work published up to that time, and at most, suggests the possibility that the virus can be transmitted through fomites. None of the papers reviewed in reference 5 showed indirect transmission through fomites. The authors must revise this sentence. My suggestion is to replace \"reported\" with \"suggested\", i.e., \"it has been suggested that SARS-CoV-2 can be transmitted indirectly through fomites or surfaces5.\"\nThe opposite situation occurs in the very next sentence. The authors write, \"However, some authors have suggested that there is a low risk of transmission of SARS-CoV-2 through fomites6,7.\" Reference 6 is more than a suggestion; the authors report the absence of infectious virus on surfaces in hospitals treating COVID-19 patients. My suggestion here is the reverse of my previous one, in this case, replace \"suggested\" with \"reported\" for reference 6, i.e., \"However, some authors have reported6 or suggested7 that there is a low risk of transmission of SARS-CoV-2 through fomites.\"\nIn the last paragraph of the methods section, the authors write: \"One reviewer (IJO) assessed the risk of bias and extracted data from the included studies, and these were independently checked by a second reviewer (EAS).\" However, the reader is not given a clue as to what the authors mean by \"bias\" in this context. The absence of a definition and/or criteria for alleged \"bias\" makes this parameter meaningless in the manuscript. If the authors are to include this parameter, they must revise the manuscript to make clear what it is they are assessing as \"bias\", and how that assessment was made.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Partly\n\nIs the statistical analysis and its interpretation appropriate? Yes\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes",
"responses": [
{
"c_id": "6570",
"date": "26 May 2021",
"name": "IGHO ONAKPOYA",
"role": "Author Response",
"response": "We thank the reviewer for the useful feedback regarding our manuscript. In line with the reviewer's suggestions, we will be making the following revisions to the manuscript: ABSTRACT We will revise the conclusions to reflect the results that the risk of transmission of SARS-CoV-2 through fomites is low. METHODS In the second paragraph, we will replace \"reported\" with \"suggested\" (ref. 5) and replace \"suggested\" with \"reported\" (refs. 6&7). In the last paragraph of this section, we will expand the reporting of the methods used for risk of bias assessment - we will include the domains of bias assessed and how each domain was scored."
},
{
"c_id": "6672",
"date": "26 May 2021",
"name": "IGHO ONAKPOYA",
"role": "Author Response",
"response": "Peer Reviewer's comment: In this manuscript, the authors have conducted an extensive comparison of many published studies attempting to assess the possibility of transmission of SARS-CoV-2 via fomites. Most of the studies reviewed involved samples from hospitals, although some studies were also from community settings. The authors report that none of the studies found infectious virus on fomites, and that viral RNA, while generally present to varying degrees, was likely of too poor quality in most instances to support infectivity anyway, based on relatively high cycle threshold (CT) values for the RNA samples. This is a useful snapshot of where we are in the pandemic, and why thinking in the field has increasingly moved towards the view that fomite transmission is not a significant source of infection. Authors' response: Thank you. Peer Reviewer's comment: This reviewer believes the authors are too timid in drawing that conclusion, only stating in the Abstract \"Lack of positive viral cultures and variation in cycle thresholds create uncertainty about fomites as a mode of transmission.\" I believe a more forceful statement about the insignificance of fomite transmission is warranted. Authors' response: We agree with the reviewer and have revised the statement. Abstract conclusion now reads thus: “Lack of positive viral cultures suggests that the risk of transmission of SARS-CoV-2 through fomites is low.” Peer Reviewer's comment: In the second paragraph of the Introduction, the authors do not adequately characterize the content of some of the references cited. The authors write, \"it has been reported that SARS-CoV-2 can be transmitted indirectly through fomites or surfaces5.\" This is inaccurate; reference 5 is a review of work published up to that time, and at most, suggests the possibility that the virus can be transmitted through fomites. None of the papers reviewed in reference 5 showed indirect transmission through fomites. The authors must revise this sentence. My suggestion is to replace \"reported\" with \"suggested\", i.e., \"it has been suggested that SARS-CoV-2 can be transmitted indirectly through fomites or surfaces5 Authors' response: We have amended the sentence. Now reads thus: “… it has been suggested that SARS-CoV-2 can be transmitted indirectly through fomites or surfaces…” Peer Reviewer's comment: The opposite situation occurs in the very next sentence. The authors write, \"However, some authors have suggested that there is a low risk of transmission of SARS-CoV-2 through fomites6,7.\" Reference 6 is more than a suggestion; the authors report the absence of infectious virus on surfaces in hospitals treating COVID-19 patients. My suggestion here is the reverse of my previous one, in this case, replace \"suggested\" with \"reported\" for reference 6, i.e., \"However, some authors have reported6 or suggested7 that there is a low risk of transmission of SARS-CoV-2 through fomites.\" Authors' response: We have amended the sentence. Now reads thus: “… some authors have reported that there is a low risk of transmission of SARS-CoV-2 through fomites [6,7] and others have reported that the risk of such transmission is exaggerated [8]”. Peer Reviewer's comment: In the last paragraph of the methods section, the authors write: \"One reviewer (IJO) assessed the risk of bias and extracted data from the included studies, and these were independently checked by a second reviewer (EAS).\" However, the reader is not given a clue as to what the authors mean by \"bias\" in this context. The absence of a definition and/or criteria for alleged \"bias\" makes this parameter meaningless in the manuscript. If the authors are to include this parameter, they must revise the manuscript to make clear what it is they are assessing as \"bias\", and how that assessment was made. Authors' response: We have expanded the section on risk of bias assessment. Now reads thus: “We assessed the risk of bias using five domains from the QUADAS-2 criteria [9]; we adapted this tool because the included studies were not designed as diagnostic accuracy studies. The domains assessed were: (i) study description - was there sufficient description of methods to enable replication of the study? (ii) sample sources – was there a clear description of sample sources? (iii) description of results - was the reporting of study results and analysis appropriate? (iv) risk of bias - did the authors acknowledge any potential biases, if yes were any attempts made to address these biases? (v) applicability – is there any concern that the interpretation of test results differs from the study question? For each bias domain, the risk was judged as “low”, “unclear” or “high”.”"
}
]
},
{
"id": "83869",
"date": "11 May 2021",
"name": "Ana Karina Pitol Garcia",
"expertise": [
"Reviewer Expertise Disease transmission",
"Quantitative Microbial Risk Assessment (QMRA)",
"fomite-mediated transmission",
"virus transfer."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 compiled and summarized many scientific publications that surveyed SARS-CoV-2 on surfaces. Surface contamination is an essential piece of information needed to understand the role of fomites in disease transmission. The authors collected data on the presence of RNA and viable SARS-CoV-2. Notable, out of the 11 identified papers that attempted viral culture, none fund cytopathic effects. Therefore, no viable SARS-CoV-2 has been recovered from surfaces up to date. The review is comprehensive, timely, and valuable for understanding the relative contribution of fomite-mediated transmission to the spread of SARS-CoV-2.\nMajor comments:\nMethods The authors mention using an adapted version of \"QUADAS-2 criteria\" to assess the quality of the studies, but the exact methodology is not reported neither in the main article nor in the extended data. More transparency is needed regarding the exact questions used to determine quality and bias.\nAdditionally, the authors criticize publications that do not report \"patient information\" such as \"symptom onset in the patients\". Nevertheless, this information is not relevant in settings with no COVID-19 patients (surfaces at gas stations, bus stations, hospital wards, etc.).\nDiscussion Regarding the following statement: \"The inability to culture the virus despite positive PCR detection tests may indicate either that surface contamination does not support viral growth and hence transmissibility or that the timing of collection was at a point of time where no viable virus would be likely to be found.\"\nThe first hypothesis is not clear, \"The inability to culture the virus despite positive PCR detection tests may indicate either that surface contamination does not support viral growth and hence transmissibility\" - We know that the virus needs a host cell to replicate. The capacity of fomites to serve as a vehicle for the transmission of SARS-CoV-2 depends on factors such as the decay rate of the virus on the surface and on the hands, the virus transfer rate (surface to hand, and hand to face), the frequency of touch between the hands and face, the dose-response curve of the virus, among other parameters. Even if the virus does not \"grow\" on the surface, there is still potential for transmission. Therefore, this sentence needs to be removed or clarified.\nSecond hypothesis: \"The inability to culture the virus despite positive PCR detection tests may indicate … that the timing of collection was at a point of time where no viable virus would be likely to be found.\" - The authors suggest throughout the discussion that the 11 studies that cultured the virus showing not cytopathic effects have \"significant fundamental methodological flaws\" (which are not clearly pointed out in the manuscript), directing the reader to conclude that this is probably the reason why no attempt at culturing viruses from surfaces has been successful. It's helpful to point out that SARS-CoV-2 RNA is much more stable on fomites than infective SARS-CoV-2 virus, and it is found in much greater concentrations. For example, in an experimental study where SARS-CoV-2 was inoculated on surfaces, Paton et al. (2021)1 found that the number of RNA recovered from the surfaces was 103 to 108 times higher than the number of viable virus in the samples. Given the relatively low concentration of RNA found on surfaces in the compiled articles, it is expected that the 11 studies that attempted to culture the virus could not find cytopathic effects. It is true, as the authors point out, that the transmission via fomites cannot be discarded. Nevertheless, the evidence that the authors compiled can already give an idea of how unlikely fomite-mediate transmission is in most settings.\nMinor comments:\nAbstract Please, clarify the statement \"SARS-CoV-2 has been detected in fomites...\" by replacing it with \"SARS-CoV-2 RNA has been detected in fomites...\"\nIntroduction The statement, \"it has been reported that SARS-CoV-2 can be transmitted indirectly through fomites or surfaces.\" is not supported by the reference. The reference only suggests the possibility of fomite transmission based on (1) the presence of SARS-CoV-2 RNA on surfaces, and (2) experimental evidence of virus survival at specific conditions and high concentrations. Up to date, no study has \"reported\" fomite-mediated transmission. Replacing the word \"reported\" by \"suggested\" would be better.\nDiscussion In the following sentence, \"We identified one non-peer-reviewed (pre-print) systematic review that assessed fomite contamination in SARS-CoV-2.\" perhaps what the authors intended to say was, \"We identified one non-peer-reviewed (pre-print) systematic review that assessed SARS-CoV-2 contamination in fomites.\"?\nFigure 3 It would be more informative for the reader if the plot could distinguish between public spaces and rooms with COVID-19 patients. The authors could break the \"other\" category and include \"isolation or quarantine room\", since the most frequently contaminated spaces were quarantine rooms.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Partly\n\nIs the statistical analysis and its interpretation appropriate? Not applicable\n\nAre the conclusions drawn adequately supported by the results presented in the review? Partly",
"responses": [
{
"c_id": "6671",
"date": "26 May 2021",
"name": "IGHO ONAKPOYA",
"role": "Author Response",
"response": "Peer reviewer's comment: The authors compiled and summarized many scientific publications that surveyed SARS-CoV-2 on surfaces. Surface contamination is an essential piece of information needed to understand the role of fomites in disease transmission. The authors collected data on the presence of RNA and viable SARS-CoV-2. Notable, out of the 11 identified papers that attempted viral culture, none fund cytopathic effects. Therefore, no viable SARS-CoV-2 has been recovered from surfaces up to date. The review is comprehensive, timely, and valuable for understanding the relative contribution of fomite-mediated transmission to the spread of SARS-CoV-2. Authors' response: Thank you. Peer reviewer's comment: Major comments: Methods The authors mention using an adapted version of \"QUADAS-2 criteria\" to assess the quality of the studies, but the exact methodology is not reported neither in the main article nor in the extended data. More transparency is needed regarding the exact questions used to determine quality and bias. Authors' response: Now reads thus: “We assessed the risk of bias using five domains from the QUADAS-2 criteria [9]; we adapted this tool because the included studies were not designed as diagnostic accuracy studies. The domains assessed were: (i) study description - was there sufficient description of methods to enable replication of the study? (ii) sample sources – was there a clear description of sample sources? (iii) description of results - was the reporting of study results and analysis appropriate? (iv) risk of bias - did the authors acknowledge any potential biases, if yes were any attempts made to address these biases? (v) applicability – is there any concern that the interpretation of test results differs from the study question? For each bias domain, the risk was judged as “low”, “unclear” or “high”.” Peer reviewer's comment: Additionally, the authors criticize publications that do not report \"patient information\" such as \"symptom onset in the patients\". Nevertheless, this information is not relevant in settings with no COVID-19 patients (surfaces at gas stations, bus stations, hospital wards, etc.). Authors' response: Now reads thus: “The latter possibility is considered highly likely on the basis of culturing without the benefit of looking at the timing of the specimens with respect to symptom onset (in study settings that had SARS-CoV-2 positive patients) …” Peer reviewer's comment: Discussion Regarding the following statement: \"The inability to culture the virus despite positive PCR detection tests may indicate either that surface contamination does not support viral growth and hence transmissibility or that the timing of collection was at a point of time where no viable virus would be likely to be found.\" The first hypothesis is not clear, \"The inability to culture the virus despite positive PCR detection tests may indicate either that surface contamination does not support viral growth and hence transmissibility\" - We know that the virus needs a host cell to replicate. The capacity of fomites to serve as a vehicle for the transmission of SARS-CoV-2 depends on factors such as the decay rate of the virus on the surface and on the hands, the virus transfer rate (surface to hand, and hand to face), the frequency of touch between the hands and face, the dose-response curve of the virus, among other parameters. Even if the virus does not \"grow\" on the surface, there is still potential for transmission. Therefore, this sentence needs to be removed or clarified. Authors' response: We have revised the statement and added a reference. Now reads thus: “The inability to culture the virus despite positive PCR detection tests suggests that SARS-CoV-2 RNA is more stable (and likely found in greater concentrations) on fomites than infective SARS-CoV-2 virus [11]”. Factors known to affect the ability of fomites to serve as transmitters of respiratory viruses include the rate of decay of the virus on the surface and on the hands, the virus transfer rate (surface to hand, and hand to face), the frequency of touch between the hands and face, the dose-response curve of the virus, temperature and humidity, amongst others [12].” Peer reviewer's comment: Second hypothesis: \"The inability to culture the virus despite positive PCR detection tests may indicate … that the timing of collection was at a point of time where no viable virus would be likely to be found.\" - The authors suggest throughout the discussion that the 11 studies that cultured the virus showing not cytopathic effects have \"significant fundamental methodological flaws\" (which are not clearly pointed out in the manuscript), directing the reader to conclude that this is probably the reason why no attempt at culturing viruses from surfaces has been successful. It's helpful to point out that SARS-CoV-2 RNA is much more stable on fomites than infective SARS-CoV-2 virus, and it is found in much greater concentrations. For example, in an experimental study where SARS-CoV-2 was inoculated on surfaces, Paton et al. (2021)1 found that the number of RNA recovered from the surfaces was 103 to 108 times higher than the number of viable virus in the samples. Given the relatively low concentration of RNA found on surfaces in the compiled articles, it is expected that the 11 studies that attempted to culture the virus could not find cytopathic effects. It is true, as the authors point out, that the transmission via fomites cannot be discarded. Nevertheless, the evidence that the authors compiled can already give an idea of how unlikely fomite-mediate transmission is in most settings. Authors' response: We have revised the statement. Peer reviewer's comment: Minor comments: Abstract Please, clarify the statement \"SARS-CoV-2 has been detected in fomites...\" by replacing it with \"SARS-CoV-2 RNA has been detected in fomites...\" Authors' response: Added “RNA” Peer reviewer's comment: Introduction The statement, \"it has been reported that SARS-CoV-2 can be transmitted indirectly through fomites or surfaces.\" is not supported by the reference. The reference only suggests the possibility of fomite transmission based on (1) the presence of SARS-CoV-2 RNA on surfaces, and (2) experimental evidence of virus survival at specific conditions and high concentrations. Up to date, no study has \"reported\" fomite-mediated transmission. Replacing the word \"reported\" by \"suggested\" would be better. Authors' response: Agreed. This was already commented on by Reviewer 1. We have revised as suggested. Peer reviewer's comment: Discussion In the following sentence, \"We identified one non-peer-reviewed (pre-print) systematic review that assessed fomite contamination in SARS-CoV-2.\" perhaps what the authors intended to say was, \"We identified one non-peer-reviewed (pre-print) systematic review that assessed SARS-CoV-2 contamination in fomites.\"? Authors' response: We have made the correction. Now reads thus: “We identified one non-peer-reviewed (pre-print) systematic review that assessed SARS-CoV-2 contamination in fomites…” Peer reviewer's comment: Figure 3 It would be more informative for the reader if the plot could distinguish between public spaces and rooms with COVID-19 patients. The authors could break the \"other\" category and include \"isolation or quarantine room\", since the most frequently contaminated spaces were quarantine rooms. Authors' response: We understand the reviewer’s point here. However, we reported the settings are described by the study authors - only 2 studies were described as “hospital and quarantine”. Therefore we have not made any changes to the figure."
}
]
}
] | 1
|
https://f1000research.com/articles/10-233
|
https://f1000research.com/articles/9-342/v1
|
11 May 20
|
{
"type": "Research Article",
"title": "Metformin improves FOXP3 mRNA expression through suppression of interferon gamma levels in pristane-induced murine models of lupus",
"authors": [
"Stevent Sumantri",
"Mochammad Hatta",
"Rosdiana Natzir",
"Haerani Rasyid",
"Iris Rengganis",
"Muh. Nasrum Massi",
"Andi Asadul Islam",
"Gatot Lawrence",
"Ilhamjaya Patellongi",
"Andi Fachruddin Benyamin",
"Mochammad Hatta",
"Rosdiana Natzir",
"Haerani Rasyid",
"Iris Rengganis",
"Muh. Nasrum Massi",
"Andi Asadul Islam",
"Gatot Lawrence",
"Ilhamjaya Patellongi",
"Andi Fachruddin Benyamin"
],
"abstract": "Background: A recent study has indicated the potential of metformin therapy for lupus in animal models, but there has been no study evaluating the effect on pristane-induced lupus. This study aims to evaluate the effect of intraperitoneal versus oral metformin on interferon (IFN)-γ levels and FOXP3 mRNA expression on pristane-induced female BALB/c mice. Methods: In total, 31 female BALB/c mice, aged 6 weeks, were intraperitoneally induced with 0.5 ml of pristane (2,6,10,14-tetramethylpentadecane). After 120 days, the mice were grouped and treated with various treatments: normal saline 100 mcl, oral metformin 100mg/kgBW, or intraperitoneal metformin 100mg/kgBW. After 60 days of treatment, all treatment groups were sacrificed, and kidney specimens prepared and stained using hematoxylin and esosin. Results: IFNγ levels of saline controls vs. oral metformin group was 309.39 vs. 292.83 pg/mL (mean difference 16.56 pg/mL; 95% CI 0.74-32.37; p=0.042), and saline control vs. intraperitoneal metformin group was 309.39 vs. 266.90 pg/mL (mean difference 42.49 pg/mL; 95% CI 29.24-55.73 pg/mL; p<0.004). FOXP3 mRNA expression changes in saline controls vs. oral metformin group was 6.90 vs. 7.79-fold change (mean difference -0.89-fold change; 95% CI -1.68-(-0.11); p=0.03) and in saline controls vs. intraperitoneal metformin group was 6.90 vs. 9.02-fold change (mean difference -2.12-fold change; 95% CI -2.99-(-1.25); p=<0.001). Correlation analysis of FOXP3 mRNA expression and IFNγ level changes revealed a Pearson correlation of -0.785 (p=0.001) and R2 value of 0.616 (p=0.001). Conclusion: Metformin is a potential new therapy to reduce the levels of IFNγ and increase FOXP3 mRNA expression in mice models of systemic lupus erythematosus. Intraperitoneal metformin, i.e intravenous administration in human, could provide a novel route of administration to improve the effect of metformin for lupus patients.",
"keywords": [
"systemic lupus erythematosus",
"pristane induced lupus",
"oral metformin",
"intraperitoneal metformin",
"AMPK/mTOR pathway"
],
"content": "Introduction\n\nSystemic lupus erythematosus (SLE) is a complex systemic disease, which is defined by multiple organ damage and dysfunction resulting from auto-antibody generation and inherited immune system dysregulation1. The complicated pathophysiology and clinical manifestations result in difficulty in reaching an effective and comprehensive management of this condition. Lupus treatment currently relies on immunosuppressants and corticosteroids to suppress the immune system and reduce disease activity. This strategy is not ideal; there are several types of patients who do not respond well to immunosuppression and this therapy also produces side effects, such as recurrent infection, bone density loss, sarcopenia and psychological disturbances. This has led to infection and cardiovascular comorbidity becoming the major cause of mortality related to SLE, and not the disease itself2.\n\nRecent studies on experimental models has shown that the key to effective SLE management doesn’t rely on suppression of immune system, but how to manage and balance the activity of several key players, such as T regulator (Treg), T autoreactive (Th17), B autoreactive, and B regulator lymphocytes3. Inflammatory cytokines and cellular components, such as tumour necrosis factor (TNF)-α, type 1 and 2 interferons, B-lymphocyte stimulator and interleukin-10 has also been known to contribute to the development of auto-antibodies and immune complexes that destroy tissues, especially in the kidneys4–6. Recently the activity of interferon (IFN)-γ and Th1 cells has been the focus of several experimental and clinical studies, especially its relationship to the development of lupus nephritis and its effect on downstream T-helper cells, such as Treg and Th177–9.\n\nSeveral studies has also shown the influence of oxidative stress from environmental exposure to the imbalance of Treg and Th1 cells, with subsequent effects on the elevation of IFNγ levels and the development of SLE in exposed murine models10. Exposure to reactive oxygen species is known to disrupt mitochondrial potential balance and activate the mTOR (mammalian Target of Rapamycin) metabolism regulation pathway by suppressing AMPK (Adenosine Monophosphate Kinase). This in turn results in a preference of Th1 pathway activation rather than Treg11–13.\n\nMetformin, an old anti-diabetic drug with a reputable safety profile, recently has been known to be able to regulate the AMPK/mTOR pathway and from several studies has been shown to be able to regulate several autoimmune-, inflammation-, malignant- and aging-related conditions14,15. Studies on mice models of rheumatoid arthritis, autoimmune encephalitis and lupus nephritis has also shown this drug’s ability as a potential therapy of autoimmune disease11,16. This study aims to evaluate the effect of intraperitoneal versus oral metformin in decreasing IFNγ and increasing FOXP3 mRNA expression levels on pristane-induced female BALB/c mice, as there no studies that have evaluated the route of metformin delivery, especially on an environmentally induced model of lupus nephritis.\n\n\nMethods\n\nIn total, 30 female BALB/c mice, aged 6 weeks and weighing approximately 25 grams, were purchased from Universitas Hasanuddin Makassar (Indonesia) and then maintained at the Animal Unit of the Molecular Biology Laboratory of Universitas Hasanuddin Makassar from January 2018. The mice was kept in a temperature controlled housing according to their study group, food and water was provided freely. The number of mice for intervention study was determined using Federer formula for 5 groups. Efforts was made to minimize suffering, such as minimal handling, less frequency of venous sampling, adequate space for living and no other experimentation or pain inducing procedures.\n\nAfter 2 weeks of acclimatization the mice were then randomly divided into five groups (6 mice/group): group 1, normal control; group 2, SLE model; group 3, normal saline; group 4, oral metformin; and group 5, intraperitoneal metformin groups. Four of the groups (all apart from normal control) were induced with 0.5 ml of pristane (2,6,10,14-tetramethylpentadecane; Sigma Aldrich) intraperitoneally. The normal control group was injected with normal saline 0.5 ml intraperitoneally as a control group. After 120 days, groups 1 and 2 were sacrificed using chloroform euthanasia methods (dose of 20 g/m3 in a closed chamber system). Kidney specimen was then fixed with neutral buffered formalin (NBF) 10%, prepared in paraffin block, sliced to 2μM thickness and then stained with haematoxylin and eosin (H&E).\n\nAll intervention, analysis and reporting conducted in this study follows the ARRIVE guidelines for animal studies. Ethical approval for animal studies was obtained from Universitas Hasanuddin’s Health Studies Ethical Committee, with protocol number UH17030037. Care and intervention conducted in the research animal, refers to Indonesian National Guidelines on Health Research Ethics and Indonesian Food and Medicine Regulatory Body Guidelines on Good Clinical Practice17.\n\nAfter 120 days, the intervention groups (groups 3–5) were given therapy every morning in the animal laboratory according to their designation: group 3, given 100 mcl normal saline via oral gavage once daily; group 4, given 100 mg/kg body weight of metformin diluted in 100 mcl normal saline via oral gavage once daily; group 5, given 100 mg/kg body weight of metformin diluted in normal saline via intraperitoneal injection once daily. Treatment lasted for 60 days and at the end of the period all three groups were sacrificed, kidney specimen fixated with NBF 10%, prepared in paraffin block and then stained with H&E.\n\nSamples for IFNγ and FOXP3 mRNA measurements was collected from tail vein sampling (0.1–0.2 ml for each sample). IFNγ was measured using the murine IFNγ ELISA kit from Abcam (ab100689) and read using ELISA Reader 270 with 450 nm wavelength (Biomerieux, France).\n\nTotal RNA was isolated from using the Qiagen RNeasy Micro Kit (DNA Genotek, Qiagen) according to the manufacturer’s instructions. Complementary DNA synthesis was performed by using iScript™ Advanced cDNA Synthesis Kit for RT-qPCR (Bio-Rad). Using cDNA synthesized from 150 ng of total RNA as a template for one amplification, real-time reverse transcriptase (RT)-PCR (CFX Connect system; Bio-Rad) was performed using SYBR® Green PCR Master Mix one step according to the instructions provided (Bio-Rad). Final reaction volume was 20 μL, and included 2 μL cDNA, 10 μL SYBR Green Master Mix, 0.5 μL each of the forward and reverse primers (10 pmol), and 7 μL nuclease-free water. Amplification conditions used for qPCR were: 95°C for 2 minutes, followed by 40 cycles of denaturation and annealing/extension cycles at 95°C for 5 seconds and 60°C for 30 seconds.\n\nThe glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene was used as an internal control for normalization, GAPDH primer, forward (5’GAAGGTGAAGGTCGGAGT-3’) and reverse (5’-GAAGATGGTGATGGGATTTC-3’). Fold change was determined by the ΔΔCt method. All measurements were conducted as per manufacturer’s instructions and repeated three times to ensure the validity. Target protein concentration was read as picogram/millilitre and mRNA expression as fold change.\n\nKidney specimens were examined by two independent and blinded histopathologists experienced in evaluating murine renal samples. Glomerular scores were evaluated by measuring the level of destruction on 50 glomerular units in each mouse and scored as 0 = normal, 1 = mesangial expansion, 2 = endocapillary proliferation, 3 = capillaritis or necrotic changes and 4 = crescents. Interstitial scoring was measured by evaluating 50 high power fields and scored as 0 = no interstitial involvement, 1 = <25% interstitial involvement, 2 = 25–50% involvement and 3 = >50% involvement18.\n\nStatistical analysis (SPSS Statistics ver. 20, IBM) was done by measuring mean difference (t-test) to evaluate the difference in IFNγ levels, FOXP3 mRNA fold change and histopathological scores between the five groups. Correlation analysis was also done to evaluate the relationship between IFNγ and FOXP3 mRNA changes to determine the strength of the causality. All tests were reported with 95% confidence interval, standard error and statistical significance score (p<0.05).\n\n\nResults\n\nTwo female mice expired in the adaptation period; therefore, only 29 mice entered the intervention period and finished the experiments without problems, analysis was done with 5 mice from each group (n=25).\n\nGroups 1 and 2 (normal control and SLE model) were sacrificed at the end of the initial 120 day induction period and IFNγ and FOXP3 mRNA expression changes are detailed in Table 1. The starting level of IFNγ shows no difference between normal control and SLE model groups (269.60 vs. 281.12 pg/mL; mean difference 11.52 pg/mL; 95% CI -17.47 – 40.52 pg/mL; p=0.386). Post-induction with intraperitoneal pristane (for group 2 only), there was a difference in IFNγ levels between normal control and SLE model groups (269.82 vs. 322.42 pg/mL; mean difference 52.59 pg/mL; 95% CI 31.23-73.96 pg/mL; p<0.001) (Figure 1A). The expression of FOXP3 mRNA at baseline shows no difference between normal control and SLE model groups (8.87 vs. 8.86-fold change; mean difference -0.00-fold change; 95% CI -0.78-0.77; p=0.983), while post-pristane induction there was a mean difference of -1.63-fold change of mRNA FOXP3 expression between groups (8.80 vs. 7.17-fold change; 95% CI -2.17 – 1.09-fold change; p<0.001) (Figure 1C).\n\nData are presented as mean (95% confidence interval). SLE, systemic lupus erythematosus; PI, post induction.\n\nPost pristane induction and post metformin intervention IFNγ levels (A and B) and FOXP3 mRNA expression (C and D).\n\nGroups 3–5 (normal saline, oral metformin and intraperitoneal metformin) entered the 60 days of intervention period. IFNγ and FOXP3 mRNA expression changes can be seen in Table 2. Comparison between saline control and oral metformin groups resulted in IFNγ levels of 309.39 vs. 292.83 pg/mL (mean difference 16.56 pg/mL; 95% CI 0.74-32.37; p=0.042; Figure 1B). Comparison between saline control and intraperitoneal metformin groups resulted in IFNγ levels of 309.39 vs. 266.90 pg/mL (mean difference 42.49 pg/mL; 95% CI 29.24-55.73 pg/mL; p<0.004; Figure 1B). Comparison between oral and intraperitoneal metformin groups resulted in IFNγ level changes of -33.34 vs. -62.70 pg/mL (mean difference 29.35 pg/mL; 95% CI -52.08 – (-6.63); p=0.018; Figure 1B).\n\nData are presented as mean (95% confidence interval). PI, post induction.\n\nFOXP3 mRNA expression changes between saline control compared with oral metformin revealed 6.90 vs. 7.79-fold change (mean difference -0.89-fold change; 95% CI -1.68-(-0.11); p=0.03; Figure 1D), while between saline control and intraperitoneal metformin there was a 6.90 vs. 9.02-fold change (mean difference -2.12-fold change; 95% CI -2.99-(-1.25); p=<0.001; Figure 1D). Comparison of FOXP3 mRNA expression between oral and intraperitoneal metformin groups was -0.94 vs. (-2.02) fold change (mean difference 1.07-fold change; 95% IC 0.16-1.99; p=0.027; Figure 1D).\n\nRatio of FOXP3 mRNA expression and IFNγ levels represents the balance between Treg (anti-inflammatory) and Th1 (pro-inflammatory) activity. Post pristane induction in BALB/c mice showed a ratio of 0.002 vs. 0.003 (mean difference -0.001; 95% CI -0.001 – (-0.0008); p<0.001) in SLE model compared to normal BALB/c group (Figure 2A). Correlation analysis of FOXP3 mRNA expression and IFNγ level changes pre and post induction with pristane in the five groups revealed a Pearson correlation of -0.776 (p<0.001) and R2 value of 0.602 (p<0.001) (Figure 2B).\n\nPost pristane induction FOXP3 mRNA/IFN-gamma ratio and correlation scatter plot (A and B) and post metformin therapy FOXP3 mRNA/IFN-gamma ratio and correlation scatter plot (C and D).\n\nPost intervention, comparison between saline control with oral metformin groups was 0.0022 vs. 0.0027 (mean difference -0.0004; 95% CI -0.0007 – (-0.0001); p=0.008; Figure 2C), while between saline control and intraperitoneal metformin groups was 0.0022 vs. 0.0034 (mean difference -0.001; 95% CI -0.0015 – (-0.0007); p<0.001; Figure 2C). Comparison between oral and intraperitoneal metformin groups revealed 0.0027 vs. 0.0034 (mean difference -0.0007; 95% CI -0.0011 – (-0.0003); p=0.002; Figure 2C). Correlation analysis of FOXP3 mRNA expression and IFNγ level changes between post induction and post treatment with metformin revealed a Pearson correlation of -0.785 (p=0.001) and R2 value of 0.616 (p=0.001) (Figure 2D).\n\nHistopathological analysis on kidney specimens resulted in a variable change in each intervention group (Figure 3). Glomerular scoring comparison between BALB/c normal and SLE model groups revealed a score of 2.2 vs. 3.0 (mean difference 0.80; 95% CI 0.33-1.26; p=0.04). Interstitial scoring comparison between BALB/c normal and SLE model groups revealed a score of 1.20 vs. 1.40 (mean difference 0.20; 95% CI 0.83-1.23; p=0.667). Total histopathological scoring between the two groups revealed a score of 4.40 vs. 3.40 (mean difference 1.00; 95% CI -0.08 – 2.08; p=0.066).\n\nAnalysis on normal BALB/c control kidney (upper and lower left) revealed mild tubulo-nephritis changes, with minimal mesangial expansion, endocapillary proliferation and capillaritis. Significant interstitial infiltration (25–50% field) only happens in one member of normal BALB/c group. In the SLE model group (upper and lower right), after induction with pristane, there was a significant change in the glomeruli, with dominant endocapillary proliferation and minimal mesangial expansion and capillaritis.\n\nHistopathological scoring between intervention groups (normal saline, oral and intraperitoneal metformin) did not reveal significant differences, although qualitative analysis by blinded pathologists revealed difference in the degree of nephritis occurring in each group (Figure 4).\n\nIn general, there was a widespread and significant glomerular and interstitial change across all groups, consistent with previous SLE models. Tubulo-nephritic changes significantly happens more than glomerulo-nephritis, although significant interstitial infiltration only happens in the normal saline group (upper right), especially in two members of its group. Qualitatively, two blinded pathologists concluded that the most severe changes happen in the normal saline group and the least severe in the intraperitoneal metformin group.\n\n\nDiscussion\n\nSLE is a multifactorial inflammatory autoimmune disease, with clinical manifestations that involves various tissues and organs. The aetiology of this autoimmune condition is linked to dysfunctional B and T lymphocyte responses to environmental stimulus in a genetically susceptible individual, which in turn determines the immune response to various autoantigens and can cause tissue damage. The application of pristane, an aromatic hydrocarbon, has an advantage to genetically modified mice, because the ability of this model to mimic SLE in humans, which in a genetically susceptible individual is usually caused by environmental exposure. Pristane mouse models also enables researchers to evaluate pathophysiological changes in a timely manner, and to give a picture of the cellular mechanism involved in the development and progressivity of SLE12.\n\nIn this study, we showed that after induction with pristane, there was a significant difference in the level of IFNγ in the normal BALB/c group compared to the SLE model (269.82 vs. 322.42 pg/mL; mean difference 52.59; 95% CI 31.23 - 73.96; p<0.001). Richards et al.12 showed that IFNγ is an important component in the development of lupus nephritis in pristane-induced murine models. Induction with pristane in an IFNγ deficient mouse (IFNγ-/-) would not result in a change of renal pathology corresponding to lupus nephritis. Furthermore, in this model of IFNγ deficient mice, post pristane induction, no antibodies characteristically associated with lupus, such as IgG anti-ssDNA and anti-chromatin antibody, were found12,19. Chiche et al.19 also noted that the activity of pathways related to IFNγ play an important role in the development of anti-dsDNA antibodies and the reduction of lymphocyte counts in patients with SLE.\n\nRegarding the expression of FOXP3 mRNA, we showed that there was a significant difference between normal BALB/c compared to the SLE model group (8.80 vs. 7.17-fold change; mean difference -1.63; 95% CI 2.17 – 1.09; p<0.001). The expression of FOXP3 mRNA in pristane induced murine models is a marker for Treg cell activity. In a study by Peixoto et al., it was shown that on day 90 and 120 post induction there was a decrease in CD4+CD25+FOXP3+ (Treg) cell count in peripheral blood samples20. These authors also showed that the reduction in Treg count was correlated with an increase in IFNγ (p=0.017), TNFα (p=0.043) and TGF-β1 (p=0.038). Furthermore, Kluger et al. also pointed out that the disturbances in Treg (FOXP3+) function contributes to the development of acute glomerulonephritis in pristane induced lupus21.\n\nIn this study, metformin intervention, whether in oral form (309.39 vs. 292.83 pg/ml; mean difference 16.56; 95% CI 0.74-32.37; p=0.042) or intraperitoneal injection (309.39 vs. 266.90 pg/ml; mean difference 42.49 pg/ml; 95% CI 29.24-55.73; p<0.001) gave a significantly superior suppression of IFNγ levels. A previous study by Mardani et al. showed that an intervention with probiotics could reduce IFNγ and IL-17 levels in pristane induced murine lupus, followed by a reduction in autoantibodies such as ANA, anti-dsDNA and anti-RNP9. Reduction of IFNγ levels could improve the outcome of lupus nephritis by inactivating B7/CD28 signalling pathway, which results in a reduction in ANA autoantibodies, IL-4 and IFNγ levels. The inactivation of B7/CD28 pathways also caused anergy, tolerance and apoptosis of T-cells, which results in a decrease of urine protein and immune complex deposition in the kidneys of pristane induced C57BL/6J mice22.\n\nThis study revealed that the administration of oral and intraperitoneal metformin gave a significantly better suppression of IFNγ than placebo, in accordance to the study conducted by Yin et al.23. In that study, intervention with metformin and 2-DG (2-deoxy-glucose) in B6.Sle1Sle2.Sle3 mice resulted in a suppression of IL-17 and IFNγ levels through a blockade on the glucose oxidation pathway. This blockade on the glucose oxidation pathway also normalized T-cell metabolism, which in turn suppresses the activation of CD4+ T-cells and returns the balance of pro/anti-inflammatory cytokines in mice models10.\n\nRegarding FOXP3 mRNA expression, this study showed that intervention with metformin via oral (6.90 vs. 7.79-fold change; mean difference -0.89; 95% CI -1.68 – (-0.11); p=0.03) or intraperitoneal route (6.90 vs. 9.02-fold change; 95% CI -2.99 – (-1.25); p<0.001) gave a significantly superior increase in FOXP3 mRNA expression compared to saline control. We also showed that there was a strong significant inverse correlation between the increase of FOXP3 mRNA expression and decrease of IFNγ resulting from metformin intervention (R=-0.785; p=0.001). Furthermore, it seems that the reduction of IFNγ explains the increase in FOXP3 mRNA expression rather strongly, as shown by the R2 value of 0.616 (p=0.001). The above result was consistent with several studies in pristane induced models; a decrease in FOXP3+ T-cells and increase in CD4+CD69+ T-cells coincide with an increase in IFNγ levels in intraperitoneal fluid20,23.\n\nTo the best of our knowledge, this is the first study that evaluates the effect of metformin on the expression of FOXP3 mRNA in lupus, although it is also known that metformin has the ability to induce AMPK pathway activity and suppress mTOR signalling24,25. Metformin has also been known to be able to improve disease activity index, histological and inflammatory profiles in several other autoimmune models, such as inflammatory bowel disease26 and autoimmune insulitis14 through the modulation of AMPK-mTOR pathway and the resulting changes in IL-17, IFNγ, IL-10 and FOXP3 associated cytokines and cells.\n\nIntraperitoneal route of metformin gave a superior effect on the suppression of IFNγ levels and increasing FOXP3 mRNA expression compared to the oral route, and to the best of our knowledge this was the first study that observed this effect in pristane induced murine model of lupus. A study by Dowling et al. on NOD/SCID mice revealed that plasma levels of metformin were higher via intraperitoneal than oral route (145 uM vs. 77 uM; range 65.8-214.7 uM vs. 41.6-99.0 uM)27. Thus it is concluded that intraperitoneal metformin gave a higher suppression of IFNγ and increase of FOXP3 mRNA expression through an plasma level rather than an oral route. In addition, a study by Wang et al. in a scleroderma model has also shown the ability of intraperitoneal metformin to dose dependently reduce IL-17A levels and RORγt expression and increase FOXP3 mRNA expression28.\n\nAlthough this study was able to prove that there was a characteristic change in accordance to lupus nephritis in pristane induced models compared to normal BALB/c, subsequent therapy with metformin failed to produce a statistically significant score change. However, qualitative analysis by blinded pathologists has confirmed that there was at least a difference in renal changes that showed better results in intraperitoneally treated mice compared with oral metformin and placebo control. This result could be caused by a short period of intervention; a longer treatment time could possibly result in a significant difference in renal scoring.\n\nWe did not perform an evaluation of autoantibodies related to SLE, such as anti-dsDNA, anti-Sm and anti-RNP1. However, several murine studies has confirmed the ability of pristane induced BALB/c in producing related auto-antibodies29,30. Our research also did not evaluate the antibody response to metformin therapy; however several studies has shown the ability of metformin in reducing autoantibodies related to SLE10,22. We also did not evaluate the expression of mRNAs related to IFNγ, but several studies has shown that Th1 activity is closely related to IFNγ levels8,31,32. Furthermore it has been recently suggested that the cytokine balance could play an important role in determining active T-cell subsets, changing the phenotype of peripheral T-cells and contributes to the pathogenesis of lupus13,33.\n\n\nConclusions\n\nA murine model of SLE by pristane induced female BALB/c mice could be used to represent a model of lupus similar to the human condition. The increased activity of Th1 and reduced activity of Treg, in this study represented by pro-inflammatory IFNγ levels and FOXP3 mRNA expression, has proven to be related to the development of lupus nephritis. Metformin is a potential new therapy to reduce the levels of IFNγ and increase FOXP3 mRNA expression in SLE and in turn inhibits the development of glomerulonephritis. Intraperitoneal metformin, intravenous in humans, could provide a novel route of administration to improve the effect of metformin on lupus patients.\n\n\nData availability\n\nOpen Science Framework: Metformin on Pristane Induced Lupus, https://doi.org/10.17605/OSF.IO/S9GRP34.\n\nThis project contains the following underlying data:\n\nIFNγ levels for all mice pre and post intervention;\n\nFOXP3 expression fold change for all mice pre and post intervention;\n\nInterstitial and glomerular scoring for all mice; and\n\nUncropped, unedited kidney images for all mice.\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\nCrispín JC, Liossis SN, Kis-Toth K, et al.: Pathogenesis of human systemic lupus erythematosus: recent advances. Trends Mol Med. 2010; 16(2): 47–57. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLateef A, Petri M: Unmet medical needs in systemic lupus erythematosus. Arthritis Res Ther. 2012; 14(Suppl 4): S4. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDolff S, Bijl M, Huitema MG, et al.: Disturbed Th1, Th2, Th17 and T(reg) balance in patients with systemic lupus erythematosus. Clin Immunol. 2011; 141(2): 197–204. PubMed Abstract | Publisher Full Text\n\nGeorge B, Ricard. C, Boumpas DT: Systemic Lupus Erythematosus: Pathogenesis and Clinical Features. Eular On-line Course Rheum Dis. 2012;(1909): 476–505. Reference Source\n\nFinzel S, Schaffer S, Rizzi M, et al.: Pathogenesis of systemic lupus erythematosus. Z Rheumatol. 2018; 77(9): 789–98.\n\nMok CC, Lau CS: Pathogenesis of systemic lupus erythematosus. J Clin Pathol. 2003; 56(7): 481–90. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLech M, Anders HJ: The pathogenesis of lupus nephritis. J Am Soc Nephrol. 2013; 24(9): 1357–66. PubMed Abstract | Publisher Full Text | Free Full Text\n\nViallard JF, Pellegrin JL, Ranchin V, et al.: Th1 (IL-2, interferon-gamma (IFN-gamma)) and Th2 (IL-10, IL-4) cytokine production by peripheral blood mononuclear cells (PBMC) from patients with systemic lupus erythematosus (SLE). Clin Exp Immunol. 1999; 115(1): 189–95. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMardani F, Mahmoudi M, Esmaeili SA, et al.: In vivo study: Th1-Th17 reduction in pristane-induced systemic lupus erythematosus mice after treatment with tolerogenic Lactobacillus probiotics. J Cell Physiol. 2018; 234(1): 642–9. PubMed Abstract | Publisher Full Text\n\nYin Y, Choi SC, Xu Z, et al.: Normalization of CD4+ T cell metabolism reverses lupus. Sci Transl Med. 2015; 7(274). PubMed Abstract | Publisher Full Text | Free Full Text\n\nNath N, Khan M, Paintlia MK, et al.: Metformin Attenuated the Autoimmune Disease of the Central Nervous System in Animal Models of Multiple Sclerosis. J Immunol. 2009; 182(12): 8005–14. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRichards HB, Satoh M, Jennette JC, et al.: Interferon-gamma is required for lupus nephritis in mice treated with the hydrocarbon oil pristane. Kidney Int. 2001; 60(6): 2173–80. PubMed Abstract | Publisher Full Text\n\nTalaat RM, Mohamed SF, Bassyouni IH, et al.: Th1/Th2/Th17/Treg cytokine imbalance in systemic lupus erythematosus (SLE) patients: Correlation with disease activity. Cytokine. 2015; 72(2): 146–53. PubMed Abstract | Publisher Full Text\n\nDuan W, Ding Y, Yu X, et al.: Metformin mitigates autoimmune insulitis by inhibiting Th1 and Th17 responses while promoting Treg production. Am J Transl Res. 2019; 11(4): 2393–402. PubMed Abstract | Free Full Text\n\nRena G, Hardie DG, Pearson ER: The mechanisms of action of metformin. Diabetologia. 2017; 60(9): 1577–85. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSon HJ, Lee J, Lee SY, et al.: Metformin attenuates experimental autoimmune arthritis through reciprocal regulation of Th17/Treg balance and osteoclastogenesis. Mediators Inflamm. 2014; 2014: 973986. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKNEPK: Pedoman Nasional Etik Penelitian Kesehatan 2011. Litbang Kementrian Kesehat. 2011. Reference Source\n\nBossaller L, Christ A, Pelka K, et al.: TLR9 Deficiency Leads to Accelerated Renal Disease and Myeloid Lineage Abnormalities in Pristane-Induced Murine Lupus. J Immunol. 2016; 197(4): 1044–53. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPeng SL, Moslehi J, Craft J: Roles of interferon-gamma and interleukin-4 in murine lupus. J Clin Invest. 1997; 99(8): 1936–46. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPeixoto TV, Carrasco S, Botte DAC, et al.: CD4+CD69+ T cells and CD4+CD25+FoxP3+ Treg cells imbalance in peripheral blood, spleen and peritoneal lavage from pristane-induced systemic lupus erythematosus (SLE) mice.Adv Rheumatol. (London, England). 2019; 59(1): 30. PubMed Abstract | Publisher Full Text\n\nKluger MA, Nosko A, Ramcke T, et al.: RORγt expression in Tregs promotes systemic lupus erythematosus via IL-17 secretion, alteration of Treg phenotype and suppression of Th2 responses. Clin Exp Immunol. 2017; 188(1): 63–78. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHuang L, Kong Y, Wang J, et al.: Reducing progression of experimental lupus nephritis via inhibition of the B7/CD28 signaling pathway. Mol Med Rep. 2015; 12(3): 4187–95. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFu D, Senouthai S, Wang J, et al.: Vasoactive intestinal peptide ameliorates renal injury in a pristane-induced lupus mouse model by modulating Th17/Treg balance. BMC Nephrol. 2019; 20(1): 350. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChung MM, Nicol CJ, Cheng YC, et al.: Metformin activation of AMPK suppresses AGE-induced inflammatory response in hNSCs. Exp Cell Res. 2017; 352(1): 75–83. PubMed Abstract | Publisher Full Text\n\nHowell JJ, Hellberg K, Turner M, et al.: Metformin Inhibits Hepatic mTORC1 Signaling via Dose-Dependent Mechanisms Involving AMPK and the TSC Complex. Cell Metab. 2017; 25(2): 463–71. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLee SY, Lee SH, Yang EJ, et al.: Metformin ameliorates inflammatory bowel disease by suppression of the stat3 signaling pathway and regulation of the between Th17/Treg Balance. PLoS One. 2015; 10(9): e0135858. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDowling RJ, Lam S, Bassi C, et al.: Metformin Pharmacokinetics in Mouse Tumors: Implications for Human Therapy. Cell Metab. 2016; 23(4): 567–8. PubMed Abstract | Publisher Full Text\n\nWang Y, Zhang S, Liang Z, et al.: Metformin attenuates bleomycin-induced scleroderma by regulating the balance of Treg/Teff cells and reducing spleen germinal center formation. Mol Immunol. 2019; 114: 72–80. PubMed Abstract | Publisher Full Text\n\nRichards HB, Satoh M, Shaw M, et al.: Interleukin 6 dependence of anti-DNA antibody production: Evidence for two pathways of autoantibody formation in pristane-induced lupus. J Exp Med. 1998; 188(5): 985–90. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSatoh M, Richards HB, Shaheen VM, et al.: Widespread susceptibility among inbred mouse strains to the induction of lupus autoantibodies by pristane. Clin Exp Immunol. 2000; 121(2): 399–405. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBalomenos D, Rumold R, Theofilopoulos AN: Interferon-gamma is required for lupus-like disease and lymphoaccumulation in MRL-lpr mice. J Clin Invest. 1998; 101(2): 364–71. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLuzina IG, Keegan AD, Heller NM, et al.: Regulation of inflammation by interleukin-4: a review of “alternatives.” J Leukoc Biol. 2012; 92(4): 753–64. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGuimarães PM, Scavuzzi BM, Stadtlober NP, et al.: Cytokines in systemic lupus erythematosus: Far beyond Th1/Th2 dualism lupus: Cytokine profiles. Immunol Cell Biol. 2017; 95(9): 824–831. PubMed Abstract | Publisher Full Text\n\nSumantri S: Metformin on Pristane Induced Lupus.2020;. http://www.doi.org/10.17605/OSF.IO/S9GRP"
}
|
[
{
"id": "63253",
"date": "26 May 2020",
"name": "Shuang Ye",
"expertise": [
"Reviewer Expertise Our group carried out proof-of-concept trial and randomised placebo-controlled trial of metformin in lupus patients."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors tried to illustrate the effect of metformin on pristane-induced mice in terms of IFN-γ levels and FOXP3 mRNA expression. However, the authors did not see the significant difference of renal histopathological score between intervention groups. It is better to provide evidence of effect of metformin on other manifestations, i.e. serological, in this model. The conclusion of \"intravenous administration in human, could provide a novel route of administration....\" could not be drawn from the data provided in the manuscript.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? 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": "5550",
"date": "26 May 2020",
"name": "Stevent Sumantri",
"role": "Author Response",
"response": "Dear Dr Shuang Ye,Many thanks for your review on the research article. Could you kindly advise in which way we could further improve the quality of this article?Regards, Stevent Sumantri MD"
},
{
"c_id": "5589",
"date": "08 Jun 2020",
"name": "shuang ye",
"role": "Reviewer Response",
"response": "1. The authors did not see the positive results of renal histopathology between intervention groups. We suggest to provide evidence of other manifestations, such as autoantibodies, in this model.2. The conclusion of \"intravenous administration in human, could provide a novel route of administration....\" could not be drawn from the data provided in the manuscript, and should be deleted."
},
{
"c_id": "6624",
"date": "11 Jun 2021",
"name": "Stevent Sumantri",
"role": "Author Response",
"response": "Dear Dr. Shuang Ye, Sorry for the late response; I will adjust the conclusion and writing of the reports according to our study limitations. Unfortunately, due to financial constraints, it was not possible to provide antibody data in our study; I will discuss the limitations in my revision. Regards, Stevent Sumantri"
}
]
},
{
"id": "83368",
"date": "27 Apr 2021",
"name": "Erin B Taylor",
"expertise": [
"Reviewer Expertise Lupus",
"autoimmunity",
"immunology",
"renal physiology",
"hypertension."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn the manuscript by Sumantri et al., the authors evaluated metformin in the pristane-inducible model of SLE. The authors tested both oral gavage and intraperitoneal administration of metformin as a treatment. Lupus was induced by a single ip injection of pristane into female BALB/c mice, after which lupus was allowed to develop for 120 days. At this point, mice were given vehicle, oral metformin, or IP metformin daily for 60 days. The experimental endpoints were as follows: the expression of mRNA for the Treg-associated transcription factor FoxP3 and circulating IFN-ɣ, both of which were assessed using blood collected from the tail vein. In addition, and histological examination of H&E stained kidneys was performed. The administration of pristane resulted in an increase in circulating IFN-ɣ and a decrease in the expression FoxP3, and treatment with metformin decreased IFN-ɣ and increased FoxP3 expression. The authors also conclude that treatment with pristane leads to renal injury, including glomerular changes, but minimal mesangial expansion. Treatment with metformin did not lead to significant changes in renal injury. Overall, this manuscript is written clearly, and the methods would be easy to follow if one were to repeat these experiments.\nOne specific concern is the statistical analyses that are used. It is stated that t-tests were used; however, there are five experimental groups. I suggest that the statistical tests be redone using one-way ANOVA, followed by Tukey’s post test for multiple comparisons. Another issue/point of confusion that I have is with the presentation of the data in the Figures and Tables. In both Figure 1 and Figure 2, I suggest adding asterisks or other markers to indicate statistically significant differences among the groups. While it is stated in the text, it would be clearer if it was also on the graphs. Also, are the marks in Figure 1B, 1C, and 2A statistical outliers? Please indicate in the figure legends. In addition, Table 2 states that it is composed of IFN-ɣ and FoxP3 expression after intervention with metformin. While I think these are the data that are presented, the table says “post induction” as in Figure 1, which was referring to post treatment with pristane. I think that Table 2 should be relabeled with “post treatment” or something similar. Finally, the kidney specimens were scored, but those scores were not presented in any format. I would suggest presenting the scoring data in a graphical format in the manuscript.\n\nThe pristane model of SLE mimics human disease in many ways, including increases in IFN-production and dysregulation of T cell subsets. The data that the authors present suggest that metformin may improve the Th subset imbalances (increasing FoxP3, decreasing IFN-ɣ), but direct evidence of this is lacking. The findings could be strengthened by the addition of flow cytometry to assess Th subsets. In addition, the authors indicate that they did not measure immunoglobulins or autoantibodies in their animals. While data may be available in other studies, it would be a good additional piece of data for this study.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\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": [
{
"c_id": "6623",
"date": "11 Jun 2021",
"name": "Stevent Sumantri",
"role": "Author Response",
"response": "Dear Dr. Taylor, Many thanks for your inputs. I will revise the statistical methods and table as soon as possible. Regarding flow cytometry and antibody measurements, unfortunately, it was not possible at this time, but I will put it in discussion for further research plans. Regards, Stevent Sumantri"
}
]
}
] | 1
|
https://f1000research.com/articles/9-342
|
https://f1000research.com/articles/8-1020/v1
|
08 Jul 19
|
{
"type": "Research Article",
"title": "Fracture resistance and 3D finite element analysis of machined ceramic crowns bonded to endodontically treated molars with two planes versus flat occlusal preparation designs: an in vitro study",
"authors": [
"Omnia Nabil",
"Carl Hany Halim",
"Ashraf Hassan Mokhtar",
"Carl Hany Halim",
"Ashraf Hassan Mokhtar"
],
"abstract": "Background: The flat occlusal preparation design (FOD) of posterior teeth offers promising results of fracture resistance and stress distribution, but its application in vital teeth is limited as there may be a danger of pulp injury. Although this danger is omitted in endodontically treated teeth, there is no research work assessing the impact of FOD on the fracture resistance and distribution of stresses among these teeth. The aim of this study was to assess the impact of FOD of endodontically treated molars on the fracture resistance and distribution of stresses among a ceramic crown-molar structure when compared to the two planes occlusal preparation design (TOD). Methods: 20 human mandibular molars were endodontically treated and distributed equally to two groups: Group I (TOD) and Group II (FOD). Ceramic CAD/CAM milled lithium disilicate (IPS e.max CAD) crowns were produced for all preparations and adhered using self-adhesive resin cement. Using a universal testing machine, the fracture resistance test was performed. The fractured samples were examined using a stereomicroscope and scanning electron microscope to determine modes of failure. Stress distribution was evaluated by 3D finite element analysis, which was performed on digital models of endodontically treated mandibular molars (one model for each design). Results: Group II recorded statistically non-significant higher fracture resistance mean values (3107.2± 604.9 N) than Group I mean values (2962.6 ±524.27 N) as indicated by Student’s t-test (t=0.55, p= 0.57). Also, Group II resulted in more favorable failure mode as compared to Group I. Both preparation designs yielded low von-Mises stresses within the factor of safety. However, the stress distribution among different layers of the model differed. Conclusions: FOD having comparable fracture strength to TOD and a more favorable fracture behavior can be used for the preparation of endodontically treated molars.",
"keywords": [
"Two planes occlusal preparation",
"Flat occlusal preparation",
"Endodontically treated molars",
"Ceramic-crown tooth structure",
"Fracture resistance",
"3D Finite Element Analysis."
],
"content": "Introduction\n\nEndodontic treatment weakens posterior teeth and ought to be covered by crowns1. The capability of these crowns to bear load relies on the preparation of an appropriate design and the selection of a crown material with adequate fracture strength and thickness2.\n\nIn vital teeth, the anatomic occlusal preparation design is followed such that the occlusal surface is reduced uniformly, maintaining the cusps, fissures and normal inclined planes but at a reduced height. This aids in minimizing the risk of pulp injury. In contrast, in non-vital teeth, this design can be modified such that the occlusal surface is prepared in two planes (buccal and lingual planes)3.\n\nA flat prepared occlusal surface provides less quantitative and better qualitative stresses when compared to an anatomically prepared surface4. Also, an anatomically prepared occlusal surface follows old preparation configurations for non-bonded crowns and more concern needs to been given to the functioning of bonded crowns, which can preserve tooth structure5.\n\nThe aim of our research was to assess the impact of a flat prepared occlusal surface (FOD) of endodontically treated molars on the fracture resistance and the distribution of stresses among the ceramic crown-molar structure when compared to a two planes prepared occlusal surface (TOD).\n\nThe hypothesis of our research was there would not be significant differences in both fracture resistance and developed stresses of the ceramic crown-molar structure of FOD when compared to TOD of endodontically treated molars (null hypothesis).\n\n\nMethods\n\nThis study was approved by the Research Ethics Committee of the Faculty of Dentistry, Cairo University. Approval number: 15636 (Extended data).\n\nExtracted teeth were obtained from the outpatient clinic, Oral Surgery Department, Faculty of Dentistry, Cairo University. Any researcher in the institute can obtain extracted teeth that meet the criteria of the research without requiring the researcher to contact the patients, since the patients give their consent for their extracted teeth to be used in future research when they are extracted.\n\nStudent’s t-test was performed to compare two groups (Group I: TOD; Group II: FOD), as per a previous study by Shahrbaf et al.5. The primary outcome of this study is the fracture resistance with an estimated mean value of 407.7±82.7 N for the control group (Group I) and 661.1±190 N for the test group (Group II) (effect size =1.7 with alpha 0.05 and power =0.8). Priori power showed that the required sample size should be above 14 (7 in each group) (calculated using G*power release 3.1.9.2). Accordingly, a total sample size of 20 (10 per group) was performed.\n\nTeeth collection, endodontic treatment and coronal build up. In total, 20 human mandibular molars free of caries, defects and cracks were chosen. The mean measurement between the maximum convexity on the buccal and lingual surfaces of the selected teeth differed by ≤ 2.5% (as measured using a digital caliber (Harbor Freight Tools, CA, USA))6. The teeth were kept in distilled water after ultrasonic scaling which was done to remove any remnants. Conventional access cavities were prepared in all teeth. Manual preparation and enlargement of root canals was performed until size # 25 (MANI, Japan)7,8. Rotary root canal preparations were then performed with a series of ProTaper Ni-Ti rotary instruments (Dentsply Maillefer, Switzerland). The matched gutta percha points (Dentsply Maillefer, Switzerland) and resin based sealer (Adseal; META BIOMED Co, Korea) were used for obturation and the excess gutta percha was removed by a heated plugger9. Coronal cavities were then treated with 37% phosphoric acid Etch (Spident, USA) for 15 seconds, rinsed for 10 seconds and dried gently using a cotton pellet. A layer of light cure bonding agent (Adper Single Bond Plus Adhesive; 3M ESPE AG, Germany) was applied with gentle agitation and light cured for 10 seconds, then packable composite resin (3M Filtek Z250 XT Nano hybrid composite resin; 3M Deutschland GmbH, Germany) was incrementally added and light cured10.\n\nTeeth mounting, grouping and preparation. A plastic ring (2.5 cm in diameter and 2 cm in length) was utilized to mount the teeth in epoxy resin (CMB, Egypt) and a custom made paralleling device (Extended data) was used to allow accurate vertical centralization of the tooth in the ring. The mounted teeth were randomly distributed into two equal groups as follows:\n\nGroup I (TOD): Prepared teeth with two planes occlusal surface.\n\nGroup II (FOD): Prepared teeth with flat occlusal surface.\n\nA special milling machine (AF30 Nouvag, Switzerland) was used to prepare all the teeth by the same operator (Figure 1). The preparation parameters are detailed in Table 1.\n\nCrown fabrication and cementation. A CAD/CAM system (CEREC AC; Sirona, Germany) was used for the fabrication of all crowns. Each prepared tooth was scanned using the CEREC Omnicam and design was carried out using CEREC Premium 4.4 software. The distance between central groove of restoration and the occlusal surface of tooth was standardized at 1.5 mm in all restorations. Milling of the crowns was done from Lithium disilicate blocks (IPS e.max CAD; Ivoclar Vivadent AG, Principality of Liechtenstein) in 4-axis milling machine CEREC MC XL. Finally, crowns were fully crystallized and glazed in Programat P510 furnace (Ivoclar Vivadent AG, Principality of Liechtenstein).\n\nSurface treatment of the fitting surface of each crown was done as follows: Porcelain Etch (BISCO, USA) application for 20 seconds, followed by water rinsing and drying, then Silane (BISCO, USA) application for 60 seconds followed by air drying for 5 seconds. Self-adhesive resin cement (RelyX Unicem; 3M ESPE AG, Germany) was used for cementation.\n\nEach crown was seated on its corresponding tooth and held with light pressure. The excess cement was cleared by an explorer after 2 seconds of tack-curing, then glycerine based gel (K-Y Jelly; Johnson & Johnson, USA) was applied at the margins of crown to prevent the oxygen inhibiting layer. A 5 kg load was applied parallel to the long axis of each tooth during cementation using a custom made loading device (Extended data)11,12. The load was applied for 5 minutes to allow the cement to self-cure as recommended by the manufacturer. This was followed by final curing of axial and occlusal surfaces with light cure for 20 seconds.\n\nThe test was carried out using a computer-controlled material testing machine (Instron, Model 3345; Instron industrial, USA). Each sample was tightened to the lower fixed compartment by screws. A compressive load was applied on the occlusal surface utilizing a metallic rod with round tip (5.8 mm diameter) attached to the upper movable compartment traveling at cross-head speed of 1mm/min with tin foil sheet in-between to achieve homogenous stress distribution and to minimize the transmission of local force peaks. The load to fracture was recorded in Newtons (N) using Instron Bluehill Lite Computer Software version 2 (Instron, USA). The fracture was manifested by an audible crack and confirmed by a sharp drop at load-deflection curve.\n\nData from the two groups were gathered, arranged and analyzed using SPSS (version 21; IBM, USA).\n\nHigh-performance Leica MZ6 Stereomicroscope (Meyer Instruments, USA) with 6.3:1 zoom was used to evaluate the fracture mode of the samples, indicating areas of interest for further examination under a scanning electron microscope (SEM; Model Quanta 250 Field Emission Gun; FEI Company, The Netherlands) attached with Energy Dispersive X-ray Analyses unit, with 30 KV accelerating voltage, 70X, 250X magnification and resolution of 1nm.\n\n3D designing of models\n\n3D scanning. Two of the prepared samples (one for each group) and their corresponding crowns were scanned before cementation to produce models with real geometrical measures. 3D reconstruction from cone beam computed tomography (CBCT) data of the teeth scans was found had high linear, volumetric, and geometric accuracy13. A CBCT scanner (Next Generation iCAT scanner; ISI, USA) was used to obtain CBCT images in this research. After scanning, data were exported in DICOM format. Mimics software version 17 (Materialise, Belgium) was useda for segmenting the scanned objects into separate elements. A definitive threshold level was set to most clearly show each element of the scanned samples with minimal interference from the surrounding structures, and once segmentation was completed the software automatically calculated the element’s volume. The resulting STL files were opened separately on Meshmixer software version 3.3.15 (Autodesk Inc., USA) for the improvement of mesh quality and its refinement.\n\nReverse engineering and assembly. Reverse engineering was performed by NX software version 10 (Siemens PLM, Texas, USA)b. The refined STL files were imported into the software and converted into solid parts. Then, cortical bone and cancellous bone were drawn as solid parts in cylindrical shapes followed by their superimposition together for Boolean subtraction. Finally, all the produced solid parts were superimposed together for Boolean subtraction and periodontal ligaments were modeled with 0.2 mm thickness to allow a fully defined simulation methodology. The generated 3D CAD geometry of all parts were then assembled using Solidworks software 2017 (Dassault Systèmes SolidWorks Corporation, France)c to produce the 3D CAD models, one for each group (Figure 2).\n\nFinite element analysis. Finite element analysis (FEA) was carried out by ANSYS R16.2 software (ANSYS, Canonsburg, USA)d using the 3D CAD models. It included 3 phases:\n\nPre-processing phase. The type of element was defined as Solid 10 node 187. All the materials’ properties were set as isotropic, homogenous and linear elastic. The modulus of elasticity and Poisson’s ratio of each material were gathered and were uploaded to the software (Table 2). A perfect rigid bonding with no-slip condition between all the elements was simulated. Each model was divided into small parts called elements connected together at points called nodes forming a mesh structure. Parabolic tetrahedral solid elements were used to form a fine solid mesh. The overall number of elements and nodes was recorded (Table 3).\n\nProcessing phase. Following the creation of the 3D meshes, a zero displacement boundary condition was set at all nodes of the cortical bone that were confined in X, Y, and Z directions. Posterior fixed restorations ought to have the capability to tolerate a 500 N occlusal load18,19. Accordingly a load of 500 N was applied by a ball model of diameter 5.8 mm equal to that of metallic rod ball of the universal testing machine used for fracture resistance test in this study. The occlusal surface of the crown was loaded at the inner inclines of the mesiobuccal, distobuccal and mesiolingual cusps20. The load was applied in vertical direction as the masticatory forces directed onto molar teeth is mostly vertical, while through the anterior guidance and lateral guidance, they are guarded by the anterior teeth21.\n\nPost-processing phase. The output of the processing phase was displayed as graphical output and numeric output.\n\n\nResults\n\nFracture resistance results as a function of preparation design are summarized in Table 4.\n\nIt was found that the fracture resistance mean ± SD value recorded for Group I was 2962.6 ± 524.2 N, with minimum value of 2206.01 N and maximum value of 4014.7 N. For Group II, the mean ± SD value recorded was 3107.2 ± 604.94 N, with minimum value of 2253.5 N and maximum value of 4153.4 N.\n\nThe difference between the mean fracture resistance between the two groups was non-statistically significant as indicated by Student’s t-test (p=0.57) (Figure 3).\n\nThe behavior of the samples upon fracture differed (Table 5). Five different modes were observed and categorized as restorable or non-restorable according to their relation to the cemento-enamel junction (CEJ). A fracture that ends before CEJ, implying that even after the occurrence of fracture, the tooth can be saved is a restorable one, while fractures that are non-restorable extend beyond CEJ and extraction of the tooth is expected22. The extensions of the cracks were verified by SEM (Figure 4). The results are tabulated in Table 6 and classified as restorable and non-restorable.\n\nRestorable remaining tooth structure: modes I, II and IV; non-restorable remaining tooth structure: modes III and V.\n\nIn each model, FEA revealed stresses at every node. These results were presented as stress contours overlaid on the model. The numeric data of stress, deformation and safety factor in the models were calculated and transformed into color graphics.\n\nEquivalent (von-Mises) stress. The \"von-Mises Stress\" at different areas were calculated and compared (Table 7). The stress distribution values were generally found to be low.\n\nRed dot marks the higher value.\n\nTotal deformation. The maximum value of total deformation denoted by the red color in Group I was 0.0158 mm. It was concentrated on the mesial half of the coronal portion of model (Crown, dentin and core) and the root (neck of the tooth) at the mesial surface and the mesial half of the lingual surface (Figure 5). While in Group II the maximum value of total deformation was 0.01409 mm. It was located on middle and the lingual half of coronal portion of model and the lingual neck of the tooth with mesiolingual and distolingual line angles (Figure 6). When comparing both groups, Group II yielded less total deformation values than Group I.\n\nSafety factor. Both groups had high safety factor where the maximum equivalent stress was less than the stress limit. In Group I: the lowest safety factor recorded was 1.5575 was at the mesial neck of the tooth denoted by the orange color (Figure 7). In Group II: the lowest safety factor recorded was 1.1571 was at the lingual neck of the tooth denoted by the orange color (Figure 8).\n\nThe stress distribution among different layers of the model differed as well as areas of total deformation. This was correlated with the fracture behavior of samples of both groups as follows:\n\nGroup I (Figure 9). The stress values were high at mid-mesial and mid-lingual axial walls, mid-mesial and mid-lingual finish line, and root’s mesial surface. Maximum total deformation was concentrated in the mesial half of the coronal portion of model (crown, dentin and core) and the neck of the tooth at the mesial surface and mesial half of the lingual surface.\n\nUpon observation of fracture behavior of Group I samples of fracture resistance, the failure in most of the samples occurred at the mesial half of the crown-tooth structure including the finish line and the root (neck of the tooth).\n\nGroup II (Figure 10). The centers of the crown and the underlying core material generated high stress values upon load application. Also, at mesiobuccal cusp, mesiolingual cusp, mesial marginal ridge, and root’s lingual surface stresses were high. Maximum total deformation was located at the middle and the lingual half of coronal portion of model (crown, dentin, and core) and the lingual neck of the tooth with mesiolingual and distolingual line angles.\n\nUpon observation of fracture behavior of Group II samples of fracture resistance, the failure in more than half of the samples occurred at the lingual half of the crown-tooth structure, not including the finish line and the root (neck of the tooth).\n\n\nDiscussion\n\nPrevious research has generally given minimal concern to the impact of the preparation configuration on the ability of the crown-tooth structure to resist fracture and distribute stresses, and instead has mainly targeted the crown material itself5. Thus, the focus of this study was to specifically address the impact of the prepared occlusal surface configuration comparing two planes occlusal preparation (TOD) versus flat occlusal preparation (FOD) of endodontically treated molars.\n\nIn our study, mandibular molars were chosen due to their high incidence for developing caries, their subjection to strong occlusal loads and greater susceptibility to fracture23. Single-cone obturation technique was followed to exclude the inordinate cutting of dentin needed to ease the entry of the endodontic plugger in vertical warm condensation technique and the wedge-acting stresses of the spreaders during lateral cold condensation technique24. Lithium disilicate ceramic was chosen for crown fabrication. This ceramic material features appropriate mechanical and esthetic qualities for making monolithic restorations, allowing conservative tooth preparation and simplicity of production25. Self-adhesive resin cement was selected as it was revealed that the use of adhesive cement raised the fracture resistance by almost 26% when utilized with lithium disilicate glass ceramic as compared to non-adhesive cement26.\n\nPeriodontal ligament (PDL) was not simulated. Upon the application of a static load, no difference was anticipated in the resistance of teeth to fracture whether their roots were covered with a PDL simulating material or not. Moreover, the thickness of the silicone PDL simulating material used to cover the roots was found to be thicker than the normal PDL thickness. Also, with the difficulty to unify the thickness of this material, there was no control on the movability of the investigated teeth and more drawbacks were expected27.\n\nInvestigation of the fracture resistance of crown-molar structure was the primary study objective. Static load fracture test was employed in an occluso-axial direction, which is viewed as the most well-known strategy for testing the integrity of a structure5.\n\nChecking the areas of stress is crucial as stress, regardless of if it is beneath the point of failure, is considered as a noteworthy reason for propagation of a crack and henceforth failure. 3D FEA has been used to investigate stress bearing and handling capabilities of various restoration materials and shapes in a safe and time saving method18.\n\nFEA simulated the test of fracture resistance performed in this investigation to demonstrate the generated points of stress subsequent to load application. A good-bond interlayer condition was assumed between the distinctive layers in the model.\n\nOur results failed to reject the null hypothesis that FOD of endodontically treated molars would not differ in both fracture resistance and the generated stresses of the ceramic crown-molar structure when compared to TOD.\n\nThe results of fracture resistance test displayed no significant difference statistically between both tested groups with an average ˃ 2900 N, which surpasses the average and maximum biting force reported in the mouth (100-600 N)28.\n\nAlso, these results exceeded those of other studies. According to Nordahl et al.29 the mean fracture resistance of e.max lithium disilicate crowns of posterior molars of thickness 1.5 mm was 1,431 N while according to Yu et al.22 it was 1827.3 N. This can be attributed to the exposure of crowns in both studies to artificial aging before loading until fracture. The exposure of the crowns to aging was stated in various investigations to diminish the resultant fracture loads significantly29,30.\n\nRegardless of the close and clinically satisfactory fracture resistance results of both investigated designs, the failure mode varied. It was found that 20% of Group I (TOD) had undergone restorable fractures, while in Group II (FOD) this was 60%. This denotes that FOD showed better stress distribution, thus more favorable fracture behavior.\n\nThe 3D FEA data recorded in this study showed that both preparation designs yielded low von-Mises stresses within the factor of safety of the model. In both groups, high stresses and deformation were induced in the lingual surface of molars. This was justified by the weakening effect of the hard tissue loss on the mandibular molars, which might predispose the lingual wall to fracture due to unfavorable distribution of stresses during chewing31. This was confirmed by Oyar et al.2 who found high stress values were generated in the lingual dentin regions in both anatomic and non-anatomic occlusal preparation designs.\n\nUpon observation of fracture behavior of samples of fracture resistance test and correlating it with the results of the FEA, the following were concluded: Group I (TOD) developed lower stresses in the center of the crown and the core, and the stresses increased upon moving apically towards the root with greater influence on the mesial half of the model. This explained the failure pattern in most of the samples that occurred at the mesial portion of the crown-molar structure including the finish line and the root (neck of the tooth). While Group II (FOD) developed higher stresses in the center of the crown and the core, and the stresses decreased upon moving apically towards the root with greater influence on the lingual half of the model. This explained the failure pattern in more than half of the samples which occurred at the lingual portion of the crown-molar structure without the inclusion of finish line and root (neck of the tooth).\n\nOur results differed than other studies regarding the stress distribution pattern. According to, Oyar et al.32 the anatomically prepared design yielded better stress distribution in dentin while the non-anatomic design yielded better distribution and less amount of stresses in the porcelain structure. Their study was carried out on mandibular second premolars restored by metal-ceramic crowns.\n\nWhile Shahrbaf et al.4 concluded that the flat occlusal configuration presented lower stresses than the anatomic configuration in all layers and a more favorable distribution. Their study was carried out on maxillary first premolars with variable amount of occlusal reduction, such that 2 mm even reduction for the anatomic design and 1.2 mm reduction from the central groove for the flat one.\n\nOyar et al.2 found that different designs did not result in differences in the generated stresses in tooth (dentin, pulp) and bone. However, the anatomic design crown had the highest value of stresses and this was attributed to the crown thickness, which was less than that of the non-anatomic. Their study was conducted on mandibular second premolar teeth.\n\nIn the current researchers’ opinion, the comparable results obtained among the two tested groups in the present study could be attributed to multiple factors: First, unifying the ceramic thickness at the fissure depth to 1.5 mm thickness, which is the most critical area for failure; second, selecting lithium disilicate monolithic crowns as the material of choice with its well-known high mechanical properties in terms of flexural strength and good bonding potential to tooth and composite resin; third, conducting adhesive bonding protocol using adhesive composite resin cement, which has a positive impact on overall fracture resistance of the ceramic-molar structure.\n\nThe fracture resistance test used in this research is considered a limitation, as it does not precisely mimic the load application inside patient’s mouth, which is a cyclic loading process. Also, another limitation is the consideration of having a perfect bond between the crown and tooth in FEA method.\n\n\nConclusions\n\n1. Flat and two planes occlusal preparation designs of endodontically treated molars had fracture resistance values surpassing the average and maximum biting force reported in the mouth.\n\n2. Flat and two planes occlusal preparation designs of endodontically treated molars showed stress values within the safety factor when subjecting the models to the average biting force.\n\n3. Flat occlusal preparation design showed more favorable mode of failure as compared to two planes occlusal preparation design based on the fractographic and 3D finite element analyses.\n\n4. Flat occlusal preparation design can be used safely with endodontically treated molars.\n\nThe occlusal reduction of endodontically treated molars can influence the functioning of the crown-molar structure. The occlusal surface preparation design has to strengthen the prepared tooth to sustain the forces being subjected to and, upon failure, it favors a restorable mode.\n\nThis study revealed that restorable fractures were higher in flat occlusal preparation design than two planes occlusal preparation design. Therefore, clinicians may choose the flat occlusal preparation design to improve the clinical performance and longevity of the restored endodontically treated molars.\n\n1. Clinical studies comparing the behavior of the two tested designs.\n\n2. Designing the same research using other contemporary metal free crown materials (hybrid materials, polycrystalline materials), which may yield different outcomes.\n\n\nData availability\n\nOpen Science Framework: Fracture Resistance and 3D Finite Element Analysis of Machined Ceramic Crowns Bonded to Endodontically Treated Molars with Two Planes versus Flat Occlusal Preparation Designs. “In-Vitro Study”, https://doi.org/10.17605/OSF.IO/WMRU433.\n\nThis project contains the following underlying data:\n\n- 3D FEA results (.xlsx files)\n\n- Fracture resistance data (.xlsx file)\n\n- SEM raw data (.doc file)\n\n- FEA output (.mechdat files)\n\n- Solidworks software 2017 files, 3D models (.x_t files)\n\n- Instron Lab fracture resistance output report\n\nOpen Science Framework: Fracture Resistance and 3D Finite Element Analysis of Machined Ceramic Crowns Bonded to Endodontically Treated Molars with Two Planes versus Flat Occlusal Preparation Designs. “In-Vitro Study”, https://doi.org/10.17605/OSF.IO/WMRU433.\n\nThis project contains the following extended data:\n\n- Ethical approval document\n\n- Custom made paralleling device\n\n- Custom made loading device",
"appendix": "Grant information\n\nThe author(s) declared that no grants were involved in supporting this work.\n\n\nAcknowledgements\n\nWe would like to express our thanks and appreciation to Mohamed Gamal Askar (MSc, Research Assistant, Mechanical Department, Faculty of Engineering, Helwan University) for his efforts, excellent work and beneficial remarks regarding 3D FEA.\n\n\nFootnotes\n\na Free alternative software that could be used for this analysis is ITK-SNAP.\n\nb Free alternative software that could be used for this analysis is FreeCAD.\n\nc Free alternative software that could be used for this analysis is FreeCAD.\n\nd Free alternative software that could be used for this analysis is OpenFoam V6.\n\n\nReferences\n\nNagasiri R, Chitmongkolsuk S: Long-term survival of endodontically treated molars without crown coverage: a retrospective cohort study. J Prosthet Dent. 2005; 93(2): 164–170. 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J Adhes Sci Technol. 2017; 31(13): 1454–1466. Publisher Full Text\n\nGarlapati TG, Krithikadatta J, Natanasabapathy V: Fracture resistance of endodontically treated teeth restored with short fiber composite used as a core material-An in vitro study. J Prosthodont Res. 2017; 61(4): 464–470. PubMed Abstract | Publisher Full Text\n\nCelikten B, Uzuntas CF, Gulsahi K: Resistance to fracture of dental roots obturated with different materials. Biomed Res Int. 2015; 2015: 591031. PubMed Abstract | Publisher Full Text | Free Full Text\n\nYu T, Wang F, Liu Y, et al.: Fracture behaviors of monolithic lithium disilicate ceramic crowns with different thicknesses. RSC Adv. 2017; 7: 25542–25548. Publisher Full Text\n\nLim MJ, Lee KW: Effect of adhesive luting on the fracture resistance of zirconia compared to that of composite resin and lithium disilicate glass ceramic. Restor Dent Endod. 2017; 42(1): 1–8. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChang CY, Kuo JS, Lin YS, et al.: Fracture resistance and failure modes of CEREC endo-crowns and conventional post and core-supported CEREC crowns. J Dent Sci. 2009; 4(3): 110–117. Publisher Full Text\n\nSadighpour L, Geramipanah F, Raeesi B: In Vitro Mechanical Tests for Modern Dental Ceramics. J Dent. 2006; 3(3): 143–152. Reference Source\n\nNordahl N, Vult von Steyern P, Larsson C: Fracture strength of ceramic monolithic crown systems of different thickness. J Oral Sci. 2015; 57(3): 255–261. PubMed Abstract | Publisher Full Text\n\nSkouridou N, Pollington S, Rosentritt M, et al.: Fracture strength of minimally prepared all-ceramic CEREC crowns after simulating 5 years of service. Dent Mater. 2013; 29(6): e70–e77. PubMed Abstract | Publisher Full Text\n\nDejak B, Młotkowski A, Romanowicz M: Finite element analysis of stresses in molars during clenching and mastication. J Prosthet Dent. 2003; 90: 591–597. PubMed Abstract | Publisher Full Text\n\nOyar P, Ulusoy M, Eskitascioglu G: Finite element analysis of stress distribution of 2 different tooth preparation designs in porcelain-fused-to-metal crowns. Int J Prosthodont. 2006; 19(1): 85–91. PubMed Abstract\n\nNabil O: Fracture Resistance and 3D Finite Element Analysis of Machined Ceramic Crowns Bonded to Endodontically Treated Molars with Two Planes versus Flat Occlusal Preparation Designs. “In-Vitro Study.” 2019. http://www.doi.org/10.17605/OSF.IO/WMRU4"
}
|
[
{
"id": "57384",
"date": "05 Dec 2019",
"name": "Gürel Pekkan",
"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 manuscript is well organised and well written. However, it needs more literature review in the introduction as well as discussion of some points that are listed below:\nIn the introduction, give more literature review about the core build-up materials and techniques.\n\nGive more info about the prosthetic materials and the reasons for the choice of different restorative materials in endodontically treated teeth.\n\nPlease discuss the ball-contact points and localization in the test configuration that would affect the force distribution in the tooth.\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": "6744",
"date": "11 Jun 2021",
"name": "Omnia Nabil",
"role": "Author Response",
"response": "Thank you very much for your careful reading and useful comments. Your effort and time are much appreciated. A second version of the article has been submitted, which has the following changes made in response: In the introduction, more literature review has been given about the core build-up materials and techniques. (Paragraphs 1 and 2) In the introduction, more info about the prosthetic materials and the reasons for the choice of different restorative materials in endodontically treated teeth has been added. (Paragraphs 3, 4 and 5) In the discussion, the ball-contact points and direction of load have been addressed. (Paragraph 4)"
}
]
},
{
"id": "50923",
"date": "09 Mar 2020",
"name": "Tarek Salah",
"expertise": [
"Reviewer Expertise Prosthodontics",
"Esthetic dentistry",
"Digital dentistry",
"Implantology"
],
"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 research and of high clinical interest and I really appreciate the work of the authors. It is definitely publishable material after some revisions.\n\nMaterials and Methods:\nWhy didn’t you consider doing mechanical cyclic loading before the fracture resistance testing? I think it would have been more clinically significant.\n\nMore details are needed concerning teeth dimensions.\n\nAccess cavity design and dimensions should be also described as all these details are important in behavior of the teeth during fracture resistance testing. And also, please mention the master apical file size.\n\nTo which level were the teeth mounted in the epoxy resin?\n\nThere should be more elaboration on specifics of teeth preparation designs, especially occlusal designs. A diagram would be highly beneficial. The photograph is not that descriptive.\n\nWhat were the details of crowns dimensions and standardization during designing?\n\nTesting:\nIndicate the points of load application during fracture resistance testing?\n\nStatistical analysis:\nThere are no details. What type of tests or analysis did you perform?\n\nFEA:\nThe model designing step needs more description especially the role of CBCT and the correlation with the 3D scanning.\n\nFig 3:\nJust mention Bar chart or column chart.\n\nFig 4:\nIndicate which mode of failure that figure is.\n\nDiscussion:\nParagraphs 2 to 6 are not necessary. Go straight for the interpretation after paragraph 1.\n\nReference 33 has no journal.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "6745",
"date": "11 Jun 2021",
"name": "Omnia Nabil",
"role": "Author Response",
"response": "Thank you very much for your careful reading, useful comments and accepting our article. Your effort and time are much appreciated. A second version of the article has been submitted, which has the following changes made in response: Materials and Methods: Why didn’t you consider doing mechanical cyclic loading before the fracture resistance testing? I think it would have been more clinically significant. In our study we focused on the impact of the occlusal preparation design only on the fracture resistance and stress distribution among a ceramic crown-molar structure. A static load fracture test was preferred to avoid the addition of any variables that can be caused by fatigue testing. More details concerning teeth dimensions. The bucco-lingual dimension of crown as measured between the buccal and lingual maximum convexities was (10.5 ± 0.25 mm), while the mesio-distal dimension at cervix was (9 ± 0.25 mm) as measured using a digital caliber (Harbor Freight Tools, CA, USA). Access cavity design and dimensions should be also described as all these details are important in behavior of the teeth during fracture resistance testing. And also, please mention the master apical file size. In all teeth, the access cavity was prepared with a round diamond bur which was directed at center. The undercuts of dentin had been removed with long shafted round bur and finally finishing and flaring was carried out by safe ended diamond bur to allow straight-line access for instrumentation of the apical part of the canal. The access cavity was triangular in case of single distal canal and trapezoidal in case of 2 distal canals, with the lesser base corresponding to the distal wall. Rotary root canal preparations were then performed with a series of ProTaper Ni-Ti rotary instruments (Dentsply Maillefer, Switzerland). The canals were prepared to F2 (D1 diameter 0.25 mm), while larger canals were shaped to F3 (D1 diameter 0.3 mm). To which level were the teeth mounted in the epoxy resin? The mid-facial extent of the cementoenamel junction was located 2 mm coronal to the resin top surface. There should be more elaboration on specifics of teeth preparation designs, especially occlusal designs. A diagram would be highly beneficial. The photograph is not that descriptive. A diagram has been added. What were the details of crowns dimensions and standardization during designing? With the purpose of standardization, the restoration parameters were fixed for all the restorations with the radial spacer set at 60 µm, minimal thickness occlusal 1500 µm and minimal thickness radial 1200 µm. The restoration’s position in 3D (buccolingually, mesiodistally and occlusocervically) was adjusted by rotation tools to follow the anatomy of the prepared tooth. The distance between central groove of restoration and the occlusal surface of tooth was standardized at 1.5 mm in all restorations. Testing: Indicate the points of load application during fracture resistance testing? 3 Loading points: 2 points on the inner inclines of the mesiobuccal and distobuccal cusps and 1 point on the inner incline of the mesiolingual cusp. A figure has been added Statistical analysis: There are no details. What type of tests or analysis did you perform? Data analysis was performed using IBM SPSS, version 21 (SPSS, Chicago, IL, USA). Student t-test was used to detect significance between two groups which was set at 5% for all statistical analyses and confidence interval at 95% such that P values ≤0.05 were considered to be statistically significant FEA: The model designing step needs more description especially the role of CBCT and the correlation with the 3D scanning. CBCT 3D scanning of two of the prepared samples (one for each group) and their corresponding crowns was done before cementation. After scanning, data were exported in DICOM format. Mimics software version 17 (Materialise, Belgium) was used for segmenting the scanned objects into separate elements. A definitive threshold level was set to show each element of the scanned samples most clearly with minimal interference from the surrounding structures, and once segmentation was completed the software automatically calculated the element’s volume. The resulting STL files were opened separately on Meshmixer software version 3.3.15 (Autodesk Inc., USA) for the improvement of mesh quality and its refinement. Now we have the components of crown-tooth structure as separate elements of known volumes that can be assembled together in STL file format of improved quality. A figure has been added to show components of STL files as separate elements Fig 3: Just mention Bar chart or column chart. Column chart. Fig 4: Indicate which mode of failure that figure is. Mode of failure III Discussion: Paragraphs 2 to 6 are not necessary. Go straight for the interpretation after paragraph 1. We think that justifying the important steps in the methodology would be beneficial for other readers to justify our choices. References: Reference 33 has no journal. It is a reference to our article account on Open Science Framework to access all the extended data of our work."
}
]
}
] | 1
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https://f1000research.com/articles/8-1020
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https://f1000research.com/articles/10-167/v1
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01 Mar 21
|
{
"type": "Study Protocol",
"title": "Estimating epidemiological and economic burden and community derived disability weights for snake bite in Kerala: a study protocol",
"authors": [
"Jaideep C. Menon",
"Denny John",
"Geeta R. Menon",
"Joseph K. Joseph",
"P. Rakesh Suseela",
"VV Pillay",
"Denny John",
"Geeta R. Menon",
"Joseph K. Joseph",
"P. Rakesh Suseela",
"VV Pillay"
],
"abstract": "Background: In India, geographical variation, lack of data and underreporting on cases and deaths due to snakebite makes it difficult to estimate socio-economic burden of snakebites. Previous studies measuring economic burden of snakebite in low-and-middle-income countries (LMICs) using different approaches have been conducted, but none so far in India. The proposed study aims to provide evidence on disability weights, epidemiological and economic burden due to snakebites in Kerala state, India. Protocol: A cross-sectional community based study for estimating epidemiological and economic burden of snakebite, recruiting victims of snakebite occurring over a nine month period prior to start and over the three month period of the study, across Ernakulam district, Kerala state, India. For the community derived disability weights, 60 adult patients admitted and treated at Amrita Institute of Medical Sciences, Kochi or Little Flower Hospital, Angamaly would be interviewed. The sample size to determine the mortality rate is calculated at 108,458 persons in Ernakulam.The study will measure annual incidence, mortality, treatment cost of snakebites along with community-derived disability weights for snakebites. Standard methods for analysis and reporting of mortality, morbidity, years of lives lost, years lived with disability, disability weights, and costs of treatment will be calculated and presented. The study will be started in March 2021 and is expected to be completed by June 2021. Discussion: This protocol is the first published for estimating epidemiological, economic burden and community derived disability weights for snakebites in India. Besides, the Global Burden of Disease has not attached a particular disability weight to snakebite and this would be an attempt to do so.The protocol has been developed using guidelines for both cross-sectional studies and for conducting community derived disability weights. The evidence generated will contribute to knowledge regarding epidemiology, economic burden and community-derived disability weights for snakebites in India and other LMICs.",
"keywords": [
"snakebite",
"epidemiology",
"economic burden",
"disability weight",
"DALY"
],
"content": "Abbreviations\n\nASHA; Accredited Social Health Activist\n\nCMO: Chief Medical Officer\n\nDALY: Disability-adjusted life years\n\nDW: Disability Weights\n\nDMO: District Medical Officer\n\nDPM: District Programme Management\n\nGBD: Global Burden of Disease\n\nNHM: National Health Mission\n\nVAS: Visual Analogue Scale\n\nYLD: Years lived with disability\n\nYLL: Years of lives lost\n\n\nIntroduction\n\nSnakebite is a major public health problem in the rural communities of Asia, Africa, and Latin America, and most neglected among all the neglected tropical diseases. Many studies on the bio-medical perspectives of snakebite exist but very few studies have been conducted from a socio-economic viewpoint1. Global estimates ofsnakebite range from 4.5 million to 5.4 million annually with an estimated 2 million of them in India, with tremendous socioeconomic consequences2. As per the Registrar General of India-Million Death Study (RGI-MDS), the number of deaths due to venomous snakebite in India is 46,900 per year3. Reports suggest that only 20–30% victims of snakebite in rural India seek treatment in hospitals4. A recent update of the MDS suggests that the number of deaths are higher still at 58,000 per year5.\n\nThe geographical variation, lack of data and underreporting on cases of snakebites and deaths makeit difficult to estimate socio-economic burden of snakebite in India. Few studies have provided data on mortality, cause of death , hospital based case series (in Maharashtra, West Bengal, Kerala and Andhra Pradesh states), compensations paid to snakebite victims and socio-economic impact6–14.\n\nAlong with mortality, snakebite may lead to physical and psychological impairment, scarring, permanent residual disability, blindness, malignant ulcers, pregnancy loss and of productivity following hospitalisation and incapacitation15. The Disability Adjusted-Life Years (DALYs) is a widely used metric for quantifying disease burden16. One DALY is equal to one lost year of healthy life. The sum of the DALYs for all diseases, across all age groups and either gender is a measure of the gap between current health status and an ideal health situation where the entire population lives to an advanced age, free of disease and disability.\n\nPrevious studies measuring economic burden of snakebites in low and middle income countries have used different approaches for estimating DALYs for snakebites. Kasturiratne et al. (2017), in measuring economic burden of snakebites in Sri Lanka, used disability weights for poisoning from the 2013 Global Burden of Disease (GBD) study as a surrogate17. The duration of an episode of snakebite with envenoming was considered to be 0.3 years. For snakebite without envenoming disability weight of 0.006 (lower estimate) and 0.108 (higher estimate) were used; the higher estimate being a surrogate for open wounds as per the GBD study. The duration of illness of snakebite without envenoming was considered to be 0.04 years. Habib et al. (2015) used a meta-analytic approach to project annual epidemiological burden of snakebite envenoming in sub-Saharan Africa using pooled rates of incidence, amputation, and mortality rates18. These estimates were applied to sub-Saharan population for deriving estimates of mortality and amputations. The standard loss functions based on projected frontier period life expectancy at birth for Japan and South Africa in the year 2050 estimated at 91.9 years (undiscounted) minus the mean age at the time of envenoming was used to calculate years of lives lost (YLL). Years lived with disability (YLD) were estimated by multiplying the number of amputations by the respective disability weight of 0.13 and applying this disability weight for the remainder of undiscounted local life expectancy. In Nigeria, Habib et al. (2015) used cost per DALY averted to measure the cost-effectiveness of antivenoms for snakebite envenoming19. The study used associated amputation-related disability weight of 0.12.\n\nThis proposed study aims to address some of these issues by conducting a retrospective incidence study to provide evidence on disability weights, epidemiological and socio-economic burden due to snakebites in Kerala state, India.\n\nThe study will be conducted in Ernakulam district of Kerala to provide a state specific estimate on incidence, mortality, pattern of injuries, treatment seeking behaviour and cost of illness among snakebite victims. Additionally, the study will conduct a health state valuation to account for societal perspectives in estimating disability weights for snakebites.\n\nThere is lack of data and underreporting on cases of snakebites and deaths that makes it difficult to estimate socio-economic burden of snakebite in India. Disability-weights (DWs) are values obtained from an individual’s perception of health states. It is to be noted that Global Burden of Disease (GBD) disability weights are not universal in nature as social and cultural contexts of health states were not accounted for in the GBD process20. This is mainly because the GBD valuers generally, were educated professionals either from medical or health fields and could easily participate in the cognitively demanding valuation methods20–25. Although of late GBD and numerous other studies started including the general population along with professionals as participants, these studies were unable to capture the community-level perception of individual health states thus eliciting over-or-under-estimation of health states20,26–31.\n\nIt is envisaged that the derived DWs from this proposed studyalong with the epidemiological and economic burden estimations, would be useful for future researchers and policymakers in the country to guide further research and policy in management of snakebites in the country.\n\nThe aim of this study is to estimate the epidemiological and socio-economic burden and community-derived disability weights due to snakebites in Kerala state, India.\n\nPrimary objectives\n\n1. To determine the prevalence, morbidity and mortality due to snakebite in Ernakulam district of Kerala state, India.\n\n2. To determine the economic burden due to snakebites in the community.\n\n3. To determine the community-derived disability weights for snakebites.\n\n\nMethods\n\nA cross-sectional study involving adult populations for estimating epidemiological and economic burden of snakebite will be conducted. These adults will be recruited over a total period of 12 months, 9 months prior to start of study and the 3 months of the study duration across various Gram Panchayats in Ernakulam district, Kerala state. For the community-derived disability weights, 60 adult patients admitted in the three months prior to start of data collection at either of Amrita Institute of Medical Sciences (AIMS), Kochi Hospital or Little Flowers Hospital (LF), Angamaly would be interviewed. The study will be started in March 2021 and is expected to be completed by June 2021.\n\nErnakulam district, with an area of 3063 sq. km, has a population of 3.47 million. Industry and service sectors are the main sources of occupation in the urban areas with agriculture being so in the eastern part of the district. Export oriented fishing industry is also a major source of revenue and occupation towards the coast.\n\nEpidemiological and economic burden. Victims and family members, identified by community health workers (ASHAs), with a history of snakebite in the preceding 12 months will be included for the socio-demographic and economic costsaspect of the study.\n\nCommunity-derived disability weights. The victims interviewed would include individuals who received treatment for snakebite either as an out or inpatient in the immediate nine months preceding the date of start of the study. The victims would include those identified at the community level by ASHA workers in addition to patients admitted and treated for snakebite within the three months of study duration in hospitals in the district treating snakebite. Victims thus identified from in-patient records of treating hospitals would be included, if residents of Ernakulam district. The length of hospital stay of individual patients would be accessed from both hospital records of patients admitted within the three month period of study and copies of discharge records of victims identified from community screening by ASHA workers.\n\nFor our study we will be using the Visual Analogue Scale (VAS) to valuate health states on a continuous graduated line segment, one end labelled as ‘death’ and the other labelled as ‘perfect health’ ranging from 0 to 100. The VAS allows the user to rate a particular health state between the mentioned anchor points, i.e. death and perfect health.\n\nFor the study component related to disability weights, victims admitted and treated for snakebite at AIMS, Kochi or Little Flower Hospital, Angamaly over the three month period prior to the start of study would be interviewed. Additionally, victims with a history of snakebite in the preceding nine months would also be interviewed for the epidemiologic and economic burden components of the study and prospectively so in victims admitted in the two afore-mentioned hospitals over the study period of three months.\n\nSymptoms related to poisoning other than due to snakebite or non-ophid bites and those not willing to provide consent will be excluded.\n\nEpidemiological and economic burden. For estimating the epidemiological and economic burden, a population-level epidemiological study will be conducted covering all gram panchayats (n= 82) in Ernakulam district of Kerala state, India, using a pre-specified questionnaire to capture demographic characteristics (area of residence, age, gender, education, household income etc), details of snakebite (envenomation, site, wound type), treatment (hospitalisation, outpatient, investigations), outcomes (number of days of hospitalisation, death) and costs (outpatient, investigations, hospitalisation, funeral). Based on the estimated population and households in a previous Sri Lankan study32, taking the prevalence of snakebite as 153 per 100,000 population (0.15%), the estimated sample size is 5868 with a precision of 0.1% from a population of 3.47 million residents32. Assuming 15% cases being unreported, a total of 6904 will need to be interviewed to identify 11 cases of snakebites. Since the mortality of snakebites is estimated at 6/100,000, the sample size to estimate a mortality of 0.006% is 92,190 persons. Assuming a 15% loss of information the actual sample size, to determine the mortality rate is 108,458 persons in Ernakulam.\n\n\n\nZ1-a/2 = Is standard normal variate [at 5% type 1 error (P<0.05) it is 1.96]. p = Expected proportion in population based on previous studies or pilot studies.\n\nd = Absolute error or precision\n\nCommunity derived disability weights. The interviews will be conducted using a purposive sampling method and the VAS would be administered in about 60 adults currently admitted in AIMS and LF hospitals or admitted three months prior to data collection.\n\nThe study will measure annual incidence, mortality, and treatment costs of snakebites in Ernakulam district of Kerala state, India. Additionally, the study will also calculate community-derived disability weights for snakebites in the district.\n\nEpidemiological components. Population based incidence rates will be calculated using the “Survey” package in R programming language. Individual level variables (e.g. age, sex) will be considered only for descriptive analysis. The explanatory variables for snakebite incidence will include population density, sex, occupation, education, and income. The categorical variables will be presented in the form of frequencies and percentages and the continuous variables will be presented as means and standard deviations.\n\n\n\n\n\n\n\nCost of treatment. The median out-of-pocket cost of different cost elements (direct medical and non-medical and indirect) will be estimated based on the data reported by the victims or a household member.\n\nHealth state valuation. For the health valuation descriptive statistics of the socio-demographic profile of the valuers will be presented using appropriate summary statistics—number with percentage for categorical variables and median with inter-quartile range for quantitative variables. The mean of the VAS scores for each disease sequelae will be calculated. The computation of DWs will be done using the formula: DW = 1 –VAS /10033. 95% Confidence Intervals will be provided for the DWs.\n\nDisability adjusted life years (DALYs). DALYs for a disease or health condition is a combined metric of mortality and morbidity/disability and can be used to compare the disease burden across different countries or across different time periods for the same country. The mortality component is estimated in terms of YLL due to premature mortality, and the morbidity component is defined by the YLD due to that condition or any of its sequelae. DALYs is the sum of YLLs + YLDs34. All the three metrics are defined for a particular health condition, for a pre-specified population whose age and sex wise population distribution, death/ mortality distribution, cause specific mortality distribution and life expectancy is known. The YLLs are then computed as the sum over all ages of the product of number of deaths at a particular age multiplied by the standard life expectancy at that age (YLL=∑x=1nNxLx) where Nx= number of deaths at age x, Lx= standard life expectancy in years at age x and x varies from 0 to n where n is the maximum years for which the population death data is available. YLDs for a particular cause (e.g. snakebite) in a particular time period, is calculated using the number of incident cases in that period multiplied by the average duration of the disease and the weight factor that reflects the severity of the disease from scale from 0 (perfect health) to 1 (death).\n\nYLDs will be calculated using the incidence approach where YLD=I × DW × L, where I = number of incident cases, DW= disability weight, L= average duration of the case until recovery or death (years).\n\nThe study would be facilitated through the offices of the District Program Manager, National Health Mission and the Chief/District Medical Officer of Ernakulam district.\n\nInformed consent from all participants will be conducted prior to administration of any data collection questionnaire (Extended data: Annexure 135). A pre-specified questionnaire developed for the research study will be used to collect data regarding socio-demographic, hospitalisation, and economic details (Extended data: Annexure 235). The questionnaire has been developed after consultation with experts working in the field of snakebites in the country, and discussion among authors. The interview schedule for valuation will have two sections: (1) socio-demographic profile of valuer, (2) ‘own health state’ valuation using VAS (Extended data: Annexure 335). Both these schedules will be pre-tested among 5-6 participants prior to any finalisation and administration to the entire sample.\n\nHowever, for information related to any family member whose age is below 18 years, the mother or the father shall be interviewed. Information about the victim, profile of envenomation and complications thereof, other related characteristics, treatment outcome and any other related details will be noted but kept coded and confidential.\n\nData entry will be conducted by a single data entry operator atthe research unit of AIMS. One of the co-authors will review the data entry to check for any discrepancies including any data entry errors from the data entry form. The data will be stored in a desktop computer with access to the data entry operator, and Principal Investigator (JCM). Once the data entry is completed and cleaned, the data sheet will be transferred to the laptops of the co-authors (JCM, GRM & DJ) for further analysis. After analysis these data sheets will be destroyed in these laptops and the data sheet would be available only with the desktop present at research unit of AIMS.\n\nData gathered at the Panchayat (village) level would be collated on a Tab PC by the field officers from where it would be synced on to the server at AIMS, accessible only to JCM,DJ and GRM. De-identified details would be used for statistical analysis and reporting. Details gathered would not be shared on any public domain and would be kept confidential.\n\n\nEthical approval\n\nParticipants will be informed about the nature of the study and will be assured that privacy will be maintained, and information provided by the respondent will be held confidentially and only be used for research purposes. Their willingness to participate will be sought and informed written consent will be taken before including them in the study. Social and cultural values of the participants will be respected and considered as needed. Information obtained during research will not be used for any other purpose except research and research findings will be disseminated as per research dissemination ethics.\n\nThe study received ethics approval from the Institutional Ethics Committee of Amrita Institute of Medical Sciences, Kochi (study reference number IRB-AIMS-2020-1 01) on 13/03/2020.\n\n\nStudy challenges\n\nSnakebite is generally a disease of the working community, being most common among farmers, rubber tappers, tea/coffee estate pickers, brick kiln workers, and plywood industry workers. The majority of bites are accidents, which occur at the workplace or at home with the lower socio-economic groups being most affected. The degree of education and comprehension of the VAS could be a challenge in this group of individuals. There could be a recall bias in victims bitten close to a year back on degree of disability and other disease details as well.\n\n\nDistribution of study results\n\nThe study results will be submitted to a suitable peer-review publication within 6#six months of study completion. Additionally, the results will also be presented in suitable national/international conferences based on resources available for participation. The study results will be presented using STROBE guidelines for cross-sectional studies.\n\n\nStudy status\n\nThe study protocol was discussed and agreed by Steering Group members (clinicians from Amrita Institute of Medical Sciences (AIMS), Kochi Hospital or Little Flowers Hospital (LF), Angamaly handling patients affected with snakebite) prior to start of data collection.\n\nTraining session of staff who would be administering the VAS score has been completed and the necessary permission for using frontline health workers in identifying victims of snakebite in the community has been secured from the District Program Manager of the National Health Mission’s office, and we expect to start the field work form the 1st March 2021.\n\n\nConclusion\n\nThis research constitutes the first published protocol for estimating epidemiological and economic burden as also community derived disability weights. The protocol has been developed using guidelines for cross-sectional studies, and international guidelines for conducting community-derived disability weights. The findings of the study will be useful to inform researchers for a proposed extension of the study in other states as part of ICMR-funded study to be initiated in 2021 (five of the authors are also investigators on this study). The evidence generated by this study will contribute significantly to knowledge regarding the epidemiology, economic burdenand community-derived disability weights for snakebite in India and other countries where incidence of snakebite is high.\n\n\nData availability\n\nNo underlying data is associated with this article.\n\nFigshare: Estimating epidemiological and economic burden and community derived disability weights for snakebite in Kerala: A study protocol, https://doi.org/10.6084/m9.figshare.14061215.v135\n\nThis project contains the following extended data:\n\nAnnexure 1. Consent Form\n\nAnnexure 2. Questionnaire\n\nAnnexure 3. VAS tool\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
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PubMed Abstract | Publisher Full Text | Free Full Text\n\nRoshnath R, Kunhiraman E, Rajan CV: Incidence of snakebite and corresponding compensation payments in the Kannur district of Kerala, India. Herpetol Bull. 2018; 26–29. Reference Source\n\nFatalities from Venomous Animals: Australian Venom Research Unit, Australian Bureau of Statistics. Accessed on 17 December 2020. Reference Source\n\nAnand S, Hanson K: Disability-adjusted life years: A critical review. J Health Econ. 1997; 16(6): 685–702. PubMed Abstract | Publisher Full Text\n\nKasturiratne A, Pathmeswaran A, Wickremasinghe AR, et al.: The socio-economic burden of snakebite in Sri Lanka. PLoS Negl Trop Dis. 2017; 11(7): e0005647. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHabib AG, Kuznik A, Hamza M, et al.: Snakebite is Under Appreciated: Appraisal of Burden from West Africa. PLoS Negl Trop Dis. 2015; 9(9): e0004088. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHabib AG, Lamorde M, Dalhata MM, et al.: Cost-effectiveness of antivenoms for snakebite envenoming in Nigeria. PLoS Negl Trop Dis. 2015; 9(1): e3381. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSommerfeld J, Baltussen RMPM, Metz L, et al.: Determinants of variance in health state valuations. In Summary Measures of Population Health Concepts, Ethics, Measurement and Applications. 2002. Reference Source\n\nRead JL, Quinn RJ, Berwick DM, et al.: Preferences for health outcomes. Comparison of assessment methods. Med Decis Making. 1984; 4(3): 315–29. PubMed Abstract | Publisher Full Text\n\nNord E: Uncertainties about disability weights for the Global Burden of Disease study. Lancet Glob Health. 2015; 3(11): e661–2. PubMed Abstract | Publisher Full Text\n\nLai T, Habicht J, Kiivet RA: Measuring burden of disease in Estonia to support public health policy. Eur J Public Health. 2009; 19(5): 541–7. PubMed Abstract | Publisher Full Text\n\nGreen C, Brazier J, Deverill M: Valuing health-related quality of life. A review of health state valuation techniques. Pharmacoeconomics. 2000; 17(2): 151–65. PubMed Abstract | Publisher Full Text\n\nStouthard MEA, Essink-Bot M, Bonsel G, et al.: Disability Weights for Diseases in the Netherlands. 1997; 1–67. (accessed September 4, 2017). Reference Source\n\nSung YT, Wu JSL: The Visual Analogue Scale for Rating, Ranking and Paired-Comparison (VAS-RRP): a new technique for psychological measurement. Behav Res Methods. 2018; 50(4): 1694–715. PubMed Abstract | Publisher Full Text | Free Full Text\n\nNeethling I, Jelsma J, Ramma L, et al.: Disability weights from a household survey in a low socio-economic setting: how does it compare to the global burden of disease 2010 study? Glob Health Action. 2016; 9: 31754. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSalomon JA, Vos T, Hogan DR, et al.: Common values in assessing health outcomes from disease and injury: disability weights measurement study for the Global Burden of Disease Study 2010. Lancet. 2012; 380(9859): 2129–43. PubMed Abstract | Publisher Full Text\n\nHaagsma JA, Maertens de Noordhout C, Polinder S, et al.: Assessing disability weights based on the responses of 30,660 people from four European countries. Popul Health Metr. 2015; 13: 10. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSackett DL, Torrance GW: The utility of different health states as perceived by the general public. J Chronic Dis. 1978; 31(11): 697–704. PubMed Abstract | Publisher Full Text\n\nGudex C, Dolan P, Kind P, et al.: Health state valuations from the general public using the visual analogue scale. Qual Life Res. 1996; 5(6): 521–31. PubMed Abstract | Publisher Full Text\n\nEdireweera DS, Kasturiratne A, Pathmeswaran A, et al.: Mapping the risk of Snakebite in Sri Lanka- A national survey with geo-spatial analysis. PLoS Negl Trop Dis. 2016; 10(7): e0004813. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLobo E, Nanda L, Akhouri SS, et al.: Describing the Development of a Health State Valuation Protocol to Obtain Community-Derived Disability Weights. Front Public Health. 2019; 7: 276. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMathers C, Vos T, Lopez E, et al.: National Burden of Diseases Studies; A Practical Guide. Geneva: 2001. Reference Source\n\nJohn D, Menon J: Estimating epidemiological and economic burden and community derived disability weights for snakebite in Kerala: A study protocol. figshare. Dataset. 2021. http://www.doi.org/10.6084/m9.figshare.14061215.v1"
}
|
[
{
"id": "81324",
"date": "23 Mar 2021",
"name": "Abul M. Faiz",
"expertise": [
"Reviewer Expertise Clinician with special interest in snakebite",
"poisoning and infectious diseases"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nSnakebite is labelled as 'injuries' which is not entirely true. This research will be used for further research and policy formulation, instead may be stated as utilized for policy decision and further research.\nTitle: aim and objectives may be mentioned/ changed as 'Objectives with division: General objective (s), and specific objectives.\nBeing an emergency situation snakebite attending at OPD is unlikely and to be replaced by emergency department or in-patient department, also better to include any victims of snakebite.\nStudy design: some contradictory statement are there: adults but mentioned that consent from a Child below 18 will be taken from parent or guardian. It would be better to include all patients irrespective of age. Why children will be excluded is not clear.\nDuration of study was 12 months with 9 months retrospective and three months prospective is a concern as the data for disability should be on a prior fixed interval from bite or else one may underestimate some sequelae. It should be clearly mentioned which time point for detection of sequelae following bite will be used. There are distinct two segments of the study- epidemiological and economic aspects- should be clarified.\n\nSnakebite is not 'poisoning' which should be corrected.\nData analytical plan to be provided.\nDisability: it should be clearly mentioned which group of patients will be interviewed retrospective or prospective or both.\nFor the data to be collected in the Case record form there should be a check list and definition for uniformity in data collection with special note on the elements of costing.\nHow the psychological disability will be identified is not clear.\nInformed consent: The consent form will be only in English or both in English and local language. For children, assent from will be required.\nAnnex 2: Clarity is needed in many fields, for example, how the species of snake will be identified, some fields are vague, example- localized reaction.\nDefinition is required in some files, for example adverse reaction.\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? Partly",
"responses": [
{
"c_id": "6724",
"date": "09 Jul 2021",
"name": "Jaideep Menon",
"role": "Author Response",
"response": "DR M Abul Faiz Abul M Faiz Snakebite is labelled as 'injuries' which is not entirely true. This research will be used for further research and policy formulation, instead may be stated as utilized for policy decision and further research. Title: aim and objectives may be mentioned/ changed as 'Objectives with division: General objective (s), and specific objectives. Response: Our study has 3 primary objectives i.e. estimating epidemiological and economic burden and community-derived disability weights. Hence we are not reporting as general and specific objectives. Being an emergency situation snakebite attending at OPD is unlikely and to be replaced by emergency department or in-patient department, also better to include any victims of snakebite. Response: The DALY study is planned in patients treated for snakebite in the immediate three months prior to the start of the study, the assessment for which would occur on follow-up visit as an out-patient. Study design: some contradictory statement are there: adults but mentioned that consent from a Child below 18 will be taken from parent or guardian. It would be better to include all patients irrespective of age. Why children will be excluded is not clear. Response: We have now added that response from the child along with those from adult parents or care-givers will be conducted. Duration of study was 12 months with 9 months retrospective and three months prospective is a concern as the data for disability should be on a prior fixed interval from bite or else one may underestimate some sequelae. It should be clearly mentioned which time point for detection of sequelae following bite will be used. There are distinct two segments of the study- epidemiological and economic aspects- should be clarified. Response: The estimation of epidemiological and economic components will be taken for 12 months duration to estimate annual incidence and economic costs. For the estimation of community-derived disability weights we have used 3 months duration in order to capture the hospitalisation details along with short-term disability aspects. We feel that using a longer time period would induce recall bias of short-term disability by the respondents. Snakebite is not 'poisoning' which should be corrected. Response: We have now corrected to injury other than due to snakebite. Data analytical plan to be provided. Response: The data analytical plan is mentioned in the Statistical Analysis sections and has detailed all the primary objectives. Disability: it should be clearly mentioned which group of patients will be interviewed retrospective or prospective or both. Response: All snakebite victims will be identified who have been bitten in the past. Patient identification is retrospective in nature. For the data to be collected in the Case record form there should be a check list and definition for uniformity in data collection with special note on the elements of costing. Response: We have used cost of illness checklist of Larg& Moss to capture cost elements. How the psychological disability will be identified is not clear. Response: Vignettes (pictorial) are used for both cognitive, anxiety and depression in line with the Euro-QoL methods. The victim identifies her level of distress from the vignettes presented and not on the basis of any other formal mental health scoring system. Informed consent: The consent form will be only in English or both in English and local language. For children, assent from will be required. Response: We will be using consent form in English or Malayalam as understood by the respondent. We have now added that an assent form for children will be used. Annex 2: Clarity is needed in many fields, for example, how the species of snake will be identified, some fields are vague, example- localized reaction. Response: Species would be reported only in case of the victim being absolutely sure of the species or if the killed/captured snake was verified and reported so. Local signs of envenomation limited to the bite site is what is intended in the Questionnaire. Definition is required in some files, for example adverse reaction. Response: The field officers responsible for entering data would be trained on entry and possible responses. The initial entries are done under supervision of one of the investigators."
}
]
},
{
"id": "81325",
"date": "06 Apr 2021",
"name": "Louis Wihelmus Niessen",
"expertise": [
"Reviewer Expertise health economics and epidemiology in particular burden of disease methods and clinical 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 study protocol describe the various sub-studies needed to estimate the health and economic burden from snakebite in Kerala, conform the global BOD approach. There are 1) hospital-based study including patients with a present snakebite or a history of snakebite, 2) a district level community study in all panchayats, target about 9000 inhabitants to identify and track people who had a recent snakebite. The study is very useful and timely for the India situation and globally in the NTD discussions. Some descriptions of some methods are not very clearly (see three points below). The additional minor points (see further below) can be addressed relatively easily.\n\nTo be addressed:\nI would recommend a patient inclusion flow diagram. The exact number of hospital patients to be included is not clear nor the expected number per panchayat. It is unclear how hospital patients with a history of snakebite are identified and included for an interview in addition to the 62 presenting patients. It is unclear if at the community level what the sample framework is (sample 108,458 or 6904 persons? Percentage of total panchayat population?). Will there be an attempt to identify the missing fatal cases in the past, through registries or verbal autopsies? Any limitations to recall bias to take into account?\n\nA DALY approach is proposed, yet, in spite of the many DALY refs, it is unclear how conform this will be to the international (Seattle-based) standards, especially the way disability-weights are established, like is done in other countries, through professionals and, possibly, at community levels. Only a (clinical) VAS approach is proposed, which is used in QALYs computations, using EuroQol versions. Presently, this sounds like quite a mixed bag. Perhaps this can be added in a better narrative in a Box. Will there be controls i.e. health matches? How will the findings be validated / compared against the present BOD weights? Against other India studies?\n\nHow is snakebite short-term and long-term morbidity defined? In clinical terms? How are the VAS and clinical data reconciled, statistically?\n\nMinor points\nHow are data queries handled?\n\nIs there a quality assurance process, collecting data at the community and/or at the hospital? How?\n\nIs the a specific pilot / testing protocol / field training on the use of VAS in illiterate participants?\n\nCan one add a scored STROBE check list, please?\n\nWhat are the challenges of generalisability? How are findings extrapolated at Kerala / all India level (as state 'country')?\n\nWhat kind of costing is taking place? Perspective? Time horizon? Which checklist is used? CHEERS?\n\nSome wording needs to be improved like in the Abstract: 'methods are calculated and presented'.\n\nCan the actual guidelines used for the BOD analysis and the community disability weights be added?\n\nIs EuroQol approval needed for use of the VAS?\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Yes\n\nAre sufficient details of the methods provided to allow replication by others? Partly\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable",
"responses": [
{
"c_id": "6725",
"date": "09 Jul 2021",
"name": "Jaideep Menon",
"role": "Author Response",
"response": "Dr Louis Niessen The study protocol describes the various sub-studies needed to estimate the health and economic burden from snakebite in Kerala, conform the global BOD approach. There are 1) hospital-based study including patients with a present snakebite or a history of snakebite, 2) a district level community study in all panchayats, target about 9000 inhabitants to identify and track people who had a recent snakebite. The study is very useful and timely for the India situation and globally in the NTD discussions. Some descriptions of some methods are not very clearly (see three points below). The additional minor points (see further below) can be addressed relatively easily. To be addressed: 1. I would recommend a patient inclusion flow diagram. The exact number of hospital patients to be included is not clear nor the expected number per panchayat. It is unclear how hospital patients with a history of snakebite are identified and included for an interview in addition to the 62 presenting patients. It is unclear if at the community level what the sample framework is (sample 108,458 or 6904 persons? Percentage of total panchayat population?). Will there be an attempt to identify the missing fatal cases in the past, through registries or verbal autopsies? Any limitations to recall bias to take into account? Response: We have now included a patient inclusion flow diagram to provide an overview of the patients included for the study. The hospitalised patients will be sub-set of the population survey however they will be subjected to EQ-6D-3L and VAS in addition to other details as mentioned in Annexure 3. The total sample in the population for the epidemiological component is 108,458 persons representing 3.18% of the total population of Ernakulam district. Our studies uses ASHAs who are attached to each Gram Panchayat to report the episodes related to snakebites, and has regular interaction with the community. Due to long collaborations of working with ASHAs by JCM in Ernakulam district it is assumed that ASHAs will have knowledge of snakebite victims in each Gram Panchayat based on questioning with villagers. We will not be able to corroborate any missing cases with registries as data for 2018 year on causes of death is only available in February 2021. We do not aim to use verbal autopsy methods as snakebite is an easily reported event due to the circumstantial and symptomatic evidence as gathered from the community/family member as well as treating clinician. 2. A DALY approach is proposed, yet, in spite of the many DALY refs, it is unclear how conform this will be to the international (Seattle-based) standards, especially the way disability-weights are established, like is done in other countries, through professionals and, possibly, at community levels. Only a (clinical) VAS approach is proposed, which is used in QALYs computations, using EuroQol versions. Presently, this sounds like quite a mixed bag. Perhaps this can be added in a better narrative in a Box. Will there be controls i.e. health matches? How will the findings be validated / compared against the present BOD weights? Against other India studies? Response: We have revised the protocol to the use of EQ-6D-3L approach using modified card sorting method to visualise the entire description of health states. The modified CS process using EQ-6D-3L which has been validated in previous studies in Indian settings will not only act as a validation tool but also as a ‘warm-up” for the entire valuation exercises. Our use of EQ-6D-3L is is also due to the fact that other techniques such as Standard Gamble,TTO, PTO, patient elicitation and DCE are complicated to administer among rural and semi-literature populations. There are other studies that have used EQ-6D-3L (Lobo et.al. 2019; Mahpatra et. al., 2000) hence our findings will be validated against these studies published previously. We will not be using any healthy controls as this is not the focus of current study, and might be something to be conducted in future. We have also used pictorial diagrams to be used in vignettes of EQ-6D-3L component so that the valuers can visualize the entire description of health states. 3. How is snakebite short-term and long-term morbidity defined? In clinical terms? How are the VAS and clinical data reconciled, statistically? We are using 1-month period as short-term morbidity and long-term morbidity between 1-3 months duration. We will be capturing clinical data of patients on whom VAS will be administered and will use severity as per definition used in our study using standard statistical methods Minor points • How are data queries handled? Any data queries will be handled by a data access committee, the details are now mentioned in the revised manuscript. • Is there a quality assurance process, collecting data at the community and/or at the hospital? How? Quality checks of Annexure 1 will be conducted by JCM on 1% of total sampled patients to corroborate data collection collected by field officers. For hospitalised cases, JKJ or VVP will reconduct among sample of patients (5% of patients) for validation of responses. In case the differences of EQ-6D-3L or VAS scores are substantial then the choice of scores will be used based on discussions with JCM, JKJ or VVP and will be arrived through consensus. • Is the a specific pilot / testing protocol / field training on the use of VAS in illiterate participants? Both the questionnaires used in the study will be pre-tested among 5-6 participants prior to any finalisation and administration to the entire sample. • Can one add a scored STROBE check list, please? STROBE checklists are used for reporting of studies hence we have not provided scores as part of the protocol. We have also added the use of cost of illness checklist by Larg and Moss (2011) to report economic components of the study. • What are the challenges of generalisability? How are findings extrapolated at Kerala / all India level (as state 'country')? Our study methods and findings will be adapted after any suitable modifications to the ICMR-funded national study that JCM is PI and other members are Co-PIs. We will also be repeating the community derived disability weights methods in other states for generalisability of findings from our study to other states. • What kind of costing is taking place? Perspective? Time horizon? Which checklist is used? CHEERS? We will be using an expenditure method to derive cost of treatment and indirect cost to calculate economic costs (i.e. a prevalence approach of cost of illness method). This will be conducted using a societal perspective with a time horizon to a maximum of 12 months prior to data collection. We will be using a questionnaire to capture the resources used for treatment along with costs. Additionally costs of funeral and any subsidy through government insurance and any other means will also be captured. We will use cost of illness checklist by Larg and Moss (2011) to report our study findings. • Some wording needs to be improved like in the Abstract: 'methods are calculated and presented'. Abstract has been revised suitably. • Can the actual guidelines used for the BOD analysis and the community disability weights be added? We have mentioned use of Vignettes and EQ-6D-3L description system along with DW calculations mentioned. The methods for calculating DW mentioned in our study has been used in previous studies in Indian settings. • Is EuroQol approval needed for use of the VAS? No. In addition Dr Amitava Banerjee (UCL) a long-term GBD collaborator in onboard the study team to help navigate the GBD part of the study. • Is the rationale for, and objectives of, the study clearly described? Yes • Is the study design appropriate for the research question? Yes • Are sufficient details of the methods provided to allow replication by others? Partly • Are the datasets clearly presented in a useable and accessible format? We have presented the datasets in an online repository available at https://doi.org/10.6084/m9.figshare.14061215.v1 ________________________________________ Competing Interests No competing interests were disclosed. ________________________________________ Reviewer Expertise health economics and epidemiology in particular burden of disease methods and clinical studies."
}
]
}
] | 1
|
https://f1000research.com/articles/10-167
|
https://f1000research.com/articles/10-387/v1
|
14 May 21
|
{
"type": "Case Report",
"title": "Case Report: Spontaneous simultaneous coronary and carotid dissection in a young cannabis user",
"authors": [
"Hassen Ibn Hadj Amor",
"Imen Touil",
"Seif Boukriba",
"Skander Bouchnak",
"Salma Kraiem",
"Ramzi Rouabhia",
"Seif Boukriba",
"Skander Bouchnak",
"Salma Kraiem",
"Ramzi Rouabhia"
],
"abstract": "Due to legalization of its consumption in some countries and its medical use as well as low toxic potential, cannabis remains the most widely used drug around the world and the rate of usage is only increasing. Nevertheless, there are several case reports of vascular complications following cannabis use even in young people without cardiovascular risk factors. We report the case of a cannabis smoker presenting to the emergency room for an ischemic stroke associated with an acute coronary syndrome related to a spontaneous simultaneous double dissection of the carotid artery and the left anterior descending artery, with a favourable outcome under medical treatment. This case shows the seriousness of complications due to the cannabis consumption, hence the need to limit or even prohibit its consumption.",
"keywords": [
"Cannabis",
"coronary dissection",
"carotid dissection",
"acute coronary syndrome",
"ischemic stroke."
],
"content": "Introduction\n\nCannabis, known as marijuana, is the most widely used illicit drug in the world. Its consumption is steadily increasing due to its legalization in several countries and its recreational and medical use1.\n\nAlthough the mechanisms are not yet well established, the devastating effect of cannabis abuse on the cardiovascular system, even in the absence of other cardiovascular risk factors, is demonstrated.\n\nDiverse cases of cannabis-related acute coronary syndrome (ACS), ischemic strokes or vascular attacks associated with cannabis use have been reported2.\n\nHerein, we present the first case of cannabis-induced spontaneous simultaneous double coronary and carotid dissection.\n\n\nCase report\n\nA 32-year-old Caucasian student male was admitted to our intensive care unit (ICU) for right total hemiplegia and aphasia evolving for 4 hours associated with chest discomfort.\n\nHis past medical history revealed no cardiovascular risk factors or symptoms. He was occasional cannabis smoker and reported daily consumption in the last 5 days.\n\nAn initial exam showed stable hemodynamic parameters, the patient was conscious and executed orders successfully with his left extremities, but he had an incomprehensive verbal response. An electrocardiogram showed ST-segment elevation in the anterior leads, compatible with an ST-elevation myocardial infarction (STEMI).\n\nEmergent contrast-enhanced computed tomography (CT) scan showed spontaneous hyper-density regarding the left frontal cortex, a sub-cortical left frontal, and multiple supratentorial regions of hypodensity in a vascular distribution occurred in the white matter- grey-matter. (Figure 1) In the cervicothoracic section, it showed thrombosed dissection of the left internal carotid artery, extending over 21 mm in height. (Figure 2)\n\nThe evolution was marked by spontaneous regression within 30 minutes of ST segment elevation and appearance of anterior negative T waves.\n\nEchocardiography showed limited left ventricular anterior and apical wall motion abnormalities with conserved systolic ejection fraction (LVEF: 55%). The laboratory results were normal except for elevated cardiac enzymes.\n\nEarly cardiac catheterization showed an acute thrombotic dissection of the proximal left descending artery with TIMI III blood flow. (Figure 3) The circumflex artery and the right coronary artery were normal. We decided to respect the lesion, and to put him under double antiplatelet therapy (clopidogrel 75 mg per day, aspirin 160 mg per day), unfractionated heparin, nitrates, and bisoprolol.\n\nA second cerebral CT scan followed 48 hours later and showed favourable evolution of the cerebral lesions, so we decided to continue conservative treatment with close follow up. In-hospital outcome was favourable, with regression of aphasia and hemiplegia starting from the fifth day of the hospitalization. He was discharged after 15 days on clopidogrel 75 mg per day, aspirin 160 mg per day, atorvastatin 40 mg per day, and bisoprolol 2.5 mg per day.\n\nAt 3-month clinical control check-up, he retained right lower limb motor sequelae. Cardiac control showed the absence of symptoms, with a good electrocardiographic and echocardiographic evolution (LVEF: 60–65%).\n\n\nDiscussion\n\nMarijuana consumption has been considered benign for a long time, but multiple cardiovascular effects have been described3.\n\nAt low or moderate doses, smoked marijuana increases sympathetic activity and reduces parasympathetic activity resulting in tachycardia, hypertension and may induce atrial fibrillation4. conversely, high doses cause bradycardia and hypotension5.\n\nIn experimental conditions, cannabis causes arteriolar vasodilation which probably explains its low toxic potential, however, this is not always the rule. Contrasting effects of cannabinoids have been shown, responsible for vasoconstriction with acute coronary syndrome, stroke, or peripherical arteriopathy as complications6.\n\nMarijuana abuse can cause myocardial ischemia by various mechanisms including rupture of high-risk pre-existing plaques7, coronary vasospasm, and coronary embolism8.\n\nHemodynamic and oxidative stress weakens arterial walls and promotes plaque rupture thus allowing platelet activation, thrombus formation, and infarction9,10\n\nArterial fragility in our case as a consequence of oxidative stress, is the most logical mechanism explaining spontaneous double dissection.\n\nA recent systematic review of all cases of cannabis-induced myocardial infarction, showed male predominance (95,2%). Angiographic findings reveal involved occluded coronary arteries in 63,2% whose involvement concerned the left anterior descending artery in 42.1% of cases. Conservative management with medical observation was sufficient in 46.7% of patients2.\n\nCerebrovascular ischemic lesions are common in marijuana abuse where reversible cerebrovascular spasm is most often the cause11.\n\nSpontaneous artery dissection is a rare cause of ACS or stoke. It is generally associated with particular clinical situations: the use of contraceptives, pregnancy, Marfan syndrome, connective tissue disorders, trauma, and cocaine abuse12.\n\nSeveral cases of cannabis-induced dissection have been reported in the literature, affecting coronary and cerebral arteries but also the aorta and renal arteries13,14.\n\nNo previous case of spontaneous simultaneous coronary and carotid dissection related to cannabis use has been reported.\n\nThere is no proven therapeutic strategy for cannabis-related dissection as the literature is limited to case studies. Double antiplatelet therapy without vascular intervention can be attempted in hemodynamically stable patients2.\n\n\nConclusion\n\nThis case highlights cannabis-related coronary and cerebral complications in in early adulthood.\n\nAn increase in such cases is to be expected in the face of legalization of cannabis consumption and medical use which is spreading in several countries. If the increase in global consumption becomes unavoidable, the search for predictive factors of complications due to cannabis consumption appears necessary to avoid these serious consequences.\n\n\nPatient consent\n\nWritten informed consent for publication of their clinical details and/or images was obtained from the patient.\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\nGoyal H, Awad HH, Ghali JK: Role of cannabis in cardiovascular disorders. J Thorac Dis. 2017; 9(7): 2079–2092. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPatel RS, Kamil SH, Bachu R, et al.: Marijuana use and acute myocardial infarction: a systematic review of published cases in the literature. Trends Cardiovasc Med. 2020; 30(5): 298–307. PubMed Abstract | Publisher Full Text\n\nFilali T, Lahidheb D, Gommidh M, et al.: Spontaneous multivessel coronary artery dissection associated with cannabis use. J Cardiol Cases. 2012; 7(1): e4–7. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSingh A, Saluja S, Kumar A, et al.: Cardiovascular complications of marijuana and related substances: a review. Cardiol Ther. 2018; 7(1): 45–59. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFisher BAC, Ghuran A, Vadamalai V, et al.: Cardiovascular complications induced by cannabis smoking: a case report and review of the literature. Emerg Med J. 2005; 22(9): 679–80. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDines AM, Wood DM, Galicia M, et al.: Presentations to the emergency department following cannabis use--a multi-centre case series from ten European countries. J Med Toxicol. 2015; 11(4): 415–21. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMittleman MA, Lewis RA, Maclure M, et al.: Triggering myocardial infarction by marijuana. Circulation. 2001; 103(23): 2805–9. PubMed Abstract | Publisher Full Text\n\nVelibey Y, Sahin S, Tanık O, et al.: Acute myocardial infarction due to marijuana smoking in a young man: guilty should not be underestimated. Am J Emerg Med. 2015; 33(8): 1114.e1–3. PubMed Abstract | Publisher Full Text\n\nUl Haq E, Shafiq A, Khan AA, et al.: \"Spice\" (Synthetic marijuana) induced acute myocardial infarction: a case series. Case Rep Cardiol. 2017; 2017: 9252463. PubMed Abstract | Publisher Full Text | Free Full Text\n\nShah PK: Mechanisms of plaque vulnerability and rupture. J Am Coll Cardiol. 2003; 41(4 Suppl S): 15S–22S. PubMed Abstract | Publisher Full Text\n\nMouzak A, Agathos P, Kerezoudi E, et al.: Transient ischemic attack in heavy cannabis smokers--how 'safe' is it? Eur Neurol. 2000; 44(1): 42–4. PubMed Abstract | Publisher Full Text\n\nSchmid J, Auer J: Spontaneous coronary artery dissection in a young man - case report. J Cardiothorac Surg. 2011; 6(1): 22. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLou JY, Randhawa MS, Hornacek D, et al.: Images in vascular medicine. Spontaneous renal artery dissection in a cannabis user. Vasc Med. 2015; 20(4): 379–380. PubMed Abstract | Publisher Full Text\n\nMason EK, Gak AE, Finno JG, et al.: Thoracic aortic dissection associated with marijuana use. J Emerg Med. 2019; 57(2): 235–7. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "85461",
"date": "01 Jun 2021",
"name": "Rania Hammami",
"expertise": [
"Reviewer Expertise interventionnal cardiologist"
],
"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 would like first to thank the authors for this interesting case of coronary and carotid Spontaneous dissection in a young patient after cannabis consumption! After reviewing the literature, this clinical case is the first to show a spontaneous and simultaneous double dissection (of coronary and carotid arteries).\nThe clinical case highlights the seriousness of cannabis-related cardiovascular complications.\nCannabis is the most widely used illicit drug in the world, its consumption is legalized in some countries.\nCannabis consumption, long considered to have a low cardiovascular risk, is sometimes responsible for serious complications in young subjects with significant sequelae and functional limitation, thus encouraging to limit or even prohibit its marketing.\nThe second strong point is to show the interest of a medical treatment comprising a double antiplatelet therapy in the treatment of these cases.\nThe discussion is rich. The authors described the cardiovascular complications associated with cannabis as described in the literature and their management with recent references on this subject.\nFigures are clear with visible dissection images in the carotid artery and the proximal left descending artery. I suggest adding an arrow to the pictures. Did you perform a cerebral or coronary imaging control in this patient, if it was the case, please add the pictures?\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/10-387
|
https://f1000research.com/articles/10-242/v1
|
26 Mar 21
|
{
"type": "Review",
"title": "A review of experimental models of focal cerebral ischemia focusing on the middle cerebral artery occlusion model",
"authors": [
"Melissa Trotman-Lucas",
"Claire L. Gibson",
"Melissa Trotman-Lucas"
],
"abstract": "Cerebral ischemic stroke is a leading cause of death and disability, but current pharmacological therapies are limited in their utility and effectiveness. In vitro and in vivo models of ischemic stroke have been developed which allow us to further elucidate the pathophysiological mechanisms of injury and investigate potential drug targets. In vitro models permit mechanistic investigation of the biochemical and molecular mechanisms of injury but are reductionist and do not mimic the complexity of clinical stroke. In vivo models of ischemic stroke directly replicate the reduction in blood flow and the resulting impact on nervous tissue. The most frequently used in vivo model of ischemic stroke is the intraluminal suture middle cerebral artery occlusion (iMCAO) model, which has been fundamental in revealing various aspects of stroke pathology. However, the iMCAO model produces lesion volumes with large standard deviations even though rigid surgical and data collection protocols are followed. There is a need to refine the MCAO model to reduce variability in the standard outcome measure of lesion volume. The typical approach to produce vessel occlusion is to induce an obstruction at the origin of the middle cerebral artery and reperfusion is reliant on the Circle of Willis (CoW). However, in rodents the CoW is anatomically highly variable which could account for variations in lesion volume. Thus, we developed a refined approach whereby reliance on the CoW for reperfusion was removed. This approach improved reperfusion to the ischemic hemisphere, reduced variability in lesion volume by 30%, and reduced group sizes required to determine an effective treatment response by almost 40%. This refinement involves a methodological adaptation of the original surgical approach which we have shared with the scientific community via publication of a visualised methods article and providing hands-on training to other experimental stroke researchers.",
"keywords": [
"Stroke",
"ischemia",
"focal ischemia",
"in vivo",
"refinement"
],
"content": "Ischemic stroke disease\n\nIn the UK alone, over 100,000 strokes occur annually and approximately 1.2 million stroke survivors live with the consequences of a stroke.1 Despite innovations in stroke research, treatment and rehabilitation, stroke remains the fourth leading cause of death within the UK.1 Stroke is one of the commonest causes of complex disabilities in the UK,2 with two thirds of patients leaving hospital with a post-stroke disability, costing the UK society an estimated £26 billion each year.3 A person who suffers a stroke is highly likely to be affected by a variety of debilitating outcomes, including physical (swallowing, pain and sensory changes) and communication difficulties (speech, reading, writing and ability to understand) along with tiredness and fatigue, impacting on the quality of an individual's daily life.4 A considerable proportion, ~85%, of strokes that occur are ischemic in nature5 occurring when a cerebral vessel becomes blocked, preventing vital blood flow to the supply area of that vessel, ultimately leading to cellular damage and death.\n\nThe only current pharmacological treatment available with proven efficacy for ischemic stroke is thrombolysis treatment with recombinant tissue plasminogen activator (rtPA). However, a low number of patients qualify for rtPA treatment, due to strict eligibility criteria, combined with a narrow therapeutic time window of 4.5 hours results in only ~15% of patients receiving intra-venous rtPA treatment, a low acceptance value further exacerbated by a recanalization success rate of <50%.6,7 In addition to pharmacological treatment, mechanical clot removal via endovascular thrombectomy is increasingly used clinically for the treatment of large vessel occlusions, particularly with patients who respond poorly to rtPA treatment.6,8 This technique involves the removal of the clot blockage from directly within the affected vessel, allowing immediate reversal of the clot's impact on blood flow. The prompt restoration of vital blood flow to the ischemic area is the primary clinical goal, with the potential to salvage vital tissue and cellular function, thus reducing the spread of increasing ischemic damage.9 This prompt recanalisation of blocked vessels is positively correlated with improved survival rates and improved recovery for ischemic stroke patients.10\n\nTo allow for the development of useful clinical therapeutics for stroke treatment, the pathophysiology and mechanisms of disease/recovery need to be elucidated. For this to lead to constructive outcomes it is essential to utilise a combined approach of in vitro and in vivo models. Preclinical ischemic stroke models closely mimic the mechanisms of injury and subsequent recovery allowing investigation of potential clinically viable treatments. Although over 1,026 potential neuroprotective therapeutics have been tested preclinically,11 breakthroughs have not passed beyond clinical trial often due to detrimental side effects, with current effective treatments concentrating on the chemical or physical unblocking of the occluded vessel. This lack of translation to the clinic of neuroprotective strategies continues, requiring us to re-examine the preclinical models used in research. Revisiting these models, to refine and evolve them to be more clinically representative and consistent between laboratories, aims to improve the robustness of preclinical studies and the reproducibility of data obtained.\n\n\nPreclinical models of ischemic stroke\n\nDue to the complex nature of ischemic stroke, it is not possible to successfully model using a single in vitro or ex vivo system. However, use of these bench-side systems allows the investigation of biochemical and molecular mechanisms involved during stroke-like ischemic conditions and to examine the resultant cellular damage. These systems can be utilised to determine pathways and cellular triggers involved in both necrotic and apoptotic cell death,12 alongside the isolated investigation of cellular cascades that occur as a result of excitotoxicity.13 Methods to induce stroke-like ischemic conditions in vitro may include chemical or enzymatic block of cellular metabolism. Metabolic inhibition is induced through application of chemicals such as 2-deoxyglucose, antimycin or sodium azide,14-16 which act to interact with the electron transport chain mimicking the energy depletion that occurs during cerebral stroke. Alternatively, a chemical-based model can use NMDA or glutamate receptor agonists to induce excitotoxic conditions via imitating the significant extracellular increase in glutamate that occurs during ischemia.17,18 Chemical or enzymatic bench-side models allow high-throughput testing, with ease of application and rapid responses, the method also allows isolated analysis of specific aspects of the molecular pathways involved. However, both approaches are reductionist in that they only attempt to mimic one aspect of the pathophysiological cascade and don't replicate the more complex interplay of mechanisms. A further disadvantage to the use of chemicals or enzymes to model ischemia is that these compounds may be difficult to wash out and therefore can disrupt the return to pre-insult conditions. The return to pre-insult conditions in vitro is undertaken to mimic the return of nutrients seen in vivo due to the return of blood flow to an area affected by stroke, known as reperfusion.\n\nThe most frequently used in vitro method to induce stroke-like ischemic conditions, is to remove all the available oxygen and glucose supply to the cells, known as oxygen-glucose deprivation (OGD). This is most often achieved by perfusing glucose-free media with a nitrogen/carbon dioxide mixture to displace oxygen, with subsequent experiments taking place inside a hypoxia chamber. Reperfusion conditions can be imitated through the reintroduction of glucose alongside a return to atmospheric oxygen. Induction of OGD leads to neuronal depolarisation within 10 minutes of onset,19 with astrocytes showing immediate progressive depolarisation over the first 30 minutes of OGD.20 OGD with reperfusion shows continued neuronal degradation over several hours following a return to 'normal' culture conditions, which combined with large extracellular glutamate increases21 are both consistent with in vivo observations.22 Experiments undertaken in hypoxic-only conditions are less representative of ischemic stroke but may better represent cerebral hypoxia conditions such as carbon monoxide poisoning.23,24 Currently, many in vitro ischemia models mimic global ischemia as they induce an insult to the overall brain slice or culture preparation and therefore do not mimic the clinical situation of a focal insult. Recently, Richard et al. have demonstrated the development of focal OGD in ex vivo cortical brain slices using targeted OGD media stream perfusion, perfusing the tissue surrounding the target area with artificial cerebrospinal fluid (aCSF) solution. They reported rapid neuronal depolarisation within the core OGD targeted area with slower progressive depolarisation in the surrounding aCSF perfused area, such as is seen in the penumbra.25 The refinement of an ex vivo slice model of stroke to better represent the clinical presentation of cerebral ischemic events, may allow preclinical bench side investigations to occur in a more representative model.\n\nTo gain better relevance from bench side in vitro/ex vivo stroke models, the physiological micro-environment of the cells is critically important to gaining a true understanding of disease process and outcomes. The influence of oxygen, nutrients (including glucose), cell to cell contact and shear forces all need to be considered. With reference to the use of OGD as a key bench side ischemia-inducing model, oxygen levels should be considered when designing and interpreting data from these experiments. Physiological arterial blood oxygen concentrations differ significantly from external atmospheric levels. Maintenance at physiologically relevant oxygen levels has been shown to increase survival, cell proliferation and dopaminergic neuron differentiation in culture.26 Whereas, high oxygen levels affect not only basal functioning but also response to challenge, potentially providing resistance to stroke related oxidative stressors.27 In addition to high oxygen levels used within in vitro culture systems, glucose is also poorly matched to physiological concentrations. Cell culture glucose concentrations are often up to 8x higher than those reported within the brain.12,28,29 Glucose is used in culture maintenance at concentrations proposed to be present within the brain during severe hyperglycaemia and shown to affect neuronal viability.28 A rethink of the use of long-standing outdated culture media maintenance and methods is required to improve physiological relevance.\n\nOne step towards improving physiological relevance of in vitro stroke models is the introduction and use of co-culture models which are based on multiple cell types, typically placed in repeated monolayers, allowing substrates and signalling molecules to pass between several cell types. This approach is common for modelling the blood brain barrier and has improved our understanding of neurovascular changes that occur during ischemia. Developments in 3D cell culture have the potential to improve the physiological relevance of bench side ischemia models even further. Cells cultured in 3D, on either scaffolds or a scaffold-free system, show natural cell shapes, prevalent cell to cell junctions, well differentiated cell types and a greater response to mechanical stimuli, overall improving physiological relevance compared to 2D culture models.12,30 Cells show lower mortality rates, resistance to nutrient deprivation and drug insults, this is alongside the presence of a gradient based availability of culture media nutrients more like that of a physiological state. Popularity and interest in the use of 3D cultures for in vitro modelling is increasing and they offer an additional way to investigate potential neuroprotective treatments prior to the need for in vivo approaches, reducing ethical impact. In addition to the use of bench side models of multiple cell types to increase physiological relevance, the use of microfluidic devices is also being explored to improve the relevance and applicability of bench side disease models, often termed organ-on-a-chip models.31 Microfluidic devices, since the advent of lithography in 2001,32 use a micro-engineered culture platform that can be utilised to mimic blood flow in health and disease models, alongside allowing the isolated investigation of upstream and downstream signalling within and between cells, due to microchannels that allow axonal growth along them. Since the early 2000s there have been multiple developments in the field of biomicrofluidics to try to overcome some of the limiting factors of this type of cell culture, as this is still constrained to the typical 2D rigid culture techniques discussed earlier. Improvements towards a brain-on-a-chip model are still required, but the use of microfluidics devices for axon-specific responses, cell-cell interaction and high-throughput screening are of great interest to the preclinical stroke research community, and with advancements in the field may prove to be another key step in the drug translation process that will help improve the positive potential of tested neuroprotective therapeutics within the clinic. Although in vitro research provides a platform to determine and understand cell-specific responses to stroke-like conditions the complexities of clinical stroke often require these methods to be combined with in vivo approaches.\n\nThe significant lack of neuroprotective therapeutics in the clinic has led to extensive work aimed at improving the reproducibility of preclinical stroke models and to ensure they reflect as closely as possible the clinical disease.33-36 To date, multiple preclinical stroke models have been developed to reproduce both global and focal ischemic stroke. Whereas global ischemia models more closely mimics the situation of cardiac arrest, focal ischemia models represent the typical clinical presentation of ischemic stroke. Various models are available for use in a variety of animal species, however the use of rodents, specifically rats and mice, is the most common. This is likely to be due to low acquisition and husbandry costs associated with these species, combined with simple effective monitoring methods and ease of tissue processing.24 To try and address the gap in clinical translation for stroke treatments the Stroke Therapy Academic Industry Roundtable (STAIR) published a number of recommendations including the need for potential therapeutics to be assessed across a number of species, initially rodents followed by studies using gyrencephalic species.33,37 The use of higher-order species is necessary to overcome the evolutionary differences between rodents and primates such as the corticospinal tract descending from the motor cortex.38 Larger species may also be suitable for investigations utilising endovascular techniques, such as clot retrieval and stenting, techniques used more frequently in the clinic. However, due to cost, availability and ethical considerations with larger higher-order species, rodents still play a key role in research to ensure experimental power in addition to testing the safety and efficacy of potential neuroprotective treatments.\n\nThe most frequently used in vivo model of focal ischemia is intraluminal suture middle cerebral artery occlusion (iMCAO),39 which has enhanced our knowledge of the pathophysiology of cerebral ischemia including penumbra development and functioning, blood brain barrier injury, cell death pathways and inflammatory processes related to cerebral ischemia. Developed initially for use in the rat,40 in which infarction success rates are 88-100%,41 the method was later modified by Longa et al.42 and subsequently adapted for use in mice43 where the model is increasingly being used particularly due to the availability of transgenic mouse strains. Induction of iMCAO is achieved by the insertion of a flexible monofilament into either the common carotid artery (CCA)40 or external carotid artery (ECA).42 Access into the CCA requires the vessel to be ligated for incision.40 Similarly, for filament access, the ECA is typically transected in the modified iMCAO method.42 Once in the vessel lumen, the filament is advanced into the internal carotid artery (ICA) and to the bifurcation of the middle cerebral artery (MCA). Once in situ, at the origin of the MCA, the filament head impedes blood flow into the MCA territory and is left in situ for the duration of ischemia. The utility of this model allows for accurate control of occlusion duration, allowing for either permanent ischemia where the filament remains in place, or transient ischemia where the filament is removed to allow reperfusion of blood flow to the MCA territory. Utilising the iMCAO model, post-stroke effects can be examined months following the initial insult. Vessel access is obtained without craniectomy and therefore avoids cranial damage associated with craniectomy which could impact on intracranial pressure changes and post-stroke outcomes such as reduced lesion volume.44,45 Use of iMCAO results in large infarct volumes encompassing both the striatum and cortex,46,47 however, longer durations of iMCAO can lead to hypothalamic damage which occurs rarely in humans and can lead to hyperthermic responses in rats and poor temperature control in mice.48,49 Following iMCAO, rodents can experience a range of side-effects that negatively impact the welfare of animals, including but not limited to, significant weight loss, abnormal or reduced motility, difficulty eating/drinking and mortality. These outcomes can be moderated through enhanced pre and post-surgery care; detailed recommendations to support this have been highlighted by the IMPROVE guidelines.50\n\nThe filament selection for use within iMCAO also plays a key role within the model, as unsuitable filament selection can lead to inadequate occlusion and filament-induced secondary subarachnoid haemorrhage due to arterial rupture.51 This has led to an increase in the use of standardised silicone-coated filaments to attempt to improve reproducibility and the use of laser doppler flowmetry to confirm correct filament placement and monitor occlusion duration.52 Although the iMCAO model is not appropriate to study the effect of thrombolysis treatment in conjunction with tested therapies it does recapitulate occlusion of the MCA in the clinic, which is the most common location of thromboembolic stroke in humans.53 However, placement of the intraluminal filament into the origin of the MCA is an all or nothing approach, which does not reflect the clinic where human stroke is frequently not caused by a complete occlusion, additionally the model does not replicate the event of partial spontaneous reperfusion that can occur in patients within 48 hours of stroke onset.54,55 Furthermore, the model does not profile the slow clot disruption that occurs following rtPA administration, instead showing surge reperfusion upon filament removal.56 More recently however, the model has become increasingly relevant due to the advent of interventional mechanical thrombectomy in the clinic. In 2015, five randomised controlled clinical trials reported beneficial effects of endovascular intervention therapy in treating patients with large vessel occlusions, with or without rtPA treatment.57 This beneficial effect was correlated with the abrupt recanalisation of the vessel and rapid reperfusion of the ischemic zone, corresponding to the mechanisms of the iMCAO model. The positive outcome of endovascular thrombectomy, as reported in the clinical trials, suggests this mechanical treatment will become the primary therapy for large vessel occlusion in the clinic;56 renewing relevance of the established iMCAO model as a model of endovascular thrombectomy.\n\nIn addition to iMCAO, focal ischemia can also be induced in vivo by direct occlusion of the vessel of interest, using a cranial window to either clamp, ligate or cauterise the vessel in situ. The most used cranial entry focal ischemia method was developed in 1981 by Tamura et al., using distal MCA occlusion, similar to the occlusion location obtained using iMCAO, inducing combined cortical and striatal lesions.58 Like the iMCAO method, craniotomy models can be used to induce either permanent or transient focal ischemia - although relying heavily on the experimenter's ability to reduce potential localised cerebral damage for both scenarios. Similarly, the return to perfusion following transient ischemia using this method results in a sudden prompt mechanical perfusion, again unlike the presentation of reperfusion in the clinic. Furthermore, access to the vessel of interest through the skull has been shown to induce cortical spreading depressions and inflammatory responses.59\n\nAdditional stroke models are available that utilise specialised mechanisms to induce ischemia, typically in rodents, including thromboembolic, endothelin-induced and photochemical models. Embolic models can be broadly categorised into thromboembolic and non-clot embolic models; the former utilising the induction of localised clots or the insertion of spontaneous/thrombin-induced clots and the latter utilising non-clot methods such as micro/macrospheres to occlude vessels.52,60,61 Since most human strokes are caused by thromboembolism, thromboembolic stroke models may more closely represent the clinical disease pathology. However, there is a lack of a single standardized embolic stroke model leading to multiple occlusion induction methods, a further method that has shown increasing use is the localised injection of thrombin directly into a craniotomy exposed MCA bifurcation.62 A significant advantage of this thromboembolic technique is the opportunity to test thrombolysis treatments alone or in combination with neuroprotective agents.63,64 Additionally, the use of rtPA to lyse the clot in thromboembolic models results in a reperfusion profile that is closer to the reperfusion profiles of rtPA treated patients, contrasting the sharp reperfusion profile following filament removal using iMCAO, increasing the relevance of clot emboli models.56,65 However, infarct location and volume can be highly variable using thromboembolic stroke models along with low seven-day survival rates,66 which impacts the reproducibility of thromboembolic stroke models and their utility for longitudinal studies. In addition to the difficulties experienced in controlling lesion location, the duration of the ischemic insult is difficult to control in these models with some animals showing spontaneous recanalisation,62,67,68 a further disadvantage to the model is the potential for spontaneous clot formation following embolism disruption.69 The severity of this preclinical stroke model also has a high mortality rate of >30%, typically within the first 24 hours preventing longitudinal study.50,70 Non-clot embolic methods can include the injection of silicone or collagen into the ICA of rodents71,72 or, for example, the injection of micro/macrospheres resulting in microembolisations causing multifocal and heterogenous lesions.73,74 Administration of micro/microspheres results in an immediate reduction in cerebral blood flow (CBF) that becomes progressively stronger over the first 3-12 hours following sphere injection, this in turn leads to a slow infarct development, suggesting a longer therapeutic time window than other stroke models for instance iMCAO.74\n\nEndothelin models of ischemia employ the peptide Endothelin-1, a long-lasting potent vasoconstrictor, to induce vessel occlusions.75,76 The peptide is typically applied using stereotaxic injection methods77,78 or craniotomy79,80 applied directly onto an exposed cerebral vessel causing a constriction of the vessel reducing CBF to the vessel territory for up to 22 hours post-injection81 followed by gradual reperfusion. The severity and duration of an insult can be adjusted according to the concentration of the peptide at application. The sustained reduction in CBF and subsequent gradual reperfusion profile, alongside gradual lesion development resembles the evolution of clinical stroke. The topical application method of the peptide is a source of variability in this model, due to the difficulty in ensuring consistent diffusion. To reduce this variability intracortical injection of the peptide to sensorimotor areas has been developed.82,83 With this injection based method, care must be taken to avoid the compound entering the ventricles to avoid significant negative welfare outcomes such as barrel rolling or seizures.69 Another targeted approach of MCA occlusion induction is the photothrombotic stroke model, which induces localised permanent infarcts of the cortex by introducing a photosensitive dye (e.g. Rose Bengal) into the cardiovascular system and illuminating this through the skull using a specific wavelength of light. Targeting small vessels, this illumination activates the photosensitive dye resulting in endothelial damage due to oxygen species formation, causing platelet activation and aggregation.84,85 These together result in the formation of an occlusion and consequently rapid ischemia to the vessel territory, leading to the development of cortical lesion.86 This method produces reproducible and localised cortical lesions, with minimal variation in lesion volume,86 the small cortical lesions and low mortality associated with the model lend well to longitudinal study however, a lack of penumbral tissue within the lesion reduces the translational impact of the model, as the penumbra is the target tissue of interest for neuroprotective strategies. Photothrombotic induction requires the use of light sources, these can act as a heat source. The illumination can have a heating effect on the skull and subsequently the brain, therefore it is important that care over temperature must be taken and where possible cold light sources used, with exposure and distance from the skull/brain considered.50,82 Furthermore, due to the systemic nature of the dye the model is unsuitable for preclinical drug studies.\n\n\nRefining the in vivo model of iMCAO\n\nThe lack of lab to clinic translation of neuroprotective therapies is an ongoing issue and understanding the reasons for this is key to improving the future clinical potential of preclinical stroke research. Many in the field have deliberated the difference in outcomes between preclinical data and the clinical trial outcomes of the many tested neuroprotective agents.35,87-90 Reasons conferred for the disparity include; variations in treatment implementation timepoints, queries about dose effectiveness between species, outcome measure disparities between preclinical (typically lesion volume) and clinical (mainly death rate and disability) also, whether in vivo models effectively model drug efficacy.89,90 Moreover, systematic meta-analyses suggest the introduction of bias into data as a result of poor study design and subsequent study implementation.90-92 With sources of bias coming from both internal (e.g. selection or, performance or attrition bias, small sample sizes and low overall power) and external (e.g. publication bias and the use of exclusion criteria such as co-morbidities, age and sex) factors, acting to weaken the strength of studies.\n\nThe most commonly used in vivo model of ischemic stroke, iMCAO, has been shown to produce lesion volumes with large standard deviations even though rigid surgical and data collection protocols are followed,88,93,94 with 40% standard deviation accepted as reproducible infarct outcomes.95 The iMCAO model relies heavily on collateral flow through the Circle of Willis (CoW), a network of vessels connecting vertebral and carotid circulation, particularly at reperfusion due to ipsilateral CCA ligation. Reliance on the CoW may afford some of the variability in lesion volume reported following iMCAO, due to anatomical variations in its structure, particularly within C57BL/6 (B6) mice commonly used in preclinical stroke studies. CoW variation has been shown to occur in B6 mice, with 90% showing one or both posterior communicating arteries (PcomA) missing.47 Kitagawa et al., reported that the patency of the PcomA is a significant determinant of ischemic damage area following iMCAO.96 Furthermore, additional models of cerebral ischemia such as the bilateral common carotid artery occlusion model also report variations attributed to PcomA patencies, in both lesion volume and CBF during ischemic events, when compared across mouse strains.97-99 Variation in experimental design and husbandry techniques may also impact the potential translational ability of iMCAO studies. Recommendations provided by the IMPROVE guidelines50 on experimental design, husbandry, enrichment, analgesia and post-operative care may go some way to improving standardisation and welfare across iMCAO studies, reducing variability not only within but between studies. This may contribute towards improving the reproducibility of preclinical stroke research, allowing the focus to be on the experimental question and assessing this across research groups with a collaborative approach to research. The IMPROVE guidelines also stress the need for comprehensive reporting of confounding factors in published research, to allow correct interpretation of presented data, improving the reliability and adding value to the information provided, not only improving welfare but also consistency across the stroke research field.\n\nWe have previously reported an alternative surgical approach to iMCAO that improves reperfusion to the ischemic hemisphere, reduces lesion volume variability and subsequently reduces group sizes estimated, using power calculation, to determine an effective treatment response in terms of lesion volume.100,101 Typically, in iMCAO, entry to the cerebrovascular system is obtained via an incision into the CCA or transection of the ECA. However ECA transection, in rats, has been shown to induce ischemic lesions within the muscles controlling mastication and swallowing,102 resulting in changes to drinking behaviour and weight-loss post-MCAO.103 Preclinical stroke models, including iMCAO, that utilise ECA transection do so to minimise interruption to circulatory flow, in an attempt to maintain anatomic integrity to improve post-stroke reperfusion.104 We reported that avoidance of ECA ligation, alongside the introduction of analgesia, appeared to reduce weight loss, without impacting lesion volume when using the modified iMCAO method.101 Although limitations in experimental design did not allow the elucidation of the direct effects of analgesia versus ECA ligation avoidance, systematic administration of an analgesia regime across all experimental groups prevented this becoming a confounding variable. Analgesia use should be utilised in preclinical stroke research as a means of good practice, particularly as many preclinical stroke models involve surgical interventions, with the type of analgesia carefully selected in relation to any potential interference with a study's scientific outputs. The IMPROVE guidelines provide a comprehensive discussion on the use of analgesics within preclinical stroke research, providing recommendations to promote analgesia use within the field.50\n\nThe alternative iMCAO method we established improves mouse well-being and removes reliance on the CoW for collateral flow during reperfusion, importantly reducing lesion volume variability.100,101,105 As lesion volume is often the primary outcome measure for neuroprotective in vivo stroke research, large variations within this data can result in low statistical power if sample sizes are not accordingly adjusted to account for this variability.93 Typically, preclinical stroke studies have low statistical power, a statement supported recently by a meta-analysis revealing that on average, studies show 59% power to detect a 30% inter-group difference.93 The low power of experimental stroke studies, in simple terms, could be improved by increasing group sizes, however, this is contrary to the research community's drive to implement the 3Rs principles, where it is important to ensure studies are correctly powered.106,107 The need to use appropriate animal numbers in experimental research, in line with ethical requirements and the 3Rs principles is leading researchers to re-address the models used and experimental designs undertaken, in addition to the need to overcome the translation roadblock in neuroprotective stroke research. The iMCAO model refinement is one step within the preclinical stroke community towards reducing animal numbers. This is due to reduced variability in outcome data, improving statistical power, and leading to reduced animal numbers required per experimental group to determine treatment effect. We demonstrated that undergoing CCA repair following iMCAO increased perfusion to the ipsilateral hemisphere compared to a typical CCA ligation iMCAO method100 and that use of the CCA repair model could require group sizes 39% smaller than with use of the traditional CCA ligation technique, to attain 80% power with a significance level of 0.05 and an anticipated 30% difference in lesion volume between groups.101 For a typical year, in this instance 2019, a Pubmed search using the search term '((MICE) OR (mouse)) and (MCAO))' determined there were 210 original research articles reporting data from mice undergoing iMCAO. Based on data we reported previously,101 a group size of 58 animals per group (control and experimental condition) per article can be assumed - this group size would result in 24,360 animals per year, but of course that does not include excluded animals alongside those animal experiments that were either not included in published studies or were never completed and analysed for publication. A 39% reduction in group size, as reported following use of the CCA repair iMCAO method,101 would reduce the number of animals required across all those studies published in 2019 by 9500.\n\n\nScientific applications of refinements\n\nThe iMCAO CCA repair method we have highlighted here could have impact on other vascular surgical models within the preclinical stroke research field and potentially beyond. For example, embolic stroke models that deposit a clot into the cerebral vascular system via a carotid artery could be adapted to incorporate the demonstrated CCA repair method. Particularly, by accessing the vessel lumen through the CCA rather than the ECA, alongside the vessel sealing aspect of the refinement allowing bilateral CCA perfusion to the affected ischemic area. The refined iMCAO model using the CCA repair technique may also be of use in additional in vivo research applications, for instance therapeutic drug delivery in experimental models or intra-arterial delivery (IA) of stem cells. Currently there have been over 50 IA cell delivery studies within the stroke field108 with potential IA applications in other research fields. Argibay et al. 2017, reported that maintaining flow through the CCA resulted in uniform cerebral cell distribution following IA cell delivery, with engraftment of labelled mesenchymal stem cells (MSC) visualised using T2-weighted magnetic resonance imaging.109 The group utilised Longa's42 transient iMCAO method in rats, with both filament insertion and MSC injection via a transected ECA, with the CCA temporarily tied for the duration of iMCAO.109 CCA repair, reported previously to be successful in rats,110,111 alongside our recent method development in mice,101,105 would negate the requirement to transect the ECA, therefore, removing the negative welfare outcomes reported following ECA transection.102,103,110 Although many IA stem cell delivery experimental models utilise rats, there are examples of these studies conducted in mice. Ge et al. 2014, utilised transgenic mice expressing green fluorescent protein to assess the impact of MSC size on neuronal health in naive animals undergoing IA MSC infusion, during which multiple arteries were transected and coagulated to enable catheter placement.112 The delicate nature and small size of mouse arteries, compared to the typically more robust nature of rat arteries, increases the difficulty and applicability of IA procedures, potentially discouraging the development of improved methods utilising mice, even though the use of mice over rats opens-up the possibility of transgenic line use, and the targeted downstream investigations the use of transgenic animals allows. Use of the CCA repair technique provides an attractive solution to the problem of vessel sealing following arterial incision in mice, removing reliance on the CoW for collateral flow across the brain. Studies using IA delivery of MSC alongside stroke induction, typically induce iMCAO via the Longa et al.42 method of ECA transection for filament introduction. This is due to the need to maintain CCA flow for microneedle injection of cells, as evidence suggests the injection of MSCs into a no flow vessel results in micro stroke lesions due to the preserved flow within the injection vessel. It is therefore possible that the repair technique could have an impact in this field, allowing the induction of stroke conditions but allowing CCA perfusion post iMCAO induction to allow IA microneedle injection. For catheter-based IA models, the sealing of the CCA vessel rather than the ligation of this vessel may be able to be undertaken with adaption of the CCA repair technique.\n\n\nDissemination and uptake of the refined in vivo model of iMCAO\n\nOur overall aim in producing a refined model of iMCAO was to achieve 3Rs impact within the field of experimental stroke. The importance of this work is in demonstrating that reduced variability in animal stroke studies has the potential to increase animal wellbeing, reduce the number of animals used and potentially increase the efficacy of animal studies in detecting treatment effects. Within a scientific field, results are typically disseminated through scientific publications and any methodological adaptations, if successful, tend to be taken up relatively slowly by the community. Researchers prefer to use 'established techniques' and are resistant to changing methods they have successfully applied for many years. However, there is a real commitment within the stroke community to improve the reliability and reproducibility of animal stroke models so that they may better inform the design and outcomes of clinical trials, evidenced by recent steering papers such as the IMPROVE guidelines.113 We have engaged proactively with the stroke community to deliver hands-on training to numerous labs in the UK, Germany and USA involving over 20 researchers. To extend the reach into the community we published a visualised method of our refined approach105 which has been viewed over 8000 times since publication in early 2019 and over 2000 times in the last six months. Subsequent work published by ourselves and others brings attention to this refined approach and we continue to offer it as our standard training model to incoming members of our group and in other research groups who contact us for training advice.50 We feel that by engaging with some of the key preclinical stroke labs worldwide we will speed up the adoption of this refined technique.\n\n\nConclusion\n\nTo further understanding of stroke pathophysiology and to develop novel clinical therapeutics experimental models of ischemic stroke are beneficial. Such models, based on both in vitro and in vivo approaches, have greatly enhanced our understanding of stroke physiology and pathology. However, there is still a lack of successful clinical therapies being translated from preclinical bench work to clinical use. As various types of in vitro and in vivo models have been developed selection of the most appropriate model to test the therapeutic is key. However, it is also necessary to constantly strive to improve the validity of the models being used in terms of their relevance to the clinical situation and to improve animal wellbeing. Here, we focus on the middle cerebral artery occlusion model which is the most commonly used in vivo stroke model. The refined surgical approach described here reduces the variability, in lesion volume, associated with this model and improves the welfare of experimental animals.\n\n\nData availability\n\nNo data are associated with this article.",
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}
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[
{
"id": "82453",
"date": "26 Apr 2021",
"name": "Lorraine M. Work",
"expertise": [
"Reviewer Expertise Preclinical models of experimental stroke"
],
"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 review by Trotman-Lucas & Gibson is comprehensive and covers the various experimental models of ischaemic stroke available having also described the in vitro models which may be used to support in vivo studies. The detail is appropriate for a review, it is well written and supported through citation of the primary research material.\n\nOne suggested addition to improve the ease of access to the information described and discussed would be the inclusion of a summary table highlighting key considerations of each model (e.g. whether reperfusion can be achieved, ease of surgical technique required, limitations).\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": "6697",
"date": "20 May 2021",
"name": "claire gibson",
"role": "Author Response",
"response": "Thank you for these thoughtful comments from the reviewer. We agree that a table would be informative and have now included this in our revision."
}
]
},
{
"id": "82456",
"date": "12 May 2021",
"name": "Ruoli Chen",
"expertise": [
"Reviewer Expertise neuroprotection",
"blood brain barrier",
"hypoxia"
],
"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 excellent review article summarising experimental models of ischaemic stroke. It not only provides introduction with critical comments on both in vitro and in vivo preclinical models of ischaemic stroke, but also puts forward some proposals to refine iMCAO, the most commonly used in vivo model of ischameic stroke. iMACO produces lesion volumes with large standard deviation, thus has low statistical power. The authors have previously reported an alterative surgical approach to iMCAO, e.g, avoidance ECA ligation, providing analgesia. In this review article, the authors highlight iMCAO CCA repair method to further reduce lesion volume variability.\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/10-242
|
https://f1000research.com/articles/10-220/v1
|
18 Mar 21
|
{
"type": "Research Article",
"title": "Spatial distribution analysis of dentists, dental technicians, and dental therapists in Indonesia",
"authors": [
"Nanda Rachmad Putra Gofur",
"Achmad Zam Zam Aghasy",
"Aisyah Rachmadani Putri Gofur",
"Achmad Zam Zam Aghasy",
"Aisyah Rachmadani Putri Gofur"
],
"abstract": "Background: Access to health services is needed around the world, from healthcare providers to doctors. One of the needs in public health is a system that is accessible for everyone, but, unequal distribution of healthcare provider and health workers, especially in dentistry fields is still a main problem in several countries, including Indonesia. The aim of this study is to analyze the spatial distribution of dentists, dental technicians, and dental therapists. Methods: This spatial analysis study was conducted after obtaining secondary data in Indonesia. All data were collected between September 1st, 2020 and October 1st, 2020 from open access sources of de-identified data. The data of dentists per area, dental technicians per area, and dental therapists per area were calculated for analysis. A spatial distribution map was prepared using the Quantum Geographic Information System (QGIS Desktop, version 3.10.6). Results: The results of this study found a ratio of dentists to members of the population in Indonesia of 1:17,105. The average number of dental technicians that work in the public health centers in each province (dental technicians per area) in Indonesia was calculated to be 0.13. The average number of dental therapists that work in the public health centers in each province (dental therapists per area) in Indonesia was calculated to be 0.40. This spatial autocorrelation illustrates that there is a relationship between values of dentists per area and dental therapists per area between provinces in Indonesia, and shows geographic clustering relationships or patterns that are grouped and have similar characteristics in adjacent locations. This spatial autocorrelation did not occur in the value of dental technicians. Conclusions: From this study we can conclude that there is an unequal distribution of dental personnel in Indonesia.",
"keywords": [
"Dentist",
"Dental technician",
"Dental therapist",
"Spatial distribution"
],
"content": "Introduction\n\nIndonesia is a country in Southeast Asia located between Indian and Pacific oceans. It has more than 17,000 islands, but the biggest islands are Sumatra, Java, Borneo or Kalimantan, Sulawesi and Papua. Indonesia is the 14th largest country in the world with a land area of 1,904,569 square kilometers or 735,358 square miles and is the world’s largest island country. Indonesia is bordered by several country such as Malaysia, East Timor, Papua New Guinea, Singapore, Vietnam, Philippines, Palau and Australia1.\n\nBased on the Global Burden of Disease (GBD) study in 20162, dental and oral health problems, especially dental caries, affects nearly half of the world's population (3.58 billion people). Gum disease (periodontal) is the 11th most common oral health disease in the world. Meanwhile, in Asia Pacific, oral cancer is the third most common type of cancer. The results of the Basic Health Research (Riskesdas) in 2018 stated that 57.6% of the Indonesian population had dental and oral problems during the last 12 months, but only 10.2% received treatment by dental medical personnel (dental nurses, dentists or specialist dentists), while the rest received no treatment2,3. The largest proportion of dental problems in Indonesia are dental caries, necrosis tooth, and toothache complaints (45.3%). Meanwhile, the majority of oral health problems experienced by Indonesians are swollen gums (14%)3,4.\n\nEffective Medical Demand (EMD) is defined as the percentage of the population who had oral health problems in the last 12 months multiplied by the percentage of the population who received dental care or treatment from dental medical personnel (specialist, dentists, dental nurses/dental therapists) and dental technicians5. The EMD in Indonesia is only 8.1%, it means that only few of the population receive dental treatments when they have dental problems. The overall ability to get services from dental medical personnel (EMD) in Indonesia is only 8.1%5,6. Three provinces of Indonesia in 2013, as South Sulawesi, South Kalimantan and Central Sulawesi had quite high levels of oral and dental problems (>35%), with EMD of 10.3%, 8.0%, and 6.4%, respectively7. Based on this finding, a clear picture of the gap between dental problems and the EMD that occur in society can be seen.\n\nA public health system is needed, whereby everyone can access public health services, including dental services, at an affordable rate including affordability of health services. Private health-care providers might help affordability of health services beside government health services. The main focus which needs attention is on curative care in single-practitioner and group practices in dentistry fields. But, unfortunately, these private health services are driven by market demands in society and are business-oriented services. The Geographic Information System (GIS) is a method commonly used in health research. This method could analyze various healthcare variables related to other fields such as physical, social and cultural environments8,9. Access to health services is very important and needed around the world. The correlation between the service provider (the health practitioner) and the consumer (the patient) is still a main problem in many other countries including Indonesia10,11.\n\nAs of 2012, from 8,975 public health centers, there are 5,439 public health centers with dentists and 3,536 public health center without dentists. Nationally, 47.4% of public health centers had one dentist and 13.2% of public health centers had more than two dentists12,13. Public health centers that have the highest efforts in dental and oral health service is in the Bali province, which is 100% and the lowest efforts in dental and oral health service in Indonesia is in Papua Province, which is 24%; the national rate for this efforts of dental and oral health services is 84%. This means, Bali is the province that is best at providing dental services and appropriately considers dentistry fields, meanwhile Papua is the worst14,15.\n\nThe residents ease to reach services and facilities based on the distance and travel time to a resource is called geographic accessibility. Optimal delivery of dental health services should take into consideration availability and accessibility, which together are referred to as spatial accessibility16–18. The aim of this study was to analyze the spatial distribution of dentists, dental technicians, and dental therapists in Indonesia.\n\n\nMethods\n\nThis spatial analysis study was conducted after obtaining secondary data in Indonesia. All data were collected between 1st September 2020 and 1st October 2020 from open access sources of de-identified data; therefore, no ethical approval was required. We sought to identify the average number of dentists, dental technicians and dental therapists working in public sectors and the main building of public health centers in each province.\n\nThis study retrieved data of the number of dentists in each province in 2018 from the national Indonesian Health Facility Research report (Riset Fasilitas Kesehatan), accessed via the Ministry of Health, Indonesia.\n\nThe geographic administrative area data of Indonesia were retrieved from the Indonesia Geospatial Portal, which is publicly available. The provincial maps of the Indonesian database were processed with the Geospatial Portal for further geographic information system (GIS) based analysis to identify spatial distribution of dentists, dental technicians, and dental therapists per area by obtaining the province level polygon map that contains information regarding latitudes and longitudes of each province. We used the map of all 34 provinces of Indonesia for the analysis. Data on the distribution of dentists, dental technicians, and dental therapists was collected from the Ministry of Health and Geospatial Portal.\n\nWe created a map using the Quantum Geographic Information System (QGIS Desktop, version 3.10.6). Global and local Moran’s indices were calculated to determine the autocorrelation value and local indicator of spatial autocorrelation (LISA). LISA was analyzed using GeoDa software, version 1.10.0.8. The level of significance was set at p-value of <0.05, Zα/2 at 1.96, and randomization run to 999 permutations. We used automatic Euclidean weight distance, which matched with the assumption that each province has at least four neighboring provinces. Interpretation of the LISA significance map includes the following categories:\n\n“high–high” indicates a clustering of high value rates (positive spatial autocorrelation)\n\n“low–high” indicates that the low value rates are adjacent to high value rates (negative spatial autocorrelation)\n\n“low–low” indicates clustering of low value rates (positive spatial autocorrelation)\n\n“high–low” indicates that high value rates are adjacent to low value rates (negative spatial autocorrelation)\n\n“not significant” indicates that there is no spatial autocorrelation.\n\nThe outcome of Moran’s I identifies the intensity of spatial autocorrelation along with the result of statistically significant test, that is, the p value. The following mathematical representation exhibits the computation of Moran’s I:\n\nWhere Wij is the spatial weight between the parameters in provinces i and j. The parameters are the number of dentists per area, dental technicians per area, and dental therapists per area. N is the total number of spatial units; S0 is the aggregate of all spatial weights; xi and xj are the amount of each dental health personnel in provinces i and j, respectively.\n\n\nResults and discussion\n\nThe total number of public health centers in Indonesia were counted at 9,831. The total number of dentists, dental technicians, and dental therapists that work in public sectors of public health center main buildings in each province was 15,833, 1,214, and 3,834, respectively (Table 1).\n\nFigure 1 shows the distribution of dental health personnel in several major islands in Indonesia. The distribution is still unequal due to the big difference in the amount of dental personnel in each island. The average number of dentists that work in public sectors and public health centers in each province (dentist per area) in Indonesia was calculated at 1.61 (Figure 2). The ratio of dentist to members of the population in Indonesia was calculated at 1:17,105. The average number of dental therapists that work in main buildings of public health centers in each province (dental therapist per area) in Indonesia was calculated at 0.40 (Figure 3). The average number of dental technicians that work in main buildings of public health centers in each province, (dental technicians per area) in Indonesia were calculated at 0.13 (Figure 4).\n\nThere are 13 provinces that have a value of dentists per area below 1, which indicates that there are areas that do not have dentists at all in public health centers. All provinces in Indonesia have a value of dental technicians per area below 1, which shows that all regions of Indonesia do not have sufficient numbers of dental technicians for each public health center area. There are 31 provinces that have a value of dental therapists per area below 1, which indicates that there are areas that do not have dental therapists at all in a health center area (Figure 1–Figure 4).\n\nThe highest number of dentists per distribution area is in the province of Bali, Java-Bali, and the lowest is in the province of West Papua, Papua. The highest number of dental technicians per distribution area is in the province of Bangka Belitung, Sumatra, and the lowest is in the province of North Maluku, Maluku. The highest number of dental therapists per distribution area is in the province of Bali, Java-Bali, and the lowest is in the province of Papua. Visualization maps of dentists, dental technicians, and dental therapist per area were developed and are presented in Figure 5.\n\nVisualization maps of dentists per area (a), dental therapists per area (b), and dental technicians per area (c). Orange = <1; red = ≥1.\n\nIndonesia had both a shortage of and an unequal distribution of dental health personnel in public health center areas. The distribution of dentists is similar to that in other studies, which have indicated maldistribution of both general practitioners (GPs) and specialists19. Maldistribution indicates inequality associated with area. Dentist and dental nurses are two health workers who play an important role in providing dental health services. The distribution of the two health workers was the highest in the Java-Bali region (60.1%), and the lowest in Papua region (10.3%). However, there are a high number of dentists and dental therapists in the Maluku Islands region (57.9%)11,12. Based on this, it appears that there is a gap that occurs between regions related to the availability of dentists and dental therapists on duty at the health centers. These results are also supported by a previous study that found an unequal distribution19–21.\n\nThe poor distribution of health workers is not only present in dental health service personnel, but in other types of health workers too. Although there is a health worker placement policy in Indonesia which uses a temporary employee system for medical personnel (doctors and dentists), the distribution is not equal especially in remote areas. From the results of the analysis conducted by Ihsan Husain, et al. (2006), on average there are more dentists in Java-Bali compared to the other regions10,15.\n\nUnequal distribution of dentists can be seen from comparing the actual number versus ideal number of dentists with the total population. The ideal ratio is one dentist for 9,090 residents. In the year of 2010, based on dentist registration data from the Indonesian Medical Council (KKI), there were 22,237 registered dentists consisting of 20,665 general dentists and 1,582 specialist dentists7. However, not all dentists that were registered at the Indonesia database work in a public health center. That means only 60.6% of dentists work for an Indonesian public health center, and the rest works in private sector. The amount of Dentists who work in the private sector is 49.4% and they might not be distributed equally around Indonesia9.\n\nMany factors cause this inequality, including the placement policy of health workers in each region (province and district / city), the quality and number of health service facilities, shifting disease patterns, especially in urban regions, high disparity in health status community between regions, and characteristics of the geographic area. From the results of a study conducted by Bappenas, there is a gap between the number of workers and public health centers who need health workers, in that the number of workers is higher than public health structure itself. Furthermore, to ensure health workers are evenly distributed, it is necessary to develop an even infrastructure10–12.\n\nHealth worker placement policy is largely determined collectively by health offices and regional civil service agencies. According to a result from a study in two districts in the province of Gorontalo, the unequal distribution of healthcare workers occurs due to lack of healthcare facilities. Increasing the number of health workers every year was not followed by an equal distribution to health facilities. The study also found that there were three factors that affected the policies and development of health facilities, namely disparities of health status, migration of population, and mutual geographic characteristics10,15.\n\nBased on the results of the spatial autocorrelation test with Moran's I, there was a significant spatial autocorrelation of dentists per area (I: 0.272, z-value: 3.20) and dental therapists per area (I: 0.238, z-value: 2.85) in Indonesia. Meanwhile, the value of dental technicians per area (I: 0.002, z-value: 0.47) did not show significant spatial autocorrelation (Figure 6).\n\nSpatial autocorrelation with Moran’s index of dentists per area (a), dental therapists per area (b), and dental technicians per area was developed (c). The X axis is referring to the number of observations and is also known as the response axis. The Y axis is referring to the average or spatial lag of the corresponding observation of dental health personnel per area of the X axis.\n\nAccording to the World Health Organization (WHO), the ideal ratio of dentists for an area is 1:8,000 people, while Indonesia currently stands at 1:17,105. Dentists per area in Indonesia have spatial autocorrelation at the provincial level and are concentrated only in the Java-Bali region, with very few in the Papua region. For example, Saudi Arabia is one of the countries that has improved the ratio of dentists to population. In 1987 the ratio of dentists to population was 1:8,906, but in 2016 this number increased to 1:1,880. The ratio of dentists to population in Saudi Arabia recently was 5.3 per 10,000 people. This number is higher than all the developing countries in Asia-Pacific region. Also, in this region, China reported the lowest ratio of dentists to population, with 0.12 per 10,000 people. And on the other side, Japan has the highest ratio of dentists to population ratio in Asia-Pacific region with 7.7 per 10,000 people18,22,23.\n\nOther studies reported that the OECD member countries, excluding Scandinavian countries and Greece, have varied dentists-to-population ratios ranging from 5 to 8 with the average of 6.1 per 10,000 people. In addition, most of the European countries have dentists-to-population ratios ranging from 5.07 to 7.3 per 10,000 people. Among Middle Eastern countries, Bahrain has the lowest dentists-to-population ratio of 1.5 per 10,000 people, and Qatar has the highest dentists-to-population ratio of 5.8 per 10,000 people19,22,24,25.\n\nBased on the distribution pattern that we found, we assumed that the distribution of dentists in Indonesia occurred due to the large population, the number of dental institutions, as well as the equitable distribution of development in each region. Java island is one of the areas with an equal distribution of dentists in Indonesia, though it is also the most populated island in Indonesia20,21. In line with the large population growth, Java Island is an area that has 18 dental institutions out of a total of 31 dental institutions throughout Indonesia. Issues of development and availability of public facilities and infrastructure are the main reasons why dentists prefer to practice in the Java area. Dental therapists per area also have spatial autocorrelation at the provincial level, where the Nusa Tenggara region has the highest distribution and the Papua region has the least26,27.\n\nThis spatial autocorrelation illustrates that there is a correlation between the number of dentists per area and dental therapists per area between provinces in Indonesia and shows geographic clustering relationships or patterns that are grouped and have similar characteristics in adjacent locations. This spatial autocorrelation did not occur in the value of dental technicians. The results of Moran's I test show that there is an autocorrelation or spatial relationship of the number of dentists per area and dental therapists per area in Indonesia. Furthermore, Moran's scatterplot also illustrates the pattern of relationships between the existing provinces (Figure 7).\n\nSpatial autocorrelation illustration of dentists per area (a), dental therapists per area (b), and dental technicians per area (c). The plots show the spatial autocorrelation between the number of dentists and dental therapists per area in every province in Indonesia. But the dental technician is not showing the spatial autocorrelation.\n\nBased on the distribution patterns, similar to what happened in the maldistribution of dentists, the maldistribution that occurs in dental therapists may also be due to the population number, the number of dental institutions, and the equal distribution of welfare in each region according to this result. In addition, we assumed that the geographical grouping of dental therapists in the Nusa Tenggara region was due to the process of substituting the role of dentists by dental therapists where the distribution of dentists in the area was low. Meanwhile, a very minimal distribution was seen in the value of dental technicians per area. In this study, it was found that all regions of Indonesia did not have a sufficient number of dental technicians for each public health center, with a mean value of less than 1 per public health center. The factor that most influences this is the very limited number of schools for dental technicians; only 10 institutions throughout Indonesia. Several conditions above then describe the minimum distribution of dental personnel in Indonesia28.\n\nA sufficient number of dental health personnel, such as dentists, dental technicians, and dental therapists in a Province is very important in efforts to ensure health service. The Indonesian government has made regulations regarding the minimum number of dentists in public health centers (minimum 1), but there is not a distribution policy for dental technicians and dental therapists. Indonesia has also implemented various policies, such as increased numbers of dental students to be trained in faculties of dentistry nationwide and pre contract for dentists to work in rural areas after graduation through the Nusantara Sehat and PTT Daerah programs, to solve the shortage of dentists. However, the inequality of dental personnel distribution is still being found29.\n\nWe determined the significance of local spatial autocorrelation through LISA. From this test, the significance of the relationship in each province was obtained. The pattern of Moran's local significance levels is presented in Figure 8. Interpretation of the LISA significance map includes the following categories:\n\n“High-high” indicates a clustering of high-value rates (positive spatial autocorrelation)\n\n“Low-high” indicates that the low-value rates are adjacent to high-value rates (negative spatial autocorrelation)\n\n“Low – low” indicates clustering of low-value rates (positive spatial autocorrelation)\n\n“High – low” indicates that high-value rates are adjacent to low-value rates (negative spatial autocorrelation)\n\n“Not significant” indicates that there is no spatial autocorrelation.\n\nAutocorrelation local indicator of spatial autocorrelation (LISA) map of dentists per area (a), dental therapists per area (b), and dental technicians per area (c). Grey = not significant, red = high-high,blue = low-low, purple = low-high, peach = high-low.\n\nSpatial analysis was used to identify dental health personnel shortages and geographical distribution. The traditional methods use administrative boundaries such as counties as the basic spatial units as well as dental health personnel to identify shortages based on those numbers30–32. Such approaches have been criticized for their inability to account for either the spatial variations of population demand and dental health personnel supply within those boundaries or for population–dental health personnel interactions across them. Spatial analysis can assist current and future dental health personnel, dental school administrators, and policymakers in making informed decisions to determine suitable practice locations, dental school admissions criteria, and target areas for public health initiatives33,34.\n\nThe problem of unequal distribution of dental health personnel should use spatial analysis to understand the issues. This study included number of dental health personnel in each public health center for the accuracy of this research. This research can be accurate because the characteristics of public health centers in each region are similar35–37. Future studies are recommended to use data of dental health personnel both in the public sector and in the private sector.\n\n\nConclusion\n\nThe number of dentists in Indonesia has increased due to the increase of dental students who have been trained in faculties of dentistry which are also done the pre-contracts for dentists to work in rural areas after graduation through the Nusantara Sehat and PTT Daerah programs, to solve the shortage of dentists. However, the inequality of dental personnel distribution is still found, there is no distribution policy for dental technicians and dental therapists, and the dentist-to-population ratios in Indonesia have not improved. Spatial analysis might help identify dental health personnel shortage and geographical distribution.\n\n\nData availability\n\nThe distribution data of the number of dentists in each province is available at https://www.litbang.kemkes.go.id/ (Ministry of Health) and geographic area data is available from https://tanahair.indonesia.go.id/portal-web (Geospatial Portal).",
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J Am Dent Assoc. 2005; 136(5): 668–77. PubMed Abstract | Publisher Full Text\n\nThanakanjanaphakdee W, Laohasiriwong W, Puttanapong N: Spatial distribution of dentists in Thailand. J Int Oral Health. 2019; 11: 340–6. Publisher Full Text\n\nSusi L, Mascarenhas AK: Using a geographical information system to map the distribution of dentists in Ohio. J Am Dent Assoc. 2002; 133(5): 636–42. PubMed Abstract | Publisher Full Text\n\nKonsil Kedokteran Indonesia (Indonesia Medical Council): Standar Kompetensi Dokter Gigi Jakarta: Konsil Kedokteran. 2006. Reference Source\n\nKementerian Kesehatan RI Keputusan Menteri Kesehatan No. 378/Menkes/SKIII/2007 tentang Standar Profesi Perawat Gigi. Jakarta: Kemenkes RI; 2007. Reference Source\n\nWright SE: The spatial distribution and geographic analysis of endodontic office locations at the national scale. J Endod. 1994; 20(10): 500–5. PubMed Abstract | Publisher Full Text\n\nPerera I, Kruger E, Tennant M: GIS as a decision support tool in health informatics: spatial analysis of public dental care services in Sri Lanka. J Health Inform Dev Ctries. 2012; 6: 422–434. Reference Source\n\nJaafar N, Hakim H, Mohd Nor NA, et al.: Is the burden of oral diseases higher in urban disadvantaged community compared to the national prevalence? BMC Public Health. 2014; 14(Suppl 3): S2. PubMed Abstract | Publisher Full Text | Free Full Text\n\nEsa R, Ong AL, Humphris G, et al.: The relationship of dental caries and dental fear in Malaysian adolescents: a latent variable approach. BMC Oral Health. 2014; 14: 19. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPetersen PE, Kwan S: Equity, social determinants and public health programmes--the case of oral health. Commun Dent Oral Epidemiol. 2011; 39(6): 481–487. PubMed Abstract | Publisher Full Text\n\nWatt RG: Social determinants of oral health inequalities: implications for action. Commun Dent Oral Epidemiol. 2012; 40 Suppl 2: 44–48. PubMed Abstract | Publisher Full Text\n\nHosny G, Sayed S, Tantawi M, et al.: Evaluation of accessibility of dental services using Geographic Information System. Sci Afric J Sci Issues. 2015; 3: 763–767.\n\nOmogunloye OG, Tijani OA, Abiodun EO, et al.: Geospatial distribution and utilization of dental facilities in Lagos State. J Biodivers Endanger Species. 2016; 4: 1–18. Reference Source"
}
|
[
{
"id": "85400",
"date": "17 May 2021",
"name": "Reny Purnama Hadi",
"expertise": [
"Reviewer Expertise Biomedical",
"Public Health of Medicine"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nFirst of all the article is unique, never discussed before and adequate. Moreover, there are some additional suggestions:\n\nThe abstract background needs to focus on spatial distribution; 3 professions.\n\nThe method is adequate and clear.\n\nThe first sentence of the conclusion should be answering on the background.\n\nThe discussion is clear and adequate.\n\nAfter all, the overall is very good.\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": "81866",
"date": "25 May 2021",
"name": "Alessandro Leite Cavalcanti",
"expertise": [
"Reviewer Expertise Public Health and 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\nI congratulate the authors for the excellent quality of the manuscript. The study is relevant and describes the profile of dental professionals in Indonesia. Some minor corrections are suggested:\nPage 1: ABSTRACT: It is not necessary to repeat the name of the country in the results, since it is already in the objective.\n\nPage 3, left column, 2nd paragraph, line 11: I suggest excluding \"while the rest received no treatment\".\n\nPage 3, right column, 1st paragraph, sentence 1: New wording \"As of 2012, from 8,975 public health centers, there are 5,439 public health centers with dentists (60.6%).\" You must delete \"and 3,536 public health center without dentists\".\n\nPage 6, left column, 2nd paragraph: I suggest that the authors inform how many dental schools there are in the country and how many dentists are trained each year. The same applies to dental therapists and technicians.\n\nPage 10: I recommend that the authors describe the limitations of the study.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-220
|
https://f1000research.com/articles/9-372/v1
|
18 May 20
|
{
"type": "Case Report",
"title": "Case Report: The efficacy of early phacoemulsification in the intraocular pressure control in primary angle closure glaucoma associated with cataract in a young female",
"authors": [
"Carmen-Ecaterina Leferman",
"Madalina Cazacut",
"Alin Dumitru Ciubotaru",
"Madalina Cazacut"
],
"abstract": "Glaucoma is a leading cause of irreversible blindness in the world, second only to cataract. Among different types of glaucoma, irreversible bilateral visual impairment is more common in primary angle closure glaucoma (PACG) patients. PACG and cataract often coexist and are both more prevalent among the elderly population, being rare in children and young adults. Here, we discuss the case of a 39-year-old Caucasian woman with unilateral PACG associated with cataract. The patient presented with a several-day history of left sided headache, decreased and blurred vision as well as pain and redness of the left eye (LE). She reported similar episodes in the previous year. Visual acuity (VA) of the LE was limited to counting fingers and intra-ocular pressure (IOP) of the LE was 42 mmHg. Anterior segment examination of the LE revealed: edematous cornea, a peripheral anterior chamber depth corresponding to Van Herick’s grade 0, mid-dilated pupil and lens opacities with visible glaukomflecken. Gonioscopic evaluation revealed iridotrabecular contact for 360º, no visible angle structures and a flat–mild convex iris contour. The digital image of the optic disc suggested only a thinning of neuro-retinal rim at the lower pole. Following treatment of the initial symptoms, phacoemulsification with intra-ocular lens implant was performed. IOP improved and no IOP-lowering medication was required. The patient was monitored for VA, IOP, field of vision changes, and optic disc evaluation every six months for 2 years and no glaucomatous change occurred. The patient also denied ocular symptoms during this period. This case supports the effectiveness of early phacoemulsification in the IOP control in patients with PACG.",
"keywords": [
"primary angle closure glaucoma",
"cataract",
"phacoemulsification"
],
"content": "Introduction\n\nGlaucoma is the second leading cause of blindness around the world, being prevalent in 3.5% in those 40 years and older. The number of people with glaucoma worldwide is expected to rise from 64 million to 76 million in 2020 and to 111 million by 2040, with Africa and Asia being affected more heavily than the rest of the world1,2. This disease is generally determined by damage to the optic nerve level as a result of abnormally high intra-ocular pressure.\n\nWith a particularly high prevalence among particular populations, primary angle closure glaucoma (PACG) is responsible for nearly half the glaucoma-related blindness in the world, despite being much less common than open angle disease3. PACG occurs as a result of an interruption in the physiological mechanism of aqueous outflow in patients with crowded anterior segment anatomy. Demographic risk factors include older age, female gender and Asiatic race1. Family history of glaucoma increases also the risk of developing the disease. Angle closure is rare in children and young adults, only isolated cases and small series, primarily composed of particular ethnicities, having been reported4–6.\n\nPACG and cataract often accompany one another and are both more common among the elderly population. The crystalline plays a critical role in the pathogenesis of the two diseases because of its anatomical proximity with angle structures. Therefore, cataract extraction can be a viable solution for both conditions, because it can deepen the anterior chamber and mechanically open the iridocorneal angle, thus reversing the underlying process in these patients7.\n\nWe present a rare case of newly diagnosed PACG associated with cataract in a young female in order to underline the efficacy of early phacoemulsification in the control of intraocular pressure.\n\n\nCase presentation\n\nA 39-year-old Caucasian woman with a family history of glaucoma in one grandparent presented with a two-day history of left sided headache, decreased and blurred vision, as well as pain and redness of the left eye (LE). The patient reported multiple self-limited episodes of headache and pain of the LE associated with blurred vision with no apparent exacerbating factors during the previous year. She was not taking prescribed topical ocular or systemic medication and no ocular trauma was declared. Ophthalmological medical history revealed hyperopia of both eyes (right eye (RE) = +1.75 D sphere, LE = +3.75 D sphere).\n\nOn presentation, visual acuity (VA) of the LE was limited to counting fingers and intraocular pressure (IOP) of the LE was 42 mmHg (Goldmann Tonometry). Slit lamp examination of the left anterior eye segment revealed the following: conjunctival hyperemia, edematous cornea, relatively normal central anterior chamber (AC) depth, a peripheral AC depth corresponding to Van Herick’s grade 0 and oval, asymmetric, poorly reactive and mid-dilated pupil. Gonioscopic evaluation revealed iridotrabecular contact for 360º, no visible angle structures and a flat–mild convex iris contour. After indentation, the iris contour slightly changed. She was diagnosed with acute primary angle closure. Also, the patient was found to have cataract with visible glaukomflecken in the left lens. Due to corneal edema and lens opacities, fundoscopic examination of the LE was difficult to perform.\n\nThe VA of the fellow eye was 100/100 cc (with correction +1.75 D sphere) and IOP 16 mmHg. Anterior segment examination revealed a narrow peripheral AC depth corresponding to Van Herick’s grade 2 and gonioscopic evaluation suggested no abnormality. The posterior segment was also normal.\n\nOn the first day only, the patient received the following medication: systemic IOP-lowering agents (mannitol 20% 250 ml x2/day intravenous, acetazolamide 250 mg x2/day per os), IOP lowering drops (brimonidine 0.2% 1 drop x2/day) and topical steroid eye drops (dexamethasone 0.1% 1 drop x4/day). The therapy response allowed IOP control using topical drops (brimonidine 0.2% 1 drop x2/day) for the next five days.\n\nAfter the resolution of the acute attack, gonioscopy of the LE revealed no anterior peripheral synechiae. Fundoscopic examination revealed the optic disc with a cup-disc ratio of 0.4. The other part of retina was normal. The digital image of the optic disc suggested only a thinning of neuro-retinal rim at the lower pole, leading to her diagnosis of PACG.\n\nOn the sixth day, biometry and of the LE was performed in order to plan cataract surgery (Table 1). A-scan biometry found the left lens thickness to be 4.21mm. The glaukomflecken could not be identified by anterior segment optical coherence tomography or ultrasound biomicroscopy. Endothelial cell count was in normal range. On the seventh day, the patient underwent uneventful phacoemulsification with an intraocular lens implant.\n\nRE, right eye; LE, left eye; AC, anterior chamber; CCT, central corneal thickness.\n\nThe day after surgery, the VA of the LE was 60/100 sc (without correction) and IOP was 17 mmHg. At discharge the VA of the LE was 80/100 sc (without correction) and the IOP was 13 mmHg. The patient followed the standard post-cataract surgery care (week 1 to 2: topical tobramycin/dexamethasone 3 mg/1 mg/ml 1 drop x4/day and topical bromfenac 0.9 mg/ml 1 drop x4/day, week 3 to 4: topical tobramycin/dexamethasone 3 mg/1 mg/ml 1 drop x2/day and topical bromfenac 0.9 mg/ml 1 drop x2/day).\n\nAt the six-week evaluation, VA of the LE was 100/100 sc (without correction) and IOP was appropriate. The field of vision investigated by automated perimetry (Humphrey) appeared normal.\n\nThe patient was monitored for VA, IOP, field of vision changes, and optic disc evaluation every six months for 2 years and no glaucomatous change occurred. She also declared no ocular symptom in all this period of time.\n\n\nDiscussion\n\nA case with unilateral PACG associated with cataract in such a young patient with no systemic co-morbidities is an unusual presentation. The diagnosis of PACG was preferred, rather than simply primary angle closure, due to the modification of the neuro-retinal rim and the risk factors of the patient, including family history.\n\nThis case of unilateral PACG associated with cataract in a young patient with no systemic diseases underlines three aspects: the importance of the risk factors in glaucoma, the relationship between the pathophysiologic mechanisms of the two conditions, and the effectiveness of the phacoemulsification in the IOP control.\n\nThe etiology of angle closure in young people is different from that of the older population and is typically associated with structural or developmental ocular particularities: plateau iris, iridociliary cysts, nanophthalmos, etc. In the presented case, the patient had moderate hyperopia in the affected eye and low hyperopia of the fellow eye. Hyperopia is mentioned in literature as a risk factor for PACG8. There are, however, studies that did not find any statistically significant correlation between refractive error and PACG9,10. Biometrical parameters such as axial length and AC depth were strongly correlated with PACG10. The small axial length (AL) with a normal size lens or even growing lens, as it is in cataract, leads to a crowded anterior segment and a shallow anterior chamber9. Thus, the uni-laterality of the condition could be explained in part by the differences in the biometrical parameters between the eyes, the affected having lower values of these parameters. Also, the fellow eye is at risk of developing primary angle closure, and should be monitored.\n\nAnother particularity of the disease is the association between the two conditions at the time of diagnosis. The way in which PACG and cataract influence each other in a young patient could be explained, in part, by the presence of glaukomflecken composed of necrotic lens epithelial cells and degenerated subepithelial cortex. These two diseases seem to reinforce each other. Thus, on one side markedly elevated IOP in PACG determined epithelial and anterior cortical lens opacities, on the other side the affected lens growth can compromise the aqueous flow between the lens and iris at the pupil11. Therefore, the pupillary block suggested as a mechanism of PACG in older patients could as well appear, even though rare, in younger patient4.\n\nInitial therapeutic approach consisted of IOP-lowering medication and, after resolution of the acute attack, phacoemulsification with intraocular lens implant. Iridotomy could have been another viable treatment option, but the presence of a cataractous lens dictated cataract extraction, which is demonstrated to have more favorable results in similar conditions, despite increased risk of corneal edema after phacoemulsification12. The patient’s IOP improved, as it is also described in the literature in other cases, after cataractous lens extraction12,13. The patient required no IOP-lowering medication and the first 2 years follow up glaucoma revealed no other glaucomatous damage.\n\n\nConclusions\n\nThe therapeutic choice in PACG (iridotomy vs. phacoemulsification) should be guided by risk factors and the subsequent pathophysiological mechanisms. As our case of PACG associated with cataract in a young patient confirmed, early phacoemulsification proved its effectiveness in the IOP management. Although the risks of surgical approach are well known, especially increased risk of corneal edema, the benefits are undeniable: a good IOP control, decrease need for IOP-lowering drugs and a significant improvement of VA with a better quality of life for 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.\n\n\nConsent\n\nWritten informed consent for the publication of this case report was obtained from the patient.",
"appendix": "References\n\nTham YC, Li X, Wong TY, et al.: Global prevalence of glaucoma and projections of glaucoma burden through 2040: a systematic review and meta-analysis. Ophthalmology. 2014; 121(11): 2081–2090. PubMed Abstract | Publisher Full Text\n\nQuigley HA, Broman AT: The number of people with glaucoma worldwide in 2010 and 2020. Br J Ophthalmol. 2006; 90(3): 262–267. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCho HK, Kee C: Population-based glaucoma prevalence studies in Asians. Surv Ophthalmol. 2014; 59(4): 434–447. PubMed Abstract | Publisher Full Text\n\nRitch R, Chang BM, Liebmann JM: Angle closure in younger patients. Ophthalmology. 2003; 110(10): 1880–1889. PubMed Abstract | Publisher Full Text\n\nChhipa SA: Angle Closure Glaucoma with Myopia. Pak J Ophthalmol. 2009; 25(3). Reference Source\n\nAlzuhairy S: Bilateral angle closure glaucoma in a teenage girl - A rare presentation in Arab population - A case report. Int J Health Sci (Qassim). 2019; 13(2): 56–58. PubMed Abstract | Free Full Text\n\nMelese E, Peterson JR, Feldman RM, et al.: Comparing Laser Peripheral Iridotomy to Cataract Extraction in Narrow Angle Eyes Using Anterior Segment Optical Coherence Tomography. PLoS One. 2016; 11(9): e0162283. PubMed Abstract | Publisher Full Text | Free Full Text\n\nShen L, Melles RB, Metlapally R, et al.: The Association of Refractive Error with Glaucoma in a Multiethnic Population. Ophthalmology. 2016; 123(1): 92–101. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKim YY, Lee JH, Ahn MD, et al.: Angle Closure in the Namil Study in Central South Korea. Arch Ophthalmol. 2012; 130(9): 1177. PubMed Abstract | Publisher Full Text\n\nvan Romunde SH, Thepass G, Lemij HG: Is Hyperopia an Important Risk Factor for PACG in the Dutch Population?-A Case Control Study. J Ophthalmol. 2013; 2013: e630481. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLowe RF: Aetiology of the anatomical basis for primary angle-closure glaucoma. Biometrical comparisons between normal eyes and eyes with primary angle-closure glaucoma. Br J Ophthalmol. 1970; 54(3): 161–169. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLam DS, Leung DY, Tham CC, et al.: Randomized trial of early phacoemulsification versus peripheral iridotomy to prevent intraocular pressure rise after acute primary angle closure. Ophthalmology. 2008; 115(7): 1134–1140. PubMed Abstract | Publisher Full Text\n\nRömkens HCS, Beckers HJM, Schouten JSAG, et al.: Early Phacoemulsification After Acute Angle Closure in Patients With Coexisting Cataract. J Glaucoma. 2019; 28(2): e34–e35. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "63522",
"date": "02 Jun 2020",
"name": "Lin Fu",
"expertise": [
"Reviewer Expertise Ophthalmic surgical research",
"Ocular tissue engineering",
"Eye-on-a-chip."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors presented an unusual but interesting case of APAC in a young female of 39 years old.\n\nMajor points:\nSince the cause of this type of APAC is important, an ultrasound biomicroscopy examination should be included to present the anterior segment structure especially the ciliary body, iris and anterior chamber angle. The difference of the AC between the affected eye and unaffected eye is relative large (2.62 vs 2.16), hence a differential diagnosis is needed in the discussion part, like the discussion on lens dislocation and zonula weakness.\n\nThe authors should provide a table or relevant figures to show the results of the eye examination about of the VA, IOP, visual field, optic disc evaluation of the LE of different visits.\nMinor points: In the Abstract,\nPlease delete “second only to cataract” in the first sentence, because the sentence structure gives a wrong impression that cataract is also a kind of irreversible blindness.\n\nDid the authors intend to stress how the presented case is so unusual as in the second sentence they mentioned PACG is usually bilateral but the presented case is unilateral?\n\nWhat does the “digital image” of the optic disc as mentioned in the 6th sentence in the second paragraph of the abstract stand for? Do you mean the fundus photo?\nIn the third paragraph of Introduction,\nPlease elaborate more about the “process” mentioned in the last sentence in this paragraph.\n\nIn Table 1,\nWhat are the units of the measurements of the parameters in Table 1?\n\nIn the third paragraph of Discussion,\nCan the authors please name the parameters specifically that being mentioned in the second last sentence?\n\nIn the fifth paragraph of Discussion,\nCan the authors provide a value about the “increased risk of corneal edema after phacoemulsification”?\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": [
{
"c_id": "6732",
"date": "10 Jun 2021",
"name": "Carmen-Ecaterina Leferman",
"role": "Author Response",
"response": "We would like to thank you for your time, for taking an interest in our article, and for your constructive feedback. All your concerns were valid, pointing out areas in which our case report needed improvement. We are therefore grateful for your valuable contribution. Kindly note our response in line with the provided comments: Since the cause of this type of APAC is important, an ultrasound biomicroscopy examination should be included to present the anterior segment structure especially the ciliary body, iris and anterior chamber angle. The difference of the AC between the affected eye and unaffected eye is relative large (2.62 vs 2.16), hence a differential diagnosis is needed in the discussion part, like the discussion on lens dislocation and zonula weakness. Thank you for your observation. Indeed, because PACG and PAC tend to be bilateral, the observation of a wide-open angle in the fellow eye suggests a diagnosis other than PAC. Ultrasound biomicroscopy ruled out other conditions which may be unilateral or bilateral, such as lens related disorders like ectopia lentis or zonula weakness that cause secondary anterior chamber angle closure. Also, we added ultrasound biomicroscopy parameters measured for both eyes at admission (Table 1 in the new version). Variation in accommodation was minimized by fixation of the contralateral eye on a standard distance target on the ceiling. The authors should provide a table or relevant figures to show the results of the eye examination about of the VA, IOP, visual field, optic disc evaluation of the LE of different visits. We provide a table (Table 3 in the new version) to show the results of the eye examination representing visual acuity (VA), intraocular pressure (IOP), visual field (VF), optic disc evaluation of the affected eye measured at different visits. VA remained unchanged compared to the 6 weeks postoperative follow-up. Regarding the IOP, the office hour IOP and diurnal variation test (DVT) were determined. Even if the office hour IOP was at target level, we repeated DVT to look for undetected IOP peaks or high fluctuations in the first year post-op. DVT was ≤ 5 mmHg. Changes in retinal nerve fiber layer (RNFL) and ganglion cell layer (GCL) thickness over the two years fall within the individual variability corresponding to age, sex, and ethnicity. Please delete “second only to cataract” in the first sentence, because the sentence structure gives a wrong impression that cataract is also a kind of irreversible blindness. We deleted “second only to cataract” in the first sentence. Did the authors intend to stress how the presented case is so unusual as in the second sentence they mentioned PACG is usually bilateral but the presented case is unilateral? Thank you for your comment. PACG and PAC tend to be bilateral. As such, the observation of a wide-open angle in the opposite eye suggests a diagnosis other than PACG. Using ultrasound biomicroscopy, we were able to rule out other unilateral and bilateral lens related disorders like ectopia lentis or zonula weakness that cause secondary anterior chamber angle closure. We added a new paragraph regarding this topic in the discussion section (second paragraph in the new version). What does the “digital image” of the optic disc as mentioned in the 6th sentence in the second paragraph of the abstract stand for? Do you mean the fundus photo? As an imaging strategy, we used the spectral domain optical coherence tomography in order to acquire retinal nerve fiber layer (RNFL) and ganglion cell layer (GCL) measurements and analyze cup-disc ratio. In the third paragraph of Introduction, please elaborate more about the “process” mentioned in the last sentence in this paragraph. Phacoemulsification can reverse structural impairment of aqueous humor drainage via the trabecular meshwork, thereby decreasing the volume of the capsular sac, increasing the size of the iridocorneal angle and, making it a viable situation for both conditions. We added this information in the text. In table 1, what are the units of the measurements of the parameters? All values in the Table 1 (Table 2 in the new version) are in mm. In the third paragraph of discussion, can the authors please name the parameters specifically that being mentioned in the second last sentence? The parameters refer to the la axial length and the lens thickness. We added them in the text. In the fifth paragraph of discussion, can the authors provide a value about the “increased risk of corneal edema after phacoemulsification”? The occurrence and severity of corneal edema after phacoemulsification depends on the associated preoperative, intraoperative and postoperative risk factors which makes it difficult to provide a single a value about the \"increased risk of corneal edema after phacoemulsification\". In our case in particular, the risk refers more to the anatomical features suggested by the biometric parameters, that may increase the risk of corneal endothelial damage during phacoemulsification, plus endothelial damage caused by recent increased intraocular pressures reported at the time of surgery."
}
]
},
{
"id": "72882",
"date": "29 Oct 2020",
"name": "Monica Kenney Ertel",
"expertise": [
"Reviewer Expertise Glaucoma surgical outcomes."
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nSummary: This was an interesting case of a young 39-year old patient who developed acute angle closure presumably phacomorphic in etiology. In order to manage her elevated intraocular pressure, the authors performed cataract surgery which successfully reduced her IOP and deepened her angle.\n\nComments:\nCan the authors elaborate on the cataract in the case presentation? Which type of cataract and which grade of cataract? It seems atypical for such a young patient to have a unilateral, visually significant cataract. Were other systemic illnesses ruled out? The authors include that the patient denies trauma but were there any other exam findings that suggest trauma? Could there be zonular insufficiency secondary to trauma which would explain the asymmetric narrow angle and the cataract?\n\nDid the authors obtain UBM to image the angle and to rule out other potential etiologies of asymmetric, unilateral narrow angles?\n\nThe first sentence in paragraph 6 in case presentation is missing information. Biometry and what were performed? Was the difference in axial length between the two eyes confirmed with A-scan?\n\nCan the authors elaborate on findings of the post-operative follow-up visits? Was formal glaucoma imaging with OCT RNFL, OCT GCC testing performed to evaluate for damage to the optic nerve?\n\nIn the second to last paragraph in the discussion, the authors seem to suggest that the anterior capsular changes that occurred during her acute angle attack led to pupillary block from the lens. However, the lens thickness between the two eyes is minimal, much smaller than the difference in axial length between the two eyes. Can the authors elaborate?\n\nWere the anterior capsular changes the only lenticular changes present? In this young patient who still has accommodation, removing her accommodation with cataract extraction seems to be a large risk when she may have done well with an LPI. I think this thought process and the authors rationale for their treatment choices is a very important part of this case. They seems to only mention that the presence of a cataract was their reasoning but it seems there are other points which should be addressed.\n\nThe authors suggest that the patient is a case of PACG, however based on her lack of optic nerve cupping and mentioned normal testing - she would not qualify as PACG. Can the authors please address?\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": [
{
"c_id": "6734",
"date": "18 Feb 2022",
"name": "Carmen-Ecaterina Leferman",
"role": "Author Response",
"response": "We would like to thank you for your time, for taking an interest in our article, and for your constructive feedback. All your concerns were valid, pointing out areas in which our case reports needed improvement. We have carefully followed your recommendations and made the necessary improvements. We will provide answers to each of your comments illustrating the changes point by point. Can the authors elaborate on the cataract in the case presentation? Which type of cataract and which grade of cataract? It seems atypical for such a young patient to have a unilateral, visually significant cataract. Were other systemic illnesses ruled out? The authors include that the patient denies trauma but were there any other exam findings that suggest trauma? Could there be zonular insufficiency secondary to trauma which would explain the asymmetric narrow angle and the cataract? Thank you for this constructive review and questions. Regarding lens opacities, the patient presented central anterior lens opacity changes and grade C3 cortical cataract according to LOCS III standardized chart. Other systemic illnesses were ruled out and there were no exam finding that suggested trauma. Other conditions causing lens related disorders- like ectopia lentis or zonula weakness- that cause secondary anterior chamber angle closure and which may be unilateral or bilateral were ruled out by ultrasound biomicroscopy. Did the authors obtain UBM to image the angle and to rule out other potential etiologies of asymmetric, unilateral narrow angles? PACG and PAC tend to be bilateral. As such, the observation of a wide-open angle in the opposite eye suggests a diagnosis other than PACG. Using ultrasound biomicroscopy, we were able to rule out other unilateral or bilateral lens related disorders like ectopia lentis or zonula weakness that cause secondary anterior chamber angle closure (Table 1 in the new version). The first sentence in paragraph 6 in case presentation is missing information. Biometry and what were performed? Was the difference in axial length between the two eyes confirmed with A-scan? The difference in axial length between the two eyes was confirmed with A-scan. A-scan ultrasound biometry and keratometry were performed for both eyes in order to plan cataract surgery for the left eye. We added this information in the text. Can the authors elaborate on findings of the post-operative follow-up visits? Was formal glaucoma imaging with OCT RNFL, OCT GCC testing performed to evaluate for damage to the optic nerve? We provide a table (Table 3 in the new version) to show the results of the eye examination representing visual acuity (VA), intraocular pressure (IOP), visual field (VF), optic disc evaluation of the left eye measured at different visits. VA remained unchanged compared to the 6 weeks postoperative follow-up. Regarding the IOP, the office hour IOP and diurnal variation test (DVT) were determined. Even if the office hour IOP was at target level, we repeated DVT to look for undetected IOP peaks or high fluctuations in the first year post-op. DVT was ≤ 5 mmHg. Changes in retinal nerve fiber layer (RNFL) and ganglion cell layer (GCL) thickness over the two years fall within the individual variability corresponding to age, sex, and ethnicity. There was also no pathological progression in cupping and no changes in the visual field. In the second to last paragraph in the discussion, the authors seem to suggest that the anterior capsular changes that occurred during her acute angle attack led to pupillary block from the lens. However, the lens thickness between the two eyes is minimal, much smaller than the difference in axial length between the two eyes. Can the authors elaborate? We want to accentuate the positioning of the lens in angle closure affect eyes. It is located more anteriorly, thus hindering the passage of the aqueous humor between the lens and the iris as it moves towards the anterior chamber. Also, increasing thickness of the lens with existing opacities or the aging of a lens may also contribute to a progressive narrowing of the angle. Were the anterior capsular changes the only lenticular changes present? In this young patient who still has accommodation, removing her accommodation with cataract extraction seems to be a large risk when she may have done well with an LPI. I think this thought process and the authors rationale for their treatment choices is a very important part of this case. They seems to only mention that the presence of a cataract was their reasoning but it seems there are other points which should be addressed. Thank you for your excellent point. As a result, we added a few lines in the text in order to highlight this important consideration. Indeed, a broader discussion of the risks and benefits of both LPI and lens extraction is necessary for patients with minimal cataractous changes. As we previously mentioned, anterior capsular changes are not the only lenticular changes (the patient presented central anterior lens opacities changes and cortical cataract C3 grade after LOCS III standardized chart in the left eye alone). Younger patients who are considering lens extraction as option should carefully ponder loss of accommodation. In the presented case, the age of the patient is at the point most people begin to notice the effect of presbyopia. The therapeutic role for lens removal was supported by the anatomy of the patient’s left eye. Also, a progressing narrowing of the angle may also be attributed to an increase in lens thickness caused by aging of the lens and existing opacities. On the other hand, iridotomy may then have been a viable treatment, however most patients retain some iridotrabecular contact, so angle closure may progress regardless. Laser iridotomy widens the anterior chamber angle, however a more effective solution, when appropriate, may be removing the lens mass, which could reduce, or even eliminate the risk of blindness from an acute attack and chronic increase in IOP. Phacoemulsification has been shown effective in some studies to prevent subsequent IOP elevations in PACG eyes presenting with IOP > 55mm Hg. The authors suggest that the patient is a case of PACG, however based on her lack of optic nerve cupping and mentioned normal testing - she would not qualify as PACG. Can the authors please address? A diagnosis of primary angle chronic glaucoma was preferred, given the slight thinning of the neuro-retinal rim at the lower pole in the 6-clock hour sector, suggested by spectral domain optical coherence tomography."
}
]
}
] | 1
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https://f1000research.com/articles/9-372
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https://f1000research.com/articles/9-1495/v1
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21 Dec 20
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{
"type": "Research Article",
"title": "Risk factors and experiences of prepartum depression among pregnant women in urban- low income in Nairobi Kenya: a mixed-method study",
"authors": [
"Beatrice A. Madeghe",
"Wambui Kogi-Makau",
"Sophia Ngala",
"Manasi Kumar",
"Wambui Kogi-Makau",
"Sophia Ngala",
"Manasi Kumar"
],
"abstract": "Background: Prepartum depression is common among pregnant women and has not been studied much in low and middle-income countries. Evidence shows that mental illnesses are more prevalent in urban than in rural areas. The study objective was to determine the magnitude of prepartum depression, risk factors, and real-life experiences of depression among pregnant women. Method: A mixed-method cross-sectional study was conducted. It included 262 pregnant women attending antenatal clinics in two public health facilities in the urban low-income settlement of Nairobi, Kenya. Edinburgh Postnatal Depression Scale (EPDS) with cut-off >13 was used to classify clinical depressive illness. Further, a focus group discussion was conducted with 20 women identified with the depression. Bivariate analysis with Odd's Ratio was used to test associations. Variables with a p<0.05 in multivariate were considered significant. Result: Out of the 262 women, 33.6% were found to have prepartum depression as indicated by an EPDS score of >13. Women's gestational age in the second trimester (87.5%) was statistically significantly associated with prepartum depression (p<0.001). Income levels <10,000 KES (58%) were statistically significantly associated with prepartum depression (p<0.001). Further, thematic analysis of qualitative data indicated that poverty, lack of social support, domestic violence, and unfriendly health care were major contributors to prepartum depression. Conclusion: Significant numbers of pregnant women were found to experience depression. This prevalence rate indicates a high disease burden of women who live with depression, which is not diagnosed because screening of depression is not done in primary health care centers. This study calls for a need and consideration for screening for perinatal depression in primary health care facilities, mainly in resource-poor areas. Interventions targeting means of resolving conflicts in families are highly needed. Such steps would help achieve key sustainable development goals where maternal and child health remains a key priority.",
"keywords": [
"Maternal",
"depression",
"risk factors",
"experiences",
"Kenya"
],
"content": "Introduction\n\nPrepartum depression has been identified as a serious health problem but is a neglected component of care for women during pregnancy1–3. While pregnancy is expected to be the most unique and happiest moments in a woman's life, to some women there is a different scenario filled with tears, fears, and confusion, including stress to severe depression4,5. Perinatal depression refers to mood disorders during pregnancy and/or after delivery within the first twelve months postpartum; thus, prepartum depression is a mood disorder during pregnancy6,7. Global prevalence indicates that at least one in ten women in developed countries and two in five women in the developing world develop depression during pregnancy8. The prevalence rates of prepartum depression range between 12.5–42% of women screened for depression symptoms in low and lower middle-income countries9,10. Systematic reviews that determined the occurrence and determinants of prepartum depression found prevalence rates that range from 15% to 65% globally4,11. In Kenya, prevalence estimates of depression are found at 32.9% among pregnant adolescents12, with postpartum depression prevalence rate of 13%13.\n\nResearch evidence reveals that the stresses of life, especially around pregnancy and childbirth, can affect the emotions of women and behavior of many mothers, hence increasing the risk of depression during pregnancy and after childbirth14. Socio-determinants, i.e. the social conditions where people are born, grow, live, work, and age, influences their health outcomes15,16. During pregnancy, maternal mental health is fundamental for the health of the mother and the infant's brain health and development; it needs to be prioritized early in the life course to prevent mental health problems later in life1. Given this backdrop, this study aims to determine the magnitude of prepartum depression, and identify risk factors for prepartum depression, and picture real-life experiences of pregnant women of low-urban income in Nairobi, the capital city of Kenya.\n\n\nMethods\n\nThis was a mixed-method cross-sectional study that involved pregnant women who attended antenatal care clinics, during the study period March 2019 to June 2019. Ethical approval was obtained from The Kenyatta National Hospital/University of Nairobi Ethical and Research Committee (KNH/UoN-ERC Ref: P56/02/2018). The study took place in two public health facilities in two urban low-income settlements, namely Kangemi and Kawangware. The two sites are both growing informal settlements, located on the outskirts of the Nairobi city center. They were chosen purposively because the antenatal clinics (ANC) at these health facilities receive a high volume of pregnant women. Eligibility criteria included all pregnant women aged 18 to 44 years who visited ANCs for antenatal check-up in Kawangware or Kangemi composed the study population.\n\nThis cross-sectional study was part of the baseline assessment of a longitudinal cohort study of pregnant women that targeted 100 depressed pregnant women, which examined the efficacy of dietary intervention for depression care among pregnant women in urban low-income Nairobi Kenya. To obtain the above sample size at baseline, consecutive sampling was used where every pregnant woman who came for checkup was assessed for depression; hence 262 pregnant women were recruited in this study.\n\nQuantitative data. Data were obtained from pregnant women by means of an interview administered questionnaire. All women who came to the ANCs and were queuing in the waiting room were approached to participate. The study purpose was explained to them that participation was voluntary, and refusal to participate will involve no penalty of benefits to which one is entitled at the clinic. The participants were assured about their privacy and confidentiality. After obtaining a written informed consent signed by the respondent based on willingness to participate, the interview commenced.\n\nSocio-demographic characteristics questionnaire: Using a questionnaire, pregnant women provided data on socio-demographic characteristics, age, marital status, maternal education level, employment status, partner's occupation, monetary decision-making, and family monthly income.\n\nMaternal depression questionnaire: Edinburgh Postnatal Depression Scale (EPDS), was used to assess maternal depression. The EPDS is a 10-item questionnaire in which women report on how they have been feeling in the past seven days17. EPDS, which has a Kiswahili translation version, has been validated for detecting depression in both prepartum and postpartum mothers in many countries, including Kenya18. EPDS is one of the most well-known and evaluated instruments for maternal depression and has demonstrated acceptable clinical utility as a screening tool. It has a sensitivity of 86%, specificity of 78% and a positive predictive value of 73%19,20. The depression scores were categorized into two levels; EPDS score higher than 13 indicated existence of clinical maternal depression17.\n\nQualitative data. A focus group discussion (FDG) was conducted with women who were identified as depressed, in order to get a deeper understanding of women's experiences during the present pregnancy. After identifying women as depressive in the questionnaire (above), we asked the pregnant women if they would be willing to participate in the FDG. Convenience sampling was used to select and invited the depressed pregnant women for FGD.\n\nThe aim of FGDs was to identify the causes of depression among pregnant women and the experiences around them. In this qualitative inquiry, 20 pregnant women with depressive symptoms (EPDS score cut-off score >13) were invited to participate. Two FGDs with a group of 10 participants were conducted from each site of Kangemi and Kawangware, respectively. Face to face discussion was conducted away from the health center by two female field researchers (BM and a research assistant) in a hired hall convenient for the women to discuss. BM has Master in Public Health, and the research assistant has MSc in Clinical Psychology. They were both trained on mental health quantitative and qualitative research methods. The relationship between researcher and pregnant women was established prior to the FDG. The FGD lasted for 60–90 minutes, and it was conducted in the Kiswahili language and was audio-recorded. The data was coded until when the ability to obtain additional new information was exhausted for the study purpose. The interview guide can be found in Extended data21.\n\nQuantitative analysis. The filled questionnaires were checked for completeness, errors, and discrepancies; this was followed by data entry, cleaning, and analysis using SPSS version 22. Descriptive statistics such as percentage means and standard deviation were used to summarize the socio-demographic data. An EPDS score of >13 pointed the likelihood of the presence of clinical depressive illness. Independent variables were categorized to analyzed, the association between independent and outcome variable, using a bivariate analysis odds ratio (OR) with 95% confidence interval (CI). Those variables that were associated with p<0.001 in the bivariate analysis were entered into multivariate analysis. Variables with p<0.05 in the multivariate analysis were considered to be significant.\n\nQualitative analysis. The FDGs in Kiswahili was transcribed and translated into English at the same time. Thematic analysis was employed to process the data. Two coders (BM and a research assistant) were involved in the coding process. The study primarily followed the inductive approach and identified the emerging codes, and to some extent, the deductive approach was also used to determine the codes22. Coding was manually done, and finally, four major themes emerged from the discussion. Informed consent was obtained from participants in this research for future uses of data, such as publication, preservation, and long-term use of research data. Confidentiality was assured. The information collected was kept confidential. Serial numbers were used instead of a name.\n\n\nResults\n\nIn total 262 women responded to the questionnaire, 134 from Kangemi and 128 from Kawangware. The mean (SD) age of the 262 women was 25.3±5.0 years (range, 18–44 years). The majority of the women (82%) were married, with 29.8% having less than high school education and 14% had tertiary level education. About 79.4% of the women had no employment but depended on their partners or parents, only 20.6% were employed. Slightly less than half of the women (43%) were first-time mothers, while 70% of them were in their second trimester during baseline assessment. Almost all the women (98%) owned a basic personal phone, and slightly less than three quarters owned a television (73%). The mean (SD) income level was 10845.8 Kenyan shillings (KES) per month, and almost half of the women (49.6%) lived on an income less than KES 15,000, equivalent of 150 USD per month, while two-fifths of the women (38.9%) had their husbands make decisions on household finances (Table 1).\n\nGuided by the EPDS scoring system, the 10 items generated a depression score ranging from 0 to 30. The depression scores were categorized into two levels (depressed and not depressed). A score greater than 13 indicated the existence of prepartum depression of various severities\n\nOut of the 262 women, about a third (33.6%; 95% CI 27.9-40.7) had depression as indicated by EPDS >13 (Figure 1). Suicidal Ideation (EPDS item 10) revealed that 24% of pregnant women had some suicidal ideation. The mean (SD) EPDS score was 11.1, interquartile range of 10 with a minimum score of 0 and a maximum score of 26. When the socio-demographic characteristics were compared between depressed women and those not depressed, results showed that women's gestation age in the second trimester (87.5%) was statistically significantly associated with maternal depression (OR 3.37; 95% CI 1.60-7.10; p<0.001). Income levels was also statistically significantly associated with maternal depression where women (58%) with income level <10,000 KES were depressed (OR 0.39; 95% CI 0.23-0.66; p<0.001; Table 2).\n\nParticipants were aged from 18 to 44 years, and these women all had an EPDS score of 13–25 and were in their second trimesters. Table 3 provides participant's characteristics in the FGDs.\n\nThe qualitative results from the FDGs were categorized into four major themes: poverty – manifested through a financial struggle, unemployment and food insecurity; social support – women reported inadequate support from their partners/husbands, the lack of a trustworthy person/friend who they could share their worries, loneliness, living far from family members, and feeling neglected; marital disharmony – issues of domestic violence (physical abuse and psychological/emotional abuse), and separation/divorce were reported; trauma experiences – women reported fear and worries about childbirth and birth outcome, considering that most of them were first-time mothers, and some women reported a previous loss of a child, previous birth difficulties, and fear of facing health care providers. Each of these themes are discussed in detail below.\n\nPoverty. Poverty is the root cause of stress and prepartum depression and contributes to other risk factors of depression. Women reported having not enough making and everything seeming difficult because of this. The three subthemes identified were financial struggles, food insecurity, and lack of employment.\n\nFinancial struggles\n\nPregnant women reported having financial struggles because they have no income, or their partner not being employed, so it becomes so difficult for them to do things.\n\n\"I don't have a job, and I'm pregnant, and my husband doesn't have a job, and we live that way looking here and there; we are supposed to pay rent, food, and different kinds of needs. So you live with questions and start questioning yourself.\" Participant 20\n\n\"Lack of money; If I have money in my pocket, I would be just fine.\" Participant 15\n\n\"By the way, you stay in the house; maybe you lack something, and when you ask for it, and the husband doesn't have money, so he begins to become harsh, then it results in quarreling, just that.\" Participant 5\n\nFood insecurity\n\nSome pregnant women reported a lack of enough food, or sometimes basic food may be available, but the food that they crave during their pregnancy they cannot get.\n\n“There is sometimes we don’t have food, and there is nothing to eat.\" Participant 12\n\n\"My husband will leave without leaving me food to eat, and I'm pregnant, whereby I don't understand whatever is happening so that one usually bores me so much.\" Participant 17\n\n\"The problem is even if it is available yet my husband stresses me, how will I eat? You cannot.\" Participant 10\n\n\"Sometimes the basic food is available, but the food I feel like eating I can't get, I love and admire eating pizza, but there is not enough money to buy it.\" Participant 11\n\n\"When I ask him about house needs, he becomes harsh and doesn't understand me.\" Participant 6\n\nSocial support. Most of the pregnant women felt that they lacked emotional and financial support from the partners responsible for the pregnancy. In addition, some of the partners denied their pregnancy, and do not want to take any responsibilities.\n\n\"I stay with a family from my husband's side, and there is no support of any kind that they offer me, and the husband himself doesn't support me, so the people who support me are neighbors when I have a problem I tell them.\" Participant 2\n\n\"So before I got pregnant, he is the one who used to insist that I should give birth, and then he will marry me and such things, so when I got pregnant up to the moment, he still doesn't do what he said to me.\" Participant 4\n\n\"Was in the hospital they rang him saying, ‘we want blood transfusion on her can you come and replace the blood?’ He said ‘I don't know EV.’ He just talks rubbish.\" Participant 12\n\n\"So for me, it is just to give birth and raise the baby by myself because he is not supporting\" Participant 19\n\n\"My husband tells me, 'what are you crying for? Just cry when you are tired you keep quiet\". Participant 5\n\nSome women reported that they do not have a trusting person around them to share their worries and talk heart to heart. Living conditions in slums where people live in one plot, some neighbors are stubborn and like making fun to others, further contributing to stress, anger and depression. Some stay away from their family members, and so they feel they lack support.\n\n\"I don't have anybody to tell my story.\" Participant 7\n\n\"They are available, but I have never trusted somebody so much.\" Participant 5\n\n\"You cannot trust someone; maybe you can tell them your problems and think that it has ended there, but you will hear it with everybody.\" Participant 15\n\n\"Then there is another person whom you can tell and maybe feel that she is a friend, you sit with her and tell her; she also supports you as if she has pity over you, but maybe after you leave she is a type that laughs at you.\" Participant 16\n\nMarital disharmony. In the FDGs, women reported hopelessness and helplessness around the experience of domestic abuse, which manifested as both physical and emotional abuse.\n\nPhysical abuse\n\n\"One day, my husband came and quarreled at me, and then he later slapped me, then pushed me. I fell on the table and hit my stomach. I started feeling pain on the stomach and thought my baby in my belly was hurt.\" Participant 6\n\n\"My husband has a lot of disrespect whereby he sometimes spends a night out when he comes back and ask him where he was then at that point we start a big fight, and he will leave without leaving you food usually that bores me so much.\" Participant 17\n\nSome women defend themselves.\n\n\"Yes; whenever he starts, we just hit each other, there is no sparing him; so he also fears me, I have a lot of energy, and he cannot quarrel with me so much.\" Participant 14\n\nSometimes women are forced to stay with abusive partners even if they are beaten as they cannot sustain themselves.\n\n\"If you go tell parents you're told that \"you cannot live a life with a husband without being beaten\" Participant 3\n\n\"When you leave, where will you go?\" Participant 9\n\n\"I don't have a job; don't have money; if I have had a job and money would get myself out. Where will I stay?\" Participant 11\n\nPsychological abuse\n\nWomen reported being psychologically abused, with many partners not wanting to offer emotional support to their wives.\n\n\"He is keeping quiet, if I don't talk, he cannot talk, and it hurts me so much.\" Participant 19\n\n\"He said that he will beat me and that he is not the one responsible for the pregnancy, then he said that I abort, but I abandoned him.\" Participant 13\n\n\"That one he doesn't want to talk when you are tired and tell him ‘Today I am not feeling well’, he tells you ‘it's up to you’. Participant 9\n\nSeparation/Divorce\n\nSome women experienced separation or divorce.\n\n\"I don't stay with him too, but he is so contemptuous; he cannot even offer you support, he has even blacklisted my number.\" Participant 12\n\n\"I don't know how to put it, but we parted ways those days when I was the first month, so all along I have been surviving, and I have become used.\" Participant 8\n\nTrauma experiences. Some women had previous trauma experiences, such as loss of a child and difficult birth.\n\n\"Fear of how it will be when I go for delivery you don't know if your child will be alive.\" Participant 3\n\n\"I fear how that situation will be, so my mind is tormented by the day that I will go to deliver.\" Participant 7\n\n\"I fear delivery that is the stress I have, since I have never had a baby, people tell me but it frightens me\" Participant 1\n\nSome women feel that health care is unfriendly. When they go to the clinic, nothing is explained to them, even during a physical examination. For example, pregnant women are not given any feedback about how they are doing, or if their babies are growing well. They reported that they are dismissed without any information given to them, only the date to come back for checkup is provided. Therefore, the women reported that health care itself is a source of stress.\n\n\"They press my belly so hard and painful, and they tell me go you are done, and another one is called; you are not told how your baby is doing, so I don't understand.\" Participant 6\n\n\nDiscussion\n\nIn our study, 33.6% of pregnant women in the study had maternal depression, as assessed by EPDS, which was associated with low-income and gestational age, specifically in the second trimester. This prevalence rate indicates a high number of women who live with depression and calls for interventions to support women with this condition. This estimate lies within the wide range of prior prepartum prevalence rates of depressive symptoms (12.5–42%) among pregnant women in low and middle-income countries9,10. Our findings revealed relatively similar prevalence rates to the study by De Oliveira et al.11, who found 37.5% depression prevalence among Hispanic pregnant women in South Florida using PHQ-9. A study by Sheeba et al.23 in Ethiopia found a prevalence rate of 35.7% among pregnant women using EPDS >13. Likewise, among Chinese women a prevalence rate of 28.5% was found among pregnant women in late pregnancy using the Self-rating Depression Scale24. A study by Shrestha20 from Nepal reported a point prevalence of 18% among pregnant women using EPDS ≥10. Another study in Ethiopia by Duko et al.25 found a prevalence rate of 21.5% among prenatal mothers using EPDS ≥13.\n\nVarious prevalence estimates of prenatal depression have been reported in various countries. The differences in estimates could be due to methodological differences in the ways the studies were conducted, or the settings where the studies conducted, the timing of pregnancy, screening instruments used, and the cut-off values used to classify mothers as depressed (see reviews16,25–27). However, the most important thing to note is that all the studies show a significant prevalence of depression during pregnancy.\n\nIn our study, low-income and gestational age, specifically during second trimester, were significantly statistically associated with prepartum depression. Furthermore, the qualitative findings revealed poverty to be the primary determinant of maternal depression, especially financial struggles due to lack of stable income and food insecurity. Our results have similarities with other studies in the literature, where the identified risk factors for prepartum depression include maternal age, socio-economic status15, domestic violence, social support, history of previous mental disorder23, and pregnancy-related complications16. The study by Shrestha in Nepal reported higher odds for health problems, gestational age, sex preference, and spousal alcohol intake to be associated with depression20; these results are similar to our study where gestational age was associated with prepartum depression. Another study by Sheeba et al. in Ethiopia23 reported that age group, educational qualification and occupation were significant predictors of prenatal depression, and socio-economic status was not significantly associated with depression; these results contrast with our findings where age, education level, and occupation were not related to prepartum depression.\n\nQualitative findings revealed financial worries and psychosocial factors to be associated with prepartum depression. In our study, most of the study participants were young mothers who belonged to the low-income group, and most of them were first-time mothers. These women were unemployed and were entirely dependent on their spouses or partners and family members. It is hypothesized that low income increases the likelihood of poor living conditions; financial struggle influences personal relationships, leading to psychosocial stress23. This hypothesis agrees with our qualitative findings where poverty, including financial struggles and food insecurity, were associated with prepartum depression. The risk factors related to prepartum depression may not be similar. Some studies may find some risk factors associated with prepartum depression are not the same16,25,26. This could be attributed due to cultural differences, population differences, study setting, and living conditions that cause people to experience different risk factors for prepartum depression.\n\nThis study used mixed methods, both quantitative and qualitative. The qualitative part was useful in gaining a better understanding of the causes of prepartum depression and has complemented the quantitative part of the study to provide a fuller story. Prepartum depression has not been studied much in low and middle-income countries, contributing to a high disease burden. Therefore, our study focus on prepartum depression contributes to filling a knowledge gap and awareness to health-care providers, researchers, policymakers, and the public about the rates and risk factors of prepartum depression. However, due to reasons that the recruitment occurred at the ANC where the attendance rate is not 100% for all residents in the settlements, many women with depressive symptoms may not been reached, and even those who came to the ANC, not all of them were screened leading to underreporting of the cases hence the result cannot be generalized.\n\n\nConclusion\n\nConsiderable numbers of pregnant women, about a third of the women, were found to experience maternal depression in the urban-low income of Nairobi, Kenya. Our study findings indicate many women who live with maternal depression, which is neither diagnosed nor treated since the ANC do not carry out routine screening for prepartum depression. Therefore, women are suffering without adequate services or timely help. This study calls for urgent consideration of screening of perinatal depression at primary health care facilities so that women can get help through counseling and be provided with social support. We strongly feel that the ANC nurses and primary health care staff also need to be trained in delivering respectful, patient-centered services where the mental health of these vulnerable women is prioritized. Interventions targeting means of resolving conflicts and intimate partner violence are highly needed. This will contribute towards efforts on global mental health and sustainable development in prioritizing perinatal mental health and childhood mental health because acting early in the life course is crucial to preventing mental health problems later.\n\n\nData availability\n\nFigshare: Socio-demography and Depression Questionnaire, https://doi.org/10.6084/m9.figshare.13265297.v128.\n\nFigshare: Maternal Depression experiences FDG transcription, https://doi.org/10.6084/m9.figshare.13265549.v129.\n\nFigshare: Maternal Depression Experiences FDGs Interview guide, https://doi.org/10.6084/m9.figshare.13265420.v221.\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 thank our study participant's pregnant women who attended the antennal clinic during the study period, numerous ANC nurses at Kangemi and Kawangware Health Centre. We thank the research assistants Ruth Mwaura and Theresia Mutisyo, for their valuable time and cooperation during fieldwork. We also acknowledge Albert Tele for his statistical support.\n\n\nReferences\n\nPatel V, Saxena S, Lund C, et al.: The Lancet Commission on global mental health and sustainable development. Lancet. 2018; 392(10157): 1553–1598. PubMed Abstract | Publisher Full Text\n\nde Vargas Nunes Coll C, da Silveira MF, Bassani DG, et al.: Antenatal depressive symptoms among pregnant women: Evidence from a Southern Brazilian population-based cohort study. J Affect Disord. 2017; 209: 140–146. PubMed Abstract | Publisher Full Text | Free Full Text\n\nOgbo FA, Eastwood J, Hendry A, et al.: Determinants of antenatal depression and postnatal depression in Australia. BMC Psychiatry. 2018; 18(1): 49. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFisher J, de Mello MC, Patel V, et al.: Prevalence and determinants of common perinatal mental disorders in women in low- and lower-middle-income countries: a systematic review. Bull World Health Organ. 2012; 90(2): 139G–149G. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBarker ED, Kirkham N, Ng J, et al.: Prenatal maternal depression symptoms and nutrition, and child cognitive function. Br J Psychiatry. 2013; 203(6): 417–421. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFord E, Lee S, Shakespeare J, et al.: Diagnosis and management of perinatal depression and anxiety in general practice: a meta-synthesis of qualitative studies. Br J Gen Pract. 2017; 67(661): e538–e546. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLeung BMY, Kaplan BJ: Perinatal depression: prevalence, risks, and the nutrition link--a review of the literature. J Am Diet Assoc. 2009; 109(9): 1566–1575. PubMed Abstract | Publisher Full Text\n\nMossie TB, Sibhatu AK, Dargie A, et al.: Prevalence of Antenatal Depressive Symptoms and Associated Factors among Pregnant Women in Maichew, North Ethiopia: An Institution Based Study. Ethiop J Health Sci. 2017; 27(1): 59–66. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWHO-UNFPA: Maternal mental health and child health and development in low and middle income countries. Geneva, Switzerland. 2008. Reference Source\n\nWoldetsadik AM, Ayele AN, Roba AE, et al.: Prevalence of common mental disorder and associated factors among pregnant women in South-East Ethiopia, 2017: a community based cross-sectional study. Reprod Health. 2019; 16(1): 173. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDe Oliveira G, Cianelli R, Gattamorta K, et al.: Social Determinants of Depression Among Hispanic Women. J Am Psychiatr Nurses Assoc. 2017; 23(1): 28–36. PubMed Abstract | Publisher Full Text | Free Full Text\n\nOsok J, Kigamwa P, Stoep AV, et al.: Depression and its psychosocial risk factors in pregnant Kenyan adolescents: a cross-sectional study in a community health Centre of Nairobi. BMC Psychiatry. 2018; 18(1): 136. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMadeghe BA, Kimani VN, Stoep AV, et al.: Postpartum depression and infant feeding practices in a low income urban settlement in Nairobi-Kenya. BMC Res Notes. 2016; 9(1): 506. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGovender D, Naidoo S, Taylor M: Antenatal and Postpartum Depression: Prevalence and Associated Risk Factors among Adolescents' in KwaZulu-Natal, South Africa. Depress Res Treat. 2020; 2020: 5364521. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWorld Health Organization: A Conceptual Framework for Action on the Social Determinant of Health. 2008. Reference Source\n\nWorld Health Organization: Thinking Healthy: A manual for psychosocial management of perinatal depression. WHO, Community Health Workers Version. 2015. Reference Source\n\nCox JL, Holden JM, Sagovsky R: Detection of postnatal depression. Development of the 10-item Edinburgh Postnatal Depression Scale. Br J Psychiatry. 1987; 150: 782–6. PubMed Abstract | Publisher Full Text\n\nKumar M, Ongeri L, Mathai M, et al.: Translation of EPDS Questionnaire into Kiswahili: Understanding the Cross-Cultural and Translation Issues in Mental Health Research. J Pregnancy Child Health. 2015; 2(1): 1000134. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTesfaye M, Hanlon C, Wondimagegn D, et al.: Detecting postnatal common mental disorders in Addis Ababa, Ethiopia: validation of the Edinburgh Postnatal Depression Scale and Kessler Scales. J Affect Disord. 2010; 122(1–2): 102–8. PubMed Abstract | Publisher Full Text\n\nJoshi D, Shrestha S, Shrestha N: Understanding the antepartum depressive symptoms and its risk factors among the pregnant women visiting public health facilities of Nepal. PLoS One. 2019; 14(4): e0214992. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMadeghe B, Kogi-Makau W, Kumar M, et al.: Maternal Depression Experiences FDGs Interview guide. figshare. Dataset. 2020. http://www.doi.org/10.6084/m9.figshare.13265420.v2\n\nIbrahim M: Thematic Analysis : A Critical Review of Its Process and Evaluation. WEI International European AcademicConference Proceedings. 2012; 1: 8–21. Reference Source\n\nSheeba B, Nath A, Metgud CS, et al.: Prenatal Depression and Its Associated Risk Factors Among Pregnant Women in Bangalore: A Hospital Based Prevalence Study. Front Public Health. 2019; 7: 108. PubMed Abstract | Publisher Full Text | Free Full Text\n\nZeng Y, Cui Y, Li J: Prevalence and predictors of antenatal depressive symptoms among Chinese women in their third trimester: a cross-sectional survey. BMC Psychiatry. 2015; 15(1): 66. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDuko B, Ayano G, Bedaso A: Depression among pregnant women and associated factors in Hawassa city, Ethiopia: an institution-based cross-sectional study. Reprod Health. 2019; 16(1): 25. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAbebe A, Tesfaw G, Mulat H, et al.: Postpartum depression and associated factors among mothers in Bahir Dar Town, Northwest Ethiopia. Ann Gen Psychiatry. 2019; 18(1): 19. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRashid A, Mohd R: Poor social support as a risk factor for antenatal depressive symptoms among women attending public antennal clinics in Penang, Malaysia. Reprod Health. 2017; 14(1): 144. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMadeghe B, Kogi-Makau W, Kumar M, et al.: Socio-demography and Depression Questionnaire. figshare. Dataset. 2020. http://www.doi.org/10.6084/m9.figshare.13265297.v1\n\nMadeghe B, Kogi-Makau W, Kumar M, et al.: Maternal Depression experiences FDG transcription. figshare. Dataset. 2020. http://www.doi.org/10.6084/m9.figshare.13265549.v1"
}
|
[
{
"id": "76447",
"date": "25 Jan 2021",
"name": "Irene Inwani",
"expertise": [
"Reviewer Expertise Pediatric",
"adolescents and maternal 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 addresses an important and to some extent neglected area of health care and research. It is a well written manuscript but there are areas that require some improvement as highlighted below:\nWhat was the rationale of recruiting women aged 18 to 44 years only when we know age is a predictor of depression?\n\nWhat was the justification for not including a sample from women identified as not depressed in the FGDs to understand if their experiences were similar to the sampled group?\n\nEligibility criteria in this study were only age and pregnancy. What criteria made participants not eligible for the study? Which confounding factors were considered?\n\nWhich quality assurance measures were put in place for qualitative data analysis?\n\nEthically; what happened to women found to have depression and especially those who had suicidal ideation as well as those experiencing violence?\n\nPlease check the following:\n\nAge range in the text is 18-44 while in the tables it is 18-42 Table 1; what does the percentage of the mean age represent? Parity is equated to the number of children below 18 years; this is erroneous, a 44 can have children above 18 and therefore be misclassified. In the table the bands for income overlap, check. Confirm the proportion of those earning less than 15000. Revise subheadings to reflect the issue being addressed and leave out the population and settings which are described in the methods. Reported range of depression score conflict some sections 0-30, others 0-26. Table 2; confirm the totals (N) for depressed and non-depressed. Table 3 categorize per site. The qualitative data need to be reworked and triangulated appropriately with the quantitative data. The themes, example poverty and financial struggles are closely related and therefore need to see which quotes fit well in each theme. Review the language in the quotes and generally in the qualitative section. Discussion section; A good discussion but can be improved by focusing on the audience and key message built from the major findings. Check findings from other countries, regions and local which used a similar and different methodology, and if possible similar context. Discuss some more weaknesses/limitations such as cross-sectional nature of the study therefore not able to establish a causal relationship, not having assessed other possible contributors to depression and neonatal outcomes\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": [
{
"c_id": "6545",
"date": "16 Apr 2021",
"name": "Beatrice Madeghe",
"role": "Author Response",
"response": "Reviewer 1: Comments and responses 1. What was the rationale of recruiting women aged 18 to 44 years only when we know age is a predictor of depression? Response: - Thank you for this comment. This was a mistake and has been corrected in the text. The study participants included Women of reproductive age of 15-49 in Kenya. The actual age range of participants who were present and recruited in the study and their data analyzed had an age range of 18 to 42. This has been corrected in the text. See method, Study participants. 2. What was the justification for not including a sample from women identified as not depressed in the FGDs to understand if their experiences were similar to the sampled group? Responses: Thank you for this comment. This cross-sectional study was part of the baseline assessment of a longitudinal cohort study that targeted depressed pregnant women for intervention. The non-depressed women were not included in this study because the study interest was to understand the experiences of depression pregnant women to provide a way forward for an intervention study. Therefore we were interested in depressed pregnant women only, and it was necessary to find out their experiences for depression to get the starting point for the intervention. That’s why non-depressed women were not included. However, I agree that including non-depressed women could be an advantage to know their experiences too. See FDGS section. 3. Eligibility criteria in this study were only age and pregnancy. What criteria made participants not eligible for the study? Which confounding factors were considered? Response: - Thank you for this comment. The eligibility criteria were pregnant women who are depressed. As explained in the comment above, this study was part of the baseline data of an intervention study that targeted women of reproductive age and who are depressed so that they can be considered for f intervention. So it included women who gave written informed consent and women who are not mentally disturbed to the extent of not giving correct information. See method 4. Which quality assurance measures were put in place for qualitative data analysis? Responses: - We used the COREQ (Consolidated criteria for Reporting Qualitative research) Checklist, a 32-item checklist for interviews and focus groups. Developed from: Tong A, Sainsbury P, Craig J. Consolidated criteria for reporting qualitative research (COREQ). A checklist of items was included to report this qualitative research. Each of the items listed in this checklist was considered in the manuscript and was reported. The completed checklist was uploaded as part of my submission with this manuscript. See FGDs section 5. Ethically; what happened to women found to have depression and especially those who had suicidal ideation as well as those experiencing violence? Responses: - This was revised and added to the text, All women who appeared to have suicidal ideation and those who were experiencing violence were referred to the mental health services available at the health facility for treatment, furthermore, the second part of the study was an intervention study so they were enrolled to proceed with the intervention study, See results depression levels. 6. Please check the following: i. Age range in the text is 18-44 while in the tables it is 18-42? Responses: - The actual age range of women recruited and their data analyzed had an age range of 18-42. See results, sociodemographic characteristics ii. Table 1: What does the percentage of the mean age represent? Response: - This was a mistake and the mistake has been corrected. See table 1 iii. Parity is equated to the number of children below 18 years; this is erroneous, a 44 can have children above 18 and therefore be misclassified? Response: - Thank you for this comment. The age range of women recruited and their data analyzed in the study was 18 to 42. None of them had a child above 18. As explained above the inclusion criteria has been corrected included women aged range of 15-49, but the actual age range of women obtained in the study was 18 - 42. Therefore there was no mix-up, and the age range here was not equated with a number of children below 18. See results. iv. In the table the bands for income overlap, check. Confirm the proportion of those earning less than 1500? Response: - This has been revised and the mistake and has been corrected in the table. v. Reported range of depression score conflict some sections 0-30, others 0-26? Response: - This has been clarified, Edinburgh Postnatal Depression Scale (EPDS), guided the scoring system17. EPDS has 10 questions which generate scores from 0 to 30 maximum. According to this tool, a score of 10/30 or greater indicates possible depression. Women who score above 13/30 are likely to be suffering from clinical depression of varying severity. On the results, the actual scores of women screened in the study and their data analyzed had EPDS scores range of 0 -26. See results prevalence of Prepartum depression vi. Table 2; confirm the totals (N) for depressed and non-depressed? Response: - Thank you for this comment; Table 2 has been revised, the labeling error for table 2 has been corrected, the number of depressed and not depressed has been confirmed. See table3 vii. Table 3 categorize per site? Response: - Table 3 has been revised and categorized per site, where the first table is depressed women from Kawangware and the second table is depressed women from Kangemi. See table 3. viii. The qualitative data need to be reworked and triangulated appropriately with the quantitative data. The themes, for example, poverty, and financial struggles are closely related and therefore need to see which quotes fit well in each theme? Response: - Thank you for this comment. The themes were only four. Poverty is one theme that was – manifested through three sub-themes identified as financial struggle, unemployment, and food insecurity, so financial struggles were the sub-theme of poverty, not a different theme. The other theme was Social support: Marital disharmony and Trauma experiences and all have sub-themes, and their experiences were discussed in details in the quotes See qualitative results ix. Review the language in the quotes and generally in the qualitative section? Responses: - I have revised my best possible the quotes in the qualitative section x. Discussion section; a good discussion but can be improved by focusing on the audience and key message built from the major findings. Check findings from other countries, regions, and local which used a similar and different methodology, and if possible similar context? Response:-Thank you. The discussion section has been revised. I have tried to improve it as suggested. See discussion xi. Discuss some more weaknesses/limitations that the cross-sectional nature of the study therefore not able to establish a causal relationship, not having assessed other possible contribution to depression and neonatal outcomes? Responses Thank you for this comment. I have discussed more weakness/ limitations of the study and added to the text / other possible confounding factors such as child preference, previous history of depression, spouse alcohol intake as a risk factor for depression and neonatal outcomes were not assessed hence limitation to this study. Moreover, this was a cross-sectional study and as a limitation, cross-sectional studies do not establish the causal relationship hence the limitation for this study. See study limitation."
}
]
},
{
"id": "76448",
"date": "04 Feb 2021",
"name": "Rahul Shidhaye",
"expertise": [
"Reviewer Expertise Psychiatric epidemiology",
"perinatal mental health",
"implementation science"
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn this paper titled, 'Risk factors and experiences of prepartum depression among pregnant women in urban-low income in Nairobi Kenya: a mixed methods study,' Madeghe and colleagues present the prevalence of prepartum depression, risk factors, and real-life experiences of depression among pregnant women. There are few concerns that need to be addressed and some suggestions to further improve this paper.\nTitle: It will be better to use the term 'antenatal depression' instead of 'prepartum depression' as the former is more commonly used in the literature. A quick pubmed search returned 609 articles for the term, 'antenatal depression' compared to 9 results when 'prepartum depression' was used. In case you agree with this suggestion, please make the changes throughout the draft. I assume you wish to say urban-low income settlements/setting? Please add an appropriate word in the title. Prepartum depression will be present ONLY in pregnant women. It will be good to say either, 'prepartum/antenatal depression in urban low......' or 'depression among pregnant women in urban low.....'\n\nAbstract: It is mentioned, 'Women's gestational age in the second trimester (87.5%) was statistically significantly associated with prepartum depression (p<0.001).' Please can you provide the measure of association (odds ratio) to support this statement? It is not clear what 87.5% means. Is it that 87.5% of women in their second trimester had depression? I have the same comment for the next statement in the abstract on income level.\n\nSample size: Please provide the rationale for recruiting 262 pregnant women in this study.\n\nIt will be good to provide the reference for the cohort study mentioned in the methods section.\n\nDid you use any conceptual framework or prior literature to select the socio-demographic characteristics? A number of factors such as domestic violence, gender preference of the child, and nutritional status of women are not included. Please clarify.\n\nGenerally, the cut-off of 11/12 is used for EPDS. Please clarify the reason for choosing 12/13 as the cut-off.\n\nThe following sentence is not clear, 'The data was coded until when the ability to obtain additional new information was exhausted for the study purpose.'\n\nHow many women were approached and what proportion of them consented to participate in the study? Please provide these details in the first paragraph of the results.\n\nAlthough 33.6% of women had depression, table 2 mentions 174 women as depressed. Please check.\n\nPlease provide actual n for each of the variables.\n\nThe percentages presented in table 2 make very little sense. The readers will be interested in knowing the proportion of women who screened positive for depression for one level of a variable compared to another level of the same variable. To illustrate this, it will be good to know what proportion of women in the age group of 18-24 screened positive for depression and also the proportion of women in the age group of 25-42 who screened positive for depression. The current numbers do not provide that information.\n\nIt seems that lower income level was a protective factor and resulted in lower odds of depression (OR: 0.39, 95% CI 0.23-0.66). This completely contradicts the findings from your qualitative study as well as from the past literature.\n\nPlease present the findings related to the univariable association of each of the explanatory variables with the outcome. I assume that the findings in table 2 are that of multivariable association? Please clarify.\n\nThe analysis undertaken is simple/univariable and multiple/multivariable logistic regression and not multivariate regression. Please correct. . One of the important limitations is the cross-sectional nature of this study which precludes any causal inferences. This needs to be included in the limitations.\n\nIt is also likely to have confounding bias as the data on key explanatory variables is not included.\n\nThe use of a screening tool for depression (EPDS) also needs to be included as one of the limitations.\n\nPlease read the paper carefully to address the grammatical errors.\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": [
{
"c_id": "6546",
"date": "16 Apr 2021",
"name": "Beatrice Madeghe",
"role": "Author Response",
"response": "Reviewer 2: Comments and responses 1. Title: It will be better to use the term 'antenatal depression' instead of 'prepartum depression' as the former is more commonly used in the literature. A quick PubMed search returned 609 articles for the term, 'antenatal depression' compared to 9 results when 'prepartum depression' was used. In case you agree with this suggestion, please make the changes throughout the draft. I assume you wish to say urban-low income settlements/setting? Please add an appropriate word in the title. Prepartum depression will be present ONLY in pregnant women. It will be good to say either, 'prepartum/antenatal depression in urban low......' or 'depression among pregnant women in urban low....? Responses:- Thank you for this suggestion and it is true pre-partum is not commonly used. I request to maintain the prepartum term because I have defined it and it has the same meaning as prenatal. I have maintained it throughout the text. I have structured the title, and I have added the words settlements as advised, now the title read as:-“Risk factors and experiences of prepartum depression in urban-low income settlements Nairobi-Kenya: a mixed-method study” see page 1. 2. Abstract: It is mentioned, 'Women's gestational age in the second trimester (87.5%) was statistically significantly associated with prepartum depression (p<0.001).' Please can you provide the measure of association (odds ratio) to support this statement? It is not clear what 87.5% means. Is it that 87.5% of women in their second trimester had depression? I have the same comment for the next statement in the abstract on income level? Response: - This was revised. I have provided the measures of associations to support the statements in the abstract and text as follows:- Women's gestational age was statistically significantly associated with prepartum depression [OR 3.37; (95% C.I 1.60 - 7.10); p <0.001]. Income levels <10,000 KES was statistically significantly associated with prepartum depression [OR 0.39; (95%; C.I 0.23 – 0.66); p <0.001. See abstract. 3.Sample size: Please provide the rationale for recruiting 262 pregnant women in this study? Response: - This was revised and explained in the text. The rationale for recruiting 262 women is because this was the baseline study for the intervention longitudinal study. So sample size was calculated using Sample size estimation for longitudinal designs with attrition (Diggle et al., 2002). We needed approximately 100 subjects in each group, where 50 would be the intervention and 50 would be the intervention group. Therefore to obtain the above sample of women, we consecutively screened 262 pregnant women at baseline and obtained 100 depressed pregnant women. See method. 4. It will be good to provide the reference for the cohort study mentioned in the methods section? Response: - Thank you for this suggestion, the intervention results for this study are not yet published and still under review, this was the baseline data that we are sharing, that’s why we are unable to provide the reference cohort. 5. Did you use any conceptual framework or prior literature to select the socio-demographic characteristics? A number of factors such as domestic violence, gender preference of the child, and nutritional status of women are not included. Please clarify? Response: - Thank you for this comment. Yes, the literature guided the process of selecting the socio-demographic factors; in this study, the association between nutritional status and prepartum depression was studied in details, and the nutritional factors/status associated with prepartum depression were evaluated and discussed in another paper, which is still under review, we also conducted the focus group discussion to understanding the real-life experiences of depressed women. I admit that as a limitation to this study some contributing factors were not included in the sociodemographic questionnaire. However, in the focus group discussion, domestic violence came up and was captured as contributing factor for depression in this study. This limitation was added as the limitation of to study, that some factors such as child sex preference, spouse alcohol intake were not assessed. 6. Generally, the cut-off of 11/12 is used for EPDS. Please clarify the reason for choosing 12/13 as the cut-off? Response: - I used The Edinburgh Postnatal Depression Scale (EPDS). According to the scoring system of this tool, a score of 10 or greater indicates possible depression. Mothers who score above 13 are likely to be suffering from clinical depression of varying severity. The maximum score is 30.17 Therefore I followed the cut-off guidance provided in this scale where an EPDS, a score of 10 to 13 indicates possible depression of moderate severity, and a score of above 13 indicates clinical depression. In this study, all women who had EPDS SCORE of 10 to 13 were classified with possible depression, and those with EPDS scores of above 13 were classified as having clinical depression. Source: Cox, J.L., Holden, J.M., and Sagovsky, R. 1987. 7. The following sentence is not clear, 'The data was coded until when the ability to obtain additional new information was exhausted for the study purpose? Response: - The sentence was reviewed and made clear. Data was coded until all the information required for the study was exhausted. See FGDs results. 8. How many women were approached and what proportion of them consented to participate in the study? Please provide these details in the first paragraph of the results? Responses:- This section was revised and added to the text. This cross-sectional study was part of the baseline assessment of a longitudinal cohort study that targeted depressed pregnant women for intervention. Therefore the sample size was calculated using Sample size estimation for longitudinal designs with attrition (Diggle et al., 2002). We needed approximately 100 subjects. To obtain the above sample size at baseline, consecutive sampling was used where every pregnant woman who came for a checkup during the study period was assessed for depression as part of service delivery, hence 262 pregnant women were recruited which enabled a sample of 100 depressed women. See method. 9. Although 33.6% of women had depression, table 2 mentions 174 women as depressed. Please check? Responses: - Thank you for this comment. This was the mistake, the table was not labeled correctly. I have revised this table and the table has been labeled correctly. 10. Please provide actual n for each of the variables? Response: - This has been revised the actual numbers in the table have been provided. See table 2. 11. The percentages presented in table 2 make very little sense. The readers will be interested in knowing the proportion of women who screened positive for depression for one level of a variable compared to another level of the same variable. To illustrate this, it will be good to know what proportion of women in the age group of 18-24 screened positive for depression and also the proportion of women in the age group of 25-42 who screened positive for depression. The current numbers do not provide that information? Response: - This comment has been revised I have provided the proportion of women who screened positive for depression for one level of a variable were compared to another level of the same variable. See table2. 12. It seems that a lower-income level was a protective factor and resulted in lower odds of depression (OR: 0.39, 95% CI 0.23-0.66). This completely contradicts the findings from your qualitative study as well as from the past literature? Response: - This was an error in the labeling of table 2, which caused results to read the opposite, this has been corrected, and the table labeled correctly. The result reads well that the lower-income level is the risk factor for depression. See table 2. 13. Please present the findings related to the univariable association of each of the explanatory variables with the outcome. I assume that the findings in table 2 are that of multivariable association? Please clarify? Response:- Thank you for this comment, the factors that were significant in the univariable association were the same as in the multivariable association, so I only provided the multivariable table because the factor that was significant was the same. See data analysis. 14. The analysis undertaken is simple/univariable and multiple/multivariable logistic regression and not multivariate regression. Please correct? Response:- Thank you for this correction, I have corrected this error. The analysis undertaken was univariable and multivariable logistic regression. See data analysis. 15. One of the important limitations is the cross-sectional nature of this study which precludes any causal inferences. This needs to be included in the limitations? Response: - Thank you for this comment. This limitation has been added to this study, This study was a cross-sectional study and as a limitation, cross-sectional studies do not establish the causal relationship hence the limitation for this study. See study limitation. 16. It is also likely to have confounding bias as the data on key explanatory variables is not included? Response: - This section has been revised and added as a limitation to the study that, other possible confounding factors such as child preference, previous history of depression, and partner alcohol intake as a risk factor for depression were not assessed hence a limitation to this study. See study limitation. 17. The use of a screening tool for depression (EPDS) also needs to be included as one of the limitations? Response: - Thank you for this comment, this limitation was added to the text that; Although EPDS is an established and widely used screening tool for maternal depression with high specificity and sensitivity, it is not as a definitive diagnosis, hence the inherent limitation of using this tool. See study limitation. 18. Please read the paper carefully to address the grammatical errors? Response: - The paper was carefully read through and all possible grammatical errors addressed. Thank you"
}
]
}
] | 1
|
https://f1000research.com/articles/9-1495
|
https://f1000research.com/articles/9-1372/v1
|
26 Nov 20
|
{
"type": "Research Article",
"title": "A new analysis approach for single nephron GFR in intravital microscopy of mice",
"authors": [
"Friederike Kessel",
"Hannah Kröger",
"Michael Gerlach",
"Jan Sradnick",
"Florian Gembardt",
"Vladimir Todorov",
"Christian Hugo",
"Friederike Kessel",
"Hannah Kröger",
"Michael Gerlach",
"Jan Sradnick",
"Florian Gembardt",
"Vladimir Todorov"
],
"abstract": "Background: Intravital microscopy is an emerging technique in life science with applications in kidney research. Longitudinal observation of (patho-)physiological processes in living mice is possible in the smallest functional unit of the kidney, a single nephron (sn). In particular, effects on glomerular filtration rate (GFR) - a key parameter of renal function - can be assessed. Methods: After intravenous injection of C57BL/6 mice with a freely filtered, non-resorbable, fluorescent dye a time series was captured by multiphoton microsopy. Filtration was observed from the glomerular capillaries to the proximal tubule (PT) and the tubular signal intensity shift was analyzed to calculate the snGFR. Results: Previous methods for this analysis relied on two manually defined measurement points in the PT and the tubular volume was merely estimated in 2D images. We extended the workflow in FIJI by adding continuous measurement of intensity along the PT in every frame of the time series. Automatic modelling of actual PT volume in a 3D dataset replaced 2D volume estimation. Subsequent data analysis in R, with a calculation of intensity shifts in every frame and normalization against tubular volume, allowed exact assessment of snGFR by linear regression. Repeated analysis of image data obtained in healthy mice showed a striking increase of reproducibility by reduction of user interaction. Conclusions: These improvements maximize the reliability of a sophisticated intravital microscopy technique for the precise assessment of snGFR, a highly relevant predictor of kidney function.",
"keywords": [
"Intravital Microscopy",
"2-Photon Microscopy",
"Kidney",
"Single Nephron GFR",
"ImageJ",
"R"
],
"content": "Introduction\n\nGlomerular filtration rate (GFR) is a key parameter of kidney function and deviations from normal GFR are a hallmark of renal diseases1,2. GFR describes the filtration of substances from blood in the glomerular capillaries, to the primary urine in the tubular system of the kidney. Therefore, changes in GFR serve to monitor disease progression. GFR is also measured in animal models to study effects of pharmacological intervention on kidney function. Advances in intravital imaging and multiphoton microscopy allow repetitive assessment of GFR and morphological changes in the smallest functional unit of the kidney – the nephron. Longitudinal imaging of single nephrons (sn) enable direct correlation of structural and functional data.\n\nAfter intravenous injection of the freely filtered, non-resorbable, fluorescent dye LuciferYellow (LY), a time series was captured by multiphoton microsopy. Filtration was observed from the glomerular capillaries to the proximal tubule (PT) and the tubular signal intensity shift is analyzed to calculate the filtration rate. Translated to an image processing task, this can be generalized as the flow rate in a tube. Previous methods for this analysis3,4 relied on two manually annotated measurement points in the PT and stereotypic estimation of PT volume in 2D images. Since results we obtained with this approach were highly variable, we expanded the analysis via 3D modelling with open source software, to increase overall reproducibility and reliability when comparing renal function of different experimental groups.\n\n\nMethods\n\nAnimal experiments were performed in accordance with the Federation of European Laboratory Animal Science Associations (FELASA) Guidelines for the Care and Use of Laboratory Animals and the Federal Law on the Use of Experimental Animals in Germany and approved by the ethical review committee at the Landesdirektion Sachsen (licence DD-24.1-5131/338/37). For microscopy, male, 10–12 week old C57BL/6 mice were prepared as previously described5,6. In brief, a titanium abdominal imaging window (AIW) covered with a coverslip is surgically implanted above the kidney. The kidney is glued to the coverslip with cyanoacrylate glue before securing the AIW by tightening the skin in the AIW groove. Microscopy was performed one day after AIW implantation.\n\nA custom-built temporary intravenous catheter (polyethylene tubing #587360 by Science Products GmbH with 0.3×12mm needle) was placed in the lateral tail vein. Fluorescent dyes were administered into the tail vein prior (Hoechst, AngioSpark) or during (LuciferYellow) microscopy (detailed information in Table 1).\n\nAll efforts were made to ameliorate harm to animals. Imaging (including injections of the fluorescent dyes) and the implantation is done under isoflurane narcosis. The image data of the five animals presented for the comparison of the extended workflow with the previous workflow in this manuscript were generated previously as part of an independent experiment (licence DD-24.1-5131/338/37).\n\nImaging was performed on an upright Leica SP8 multiphoton laser scanning microscope of the Core Facility Cellular Imaging. Settings for signal acquisition are summarized in Table 2.\n\nImage processing and analysis was done in ImageJ7–9 (1.53c) with 3D ImageJ Suite10 and Bio-Formats11 for the use of 3D image processing plugins and the Bio-Formats Importer. Data analysis was performed in R12 (4.0.2), with RStudio13 (1.2.5033) with ggplot214 (including dependencies) installed as additional library. The script executed the ImageJ macro from command line and subsequently analyzed and visualized the results. A detailed description of the algorithm is associated with the scripts on GitHub15.\n\nThe line region of interest (ROI) set for the extended workflow to manually define direction and position of the proximal tubule (PT) was also used to determine the two measuring points (beginning and end of line) for analysis of image material based on the previously described approach3,4. Tubular diameter was calculated as the mean of five manually measured diameters.\n\n\nResults\n\nIn the time series acquired after application of LuciferYellow (LY), a line region of interest (ROI) was set to manually define the position and direction of the measurement. Along this line ROI, x-y plots measured the dye intensity in the proximal tubule (PT) in every frame (Figure 1) and numerical results were saved.\n\nSignal intensity of LuciferYellow (LY) was measured along a line region of interest (magenta) in every frame (here only frame 0 - before LY injection, frame 13 and 26).\n\nFor the automatic 3D modelling of PT volume the z-stack of the same field of view was acquired. Additional channels (Ch3: AngioSpark - vessels, Ch4: Hoechst - nuclei, Figure 2A) were subtracted from Ch2 (target channel, LuciferYellow intensity) to remove spectral bleed-through artifacts (Figure 2B). With the 3D watershed, the PT was segmented (Figure 2C, 3D-model) and saved for visual verification. The cumulative PT volume was measured over the distance along the line ROI and interpolated for every measurement position along the line ROI in the PT (Figure 3A) in subsequent data analysis. From intensity measurements a threshold intensity was set to the turning point of fluorescence intensity over time at every position (maximum slope, Figure 3B). The position with this intensity was approximated in each frame and used for linear regression (Figure 3C). The slope of the regression line equals the snGFR. Together with information about PT length, PT volume and R-squared the results were summarized and saved in a data table.\n\nA) After applying a 3D median filter, the channel 3 and channel 4 z-stacks were substracted from channel 2 to eliminate spectral bleedthrough artifacts (B). The proximal tubule (PT) was segmented with the help of a 3D watershed (3D model of the resulting z-stack, C).\n\nA) For every position along the line region of interest (ROI), the cumulative volume was measured. B) Numerical data underlying the x-y plots was saved and used to subsequently plot changes of signal intensity over time for every position along the line ROI. The dashed line represents the threshold value (intensity with maximum slope across all positions), at which position and corresponding volume of the proximal tubule (PT) was approximated for every frame. C) Using linear regression the GFR could be calculated as the volume with the intensity threshold at the frames of interest. Regression line is displayed with 95% confidence interval.\n\nRepeated analysis of 15 indiviudal glomeruli by the same researcher (five times) showed that results obtained with the presented workflow had higher consistency (lower intrasample variance, CV=10.35%) compared to the previous approach (CV=38.75%, Figure 4). Due to the high variance with the previous approach a direct correlation of the workflows was not possible; however, the final result - the mean snGFR - was comparable (previous workflow: 1.71±0.91, extended workflow: 1.70±0.78) and a two-sample Kolmogorov-Smirnof test of both result vectors showed that the distributions were not different (p=0.4662).\n\nImage data of healthy mice (five animals, 15 glomeruli) was analysed five times by the same researcher using the previous and the extended workflow. Scatter plot of results of the previous (x-axis) and extended workflow (y-axis) with rectangles used to indicate the range of results obtained in one glomerulus. Colours indicate data obtained from individual glomeruli. Intrasample variance with the extended workflow (variance along the y-axis, mean CV=10.35%) was smaller than with the previous workflow (variance along the x-axis, mean CV=38.75%). Both analysis workflows showed similar results (mean snGFR, previous workflow: 1.71±0.91, extended workflow: 1.70±0.78) and a two-sample Kolmogorov-Smirnof test of both result vectors showed that the distributions were not different (p=0.4662).\n\n\nConclusions\n\nThe progressive development of microscopy techniques like measurement of snGFR in experimental animals needs to be accompanied by improvements in analysis algorithms to use their full potential. In this manuscript we present a workflow by extending an existing analysis via 3D modelling, for increased reproducibility, accuracy, but also transparency in the measurement of snGFR. By reducing user interaction, intrasample variance was markedly improved.\n\nAdditionally, the automatically saved user input and intermediate results (z-stack of watershed of PT as shown in Figure 2C and graphs in Figure 4) for every analyzed dataset provide full possibility to verify every analysis step. These results can be used to objectively evaluate the measurement. Although the snGFR in this manuscript was very low for healthy animals compared to previously published values3, the range was comparable in both methods and not an artifact produced by the workflow but more likely caused by the general experimental setup.\n\nTaken together, this workflow extension contributes to an overall improvement of snGFR measurement. Applied to experimental data this can cumulate in a higher power to detect statistically significant differences between experimental groups and even decrease the necessary sample size, thus having an impact on animal welfare.\n\n\nData availability\n\nZenodo: Sample dataset - cont-3D-snGFR. https://doi.org/10.5281/zenodo.427559616.\n\nThis project contains the following underlying data:\n\n- Sample_Dataset_cont-3D-snGFR.lif (Sample file with time series and z-stack of three different glomeruli after injection of LuciferYellow for the analysis of single nephron GFR)\n\n- Results.zip (Sample file for the selection (ROI sets) of the proximal tubulus in the sample dataset, including the resulting measurements (text files) in the time series and 3D modelling of the proximal tubules (tiff files))\n\n- Graphs_2020-09-30.zip (Intermediate results and graphs (png files) as obtained from the sample dataset with selections and measurement data in the results file)\n\n- 2020-09-30-Result_summary.txt (Final summary (text file) of calculated single nephron GFR for the three sample glomeruli based on selections from the results file)\n\n- Dataset1.lif (Image data used for the comparison of previous and extended workflow in Figure 4, includes 15 time series and the corresponding z-stacks)\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\nSource code available from: https://github.com/NephrologieDresden/cont-3D-snGFR\n\nArchived source code at time of publication: https://doi.org/10.5281/zenodo.405954915.\n\nLicense: GNU General Public License v3.0",
"appendix": "Acknowledgments\n\nThe authors acknowlegde the support of the Core Facility Cellular Imaging (CFCI) at the Medical Faculty Carl Gustav Carus, Technical University Dresden. This publication was supported by COST Action NEUBIAS (CA15124), funded by COST (European Cooperation in Science and Technology).\n\n\nReferences\n\nTrevisan R, Dodesini AR: The Hyperfiltering Kidney in Diabetes. Nephron. 2017; 136(4): 277–280. PubMed Abstract | Publisher Full Text\n\nEarle DP Jr: Renal function tests in the diagnosis of glomerular and tubular disease. Bull N Y Acad Med. 1950; 26(1): 47–65. PubMed Abstract | Free Full Text\n\nKidokoro K, Cherney DZI, Bozovic A, et al.: Evaluation of Glomerular Hemodynamic Function by Empagliflozin in Diabetic Mice Using In Vivo Imaging. Circulation. 2019; 140(4): 303–315. PubMed Abstract | Publisher Full Text\n\nKang JJ, Toma I, Sipos A, et al.: Quantitative imaging of basic functions in renal (patho)physiology. Am J Physiol Renal Physiol. 2006; 291(2): F495–502. PubMed Abstract | Publisher Full Text\n\nHickmann L, Steglich A, Gerlach M, et al.: Persistent and inducible neogenesis repopulates progenitor renin lineage cells in the kidney. Kidney Int. 2017; 92(6): 1419–1432. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSchiessl IM, Fremter K, Burford JL, et al.: Long-Term Cell Fate Tracking of Individual Renal Cells Using Serial Intravital Microscopy. Methods Mol Biol. 2020; 2150: 25–44. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSchindelin J, Rueden CT, Hiner MC, et al.: The ImageJ ecosystem: An open platform for biomedical image analysis. Mol Reprod Dev. 2015; 82(7–8): 518–529. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSchneider CA, Rasband WS, Eliceiri KW: NIH Image to ImageJ: 25 years of image analysis. Nat Methods. 2012; 9(7): 671–675. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSchindelin J, Arganda-Carreras I, Frise E, et al.: Fiji: an open-source platform for biological-image analysis. Nat Methods. 2012; 9(7): 676–682. PubMed Abstract | Publisher Full Text | Free Full Text\n\nOllion J, Cochennec J, Loll F, et al.: TANGO: a generic tool for high-throughput 3D image analysis for studying nuclear organization. Bioinformatics. 2013; 29(14): 1840–1841. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGoldberg IG, Allan C, Burel JM, et al.: The Open Microscopy Environment (OME) Data Model and XML file: open tools for informatics and quantitative analysis in biological imaging. Genome Biol. 2005; 6(5): R47. PubMed Abstract | Publisher Full Text | Free Full Text\n\nR: A Language and Environment for Statistical Computing. (Vienna, Austria, 2017). Reference Source\n\nRStudio: Integrated Development Environment for R. (Boston, MA, 2019). Reference Source\n\nggplot2: Elegant Graphics for Data Analysis. (Springer-Verlag New York), 2016. Reference Source\n\nKessel F, Kröger H, Hugo C: Continuous analysis of single nephron GFR. 2020. http://www.doi.org/10.5281/zenodo.4059549\n\nKessel F, Kröger H, Hugo C: Sample dataset - cont-3D-snGFR. 2020. http://www.doi.org/10.5281/zenodo.4275596"
}
|
[
{
"id": "75572",
"date": "16 Dec 2020",
"name": "Bruce A. Molitoris",
"expertise": [
"Reviewer Expertise Nephrology",
"imaging"
],
"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\nMeasurement of SNGFR is an important undertaking and adding a 3D component to tubular volume is interesting. However, viewing glomeruli in mice of 10-12 weeks is not possible without significant invasive proceedures. Ureteral obstruction has been used by some, but this author uses removal of 1 mm of cortical tissue to get down to cortical glomeruli. They do not say this but reference an existing paper. Since you can only see up to 100 microns with the 2-photon scope with high resolution, it is difficult to imaging tissue injury is not altering function of the glomerulus and tubules. This has to be discussed and if controls are available they should be mentioned. In the referenced paper the sieving Coefficient for albumin was very high and likely due to tissue injury. No glomerulus is shown in the present work and yet the authors indicate they followed from glom and then along the tubule. Were they measuring flow in S1 or S2 segments as flow would vary due to reabsorption?\nAlso, the subtraction of 3D volumes from each other for background subtraction is not recommended. It is best to subtract each individual plane from the corresponding channels.\nIt would also be helpful if they put figure 4 data into a table for easier and direct comparison.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? No source data required\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": [
{
"c_id": "6299",
"date": "12 Apr 2021",
"name": "Friederike Kessel",
"role": "Author Response",
"response": "We thank Prof. Molitoris for his time and the detailed review. However there seems to be a misunderstanding of the intentions of the submitted manuscript. We present and validate a workflow and an algorithm to process image data obtained from single nephron GFR measurements by intravital microscopy. The measurement itself is not the focus of the manuscript. A detailed protocol on animal preparation and image data acquisition was merely cited (1), however the experimental setup is reproducible using these protocols. In our setup, superficial glomeruli can be imaged in the intact kidney of 10-12 week old animals with 2-photon microscopy with sufficient quality. We want to specifically point out that removing parts of the kidney cortex prior imaging is not included in the cited protocols and we did not perform this in our study either. Prof. Molitoris is possibly referring to the paper of Kidokoro et al. (2) which was cited by us in the context of illustrating an existing analysis approach for image data obtained from the snGFR measurement. With the focus of the manuscript in mind: We compare results obtained from the analysis of the same image datasets with two different workflows (but using the same segments of the proximal tubule) – and not different experimental groups of differently treated animals. With all raw image data (openly accessible at Zenodo), the source code (openly accessible at GitHub) and open source software (ImageJ and R) the data we present are completely reproducible. We agree with Prof. Molitoris that presenting more image data in the manuscript might be beneficial. The challenges of depicting time series and complex 3D image data in a 2D representation led us to the decision to upload all raw image data (time series and 3D datasets) to Zenodo, where it can be freely accessed. Lastly we rephrase the description of one of the image processing steps: As Prof. Molitoris pointed out correctly, the subtraction of one z-stack from the other is performed plane by plane, and not with 3D volumes. Clarifying changes in the manuscript on the emphasis of the intention (presenting an image analysis workflow) will be made in an upcoming version. We would gladly invite Prof. Molitoris to review the updated manuscript again with this perspective. Kidokoro K, Cherney DZI, Bozovic A, et al.: Evaluation of Glomerular Hemodynamic Function by Empagliflozin in Diabetic Mice Using In Vivo Imaging. Circulation. 2019; 140(4): 303–315. Schiessl IM, Fremter K, Burford JL, et al.: Long-Term Cell Fate Tracking of Individual Renal Cells Using Serial Intravital Microscopy. Methods Mol Biol. 2020; 2150: 25–44."
}
]
},
{
"id": "76548",
"date": "28 Jan 2021",
"name": "Christopher Schmied",
"expertise": [
"Reviewer Expertise Bioimage analysis",
"Computer vision",
"Data 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 authors describe a semi-automated analysis for measuring single nephron glomerular filtration rate (snGFR). An important parameter for assessing renal function. Intravital microscopy was used to record the filtration of a fluorescent dye along glomerular vessels to the proximal tubule. The aim of the analysis is to measure the flow rate. To achieve this the user first sets a line ROI to determine the position and direction for the measurement of the intensity change across the time course. Then the entire 3D volume is segmented in a separate z-stack. The analysis is smart and tries to use all available information in their experimental setup to ensure a robust analysis. The generation of the 3D volume based on a 3D watershed uses the information from different channels to ensure a robust segmentation. Using a regression analysis makes sure that not only 2 points alone will contribute to the final measurement of the snGFR. I think this is a good image and data analysis approach to reduce measurement variability and increase statistical power.\nThe workflow runs as R script that also calls a Fiji macro. The interaction runs via sequential GUI prompts. This increases the ease of use.\n\nThe article is, in general, well written and contains most of the important information to understand the method and how it compares to previously used methods. The detailed description of the algorithm is sometimes a bit confusing but one can understand the rational of the authors. My main problem is with the lack of documentation that allows one to access and implement the tools. Here are my points for revision:\n\nMAJOR: The algorithm makes sense. The description in the text and figure legends is however a bit hard to understand.\nThis sentence is particularly unclear: \"The position with this intensity was approximated in each frame and used for linear regression (Figure 3C)\". I guess what the authors wanted to express is that the volume was approximated at this position. Then the approximated volume was plotted over time and based on that linear regression was performed?\nFigure 3 B&C and their legends are rather confusing:\n\nFigure 3B mixes in the volume of the segmentation, although this is not the message of the figure (Intensity and computation of threshold on slope). The color code of Figure 3B&C corresponds I guess to the positions? This is not explained anywhere. In Figure 3A first µm³ is used and then in Figure 3C nl?\nMAJOR: I downloaded the material and it took me about 4 tries to get the scripts to work correctly. Here are the key impediments:\n\nDoes not execute on ubuntu 20.04: the R script uses functions that only work under Windows. This limitation needs to be explicitly stated. This also abolishes the advantage of cross platform tools such as Fiji and R.\n\nThe 3D watershed is not explicitly stated as dependency of Fiji. It needs to be clearly stated what needs to be installed and how.\n\nThe direction of the ROI is important but this was not clear from the documentation.\n\nMAJOR: The Documentation word file provided is not helpful for actually using the scripts. It rather contains a code documentation that has some directions of using the program included. People with little expertise have no clear guidance for the usage and the important settings of the usage are entirely lost in all the detail.\n\nThe usage needs to be documented separately from the code.\n\nThe actual interaction with the program needs to be documented also via screenshots.\n\nThe important settings need to be explained clearly and in sufficient detail.\n\nMAJOR: That one needs to draw the ROI in the direction of the wave was not really obviously documented or it got lost in the complexity of the code documentation. Please use screenshots or describe with words.\n\nMAJOR: How the data needs to be acquired and structured for this workflow to function is not explained anywhere. The prompt for selecting a corresponding z-stack made initially zero sense. Since it was not clear that the .lif file must contain the multichannel time series AND the z-stack. Are the channels settings hard coded then? If the analysis is inflexible in its data input (which can be ok), it needs to be mention explicitly as an important prerequisite.\nMAJOR: Reproducing the workflow using the provided .lif file resulted mostly in snGFR that were in a similar range. But still off. Maybe drawing the ROIs seems to be still an important source of variability. It would be good if there would be an easy way to load and visualize the ROIs provided by the authors. This shows easily how the authors intend users to set ROIs. One can load them via the ROI Manager during the GUI interactions but this produces an error later on:\n\nComposite selections cannot be converted to lines. in line 520:\n\n(called from line 193) run ( \"Area to Line\" <)>\n\nMaybe it would also be good to document in words along example screenshots how one best should set the ROI.\nMAJOR: I am not in the kidney field. Maybe certain statements are common knowledge there and it is practice not to cite them. But the following statements in the introduction would strike me as requiring citations:\n\n\"Therefore, changes in GFR serve to monitor disease progression.\"\n\n\"GFR is also measured in animal models to study effects of pharmacological intervention on kidney function.\"\n\n\"Advances in intravital imaging and multiphoton microscopy allow repetitive assessment of GFR and morphological changes in the smallest functional unit of the kidney – the nephron.\"\n\n\"Longitudinal imaging of single nephrons (sn) enable direct correlation of structural and functional data.\"\n\n\"Since results we obtained with this approach were highly variable.\"\n\nMINOR: All the result files produced by the workflow and how to interpret them and recognize issues are not described anywhere in the documentation.\n\nMINOR: It would be nice, at least in the documentation, to layout graphically the flow of the workflow.\nMINOR: Please include a brief description of the usage in the README. What needs to be installed (also the 3D watershed update site) and how to run the workflow. Also any important prerequisites should be mentioned there as well.\n\nMINOR: Selecting the \"executable Fiji file\" needs to be described better and documented with a screenshot. Users that have Fiji preinstalled or rarely use Fiji will not know this.\n\nMINOR: Figure 4 is hard to interpret and one cannot easily compare own results for reproducing the workflow. The result of the automatic analysis are included as an extra file. It would be nice to have the results of this automatic and manual analysis available as a table for a direct comparison.\n\nMINOR: I miss an explicit point of contact or means of support for any users such as github, forum or Email.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "6502",
"date": "12 Apr 2021",
"name": "Friederike Kessel",
"role": "Author Response",
"response": "First of all we thank the reviewer for the extensive report and constructive feedback. We agree that a lack of documentation, guidance and also support information notably impaired the usability of the workflow. In this context, the patience of the reviewer to implement the algorithm is highly appreciated. Since most of the remarks were directly linked with lack of documentation, we uploaded detailed instructions to the GitHub repository and updated the associated release on Zenodo. This documentation now includes: A paragraph on the structure of the raw data System requirements (operating system) Software requirements (ImageJ, including update sites, R and RStudio with additional libraries) Instructions on how to run the workflow with screenshots Explicitly pointing out the importance of the direction of the line ROI With additional screenshots of example line ROIs for the images included in the sample dataset Information on all output files (ROI sets, result files, graphs) Suggestions for data interpretation and troubleshooting Contact information Since this analysis was only recently developed and experiences when applying it to different image data are still limited we are determined to continuously expand the documentation and troubleshooting suggestions. We recognize that there is also room for improvement for the programming itself, regarding the limitation to Windows and hard-coded requirements of the raw data. We plan to support the gradual expansion of the workflow to be more adaptable – and applicable – in the future (as mentioned in the documentation). Since the reviewer pointed out that some of the descriptions in the manuscript and figure legends were hard to understand, we rephrased some points. We hope it is now more understandable. Description of Figure 3C: Approximation of the volume for every position and plotting against time for linear regression Legends for Figures B and C: Colour code Conversion of units: µm³ to nl in Figure 3C We also included the table with the numerical results as shown in Figure 4. Finally, the statements on GFR and methods in intravital microscopy in the introduction can be supported with references that were already used in other contexts in the manuscript. Therefore, we additionally refer to them in the introduction."
}
]
}
] | 1
|
https://f1000research.com/articles/9-1372
|
https://f1000research.com/articles/10-184/v1
|
05 Mar 21
|
{
"type": "Research Article",
"title": "Quadriceps muscle power and optimal shortening velocity are inversely related to angiotensin converting enzyme activity in older men",
"authors": [
"Joanna Kostka",
"Joanna Sikora",
"Agnieszka Guligowska",
"Tomasz Kostka",
"Joanna Sikora",
"Agnieszka Guligowska",
"Tomasz Kostka"
],
"abstract": "Background: Methods which potentially could prevent age-related loss of muscle mass and function are still being sought. There are various attempts to use pharmacological agents to prevent loss of muscle mass, but the effectiveness of many of them still needs to be confirmed. One of the promising therapeutics are Angiotensin Converting Enzyme Inhibitors (ACEIs) and lowering of serum ACE activity. The goal of this study was to assess if taking Angiotensin Converting Enzyme Inhibitors (ACEI) and other angiotensin system blocking medications (ASBMs) can modify muscle performance in older men as well as to assess the association of serum ACE activity with muscle strength, power, muscle contraction velocity and functional performance. Methods: Seventy-nine older men took part in the study. Muscle function was assessed with hand grip strength, maximum power relative to body mass (Pmax) and optimal shortening velocity (Ʋopt) of the knee extensor muscles. Anthropometric data, ACE activity and functional performance were also measured. Results: Negative correlations between ACE activity and Pmax (rho=-0.29, p=0.04) as well as Ʋopt (rho=-0.31, p=0.03) in a group of patients not taking ACEI and between ACE activity and Ʋopt (rho=-0.22, p=0.05) in the whole group of men were found. Positive relationship between age and ACE activity was demonstrated (rho=0.26, p=0.02). Age was the only selected variable in the multiple regression analyses to determine both Pmax and Ʋopt. Conclusions: Taking ACEI is not associated with a functional performance in older men of the same age and with the same anthropometric parameters. Serum ACE activity negatively associates to muscle power and muscle contraction velocity.",
"keywords": [
"sarcopenia",
"muscle function",
"muscle strength",
"ageing",
"ACE inhibitors"
],
"content": "Introduction\n\nAge-related sarcopenia, connected with deteriorating in muscle mass and function, is one of the most important factors determining functional status1–3. That is why methods used to prevent age-related loss of muscle mass and function are still being sought. Physical activity especially with proper nutritional intervention may be potentially an effective management for sarcopenia4, but it is difficult to convince seniors to follow these recommendations. There are various attempts to use pharmacological agents to prevent loss of muscle mass, but the effectiveness of many of them still needs to be confirmed5. Taking Angiotensin Converting Enzyme Inhibitors (ACEI) is also being considered. ACEI are traditionally used among others as anti-hypertensive medications and in cardiovascular diseases or diabetic nephropathy treatment6, but there are also some hypotheses that using ACEI may modify muscle aging. For example, Onder et al.7 in a three-year observational study in a group of older women with hypertension and without congestive heart failure have shown that ACEI treatment may slow age-related decline in muscle strength.\n\nTaking ACEI as well as the ACE genotype with insertion (II) of allele in gene, is associated with lower serum ACE activity8,9 and with predispositions for practicing some sports10. ACE is a basic component of renin-angiotensin system (RAS), which converts angiotensin I (ang I) in angiotensin II (ang II). Ang II may in turn influence muscle performance11. Williams et al.12 reported that circulating ACE activity was correlated with isometric and isokinetic strength of quadriceps muscle strength in untrained man.\n\nEven more important than muscle strength factor affecting functional performance in elderly population are muscle power and muscle contraction velocity1,2. These factors are also more influenced by aging than muscle strength13. In addition to our recent research14, there are no reports on the effect of ACEI taking and serum ACE activity on muscle power and muscle contraction velocity in older population. In that study we have found association between serum ACE activity with optimal shortening velocity of quadriceps muscles in older women, but not with muscle strength and power. Because various sex-related factors can modify age-related muscle changes15, earlier reported sex-related differences in ACE activity16, as well as possible differences in absorption of medications (absorption in women may be slower due to reduced gastric acid secretion and gastrointestinal motility)17 we conducted similar study in the group of older men.\n\nThe goal of our study was to assess if taking ACEI can modify muscle performance in older man as well as to assess the association of serum ACE activity with muscle strength, power, muscle contraction velocity and functional performance\n\n\nMethods\n\nSeventy-nine community-dwelling older men took part in the study. Participants were recruited through the local media by the Medical University of Lodz, Department of Geriatrics. The study included men aged ≥ 60 years, with the inclusion criteria of those with the ability to understand and execute commands, the ability to perform exercise testing, and those who signed the informed consent to participate in the study. Exclusion criteria were as follows: recent (<three months) diagnosis of myocardial infarction, stroke or orthopaedic surgery, cardiac contraindications to exercise tests, or lack of ability to perform tests because of motor system dysfunctions (limited range of motion, pain).\n\nThe study was approved by the Bioethics Committee of the Medical University of Lodz No RNN/647/14/KB.\n\nParticipants were asked to report to the Research Center in the morning (8–9 a.m.) on an empty stomach (at least 12 hours fasting), after a night’s sleep. They were also asked for avoid smoking, drinking alcohol and taking heavy physical exertion for at least 12 hours. After fasting blood drawing and a light breakfast, a comprehensive assessment was carried out with each participant. The assessment included: interview (information on socio-economic status, current and previous illnesses, and current medication), anthropometric measurements, evaluation of muscle function (muscle strength, power and shortening velocity), as well as functional status assessment.\n\nMeasurements of height, weight, and skinfold thickness (from: triceps, biceps, sub-scapula, and supra-ileum) were performed using standard methods. Body mass index – BMI (kg∙m-2) was calculated and the percentage of body fat was estimated according to Durnin & Womersley18.\n\nThe Jamar® hydraulic hand dynamometer (Sammons Preston Rolyan, Bolingbrook, Canada) was used for handgrip strength evaluation. The test was preceded by a demonstration of the researcher and performed twice (on both sides), with 30 second pauses between measurements. During the test, the participant was in a standing position, with shoulder in neutral position and elbow in flexion (90°) with no radioulnar deviation, and was encouraged to squeeze the device as hard as possible. Results were given in kilograms (kg). A better record was used for analysis19.\n\nMuscle power and optimal shortening velocity evaluations were performed with especially prepared ergometer (Monark type 818E Stockholm, Sweden). The methodology used in this measurement has been previously described in detail20. Pmax was presented in relation to body mass (W·kg-1). Ʋopt was given in number of rotations per minute (rot·min-1).\n\nActivities of Daily Living (ADL)21, the Lawton Instrumental Activities of Daily Living (IADL)22, and Timed Up & Go test (TUG)23 were used to assess functional status of the participants.\n\nADL and IADL are scales based on questions concerning ability to perform basic and complex (instrumental) daily activities. ADL scale consists of six questions about activities such as eating, dressing, bathing, continence, toileting, and transferring. IADL contains questions about more complex activities enabling independent functioning, such as ability to use telephones, shopping, food preparation, cleaning, washing, use of public transport, responsibility for own medications, and ability to handle finances.\n\nTimed Up & Go test is a simple and very popular functional test. It involves standing up from a sitting position, walking forth and back three meters, and sitting back on time. Time is given in seconds. After a familiarization test, this was performed twice and the better result was chosen for further analysis.\n\nFasting blood samples were collected from every man at the Research Center in the morning hours into vacuum tubes. The blood was centrifuged and then stored at -20 °C until measurement. The reagents used and the method of analysis were described in our previous work14. Results were given in U/L.\n\nThe descriptive statistics are presented as mean ± standard deviation for data with a normal distribution, and for data without a normal distribution they were additionally shown as median (lower quartile - upper quartile). After the normality check, the one-way analysis of variance (ANOVA) or Mann-Whitney test (for quantitative data) and Chi2 with Yates’ correction test (for qualitative data - prevalence of diseases) were used for group comparison. Spearman’s correlation coefficients were calculated to assess the relationships between numerical variables. To establish the most important determinants of Pmax and Ʋopt, the multiple regression analyses were made. For these analyses, ACE activity results were transformed logarithmically due to the non-normal distribution. Significance was set at a p value of p<0.05.\n\n\nResults\n\nBaseline characteristics of the men taking and not taking ACEI as well as taking and not taking angiotensin system blocking medications (ASBMs) are shown in Table 1. Participants taking ACEI did not differ in terms of age, anthropometric indicators, education level, grip strength, muscle power, contraction velocity, and ADL results. Patients taking ACEI took more medications and were characterized by lower level of ACE in blood samples and lower IADL status. Men from both groups did not differ with regard to the prevalence of most diseases (ischemic heart disease, stroke, cancer, osteoporosis, COPD, heart failure, diabetes, myocardial infarction), but men talking ACEI more often suffered from hypertension (p=0.0003).\n\nNote: The results for data with a normal distribution are presented as mean ±SD. The results for data without a normal distribution are presented as mean ± SD and additionally as median and quartiles\n\n*p<0.05; †p<0.01; #p<0.001 – ACEI compared to non ACEI and ASBMs compared to non ASBMs\n\nAbbreviations: Pmax, maximum power; Ʋopt, optimal shortening velocity of the knee extensor muscles; ACE, angiotensin-converting enzyme; ACEI, Angiotensin Converting Enzyme Inhibitors; ASBMs, angiotensin system blocking medications; ADL, Activities of Daily Living; IADL, Instrumental Activities of Daily Living; TUG, Timed Up and Go test; ACEI - men taking ACEI; non ACEI – men not taking ACEI; ASBMs - men taking ASBMs; non ASBMs - men not taking ASBMs\n\nWhereas participants taking ASBMs were more than two years older than subjects not taking ASBMs, they took more medications, had greater BMI, and did not differ in terms of majority of muscles function parameters (Pmax, Ʋopt, right handgrip strength), except for the left handgrip strength.\n\nWe have found a positive relationship between age and ACE activity in men not taking ACEI and in all studied patients. We have also found a negative correlation between ACE activity and Pmax (Figure 1) as well as with Ʋopt (Figure 2) in group of patients not taking ACEI and in the whole group of men (Table 2). Similar relationships were observed in group of men not taking any ASBMs – both Pmax (borderline significance) and Ʋopt were negatively correlated with serum ACE activity (Table 2).\n\nAbbreviations: Pmax, maximum power; Ʋopt, optimal shortening velocity of the knee extensor muscles; ACE, angiotensin-converting enzyme; ACEI, Angiotensin Converting Enzyme Inhibitors; ASBMs, angiotensin system blocking medications; TUG, Timed Up and Go test; ACEI - men taking ACEI; non ACEI – men not taking ACEI; ASBMs - men taking ASBMs; non ASBMs - men not taking ASBMs\n\nHowever, when ACE activity and age were entered into the multiple regression analyses, age was the only selected variable to determine both Pmax and Ʋopt.\n\n\nDiscussion\n\nIn this study we have shown that muscle power and muscle contraction velocity were negatively correlated with ACE activity in patients not taking ACEI and in patients not taking any ASBMs. However, taking ACEI was not consistently associated with handgrip strength, muscle power, muscle contraction velocity, and functional performance in older men of the same age and with comparable anthropometric parameters.\n\nIn 2002, Onder et al.7 published an article suggesting that treatment with ACEI may be associated with slower decline in muscle strength and function in older women with hypertension. During the three-year observation the reduction in the muscle strength of the knee extensors and in walking speed was significantly lower in women who continuously used ACEI than in those who used other or did not used any hypertensives. Buford et al. also reported greater exercise-derived improvements in physical function for older ACEI users24. In EELO Project, taking medicines modulating the effect of angiotensin II (both ACEI and angiotensin receptors blockers) was connected with better functional capacity and muscle strength in people over 60 year of age25. In the present study, despite the fact that patients receiving any ASBMs were more than two years older than those who did not take ASBMs, they did not differ in terms of muscle power and Ʋopt. This is consistent with our last study in older women14. Women taking ACEI were almost two years older, had lower health status than women not taking ACEI, but these two groups did not differ in terms of handgrip strength, Pmax, Ʋopt and functional performance. These results may suggest effect of RAS system on muscle performance.\n\nHowever, there are some studies which do not confirm clearly the protective effect of ACEI on muscle and functional performance and on improvement of the response to exercises training. Sumukadas et al.26 did not find effects of ACEI therapy on functional status as well as on improvement in handgrip and quadriceps muscle strength in older people undergoing 20-week progressive exercise training in comparison with placebo. In nine-month follow-ups taking ACEI was connected with decreasing of ACE activity but there was no association between the changes in ACE activity and changes in muscle strength or functional capacity in older community dwelling subjects27. Similarly, in the TRAIN study, the authors did not observe significant modifications in physical performance and handgrip strength after six-months of fosinopril use in older persons with high cardiovascular risk profile28. In 4.4 years, a follow-up study29 taking any from cardiovascular drugs (ACEI, statins or thiazides) was not associated with differences in handgrip strength decline in healthy older people.\n\nTherefore, the results regarding the relationship between ACEI and maintaining/improving muscle mass and strength in older age are still inconsistent. Many additional factors can potentially influence this relationship, like concomitant diseases, the type and dosage of the drugs, genetic predisposition, lifestyle, etc. The key point may be the observation time. The longest period of observations mentioned above was 4.4 years29, but some of them were shorter - even six months28. Decreasing muscle mass and function is not a rapid process. It has been reported that the strength loss in older men is 2–3.4% per year and is modulated by some other factors30. Moreover, in one observation 15% of subjects older than 60 did not at all decline handgrip strength during the average nine-year follow-up31. Therefore, taking ACEI may be too weak a factor to notice its impact on maintaining muscle mass and function in a relatively short period of time and a longer follow-up is needed to confirm the importance of ACEI in this area.\n\nThis seems also likely in the context of our research. The main effect of ACEI use is the decrease of ACE activity8. Our results show that men with higher serum ACE activity are characterized by lower Pmax as well as lower Ʋopt. These correlations apply only to groups of patients not taking ACEI, not taking any ASBMs and all studied men, but not men taking ACEI or ASBMs. In men taking ACEI or other ASBMs in whom pharmacotherapy modulated ACE activity, this relationship is not clear. We also did not observe a similar relationship in relation to the handgrip strength. Interestingly, even if the relationships between ACE activity and muscle function (strength, power, contraction velocity) did not reach statistical significance, the direction of the association has always been the same - lower ACE activity was associated with better muscle function. This observation applies to all indicators of muscle function and to all analyzed patients’ subgroups in both our latest14 and current study. Statistically significant dependence in our last work in older women was demonstrated only for ACE activity and Ʋopt14. In the current study, in addition to Ʋopt also Pmax is negatively correlated with ACE activity, but handgrip strength is not. Ʋopt may be a more sensitive indicator of muscle function than strength and Pmax (force and velocity indicator), decreases with age faster than strength13. Our male group is older than previous group of women. Therefore, higher ACE activity had a chance to have a longer impact on the muscles. In both male groups (taking and not taking ACEI) higher ACE activity was also seen as compared to women.\n\nThis data seems also consistent with studies based on genetic tests. Serum ACE concentration is genetically determined (an insertion/deletion – I/D polymorphism in the ACE gene)9, so depending on the genetic predisposition, reduced or increased ACE activity has been acting on the studied men for their entire life. ACE genotype and activity may be not related to muscle function tests in young subjects32. In contrast, among older people deletion polymorphism of ACE gene (DD), connected with higher level of angiotensin II, was associated with low muscle mass33. Similarly, advanced cancer patients with DD ACE gene polymorphism were characterized by higher serum ACE activity but lower hand grip strength compared with ACE insertion group34,35.\n\nThere are mechanisms potentially affecting muscle function that are associated with an increased ACE activity, and thus with the hyper-activity of the RAS system. This hyper-activity may be associated with tissue insulin resistance, muscle atrophy, and fibrosis. RAS may also stimulate mitochondrial dysfunction, oxidative stress, and promote inflammatory processes36. ACE inhibition may also have a neuroprotective effect37,38 what is crucial because neural mechanisms are important factors in the development of sarcopenia39.\n\nSince ACE activity in our study was positively correlated with age, we decided to conduct multiple regression analyses for determinants of both Pmax and Ʋopt including ACE activity and age as independent variables. In these analyses age was the only selected variable determining Pmax and Ʋopt. The positive relationship between ACE activity and age was surprising, but there were no studies in such advanced age so far. In a few works on this subject, serum ACE activity increased with age in children up to 18 years old40 but did not vary with age in adults41,42 or even decreased in rats43 and in adult men44.\n\n\nConclusions\n\nSerum ACE activity negatively determines muscle power and muscle contraction velocity but not muscle strength in older men. Taking ACEI is not associated with functional performance in older men. This problem requires further studies with long-term follow-up, and determining the type and dose of the treatment.\n\n\nData availability\n\nZenodo: Quadriceps muscle power and optimal shortening velocity are inversely related to angiotensin converting enzyme activity in older men, http://doi.org/10.5281/zenodo.449309545.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "References\n\nClémençon M, Hautier CA, Rahmani A, et al.: Potential role of optimal velocity as a qualitative factor of physical functional performance in women aged 72 to 96 years. Arch Phys Med Rehabil. 2008; 89(8): 1594–1599. PubMed Abstract | Publisher Full Text\n\nKostka JS, Czernicki JW, Kostka TJ: Association of muscle strength, power, and optimal shortening velocity with functional abilities of women with chronic osteoarthritis participating in a multi-modal exercise program. J Aging Phys Act. 2014; 22(4): 564–570. PubMed Abstract | Publisher Full Text\n\nBahat G, Tufan A, Kilic C, et al.: Prevalence of sarcopenia and its components in community-dwelling outpatient older adults and their relation with functionality. Aging Male. 2018; 5: 1–7. PubMed Abstract | Publisher Full Text\n\nSgrò P, Sansone M, Sansone A, et al.: Physical exercise, nutrition and hormones: three pillars to fight sarcopenia. Aging Male. 2019; 22(2): 75–88. 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PubMed Abstract | Publisher Full Text\n\nKrasowski MD, Savage J, Ehlers A, et al.: Ordering of the Serum Angiotensin-Converting Enzyme Test in Patients Receiving Angiotensin-Converting Enzyme Inhibitor Therapy: An Avoidable but Common Error. Chest. 2015; 148(6): 1447–1453. PubMed Abstract | Publisher Full Text\n\nNakai K, Itoh C, Miura Y, et al.: Deletion polymorphism of the angiotensin I-converting enzyme gene is associated with serum ACE concentration and increased risk for CAD in the Japanese. Circulation. 1994; 90(5): 2199–2202. PubMed Abstract | Publisher Full Text\n\nNazarov IB, Woods DR, Montgomery HE, et al.: The angiotensin converting enzyme I/D polymorphism in Russian athletes. Eur J Hum Genet. 2001; 9(10): 797–801. PubMed Abstract | Publisher Full Text\n\nYoshida T, Tabony AM, Galvez S, et al.: Molecular mechanisms and signaling pathways of angiotensin II-induced muscle wasting: potential therapeutic targets for cardiac cachexia. Int J Biochem Cell Biol. 2013; 45(10): 2322–2332. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWilliams AG, Day SH, Folland JP, et al.: Circulating angiotensin converting enzyme activity is correlated with muscle strength. Med Sci Sports Exerc. 2005; 37(6): 944–948. PubMed Abstract\n\nMetter EJ, Conwit R, Tobin J, et al.: Age-associated loss of power and strength in the upper extremities in women and men. J Gerontol A Biol Sci Med Sci. 1997; 52(5): B267–276. PubMed Abstract | Publisher Full Text\n\nKostka J, Sikora J, Kostka T: Relationship of quadriceps muscle power and optimal shortening velocity with angiotensin-converting enzyme activity in older women. Clin Interv Aging. 2017; 12: 1753–1760. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPhillips SK, Rook KM, Siddle NC, et al.: Muscle weakness in women occurs at an earlier age than in men, but strength is preserved by hormone replacement therapy. Clin Sci (Lond). 1993; 84(1): 95–98. 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PubMed Abstract | Publisher Full Text\n\nKozicka I, Kostka T: Handgrip strength, quadriceps muscle power, and optimal shortening velocity roles in maintaining functional abilities in older adults living in a long-term care home: a 1-year follow-up study. Clin Interv Aging. 2016; 11(11): 739–747. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKatz S, Ford AB, Moskowitz RW, et al.: Studies of illness in the aged. the index of ADL: a standardized measure of biological and psychosocial function. JAMA. 1963; 185: 914–919. PubMed Abstract | Publisher Full Text\n\nLawton MP, Brody EM: Assessment of older people: self-maintaining and instrumental activities of daily living. Gerontologist. 1969; 9(3): 179–186. PubMed Abstract | Publisher Full Text\n\nPodsiadlo D, Richardson S: The timed “up & go”: a test of basic functional mobility for frail elderly persons. J Am Geriatr Soc. 1991; 39(2): 142–148. PubMed Abstract | Publisher Full Text\n\nBuford TW, Manini TM, Hsu FC, et al.: Angiotensin-converting enzyme inhibitor use by older adults is associated with greater functional responses to exercise. J Am Geriatr Soc. 2012; 60(7): 1244–1252. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCoelho VA, Probst VS, Nogari BM, et al.: Angiotensin-II blockage, muscle strength, and exercise capacity in physically independent older adults. J Phys Ther Sci. 2016; 28(2): 547–552. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSumukadas D, Band M, Miller S, et al.: Do ACE inhibitors improve the response to exercise training in functionally impaired older adults? A randomized controlled trial. J Gerontol A Biol Sci Med Sci. 2014; 69(6): 736–743. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBunout D, Barrera G, de la Maza MP, et al.: Effects of enalapril or nifedipine on muscle strength or functional capacity in elderly subjects. A double blind trial. J Renin Angiotensin Aldosterone Syst. 2009; 10(2): 77–84. PubMed Abstract | Publisher Full Text\n\nCesari M, Pedone C, Incalzi RA, et al.: ACE-inhibition and physical function: results from the Trial of Angiotensin-Converting Enzyme Inhibition and Novel Cardiovascular Risk Factors (TRAIN) study. J Am Med Dir Assoc. 2010; 11(1): 26–32. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWitham MD, Syddall HE, Dennison E, et al.: ACE inhibitors, statins and thiazides: no association with change in grip strength among community dwelling older men and women from the Hertfordshire Cohort Study. Age Ageing. 2014; 43(5): 661–666. PubMed Abstract | Publisher Full Text\n\nForrest KYZ, Zmuda JM, Cauley JA: Patterns and determinants of muscle strength change with aging in older men. Aging Male. 2005; 8(3–4): 151–156. PubMed Abstract | Publisher Full Text\n\nKallman DA, Plato CC, Tobin JD: The role of muscle loss in the age-related decline of grip strength: cross-sectional and longitudinal perspectives. J Gerontol. 1990; 45(3): M82–88. PubMed Abstract | Publisher Full Text\n\nMcCauley T, Mastana SS, Hossack J, et al.: Human angiotensin-converting enzyme I/D and alpha-actinin 3 R577X genotypes and muscle functional and contractile properties. Exp Physiol. 2009; 94(1): 81–89. PubMed Abstract | Publisher Full Text\n\nHandayani MDN, Sadewa AH, Farmawati A, et al.: Deletion Polymorphism of Angiotensin-Converting Enzyme Gene Is Associated with Low Muscle Mass in Elderly People in Jakarta, Indonesia. Kobe J Med Sci. 2018; 64(3): E119–E125. PubMed Abstract | Free Full Text\n\nVigano A, Trutschnigg B, Kilgour RD, et al.: Relationship between angiotensin-converting enzyme gene polymorphism and body composition, functional performance, and blood biomarkers in advanced cancer patients. Clin Cancer Res. 2009; 15(7): 2442–2447. PubMed Abstract | Publisher Full Text\n\nKang HJ, Kim CH, Park DS, et al.: The Impacts of ACE Activity according to ACE I/D Polymorphisms on Muscular Functions of People Aged 65. Ann Rehabil Med. 2012; 36(4): 433–446. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCabello-Verrugio C, Morales MG, Rivera JC, et al.: Renin-angiotensin system: an old player with novel functions in skeletal muscle. Med Res Rev. 2015; 35(3): 437–463. PubMed Abstract | Publisher Full Text\n\nHanif K, Bid HK, Konwar R: Reinventing the ACE inhibitors: some old and new implications of ACE inhibition. Hypertens Res. 2010; 33(1): 11–21. PubMed Abstract | Publisher Full Text\n\nMansoor Q, Javaid A, Bilal N, et al.: Angiotensin-converting enzyme (ACE) gene II genotype protects against the development of diabetic peripheral neuropathy in type 2 diabetes mellitus. J Diabetes. 2012; 4(3): 257–261. PubMed Abstract | Publisher Full Text\n\nKwon YN, Yoon SS: Sarcopenia: Neurological Point of View. J Bone Metab. 2017; 24(2): 83–89. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBénéteau-Burnat B, Baudin B, Morgant G, et al.: Serum angiotensin-converting enzyme in healthy and sarcoidotic children: comparison with the reference interval for adults. Clin Chem. 1990; 36(2): 344–346. PubMed Abstract | Publisher Full Text\n\nFaure-Delanef L, Baudin B, Bénéteau-Burnat B, et al.: Plasma concentration, kinetic constants, and gene polymorphism of angiotensin I-converting enzyme in centenarians. Clin Chem. 1998; 44(10): 2083–2087. PubMed Abstract | Publisher Full Text\n\nZdrojewicz Z: [Does the activity of angiotensin converting enzyme depend on sex, age, body weight and phase of the menstruation cycle in women?] Pol Tyg Lek. 1992; 47(44–45): 1016–1017. PubMed Abstract\n\nChallah M, Nadaud S, Philippe M, et al.: Circulating and cellular markers of endothelial dysfunction with aging in rats. Am J Physiol. 1997; 273(4): H1941–1948. PubMed Abstract | Publisher Full Text\n\nFernández-Atucha A, Izagirre A, Fraile-Bermúdez AB, et al.: Sex differences in the aging pattern of renin-angiotensin system serum peptidases. Biol Sex Differ. 2017; 8: 5. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKostka J, Sikora J, Guligowska A, et al.: Quadriceps muscle power and optimal shortening velocity are inversely related to angiotensin converting enzyme activity in older men [Data set]. Zenodo. 2021. http://www.doi.org/10.5281/zenodo.4493095"
}
|
[
{
"id": "81534",
"date": "29 Mar 2021",
"name": "Ida Wiszomirska",
"expertise": [
"Reviewer Expertise Physiotherapy",
"Physical Rehabilitation",
"Muscle Function"
],
"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\nReview of the article “Quadriceps muscle power and optimal shortening velocity are inversely related to angiotensin-converting enzyme activity in older men.”\nThe topic undertaken in this article is important. Aging is associated with a gradual loss of muscle function and, consequently, deterioration of functional efficiency. Identification of factors that could slow down this process may contribute to the improvement of the functioning of the elderly.\nIntroduction The introductory part contains a factual and correct justification of the topic undertaken in the study, taking into account correctly selected items of the literature. The objectives of the work formulated correctly.\nOne sentence requires an explanation:\n\"Taking ACEI as well as the ACE genotype with insertion (II) of allele in gene, is associated with lower serum ACE activity and with predispositions for practicing some sports.\" – there is no evidence, that taking ACEI is associated with predispositions for practicing some sports (in fact, there are some reports about the ACE genotype) - this sentence suggests such a relationship. Please formulate this sentence in a different way.\nMethodology Methodology is generally well described, but it is worth supplementing some information:\nPlease add \"for each hand separately\" to the sentence \"A better record was used for analysis\" (last sentence of the section \"Muscle strength\").\n\nDespite the reference to the literature, in this part it is worth describing the measurement of Pmax and Ʋopt in a little more detail.\nResults are shown as a text, in tables and in 2 figures. This section is presented clearly.\nIn the discussion, the results of own research were compared to the current literature. In this section, it is worth discussing the limitations of the study. Correctly formulated conclusions.\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": "6730",
"date": "09 Jun 2021",
"name": "Joanna Kostka",
"role": "Author Response",
"response": "Dear Reviewer, We would like to thank you for the analysis of this manuscript and your valuable remarks. The manuscript has been corrected according to the comments. All changes are described below. 1. One sentence requires an explanation: \"Taking ACEI as well as the ACE genotype with insertion (II) of allele in gene, is associated with lower serum ACE activity and with predispositions for practicing some sports.\" – there is no evidence, that taking ACEI is associated with predispositions for practicing some sports (in fact, there are some reports about the ACE genotype) - this sentence suggests such a relationship. Please formulate this sentence in a different way. Answer: This sentence was modified to: “Taking ACEI as well as the ACE genotype with insertion (II) of allele in gene, is associated with lower serum ACE activity8,9. There are suggestions that the ACE genotype type predisposes one to be successful in certain sports10.” 2. Methodology Please add \"for each hand separately\" to the sentence \"A better record was used for analysis\" (last sentence of the section \"Muscle strength\"). Answer: We have added this sentence in line with the Reviewer's comment. 3. Despite the reference to the literature, in this part it is worth describing the measurement of Pmax and Ʋopt in a little more detail. Answer: The description of the Pmax and Ʋopt measurement methodology has been supplemented: “Muscle power and optimal shortening velocity evaluations were performed with especially prepared ergometer (Monark type 818E Stockholm, Sweden), during two 8-second attempts to pedal at the maximum possible speed with friction loads of 0.25 N·kg−1 and 0.35 N·kg−1 of body mass. Instantaneous pedaling velocity (Ʋ), force (F) and power output (P) were calculated each 5ms and then averaged over each downstroke period. The highest value of P (maximal short-term power – Pmax) and optimal shortening velocity (Ʋopt - velocity at which the power reaches a maximum value) were calculated from a 3rd order polynomial function. The methodology …” 4. Discussion In this section, it is worth discussing the limitations of the study. Answer: A \"limitation of the study\" section was added to the discussion. Best regards Joanna Kostka"
}
]
},
{
"id": "81773",
"date": "17 May 2021",
"name": "Christophe A. Hautier",
"expertise": [
"Reviewer Expertise Sport Sciences",
"physiology",
"biomechanics"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 focused about the effects of angiotensin Converting Enzyme Inhibitors (ACEI) and other angiotensin system blocking medications (ASBMs) on the strength and speed capacities of the skeletal muscle in the elderly. The subject is remarkably interesting in the prevention of dependence in the elderly because the means of combating sarcopenia and dynapenia are still poorly understood. Of course, exercise and diet have a significant effect on the muscle mass and strength and functionality of the elderly, on the other hand it seems interesting to continue to look for medicinal methods that can help maintain autonomy.\nSeventy-nine elderly men took part in the study, which is still an interesting sample and suggests that the results can be extrapolated to a larger population. Positive relationship between age and ACE activity was demonstrated and, relatively weak negative correlations were observed between ACE activity and Maximum Power or optimal speed. However, taking Angiotensin Converting Enzyme Inhibitors (ACEI) did not modify muscle performance in this population.\nThis article is well written however, the rationale of taking converting Enzyme Inhibitors (ACEI) to maintain muscle mass and strength should be reinforced with some mechanistic hypotheses. Even if the authors previously published an article about the relationship of quadriceps muscle power and optimal shortening velocity with angiotensin-converting enzyme activity in older women, there is only indirect evidence generally associating the functional status of the senior and ACE activity.\nThe method of constituting the groups of subjects (ACEI vs non ACEI and ASBMs vs non ASBMs) is not presented and moreover the different categories appear only in the results and not in the method. This seems to be an important limitation of this work, for interpreting differences in strength and/or BMI. I think it can be improved a lot by better explaining the constitution of groups in the method part. The fact that patients taking ACEI took more medications and were characterized by lower level of ACE in blood samples and lower IADL status is a major concern that should be better discussed in the limitations of the study. Nevertheless, the correlations are interesting and provide additional evidence about the significance of ACE in ageing.\nI think it is necessary to do a paragraph on the limitations of the study and better discuss the fact that these results are a bit like preliminary results that require further study given the potential role of ACE in aging. I would have liked the authors to touch very lightly on the mechanistic assumptions that might explain the effects of ACE on optimal speed and maximum power. These hypotheses are they neuromuscular, systemic, cardiovascular or else indirect because of the improvement in the quality of life and spontaneous activity. I do not think the authors can conclude on the ineffectiveness of taking ACEI in maintaining functional performance in older men.\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? Yes\n\nAre the conclusions drawn adequately supported by the results? No",
"responses": [
{
"c_id": "6731",
"date": "09 Jun 2021",
"name": "Joanna Kostka",
"role": "Author Response",
"response": "Dear Reviewer, We would like to thank you for the analysis of this manuscript and your valuable remarks. The manuscript has been corrected according to the comments. All changes are described below: 1: \"This article is well written however, the rationale of taking converting Enzyme Inhibitors (ACEI) to maintain muscle mass and strength should be reinforced with some mechanistic hypotheses. Even if the authors previously published an article about the relationship of quadriceps muscle power and optimal shortening velocity with angiotensin-converting enzyme activity in older women, there is only indirect evidence generally associating the functional status of the senior and ACE activity.\" Answer: We supplemented the Introduction section with suggested information: The authors of the article explain this effect with several mechanisms, such as: direct influence on mechanical and metabolic changes in muscles (shift of the myosin heavy chains of skeletal muscle toward the fatigue-resistant forms; increasing insulin sensitivity, glycogen storage and glucose uptake in skeletal muscle; reduction of kinin breakdown and, consequently, improved circulation and better glucose and amino acid uptake), suppression of inflammatory activation connected with muscle catabolism, beneficial effect on the nutritional status (inhibition of interleukin-6, which, among others, reduces appetite and, consequently, may cause malnutrition). 2: \"The method of constituting the groups of subjects (ACEI vs non ACEI and ASBMs vs non ASBMs) is not presented and moreover the different categories appear only in the results and not in the method. This seems to be an important limitation of this work, for interpreting differences in strength and/or BMI. I think it can be improved a lot by better explaining the constitution of groups in the method part.\" Answer: Suggested information has been added to the “Methods” section: Based on the analysis of medications taken, men were assigned to the following groups: ACEI - if they were taking any medications belonging to the ACEI group (n = 26) and to the non ACEI group - if they were not taking ACEI (n = 53). Similarly, if men were taking any drugs from the angiotensin system blocking medications (ASBMs) group, they were assigned to the ASBMs group (n = 34), if not, then to the non ASBMs group (n = 45). 3. \"The fact that patients taking ACEI took more medications and were characterized by lower level of ACE in blood samples and lower IADL status is a major concern that should be better discussed in the limitations of the study.\" Answer: This problem is discussed in the section “Limitation of the study” as suggested. 4. \"I think it is necessary to do a paragraph on the limitations of the study and better discuss the fact that these results are a bit like preliminary results that require further study given the potential role of ACE in aging.\" Answer: A \"Limitation of the study\" section was added to the discussion. Limitation of the study This study has some limitations. First, the ACEI intake period was not analyzed. We only recorded taking or not taking ACEI and other medications. Therefore, it is worth conducting research taking into account the time of taking medications, because the duration of the effect of drugs on the muscles may be important in this case. When interpreting the data, it should be taken into account that men taking ACEI took more medications and performed worse in the assessment of functional status in the IADL scale. This may indicate the poorer health status of these men and affect the interpretation of the results related to muscle function (muscle function may be determined by health status not only by ACE level). On the other hand, the relationship between serum ACE levels and muscle function occurred only in the non-ACEI group, i.e. in the group in which the drugs did not modify ACE levels. Finally, due to the size of the group and the limitations mentioned above, this work should be regarded as preliminary results that require further research, given the potential role of ACEs in aging. 5. \"I would have liked the authors to touch very lightly on the mechanistic assumptions that might explain the effects of ACE on optimal speed and maximum power. These hypotheses are they neuromuscular, systemic, cardiovascular or else indirect because of the improvement in the quality of life and spontaneous activity.\" Answer: We slightly modified and expanded part of the discussion on this topic: There are several mechanisms that can explain the effects of ACE activity on Ʋopt and Pmax potentially affecting muscle function that are associated with an increased ACE activity, and thus with the hyper-activity of the RAS system. ACE is responsible for the conversion of angiotensin I (ang-I) to angiotensin II (ang-II). Ang-II has vasoconstrictor effect, may decrease muscle blood flow and impair the delivery of insulin and glucose to skeletal muscle. The hyper-activity of RAS system may be therefore associated with tissue insulin resistance36, muscle atrophy, and fibrosis. RAS In addition it may also stimulate mitochondrial dysfunction, oxidative stress, and promote inflammatory processes 36 what may be connected with muscle atrophy. Ang-II also induces protein degradation through reactive oxygen species accumulation36. Thus, lower ACE activity may limit muscle atrophy and the associated decline in muscle function (strength, power, contraction velocity). Lower ACE activity may also have a neuroprotective effect 37, 38 what is crucial because neural mechanisms are important factors in the development of sarcopenia 39 . Conditions such as heart failure, renal failure, chronic obstructive pulmonary disease, and cancer are associated with increased activation of the RAS pathway. These conditions can contribute to muscle atrophy, and thus also the decline in muscle function36. 6. \"I do not think the authors can conclude on the ineffectiveness of taking ACEI in maintaining functional performance in older men.\" Answer: We modified the conclusions (also in the abstract): The issues related to the impact of taking ACEI on the maintenance of muscle function and functional performance in older man require further studies with long-term follow-up, and determining the type and dose of the treatment. Best regards Joanna Kostka"
}
]
}
] | 1
|
https://f1000research.com/articles/10-184
|
https://f1000research.com/articles/10-182/v1
|
05 Mar 21
|
{
"type": "Research Article",
"title": "Pan-cancer chromatin analysis of the human vtRNA genes uncovers their association with cancer biology",
"authors": [
"Rafael Sebastián Fort",
"María Ana Duhagon",
"Rafael Sebastián Fort"
],
"abstract": "Background: The vault RNAs (vtRNAs) are a class of 84-141-nt eukaryotic non-coding RNAs transcribed by RNA polymerase III, associated to the ribonucleoprotein complex known as vault particle. Of the four human vtRNA genes, vtRNA1-1, vtRNA1-2 and vtRNA1-3, clustered at locus 1, are integral components of the vault particle, while vtRNA2-1 is a more divergent homologue located in a second locus. Gene expression studies of vtRNAs in large cohorts have been hindered by their unsuccessful sequencing using conventional transcriptomic approaches. Methods: VtRNA expression in The Cancer Genome Atlas (TCGA) Pan-Cancer cohort was estimated using the genome-wide DNA methylation and chromatin accessibility data (ATAC-seq) of their genes as surrogate variables. The association between vtRNA expression and patient clinical outcome, immune subtypes and transcriptionally co-regulated gene programs was analyzed in the dataset. Results: VtRNA1-1 has the most accessible chromatin, followed by vtRNA1-2, vtRNA2-1 and vtRNA1-3. Although the vtRNAs are co-regulated by transcription factors related to viral infection, vtRNA2-1 is the most independently regulated homologue. VtRNA1-1 and vtRNA1-3 chromatin status does not significantly change in cancer tissues. Meanwhile, vtRNA2-1 and vtRNA1-2 expression is widely deregulated in neoplastic tissues and its alteration is compatible with a broad oncogenic role for vtRNA1-2, and both tumor suppressor and oncogenic functions for vtRNA2-1. Yet, vtRNA1-1, vtRNA1-2 and vtRNA2-1 promoter DNA methylation predicts a shorter patient overall survival cancer-wide. In addition, gene ontology analyses of vtRNAs co-regulated genes identify a chromosome regulatory domain, epithelial differentiation, immune and thyroid cancer gene sets for specific vtRNAs. Furthermore, vtRNA expression patterns are associated with cancer immune subtypes and vtRNA1-2 expression is positively associated with cell proliferation and wound healing. Conclusions: Our study presents the landscape of vtRNA expression cancer-wide, identifying co-regulated gene networks and ontological pathways associated with the different vtRNA genes that may account for their diverse roles in cancer.",
"keywords": [
"vault RNA",
"vtRNA1-1",
"vtRNA1-2",
"vtRNA1-3",
"vtRNA2-1",
"nc886",
"mir-886",
"cancer",
"TCGA",
"DNA methylation",
"chromatin accessibility"
],
"content": "Abbreviations\n\nvtRNA vault RNA\n\nTCGA The Cancer Genome Atlas\n\nATAC-seq Assay for Transposase Accessible Chromatin with high-throughput sequencing\n\nNoMe-seq Nucleosome Occupancy and Methylome sequencing\n\nOG Oncogene\n\nTSG Tumor Suppressor Gene\n\nTCGA The Cancer Genome Atlas\n\nTSS Transcription Start Site\n\nAve Average\n\nSD Standard Deviation\n\nACC Adrenocortical carcinoma\n\nBLCA Bladder Urothelial Carcinoma\n\nBRCA Breast invasive carcinoma\n\nCESC Cervical squamous cell carcinoma and endocervical adenocarcinoma\n\nCHOL Cholangiocarcinoma\n\nCOAD Colon adenocarcinoma\n\nDLBC Lymphoid Neoplasm Diffuse Large B-cell Lymphoma\n\nESCA Esophageal carcinoma\n\nGBM Glioblastoma multiforme\n\nHNSC Head and Neck squamous cell carcinoma\n\nKICH Kidney Chromophobe\n\nKIRC Kidney renal clear cell carcinoma\n\nKIRP Kidney renal papillary cell carcinoma\n\nLGG Brain Lower Grade Glioma\n\nLIHC Liver hepatocellular carcinoma\n\nLUAD Lung adenocarcinoma\n\nLUSC Lung squamous cell carcinoma\n\nMESO Mesothelioma\n\nOV Ovarian serous cystadenocarcinoma\n\nPAAD Pancreatic adenocarcinoma\n\nPCPG Pheochromocytoma and Paraganglioma\n\nPRAD Prostate adenocarcinoma\n\nREAD Rectum adenocarcinoma\n\nSARC Sarcoma\n\nSKCM Skin Cutaneous Melanoma\n\nSTAD Stomach adenocarcinoma\n\nTGCT Testicular Germ Cell Tumors\n\nTHCA Thyroid carcinoma\n\nTHYM Thymoma\n\nUCEC Uterine Corpus Endometrial Carcinoma\n\nUCS Uterine Carcinosarcoma\n\nUVM Uveal Melanoma\n\n\nIntroduction\n\nThe vault RNAs (vtRNAs) are a class of eukaryotic middle size non-coding RNAs (84-141 nt) transcribed by the RNA polymerase III, which associates to the vault particle (<5 % of the total mass of the vault particle) (Boivin et al., 2019; Kedersha & Rome, 1986; Kedersha et al., 1991). Although this particle is the largest cellular ribonucleoprotein complex, its function remains scarcely understood. Most mammals have a single vtRNA gene (i.e., mouse and rat), but the human genome has three copies, annotated as vtRNA1-1 (98bp), vtRNA1-2 and vtRNA1-3 (88bp) genes, which are located in the chromosome region 5q31.3 (locus vtRNA1) and code for the RNAs that are integral components of the vault particle. Another vault RNA gene located in chromosome X, was classified as a pseudogene (vtRNA3-1P) due to the absence of expression in several cell lines and the presence of silencing mutations at the B box element of its promoter (van Zon et al., 2001). Lately, a transcript initially annotated as the human microRNA precursor hsa-mir-886 (Landgraf et al., 2007), was re-classified as another human vtRNA homologue and consequently renamed as vtRNA2-1 (Stadler et al., 2009). VtRNA2-1 is also located in chromosome 5 (5q31.1, locus vtRNA2) at 0.5Mb distance from the vtRNA1 cluster, where is placed between SMAD5 and TGFB1 genes in an antisense direction. Existing evidence indicates that despite being a duplication of the vtRNAs of locus 1, the vtRNA2-1 is neither associated with the vault particle nor co-regulated with the vtRNA1 locus (Lee et al., 2011; Stadler et al., 2009). Nevertheless, the realization that only 5–20% of all the cellular vtRNA transcripts are associated to the vault particle suggests additional roles for the majority of vtRNA transcripts, independent of the vault particle (Kickhoefer et al., 1998; Nandy et al., 2009; van Zon et al., 2001).\n\nMost of the current knowledge of vtRNA function focuses on vtRNA1-1 and vtRNA2-1 roles in viral infection and cancer. Functional studies found that vtRNA1-1 and vtRNA1-2 (but not vtRNA1-3) can interact directly with drugs as mitoxantrone, doxorubicin and etoposide (Gopinath et al., 2005; Gopinath et al., 2010; Mashima et al., 2008). In addition, p62 protein interacts with vtRNA1-1 and inhibits the p62 dependent autophagy in vitro and in vivo (Horos et al., 2019). The vault RNAs have also been linked to native immune response, because of their strong upregulation during the infection of Influenza A virus (IAV) and Epstein-Barr virus (EBV) (Amort et al., 2015; Li et al., 2015; Nandy et al., 2009). These studies proposed a viral activation of host vtRNAs as a mechanism to maintain the inhibition of PKR signaling pathway, representing a viral strategy to circumvent host innate immunity.\n\nInitial reports about vtRNA2-1 (locus vtRNA2) revealed that it is abundant in normal tissues while lowly expressed in cancer cell lines from different tissue origin (breast, melanoma, cervix, lung, oral and prostate), which is consistent with a tumor suppressive role in cancer (Lee et al., 2011; Treppendahl et al., 2012). Moreover, vtRNA2-1 was proposed as a new type of ncRNA functioning as a tumor suppressor gene (TSG) that inhibits PKR, and was consequently renamed as “nc886” (Golec et al., 2019; Jeon et al., 2012a; Jeon et al., 2012b; Lee et al., 2011). Then, its anti-proliferative and TSG function was described in prostate (Aakula et al., 2016; Fort et al., 2018; Ma et al., 2020), skin (Lee et al., 2019), gastric (Lee et al., 2014b) esophageal (Im et al., 2020; Lee et al., 2014a) and cholangiocarcinoma cells (Kunkeaw et al., 2012). Conversely, a pro-proliferative and anti-apoptotic oncogenic role was proposed for vtRNA2-1 in renal (Lei et al., 2017), ovarian (Ahn et al., 2018), thyroid (Lee et al., 2016), cervical (Li et al., 2017) and endometrial (Hu et al., 2017) tissues. A recent finding proposing a vtRNA2-1/PKR loss mediated doxorubicin cytotoxicity introduced a novel view about its contribution to chemotherapy response (Kunkeaw et al., 2019). In addition, a potential TSG role has been put forward for vtRNA1-3 in Myelodysplastic syndrome (MDS) (Helbo et al., 2015).\n\nApart from their role as full length RNAs, vtRNAs are precursors of small RNAs. Indeed, small RNAs with microRNA like function were demonstrated to derive from vtRNA1-1 (svRNAs) and to repress the expression CYP3A4, a key enzyme of drug metabolism (Meng et al., 2016; Persson et al., 2009). VtRNA2-1 has also been shown to act as a microRNA precursor in different tissues, serving both as TSG in prostate (Aakula et al., 2016; Fendler et al., 2011; Fort et al., 2020), bladder (Nordentoft et al., 2012), breast (Tahiri et al., 2014), colon (Yu et al., 2011), lung (Bi et al., 2014; Cao et al., 2013; Gao et al., 2011; Shen et al., 2018) and thyroid cancers (Dettmer et al., 2014; Xiong et al., 2011) and as oncogene (OG) in renal (Yu et al., 2014), colorectal (Schou et al., 2014) and esophagus cancer (Okumura et al., 2016) through the repression of specific mRNA transcripts in human cancer.\n\nDifferent lines of evidence revealed that the vtRNA transcription can be controlled by promoter DNA methylation. The epigenetic control of vtRNA2-1 is complex and owns clinical relevance in several tissues solid tumors including breast, lung, colon, bladder, prostate, esophagus, hepatic and stomach cancer (Cao et al., 2013; Fort et al., 2018; Lee et al., 2014a; Lee et al., 2014b; Romanelli et al., 2014; Treppendahl et al., 2012; Yu et al., 2020). Intriguing aspects of the epigenetic regulation of vtRNA2-1 locus comprise its dependence on the parental origin of the allele (Joo et al., 2018; Paliwal et al., 2013), and its sensitivity to the periconceptional environment ((Silver et al., 2015) and subsequent independent studies (Richmond et al., 2018; van Dijk et al., 2018)). In addition, vtRNA1-3 promoter methylation was associated with significantly poor outcome in lower risk myelodysplastic syndrome patients (Helbo et al., 2015).\n\nCurrently, transcriptomic sequencing is the benchmark technique to study global RNA expression (Stark et al., 2019). Nonetheless, some classes of RNAs are elusive to the standard transcriptomics due to their stable RNA structure and the presence of modified bases or ends, which impair the cDNA synthesis and/or adapter ligation during the sequencing library preparation (Sendler et al., 2011; Zheng et al., 2015). The vtRNAs belong to this group due to their conserved stable stem/hairpin loop secondary structure. The latter, together with the lack of sequencing of 40–200bp-long RNAs in the conventional transcriptomic studies, which are mostly intended for small and long RNAs, probably delayed their study in comparison with other regulatory RNAs. In fact, the 50–300 nucleotides long RNAs are considered the black hole of RNA biology (Boivin et al., 2018; Steitz, 2015). Nonetheless, since chromatin accessibility plays a critical role in the regulation of gene expression, at some extent the transcription of an RNA can be inferred from the chromatin status of its promoter (Corces et al., 2018; Duren et al., 2017; Liu et al., 2018; Park et al., 2017b). Since mounting evidence has shown that vtRNAs expression is tightly controlled by chromatin accessibility, dependent on nucleosome positioning and promoter DNA methylation (Ahn et al., 2018; Fort et al., 2018; Helbo et al., 2015; Helbo et al., 2017; Lee et al., 2014a; Lee et al., 2014b; Park et al., 2017a; Park et al., 2017b; Sallustio et al., 2016; Treppendahl et al., 2012), the chromatin structure is a suitable surrogate marker of vtRNA transcription and could be used as a proxy of their expression.\n\nThe expression, regulation, and role of the four human vtRNAs in normal and disease conditions are still poorly understood, and available knowledge indicates that they hold diverse tissue specific activities. The availability of genomic data of large sets of human tissues provided by The Cancer Genome Atlas (TCGA), allows the study of the human vtRNAs across 16 tissue types and normal/cancer conditions. Here, we analyze vtRNA genes chromatin of the TCGA patient cohort withdrawn from two approaches: the assay for transposase-accessible chromatin followed by NGS sequencing (ATAC-seq) to analyze chromatin accessibility (Buenrostro et al., 2013; Buenrostro et al., 2015; Corces et al., 2018; Thurman et al., 2012) and the Illumina Infinium Human Methylation 450K BeadChip to analyze the CpG methylation of DNA (Moran et al., 2016). This led us to determine the patterns of transcriptional regulation of the four human vtRNAs throughout cancer tissues. We also evaluate the association between vtRNA expression and the patient clinical outcome in all the available cancer types. Finally, looking for functional discoveries, we analyze vtRNA relations with immune subtypes and transcriptionally co-regulated gene programs. Our study reveals specific patterns of expression for each vtRNA that support previous evidence and poses potential new roles and molecular programs in which they may participate across and intra cancer types, increasing the comprehension of the role of the human vtRNAs in health and disease.\n\n\nMethods\n\nThe ATAC-seq data obtained by The Cancer Genome Atlas (TCGA) consortium were retrieved from UCSC Xena Browser (Goldman et al., 2020) on 03/10/2018. It comprises the genomic matrix TCGA_ATAC_peak_Log2Counts_dedup_promoter with normalized count values for 404 samples (385 primary solid tumor samples across 23 tissues). As is described in UCSC Xena Browser to calculate the average ATAC-seq values a prior count of 5 was added to the raw counts, then put into a \"counts per million\", then log2 transformed, then quantile normalized; the result is the average value in the file (log2(count+5)-qn values) across all technical replicates and all biospecimens belonging to the same TCGA sample group. The gene promoter for ATAC-seq is defined as a region within -1000 to +100bp from the TSS site. Assignment of promoter peak to gene mapping information derives from the peak summit within the promoter region. Peak location information of the ATAC-seq values for 500 bp gene promoter regions was retrieved from the file TCGA_ATAC_Log2Counts_Matrix.180608.txt.gz. All the analyses were performed for tissues with at least five primary tumor samples (21 tissues), which resulted in the exclusion of CESC (2 primary tumor samples) and SKCM (4 primary tumor samples). Correlations between ATAC-seq and DNA promoter methylation were performed for the 329 primary tumors that are studied by both strategies (Extended Data: Tables S1 and S2).\n\nThe DNA methylation data obtained from The Cancer Genome Atlas (TCGA) consortium was retrieved from UCSC Xena Browser (Goldman et al., 2020) on date 03/10/2018. It comprises the normalized beta-value of DNA methylation obtained using Illumina Infinium Human Methylation 450 BeadChip arrays of the total (9149 samples) normal adjacent tissues (746 samples across 23 tissues) and primary solid tumors (8403 samples across 32 tissues) of the Pan-Cancer TCGA cohort. The current study is limited to solid tumors since only AML DNA methylation is available at the TCGA. All the analyses were performed for tissues with at least five samples. Normal adjacent tissues comprise 16 tissues, excluding CESC (two samples), GBM (two samples), PCPG (three samples), SARC (four samples), SKCM (two samples), STAD (two samples) and THYM (two samples). Primary tumors comprise 32 tissues. The normalized promoter average beta-values (500 bp bin) comprise the following CpG sites for vtRNA1-1: cg12532653, cg05913451, cg14633504, cg16615348, cg25602765, cg13323902, cg18296956; for vtRNA1-2: cg21161173, cg13303313, cg00500100, cg05174942, cg25984996, cg11807153, cg15697852; for vtRNA1-3: cg23910413, cg19065177, cg02053188, cg01063759, cg07379832, cg07741016; and for vtRNA2-1: cg16615357, cg08745965, cg00124993, cg26896946, cg25340688, cg26328633, cg06536614, cg18678645, cg04481923 (Extended Data: Tables S2–S5).\n\nThe transcription factors (TFs) occupancy analysis of vtRNAs was performed at a ± 3000 bp region centered at each vtRNA gene. The CHIP-seq data was retrieved from the UCSC genome browser (GRCh37/hg19) (Kent et al., 2002) and the K562 chronic myelogenous leukemia cell line was chosen since it has the richest TFs data of ENCODE dataset (ENCODE Transcription Factor Binding tracks - ENCODE 3 TFBS) (Euskirchen et al., 2007). The KEGG pathways enrichment analysis of the core 23 TFs common to all vtRNAs was done using STRING software (Szklarczyk et al., 2017) (Extended Data: Table S6).\n\nThe Kaplan Meier curve analysis (Bland & Altman, 1998) was performed with software GraphPad Prism 6 using Log-ranked Mantel-Cox test. We analyzed the ATAC-seq normalized values and DNA methylation average normalized beta-values for vtRNA promoters and survival data until 4000 days (99% of data). The log-rank statistics was calculated for quartiles of vtRNAs promoter chromatin accessibility comparison groups (25th and 75th) (Extended Data: Tables S7 and S8).\n\nThe genome wide correlation analysis of promoter chromatin accessibility (ATAC-seq normalized values) for each vtRNA in comparison with all the annotated genes was performed using the genomic matrix TCGA_ATAC_peak_Log2Counts_dedup_promoter retrieved from UCSC Xena Browser (385 primary tumor samples across 23 tissues) (Goldman et al., 2020) on date 03/10/2018. The protein coding genes showing a Spearman correlation r ≥ 0.4 were selected for pathway and cluster location analysis. The pathway enrichment analysis was done using STRING software for the Gene Ontology Biological Process and KEGG pathways categories (Szklarczyk et al., 2017). The cluster localization analysis was performed with two approaches, the Cluster Locator algorithm (Pazos Obregón et al., 2018) and the Enrichr software (Kuleshov et al., 2016) (Extended Data: Tables S9 and S10).\n\nThe data of Immune Subtypes defined by Thorsson et al. (Thorsson et al., 2018) is available at the Pan-Cancer TCGA and was retrieved from UCSC Xena Browser (Goldman et al., 2020) on date 03/10/2018 and from the supplementary material of Thorsson et al. article (Thorsson et al., 2018). ATAC-seq data of vtRNA promoters for the six Immune Subtype comprised a total of 364 samples: wound healing (105 samples), IFN-g dominant (93 samples), inflammatory (110 samples), lymphocyte depleted (43 samples), immunologically quiet (nine samples), TGF-b dominant (four samples). DNA methylation average normalized beta-values of vtRNA promoters for the six Immune Subtype comprised 7693 samples including wound healing (1963 samples), IFN-g dominant (2137 samples), inflammatory (2126 samples), lymphocyte depleted (933 samples), immunologically quiet (383 samples), TGF-b dominant (151 samples) (Extended Data: Tables S11–S14).\n\nUnless specified all the variables are expressed as average value ± standard deviation (SD). Statistical analyses were performed with one-way ANOVA for multiple comparison tests, including Sidak’s Honest Significant Difference test as a post-hoc test, as referred in the legend of the Figures. Spearman equations were applied to determine the correlations. All the analyses were done in R software (version 3.6) using libraries ggcorrplot, corrplot, xlsx, heatmap.2 (clustering distance measured by Euclidean and Ward clustering algorithms) and software GraphPad Prism 6. The statistical significance of the observed differences was described using the p-value (* p < 0.05, ** p < 0.01, *** p < 0.001, **** p-value < 0.0001). Differences with a p-value of < 0.05 were considered significant.\n\n\nResults\n\nThe Cancer Genome Atlas consortium incorporated ATAC-seq data for tumor samples of the GDC Pan-Cancer dataset (385 primary tumors samples across 23 cancer types (Corces et al., 2018)). The ATAC-seq strategy is a genome-wide sequencing profiling approximation to chromatin accessibility using the hyperactive Tn5 transposase that simultaneously cut and ligate adapters preferentially to the accessible DNA regions. The counts of sequencing reads in a particular genomic region provides a direct measurement of chromatin accessibility (Buenrostro et al., 2015; Tsompana & Buck, 2014). For those gene promoters regulated by DNA methylation, ATAC-seq is a more direct approximation to chromatin accessibility than promoter CpG DNA methylation measurements because the latter is well correlated but not an exact measurement of chromatin accessibility. Indeed, the effect of DNA methylation on chromatin structure depends on the gene and the distribution of the methylation sites along it. It is also important to mention that gene expression interpretations based solely on chromatin accessibility are blind to post-transcriptional regulatory events such as processing, localization, and stability of the RNA transcript. Nevertheless, since the chromatin status of the different vtRNA promoters has been positively correlated with the abundance of their transcripts (Ahn et al., 2018; Fort et al., 2018; Helbo et al., 2015; Lee et al., 2014a; Lee et al., 2014b; Park et al., 2017a; Park et al., 2017b; Sallustio et al., 2016; Treppendahl et al., 2012), ATAC-seq is likely a good surrogate of vtRNA expression. DNA CpG methylation data is available for 746 normal adjacent (across 23 tissues) and 8403 primary tumor (across 32 tissues) tissue samples of the Pan-Cancer TCGA cohort (Extended Data: Tables S1–S5 and Figure S1). The full data is listed in Tables S1–S5 and the tissue composition of the three datasets of the cohort, comprising tumor ATAC-seq, normal and tumor DNA methylation, is shown in Figure S1. The DNA methylation data has nine more tissue types and a higher number of samples than the others, while the abundance of some tissues is skewed to twice enrichment in 1-4 specific tissue types.\n\nAlthough several reports demonstrated that the DNA methylation of vtRNA promoters is well correlated to vtRNA transcript expression in various tissues (Ahn et al., 2018; Fort et al., 2018; Helbo et al., 2015; Helbo et al., 2017; Lee et al., 2014a; Lee et al., 2014b; Park et al., 2017b; Sallustio et al., 2016; Treppendahl et al., 2012), the association between the DNA methylation and chromatin accessibility at their promoters was not previously investigated.\n\nTo assess the expression of vtRNAs in cancer tissues, we analyzed a 500 bp region, containing the full vtRNA genes, the proximal promoter region and the RNA polymerase lII A and B box elements located downstream of the transcription start site (TSS) (Figure 1). Indeed, Vilalta et al., 1994 demonstrated that the deletion of the 300bp 5´-flanking region of the rat vtRNA transcript largely reduced its transcription greater than 30-fold (Vilalta et al., 1994). As depicted in Figure 1, this region bears epigenetic marks of transcriptionally active chromatin (Li et al., 2007), including histone H3K27ac, H3K4me1, H3K4me3 at the promoters and DNaseI hypersensitivity clusters around the TSS in the cell types compiled by UCSC browser (Goldman et al., 2013). Interestingly, vtRNA2-1 is the only vtRNA immersed in a CpG island and vtRNA1-1 displays the strongest epigenetic marks of transcriptional activity (Figure 1). The analysis of the ATAC-seq values of this 500 bp region of all the TCGA primary tumors reveals that the four human vtRNAs have different levels of chromatin accessibility (Figure 2A). Moreover, the average DNA methylation of the promoters (Figure 2B) in primary tumor samples supports this finding (32 tissues, Extended Data: Figure S1 and Tables S2 and S4). VtRNA1-1 promoter has the highest chromatin accessibility and the lowest DNA methylation, showing the smallest dispersion of values among the samples (Ave. 4.1, 0.6 SD) relative to the other three vtRNAs. Meanwhile, vtRNA1-2 (Ave. 2.9, 1.6 SD), vtRNA1-3 (Ave. 1.7, 1.2 SD) and vtRNA2-1 (Ave. 2.5, 1.4 SD) have broader ranges of ATAC-seq and DNA methylation values (Figure 2, Table 1, Extended Data: Tables S1 and S2 and Figure S1). A comparison among the vtRNAs shows that the average chromatin accessibility of their promoters is inversely proportional to their average DNA methylation (Table 1 and Figure 2) (relative ATAC-seq values are vtRNA1-1 (4.1) > vtRNA1-2 (2.9) > vtRNA2-1 (2.5) and accordingly, relative DNA methylation are vtRNA1-1 (0.09) < vtRNA1-2 (0.4) < vtRNA2-1 (0.5)). Yet vtRNA1-3 average low chromatin accessibility is not accompanied by a comparatively denser promoter methylation (values 1.7 and 0.22 respectively). Nevertheless, the intra-sample correlation between the ATAC-seq and DNA methylation for the vtRNAs is between -0.24 and -0.78 (see rs-values in Table 1 and Extended Data: Figure S2), suggesting that regardless of the relatively smaller average effect of DNA methylation on vtRNA1-3 promoter accessibility, all the vtRNAs are regulated by DNA methylation to some extent (Table 1). In addition, the CpG DNA methylation negatively correlates with ATAC-seq values in the 500bp of the promoters of the four vtRNAs (Table 1 and Extended Data: Figure S2). The strength of the correlation for each vtRNA is higher for the two vtRNAs that have a broader spectrum of DNA methylation, i.e. vtRNA1-2 and vtRNA2-1 (rs = -0.74 and rs = -0.78 respectively) (Table 1 and Extended Data: Figure S2B and S2D). Meanwhile, vtRNA1-1 and vtRNA1-3 promoters, which have narrower range of DNA methylation (vtRNA1-1 has also a small range of chromatin accessibility) present a smaller association between both values (rs = -0.24 and rs = -0.54 respectively) (Table 1 and Extended Data: Figure S2A and S2C). Technical differences in ATAC-seq and DNA methylation array approaches, as well as naturally occurring non-linear correlation between average DNA methylation and chromatin structure may account for these differences (Corces et al., 2018; Liu et al., 2018). The low ATAC-seq value of the vtRNA3-1P pseudogene (Ave. -1.2, 0.6 SD), represents a proof of concept of the analyses (Extended Data: Figure S3 and Tables S1–S5).\n\nGenomic view of 1.5 kb region of human vtRNA genes in UCSC Genome browser (GRCh37/hg19) centered at the 500bp bin highlighted in yellow, which was used for ATAC-seq and CpG methylation analyses. VtRNAs of locus 1 cluster (vtRNA1-1, vtRNA1-2, vtRNA1-3) and of locus 2 (vtRNA2-1) are in the sense and antisense orientation respectively. Several Gene annotation and ENCODE Project tracks for seven cell lines (GM12878, H1-hESC, HSMM, HUVEC, K562, NHEK, NHL) are displayed: DNA accessibility (DNaseI hypersensitivity clusters (color intensity is proportional to the maximum signal strength)), DNA methylation (for CpG islands length greater than 200 bp), histone modification (H3K27Ac, H3K4me1, H3K4me3 marks), conservation of the region in 100 Vertebrates (log-odds Phylop scores). The vertical viewing range of the tracks displays the default settings of the browser for each variable.\n\nAnalysis of vtRNA 500bp promoter region. A. Average chromatin accessibility ATAC-seq values for the 385 primary tumors available at the Pan-Cancer TCGA dataset (23 tissues types). B. Average DNA methylation beta-values for the 8403 primary tumors (32 tissues types). Dashed horizontal lines denote unmethylated (bottom gray, average beta-value ≤ 0.2), 50% methylated (middle red, average beta-value = 0.5) and highly methylated (top gray, average beta-value ≥ 0.8) promoters. The box plots show the median and the lower and upper quartile, and the whiskers the 2.5 and 97.5 percentile of the distribution.\n\nAiming to investigate a possible transcriptional co-regulation of vtRNA genes, we determined the pairwise correlations in chromatin accessibility and DNA methylation among the four vtRNA promoters. We found that all pairs of vtRNAs, except vtRNA1-2 and vtRNA2-1, show positive correlations in both datasets (Figure 3A and 3B) (rs-values 0.23-0.41 for ATAC-seq and rs-values 0.20-0.50 for DNA methylation). The unsupervised clustering of these epigenetic marks indicates that the three vtRNAs clustered at vtRNA1 locus (vtRNA1-1, vtRNA1-2 and vtRNA1-3), which are the vault particle associated vtRNAs, are more similar than vtRNA2-1 (Figure 3A and 3B).\n\nA-B Matrix of pairwise Spearman correlations (two-way hierarchical clustering distance measured by Euclidean and Ward clustering algorithms) of vtRNA 500 bp promoter region for ATAC-seq data (385 primary tumors samples across 23 tissues) (A) and DNA methylation average beta-values data (8403 primary tumors samples across 32 tissues) (B). C. Venn diagram of transcription factors identified as ChIP-seq Peaks by ENCODE 3 project in the cell line K562 (Venny 2.1; https://bioinfogp.cnb.csic.es/tools/venny/index.html). The region for TFs assignment was defined as ±3000 bp from the vtRNA transcript sequence boundaries. D. Interaction cluster of the core 23 TFs common to all vtRNAs performed with STRING (Szklarczyk et al., 2017). The colored labels of the top 3 enriched KEGG pathway terms (FDR < 0.05) are indicated.\n\nGiven that the chromatin accessibility of a DNA region is partially controlled by transcription and chromatin remodeler’s factors (Corces et al., 2018; Klemm et al., 2019), we analyzed transcription factors (TFs) occupancy at a ± 3000 bp region centered at each vtRNA gene. Since there is no such study of the TCGA samples, we investigated the CHIP-seq data of the K562 chronic myelogenous leukemia cell line, which has the richest TF data at ENCODE dataset (Euskirchen et al., 2007; Goldman et al., 2013). We observed that the four vtRNAs share a common core of 23 TFs (26%). The three members of the vtRNA1 cluster share 16 additional TFs (18%), reaching 39 common TFs (44%), while only 2-4 TFs with vtRNA2-1 (Figure 3C and 3D and Extended Data: Table S6). We finally asked whether this common core of TFs is linked to a specific biological process. The STRING enrichment analysis of the core of 23 TFs common to all vtRNAs identified HTLV-I infection (ATF1, ATF3, E2F1, EP300, NFATC3, TBP), Hepatitis B (E2F1, EP300, NFATC3) and Transcriptional misregulation in cancer (AFF1, ATF1, MAX) as the top three enriched KEGG pathway terms (FDR < 0.05) (Figure 3D and Extended Data: Table S6).\n\nTaken together these findings indicate that the transcriptional activity of the vtRNAs is gene specific, being vtRNA1-1 the most accessible and possibly the most expressed. In addition, the data suggest that the regulatory status of the vtRNA promoters is coordinately controlled, and the three vtRNA1s are more co-regulated among themselves. Yet, the core of TFs shared by the four vtRNAs is associated with viral infection and cancer related terms in the myeloid cell line K562.\n\nIn order to investigate the expression of vtRNAs in different tissues we analyzed the Pan-Cancer TCGA ATAC-seq data discriminating the tissue of origin. As expected, vtRNA1-1 has the highest promoter chromatin accessibility among tissues and the smallest variation (Figure 4A, Extended Data: Tables S1-S5 and Figure S1). Remarkably, low-grade glioma tumor samples (LGG) show a global reduction in chromatin accessibility at the four vtRNA gene promoters (Figure 4A). An opposite pattern is seen in adrenocortical carcinoma tissue (ACC), where the vtRNAs have the highest concerted chromatin accessibility (Figure 4A). Individually, vtRNAs promoter accessibility is maximum and minimum in THCA (4.7) and LGG (3.3) for vtRNA1-1, ACC (4.2) and LGG (0.29) for vtRNA1-2, ACC (3.7) and LGG (0.24) for vtRNA1-3 and KIRC (4.2) and LGG (1.0) for vtRNA2-1 (Figure 4A). VtRNA3-1P reaches a maximum of promoter chromatin accessibility in Testicular Germ Cell Tumors (TGCT) (0.65) with an extremely low average ATAC-seq value and its minimum in PRAD (-1.5) (Extended Data: Figure S3C). Remarkably, although vtRNA1-1 and vtRNA1-3 have the highest and lowest promoter accessibility in the majority of tissues respectively, vtRNA1-2 and vtRNA2-1 are the most variable (vtRNA1-1 SD = 0.34, vtRNA1-2 SD = 1.4, vtRNA1-3 SD = 0.75 and vtRNA2-1 SD = 0.78) (Figure 4A). In addition, in 12 tissues the chromatin accessibility of vtRNA1-2 is higher than vtRNA2-1 (57%) whereas in nine tissues the chromatin accessibility of vtRNA1-2 is lower than vtRNA2-1 (43%) (Figure 4A).\n\nA. ATAC-seq values for vtRNA promoters in 21 primary tumor tissues. B. Average beta-values of promoter DNA methylation for vtRNAs in 32 primary tumors tissues. C. Average beta-values of promoter DNA methylation for vtRNAs in 16 normal adjacent tissues. The charts show the average value and standard deviation of each vtRNAs for the tissues with at least five samples available at Pan-Cancer TCGA dataset.\n\nUsing the vtRNAs promoter DNA methylation data, we extended the analysis to 32 primary tumor tissues, incorporating nine more tissues than ATAC-seq samples (DLBC, KICH, OV, PAAD, READ, SARC, THYM, UCS, UVM) (Figure 4B, Extended Data: Figure S1) and 16 normal adjacent tissues (Figure 4C, Extended Data: Figure S1). Again, the DNA methylation profile mirrors the chromatin accessibility in the individual tissue types (Figure 4). Remarkably, the association between the average vtRNA promoter chromatin accessibility and DNA methylation of the vtRNA1 cluster in each tissue type is higher than that observed for the average of all tissues (vtRNA1-1 rs = -0.28, vtRNA1-2 rs = -0.90 vtRNA1-3 rs = -0.74 and vtRNA2-1 rs = -0.58) (Table 1 and Extended Data: Figure S4). The opposite finding for vtRNA2-1 may be explained by the impact of the previously recognized chromatin polymorphisms in the locus (Silver et al., 2015), which may prevail over the tissue specific variation for this gene.\n\nIn primary tumor tissues, promoter DNA methylation of vtRNA2-1 is higher than vtRNA1-2 in 17 tissues (53%) and the opposite is observed in the remaining 15 tissues (47%) (Figure 4B). Meanwhile in normal tissues, promoter DNA methylation of vtRNA2-1 is higher than vtRNA1-2 in 4 tissues (25%) and lower in 12 tissues (75%) (Figure 4C), indicating that although vtRNA1-2 is more methylated in normal samples, vtRNA2-1 gains methylation in neoplastic tissue, becoming more methylated than vtRNA1-2 (in 7 tissue types and vtRNA1-2 loose methylation: BLCA, BRCA, CHOL, HNCSC, LUAD, LUSC, UCEC). Indeed, the Fisher's exact test identifies a mirrored profile of chromatin accessibility between normal (4 tissues with high vtRNA1-2 and 12 tissues with high vtRNA2-1 from 16 total tissues) and tumor tissues (17 tissues with high vtRNA1-2 and 15 tissues with high vtRNA2-1 from 32 total tissues) for vtRNA1-2 and vtRNA2-1 (p-value = 0.07). Despite this deregulation in transformed tissues, we wondered if the tissue specific differences in vtRNA promoters were explained by their pre-existing status in the normal tissues. The correlation among average vtRNA promoter DNA methylation in normal and tumor tissues suggest that the variation in chromatin accessibility among tissue types is already established in the normal tissue counterparts (vtRNA1-1 rs = 0.53, vtRNA1-2 rs = 0.84, vtRNA1-3 rs = 0.47 and vtRNA2-1 rs = 0.75, Extended Data: Figure S5).\n\nThe assessment of differential vtRNA expression from normal to tumor condition at the TCGA cohort can only be performed using DNA methylation dataset since no ATAC-seq analyses were performed in the normal tissues. The average beta-value of CpG sites in the 500bp vtRNAs promoter of normal and tumor tissue evidenced gene specific patterns of deregulation in neoplastic tissues (Figure 5). As depicted in Figure 4, vtRNA1-1 and vtRNA1-3 promoter DNA methylation and chromatin accessibility is low and high tissue-wide respectively, in both normal and tumor tissues (yet, there are highly methylated tumor outliers as LGG, that lack normal counterpart) (Figure 4 and Figures 5A and 5C). Conversely, vtRNA1-2 and vtRNA2-1 revealed significant differences in average promoter DNA methylation among the tissue categories (Figures 5B and 5D). In agreement with previous results, the methylation of vtRNA1-2 promoter decreases from normal to tumor samples, while vtRNA2-1´s increases (Figures 5B and 5D and Figure 4).\n\nAverage beta-values of promoter DNA methylation of vtRNA1-1 (A), vtRNA1-2 (B), vtRNA1-3 (C) and vtRNA2-1 (D), assessed in 746 normal and 8403 tumor tissues respectively. The box plots show the median line and lower and upper quartile and the whiskers the 2.5 and 97.5 percentile. Horizontal grey striped and red dotted lines denote unmethylated (average beta-value ≤ 0.2), 50% methylated (average beta-value = 0.5) and highly methylated (average beta-value ≥ 0.8) promoters. One-way ANOVA multiple test analysis with Sidak as posthoc test was performed. **** p-value < 0.0001.\n\nWe next asked whether the promoter status of the vtRNAs is deregulated during the normal and tumor transformation of different tissue types. This comparison was restricted to the 16 tissues with normal samples (with data of at least five samples, Figure 6 and Extended Data: Figure S1, Table S5). The results revealed that vtRNA1-1 is globally unmethylated in normal and tumor from different tissue origins, but presents small but statistically significant changes in 4 tissue types (OG profile in BLCA, THCA UCEC and TSG in LUSC), whose biological impact remains to be determined (Figure 6A). Similarly, vtRNA1-3 is globally unmethylated, showing larger variability and significant upregulation in BRCA and PRAD, compatible with a TSG function (TSG trends for LIHC p-value = 0.08 and LUSC p-value = 0.09, Figure 6C). In agreement with the literature, vtRNA2-1 presents a TSG pattern of deregulation in PRAD, LUSC and BRCA (Cao et al., 2013; Fort et al., 2018; Romanelli et al., 2014), and an OG pattern in KIRP that has not been previously described (Figure 6D). Finally, a statistically significant dysregulation of vtRNA1-2 promoter DNA methylation across almost all cancer types (13 out of 16 tissues analyzed) poses it as a candidate OG in cancer (Figure 6B).\n\nAverage beta-values of promoter DNA methylation for vtRNA1-1 (A) vtRNA1-2 (B), vtRNA1-3 (C) and vtRNA2-1 (D). Acronyms indicate the tissue condition (normal (N) and tumor (T)). Blue and red colors indicate an increase or reduction in promoter methylation in tumor vs their normal tissues counterparts. The box plots show the median and the lower and upper quartile, and the whiskers the 2.5 and 97.5 percentile of the distribution. Horizontal, lines denote the methylation level of the promoters: grey striped bottom and top for unmethylated (average beta-value ≤ 0.2) or highly methylated (average beta-value ≥ 0.8) respectively, and red dotted for 50% methylated (average beta-value = 0.5)) promoters. One-way ANOVA multiple test analysis with Sidak as posthoc test was performed. * p-value < 0.05; ** p-value < 0.01; **** p-value < 0.0001.\n\nOverall, the data shows different DNA methylation changes in the vtRNAs promoters upon malignant transformation in several tissues. In addition, the deregulation of each vtRNA occurs mostly in a gene specific direction, where vtRNA1-2 has an OG like epigenetic de-repression while vtRNA2-1 (and to a lesser extent vtRNA1-1, vtRNA1-3) has a TSG like repressive methylation in tumor tissues.\n\nSeeking for a possible clinical significance of the chromatin accessibility change of the vtRNA promoters, we studied its association with the overall survival of patients (Figure 7 and Extended Data: Tables S7 and S8). The analysis of patients stratified by vtRNA promoter accessibility quartiles did not show differences in overall survival (data available at Extended Data: Table S8). However, a significantly lower patient survival probability when patient tumors have lower promoter DNA methylation is observed for vtRNA1-1 (p-value = 0.003), vtRNA1-2 (p-value = 0.004) and vtRNA2-1 (p-value = 0.002) (patient stratified in quartiles of the promoter DNA methylation cohort values, Figure 7). Therefore, a lower promoter DNA methylation of vtRNA1-1, vtRNA1-2 and vtRNA2-1, a surrogate of their high expression, might be associated with poor patient overall survival cancer-wide.\n\nKaplan-Meier curves of overall patient survival probability over the time (4000 days) discriminating the primary tumors into two cohorts with relatively higher (75th) and lower (25th) DNA methylation at each vtRNA promoter. Promoter DNA methylation data of the 8060 primary tumors was used to stratify the patients in two quartiles, based on the expression of vtRNA1-1 (A) vtRNA1-2 (B), vtRNA1-3 (C) and vtRNA2-1 (D). Patient survival probability of the two groups was analyzed using Log-rank (Mantel-Cox) test. The dotted lines represent the 95% confidence interval for each curve.\n\nSeeking to get insight into the function of the vtRNAs from their transcription regulatory marks, we searched for the genes co-regulated at chromatin level. We calculated the correlation of the ATAC-seq promoter values of each vtRNA and all the individual genes in the 385 primary tumor cohort and selected those showing a Spearman correlation rs ≥ 0.4. Using STRING software analysis, we then investigated their connection with Biological Process categories and KEGG pathways (Szklarczyk et al., 2017). A few enriched terms for the genes correlated with vtRNA1-2, vtRNA1-3 and vtRNA2-1 is identified (FDR < 1×10-3) (Extended Data: Tables S9 and S10). The 196 protein coding genes correlated with vtRNA1-2 are enriched in the Biological Process “Epithelial cell differentiation” (FDR < 1×10-4) (Extended Data: Table S10). Meanwhile, the 358 protein coding genes correlated with vtRNA2-1 are enriched in the Biological Processes “Immune system process”, “Inflammatory response” and “Immune response” (FDR < 1×10-5) and the KEGG pathways term “Cytokine-cytokine receptor interaction” (FDR < 1×10-4) (Extended Data: Table S10). The only six protein coding genes correlated with vtRNA1-3 are enriched in the “Thyroid cancer” KEGG pathway term (FDR < 1×10-4). Remarkably, although STRING analysis of the vtRNA1-1 associated 37 protein coding genes did not find enriched process or pathways, 36 of the 37 correlated genes are located at chromosome 5q region. Using the Cluster Locator algorithm (Pazos Obregón et al., 2018), we found a statistically significant non-random clustering behavior for the chromosomal location of the genes co-regulated with vtRNA1-1 (p-value < 1×10-10). Indeed, when the analysis was extended to 173 protein coding genes with Spearman correlation rs ≥ 0.3, 139 genes of 173 were situated at chromosome 5q region (p-value < 1×10-10). These genes are positioned in particular regions at chr5q31, chr5q35, chr5q23, chr5q14, chr5q32, chr5q34 (FDR < 1×10-4) (Kuleshov et al., 2016) (Extended Data: Table S10). We did not find a similar phenomenon for the other three vtRNAs. In summary, vtRNA1-3, vtRNA1-2 and vtRNA2-1 transcription may be co-regulated with genes belonging to specific biological processes located elsewhere, while vtRNA1-1 transcription may be controlled by a locally specialized chromatin domain at chromosome 5q region lacking apparent functional relatedness.\n\nTaking into account that vtRNAs have been previously related to the immune response (Golec et al., 2019; Li et al., 2015; Nandy et al., 2009), and that we found an association of vtRNA2-1 with immune related terms, we sought to investigate a putative relation between the vtRNAs expression and the six Immune Subtypes defined by Thorsson et al. (Thorsson et al., 2018), compiled at Pan-Cancer TCGA (Extended Data: Tables S11-S14). These six Immune Subtypes are named because of the foremost immune characteristic, comprising wound healing, IFN-g dominant, lymphocyte depleted, inflammatory, immunologically quiet and TGF-b dominant types (Thorsson et al., 2018). As was expected, mirrored patterns were observed for promoter ATAC-seq and DNA methylation data of the six groups (Figure 8). The immunologically quiet subtype shows a concerted shutdown of all vtRNA promoters (Figure 8), which is largely composed by LGG samples showing low vtRNA ATAC-seq and high promoter methylation average values in LGG tumors (Figures 4A and 4B). The immunological quiet subtype exhibits the lowest leukocyte fraction (very low Th17 and low Th2) and the highest macrophage:lymphocyte ratio (high M2 macrophages) (Thorsson et al., 2018). The remaining subtypes present a similar vtRNA profile except for the inversion of vtRNA1-2/vtRNA2-1 accessibility ratio, which is higher than 1 for the wound healing and IFN-g dominant subtypes while is lower than 1 for the lymphocyte depleted and inflammatory subtypes (Figure 8A). As expected, a mirrored pattern was observed for vtRNA1-2 and vtRNA2-1 at DNA methylation data (Figure 8B). Since the wound healing and IFN-g dominant subtype have high proliferation rate opposite to the lymphocyte depleted and inflammatory subtypes (Thorsson et al., 2018), we evaluated the correlation between vtRNA1-2 and vtRNA2-1 chromatin status and proliferation rate or wound healing status defined by Thorsson et al. (Extended Data: Tables S12 and S14) (Thorsson et al., 2018). A negative correlation between vtRNA1-2 promoter DNA methylation and the proliferation rate (rs = -0.44) and wound-healing features of the tumors is revealed (rs = -0.48) (Extended Data: Tables S12 and S14). These findings suggest that vtRNA transcriptional regulation may be associated with tumor immunity.\n\nA. ATAC-seq values expressed as log2 normalized values for vtRNA promoters grouped in six Immune Subtype: wound healing (105 samples), IFN-g dominant (93 samples), inflammatory (110 samples), lymphocyte depleted (43 samples), immunologically quiet (9 samples), TGF-b dominant (4 samples). B. DNA methylation average beta-values for vtRNA promoters grouped in six Immune Subtype: wound healing (1963 samples), IFN-g dominant (2137 samples), inflammatory (2126 samples), lymphocyte depleted (933 samples), immunologically quiet (383 samples), TGF-b dominant (151 samples) (Thorsson et al., 2018). The charts show the average and standard deviation for each vtRNA promoter in each Immune Subtype group.\n\n\nDiscussion\n\nAlthough important insight into the vtRNA function has been recently gained, the landscape of vtRNA expression in human tissues and cancer was unknown, perhaps for the absence of vtRNA data in transcriptomic studies. Here we used ATAC-seq and methylation arrays data from the Pan-Cancer TCGA consortium (Weinstein et al., 2013), as surrogate variables to uncover the expression of vtRNAs across multiple cancer types. A limitation of our study is its blindness to post-transcriptional controls of vtRNA expression, such as RNA processing, transport, localization and/or stability. Indeed, there is evidence of vtRNA transcript regulation via RNA methylation by NSUN2, or via its association to other proteins like DUSP11, DIS3L2, SSB, SRSF2 and DICER (Burke et al., 2016; Hussain et al., 2013; Kickhoefer et al., 2002; Łabno et al., 2016; Persson et al., 2009; Sajini et al., 2019). Nonetheless, the chromatin status of the vtRNA promoters has been correlated with the expression of their transcripts in several reports (Ahn et al., 2018; Fort et al., 2018; Helbo et al., 2015; Helbo et al., 2017; Lee et al., 2014a; Lee et al., 2014b; Sallustio et al., 2016; Treppendahl et al., 2012). These evidences unequivocally stand for the use of chromatin structure as a suitable proxy for vtRNA expression.\n\nAn integrated genomic view of the regulatory features of the vtRNA genes compiled in UCSC genome browser indicates that the four vtRNAs have chromatin signs of active transcription in different cell lines and defines a proximal promoter regulatory region of approximately 500 bp (Nikitina et al., 2011; Vilalta et al., 1994). High resolution chromatin accessibility mapping studies by NOMe-Seq of the vtRNA promoters in cell lines validate this assumption (Helbo et al., 2017). Particularly, vtRNA2-1 is singular for being immersed in a CpG island, for lacking the TATA box, DSE or PSE elements characteristic of the others vtRNA promoters, and for bearing a cAMP-response (CRE) element (Canella et al., 2010; Helbo et al., 2017; Nandy et al., 2009). Since ATAC-seq approach is currently the best high throughput method to determine the chromatin accessibility of a DNA region directly (Chen et al., 2016; Sun et al., 2019; Tsompana & Buck, 2014), we interrogated the ATAC-seq data of TCGA samples as a surrogate marker of vtRNA expression (Corces et al., 2018). Although DNA methylation is a less direct and less accurate measurement of chromatin accessibility compared to ATAC-seq, 25 times more TCGA samples have been analyzed by DNA Methylation Arrays, including matched normal tissues samples, thus this dataset is of great worth for the current study. Our analyses revealed that vtRNA1-1 has accessible chromatin and small variation in all the evaluated tissues, which is consistent with its identity as the ancestor vtRNA gene and its significance as the major RNA component of the ubiquitous vault particle (Stadler et al., 2009; van Zon et al., 2001). In addition, vtRNA1-2, vtRNA1-3 and vtRNA2-1 have lower chromatin accessibility at their promoters and a larger variation among the samples. As expected, the average DNA methylation assessed by microarrays is negatively correlated with the chromatin accessibility assessed by ATAC-seq. Therefore, the landscape of vtRNA chromatin status was corroborated by both approaches. Yet, the low chromatin accessibility of vtRNA1-3 promoter is not reflected by a concomitant high DNA methylation, suggesting that additional regulatory features of this gene, acting in trans or cis, play a major influence in its chromatin structure. As was reported by Helbo et al. using NOMe-seq assay (Nucleosome Positioning), the chromatin at vtRNA1-3 may be poised for transcription, and still require TFs to achieve physiological levels of transcription (Helbo et al., 2017).\n\nThe relative abundance of the four vtRNAs determined in the current study has been previously observed in various cell lines, including H157, H1299, CRL2741, WI-38 and NTera-2 (Lee et al., 2011), HSC CD34+, HL60 (Helbo et al., 2015), T24, colorectal RKO, human diploid fibroblasts IMR90 (Helbo et al., 2017) and MCF7 (Chen et al., 2018). Yet, others found different comparative levels of the vtRNAs in MCF7, SW1573, GLC4, 8226, KB, SW620, MCF-7, HeLa, HEK-293 and L88/5 (van Zon et al., 2001), CBL, BL2 and BL41 (Nandy et al., 2009), EBV-negative Burkitt's lymphoma cell lines and A549 (Li et al., 2015) and in LNCaP, PC3, DU145, RWPE-1, HEK, HeLa and MCF-7 (Stadler et al., 2009) cell lines, suggesting that the expression of vtRNAs may differ in laboratory cell lines compared to tissues. Alternatively, the methods used to quantify the vtRNAs are not comparable among the studies.\n\nSeeking to investigate regulatory connections between the vtRNAs as a valuable tool to study their function, we determine the pairwise correlations between the promoters of the vtRNAs. The positive correlations found are compatible with a coordinated transcriptional control of the vtRNAs, that is greater for the three members of the vtRNA1 cluster (specially vtRNA1-1 and vtRNA1-3). The exception is the pair vtRNA1-2 and vtRNA2-1, whose chromatin accessibility and promoter methylation are not linked in the cohort and can be indeed negatively associated.\n\nAs an alternative approach to investigate the vtRNA transcriptional co-regulation, we analyzed transcription and chromatin remodeling factors associated with their proximal promoter region. In agreement with their higher chromatin correlation, the vtRNA1 cluster have a larger core of common TFs (39) in comparison with vtRNA2-1 (23 TFs). The divergence of the transcriptional control of vtRNA2-1 was previously recognized given its unique regulatory elements and the complex developmental methylation it undergoes (Canella et al., 2010; Carpenter et al., 2018; Helbo et al., 2017; Nandy et al., 2009). Remarkably, the 23 TFs common to all vtRNAs are related to viral infections and cancer. The upregulation of the four vtRNAs upon viral infection has been reported for several viruses, so it is possible that this core of TFs participate in the coordinated expression of vtRNA during viral infection and related responses (Amort et al., 2015; Li et al., 2015; Nandy et al., 2009). These TFs regulate cell cycle and translational arrest as well as the inhibition of host innate immune response (Attar & Kurdistani, 2017; Ertosun et al., 2016; Horsley & Pavlath, 2002; Jean et al., 2000; Persengiev & Green, 2003; Rohini et al., 2018). Since these processes are also hallmarks of cancer, the dysregulation of the normal function of vtRNAs in viral response may provide a selective advantage for cancer cell to overcome the many sources of stress faced during neoplastic evolution. If that holds true, the core vtRNA TFs may be co-opted in the malignant context to tune vtRNA expression favoring tumor progression. In agreement with that hypothesis, ATF1 and ATF3 were associated with CREB response and increased cell viability (Persengiev & Green, 2003). Likewise, Golec et al. showed that altered levels of vtRNA2-1 modulate PKR activation and consequently altered the levels of CREB phosphorylation during T cell activation, which is a prerequisite for IFN-g activity (Golec et al., 2019). Furthermore, E2F1, a cell cycle regulator, was described as a direct transcriptional regulator of vtRNA2-1 in cervical cancer cells (Li et al., 2017). Moreover, it was shown that MYC binding to vtRNA2-1 promoter raises its expression and could be the explanation for the increased levels of vtRNA2-1 in some tumors (Park et al., 2017a). Similarly, TGFB1 provokes the demethylation of vtRNA2-1 promoter and consequently increases its expression in ovarian cancer (Ahn et al., 2018).\n\nDue to its importance for cancer biology, vtRNA2-1 transcriptional regulation was recently more investigated (Yeganeh & Hernandez, 2020). Various studies reported tissue specific roles of vtRNA2-1 in normal (Golec et al., 2019; Lee et al., 2019; Miñones-Moyano et al., 2013; Sallustio et al., 2016; Suojalehto et al., 2014) and cancer tissues (Ahn et al., 2018; Fort et al., 2018; Hu et al., 2017; Im et al., 2020; Jeon et al., 2012a; Kunkeaw et al., 2012; Lee et al., 2011; Lee, 2015; Lee et al., 2016; Lee et al., 2014a; Lee et al., 2014b; Lei et al., 2017; Li et al., 2017; Ma et al., 2020; Treppendahl et al., 2012) and epigenetic alterations of the locus have been described in different malignancies (Ahn et al., 2018; Cao et al., 2013; Fort et al., 2018; Helbo et al., 2015; Helbo et al., 2017; Joo et al., 2018; Lee et al., 2014a; Lee et al., 2014b; Park et al., 2017a; Romanelli et al., 2014; Treppendahl et al., 2012). Meanwhile, except for Kirsten Grønbæk group´s contributions on the chromatin characterization of vtRNA1-3 and vtRNA1-2 promoters (Helbo et al., 2015; Helbo et al., 2017), little is known about the transcriptional regulation and expression of the other vtRNAs. Likewise, to our knowledge, the global landscape of vtRNA expression across different cancer types has not been investigated. Our study shows that, except for vtRNA1-1, which has a high promoter chromatin accessibility and low DNA methylation in all the tissues, the other vtRNA promoters exhibit different levels of chromatin accessibility and DNA methylation among the tissue types. The relative status of the chromatin in different tissues is accurately mirrored by both approaches in the tissues examined by ATAC-seq and Illumina DNA methylation arrays. Interestingly, the same analysis performed in the normal tissue samples reveals that the tissue specific variation in DNA methylation of vtRNA promoters in the neoplastic tissues is already established in their normal tissue counterparts, indicating that the regulation of vtRNA expression is tuned during normal development and cell differentiation.\n\nWhile there is no apparent concerted modulation of the chromatin accessibility of the vtRNA promoters in most tissues, ACC and LGG tumors seem to be the exception. Concordantly, a global hypomethylation of malignant ACC tumors (Legendre et al., 2016; Rechache et al., 2012), and an aberrantly methylation processes associated to altered DNMTs activity in LGG tumors were reported (Nomura et al., 2019). However, more research is necessary to understand the molecular basis of these observations.\n\nThe differential expression of the vtRNAs from normal to primary tumor tissues revealed different patterns depending on tissue origin. The average DNA methylation of the vtRNA1-1 and vtRNA1-3 promoters is not significantly deregulated, whereas vtRNA1-2 and vtRNA2-1 are decreased and increased respectively in tumor tissues. The latter finding favors a candidate OG and TSG function of vtRNA1-2 and vtRNA2-1 in cancer, respectively. Indeed, the epigenetic repression of vtRNA2-1 was previously reported by Romanelli et al. in BLCA, BRCA, COAD and LUSC analyzing the same data from TCGA (Romanelli et al., 2014). Furthermore, functional studies in LUSC, PRAD, ESCA and AML provided experimental support to that hypothesis (Cao et al., 2013; Fort et al., 2018; Lee et al., 2014a; Treppendahl et al., 2012). Yet, vtRNA2-1 has been also proposed as an OG in ovarian, thyroid, endometrial, cervical and renal cancer (Ahn et al., 2018; Hu et al., 2017; Lee et al., 2016; Lei et al., 2017; Li et al., 2017; Yeganeh & Hernandez, 2020). In agreement with the functional data found by Lei et al. (Lei et al., 2017), we found an epigenetic de-repression of vtRNA2-1 promoter DNA methylation in renal carcinoma (KIRP). Likewise, a closer look at THCA samples, shows an average decrease in the DNA methylation of vtRNA2-1 promoter that supports the OG function described in this tissue (Lee et al., 2016). Unfortunately, normal ovarian, cervical and endometrial tissues are not available at the TCGA. Finally, vtRNA1-2 has an oncogenic pattern of inferred expression between normal and tumor tissues for 13 of 16 tissues analyzed, raising a possible oncogenic function for this RNA.\n\nOur study found also an association of DNA methylation at the promoter with a shorter overall survival for vtRNA1-1, vtRNA1-2 and vtRNA2-1. This is surprising for vtRNA2-1, since it has both TSG and OG roles and TSG compatible expression profiles in three cancer types, inferred by DNA methylation of its promoter in tumor vs normal tissues and the average promoter DNA methylation is increased in tumor compared to normal tissue. A higher impact of vtRNA2-1 expression in patient survival in the oncogenic context may justify this discrepancy. On the contrary, the association between vtRNA1-2 low promoter DNA methylation and low patient survival is in agreement with its OG expression in cancer. The lack of survival association with the ATAC-seq values may be due to the small number of patients studied by this approach.\n\nVtRNA expression in individual cancer types, inferred from the epigenetic status of their promoters, has been associated with patient survival in several studies of vtRNA2-1, one of vtRNA1-3 and none for vtRNA1-1 or vtRNA1-2. Low methylation or high expression of vtRNA2-1 promoter were associated with good prognosis or overall survival in lung (Cao et al., 2013), esophageal (Lee et al., 2014a), prostate (Fort et al., 2018), AML (Treppendahl et al., 2012), gastric (Lee et al., 2014b) and liver (Yu et al., 2020). Conversely, a worse prognosis or overall survival association of vtRNA2-1 was reported in thyroid (Lee et al., 2016) and ovarian (Ahn et al., 2018). From these reports, only prostate (Fort et al., 2018) and gastric (Lee et al., 2014b) studies used the TCGA data. Likewise, the methylation status of the vtRNA1-3 promoter associates with overall survival in the lower risk Myelodysplastic Syndrome patients (Helbo et al., 2015). Additionally, vtRNA1-1 and vtRNA1-2 correlate to chemotherapeutic resistance by direct interaction with drugs (doxorubicin, etoposide and mitoxantrone) and the modulation of vtRNA1-1 confirmed this finding in osteosarcoma cell lines (Gopinath et al., 2005; Gopinath et al., 2010; Mashima et al., 2008; van Zon et al., 2001). Furthermore, increased levels of vtRNA1-1 were associated with increased proliferation and chemoresistance due to GAGE6 induction in MCF-7 cells (Chen et al., 2018). Besides, Norbert Polacek group showed that vtRNA1-1 expression confers apoptosis resistance in several human cell lines (BL2, BL41, HS578T, HEK293, A549 and HeLa) and revealed it capacity to repressed intrinsic and extrinsic apoptosis pathway (Amort et al., 2015; Bracher et al., 2020). The later findings are in agreement with the lower patient survival associated with high levels of vtRNA1-1 expression cancer-wide observed in our analysis.\n\nSeeking to get insights into the cancer related function of the vtRNAs we performed a genome wide search for genes co-regulated at the level of promoter chromatin accessibility. Remarkably, we identified immune and cytokine related terms for the genes co-regulated with vtRNA2-1. This association agrees with its proposed roles in innate immune modulation via PKR repression or OAS1 regulation and in cytokine production (Calderon & Conn, 2018; Golec et al., 2019; Lee et al., 2020; Li et al., 2015). Furthermore, vtRNA2-1 has been associated with autoimmune disorders (Renauer et al., 2015; Weeding & Sawalha, 2018) and tumor engraftment in prostate cancer (Ma et al., 2020). This enrichment in viral infection pathways, together with the viral infection involvement of the core TFs common to all vtRNAs, reinforces the hypothesis of the re-utilization of a regulatory RNA induced upon viral response in favor of cancer development at upstream and downstream regulatory steps. Additionally, we found a non-random clustering localization at chromosome arm 5q for genes co-regulated with vtRNA1-1. The chromosome arm 5q and regions chr5q31 and chr5q32-q33 were found frequently deleted in myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML) (Fuchs, 2012; Treppendahl et al., 2012). Furthermore, the modulation of vtRNA2-1 and vtRNA1-3 was previously associated with human bone marrow CD34+ cells, AML and MDS (Helbo et al., 2015; Treppendahl et al., 2012). Yet, our analysis points to vtRNA2-1 and vtRNA1-2, and to a lesser extent to vtRNA1-1 and vtRNA1-3, as the most relevant drivers across cancer types.\n\nSupport for the involvement of the vtRNAs in the immune responses in the context of cancer came from the association of their chromatin status with the immune subtype categories defined by Thorsson et al. (Thorsson et al., 2018). Our findings suggest a possible role of the vtRNAs in lymphocyte response in tumor samples, since the immunologically quiet subtype shows the lowest leukocyte fraction and vtRNAs promoter chromatin accessibility (Thorsson et al., 2018). Meanwhile, the vtRNA2-1 and vtRNA1-2 expression distinguishes two groups among the remaining four subtypes. The participation of vtRNA2-1 in the induction of the IFN-g and IL-2 expression in activated T cells through PKR modulation (Golec et al., 2019) goes in agreement with this hypothesis. Although the same study demonstrated that vtRNA1-1 expression was unchanged during T cell activation, it is remarkable that the 5q31-q33 region, comprising the vtRNA1 locus and chromatin co-regulated genes, encodes several cytokines that regulate the differentiation of Th1 and Th2 lymphocytes and has been linked with susceptibility to infections (Jeronimo et al., 2007; Lacy et al., 2000; Naka et al., 2009; Rodrigues et al., 1999). Furthermore, vtRNA2-1 levels were recently associated with macrophages M1/M2 fates in prostate PC3 cell line mice xenografts via TGF-b (Ma et al., 2020), two pathways that define the six immune subtypes (Thorsson et al., 2018). Finally, we found that the proliferation rate and wound healing of the tumors are associated with the levels of vtRNA1-2 chromatin accessibility, which reinforces an OG role of vtRNA1-2 in cancer. Nonetheless, the participation of the vtRNAs in immune cells response inside the neoplastic niche needs to be further investigated.\n\n\nConclusion\n\nTaken together our analysis reveals the pattern of chromatin accessibility and DNA methylation at the four vtRNA promoters, analyzed by tissue of origin in the TCGA cohort. The agreement between both dataset and previous related literature endorses the use of these variables as surrogates of the vtRNA transcripts expression. The four vtRNAs seem to be co-regulated at the transcriptional level, and TFs involved in viral infection are likely to take part in their coordinated transcription. The pattern of expression in normal vs tumor tissue and the association with cancer cell pathways and patient survival suggest that vtRNA2-1 and vtRNA1-2 are possibly the more relevant contributors to cancer. The results favor tissue specific TSG and OG roles for vtRNA2-1, a still not investigated oncogenic role of vtRNA1-2 and a limited cancer driver effect of vtRNA1-1/3 in specific tissue types. Lastly, we uncovered new evidence linking the vtRNAs with the immune response, cell proliferation and overall survival in cancer, which guarantees further investigation.\n\n\nData availability\n\nAll raw data used in this study can be downloaded from Xena Browser, a tool to explore functional genomic data sets (Goldman et al., 2020) (https://xenabrowser.net/), and UCSC genome browser (Kent et al., 2002) (https://genome.ucsc.edu/).\n\nZenodo: Pan-Cancer chromatin analysis of the human vtRNA genes - Supplementary Figures, http://doi.org/10.5281/zenodo.4501382 (Fort & Duhagon, 2021a)\n\nThis project contains the following extended data:\n\nFigure S1. Data type and tissue sample distribution. Sample distribution per tissue type in the ATAC-seq, DNA methylation, ATAC-seq & DNA methylation and Normal adjacent tissue sample groups. A. Number of samples. B. Percentage of samples. The color reference, the number of samples of this tissue and the accounted percentage are presented to each tissue. Names references: ACC (Adrenocortical carcinoma), BLCA (Bladder Urothelial Carcinoma), BRCA (Breast invasive carcinoma), CESC (Cervical squamous cell carcinoma and endocervical adenocarcinoma), CHOL (Cholangiocarcinoma), COAD (Colon adenocarcinoma), DLBC (Lymphoid Neoplasm Diffuse Large B-cell Lymphoma), ESCA (Esophageal carcinoma), GBM (Glioblastoma multiforme), HNSC (Head and Neck squamous cell carcinoma), KICH (Kidney Chromophobe), KIRC (Kidney renal clear cell carcinoma), KIRP (Kidney renal papillary cell carcinoma), LGG (Brain Lower Grade Glioma), LIHC (Liver hepatocellular carcinoma), LUAD (Lung adenocarcinoma), LUSC (Lung squamous cell carcinoma), MESO (Mesothelioma), OV (Ovarian serous cystadenocarcinoma), PAAD (Pancreatic adenocarcinoma), PCPG (Pheochromocytoma and Paraganglioma), PRAD (Prostate adenocarcinoma), READ (Rectum adenocarcinoma), SARC (Sarcoma), SKCM (Skin Cutaneous Melanoma), STAD (Stomach adenocarcinoma), TGCT (Testicular Germ Cell Tumors), THCA (Thyroid carcinoma), THYM (Thymoma), UCEC (Uterine Corpus Endometrial Carcinoma), UCS (Uterine Carcinosarcoma) and UVM (Uveal Melanoma).\n\nFigure S2. Correlation between ATAC-seq values and promoter methylation values of vtRNAs in Pan-Cancer TCGA dataset. A–D. The correlation between ATAC-seq and DNA methylation average normalized beta values was calculated for vtRNAs (vtRNAs1-1 (A), vtRNA1-2 (B), vtRNA1-3 (C) and vtRNA2-1 (D)), in 329 primary tumors samples. The box plots show the median line and lower and upper quartile and the whiskers the 2.5 and 97.5 percentile. Horizontal grey striped and red dotted lines are shown to denote unmethylated (average beta-value ≤ 0.2), 50% methylated (average beta-value = 0.5) and highly methylated (average beta-value ≥ 0.8) levels. Spearman correlation value and the best-fit line (red line) with 95% confidence bands (black dot lines) are shown.\n\nFigure S3. Genomic context and chromatin accessibility of human vtRNA3-1P. Genomic view of the 1.5 kb region of human vtRNA3-1P gene in UCSC Genome browser (GRCh37/hg19) centered at the 500bp of the ATAC-seq. Highlighted in yellow is the 500 bp ATAC-seq region used in the posterior analyses. The following Gene annotation and ENCODE Project tracks for seven cell lines (GM12878, H1-hESC, HSMM, HUVEC, K562, NHEK, NHL) are displayed: DNA accessibility (DNaseI hypersensitivity clusters (color intensity is proportional to the maximum signal strength)), DNA methylation (CpG islands length greater than 200 bp), histone modification (H3K27Ac, H3K4me1, H3K4me3 marks), conservation of the region in 100 Vertebrates (log-odds Phylop scores). The vertical viewing range of the tracks displays the default settings of the browser for each variable. B. The distribution of (ATAC-seq) values for vtRNA3-1P in PANCAN TCGA dataset (385 tumors samples across 23 cancer types) expressed as log2 normalized values. The box plots show the median and the lower and upper quartile, and the whiskers the 2.5 and 97.5 percentile of the distribution. C. ATAC-seq values for vtRNA3-1P in 21 different tumors with at least 5 tumor samples present in Pan-Cancer TCGA dataset (385 tumors samples) expressed as log2 normalized values. The chart shows the average and standard error for each vtRNAs in each tumor type.\n\nFigure S4. VtRNA promoter’s chromatin accessibility (ATAC-seq and DNA methylation) average values for tumor tissues from Pan-Cancer TCGA dataset. The average vtRNA promoters ATAC-seq and DNA methylation values for each primary tumor tissue type (21 tissues). VtRNA1-1 (A), vtRNA1-2 (B), vtRNA1-3 (C) and vtRNA2-1 (D). The Spearman correlation between averages ATAC-seq and DNA methylation values was calculated for each vtRNA. The chart shows the average and standard deviation for each tissue with at least five samples available at Pan-Cancer TCGA.\n\nFigure S5. VtRNA promoter’s DNA methylation for normal and tumor tissues from Pan-Cancer TCGA dataset. The average promoter DNA methylation beta-values of normal adjacent (Normal) and primary tumor (Tumor) tissues (16 tissue types) for vtRNA1-1 (A), vtRNA1-2 (B), vtRNA1-3 (C) and vtRNA2-1 (D) is shown. The Spearman (r) correlation between normal and tumor values was calculated. The chart shows the average and standard deviation for each tissue with at least five samples available at Pan-Cancer TCGA.\n\nZenodo: Pan-Cancer chromatin analysis of the human vtRNA genes - Supplementary Tables, http://doi.org/10.5281/zenodo.4501399 (Fort & Duhagon, 2021b)\n\nThis project contains the following extended data:\n\nTables S1–S5. ATAC-seq and DNA methylation data for vtRNA promoters in primary tumors and normal adjacent tissues. CSV spreadsheets: Table_S1_ATAC-seq_data_500bp: All ATAC-seq data of vtRNAs promoter (500bp) data for primary tumor samples; Table_S2_DNA_methylation_500bp: All DNA methylation data and ATAC-seq data of vtRNAs promoter (500bp) data for total primary tumor and normal adjacent samples; Table_S3_DNA_methylation_NORMAL: All DNA methylation data of vtRNAs promoter (500bp) data for normal adjacent samples; Table_S4_DNA_methylation_TUMOR: All DNA methylation data of vtRNAs promoter (500bp) data for primary tumor samples; Table_S5_Normal_&_Tumor_matched: All DNA methylation data of vtRNAs promoter (500bp) data for primary tumor and normal adjacent samples.\n\nTable S6. VtRNAs Transcription Factor Binding and KEEG enriched terms. CSV spreadsheets: Table_S6_Binding_Factors: Transcription factors identified in the cell line K562 as ChIP-seq Peaks by ENCODE 3 project and KEEG_terms: enriched KEGG pathway terms (FDR < 0.05).\n\nTables S7–S8. DNA methylation, ATAC-seq data and associated survival data for primary tumors. CSV spreadsheets: Table_S7_DNA-methylation_Survival_data: All DNA methylation data of vtRNAs promoter (500bp) and survival data for primary tumor samples; Table_S8_ATAC-seq_Survival_data: ATAC-seq data of vtRNAs promoter (500bp) and survival data for primary tumor samples.\n\nTables S9–S10. Correlation of ATAC-seq values between vtRNA and all genome promoters in primary tumor samples. CSV spreadsheets: Table_S9_ATAC-seq_gene_promoter_spearman_correlation: Spearman correlation values of all promoter genes and vtRNAs in primary tumors samples; Table_S10_vtRNAs_pathway_enrichment_and_cluster_chromosome_localization_analysis: vtRNAs vtRNA1-1, vtRNA1-2, vtRNA1-3 and vtRNA2-1 pathway enrichment and cluster chromosome localization data.\n\nTables S11–S14. ATAC-seq and DNA methylation data for vtRNA promoters in primary tumors and the associated Immune Subtypes data. CSV spreadsheets: Table_S11_Immune_Subtypes_DNA_methylation_data: All DNA methylation data of vtRNAs promoter (500bp) and Immune Subtypes data for primary tumor samples; Table_S12_Spearman_corr_vtRNAs_Immune_Subtypes_DNA_methylation_data: Spearman correlation values of DNA methylation data of vtRNAs promoter (500bp) and Immune Subtypes data for primary tumor samples; Table_S13_Immune_Subtypes_ATAC-seq_data: All ATAC-seq data of vtRNAs promoter (500bp) and Immune Subtypes data for primary tumor samples; Table_S14_Spearman_corr_vtRNAs_Immune_Subtypes_ATAC-seq_data: Spearman correlation values of ATAC-seq data of vtRNAs promoter (500bp) and Immune Subtypes data for primary tumor samples.\n\nData are available under the terms of the Creative Commons Zero \"No rights reserved\" data waiver (CC0 1.0 Public domain dedication).",
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Nat Rev Genet. 2019; 20(4): 207–220. PubMed Abstract | Publisher Full Text\n\nKuleshov MV, Jones MR, Rouillard AD, et al.: Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. Nucleic Acids Res. 2016; 44(W1): W90–W97. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKunkeaw N, Jeon SH, Lee K, et al.: Cell death/proliferation roles for nc886, a non-coding RNA, in the protein kinase R pathway in cholangiocarcinoma. Oncogene. 2012; 32(32): 3722–3731. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKunkeaw N, Lee YS, Im WR, et al.: Mechanism mediated by a noncoding RNA, nc886, in the cytotoxicity of a DNA-reactive compound. Proc Natl Acad Sci U S A. 2019; 116(17): 8289–8294. PubMed Abstract | Publisher Full Text | Free Full Text\n\nŁabno A, Warkocki Z, Kulinski T, et al.: Perlman syndrome nuclease DIS3L2 controls cytoplasmic non-coding RNAs and provides surveillance pathway for maturing snRNAs. Nucleic Acids Res. 2016; 44(21): 10437–10453. 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}
|
[
{
"id": "82633",
"date": "14 Apr 2021",
"name": "Daniele Hasler",
"expertise": [
"Reviewer Expertise RNA biology"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe study by Fort and Duhagon estimates the expression of a class of non-coding (nc)RNAs termed 'vault RNAs' (vtRNAs) across different cancer types. Since vtRNAs might be underrepresented applying conventional RNA sequencing techniques, the authors infer vtRNAs expression by analyzing chromatin characteristics at promoter regions of vtRNA genes. In more detail, Fort and Duhagon use genome-wide chromatin accessibility data (ATAC-seq) as well as DNA methylation data sets from The Cancer Genome Atlas (TCGA) consortium to provide a comprehensive comparison between the four annotated vtRNA genes. By this approach, the authors determine the correlation between chromatin accessibility and DNA methylation of vtRNA promoters and compare their chromatin characteristics across different cancer types. Furthermore, Fort and Duhagon use publically available CHIP-seq datasets originating from a leukemia cell line to determine transcription factors (TFs) binding to vtRNA genes and identify a set of 23 core TFs common to all vtRNAs which might govern chromatin accessibility at these genomic sites.\nFurther analyses of the TCGA DNA methylation data sets provide evidence for vtRNA-specific deregulation upon malignant transformation in specific cancer types, as well as lower patient survival probability associated with reduced vtRNA promoter methylation. Finally, the authors determine genes that are co-regulated with vtRNAs in terms of chromatin accessibility and the also profile chromatin accessibility and DNA methylation of vtRNA promoters in six immune subtypes of the pan-cancer TCGA datasets.\nVtRNAs are a class of ncRNAs with rather enigmatic functions, albeit they have been recently implicated in important cellular processes1,2 and in cancer biology[ref-]. The work by Fort and Duhagon is the first pan-cancer study focusing on vtRNAs and it provides a nice and comprehensive overview for the potential function of the single vtRNA transcripts as tumor suppressors or oncogenes in specific cancer types.\nThe manuscript is well written, although some aspects could have been presented a bit more concisely. In particular, the authors dedicate special emphasis to the relative comparison between vtRNA genes (e.g. Figures 3A and 3B and result section related to Figures 4 and 8). The question arises whether a key message of the study is that specific vtRNA genes are up- or down-regulated in certain cancer conditions or whether a key point is that the relative expression levels of the four vtRNA genes are altered. If so, the authors should propose a model in the discussion section.\n\nAdditional major points:\nThe major limitation of this study is that vtRNA expression was not analyzed directly but was inferred from chromatin accessibility data (ATAC-seq) as well as DNA methylation data. Nevertheless, the authors honestly point out this limitation and provide convincing evidences from literature that support the validity of their study. Taken together, this approach sounds reasonable. Nevertheless, the findings could be further strengthened by analyzing TCGA miRNA-seq datasets for the expression of vtRNA-derived small RNA fragments. This strategy has been applied in previous studies to infer the expression of snoRNAs4 and tRNAs5 across different cancer types, assuming that small processing products correlate with expression levels of the full-length transcripts. Indeed snoRNAs and in particular tRNAs are ncRNA with similar sequencing biases as vtRNAs.\nFurthermore, since a small RNA derived from vtRNA-2-1 has been linked to different cancers (see references within the manuscript), this additional pan-cancer analysis would be informative not only concerning this specific fragment but might also uncover the relevance of additional vtRNA-derived small RNAs.\nThe analysis of TF occupancy at vtRNA loci is, in my opinion, rather speculative and vague. Since vtRNAs are transcribed by RNA polymerase III (pol III), is there any clear and direct evidence from literature that the identified TFs regulate Pol III activity (except for the TFIIIA, TFIIIB and TFIIIC complexes)? Could the binding of these TFs rather regulate transcription of adjacent RNA polymerase II genes and not of vtRNAs? The authors might at least briefly touch these aspects in the discussion.\nIt would be also worth to determine whether deregulation (e.g. of any of the 9 vtRNA1-2-specific TFs or any of the 4 vtRNA2-1-specific TFs) correlates with the changes of vtRNA promoter DNA methylation in normal vs tumor samples (Figure 6). This would be more informative than the current conclusions concerning shared TFs between vtRNA loci and their co-regulated expression. Indeed, this analysis might help to understand, e.g., how the expression of a single vtRNA locus is regulated within the vtRNA1 cluster.\nInterestingly, the chromatin profile of vtRNAs in brain lower grade glioma (LGG) indicates that vtRNA expression is strongly reduced in this condition. Does this effect hold true also for other classes of pol III transcripts (e.g. Y RNAs)? If so, this finding might point towards a general reduction of pol III activity in LGG.\nMinor points:\nThe authors should reformulate their statement in the introduction “VtRNA2-1 has also been shown to act as a microRNA precursor”, as the vtRNA2-1-derived fragment was not convincingly proven to be a bona fide microRNA and the hsa-miR-886 entry has been retracted in the current miRBase release 22.16.\nPlease correct the typo on page 3 replacing “TGFB1” by “TGFBI”; i.e. Transforming Growth Factor Beta Induced (TGFBI) and not Transforming Growth Factor Beta 1 (TGF1).\nSince lower patient survival of cancer patients was associated with lower vtRNA promoter methylation and not with higher promoter accessibility, the paragraph “High chromatin accessibility at the promoter of vtRNA1-1, vtRNA1-2 and vtRNA2-1 is associated with low patient overall survival” should be renamed. In light of the statement “DNA methylation is a less direct and less accurate measurement of chromatin accessibility compared to ATAC-seq” (page 16), it is questionable whether the relationship between DNA methylation and patient survival is due to increased vtRNA expression, as a similar result would be expected also from the analysis of the ATAC-seq data. Is this simply due to a larger samples size of the DNA methylation dataset?\nThe authors do not mention that a pseudogene of vtRNA2-1 (vtRNA2-2P) has been annotated at chr2:65,555,432-65,555,534. Is there any reason for that? VtRNA2-2P could be included as proof of concept similarly to vtRNA3-1P on page 8.\nPage 3: “…the presence of silencing mutations at the B box element of its promoter B-box”. Since the organization of RNA polymerase III promoters has not been explained before, it would be better to keep this statement more general without mentioning the B-box.\nThe abbreviation “PANCAN” in the title of the legend to Figure 8 was not used before in the text.\nI am not sure whether the term “chromatin polymorphism” on page 10 is correct. The referenced publication refers to epigenetic variations.\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": [
{
"c_id": "6807",
"date": "16 Jun 2021",
"name": "Maria Ana Duhagon",
"role": "Author Response",
"response": "Reviewer: Daniele Hasler, Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, Regensburg, Germany. Reviewers’ comment: The study by Fort and Duhagon estimates the expression of a class of non-coding (nc)RNAs termed 'vault RNAs' (vtRNAs) across different cancer types. Since vtRNAs might be underrepresented applying conventional RNA sequencing techniques, the authors infer vtRNAs expression by analyzing chromatin characteristics at promoter regions of vtRNA genes. In more detail, Fort and Duhagon use genome-wide chromatin accessibility data (ATAC-seq) as well as DNA methylation data sets from The Cancer Genome Atlas (TCGA) consortium to provide a comprehensive comparison between the four annotated vtRNA genes. By this approach, the authors determine the correlation between chromatin accessibility and DNA methylation of vtRNA promoters and compare their chromatin characteristics across different cancer types. Furthermore, Fort and Duhagon use publically available CHIP-seq datasets originating from a leukemia cell line to determine transcription factors (TFs) binding to vtRNA genes and identify a set of 23 core TFs common to all vtRNAs which might govern chromatin accessibility at these genomic sites. Further analyses of the TCGA DNA methylation data sets provide evidence for vtRNA-specific deregulation upon malignant transformation in specific cancer types, as well as lower patient survival probability associated with reduced vtRNA promoter methylation. Finally, the authors determine genes that are co-regulated with vtRNAs in terms of chromatin accessibility and the also profile chromatin accessibility and DNA methylation of vtRNA promoters in six immune subtypes of the pan-cancer TCGA datasets. VtRNAs are a class of ncRNAs with rather enigmatic functions, albeit they have been recently implicated in important cellular processes1,2 and in cancer biology[ref-]. The work by Fort and Duhagon is the first pan-cancer study focusing on vtRNAs and it provides a nice and comprehensive overview for the potential function of the single vtRNA transcripts as tumor suppressors or oncogenes in specific cancer types. The manuscript is well written, although some aspects could have been presented a bit more concisely. In particular, the authors dedicate special emphasis to the relative comparison between vtRNA genes (e.g. Figures 3A and 3B and result section related to Figures 4 and 8). The question arises whether a key message of the study is that specific vtRNA genes are up- or down-regulated in certain cancer conditions or whether a key point is that the relative expression levels of the four vtRNA genes are altered. If so, the authors should propose a model in the discussion section. Authors response: We are grateful for the evaluation of our manuscript entitled “Pan-Cancer chromatin analysis of the human vtRNA genes uncovers their association with cancer biology”, since we find these constructive comments rather pertinent and valuable. We tried to answer all the points raised by the Reviewer and hope it led us to the improved of the manuscript. It is true that the article is long. We believe the length is justified by the type of information it provides. In particular, the description of the patterns of vtRNA inferred expression involves four genes in 20 cancer types assessed by two methods, plus normal tissues data for DNA methylation. We think that the message of the study is fairly written in the abstract and conclusion, neither of which prioritize the inferred relative expression of the vtRNAs per se, but what in the inferred expression pattern is suggestive of the involvement of the four genes in cancer. The article aimed to use the chromatin status of the genes to withdraw their candidate roles in cancer tissue. In our view the figures mentioned by the Reviewer are about their pattern of expression in cancer and immune subtypes, regulation, and the derived functional implications of those findings. Nevertheless, the narrative requires a description of their relative abundance and change, while their comparison helps to visualize how different they are expressed and the implication for their function in normal and tumor tissue. Additional major points: Reviewers’ comment: The major limitation of this study is that vtRNA expression was not analyzed directly but was inferred from chromatin accessibility data (ATAC-seq) as well as DNA methylation data. Nevertheless, the authors honestly point out this limitation and provide convincing evidences from literature that support the validity of their study. Taken together, this approach sounds reasonable. Nevertheless, the findings could be further strengthened by analyzing TCGA miRNA-seq datasets for the expression of vtRNA-derived small RNA fragments. This strategy has been applied in previous studies to infer the expression of snoRNAs4 and tRNAs5 across different cancer types, assuming that small processing products correlate with expression levels of the full-length transcripts. Indeed snoRNAs and in particular tRNAs are ncRNA with similar sequencing biases as vtRNAs. Authors response: We agree the small RNA sequencing analysis proposed by the Reviewer would be valuable to provide further support for the expression of the vtRNAs inferred from the chromatin status. Indeed, we have done it previously while studying snc886-3p, a microRNA-like RNA derived from vtRNA2-1 (published in Fort et al., 2020). There we showed that nc886 and snc886-3p expression (determined by qRT-PCR) negatively correlate with DNA methylation in six PrCa cell lines analyzed (r Spearman -0.71). Nevertheless, since vtRNAs derived fragments are not quantified with the TCGA small RNA workflow, we need to request access to protected controlled-access data - primary sequencing data (BAM or FASTQ files) to identify them. We understand that this approach and the subsequent data analyses exceed the extent of the current manuscript. Attempting to follow the Reviewer’s recommendation using readily available data, we analyzed the NCI-60 cell lines panel, whose genome DNA methylation and small RNA-seq data is published. Indeed, the 4 vtRNA are known to be subject to posttranscriptional processing at some extent (Hussain et al., 2013; Sajini et al., 2019). We found that vtRNA2-1 produces more specific small RNAs than the other three vtRNAs, thus arguing in favor of a specialization of vtRNA2-1 as a Dicer substrate, which may explain the better correlation between the precursor and the small RNAs derived from it (see Panel A of the figure attached to this response; Figure_reviewer_response-I. Zenodo. http://doi.org/10.5281/zenodo.4784690). In addition, vtRNA2-1 generates more than 30 times small RNAs that the other vtRNAs (see Panel B of the figure attached to this response). As anticipated, the expression of the small RNA fragments derived from vtRNA2-1 shows a better correlation with promoter methylation in the NCI-60 cell lines (r= -0.77). Meanwhile, the small RNAs derived from vtRNAs of cluster 1 are less abundant and less associated to promoter methylation (r= -0.19- -0.24) (see Panel C of the figure attached to this response). In addition, the average abundance of the small RNAs derived from the vtRNAs of cluster 1 correlates with the relative methylation of their promoters (small RNAs derived from vtRNA1-1> vtRNA1-2> vtRNA1-3 and promoter methylation vtRNA1-1< vtRNA1-2< vtRNA1-3) (see Panel B of the figure attached to this response), in agreement with the TCGA data presented in our manuscript. Since small RNAs derived from vtRNA2-1 are more abundant than those derived from the other three vtRNAs, the relative expression of its fragments does not correlate with the relative DNA methylation of the others. In summary, the analysis of NCI-60 cell lines, a panel comprising all tissue types, confirms that the abundance of the small RNAs derived from vtRNAs negatively correlates with their promoter methylation but indicated it may be useful just for vtRNA2-1. The latter, together with the low abundance of the small RNAs derived from the vtRNAs and their processing (Hussain et al., 2013; Sajini et al., 2019), suggest that the abundance of small RNAs in the TCGA small RNA-seq data may not be a good proxy for vtRNA expression. As discussed above, the post-transcriptional regulation of vtRNA seems to represent an additional layer of complexity of vtRNA biology that includes the processing into small RNAs. We speculate that only some of the fragments derived from specific vtRNAs may have functional significance, but it is likely reached by mechanisms different from those in which their precursors vtRNAs participate. We believe small RNAs derived from vtRNA are an interesting subject of investigation, requiring an independent study, which incorporates the biological mechanism in which they play a part. Reviewers’ comment: Finally, in order to be more accurate about the limitation of the study mentioned by the Reviewer, we substituted the term “expression” for “chromatin status” or related terms when was appropriate. The analysis of TF occupancy at vtRNA loci is, in my opinion, rather speculative and vague. Since vtRNAs are transcribed by RNA polymerase III (pol III), is there any clear and direct evidence from literature that the identified TFs regulate Pol III activity (except for the TFIIIA, TFIIIB and TFIIIC complexes)? Could the binding of these TFs rather regulate transcription of adjacent RNA polymerase II genes and not of vtRNAs? The authors might at least briefly touch these aspects in the discussion. Authors response: We welcome the Reviewers comment since we had a similar concern about the significance of these observations. Yet, we reasoned that the identification of viral related transcription factors (TFs) near vtRNA genes was a provocative finding in the context of their involvement in viral infection and innate immune response. In addition, RNA Pol III (Pol III) has been linked to the innate immune response at different levels, thus it is tempting to speculate that the Pol III regulated genes are coordinately regulated by viral related TFs dependently or independently of RNA Pol II (Pol II) action. The identified TFs that are shared by the vtRNA (23 TFs) comprise TFs known to be part of the Pol III basal machinery (3/23), or to be direct (6/23) or indirect interactors (3/23) of Pol III machinery. This observation endorses their participation in the vtRNA genes transcription. There are no Pol II genes near or overlapping the vtRNA genes, thus this in an unlikely explanation for TF occupancy in the vicinity of the genes. Indeed, several lines of evidence have shown that Pol II and some of its specific TFs affect Pol III activity (White, 2011). The localization of the Pol II and its specific TFs (FOS, JUN, ETS1) near Pol III promoters (200bp upstream of TSS) in human cell lines, the global regulation by Pol II specific TFs (p53, MAF1, MYC, RB), the regulation of Pol III by Pol II activity, the sharing chromatin marks and the basal TFIIIB component TBP. The direct interaction between specific TFs and TFIIIB is also known to modulate Pol III transcription. It has been proposed that Pol II may assist RNA pol III activity by either binding, transcription, or stalling, contributing to make the chromatin more permissive for transcription by Pol III. Curiously, Raha et al demonstrated a reduction of the three vtRNAs of locus 1 after α-amanitin treatment and the co-localization of Pol III and Pol II near these genes (Raha et al., 2010). Additional evidence of the Pol II regulation of specific Pol III transcribed genes has been published, including tRNAs (mediated by MAF1 (Gerber et al., 2020), GAF1 (Rodríguez-López et al., 2020), U6 RNA (OCT1, SP1, STAF, reviewed in (Hirsch et al., 2000)) Alu elements (mediated by YY1, SP1, MEG2, FOS, EP300, AP-1, (Zhang et al., 2019 and references therein). Finally, the crosstalk between the two polymerases seems to be tissue and gene specific, suggesting that Pol II-Pol III crosstalk may be finer that previously envisioned. To amend the lack of discussion of this aspect we included the following sentence in the Discussion of the manuscript: “It is worth to mention that RNA polymerase II TFs clustered near TSS of RNA polymerase III transcripts could modulate occupancy and transcription rate of RNA polymerase III through RNA pol II activity (Campbell and White, 2014; Gerber et al., 2020; Raha et al., 2010; Zhang et al., 2019). Specifically, RNA polymerase II could assist chromatin opening, thus allowing accessibility of RNA polymerase III or its associated factors in the human genome (Raha et al., 2010).” Reviewers’ comment: It would be also worth to determine whether deregulation (e.g. of any of the 9 vtRNA1-2-specific TFs or any of the 4 vtRNA2-1-specific TFs) correlates with the changes of vtRNA promoter DNA methylation in normal vs tumor samples (Figure 6). This would be more informative than the current conclusions concerning shared TFs between vtRNA loci and their co-regulated expression. Indeed, this analysis might help to understand, e.g., how the expression of a single vtRNA locus is regulated within the vtRNA1 cluster. Authors response: Following the Reviewer´s suggestion, we determined the correlation between vtRNAs chromatin accessibility and the specific TFs associated with vtRNAs (Table attached to this revision, Table_TFs_Binding_Factors.csv Zenodo. http://doi.org/10.5281/zenodo.4784690), but we did not find significant associations. It is worth to recall that TF activity is strongly regulated at the post-transcription level, thus TF abundance may not be a good indicator of TF activity. It might be also reasoned that TFs may be poised in an inactive state, to turn active upon the proper signalling, which might well be a viral invasion or an immune system response mediator. Weather this TF DNA occupancy is relevant in cancer remains to be dilucidated. While reviewing the literature to respond to this point it came to our attention that there is a link between RNApol III and innate immune response (Graczyk et al., 2015), that could be an alternative explanation of the viral TF enrichment at the vicinity of vtRNAs. Therefore, we decided to introduce this phrase at the end of the discussion of this aspect: “Alternatively, since RNA polymerase III transcripts are involved in virus replication and immune response (Graczyk et al., 2015), it is possible that the TF bound to vtRNA vicinity are part of a global and not a vtRNA specific viral response.” In view of the above, in an attempt to reduce the conjectures derived from the TFs analysis we modified the abstract and the conclusion of the paper as explained below. Abstract: We substituted the sentence “Although the vtRNAs are co-regulated by transcription factors related to viral infection, vtRNA2-1 is the most independently regulated homologue.” for the following: “VtRNAs promoters are enriched in transcription factors related to viral infection. VtRNA2-1 is likely the most independently regulated homologue.” Conclusion: We substituted the sentence “The four vtRNAs seem to be co-regulated at the transcriptional level, and TFs involved in viral infection are likely to take part in their coordinated transcription.” for the following: “VtRNA genes are enriched in viral related TFs. The comparison of TFs and chromatin status of the vtRNAs suggest that vtRNA2-1 is likely the most independently regulated vtRNA locus.” Reviewers’ comment: Interestingly, the chromatin profile of vtRNAs in brain lower grade glioma (LGG) indicates that vtRNA expression is strongly reduced in this condition. Does this effect hold true also for other classes of pol III transcripts (e.g. Y RNAs)? If so, this finding might point towards a general reduction of pol III activity in LGG. Authors response: In order to answer the Reviewer, we determined the ATAC-seq chromatin accessibility of RNYs (RNY1, RNY3, RNY4 and RNY5). As seen in the new Supplementary Figure 3 and modified Supplementary Table 1, the RNYs showed a different chromatin accessibility profile within different tissues, among them and compared to vtRNAs. Interestingly, RNY3 and RNY4 show a conspicuously higher chromatin accessibility in LGG compared with other tissues, which is opposite to the lower accessibility observed for the vtRNAs These observations raise a possible RNA pol III misregulation in LGG tumors, which must be gene specific to justify opposite outcomes for RNAY and vtRNAs. The modified Supplementary Figure 3 and modified Supplementary Table 1 are now included in the manuscript. To incorporate these findings in the text, the following sentence was included the results section: “The same approach was performed for the Y-RNAs genes RNY1 (Ave. 3.7, 0.4 SD), RNY3 (Ave. 2.1, 0.6 SD, RNY4 (Ave. 1.9, 0.6 SD) and RNY5 (Ave. 3.1, 0.4 SD) (Canella et al., 2010), which code for produce ubiquitously expressed RNA polymerase III transcripts (Extended Data: Figure S3 and Tables S1).”. Minor points: Reviewers’ comment: The authors should reformulate their statement in the introduction “VtRNA2-1 has also been shown to act as a microRNA precursor”, as the vtRNA2-1-derived fragment was not convincingly proven to be a bona fide microRNA and the hsa-miR-886 entry has been retracted in the current miRBase release 22.16. Authors response: Following the advice, we modified the sentences related to small RNAs derived from vtRNA2-1. “VtRNA2-1 has also been shown to generate small RNAs that could act like microRNAs in different tissues,…”. Reviewers’ comment: Please correct the typo on page 3 replacing “TGFB1” by “TGFBI”; i.e. Transforming Growth Factor Beta Induced (TGFBI) and not Transforming Growth Factor Beta 1 (TGF1). Authors response: We are sorry for the mistake; we have corrected the name of the gene. Reviewers’ comment: Since lower patient survival of cancer patients was associated with lower vtRNA promoter methylation and not with higher promoter accessibility, the paragraph “High chromatin accessibility at the promoter of vtRNA1-1, vtRNA1-2 and vtRNA2-1 is associated with low patient overall survival” should be renamed. In light of the statement “DNA methylation is a less direct and less accurate measurement of chromatin accessibility compared to ATAC-seq” (page 16), it is questionable whether the relationship between DNA methylation and patient survival is due to increased vtRNA expression, as a similar result would be expected also from the analysis of the ATAC-seq data. Is this simply due to a larger samples size of the DNA methylation dataset? Authors response: We amended the title of the paragraph to “Low DNA methylation at the promoter of vtRNA1-1, vtRNA1-2 and vtRNA2-1 is associated with low patient overall survival.” Despite no statistically significant differences in overall survival were observed using ATAC-seq patient data the curves were like those observed using the promoter DNA methylation. The lack of significance is likely due to the smaller ATAC-seq sample size as anticipated by the Reviewer. In addition, the association between OS and vtRNA promoter DNA methylation is weak per se, so sample size is likely critical to sense significant differences. Reviewers’ comment: The authors do not mention that a pseudogene of vtRNA2-1 (vtRNA2-2P) has been annotated at chr2:65,555,432-65,555,534. Is there any reason for that? VtRNA2-2P could be included as proof of concept similarly to vtRNA3-1P on page 8. Authors response: We have previously looked for vtRNA2-2P in ATAC-seq data but there is no ATAC-seq region determined for this gene in the TSS, so we decided to do not include it. However, we now extended the analysis to the ATAC-seq region nearest to the TSS of vtRNA2-2P. As can be seen in modified Supplementary Figure 3 and modified Supplementary Table 1, the vtRNA2-2P has a very low and stable pattern of ATAC-seq chromatin accessibility across the different tissues that agrees with its pseudogene annotation. These results were now included in the manuscript and the text was modified accordingly. In the introduction section we added: “The vtRNA3-1P and vtRNA2-2P are two additional vault RNA genes situated in chromosome X and 2 respectively, but were classified as a pseudogenes due to the absence of expression in cell lines and the presence of silencing mutations at the promoter (Büscher et al., 2020; van Zon et al., 2001).”. In the results section we added: “The low ATAC-seq value of the pseudogenes vtRNA3-1P (Ave. -1.2, 0.6 SD) and vtRNA2-2P (Ave. 0.1, 0.6 SD), represents a proof of concept of the analyses (Extended Data: Figure S3 and Tables S1-S5). The same approach was performed for the Y-RNAs genes RNY1 (Ave. 3.7, 0.4 SD), RNY3 (Ave. 2.1, 0.6 SD, RNY4 (Ave. 1.9, 0.6 SD) and RNY5 (Ave. 3.1, 0.4 SD) (Canella et al., 2010), which code for produce ubiquitously expressed RNA polymerase III transcripts (Extended Data: Figure S3 and Tables S1).” and “VtRNA2-2P reaches a maximum and minimum promoter chromatin accessibility in Lung Adenocarcinoma (LUAD) (1.0) and ACC (-0.34) respectively (Extended Data: Figure S3C).” Reviewers’ comment: Page 3: “…the presence of silencing mutations at the B box element of its promoter B-box”. Since the organization of RNA polymerase III promoters has not been explained before, it would be better to keep this statement more general without mentioning the B-box. Authors response: To attend the Reviewer´s suggestion, we modified the sentence to “the presence of silencing mutations at the promoter”. Reviewers’ comment: The abbreviation “PANCAN” in the title of the legend to Figure 8 was not used before in the text. Authors response: Due the Reviewer´s comment, we modified “PANCAN” for “Pan-Cancer”. Reviewers’ comment: I am not sure whether the term “chromatin polymorphism” on page 10 is correct. The referenced publication refers to epigenetic variations. Authors response: Due the Reviewer´s comment, we modified the term “chromatin polymorphism” for “epigenetic variation”. References: Fort, R.S., Garat, B., Sotelo-Silveira, J.R., & Duhagon, M.A. (2020). vtRNA2-1/nc886 Produces a Small RNA That Contributes to Its Tumor Suppression Action through the microRNA Pathway in Prostate Cancer. Non-Coding RNA 6, 7. Gerber, A., Ito, K., Chu, C.S., & Roeder, R.G. (2020). Gene-Specific Control of tRNA Expression by RNA Polymerase II. Mol. Cell 78, 765–778. Graczyk, D., White, R.J., & Ryan, K.M. (2015). Involvement of RNA Polymerase III in Immune Responses. Mol. Cell. Biol. 35, 1848–1859. Hirsch, H.A., Gu, L., & Henry, R.W. (2000). The Retinoblastoma Tumor Suppressor Protein Targets Distinct General Transcription Factors To Regulate RNA Polymerase III Gene Expression. Mol. Cell. Biol. 20, 9182–9191. Hussain, S., Sajini, A.A., Blanco, S., Dietmann, S., Lombard, P., Sugimoto, Y., Paramor, M., Gleeson, J.G., Odom, D.T., Ule, J., et al. (2013). NSun2-mediated cytosine-5 methylation of vault noncoding RNA determines its processing into regulatory small RNAs. Cell Rep. 4, 255–261. Raha, D., Wang, Z., Moqtaderi, Z., Wu, L., Zhong, G., Gerstein, M., Struhl, K., & Snyder, M. (2010). Close association of RNA polymerase II and many transcription factors with Pol III genes. Proc. Natl. Acad. Sci. U. S. A. 107, 3639–3644. Rodríguez-López, M., Gonzalez, S., Hillson, O., Tunnacliffe, E., Codlin, S., Tallada, V.A., Bähler, J., & Rallis, C. (2020). The GATA Transcription Factor Gaf1 Represses tRNAs, Inhibits Growth, and Extends Chronological Lifespan Downstream of Fission Yeast TORC1. Cell Rep. 30, 3240-3249.e4. Sajini, A.A., Choudhury, N.R., Wagner, R.E., Bornelöv, S., Selmi, T., Spanos, C., Dietmann, S., Rappsilber, J., Michlewski, G., & Frye, M. (2019). Loss of 5-methylcytosine alters the biogenesis of vault-derived small RNAs to coordinate epidermal differentiation. Nat. Commun. 10. White, R.J. (2011). Transcription by RNA polymerase III: More complex than we thought. Nat. Rev. Genet. 12, 459–463. Zhang, X.O., Gingeras, T.R., & Weng, Z. (2019). Genome-wide analysis of polymerase III–transcribed Alu elements suggests cell-type–specific enhancer function. Genome Res. 29, 1402–1414."
}
]
}
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https://f1000research.com/articles/10-182
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https://f1000research.com/articles/10-4/v1
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06 Jan 21
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{
"type": "Software Tool Article",
"title": "BioPAN: a web-based tool to explore mammalian lipidome metabolic pathways on LIPID MAPS",
"authors": [
"Caroline Gaud",
"Bebiana C. Sousa",
"An Nguyen",
"Maria Fedorova",
"Zhixu Ni",
"Valerie B. O’Donnell",
"Michael J.O. Wakelam",
"Simon Andrews",
"Andrea F. Lopez-Clavijo",
"Caroline Gaud",
"Bebiana C. Sousa",
"An Nguyen",
"Maria Fedorova",
"Zhixu Ni",
"Valerie B. O’Donnell",
"Michael J.O. Wakelam",
"Simon Andrews"
],
"abstract": "Lipidomics increasingly describes the quantitation using mass spectrometry of all lipids present in a biological sample. As the power of lipidomics protocols increase, thousands of lipid molecular species from multiple categories can now be profiled in a single experiment. Observed changes due to biological differences often encompass large numbers of structurally-related lipids, with these being regulated by enzymes from well-known metabolic pathways. As lipidomics datasets increase in complexity, the interpretation of their results becomes more challenging. BioPAN addresses this by enabling the researcher to visualise quantitative lipidomics data in the context of known biosynthetic pathways. BioPAN provides a list of genes, which could be involved in the activation or suppression of enzymes catalysing lipid metabolism in mammalian tissues.",
"keywords": [
"LIPID MAPS",
"Lipidomics",
"Biosynthetic pathway analysis",
"lipids",
"lipid profiling."
],
"content": "Introduction\n\nLipids (fats) are essential and diverse families of molecules that play structural, energy storage and signalling roles. They are connected through complex metabolic pathways, which comprise linked series of enzymatic reactions (several are outside cells, e.g. PLA2 isoforms, autotaxin). Thus, lipids can be substrates, products or intermediates. It has been estimated that there are approximately 3–5000 different lipid species in mammalian cells although the true number is still unknown and extremely difficult to reliably measure1,2. In recent years, great advances have been made in our ability to experimentally determine the elemental composition and quantitation of lipid levels in biological samples, with the advent of rapid scanning benchtop mass spectrometers (MS), in particular high-resolution configurations such as Orbitrap, and ToF. Liquid chromatography-MS, either tandem or high resolving power, interfaced with processing pipelines such as Lipid Data Analyser (LDA), LipidFinder, LipidHunter, MS-Dial, XCMS and many others makes it feasible to simultaneously monitor the dynamic changes in hundreds of lipid molecular species in biological samples3–7.\n\nAs the quantity and detail of quantitative lipid data continue to grow it has become considerably more challenging to interpret the complex sets of changes within the lipidome8. Relevant biological perturbations usually happen not at the level of a single lipid molecular species in isolation, but as broad sets of changes over entire lipid classes and subclasses9. For example, a group of phosphatidylcholines will tend to change together in the same direction, since they are being regulated by the same enzyme isoform(s). This introduces characteristic patterns in the data that can reveal important clues as to the underlying level of genetic and transcriptomic regulation. Consequently, there is a need for software tools to automate and facilitate biosynthetic pathway scale analyses with lipids grouped according to structural motifs. Nguyen et al. and Hann et al. described the analysis of quantitative lipidomics datasets at pathway levels10–12. Here, we have integrated the biosynthetic metabolic levels into BioPAN. So, BioPAN combines current knowledge of lipid metabolism with a statistical analysis functionality, by comparing two biological conditions to identify activated or suppressed pathways, and present the results in an interactive graphical display. BioPAN works with data resolved to the level of individual lipid molecular species, but it can aggregate results at the subclass level to simplify the interpretation. Mammalian reaction information is converted into a metabolic pathway within BioPAN, allowing it to predict the most likely lipid transforming genes modulated by an experiment, to provide direct biological insight and generate hypotheses that can be experimentally tested.\n\nBioPAN is openly available on the LIPID MAPS® Lipidomics Gateway, at https://lipidmaps.org/biopan/. The tool is designed to allow users to upload and analyse their own data, and example datasets are also provided for evaluation. BioPAN is fully integrated with LipidLynxX, allowing users to convert different naming (short notation) conventions from diverse software inputs to be able to make it readable on BioPAN. Additionally, LipidLynxX will convert lipid results with fatty acid position, double bond location, and stereochemistry into a sum composition of carbon number and double bond equivalents. For example, DAG (16:0/20:1(Z11)), is converted by LipidLynxX to DG 36:1. BioPAN offers a link with LIPID MAPS Structure Database (LMSD)9.\n\n\nMethods\n\nThe statistical model used in BioPAN was originally described by Nguyen et al.10. In brief, BioPAN uses data from replicated quantitative lipidomics experiments with two biological experiments: a condition of interest (treated) and a control condition. BioPAN calculates statistical scores for all possible lipid pathways to predict which are active or suppressed in the treated samples compared to the control set.\n\nThe BioPAN workflow relies on the calculation of the Z-score, which considers the mean and the standard deviation of the experiment assuming a normally distributed data of lipid subclasses. A probability function (P) is computed and subtracting from one to obtain Q, which in turn is the probability that a Z-score is due to chance. The Z-score is then used to predict whether a particular reaction is significantly (p < 0.05) changing between control and treated conditions. Z-scores for all reactions in a pathway are combined using a cumulative function (CDF) to give a global pathway Z-score The set of equations used to calculate Z-scores are presented and discussed elsewhere10. Changing reactions are classified as activated or suppressed depending upon the direction of change. BioPAN, by default, calls a reaction or pathway as significantly modified at a level of p < 0.05 (Z > 1.645).\n\nBioPAN is implemented as an open access web-based tool. The front end uses HTML, jQuery (v3.5.1) for the interface and the Cytoscape.js library (v3.10.2)13 to draw and manipulate the results graphs. The server-side code uses PHP (v7.4.11) for request handling and R (v4.0.2) for data processing and statistical analysis. BioPAN runs on all modern web browsers and is available at https://lipidmaps.org/biopan/.\n\nBioPAN allows uploading of lipidomics datasets containing quantitative data from two different experiments or conditions (e.g. wild type against treated/knock-out). The use of BioPAN is simple and intuitive with a user-friendly interface. The data files should have minimum two replicas per condition, as BioPAN compares the changes between the experiments. BioPAN takes an input file in .csv (Comma-Separated Values). The first column on the file should include the lipid abbreviation subclass followed by the notation e.g. PC 38:4, PC 18:0_20:4, PC 18:0/20:4, or PC 18:0/20:4(5Z,8Z,11Z,14Z), for glycerophopholipids, glycerolipids, and sterol lipids. Sphingolipid molecular species written as e.g. d18:1/20:4, or 18:1;O2/20:4, where 18:1;O2 is the sphingosine base and 20:4 is the N-acyl chain liked to the sphingosine base are also recognised in BioPAN. Non-conventional nomenclature like DG(aa-34:0, DG(ea-34:1) is not recognised by BioPAN and the user manually need to change the lipid subclass abbreviation14. There are additional instructions about the structure of the data file following the link https://lipidmaps.org/biopan/doc/step1.html, which directs the user to each lipid subclass abbreviation in LIPID MAPS® Lipidomics Gateway.\n\nThe first step in BioPAN is to load a file of quantitative lipidomics data. After uploading, BioPAN uses the LipidLynxX15 tool to cross-match some lipid names into the LIPID MAPS® Lipidomics Gateway nomenclature style according to the guidelines from COMP_DB (https://www.lipidmaps.org/resources/tools/bulk_structure_searches_documentation.php)9,14,16. BioPAN then classifies the submitted lipids as either unrecognised, processed, or unprocessed. Unrecognised molecular species are lipids whose subclasses are not included into BioPAN database, while unprocessed species are part of BioPAN, but were not associated with any reactions. BioPAN’s database was manually collated followed by a validation using available literature. The database currently contains 94 lipid reactions identified in mammals, covering 41 lipid subclasses. Only processed molecular species, e.g. those which can be associated with at least one reaction, are used for downstream analysis.\n\nThe second step within BioPAN requires users to associate each sample with a condition. (e.g. sample names: control1, treated1, or control2, treated2, and so on, with their respective replicates). Each condition requires a minimum of two replicas (three or more replicas per condition are strongly recommended). Once assignments have been made, BioPAN searches for reactions and pathway changes between these. Following analysis completion, the user is directed to the results page (Figure 1). The main viewport shows an interactive graph comprising lipids and reactions assigned to the lipids included in the input file uploaded. The user can select how the pathways are displayed in the interactive graph by manually moving the nodes in the graph, while the link between product and substrate is maintained. Thus, providing a view of all possible reaction pathways. The side panel provides a legend for the graph and controls to modify the specifics of the analysis performed and the level of detail in the graph. The legend describes the shape of the nodes, which denote the lipid subclass, and the colour of the nodes represent the pathway status (active/suppressed or none). Each arrow between two nodes (lipid subclass/lipid molecular species) depicts the reaction direction between the two lipids. The colour of the arrows depends on the value of the Z-score (see the Implementation section), where green indicates a positive Z-score and purple negative, as shown in Figure 1. The user can click in the arrows connecting each node and a pop table is generated by BioPAN showing all the lipid molecular species selected and non-selected in the reaction between two nodes (see Extended Data, Table S-1). Selecting the arrow is only functional when selecting the lipid subclass level in the pathway options (described in the section below). Additionally, information on lipid subclasses and molecular species are available by clicking on the nodes, linking to the LMSD database (https://www.lipidmaps.org/data/structure/index.php).\n\nPathways are displayed as an interactive graph at the centre of the screen. Users have control over the information presented in the graph using the menus on the left side panel and results tables are displayed at the bottom of the screen.\n\nThe bottom panel shows a tabular view of statistically significant (p < 0.05 equivalent to Z-score > 1.645) results.\n\nDisplay options. The pathway options on the left of the screen allow users to customize the display of results in the graph. BioPAN arbitrarily chooses two conditions to compare (condition of interest and control condition, see Figure 1. The user can change conditions to compare using the drop-down menu (Figure 1). Users can choose to view pathways based on either the lipid subclass or on the fatty acyl composition. They can also choose which pathways to highlight in the main graph. Users can opt for either significantly active (condition of interest > control) or significantly suppressed (condition of interest < control) pathways. Where the same reaction can participate in multiple pathways, users can also choose to view only the most active (or most suppressed) pathway. This will highlight only the pathway with the highest individual pathway level Z-score for pathways containing reactions where a substrate is the starting agent in a reaction. In other words, selecting most active or most suppressed status still follow the rule for the active/suppressed status in terms of colours and Z-scores as discussed above. However, the Z-scores in an active/suppressed single reaction (e.g. PC→DG) are compared for substrates, intermediates, and products following each step of the pathway. For example, in the cerebral cortex (with pathway options: active status, subclass level, reaction subset of lipid data, 0.05 p value, no paired-data), reactions within multiple pathways like PC→DG→MG and PC→DG→PA. PC is the initial substrate and have individual reaction Z-scores of 3.083 (PC→DG), 2.054 (DG→MG), and -0.408 (DG→PA). It can be observed above that PC→DG is common for the first step in both pathways, and then BioPAN selects the most active reaction with the highest Z-score for the second part of the pathway. So, the Z-score of DG→MG is greater than the score for DG→PA. Thus, PC→DG→MG is most active pathway compared to PC→DG→PA. There might be more than one active pathway with one lipid-initiated substrate (e.g. DG→TG, DG→PE→PS, and DG→PC→CL), the same principle is applied, and BioPAN will consider only one of those pathways as most active.\n\nUsers can also choose to have the nodes in the graph aggregated into lipid subclasses, or they can view individual lipid molecular species. All views allow for filtering to display only a user-selected subset of lipids. These can be chosen either from a tree of checkboxes for each subclass, or using a free text search, allowing users to focus on particular lipids of interest (see Extended Data, section S-2, Figure S-1). Alternatively, the user can opt to view only reaction chains which occur within the context of a set of curated named pathways stored within BioPAN (e.g. biosynthesis of PC and Kennedy pathway). Changing pathway options affects both the graph and results tables.\n\nCalculation options. Under the Pathway Calculation section, the user can control details of the statistical calculation. They can alter the groups to be compared as well as changing the threshold for significance from the default of p < 0.05. If replicates in the uploaded data were generated as matched pairs (e.g. control and treated sample coming from the same animal) then the calculation can also take this into account in the t-test step of the analysis.\n\nExporting results. Results of the statistical analysis of active/suppressed pathways are presented in four tables at the bottom of the page, where predicted gene changes can be visualized. Export options are also available on the top right corner in the BioPAN viewport, where the main graph can be exported in several formats (JPEG / PNG / JSON / TXT) and tables are exported as TSV files.\n\n\nExample use case\n\nLipidomics data from cerebral cortex and liver of young and aged mice17 were used here as an example to illustrate how to use BioPAN and interpret its results. Ando et al.17 compared the lipid profile of different tissues in young and aged mice with the aim of detecting age-related as well as tissue-specific lipid modifications. The authors clustered alkylacyldiacylglycerols and deoxysphingolipids molecular species, reporting accumulation of deoxysphingolipids and ether-linked diacylglycerols in both tissues. Additional lipid subclasses were measured from Ando et al. (Additional information file 3), but those results were not discussed in the original publication10. The results from Ando et al. are used here to show how BioPAN can provide a wider analysis of the lipid level changes and the interrelation between different lipid subclasses.\n\nThe datasets from the original paper, were downloaded as TXT files from Metabolomics Workbench (Project ID PR000713, Studies ID ST001065 and ST001066) and are available as underlying data (see data availability section). Each file was imported as described in the method implementation section. Pathway options and pathway calculations settings were as follows: Type: Lipid; Status: Active; Level: Lipid subclass; Subset of lipid data: Reactions; Condition of interest: Aged; Control condition: Young; p value: 0.05; Paired data: No.\n\nThe lipid network at the lipid subclass level is shown in Figure 2A for the liver and Figure 2B for the cerebral cortex. The lipid pathway graph allows the user to quickly spot trends and differences between the two sets of samples. Figure 2 shows that reactions using ether-linked diacylglycerol (O-DG) as a substrate are suppressed in both liver and cerebral cortex in old versus young, which agrees with the reported accumulation of this particular lipid subclass by Ando et al.17. Here, BioPAN also found tissue-specific differences in lipid metabolism. For example, the reaction pathway results of aged mouse liver suggest active metabolism leading to accumulation of triacylglycerols (TG, Z-score = 2.301), a form of energy storage, contrary to a catabolic metabolism of TG observed in the cerebral cortex (Z-score = -2.612).\n\nLipid network graphs exported from BioPAN for the liver (A) and the cerebral cortex (B) of aged mice compared to young mice17. Green nodes correspond to active lipids and green shaded arrows to active pathways. Reactions with a positive Z score have green arrows while negative Z scores are coloured purple. Pathways options: aged condition of interest, young control condition, lipid type, active status, subclass level, reaction subset of lipid data, p value 0.05, and no paired-data.\n\nBioPAN also shows more differences in the metabolism of sphingolipids between the tissues. Specifically, in the liver the pathway is shifted towards the formation of ceramide-1-phosphate (Cer1P), while in the cerebral cortex sphingolipid metabolism points towards the formation of sphingomyelin (SM). Moreover, in the liver, glycerophospholipids and lysophospholipids synthesis is active with exception of LPA, contrary to what it is observed in the cerebral cortex, where glycerophospholipids and lysophospholipids pathways are suppressed, but production of LPA is favoured.\n\nBioPAN provides tables showing the suggested genes known to be involved in each reaction. Table 1 shows the lipid subclass active reaction results generated for the liver dataset. For example, the pathway PE→PC→PS→LPS designates the genes PEMT, PTDSS1, PLA2G2E, PLA2G2A, PLA2G2F. It should be noted that the default nomenclature of the genes in BioPAN corresponds to human species. In the example case presented here, the lipidomics data was obtained from mice, and although most often human and mouse genes are the same, there can be subtle differences between species. Thus, the user is encouraged to assign the gene according to the species in their own study. To aid the user in identifying the species each gene in Table 1 has a link that exists in the LIPID MAPS® Proteome Database (LMPD) (https://lipidmaps.org/resources/databases/index.php?tab=lmpd). For example, in Table 1 PEMT gene refers to a table containing the name and species of the gene, including a unique LMP ID for each gene/species pair. Thus, LMP002477 is assigned to the gene Pemt for mouse, which converts PE to PC. The status of this pathway might be changed by the loss of function or altered activity in any of the enzymes involved. Therefore, the list provided by BioPAN might help guide integration of lipidomics with proteomics or transcriptomics data as it directly suggests target proteins for further analysis.\n\nTable contains the active reactions chains found by BioPAN according to the Z-score values. Several genes are predicted as being involved in the current status of each reaction based on their function. Pathway options: aged condition of interest, young control condition, lipid type, active status, subclass level, reaction subset of lipid data, p value 0.05, no paired-data.\n\nLooking at fatty acids (FA) pathways at the molecular species level with BioPAN (Figure 3) shows the FA network obtained for liver and cerebral cortex of aged in comparison to young mice. The results show active metabolism towards the production of monounsaturated FA 16:1 and polyunsaturated FA 20:4, FA 20:5, and FA 22:4 in the cerebral cortex compared to the liver. Additionally, BioPAN has highlighted accumulation of the long acyl chain, polyunsaturated FA 24:5 in liver, which is associated with the activation of the ELOVL2 gene found in Table 2. Moreover, the results shown in Table 2 suggest a general activation of elongases (ELOVL) rather than desaturases (SCD) which was found to be a common trait in both tissues.\n\nFA graphs exported from BioPAN tool for the liver (A) and the cerebral cortex (B) of aged mice compared to young mice17. Green nodes correspond to active lipids and green shaded arrows to active pathways. Reactions with a positive Z score have green arrows while negative Z scores are coloured purple. Pathways options: aged condition of interest, young control condition, lipid type, active status, subclass level, reaction subset of lipid data, p value 0.05, and no paired-data.\n\nTable contains the active reaction chains found by BioPAN according to the Z-score values. Several genes are predicted as being involved in the current status of each reaction based on their function. Pathway options: aged condition of interest, young control condition, fatty acid type, active status, p value 0.05, no paired-data.\n\n\nConclusion\n\nModern lipidomics techniques generate a huge amount of data and information on many lipid subclasses, making the interpretation of results challenging. BioPAN provides several advantages over simpler analyses of individual lipids. The mapping of the lipid network graph provides a bigger picture allowing a new perspective on the data where new connections can be made, and a study can be moved forward into particular areas of interest. BioPAN offers a quick visualisation of differences in lipid pathways in mammal studies as well suggesting genes and their enzyme products involved in those differences.\n\n\nData availability\n\nThe datasets analysed as an example are available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org/ where it has been assigned Project ID PR000713 (studies ST001065 and ST001066).\n\nThe data can be accessed directly via its Project DOI: https://dx.doi.org/10.21228/M8HM48, https://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=SetupDownloadResults&StudyID=ST001065 and https://www.metabolomicsworkbench.org/data/DRCCMetadata.php?Mode=SetupDownloadResults&StudyID=ST001066.\n\nOpen Science Framework: BioPAN: a web-based tool to explore mammalian lipidome metabolic pathways on LIPID MAPS, https://doi.org/10.17605/OSF.IO/PKD6B18.\n\nThis project contains the modified dataset from Ando et al.17 according to BioPAN’s requirements:\n\nCerebral cortex dataset: https://osf.io/reavk/\n\nLiver dataset: https://osf.io/zd4as/\n\nOpen Science Framework: BioPAN: a web-based tool to explore mammalian lipidome metabolic pathways on LIPID MAPS, https://doi.org/10.17605/OSF.IO/PKD6B18.\n\nThis project contains the following extended data:\n\nTable S1, reaction table.\n\nSection S2, filtering and tree checkbox discussion.\n\nFigure S1, Filter tool example for acyl chains 38:4 and 38:5.\n\n\nSoftware availability\n\nSoftware, documentation and tutorial video are available from: https://lipidmaps.org/biopan/.\n\nArchived source code at the time of the publication: https://doi.org/10.17605/OSF.IO/PKD6B18.\n\nThe user can try BioPAN locally by following the readme instruction file located in: https://osf.io/7g2dx/.\n\nLicense: GNU GPL 3.0",
"appendix": "Acknowledgements\n\n“In memorium” The authors would like to dedicate this software application note to Michael J. O. Wakelam, who devoted his 40 years academic career to the field of lipidomics and mass spectrometry. This document is a testament to Michael’s depth knowledge in lipidomics and his immense capacity to translate lipid data into biological meaning. We ought the development of BioPAN’s database to Michael’s dream of integrating lipids with enzymatic changes. BioPAN is Michael’s legacy to the whole world as an open access tool he envisioned many moons ago. He is truly missed!\n\n\nReferences\n\nSlatter DA, Aldrovandi M, O’Connor A, et al.: Mapping the Human Platelet Lipidome Reveals Cytosolic Phospholipase A2 as a Regulator of Mitochondrial Bioenergetics during Activation. Cell Metab. 2016; 23(5): 930–944. PubMed Abstract | Publisher Full Text | Free Full Text\n\nQuehenberger O, Armando AM, Brown AH, et al.: Lipidomics reveals a remarkable diversity of lipids in human plasma. J Lipid Res. 2010; 51(11): 3299–3305. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHartler J, Trötzmüller M, Chitraju C, et al.: Lipid data analyzer: Unattended identification and quantitation of lipids in LC-MS data. Bioinformatics. 2011; 27(4): 572–577. PubMed Abstract | Publisher Full Text\n\nNi Z, Angelidou G, Lange M, et al.: LipidHunter Identifies Phospholipids by High-Throughput Processing of LC-MS and Shotgun Lipidomics Datasets. Anal Chem. 2017; 89(17): 8800–8807. PubMed Abstract | Publisher Full Text\n\nTsugawa H, Cajka T, Kind T, et al.: MS-DIAL: Data Independent MS/MS Deconvolution for Comprehensive Metabolome Analysis. Nat Methods. HHS Public Access. 2015; 12(6): 523–526. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTautenhahn R, Patti GJ, Rinehart D, et al.: XCMS Online: A Web-Based Platform to Process Untargeted Metabolomic Data. Anal Chem. 2012; 84(11): 5035–9. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTsugawa H, Ikeda K, Takahashi M, et al.: A lipidome atlas in MS-DIAL 4. Nat Biotechnol. 2020; 38(10): 1159–1163. PubMed Abstract | Publisher Full Text\n\nSpener F, Lagarde M, Géloên A, et al.: What is lipidomics? Eur J Lipid Sci Technol. 2003; 105(9): 481–482. Publisher Full Text\n\nFahy E, Subramaniam S, Murphy RC, et al.: Update of the LIPID MAPS comprehensive classification system for lipids. J Lipid Res. 2009; 50 Suppl(Suppl): S9–14. PubMed Abstract | Publisher Full Text | Free Full Text\n\nNguyen A, Rudge SA, Zhang Q, et al.: Using lipidomics analysis to determine signalling and metabolic changes in cells. Curr Opin Biotechnol. 2017; 43: 96–103. PubMed Abstract | Publisher Full Text\n\nNguyen A, Guedán A, Mousnier A, et al.: Host lipidome analysis during rhinovirus replication in HBECs identifies potential therapeutic target. J Lipid Res. 2018; 59(9): 1671–1684. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHahn O, Drews LF, Nguyen A, et al.: A nutritional memory effect counteracts benefits of dietary restriction in old mice. Nat Metab. 2019; 1(11): 1059–1073. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFranz M, Lopes CT, Huck G, et al.: Cytoscape.js: A graph theory library for visualisation and analysis. Bioinformatics. 2016; 32(2): 309–311. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLiebisch G, Vizcaíno JA, Köfeler H, et al.: Shorthand notation for lipid structures derived from mass spectrometry. J Lipid Res. 2013; 54(6): 1523–30. PubMed Abstract | Publisher Full Text | Free Full Text\n\nNi Z, Fedorova M: LipidLynxX: a data transfer hub to support integration of large scale lipidomics datasets. bioRxiv. 2020; 2020.04.09.033894. Publisher Full Text\n\nFahy E, Subramaniam S, Alex Brown H, et al.: A comprehensive classification system for lipids. J Lipid Res. 2005; 46(5): 839–861. PubMed Abstract | Publisher Full Text\n\nAndo A, Oka M, Satomi Y: Deoxysphingolipids and ether-linked diacylglycerols accumulate in the tissues of aged mice. Cell Biosci. 2019; 9: 61. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGaud C, Sousa BC, Nguyen A, et al.: BioPAN: a web-based tool to explore mammalian lipidome metabolic pathways on LIPID MAPS. 2020. https://www.doi.org/10.17605/OSF.IO/PKD6B"
}
|
[
{
"id": "76702",
"date": "26 Jan 2021",
"name": "Amaury Cazenave Gassiot",
"expertise": [
"Reviewer Expertise Lipidomics."
],
"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 entitled “BioPAN: a web-based tool to explore mammalian lipidome metabolic pathways on LIPID MAPS” described an online tool for visualisation of biological pathways from quantitative lipidomics data. The tool is an important contribution to lipidomics data analysis pipeline that could help make sense of ever more complex dataset.\nGeneral comments\nWell-written manuscript and an interesting contribution for those studying quantitative lipidomics datasets.\n\nRecommendation is to accept with minor revision and, if possible, implementation of a few suggestions.\nSuggestions\nWith regards to the statistical model used by the software. Could the authors elaborate on whether correction for multiple testing is done for p-value calculations? In the “Pathway calculation” section, would it be possible to let the user input any value for the significance threshold, rather than choosing from a few drop-down options?\n\nThe “Filter” field in the “Pathway options” section is very useful; however, it seems to take only one value at a time. Would it be possible to include logical operators? For instance, one could filter for “PC 32:1 AND PE 32:1”, or “38:5 OR 38:6”.\n\nUltimately, the tool relies on information contained in the pathway database. While using an in-house dataset for testing the tool, a large number of species were unfortunately “unprocessed”. Could the authors suggest how community users could help enriching the database?\n\nThe export function is useful, but only allows for exports of .png and .jpg graphics, the resolution of which seems to depend on the zoom status in the display window. Would it be possible to add an option to export as vector graphics, .svg for example?\nMinor comments\nPage 1, Abstract, line 3: change “increase” to “increases”.\n\nPage 2, Authors roles, line 1: change “visualization” to “visualisation”.\n\nPage 5, right column, 3rd paragraph, line 3-4: change “visualized” to “visualised”.\n\nPage 9, Acknowledgements: change “In memorium” to “In memoriam”.\n\nIs the rationale for developing the new software tool clearly explained? Yes\n\nIs the description of the software tool technically sound? Yes\n\nAre sufficient details of the code, methods and analysis (if applicable) provided to allow replication of the software development and its use by others? Yes\n\nIs sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool? Yes\n\nAre the conclusions about the tool and its performance adequately supported by the findings presented in the article? Yes",
"responses": [
{
"c_id": "6693",
"date": "09 Jun 2021",
"name": "Andrea F. Lopez-Clavijo",
"role": "Author Response",
"response": "We thank you reviewer Amaury Cazenave Gassiot for his comments. Suggestions: With regards to the statistical model used by the software. Could the authors elaborate on whether correction for multiple testing is done for p-value calculations? --> BioPAN does not correct for multiple testing as it calculates a Z-score to find stronger relationships within the data, hence higher Z-scores represent a more interesting result than others. In the “Pathway calculation” section, would it be possible to let the user input any value for the significance threshold, rather than choosing from a few drop-down options? --> The drop-down menu has been replaced to a text box and it has been incorporated into BioPAN. The “Filter” field in the “Pathway options” section is very useful; however, it seems to take only one value at a time. Would it be possible to include logical operators? For instance, one could filter for “PC 32:1 AND PE 32:1”, or “38:5 OR 38:6”. --> A paragraph was added in the Display options section: “The search box allows the user to search for one or two queries using the logical operators AND / OR. Selecting the AND operator, the user can view lipid subclasses or molecular species for which the name implies both queries. For example, searching for “PC” and “34:0” on the lipid molecular species graph displays lipids “PC(34:0)” and “O-PC(34:0)”. Choosing the OR operator allow the user to visualise lipids whose names includes one of the two searches. For instance, searching “LPC” or “LPA” on the subclasses graph displays lipids “LPC”, “O-LPC” and “LPA”.”. Ultimately, the tool relies on information contained in the pathway database. While using an in-house dataset for testing the tool, a large number of species were unfortunately “unprocessed”. Could the authors suggest how community users could help enriching the database? --> A paragraph was added in the operation section to address the “unprocessed” molecular species within BioPAN: “The unprocessed category corresponds to lipid molecular species that did not have a matching molecular species, as a reactant and product, with the same number of carbons and double bonds. For example, a substrate molecular species, such as PA 34:2 should have a matching product with the same sum composition (e.g. DG 34:2). Additionally, some biological reactions require fatty acid or fatty-acyl-CoA molecular species. So, a lack of these subclasses in the input file prevents BioPAN to build up the reaction between substrates and products. If the substrate or product is not part of other reaction within the pathway, BioPAN will report it as unprocessed, such is the case of triacylglycerides (TG) subclasses. On other instances, like phosphatidylcholine (PC) and lysophosphatidylcholine (LPC), where PC is the substrate in the reaction to produce phosphatidic acid (PA) and LPC is the substrate to produce lysophosphatidic acid (LPA), those lipid subclasses molecular species can be considered as processed by BioPAN.”. The export function is useful, but only allows for exports of .png and .jpg graphics, the resolution of which seems to depend on the zoom status in the display window. Would it be possible to add an option to export as vector graphics, .svg for example? --> This capability of export graphics in SVG has been added and a sentence was included in the text “in several formats (JPEG / PNG / SGV / JSON / TXT)”. Minor comments 1. Page 1, Abstract, line 3: change “increase” to “increases”. Done, thank you 2. Page 2, Authors roles, line 1: change “visualization” to “visualisation”. Done, thank you 3. Page 5, right column, 3rdparagraph, line 3-4: change “visualized” to “visualised”. Done, thank you 4. Page 9, Acknowledgements: change “In memorium” to “In memoriam”. Done, thank you"
}
]
},
{
"id": "76703",
"date": "29 Jan 2021",
"name": "Phillip Whitfield",
"expertise": [
"Reviewer Expertise Lipidomics."
],
"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 Gaud et al. is focused on BioPAN, a software tool designed for the mapping of lipid networks in mammalian systems. In order to demonstrate the utility of the software an exemplar analysis is outlined using publicly available lipidomic data sets acquired from the cerebral cortex and liver of young and aged mice. This is an interesting article and the BioPAN software will be useful in visualisation outputs from lipidomic experiments. There are a few minor suggestions:\nIntroduction: A sentence could be added to the end of the introductory text summarising the overall objective of the presented work.\nMethods: It would be useful to clarify whether p<0.05 is always equivalent to Z-score>1.645.\nConclusion: The authors may wish to indicate how the software could be further developed.\n\nIs the rationale for developing the new software tool clearly explained? Partly\n\nIs the description of the software tool technically sound? Yes\n\nAre sufficient details of the code, methods and analysis (if applicable) provided to allow replication of the software development and its use by others? Yes\n\nIs sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool? Yes\n\nAre the conclusions about the tool and its performance adequately supported by the findings presented in the article? Yes",
"responses": [
{
"c_id": "6694",
"date": "09 Jun 2021",
"name": "Andrea F. Lopez-Clavijo",
"role": "Author Response",
"response": "We thank you reviewer Phillip Whitfield for his comments. There are a few minor suggestions: Introduction: A sentence could be added to the end of the introductory text summarising the overall objective of the presented work. --> A sentence was added: “So, BioPAN aids for automatic integration of lipid metabolism with lipid profiles, finding strong relationships between lipid substrates and lipid products catalysed by active or suppressed enzymes.” Methods: It would be useful to clarify whether p<0.05 is always equivalent to Z-score>1.645. --> It was added: “…corresponding to Z > 1.645).” Conclusion: The authors may wish to indicate how the software could be further developed. --> A sentence was added: “Further work into the BioPAN database will be carried out to incorporate new biosynthetic pathways, such as: cholesterol, eicosanoids, and oxidised lipid subclasses, among others. Addition of glucosyl and galactosyl ceramides (Glc/Gal-Cer) to complement to the existing sphingolipids pathway in BioPAN will also be considered.”"
}
]
},
{
"id": "76705",
"date": "09 Mar 2021",
"name": "Ginger Milne",
"expertise": [
"Reviewer Expertise Lipidomics",
"mass spectrometry",
"oxidized lipid mediators",
"lipid metabolism."
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe submitted manuscript explains a web-based tool on the Lipid Maps website that helps the user to follow biosynthetic and metabolic pathways of endogenous lipids (the lipidome) following mass spectrometric analysis. This program will help the user link lipidomics data with underlying endogenous processes. The authors have taken care to cite appropriate references and give examples of how to use this tool. Further, the tool itself has a link to an excellent web-based tutorial.\nRecommendation:\nThe introduction ends abruptly. It reads as if there is a paragraph missing emphasizing the importance and expected use of this tool.\n\nIs the rationale for developing the new software tool clearly explained? Partly\n\nIs the description of the software tool technically sound? Yes\n\nAre sufficient details of the code, methods and analysis (if applicable) provided to allow replication of the software development and its use by others? Yes\n\nIs sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool? Yes\n\nAre the conclusions about the tool and its performance adequately supported by the findings presented in the article? Yes",
"responses": [
{
"c_id": "6695",
"date": "09 Jun 2021",
"name": "Andrea F. Lopez-Clavijo",
"role": "Author Response",
"response": "We thank you the reviewer Ginger Milne for her comments. Recommendation: The introduction ends abruptly. It reads as if there is a paragraph missing emphasizing the importance and expected use of this tool. --> A sentence was added: “So, BioPAN aids for automatic integration of lipid metabolism with lipid profiles, finding strong relationships between lipid substrates and lipid products catalysed by active or suppressed enzymes.”"
}
]
}
] | 1
|
https://f1000research.com/articles/10-4
|
https://f1000research.com/articles/9-419/v1
|
22 May 20
|
{
"type": "Case Report",
"title": "Case Report: Peptic ulcer disease following short-term use of nonsteroidal anti-inflammatory drugs in a 3-year-old child",
"authors": [
"Alin Dumitru Ciubotaru",
"Carmen-Ecaterina Leferman"
],
"abstract": "Background: Peptic ulcer disease (PUD) affects 1-2 per 1000 people annually in the USA, the UK and Europe, and occurs less frequently in children than in adults. PUD in children occurs mainly during the second decade of development. Among risk factors, nonsteroidal anti-inflammatory drugs (NSAIDs), commonly used to manage acute febrile illness or pain in healthy children, is rarely reported to lead to PUD and upper gastrointestinal bleeding. Case presentation: We present a rare case of upper gastrointestinal bleeding following a low dose ibuprofen treatment in a 3-year-old female. The patient with a family history of peptic ulcer was admitted for fever, coffee-ground vomiting and abdominal pain. The clinical examination revealed an altered general health status with a distended and mildly tender abdomen moving normally with respiration as well as normal stool. The initial laboratory test indicated anemia with reticulocytosis. During the first hours of hospitalization, the patient had a second episode of coffee-ground vomiting. An upper digestive endoscopy with biopsy was performed in the following six hours revealing a non-bleeding gastric ulcer at 2 cm from pylorus. Helicobacter pylori testing was negative. The patient was treated with a proton pump inhibitor (esomeprazole 10 mg/day) for 2 months. There were no further gastrointestinal symptoms and hemoglobin values returned to normal, indicating resolution of her gastrointestinal bleeding. Conclusion: The short-term utilization of NSAIDs in the appropriate dosage can lead to PUD, and considering the risk factors before administration can lead to an appropriate management.",
"keywords": [
"peptic ulcer disease",
"upper gastrointestinal bleeding",
"nonsteroidal anti-inflammatory drugs",
"proton pump inhibitors",
"children"
],
"content": "Introduction\n\nPeptic ulcer disease (PUD) affects 1–2/1000 people annually in the USA, UK and Europe and has been gradually decreasing1. An explanation could be the declining prevalence of Helicobacter pylori infection. While the rate of infections is decreasing, the rate of complications remains static, likely due to an aging population which has an elevated usage of ulcerogenic medication1.\n\nPUD occurs less frequently in children than adults. Epidemiological data are limited due to the rareness of the disease. An extensive study estimated the prevalence of ulcers and/or erosions in European children at 8.1%2, occurring mainly during the second decade of development. In the USA, 17.4% of pediatric patients are diagnosed with upper gastrointestinal ulcers each year3.\n\nPUD is a heterogenous disease defined by an imbalance between mucosa-protective and aggressive factors in the presence of risk factors including: H. pylori infection, chronic disease (inflammatory bowel disease, rheumatic diseases) and drug use, particularly nonsteroidal anti-inflammatory drugs (NSAIDs)2. In practice, NSAIDs are commonly used to manage acute febrile illness or pain in healthy children. One adverse reaction is acute gastrointestinal bleeding associated with short-term NSAIDs use, with a high rate of hospitalization and mortality in developed countries4. The adverse effect of short-term utilization of NSAIDs among children and their association with PUD are less clear.\n\nWe present a rare case of upper gastrointestinal bleeding following a low dose of ibuprofen in a 3-year-old to underline potentially severe side-effects of short-term NSAIDs use at appropriate doses in children.\n\n\nCase presentation\n\nA 3-year-old-female, with a family history of peptic ulcers, was admitted with fever, coffee-ground vomiting and abdominal pain. The mother stated the patient received two weight-appropriate doses of ibuprofen and a dose of paracetamol, both administered within an appropriate time interval in the previous 24 hours for fever control. The patient had a positive medical history of upper respiratory tract infections with febrile seizures and interstitial pneumonia treated with antypiretics and clarithromycin, respectively. The patient is allergic to cephalosporin and Augmentin. No immune deficiency disease was documented.\n\nClinical examination revealed general malaise, pallor, fever, pharyngotonsillar congestion and productive cough, normal breath sound, a distended and mildly tender abdomen moving normally with respiration and normal stool. The patient weighed 15 Kg and measured 88 cm tall.\n\nInitial laboratory tests indicated anemia with reticulocytosis (Hematocrit 29.7%, Hemoglobin 9.6 g/dl, reticulocytes 36/1000) and lower total protein (55.2 g/L), characteristic of bleeding. Remaining laboratory results were normal, including coagulation tests.\n\nSoon after hospitalization, the patient had a second episode of coffee-ground vomiting.\n\nAn upper digestive endoscopy with biopsy was performed revealing a non-bleeding gastric ulcer at 2 cm from pylorus (Figure 1). H. pylori testing was negative.\n\nThis shows a non-bleeding gastric ulceration measuring 2.5 × 2 cm with edematous rim located 2 cm from the pyloric ring; pale gastric mucosa, fluid stasis and food debris; snake skin appearance of gastric mucosa in the fundus.\n\nBased on this data, a diagnosis was made of NSAID-induced gastric ulcer, causing upper gastrointestinal bleeding.\n\nDuring hospitalization, perfusion with glucose and electrolytes was administered in order to compensate for fluid loss. The patient was treated with a proton pump inhibitor (esomeprazole 10 mg/day) for 2 months.\n\nThere were no further gastrointestinal symptoms. Hemoglobin values returned to normal, indicating resolution of gastrointestinal bleeding.\n\n\nDiscussion\n\nUpper gastrointestinal bleeding in a 3-year-old following short-term NSAIDs use is an uncommon presentation. Similar cases5 have been reported in literature, but the adverse effects of short-term NSAIDs use among children and their association with PUD is not completely understood. However, some studies offer compelling data indicating certain risk factors, primarily: the child’s age2, NSAIDs consumption2,4,6,7 and H. pylori infection2,6–8.\n\nPUD seems to primarily affect patients between 10–20 years old2. A retrospective cohort study reported a lower median age for those with gastric ulcers, than those with duodenal ulcers8. Our patient confirms this ratio.\n\nThe second important factor is NSAIDs consumption. The probability of PUD increases with the duration of therapy, dose and presence of risk factors, including positive familial history or drugs coadministration7,9. Thus, despite a low dose of ibuprofen, the gastric ulcer (GU) in this case can be explained in part by a positive family history and association with a dose of paracetamol. Moreover, some studies conclude that short-term NSAIDs use is highly correlated with GU6.\n\nThe association between short-term NSAIDs use and proton pump inhibitors (PPIs) can theoretically reduce the risk of upper gastrointestinal bleeding in children. Although coadministration of NSAIDs and PPIs is considered safe to reduce adverse gastrointestinal effects in adults10, there is not sufficient data about this drugs association in the prevention of short-term NSAIDs-PUDs in children.\n\nThe third important risk factor in PUD, H. pylori infection, was negative in our case. Some studies suggest a weaker association between H. pylori and PUD in children as compared with adults2,11. However, this infection is a well-recognized cause of chronic gastritis and plays an important role in the pathogenesis of PUD in children12.\n\nPatients who develop gastrointestinal bleeding caused by NSAIDs-associated ulcers should discontinue use. Therapeutic strategies in these cases depend on the severity of presentation. Pharmacologic, endoscopic and surgical techniques have been developed to achieve hemostasis. In cases of massive bleeding, immediate endoscopic or surgical intervention is required. Scoring systems for upper gastrointestinal bleeding in children, laboratory tests and blood transfusion requirements are still under development13–15. In the present case, clinical presentation with two episodes of isolated hematemesis (coffee-ground vomiting) and endoscopic examination findings (non-bleeding gastric ulcer) correlated with laboratory tests indicated pharmacologic management.\n\n\nConclusion\n\nShort term NSAIDs use in appropriate doses, commonly prescribed to control fever in children, can lead to PUD. Before administration, risk factors such as other antipyretic medication use, or a suggestive familial history must be considered. Doctors should inform caregivers of the risks involved and encouraging limited NSAIDs use.\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 the publication of this case report was obtained from the parents of the patient.",
"appendix": "References\n\nSverdén E, Agréus L, Dunn JM, et al.: Peptic ulcer disease. BMJ. 2019; 367: l5495. PubMed Abstract | Publisher Full Text\n\nKalach N, Bontems P, Koletzko S, et al.: Frequency and risk factors of gastric and duodenal ulcers or erosions in children: a prospective 1-month European multicenter study. Eur J Gastroenterol Hepatol. 2010; 22(10): 1174–1181. PubMed Abstract | Publisher Full Text\n\nBrown K, Lundborg P, Levinson J, et al.: Incidence of peptic ulcer bleeding in the US pediatric population. J Pediatr Gastroenterol Nutr. 2012; 54(6): 733–736. PubMed Abstract | Publisher Full Text\n\nGrimaldi-Bensouda L, Abenhaim L, Michaud L, et al.: Clinical features and risk factors for upper gastrointestinal bleeding in children: a case-crossover study. Eur J Clin Pharmacol. 2010; 66(8): 831–837. PubMed Abstract | Publisher Full Text\n\nBerezin SH, Bostwick HE, Halata MS, et al.: Gastrointestinal bleeding in children following ingestion of low-dose ibuprofen. J Pediatr Gastroenterol Nutr. 2007; 44(4): 506–508. PubMed Abstract | Publisher Full Text\n\nHuang SC, Sheu BS, Lee SC, et al.: Etiology and treatment of childhood peptic ulcer disease in taiwan: a single center 9-year experience. J Formos Med Assoc. 2010; 109(1): 75–81. PubMed Abstract | Publisher Full Text\n\nCardile S, Martinelli M, Barabino A, et al.: Italian survey on non-steroidal anti-inflammatory drugs and gastrointestinal bleeding in children. World J Gastroenterol. 2016; 22(5): 1877–1883. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRoma E, Kafritsa Y, Panayiotou J, et al.: Is peptic ulcer a common cause of upper gastrointestinal symptoms? Eur J Pediatr. 2001; 160(8): 497–500. PubMed Abstract | Publisher Full Text\n\nAutret-Leca E, Bensouda-Grimaldi L, Maurage C, et al.: Upper gastrointestinal complications associated with NSAIDs in children. Therapie. 2007; 62(2): 173–176. PubMed Abstract | Publisher Full Text\n\nGwee KA, Goh V, Lima G, et al.: Coprescribing proton-pump inhibitors with nonsteroidal anti-inflammatory drugs: risks versus benefits. J Pain Res. 2018; 11: 361–374. PubMed Abstract | Publisher Full Text | Free Full Text\n\nElitsur Y, Lawrence Z: Non-Helicobacter pylori related duodenal ulcer disease in children. Helicobacter. 2001; 6(3): 239–243. PubMed Abstract | Publisher Full Text\n\nBlecker U, Gold BD: Gastritis and peptic ulcer disease in childhood. Eur J Pediatr. 1999; 158(7): 541–546. PubMed Abstract | Publisher Full Text\n\nNasher O, Devadason D, Stewart RJ: Upper Gastrointestinal Bleeding in Children: A Tertiary United Kingdom Children’s Hospital Experience. Children (Basel). 2017; 4(11): pii: E95 PubMed Abstract | Publisher Full Text | Free Full Text\n\nThomson MA, Leton N, Belsha D: Acute upper gastrointestinal bleeding in childhood: development of the Sheffield scoring system to predict need for endoscopic therapy. J Pediatr Gastroenterol Nutr. 2015; 60(5): 632–636. PubMed Abstract | Publisher Full Text\n\nGarber A, Jang S: Novel Therapeutic Strategies in the Management of Non-Variceal Upper Gastrointestinal Bleeding. Clin Endosc. 2016; 49(5): 421–424. PubMed Abstract | Publisher Full Text | Free Full Text"
}
|
[
{
"id": "75153",
"date": "01 Dec 2020",
"name": "Parijat Ram Tripathi",
"expertise": [
"Reviewer Expertise Pediatric gastroenterology and hepatology"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 emphasized the possibility of the development of gastric ulcers even on short and adequate doses of NSAIDs. The case report needs more information and clarity regarding certain aspects of predisposing factors, diagnostic tests, treatment, and follow-up.\n\nThere are multiple major and minor concerns which are mentioned below point by point:\nMajor concerns:\nIn the introduction, the second paragraph, “An extensive study estimated the prevalence of ulcers and/or erosions in European children at 8.1%, occurring mainly during the second decade of development. In the USA, 17.4% of pediatric patients are diagnosed with upper gastrointestinal ulcers each year.” In both the studies endoscopies were performed for specific indications rather than in the general pediatric population. Please mention the indications for better clarity of information.\n\nWhat were the hemodynamic parameters of the patient at admission?\n\nWhat tests were performed for H. pylori in the patient?\n\nPlease give details of family history of peptic ulcer disease (PUD) and how was it diagnosed? Was that person H. pylori-positive?\n\nIn the discussion, the second paragraph, “A retrospective cohort study reported a lower median age for those with gastric ulcers, than those with duodenal ulcers. Our patient confirms this ratio.” This is not right to say that this case report confirms this ratio. Please change or remove it.\n\nHow do authors think that the presence of positive family history (in absence of H. pylori) and paracetamol intake can explain the presence of gastric ulcer even with a low dose of NSAID? Please explain in more detail.\n\nWhy a repeat endoscopy was not performed to confirm the healing of gastric ulcer?\n\nMinor concerns:\nPlease mention doses (in per kg) and interval of ibuprofen used in the patient.\n\nPlease do not write the brand name until significant or important (e.g. Augmentin).\n\nDuration and severity of respiratory tract infection are not mentioned. Please give details.\n\nThe patient’s weight and height interpretation should be mentioned as per Z score.\n\nMention corrected reticulocyte count.\n\nHow laboratory reports (hemoglobin, hematocrit, total protein, and reticulocyte count) are suggesting bleeding characteristics? Please explain.\n\nPlease mention the dose of esomeprazole in mg/kg/day along with the dose written in case details.\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? Partly\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Partly\n\nIs the case presented with sufficient detail to be useful for other practitioners? Partly",
"responses": [
{
"c_id": "6738",
"date": "09 Jun 2021",
"name": "Carmen-Ecaterina Leferman",
"role": "Author Response",
"response": "We are appreciative of the opportunity and your support in improving upon the initial article. We have carefully followed your recommendations and made the necessary improvements, including relevant information regarding drugs administration, family history, medical history and nutritional status of the patient. Also, we elaborate more about the risk factors of peptic ulcer disease (PUD) in the discussion section. In the introduction, the second paragraph, “An extensive study estimated the prevalence of ulcers and/or erosions in European children at 8.1%, occurring mainly during the second decade of development. In the USA, 17.4% of pediatric patients are diagnosed with upper gastrointestinal ulcers each year.” In both the studies endoscopies were performed for specific indications rather than in the general pediatric population. Please mention the indications for better clarity of information. Thank you for your observation. Regarding clarity of information related to epidemiology, we elaborated more about the indications for endoscopies mentioned in the two studies to which we referred in the second paragraph of the first version. What were the hemodynamic parameters of the patient at admission? We added the hemodynamic parameters of the patient at admission (Case presentation, first paragraph, first sentence). What tests were performed for H. pylori in the patient? A biopsy was performed during the initial upper endoscopy and the results were negative for H. pylori (Case presentation, fifth paragraph, last sentence). Please give details of family history of peptic ulcer disease (PUD) and how was it diagnosed? Was that person H. pylori positive? The father of the patient was diagnosed with PUD, but was unable to confirm whether he was H. Pylori positive. In the discussion, the second paragraph, “A retrospective cohort study reported a lower median age for those with gastric ulcers, than those with duodenal ulcers. Our patient confirms this ratio.” This is not right to say that this case report confirms this ratio. Please change or remove it. We removed the sentence. How do authors think that the presence of positive family history in absence of H. pylori) and paracetamol intake can explain the presence of gastric ulcer even with a low dose of NSAID? Please explain in more detail. Thank you for your excellent point. As a result, we added in the text few lines in order to highlight this important consideration. The accumulation of more risk factors, like positive family history, NSAID administration or H. Pylori infection in pediatric population affected by PUD, has been well documented. A joint effect of paracetamol (a dosage higher than 2g) combined with NSAIDs was reported in adults that had both compounds prescribed together. Conversely, the risk for GI ulcers and ulcer complications due to normal paracetamol intake has not been yet supported by available clinical data. Why a repeat endoscopy was not performed to confirm the healing of gastric ulcer? Follow-up upper GI endoscopy is mandatory in the case of complicated duodenal ulcers. The report of the endoscopy performed at the end of the treatment period confirmed the healing of the gastric ulceration area. We did not have access to the images. Please mention doses (in per kg) and interval of ibuprofen used in the patient. Two doses of 100 mg -6,66 mg/kg- Ibuprofen by mouth, 8 hours apart. Please do not write the brand name until significant or important (e.g. Augmentin). We replaced the brand name with amoxicillin/clavulanic acid. Duration and severity of respiratory tract infection are not mentioned. Please give details. The patient had a positive medical history of upper respiratory tract infections with febrile seizures and interstitial pneumonia treated with antipyretics and clarithromycin, respectively. The duration of the symptoms was 2 weeks, three weeks prior to the GI bleeding episode. We added this information in the new version. The patient’s weight and height interpretation should be mentioned as per Z score. The 3 year-old patient weighed 15 Kg (z-score 0.65) and measured 88 cm tall (z-score -1.63) . She is at the 5th percentile for stature, 72nd percentile for weight. She has a body mass index (BMI) of 19.4 (z-score 2.15), placing the BMI-for-age at the 98th percentile. (Case presentation, fourth paragraph, last sentence). Mention corrected reticulocyte count. We mentioned corrected reticulocyte count in the new version (Case presentation, fifth paragraph). How laboratory reports (hemoglobin, hematocrit, total protein, and reticulocyte count) are suggesting bleeding characteristics? Please explain. As mentioned in the text, lower values of hemoglobin (9.6 g/dl) and hematocrit (29.7%) suggest anemia, a potential sign of hemorrhage. In order to differentiate between different possible causes of anemia in children, additional parameters like reticulocyte count and protein levels were evaluated, identifying the reticulocytosis (corrected reticulocyte count of 3.24) and the hypoproteinemia (5.52 g/dL). Reticulocytosis is a compensatory mechanism of the bone marrow to increase production in order to compensate the red blood cell loss. Hypoproteinemia is associated with blood loss. Please mention the dose of esomeprazole in mg/kg/day along with the dose written in case details. The esomeprazole dosage was 10 mg/day (0.66 mg/kg/day). (Case presentation, ninth paragraph)"
}
]
},
{
"id": "75841",
"date": "09 Feb 2021",
"name": "Vera L. Sdepanian",
"expertise": [
"Reviewer Expertise Pediatric Gastroenterologist"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 a case report of a 3-year-old-female that presented upper gastrointestinal bleeding, that the upper digestive endoscopy revealed a non-bleeding gastric ulcer at 2 cm from pylorus, and negative Helicobacter pylori testing. The patient received two weight-appropriate doses of ibuprofen and a paracetamol dose, both administered within an appropriate time interval in the previous 24 hours for fever control. Based on this data, the authors attributed the nonsteroidal anti-inflammatory drugs (NSAIDs) – ibuprofen – to the cause of the gastric ulcer.\nIn paragraph 3 of the Discussion section, the authors pointed out that positive family history of peptic ulcer and association with a dose of paracetamol could explain the gastric ulcer. First of all, the positive family history should be clarified, and secondly what should be the importance of using one dose of paracetamol.\n\nThe authors should emphasize all drugs used during at least in the last month because the patient “had a positive medical history of upper respiratory tract infections with febrile seizures and interstitial pneumonia treated with antipyretics and clarithromycin, respectively”.\n\nThe patient was treated with a proton pump inhibitor (esomeprazole 10 mg/day) for two months. Although there were no further gastrointestinal symptoms, and hemoglobin values returned to normal, there is no assurance that the ulcer improved. Therefore, the authors have to explain if another upper endoscopy was done and justify the reason do not perform it.\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? Partly\n\nIs the case presented with sufficient detail to be useful for other practitioners? Partly",
"responses": [
{
"c_id": "6739",
"date": "09 Jun 2021",
"name": "Carmen-Ecaterina Leferman",
"role": "Author Response",
"response": "We would like to thank you for your time, for taking an interest in our article, and for your constructive feedback. All your concerns were valid, pointing out areas in which our case presentation needed improvement. We are therefore grateful for your valuable contribution. We will provide answers to each of your comments illustrating the changes point by point. In paragraph 3 of the Discussion section, the authors pointed out that positive family history of peptic ulcer and association with a dose of paracetamol could explain the gastric ulcer. First of all, the positive family history should be clarified, and secondly what should be the importance of using one dose of paracetamol. Thank you for your excellent point. As a result, we added in the text few lines in order to highlight this important consideration. The accumulation of more risk factors, like positive family history, NSAID administration or H. Pylori infection in pediatric population affected by PUD, has been well documented. The father of the patient was diagnosed with PUD, but was unable to confirm whether he was H. Pylori positive. A joint effect of paracetamol (a dosage higher than 2g) combined with NSAIDs was reported in adults that had both compounds prescribed together. Conversely, the risk for GI ulcers and ulcer complications due to normal paracetamol intake has not been yet supported by available clinical data. The authors should emphasize all drugs used during at least in the last month because the patient “had a positive medical history of upper respiratory tract infections with febrile seizures and interstitial pneumonia treated with antipyretics and clarithromycin, respectively”. Thank you for your suggestion. The mother declared that beside what we already mentioned, in the last month no other antipyretic medication was administered. In the first days of the upper respiratory infection (5 weeks prior to the bleeding episode) Ibuprofen 100 mg every 8 hours for three days was administered, and the next two days when needed (two doses a day at an eight-hour interval). For the convulsion episode no antiseizure medication was needed. Also, clarithromycin 7.5 mg/kg/day was administered 10 days. The patient was treated with a proton pump inhibitor (esomeprazole 10 mg/day) for two months. Although there were no further gastrointestinal symptoms, and hemoglobin values returned to normal, there is no assurance that the ulcer improved. Therefore, the authors have to explain if another upper endoscopy was done and justify the reason do not perform it. Follow-up upper GI endoscopy is mandatory in the case of complicated duodenal ulcers. The report of the endoscopy performed at the end of the treatment period confirmed the healing of the gastric ulceration area. We did not have access to the images."
}
]
}
] | 1
|
https://f1000research.com/articles/9-419
|
https://f1000research.com/articles/10-458/v1
|
08 Jun 21
|
{
"type": "Case Report",
"title": "Case Report: The first familial hCG syndrome in a Chinese family",
"authors": [
"Ling-Yin Hung",
"Mei-Tik Leung",
"Toby Chun-Hei Chan",
"Hoi-Ning Cheung",
"Wai-Hon Li",
"Yui-Shing Cheung",
"Assumpta Sze-Man Wong",
"Chi-Chung Shek",
"Sammy Pak-Lam Chen",
"Ling-Yin Hung",
"Mei-Tik Leung",
"Toby Chun-Hei Chan",
"Hoi-Ning Cheung",
"Wai-Hon Li",
"Yui-Shing Cheung",
"Assumpta Sze-Man Wong",
"Chi-Chung Shek"
],
"abstract": "Familial hCG syndrome is a rare and benign cause of elevated serum beta human chorionic gonadotropin (hCG). We present here a case of familial hCG syndrome diagnosed in a Hong Kong Chinese family, which we believe to be the first reported in Chinese. A 38-year-old woman presented with incidental finding of persistently elevated hCG, analytically confirmed both in urine and blood. Extensive radiological and biochemical work-up were performed but were negative for pregnancy and malignancy. Testing of another asymptomatic family member revealed unexplained elevation of serum hCG, confirming the diagnosis of familial hCG syndrome. Knowledge and awareness of this entity among clinicians are important to avoid unnecessary investigations and treatment in affected families.",
"keywords": [
"familial hCG syndrome",
"hCG",
"human chorionic gonadotropin",
"gestational trophoblastic disease",
"ectopic pregnancy",
"tumour marker",
"autosomal inheritance"
],
"content": "Introduction\n\nFamilial hCG syndrome is a rare but benign cause of elevated serum/urine hCG. To date, fewer than 20 families have been reported worldwide in the literature1–3. Patients present with an otherwise unexplained elevation in serum/urine hCG, and diagnosis is established by exclusion of other causes of elevated hCG and testing of family members. An autosomal dominant pattern of inheritance was observed, although the molecular mechanism has been poorly defined. We present here a case of familial hCG syndrome diagnosed in Hong Kong, which we believe to be the first reported family in Chinese.\n\n\nCase presentation\n\nA 38-year-old Chinese woman, a veterinary surgeon, was referred for investigation of persistent unexplained elevation in serum beta human chorionic gonadotropin (hCG) levels first revealed in a positive urine pregnancy test for the investigation of abdominal pain in August 2020. Apart from a history of menorrhagia and iron deficiency anaemia, the patient had unremarkable past health. She was not on any drugs or supplement and had never been sexually active. Family history was unremarkable. Blood tests showed stable elevation of total beta-hCG ranging from 93–112 IU/L by Roche Elecsys HCG+β assay over the subsequent five months. Transabdominal ultrasound of the pelvis showed no intrauterine sac, and no abnormality was detected in the uterus and ovaries. Pituitary hormones, including serum thyroid-stimulating hormone (TSH), luteinizing hormone (LH), follicle stimulating hormone (FSH) and prolactin levels were normal. Biochemical findings of the patient are summarized in Table 1.\n\nhCG: human chorionic gonoadotropin\n\nLH: Luteinizing hormone\n\nFSH: Follicle stimulating hormone\n\nTSH: Thyroid stimulating hormone\n\nCEA: Carcinoembryonic antigen\n\nCA125: Cancer antigen 125\n\nAFP: Alpha fetoprotein\n\nDue to the discordant clinical and biochemical findings, analytical interference of hCG assay was suspected and a series of interference studies were performed (Table 2). Serial dilution study was performed on the Roche Elecsys HCG+β assay with manufacturer diluent in 1:4 and 1:9 dilutions, which showed linear recovery. Satisfactory recovery was observed in serum hCG level on the Roche assay after treatment with heterophilic blocking tube (Scantibodies Laboratory, Inc). Polyethylene glycol (PEG) precipitation study was performed by mixing 200μL of patient sample with 200μL of 25% (w/v) PEG 6000 (Sigma Aldrich). The sample was then incubated at room temperature for 10 minutes and centrifuged at 9500 × g for 10 minutes. hCG levels were assayed by the Roche Elecsys HCG+β assay in the supernatant. Recovery was satisfactory compared to the hCG result in the neat untreated serum sample. Aliquots of serum were sent to three local laboratories for analyses using different analytical platforms (Abbott Architect, Beckman DxI and Siemens Immulite 2000), all confirming elevation in beta-hCG but to variable extents, with the highest hCG result obtained using Siemens Immulite 2000 (Table 1). Spot urine total beta-hCG was checked by the Roche Elecsys HCG+β assay and measured 168 IU/L.\n\nhCG: human chorionic gonoadotropin\n\nPEG: Polyethylene glycol (PEG 6000)\n\nTo look for underlying tumours, tumour markers including carcinoembryonic antigen, cancer antigen 125 and alpha fetoprotein were checked but were not elevated. Hyperglycosylated hCG (hCG-H) was undetectable (<0.5 μg/L) using the Nichols Advantage hCG-H assay (Nichols Institute Diagnostics, San Clemente, California). Whole body positron emission tomography-computed tomography, magnetic resonance imaging of the pituitary, abdomen and pelvis were unrevealing. Oesophagogastroduodenoscopy was negative.\n\nAs biochemical and radiological work-up could not explain the persistently elevated hCG, familial hCG syndrome was considered in this otherwise asymptomatic patient. Blood hCG test was arranged for one female sibling who also had never been sexually active, and the level was elevated (37 IU/L). There were no other family members available for testing. The diagnosis of familial hCG syndrome was thus established. This is to the best of our knowledge the first case of familial hCG syndrome reported in Chinese.\n\n\nDiscussion\n\nHuman chorionic gonadotropin is a heterodimeric glycoprotein hormone produced by placental syncytiotrophoblast during pregnancy4. It comprises of a common alpha subunit shared between LH, FSH and TSH, and a unique beta subunit that has been shown to be encoded by at least seven genes4,5. In blood circulation, hCG exists in various forms arising from post-translational glycosylation and its degradation in the liver and kidneys4. Apart from pregnancy, increased levels may be seen in gestational trophoblastic diseases, and a number of tumours including germ cell tumours, non-small cell lung cancer6, as well as squamous cell carcinoma of the head and neck region7,8, in which other hCG forms such as free beta-subunit or hyperglycosylated form may predominate4. In postmenopausal women or patients with gonadal insufficiency, sulfated hCG secreted from the pituitary is a frequent cause of mildly elevated hCG. Occasionally, elevated hCG may arise from exogenous administration in doping athletes or as a dietary supplement. In a patient who has otherwise unexplained elevation of hCG discordant with clinical findings, analytical interferences, such as heterophilic antibody interference, are important causes that should be excluded. According to data from USA, hCG Reference Service, among 424 cases of positive hCG with no history of gestational trophoblastic disease or malignancy and pregnancy excluded, the commonest aetiologies were quiescent gestational trophoblastic disease (32%), analytical interference (25%) and pituitary hCG (23%), followed by other malignant conditions (15%) and exogenous intake (1%)1.\n\nThe above differentials were, however, unlikely in our patient based on the extensive negative biochemical and radiological work-up. Intrauterine and extrauterine pregnancies were unlikely given the negative pelvic imaging. Active gestational trophoblastic disease and occult malignancies were less likely with the negative findings on extensive whole-body imaging and undetectable hyperglycosylated hCG. The normal LH and FSH ruled out pituitary hCG. Analytical interferences were less likely although not entirely excluded by the normal recovery on serial dilution, treatment with heterophilic antibody blocking tube and PEG precipitation. The detection of hCG in the urine provides further evidence for a genuine increase in endogenous hCG levels. The negative work-up and persistent elevation in hCG led to the suspicion of familial hCG syndrome, which was subsequently confirmed with testing of hCG level in an asymptomatic family member.\n\nFamilial hCG syndrome is a rare but benign cause of elevated hCG. Serum hCG from reported cases in literature ranged from <1.0 – 216 IU/L, and levels showed fluctuation with time on serial testing2. Antibody profiling by Cole demonstrated the predominance of free β-subunit and β-subunit missing the C-terminal peptide in affected patients1. Both forms are biologically inactive, thus explaining the unaffected fertility in these patients. The presence of these uncommon hCG variants may account for the difference in hCG results across different analytical platforms. Studies comparing the reactivity of available international standards and international reference preparations with sandwich immunoassays on major analyzers have shown vastly different recoveries towards different hCG variants9–11. For instance, the Siemens Immulite 2000 total β-hCG assay, which was shown to have equimolar detection of β-subunit missing C-terminal peptide and nicked hCGβ, consistently returned the highest hCG result among the four platforms tested in our patient. The incongruent results across multiple immunoassay platforms may provide additional support to the diagnosis of familial hCG syndrome, as direct measurements of the various hCG subtypes are not readily available in routine clinical practice. Knowledge of the assay reactivity towards the different variants may aid in the interpretation of discordant results.\n\nReliable markers or diagnostic tests specific to familial hCG syndrome are lacking. Diagnosis relies on careful exclusion of common causes and testing of family members, the former often includes performing a number of costly diagnostic imaging. Of note, a lack of response to a trial of methotrexate therapy has been proposed as one of the diagnostic criteria for familial hCG syndrome in female patients of reproductive age to exclude ectopic pregnancy1, which, however, is not without risk. Further research into the underlying molecular mechanisms and structural characterization of the variants may identify better means of establishing a diagnosis, and may allow detection of concurrent physiological or pathological hCG elevations in diagnosed patients.\n\nIn conclusion, we report here the first case of familial hCG syndrome in a Chinese family. Given the rarity of the entity and the lack of readily available biochemical markers, familial hCG syndrome remains a diagnosis by exclusion. Knowledge and awareness of this disorder among clinicians are important to avoid over investigations and unnecessary treatment, and in offering reassurance to affected patients and family members.\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 clinical and laboratory details was obtained from the patient.",
"appendix": "References\n\nCole LA: Familial hCG Syndrome. J Reprod Immunol. 2012; 93(1): 52–7. PubMed Abstract | Publisher Full Text\n\nCole LA, Butler S: Familial hcg syndrome: Production of variable, degraded or mutant forms of hcg. J Reprod Med. 2014; 59(9–10): 435–42. PubMed Abstract\n\nTan A, van der Merwe AM, Low X, et al.: Familial HCG syndrome: A diagnostic challenge. Gynecol Oncol Rep. 2014; 10: 47–8. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCole LA: Biological functions of hCG and hCG-related molecules. Reprod Biol Endocrinol. 2010; 8: 102. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTalmadge K, Boorstein WR, Fiddes JC: The Human Genome Contains Seven Genes for the beta-Subunit of Chorionic Gonadotropin but Only One Gene for the beta-Subunit of Luteinizing Hormone. DNA. 1983; 2(4): 281–9. PubMed Abstract | Publisher Full Text\n\nKhattri S, Vivekanandarajah A, Varma S, et al.: Secretion of beta-human chorionic gonadotropin by non-small cell lung cancer: A case report. J Med Case Rep. 2011; 5: 19. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMiller C, McQuade M, MacCallum J, et al.: Persistently elevated hCG in a patient with no clear evidence of pregnancy. Clin Chim Acta. 2020; 510: 703–6. PubMed Abstract | Publisher Full Text\n\nTurner JH, Ross H, Richmon J: Secretion of beta-HCG from squamous cell carcinomas of the head and neck. Otolaryngol Head Neck Surg. 2010; 143(1): 169–70. PubMed Abstract | Publisher Full Text\n\nSturgeon CM, Berger P, Bidart JM, et al.: Differences in recognition of the 1st WHO international reference reagents for hCG-related isoforms by diagnostic immunoassays for human chorionic gonadotropin. Clin Chem. 2009; 55(8): 1484–91. PubMed Abstract | Publisher Full Text\n\nWhittington J, Fantz CR, Gronowski AM, et al.: The analytical specificity of human chorionic gonadotropin assays determined using WHO International Reference Reagents. Clin Chim Acta. 2010; 411(1–2): 81–5. PubMed Abstract | Publisher Full Text\n\nCole LA, DuToit S, Higgins TN: Total hCG tests. Clin Chim Acta. 2011; 412(23–24): 2216–22. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "87096",
"date": "16 Jun 2021",
"name": "Weldon Chiu",
"expertise": [
"Reviewer Expertise Gastrointestinal and liver related clinical biochemistry",
"General chemical pathology. Had encountered 2 families with familial hCG syndrome."
],
"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 very well written and worked-up case report on this rare but clinically important condition to avoid over-investigation or worse still, potentially invasive and harmful treatments offered for a benign condition. Though there is no gold standard test, the arguments in favour of this diagnosis are scientifically sound. My only suggestion is that especially with the rarity of this condition, if there are any additional information including serial hCG results and/or any free beta HCG results e.g. from Autodelfia or Johnson and Johnson free beta-hCG platform (designed mainly for maternal serum screening), they would be worth mentioning in the report too.\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": "87100",
"date": "28 Jun 2021",
"name": "Ravi Krishna Cheemakurthi",
"expertise": [
"Reviewer Expertise My area of research is in the field of reproductive genetics especially in the pharmocogenomic aspects of LH and FSH supplementation in COS protocols"
],
"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 appreciate authors for their effort in presenting the case report with clinical findings and proper diagnostic parameters. My suggestion is it would have been more exciting if authors would have tried to find the genetic cause behind the clinical condition, because in many rare disorders it is very difficult to find a family member with similar clinical condition. As of now it is just a case with familial hCG syndrome which was first case in a Chinese family.\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/10-458
|
https://f1000research.com/articles/10-457/v1
|
08 Jun 21
|
{
"type": "Research Article",
"title": "Factors in an Auto-Brewery Syndrome group compared to an American Gut Project group: a case-control study",
"authors": [
"Barbara Cordell",
"Anup Kanodia",
"Gregory K. Miller",
"Anup Kanodia",
"Gregory K. Miller"
],
"abstract": "Background: Auto-Brewery Syndrome (ABS), also known as Gut Fermentation Syndrome, is a rare but underdiagnosed condition. While scores of case studies of ABS are published, only one previous study examined ABS patients’ demographics, health history, lifestyle factors, and diet compared to a control group of household members. Methods: We designed a case-control study to identify factors that individuals with a diagnosis of ABS and those who live with them might have that differ from a larger general group. We administered a survey to 46 patients known to have a diagnosis of ABS and their household members. Here, we compare our group of survey takers to a cohort of the American Gut Project (AGP) participants (N=11,297) for the 30 questions that were identical. Results: With a response rate of 88% and using Rank Sum Tests, the data demonstrate that patients with ABS and their household members are more likely than participants of the AGP to own a pet (p=.03 for cat; p=.0001 for dog), get less sleep (p=.0001), and have lesser quality of bowel movements (p=.03). In addition, the ABS group consumes more water (p=.02) and less alcohol (p=.0004), eats at home more often (p=.0056), and reports more aversion to sweets (p=.01). The most striking difference is a higher presence of non-food allergies in all five subcategories of the survey in the ABS group compared to the AGP group. Conclusion: Patients with ABS and their household members show several significant differences in their lifestyle and health, diet, and medical history compared to a large group of AGP participants. These differences lead to several hypotheses about co-morbidities that warrant further research.",
"keywords": [
"Auto-Brewery Syndrome",
"Gut Fermentation",
"Yeast Overgrowth",
"American Gut Project",
"Microsetta",
"Endogenous Alcohol"
],
"content": "Introduction\n\nAuto-Brewery Syndrome (ABS), also known as Gut Fermentation Syndrome and ‘endogenous ethanol fermentation’, is a rare but underdiagnosed syndrome1. An overgrowth of fermenting yeast or bacteria in the intestines causes patients to ferment carbohydrates and sugars into ethanol. Patients test positive for blood alcohol, often at very high levels, without ingesting alcohol but may or may not exhibit signs and symptoms of intoxication.\n\nThe earliest cases were reported in France in 1894 and translated from French into English in 1906 in the book Auto-Intoxication in Disease2. Since then, at least 68 case studies in Japan, Canada, the United States, Italy, and other countries were published in the post-1950s academic literature3. Of those, 14 individual cases have been published in the last decade and the disease is finally starting to be recognized as a rare but treatable syndrome4.\n\nWe observe that ABS is often reported in people with co-morbidities, such as gastroparesis, Crohn’s disease, short bowel syndrome, and obesity-related liver disease5,6 but otherwise-healthy people are being diagnosed as well7,8. While numerous case studies describe the diagnosis and treatment, little is known about the factors that cause or even contribute to ABS.\n\nThe scores of published cases of ABS, with two exceptions, all point to an over-colonization of fermenting yeast in the gastrointestinal tract. The first anomaly is the case of a man in China with severe non-alcoholic steatohepatitis and bacterial ABS9. Strains of a high alcohol-producing Klebsiella pneumoniae (HiAlc KPN) were strongly associated with his endogenous production of alcohol. With further research, the HiAlc KPN was associated with 60% of people with non-alcoholic fatty liver disease (NAFLD) in a cohort of Chinese people. Furthermore, isolates of the microbes transferred from the subjects to healthy mice induced NAFLD. The second deviation from the norm is a case study published with the location of the fermenting yeast, Candida glabrata, in the patient’s urinary system10. The authors demonstrated high levels of ethanol production in the patient’s urine that was confirmed with an in vitro experiment.\n\nOf the thousands of different species of microbes in an individual’s gut, an estimate of less than 0.1% are considered rare, and fungi belong to the rare biosphere known as the mycobiome. Most of the reports of fungal infections focus on yeast and fungal overgrowth in immunocompromised patients but the incidence of fungemia is increasing. Symptoms of yeast overgrowth include fatigue, headaches, poor concentration, gastrointestinal distress, muscle pain, joint pain, and urogenital symptoms11.\n\nWe now know that underlying genetic susceptibility to Candida plays an important role in infections. Normally, natural defense mechanisms prevent the commensal Candida and other yeasts from becoming pathogenic. But loss of barrier function, imbalances in the gut microbiome, or inadequate immunity may lead to increased susceptibility to invasive candidiasis12.\n\nIn addition to the universally demonstrated overgrowth of fermenting yeast or bacteria, patients with ABS often have signs of yeast infections in their integumentary, genitourinary, or oral systems. Some patients with ABS respond to dietary changes alone, while others require anti-fungal medication, dietary changes, supplements, probiotics, and lifestyle modifications such as adequate sleep, stress-reduction, and moderate exercise. A small number of patients do not seem to respond to any of the mentioned treatments or will persistently relapse. For these chronic patients, a Fecal Microbiota Transplant (FMT) appears to be a promising treatment. A patient in Belgium received what we believe is the first published case of a successful FMT for ABS13.\n\nOf four previous studies on groups of fermenting patients, only one looked at ABS patients’ demographics, health history, lifestyle factors, and diet to determine factors that might contribute to ABS14. The study demonstrates that patients with ABS or symptoms have significant differences in their lifestyle and health, diet, and past medical history compared to household participants who live with someone with ABS but do not have clinical ABS.\n\nThe purpose of the current research project is to identify the health history and lifestyle factors of subjects diagnosed with ABS and their household members and compare those factors in subjects of a large control group from the database of the American Gut Project (AGP). The AGP is a crowd-funded science project to analyze the gut microbiomes of a large cross section of American citizens and determine what health and lifestyle factors correlate to different microbiomes15. The null hypothesis is that there will be no differences between the ABS and household members compared to the AGP group on thirty questions related to health and lifestyle.\n\n\nMethods\n\nWe designed a case-control study in 2016 to identify factors that individuals with a diagnosis of gut ABS and those who live with them might have that differ from a more general group in the AGP. We developed a survey that included 30 questions identical to those used in the AGP group and could be easily administered online. The 30 identical questions were used for analysis in this study. Our study design was submitted to and approved by the Institutional Review Board at Panola College in Carthage, TX, USA with approval number PC-IRB-08032016.\n\nA 78-item survey titled, Gut Fermentation Survey, was developed using questions from the AGP as well as questions from other well-known survey sources detailed below. In addition to questions for demographics and diagnosis, we used 30 of the AGP questions and these comprise the questions for the current statistical analysis between the two groups. The AGP supplied us with their questionnaire and permission to use any of their questions. In addition, they supplied data on 11,297 respondents who also answered the 30 questions as they participated in a volunteer study that used a longer questionnaire and collected stool samples16. Bias is minimized in the questionnaire by using questions from well-known questionnaire sources that have validity and reliability.\n\nQuestions 1–8 are demographic questions patterned after the Integrated Postsecondary Education Data System17 from the National Center for Education Statistics (NCES) of the Department of Education. Questions 9–11 ask about diagnosis and symptoms of ABS and serve to divide the group of respondents into the ABS group and those who live with someone with ABS. Questions 12–37 query Lifestyle and Health factors such as living arrangements, dental care, tobacco use, bowel habits, sleep habits, and pet ownership. The tobacco questions come from the World Health Organization18. The bowel habit questions are from the AGP, and the sleep questions are from the Mini-Sleep Questionnaire19.\n\nQuestions 38–55 ask about General Diet Information such as type of diet followed, amount and type of liquids consumed, alcohol consumption, and food allergies. The dietary questions are from the AGP except for the questions on alcohol use that came from the National Institute on Alcohol Abuse and Alcoholism20. Questions 56–72 concern the individual’s Health History such as the method of birth, whether the subject was breast-fed or given formula and how long, past surgeries, medical conditions past and present, as well as non-food allergies. The questions on breastfeeding came from the survey methods of breastfeeding from the Centers for Disease Control and Prevention21 and the other questions are from the AGP. Questions 73–77 inquire about medications and supplements and question 78 asks if the respondent would be willing to be contacted concerning future research opportunities. Information on access to the questionnaire is provided at the end of the article.\n\nBetween September 2016 and January 2017, we emailed requests to participate in the study to people known to the authors to either have a diagnosis of ABS or share a household with a person diagnosed with ABS. A hyperlink to the survey was included in the email request. Because ABS is very rare, we invited everyone we knew from various medical practices treating ABS, from a Facebook support group for ABS, as well as from emails sent to the author from her website on ABS. Diagnosis was confirmed by the diagnosing provider or a medical record. A $25 Amazon gift card was offered as an incentive to those who completed the survey. Bias was minimized by using a standard email message, one person to answer questions, and a uniform informed consent.\n\nIn total, all 52 people known to the authors to have ABS or to live with someone with ABS were invited to participate in the study. People with ABS were included if they were at least 18 years of age and had been formally diagnosed by a professional licensed to diagnose in their state or country. Household members were included if they lived in the same house as a person diagnosed with ABS and were at least 18 years of age. Potential participants were excluded if they were under 18 or unable to complete a survey, even with assistance. Of those invited, 46 agreed to participate, received the informed consent document, and completed the electronic Gut Fermentation Survey for an 88% response rate. The informed consent was included as the page prior to the survey and subjects were told that proceeding with the survey served as their consent. Of the 46 respondents, 28 had a history of ABS and the other 18 respondents lived in the same dwelling as one of the people with ABS. Hereinafter, the ABS and household groups are combined and labeled as the ABS group that comprised the group we compared to the data from the AGP.\n\nThe statistical analysis compared the answers for the 30 questions from the ABS and household respondents (N=46) to the answers on identical questions administered by the AGP survey (N=11,297). For those 30 questions on the two surveys, 2 by c contingency tables were created to tabulate question responses and test for row homogeneity (ABS vs. AGP group) using a permutation chi-square test.\n\nAll such permutation chi-square tests were performed using StatXact Version 4.0.1. Additional permutation Kruskal-Wallis tests reduced to Rank Sum Tests (also known as Mann-Whitney Wilcoxon Rank Sum Tests) were used to analyze row homogeneity between the ABS and AGP groups in the cases where survey questions generate ordinal responses.\n\nWe note that with such a large sample size in the control group from the AGP, our focus is less on p-values and more on the actual differences (observed effect sizes) seen in the percentages. These are provided in subsequent sections.\n\n\nResults\n\nThe demographics of the 46 ABS participants are detailed in Table 1. All participants were over the age of 18 as verified in the informed consent. The majority of participants were White, not Hispanic or Latino, and were born and lived most of their lives in the United States.\n\nLifestyle and Health: In the Lifestyle and Health section of the Gut Fermentation Survey, there are three statistically significant differences between the responses from the ABS group and those in the AGP group. Data show that those in the ABS group are: (1) more likely to own a traditional pet (41% vs. 27%, p = .03 for cat, 57% vs. 29%, p = .0001 for dog); (2) less likely to get 7 hours or more of sleep per night on average (31% vs. 59%, p = .0001); and (3) less likely to report typically having normal bowel movements (55% vs. 72%, p = .03) than those in the AGP group.\n\nGeneral Diet Information: Regarding dietary intake, those in the ABS group tend to report a higher tendency to typically consume at least one liter of water per day (62% vs. 50%, p = .02). The ABS group tends to consume less alcohol than the AGP group with a higher percentage reporting complete abstinence (47% vs. 24%, p = .0004). We see a difference in the distribution of frequency of eating out between the two groups (p = .0056) with 16% of ABS respondents stating they never eat out compared to 8% for the AGP participants. The ABS group also stated an aversion to sweets with 36% stating they refrain compared to 13% in AGP group (p = .01).\n\nHealth History: A sweeping difference between the ABS and AGP group is seen concerning the presence of allergies. The ABS group is far more of an allergic group than the AGP respondents. We see a theme where for each subcategory of non-food allergy, the ABS group shows a higher presence of an allergic reaction. Table 2 details the five subcategories of allergies with the comparison of the ABS group percentages to those of the AGP group. P-values for each comparison resulting from the associated 2 by 2 contingency table are provided. The ABS group was more likely to have seasonal allergies, drug allergies, and pet dander allergies. They were also more likely to have an allergy to bee or wasp stings and poison ivy or poison oak.\n\nAs telling as the significant results are, the items without statistical significance are still important to consider. Much research about how the microbiome develops and differs between cultures has to do with factors such as the method of birth (vaginal vs. cesarean), infant feeding (breast vs. formula), and childhood illnesses such as chickenpox. Even though the data show no significance on these three items between the ABS group and the AGP group, these factors should not be dismissed but be examined further. Perhaps a larger group of people with ABS would reveal different results.\n\nIssues of immunity such as presence or absence of tonsils and appendix, and history of flu vaccine were also assessed, and the lack of significant differences does not mean those factors do not influence ABS\n\n\nDiscussion\n\nUsing the 30 identical questions from the Gut Fermentation Survey and AGP survey, we found 12 statistically significant differences between people with ABS or living with someone with ABS and the more general group of persons participating in the AGP.\n\nIn the Lifestyle and Health section, the fact that people in the ABS group are more likely to have a lesser quality of bowel movements than the large data set (N=11,297) from the AGP, supports the idea that gut dysbiosis is the underlying cause of ABS. This a similar finding to previous research we conducted and strengthens the finding14. People with perturbations in the gut microbiota would be expected to have changes in bowel habits and conversely changes in bowel habits reflect gut dysbiosis. There is evidence that changing the gut microbiota through fecal transplant, often relieves symptoms such as diarrhea, indigestion, and abdominal pain22.\n\nThe strongly significant difference that subjects in the ABS group get less sleep than the control group may indicate there are factors of ABS such as intoxication, that cause patients to lose sleep. A study of 393 participants who visited a hospital demonstrated a high correlation in men between alcohol use and sleep disturbances as well as the perception of poor quality of sleep23. People who generate their own alcohol would likely suffer the same ill effects.\n\nThe General Diet Information section provides data similar to previous research in that people with ABS consume more water and less alcohol. In addition, they are less likely to eat meals away from home and more likely to avoid sweets. Candida overgrowth in the gut is associated with inflammation and other gastrointestinal diseases such as Crohn’s disease, ulcerative colitis, and gastric ulcers, which can lead to painful symptoms and loss of appetite24.\n\nThese findings could also be due to the dietary changes made by patients who have become aware of dietary triggers and are making informed decisions to change their eating habits. Additional information should be collected on these and other patients to determine what dietary habits they had historically, versus the dietary patterns adopted once they became aware of ABS symptoms, triggers, and treatments.\n\nThe most interesting segment of the survey comparison is the Health History section. The participants in the ABS group are much more allergic overall than the 11,297 respondents of the AGP. The ABS group is more likely to have seasonal allergies, have drug allergies, be allergic to pet dander, be allergic to bee stings, and be allergic to poison ivy or poison oak. Overall, people who suffer from ABS and those who live with them are a much more atopic group than those in the AGP. These data suggest a possible link to immune systems that may be interacting with gut dysbiosis in the expression of symptoms.\n\nFood sensitivities are closely related to other types of allergic reactions. Fermentable carbohydrates termed ‘FODMAPs’ (fermentable oligo- di- mono-saccharides and polyols) occur in many foods and are associated with many gastrointestinal symptoms such as IBS. Such sensitivities and even intolerances have been linked to eczema, asthma, food allergies, and allergic rhinitis25.\n\nPeople with ABS have gut dysbiosis by the very presence of an over-colonized fermenting yeast or bacteria and by the production of endogenous alcohol. Symptoms of gut fermentation may mimic food sensitivities and it would make sense that fermentable carbohydrates would create additional gastrointestinal symptoms. The fact that the ABS group is more allergic follows the theory of ‘allergic march’ where there are patterns of co-morbidities of allergic disease and even progression rather than a single disease26. This hypothesis should be explored further.\n\nThe significant difference that people in the ABS group are more likely to own a pet, indicates animals could be a possible contributing factor. Even though people with ABS are more likely to be allergic to pet dander, they are also more likely to own a pet. This raises the question of whether owning a pet further exacerbates fermentation and symptoms. And it also raises the question whether an allergy to pet dander contributes somehow to gut fermentation.\n\nOne limitation to the study is the online nature of the survey. Not all potential participants have access to a computer or are willing to take an online survey. These people may differ from those who do have a computer and are willing to take an online survey. Another limitation to the study is the small sample size. Significance from other questions may not have been detected with such a small ABS sample. The lack of significant results in the factors mentioned above leads us to believe these factors are not related to the development of ABS but they might still be important in future studies. While we certainly need to focus in on the significant differences, we should dig deeper into other factors to see how ABS develops. An important study would be to look at these and other factors in patients when they are first diagnosed prior to treatment.\n\nOur ABS sample size is seemingly small but considering the rarity of ABS, we felt fortunate to have as many participants as we did. Because our analysis contained patients from four continents and our response rate was 88%, we are confident in generalizing our results to the growing field of ABS.\n\n\nConclusion\n\nAuto-Brewery Syndrome is a rarely diagnosed syndrome affecting people worldwide. While many case studies have been published there is scant research on ABS. Very little is known about lifestyle factors such as health, diet, and past medical history of ABS patients that may contribute to symptoms. Using questions from the nationwide AGP survey, our research showed 12 statistically significant differences between the group of ABS patients and housemates, and the more general group from the AGP.\n\nThe findings in this case control study give insights into common factors experienced by people with ABS and their household members. We believe our findings raise interesting hypotheses about co-morbidities. These hypotheses warrant additional research into influences that may impact the microbiome and lead to ABS. We recommend that providers in emergency departments and gastroenterology practices retain an open mind when they meet intoxicated patients who insist they have not been drinking. The more we learn about ABS the more we can respond with compassion and science-based information.\n\n\nData availability\n\nDryad: ABS Questionnaire 2016 and Questionnaire results 2018, https://doi.org/10.5061/dryad.vq83bk3sg27.\n\n- This project contains the survey responses from the 46 participants for the 78 questions of the Gut Fermentation Survey.\n\n- Data are available under the terms of the Creative Commons Zero \"No rights reserved\" data waiver (CC0 1.0 Public domain dedication).\n\nQiita: American Gut Project – ID 10317, Accession number 10317: https://qiita.ucsd.edu/study/description/10317#\n\n- This project contains the survey responses from the 11,297 American Gut Project (AGP) participants prior to 2016.\n\n- Qiita is free to use but requires the registration before access. Users can register for free here.\n\nEuropean Nucleotide Archive: American Gut Project. Accession number ERP012803, https://www.ebi.ac.uk/ena/browser/view/PRJEB11419\n\nDryad: datadryad.org, ABS Questionnaire 2016 and Questionnaire results 2018, https://doi.org/10.5061/dryad.vq83bk3sg27.\n\n- This project contains the survey sent to participants\n\n- Data 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 wish to thank the American Gut Project, now the Microsetta Initiative, within the Knight Lab at UCSD Medical School, for sharing their questionnaire and data with us for this study.\n\n\nReferences\n\nMalik F, Wickremesinghe P, Saverimutti J: Case report and literature review of auto-brewery syndrome: probably an underdiagnosed medical condition. BMJ Open Gastroenterol. 2019; 6(1): e000325. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBouchard C: Lectures on Auto-Intoxication in Disease. FA Davis, Philadelphia; 1906. Reference Source\n\nCordell B: My Gut Makes Alcohol! The Science and Stories of Auto-Brewery Syndrome. Published by author; 2019. Reference Source\n\nPainter K, Cordell B, Sticco K: Auto-brewery syndrome (gut fermentation). NCBI Bookshelf, NLM, NIH. StatPearls Publishing, Treasure Island, FL; 2019. Reference Source\n\nHafez EM, Hamad MA, Fouad M, et al.: Auto-brewery syndrome: ethanol pseudo-toxicity in diabetic and hepatic patients. Hum Exp Toxicol. 2017; 36(5): 445–50. PubMed Abstract | Publisher Full Text\n\nWelch BT, Prabhu NC, Walkoff L, et al.: Auto-brewery syndrome in the setting of long-standing Crohn's disease: a case report and review of the literature. J Crohns Colitis. 2016; 10(12): 1448–450. PubMed Abstract | Publisher Full Text\n\nCordell B, McCarthy J: A case study of gut fermentation syndrome (auto-brewery) with saccharomyces cerevisiae as the causative organism. Int J Clin Med. 2013; 4(7): 309–312. Publisher Full Text\n\nCordell B, Kanodia A: Auto-brewery as an emerging syndrome: three representative case studies. J Clin Med Case Rep. 2016; 2: 5. Reference Source\n\nYuan J, Chen C, Cui J, et al.: Fatty liver disease caused by high alcohol-producing klebsiella pneumoniae. Cell Metab. 2019; 30(6): 1172. PubMed Abstract | Publisher Full Text\n\nKrukenberg KM, DiMartini AF, Rymer JA: Urinary auto-brewery syndrome: a case report. Ann Intern Med. 2020; 172(10): 702–04. PubMed Abstract | Publisher Full Text\n\nLewith GT, Chopra S, Radcliffe MJ, et al.: Elevation of candida IgG antibodies in patients with medically unexplained symptoms. J Altern Complement Med. 2007; 13(10): 1129–33. PubMed Abstract | Publisher Full Text\n\nDavidson L, Netea MG, Kullberg BJ: Patient susceptibility to candidiasis–a potential for adjunctive immunotherapy. J Fungi (Basel). 2018; 4(1): 9–29. PubMed Abstract | Publisher Full Text | Free Full Text\n\nVandekerckhove E, Janssens F, Tate D, et al.: Treatment of gut fermentation syndrome with fecal microbiota transplantation. Ann Intern Med. 2020; 173(10): 855. PubMed Abstract | Publisher Full Text\n\nCordell BJ, Kanodia A, Miller GK: Case-control research study of auto-brewery syndrome. Glob Adv Health Med. 2019; 8: 2164956119837566. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMicrosetta, Knight Lab, UCSD School of Medicine: American Gut Project. 2020; Accessed: December 3, 2020. Reference Source\n\nMcDonald D, Hyde E, Debelius JW, et al.: American Gut: an open platform for citizen science microbiome research. 2018. Publisher Full Text\n\nNational Center for Education Statistics – NCES: IPEDS 2015-2016 Data Collection System. Accessed: May 24, 2016. Reference Source\n\nWorld Health Organization: Global tobacco surveillance system. Accessed: May 24, 2016. Reference Source\n\nNatale V, Fabbri M, Tonetti L, et al.: Psychometric goodness of the Mini Sleep Questionnaire. Psychiatry Clin Neurosci. 2014; 68(7): 568–573. PubMed Abstract | Publisher Full Text\n\nNational Institute on Alcohol Abuse and Alcoholism. Accessed: May 24, 2016. Reference Source\n\nCenters for Disease Control and Prevention: Survey: Breastfeeding Rates. Accessed: May 24, 2016. Reference Source\n\nKang D, Adams J, Gregory A, et al.: Microbiota transfer therapy alters gut ecosystem and improves gastrointestinal and autism symptoms: an open-label study. Microbiome. 2017; 5(1): 10. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPark SY, Oh MK, Lee BS, et al.: The effects of alcohol on quality of sleep. Korean J Fam Med. 2015; 36(6): 294–99. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKumamoto CA: Inflammation and gastrointestinal Candida colonization. Curr Opin Microbiol. 2011; 14(4): 386–391. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAl-Abri R, Al-Amri AS, Al-Dhahli Z, et al.: Allergic rhinitis in relation to food allergies: pointers to future research. Sultan Qaboos Univ Med J. 2018; 18(1): e30–e33. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGoksör E, Loid P, Alm B, et al.: The allergic march comprises the coexistence of related patterns of allergic disease not just the progressive development of one disease. Acta Paediatr. 2016; 105(12): 1472–79. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCordell, et al.: ABS Questionnaire 2016 and Questionnaire results 2018. Dryad. [dataset]. http://www.doi.org/10.5061/dryad.vq83bk3sg"
}
|
[
{
"id": "89070",
"date": "27 Jul 2021",
"name": "Kenichi Tamama",
"expertise": [
"Reviewer Expertise Chemical pathology",
"clinical toxicology",
"laboratory medicine",
"stem cell biology"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe corresponding author has been very active in the research about auto-brewery syndrome (ABS) or gut fermentation syndrome. In this article, the authors tried to identify novel factors associated with ABS by conducting a survey-based case-control study for 46 ABS patients and their household members and comparing the survey results with a cohort of the American Gut Project participants (N=11,297).\nThe article is well-written and the relevant articles are appropriately cited. Their data indicate the possible presence of allergic components in the ABS pathogenesis. This is a novel finding, but its significance is uncertain at the moment. This hypothesis should be further explored, as the authors state in the article.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
},
{
"id": "87176",
"date": "06 Sep 2021",
"name": "Jing Yuan",
"expertise": [
"Reviewer Expertise Microbial infection and intestinal flora"
],
"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\nAuto-brewery syndrome (ABS), also named gut fermentation syndrome, drunkenness disease or endogenous ethanol fermentation, is a syndrome in which patients become intoxicated without ingesting alcohol. As a rare case, the pathogenesis and inducement of ABS are not fully understood. In this study, the author investigated the health history and lifestyle factors of subjects between ABS and control group (AGP). As most of the ABS cases could be control through dietary control and lifestyle changes, the design of the subject can help us to understand the disease induce factors of the ABS group, so as to prevent the development. They found that ABS group are more likely than to own a pet, get less sleep, and have lesser quality of bowel movements. In addition, the ABS group consumes more water and less alcohol, eats at home more often, and reports more aversion to sweets.\nThis study was well designed and the result has certain reference significance to the following research for ABS. The manuscript is well written and attractive, but I have some minor concerns on diet Information. They showed that ABS group more likely to avoid sweet. But the onset of most ABS cases was reported to consuming more carbohydrate, especially sugar. The author explained that this may due to the dietary changes made by patients who have become aware of dietary triggers and are making informed decisions to change their eating habits. I recommended to add more detail questions in this part, like the diet before and after ABS diagnosis. It will have a good help for clinician and epidemiologist to understand the dietary triggers for ABS.\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": "89069",
"date": "16 Sep 2021",
"name": "Gaku Takahashi",
"expertise": [
"Reviewer Expertise Infection"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 had a very interesting look at the relationship between homebrewing syndrome and allergic constitution. I have read your treatise and have some questions. A recent treatise suggested a link between homebrewing syndrome and alcohol-degrading enzymes. Therefore, in this study as well, I think it is necessary to further investigate the strength of individual reactions to alcohol. It may not be possible to conduct a survey at the genetic level, but I think an additional questionnaire survey is necessary. In addition, I think it is necessary to list all the items and results of the questionnaire survey in the table. Please consider these points.\nI have some further questions, so please consider and improve. From the results of the questionnaire, it was said that there is a relationship between autobrewing syndrome and allergies. I think it is necessary to consider the reason for this. I also speculate that autobrewing syndrome is associated with alcohol-degrading enzyme function, periodontal disease, and gut microbiota. If possible, please consider the constitution of each case with alcohol and the presence or absence of periodontal disease. Please consider referring the following paper of mine. Gaku T, et al. Auto-brewery syndrome caused by oral fungi and periodontal disease bacteria. Acute med Surg.\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
|
https://f1000research.com/articles/10-457
|
https://f1000research.com/articles/10-456/v1
|
08 Jun 21
|
{
"type": "Opinion Article",
"title": "Moving forward with forward genetics: A summary of the INFRAFRONTIER Forward Genetics Panel Discussion",
"authors": [
"Asrar Ali Khan",
"Michael Raess",
"Martin Hrabe de Angelis",
"Michael Raess",
"Martin Hrabe de Angelis"
],
"abstract": "In the last few decades, forward genetics approaches have been extensively used to identify gene function. Essentially, forward genetics is the elucidation of the genetic basis of a specific phenotype by screening a population containing random genomic modifications that alter gene function. These approaches have shed light on some essential gene functions in development and disease and have expanded the realm of understanding for genetic disorders. Due to the availability of efficient mutagenesis methods, phenotyping techniques, reliable validation, comprehensive sequence information and translational potential, mouse models are favored for forward genetics approaches. However, in this post-genomic CRISPR-Cas9 era, the relevance and future of forward genetics was brought into question. With more than 7300 mouse strains archived and close interactions with several leading mouse researchers around the world, INFRAFRONTIER - the European Research Infrastructure for mouse models organised a panel discussion on forward genetics at the International Mammalian Genome Conference 2018 to discuss the future of forward genetics as well as challenges faced by researchers using this approach in the current research environment. The commentary presents an overview of this discussion.",
"keywords": [
"Forward genetics",
"mouse models",
"INFRAFRONTIER",
"IMPC"
],
"content": "Introduction\n\nForward genetics is an approach that identifies the genetic basis of a specific phenotype. In medicine, this translates to the discovery of mutations that are responsible for a genetic disease. Contrary to reverse genetics that starts with a specific gene and studies the effects of its altered expression on phenotype, forward genetics uncovers the genes behind a particular phenotype (Figure 1). Briefly, such an approach starts with a screen to identify a mutant phenotype that is either naturally occurring or artificially induced, for example by N-ethyl-N-nitrosourea (ENU), a potent mutagen (de Angelis et al., 2000) (Acevedo-Arozena et al., 2008). Next, the phenotype producing population is mapped followed by mapping of responsible candidate genes and sequencing to find the causative mutation. In the final step, the candidate mutation is validated using genetic engineering approaches.\n\nForward genetics (e.g., mutagenesis screens) involves identifying the genetic basis of a phenotype while reverse genetics (e.g., ectopic expression) involves genetic manipulation and study of the resulting phenotype.\n\nOver the years, forward genetics has made significant contributions to human genetics research. For example, the etiology of several monogenic diseases like Rett syndrome (Buchovecky et al., 2013) and Huntington’s disease (Macdonald et al., 1993) have been successfully discovered using forward genetics approaches. The mutations responsible for complex phenotypes and disorders like obesity (Zhang et al., 1994), infertility (Hu et al., 2019) and circadian rhythm dysregulation (Vitaterna et al., 1994) were also successfully identified using model organisms like mice. The biggest advantage of this approach is its unbiased nature for establishing a clear relationship between a mutation and disease phenotype.\n\nAt a scientific review meeting of the Helmholtz Center Munich in February 2018, an interesting discussion was initiated about the current status and future directions of forward genetics. ‘Where does forward genetics fit in other technologies in this post-genomic era and what is its relevance?’. This initial discussion led to the organization of the Forward Genetics Panel Discussion at the International Mammalian Genome Conference 2018 (IMGC 2018). The objective of the panel discussion was to explore the current state and future of forward genetics in the light of the recent developments in (functional) genomics and data-driven science. The panellists consisted of international leaders in the field of mouse genetics and pioneers in forward genetics approaches. The panel discussion was chaired by Prof. Dr. Martin Hrabě de Angelis.\n\nThe panel discussion was preceded by a lecture from Prof. Dr. Bruce Beutler (Nobel Prize in Physiology or Medicine, 2011) on his ongoing state-of-the-art forward genetics screens to uncover mutations leading to immunological phenotypes. This entire session on Forward Genetics at the IMGC 2018 was hosted by INFRAFRONTIER via the IPAD-MD project.\n\n\nPanellists\n\nProf. Dr. Bruce Beutler, director of the Center for the Genetics of Host Defense (UT Southwestern Medical Center), has been one of the foremost leaders in the field of forward genetics and has made several key discoveries in immunology using this approach. Currently, his team conduct robust and automated forward genetics screens to identify genes responsible for specific physiological processes like immunity, metabolism, developmental and neurobehavioral functions.\n\nProf. Dr. Monica Justice is the head of the Genetics and Genome Biology Program at the Hospital for Sick Children (SickKids). Prof. Justice pioneered the use of ENU-based chemical mutagenesis approaches in mice and she has recently shown DNA damage response contributes to the pathology of Rett Syndrome.\n\nDr. Laura Reinholdt is an associate professor at the The Jackson Laboratory and has led the cloning of several ENU alleles responsible for aberrant meiotic chromosome dynamics under the Reprogenomics ENU program. Her group is widely interested in the development and application of both forward and reverse genetic approaches for understanding the etiology of genome variation and its role in health and disease.\n\nProf. Dr. David Beier, director of the Center for Developmental Biology and Regenerative Medicine at the Seattle Children's Research Institute, has been on the forefront of several major developments in the genetic analysis of model organisms including the application of ENU mutagenesis for developmental investigation and for sequence-based analysis.\n\nProf. Dr. Nadia Rosenthal is the scientific director of The Jackson Laboratory and a renowned expert in the use of mice for targeted mutagenesis in the study of muscle development, disease and repair. An integral part of EUCOMM, the European Conditional Mouse Mutagenesis Program, she coordinated the selection and production of new Cre driver strains for the international mouse genetics community.\n\nDr. Ruth Arkell heads the Early Mammalian Development Laboratory at the John Curtin School of Medical Research (ANU) and has conducted several forward genetics genome-wide ENU mutagenesis screens at MRC Harvell and ANU. She now focuses on the genetic mechanisms that control mammalian gastrulation and the consequences of incorrect gastrulation.\n\nProf. Dr. Martin Hrabě de Angelis, director of the European Mouse Mutant Archive (EMMA) and the Institute of Experimental Genetics at the Helmholtz Center Munich, is a strong proponent of forward genetics and has made several prominent discoveries in the field of genetics using ENU mutagenesis forward genetics screens.\n\n\nContribution of forward genetics towards understanding the genetic basis of human disease\n\nAccording to the panellists, there was no one particular forward genetics contribution that was the important towards the better understanding of human diseases and mammalian physiology. Some of the notable contributions of forward genetics were the discovery of Toll-like receptor (TLR)-4 as the lipopolysaccharide sensor (Poltorak et al., 1998) and discovery of Clock gene as the central regulator of mammalian circadian rhythm (Daxinger et al., 2013), discovery of early mammalian development genes (Anderson, 2000) and models for metabolic bone diseases (Sabrautzki et al., 2012).\n\nIn their view, forward genetics is the re-evaluated application of classical mendelian genetics because it also deals with the heritability of quantifiable traits. It has gained more importance in the last few decades as the actual complexity of the genome has started to become evident.\n\n\nRelevance of forward genetics in the post-genomic era\n\nForward genetics is remains highly relevant in the post-genomic era. Human geneticists are realising the importance of mouse models replicating the exact mutation found in human patients whereas previously they heavily relied on sequencing, association studies and reverse genetics to understand complex human diseases. The impact of environment and diet on diseases is widely acknowledged now. In addition, in most cases it is not a single gene but a network of genes that is responsible for a disease. Therefore, more sophisticated human diseases models are needed to accurately emulate complex human pathologies. One of the main advantages of forward genetics approaches is their unbiased nature, requiring no prior knowledge of a biological pathway. In addition, a wide spectrum of mutations is possible using mutagens that can create a variety of alleles (hypomorphicm hypermorphic, neomorphic and conditional) alleviating the problems of lethality. With their unbiased nature, forward genetic approaches can determine which genetic regulatory networks have pathogenic consequences and also employ complex mouse models which would be immensely helpful to human geneticists.\n\n\nAdvancements in forward genetics\n\nIn the last few decades, several advancements have led to significant progression of forward genetic screens. Some of them are listed below:\n\nPositional cloning: The process of positional cloning, i.e. the identification of the causative mutation, was expedited by the publication of the annotated mouse genome in 2002 and sequencing of whole mammalian exomes. Previously, such sequencing endeavours required more than 9 years to complete and now can be accomplished in a few weeks.\n\nGenetic mapping: Another breakthrough was the ‘instant positional cloning’ technique that could resolve disease phenotypes almost instantaneously (Wang et al., 2015) thereby removing the bottleneck of genetic mapping. High-throughput sequencing (HTS) technologies have expedited forward genetic screens with rapid mutation discovery (as reviewed by Simon et al., 2012). An approach called mapping-by-sequencing uses next-generation sequencing to simultaneously map and identify causal mutation by sequencing bulk populations of recombinant offspring (Schneeberger et al., 2009). A number of recent advancements of this approach have made forward genetic screens more accessible. These advancements include methods that are independent of reference genome sequences, genetic crosses and any kind of linkage information (as reviewed by Schneeberger, 2014). The use of whole-genome sequencing (WGS) has also made it possible to study mutant lines in an inbred genetic background and identify elusive genetic modifiers (Geister et al., 2018).\n\nMutant production: CRISPR-Cas9 genome editing has been used in forward genetics screens to create genome-wide mutant libraries because to its easier scalability. In addition, unlike chemical mutagens or radiation, CRISPR allows the generation of mutant libraries with known mutation sites. On one side, the development and use of inbred mice also made forward genetic screens easier. These strains possess a near overall homozygosity in their genetic loci making the identification of the causative mutation faster and cheaper. While on the other side, genetic screens have also started to utilize genetically diverse mouse strains that are generated by out-breeding and not by mutagenesis. These offer the advantage of replicating the genetic diversity found in humans to a certain extent and also capture structural genetic variants that are missed by mutagenesis (Saul et al., 2019).\n\nPhenotype screening: Several new technologies have greatly improved the efficacy of phenotype screening methods used in forward genetics screens. These include induced pluripotent stem cells, 3D-culture systems and organ-on-a-chip. In addition, the use of in vivo models, like fruit flies, C. elegans and mice, in phenotypic screens have opened up new avenues for forward genetics by standardising phenotyping pipelines. These technologies and advancements have enabled forward genetic screens to realistically recapitulate human disease biology.\n\nValidation: The use of CRISPR also enabled efficient validation of disease mutations by the rapid generation of specific mouse models reproducing the disease phenotype.\n\nThus, the last few decades of advancements in genome editing, in vitro and in vivo models, and sequencing technologies collectively propelled forward genetic screens.\n\n\nFuture of forward genetics\n\nHuman geneticists primarily rely on mapping of genetic variants (genome-wide association studies) to determine pathogenic genetic changes. As mentioned previously, forward genetics is invaluable in this regard and can provide an efficient way to molecularly assess and validate such mutations thereby bridging the relationship between functional genetic variation and human diseases.\n\nCRISPR-Cas9 has been a disruptive technology in field of genetic engineering. The efficiency, accuracy and ease of operation compared to previous technologies has also brought CRISPR-Cas9 into functional genomics screens as well. Not only has it improved reverse genetics, i.e. the validation of discovered mutations (mentioned above), but several studies have also shown its usefulness in forward genetics screens. As reviewed by Sharma & Petsalaki (2018), these pooled CRISPR-Cas9 screens offer the possibility to investigate a very large number of genetic changes in one screen.\n\nForward genetics screens are in fact promising classical genetics tools that are customizable and easy to use. This aspect is especially enticing for various research groups to undertake smaller customized screens that are specifically tailored to a scientific question. Subsequent services like cloning, phenotyping, genetic mapping and sequencing can be supported by larger core centres or infrastructures.\n\n\nChallenges (technical and financial) in the field of forward genetics\n\nAs stated earlier, positional cloning was a major rate limiting step in forward genetics screen which has been overcome with the ‘instant positional cloning’ method. The speed and affordability of current-generation sequencing technologies has also greatly helped in this direction. However, these advancements have led to the generation of large amount of genotypic and phenotypic data increasing the demand for the mechanistic analyses needed to make sense of precisely how specific mutations lead to specific phenotypes. As mentioned earlier, CRISPR is a promising tool for forward genetics. However, its use in forward genetics can still be improved by minimising off-target effects, and by targeting isoforms or splice variants and non-coding sequences like regulatory elements.\n\nOne of the main challenges faced in forward genetics today is the competition for funding from human geneticists with funding agencies arguing that animal models like mice are not suitable tools to discover, validate and study disease causing mutations. As mentioned earlier, human geneticists require allele-specific models for translational research of human diseases that can also be used for preclinical studies. The generation of such ‘synthetic complex disease models’ is currently only possible in mice.\n\nOne aspect that still requires improvements is the automated handling of animal models in these screens as they involve breeding and housing of large number of mutant animals and their subsequent progeny which is labour-, time-, and cost-intensive.\n\n\nPossible cooperative efforts from the forward genetics community\n\nIt was agreed upon that a collective effort is required to bring back forward genetics into the limelight and promote its use in present and future biomedical research. One such cooperative effort would be to develop a precision model generation and robust phenotyping pipeline for characterizing human functional genetic variation in mouse models. This pipeline could be used by human geneticists to investigate pathogenic allelic variations and enable mouse geneticists to provide valuable and reliable support to human geneticists.\n\nMore focus should be placed on gene regulatory pathways and not on individual genes, especially when involving model organisms. This would circumvent the problem of missing orthologs in humans. In addition, more effective ways need to be applied to translate molecular mechanisms to phenotypes.\n\nApart from deciphering the relationship between functional genetic variation and disease, it is also important to focus on the biology of the disease as a whole.\n\n\nClosing remarks\n\nIt was evident from the panel discussion that forward genetics is still valuable to human genetics and is needed to understand the genetic basis of human diseases. In addition, animal models (especially mouse models) hold enormous potential when combined with forward genetics screens and can efficiently complement human genetics research in the form of precise disease models. Recent advances in genome editing, sequencing technologies and mutant generation have made forward genetics screens accessible to the wider community of biomedical researchers. Consequently, this needs to be effectively communicated to the scientific community and policy officials. The panellists agreed that a review or commentary highlighting the outcomes of the panel discussion would be a logical next step. Another tangible outcome was the renewed focus on bringing together and strengthening interactions between forward, mouse and human geneticists in upcoming INFRAFRONTIER stakeholder meetings and conferences.\n\n\nData availability\n\nNo data are associated with this article.",
"appendix": "Acknowledgements\n\nSpecial thanks to the panellists for their expert discussion and to the chair Prof. Hrabě de Angelis for moderating the session. The IMGC 2018 organisers, especially Darla Miller and Ginger Shaw, helped immensely with setting up the panel discussion.\n\n\nReferences\n\nAcevedo-Arozena A, Wells S, Potter P, et al.: ENU mutagenesis, a way forward to understand gene function. Annu Rev Genomics Hum Genet. 2008; 9: 49–69. PubMed Abstract | Publisher Full Text\n\nAnderson KV: Finding the genes that direct mammalian development : ENU mutagenesis in the mouse. Trends Genet. 2000; 16(3): 99–102. PubMed Abstract | Publisher Full Text\n\nBuchovecky CM, Turley SD, Brown HM, et al.: A suppressor screen in Mecp2 mutant mice implicates cholesterol metabolism in Rett syndrome. Nat Genet. 2013; 45(9): 1013–1020. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDaxinger L, Harten SK, Oey H, et al.: An ENU mutagenesis screen identifies novel and known genes involved in epigenetic processes in the mouse. Genome Biol. 2013; 14(9): R96. PubMed Abstract | Publisher Full Text | Free Full Text\n\nde Angelis MHH, Flaswinkel H, Fuchs H, et al.: Genome-wide, large-scale production of mutant mice by ENU mutagenesis. Nat Genet. 2000; 25(4): 444–447. PubMed Abstract | Publisher Full Text\n\nGeister KA, Timms AE, Beier DR: Optimizing Genomic Methods for Mapping and Identification of Candidate Variants in ENU Mutagenesis Screens Using Inbred Mice. G3 (Bethesda). 2018; 8(2): 401–409. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHu J, Lessard C, Longstaff C, et al.: ENU-induced mutant allele of Dnah1, ferf1, causes abnormal sperm behavior and fertilization failure in mice. Mol Reprod Dev. 2019; 86(4): 416–425. PubMed Abstract | Publisher Full Text\n\nMacdonald ME, Ambrose CM, Duyao MP, et al.: A novel gene containing a trinucleotide repeat that is expanded and unstable on Huntington's disease chromosomes. The Huntington's Disease Collaborative Research Group. Cell. 1993; 72(6): 971–983. PubMed Abstract | Publisher Full Text\n\nPoltorak A, He X, Smirnova I, et al.: Defective LPS signaling in C3H/HeJ and C57BL/10ScCr mice: mutations in Tlr4 gene. Science. 1998; 282(5396): 2085–2088. PubMed Abstract | Publisher Full Text\n\nSabrautzki S, Rubio-Aliaga I, Hans W, et al.: New mouse models for metabolic bone diseases generated by genome-wide ENU mutagenesis. Mamm Genome. 2012; 23(7–8): 416–430. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSaul MC, Philip VM, Reinholdt LG, et al.: High-Diversity Mouse Populations for Complex Traits. Trends Genet. 2019; 35(7): 501–514. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSchneeberger K: Using next-generation sequencing to isolate mutant genes from forward genetic screens. Nat Rev Genet. 2014; 15(10): 662–676. PubMed Abstract | Publisher Full Text\n\nSchneeberger K, Ossowski S, Lanz C, et al.: SHOREmap: simultaneous mapping and mutation identification by deep sequencing. Nat Methods. 2009; 6(8): 550–551. PubMed Abstract | Publisher Full Text\n\nSharma S, Petsalaki E: Application of CRISPR-Cas9 Based Genome-Wide Screening Approaches to Study Cellular Signalling Mechanisms. Int J Mol Sci. 2018; 19(4): 933. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSimon MM, Mallon AM, Howell GR, et al.: High throughput sequencing approaches to mutation discovery in the mouse. Mamm Genome. 2012; 23(9–10): 499–513. PubMed Abstract | Publisher Full Text | Free Full Text\n\nVitaterna MH, King DP, Chang AM, et al.: Mutagenesis and mapping of a mouse gene, Clock, essential for circadian behavior. Science. 1994; 264(5159): 719–725. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWang T, Zhan X, Bu CH, et al.: Real-time resolution of point mutations that cause phenovariance in mice. Proc Natl Acad Sci U S A. 2015; 112(5): E440–449. PubMed Abstract | Publisher Full Text | Free Full Text\n\nZhang Y, Proenca R, Maffei M, et al.: Positional cloning of the mouse obese gene and its human homologue. Nature. 1994; 372(6505): 425–432. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "87083",
"date": "30 Jun 2021",
"name": "Martin S Denzel",
"expertise": [
"Reviewer Expertise forward genetic screens",
"aging"
],
"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 commentary by Khan et al. is an interesting and timely reminder about the strengths of forward genetic screens in mice and nicely points out recent developments in the field that assure that such screens remain valuable in understanding gene function and disease mechanisms.\nI have a few suggestions below:\nAbstract: “in development and diseases”, I would suggest adding “in the maintenance of homeostasis”.\n\nThe section: “Briefly, such an approach starts with a screen to identify a mutant phenotype that is either naturally occurring or artificially induced, for example by N-ethyl-N-nitrosourea (ENU), a potent mutagen” should also mention transposons and CRISPR as means to introduce mutations in forward screens.\n\nFigure 2 is not very useful – I would suggest making a figure with portrait pictures of the panelists that could nicely go with their introductions.\n\nContributions of… section: The first sentence “According to the panelists, there was no one particular forward genetics contribution that was the important towards the better understanding of human diseases and mammalian physiology” is not clear and perhaps it might be a better read to start the section with a positive notion.\n\nThe following sentence should be re-phrased for clarity: “CRISPR-Cas9 genome editing has been used in forward genetics screens to create genome-wide mutant libraries because to its easier scalability.”\n\nOne way to cope with the challenges of forward genetic screens in mice it to use the same methodologies (ENU, crispr etc) in cultured cells, and the use of haploid cells for mutagenesis (as described by the Jackson lab, PMID: 27820796 1 and my lab PMID: 29515774 2 and PMID: 32690882 3) provides a serious alternative for cellular phenotypes.\n\nTypos:\nIn the intro section for Prof B Beutler, “Currently, his team conduct robust...” should be “Currently, his team conducts robust…”\n\n“Therefore, more sophisticated human diseaseS models are needed to accurately emulate complex human pathologies.” should be “Therefore, more sophisticated human disease models are needed to accurately emulate complex human pathologies.”\n\n“As stated earlier, positional cloning was a major rate limiting step in forward genetics screen which has been overcome with the ‘instant positional cloning’ method.” should be “As stated earlier, positional cloning was a major rate limiting step in forward genetic screens, which was overcome by ‘instant positional cloning’.”\n\n“…hold enormous potential when combined with forward genetics screens” should be “…hold enormous potential when combined with forward genetic screens”\n\nIs the topic of the opinion article discussed accurately in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? No\n\nAre arguments sufficiently supported by evidence from the published literature? Yes\n\nAre the conclusions drawn balanced and justified on the basis of the presented arguments? Yes",
"responses": []
},
{
"id": "97639",
"date": "03 Nov 2021",
"name": "Anton Wutz",
"expertise": [
"Reviewer Expertise Mouse genetics",
"dosage compensation",
"development",
"stem cells"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 \"Moving forward with forward genetics: A summary of the INFRAFRONTIER Forward Genetics Panel Discussion\" provides a summary and visions arising from the panel discussion of the INFRAFRONTIER program on forward genetics. The authors were panelists at the occasion and have submitted a well-structured synopsis that can be used as a reference for the present state and future directions. As such it will be useful for transparently documenting for the interested scientific community and policy makers in Europe. Although the article is well written, some details below could be considered by the authors for further improving the readability.\nSpecific points:\nThe title raises expectations of insights into how to perform forward genetics but the article falls a bit short of delivering on this. The authors could consider including more information on new technologies that might be incorporated into forward genetics such as CRISPR Cas systems that have seen tremendous success in the past few years. Is it conceivable that both field synergies such that onboarding of base editors into forward genetics could provide an opportunity for developing the CRISPR applications further?\n\nThe present version of the article does not make it easily accessible to a wide readership as to the commendable accomplishments in the past. For improving the impact of the manuscript it could be suggested to provide a concrete example. Maybe from one of the works of the panelists.\n\nResearch on the organism level has the great advantage of allowing to study physiology questions. This appears to come at of cost and one wonders if over time methods and technologies have come forth that would make the endeavour more efficient going into the future. Could the authors briefly introduce the limitations and bottlenecks of forward genetics in mice at present? This could then serve to position the present proposal of future-forward genetic studies. Citing current research of new ways for introducing mutations more efficiently or unmasking phenotypes would provide the reader with concrete ideas and make the text more exciting.\n\nIn general, it seems clear that genetics is an important method for gaining insights into disease and developmental biology. The text appears to focus specifically on forward genetics. On one hand, this appears to artificially limit discussion and on the other hand, the authors themselves cite applications that seem to be not clearly forward genetically in nature. Page 4, right column, beginning of the last paragraph discusses the analysis of human disease mutations in mice. This likely could be seen as a reverse genetics approach. It would appear important to specifically define this in order to avoid confusing readers.\n\nPage 5, right column, beginning of the last paragraph briefly refers to CRISPR technology and raises current problems. It would be interesting to briefly state how this system could be used and a promising tool as it appears that limitations might be overcome quickly in this rapidly progressing field. A comparison of the advantages and disadvantages of both systems could be informative for the reader.\n\nIn the introduction, the authors refer to the MeCP2 mutation in mice as a model of human RETT syndrome. It might be wise to consider more careful wording as in strict genetics terms the disease is caused by heterozygosity in female patients whereas it is a homozygous / hemigynous mutation that leads to motor impairment in mice. Maybe a sentence reconciling the phenotypic and genetic differences could be included for factual correctness.\n\nAs the manuscript is considered as a policy document it would appear of importance to position the proposed method against related approaches. Given the enormous efforts in time and cost for maintaining mice, the authors might wish to explain the big advantages over culture-based approaches. Firstly, redundancy among genes can be unmasked by observing the phenotype in different tissues where redundant factors might not be masked. Secondly, complex physiological interactions can only be studied in the tissues and organs of the organism and therefore the proposed approach would extend competing approaches that aim to identify the molecular basis of human disease in culture systems. Would a proposal based on large numbers of animals not appear untimely without considering alternative approaches?\n\nIs the topic of the opinion article discussed accurately in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? Partly\n\nAre arguments sufficiently supported by evidence from the published literature? Yes\n\nAre the conclusions drawn balanced and justified on the basis of the presented arguments? Partly",
"responses": []
},
{
"id": "97637",
"date": "30 Nov 2021",
"name": "Camron D Bryant",
"expertise": [
"Reviewer Expertise addiction genetics in rodent model organisms"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 much needed discussion/summary as it addresses the ongoing backlash against forward genetics of complex traits and disease models that human geneticists have instigated against quantitative geneticists that employ model organisms.\nMany of my comments below are with regard to proofing, with a few conceptual comments/suggestions\nDefinition of “forward genetics” at the beginning seems ENU-centric and does not sound like it includes QTL and GWAS. “random genomic modifications that alter gene function” (includes both naturally occurring and artificially induced).\n\nThere must be a word missing here: “the phenotype producing population is mapped…” the phenotype producing population variance is mapped? Also, too many “mapped”s in this sentence.\n\n“The mutations responsible for complex phenotypes and disorders…” I would change to “Mutations contributing to complex phenotypes and disorders…” (We do not know the full genetic architecture yet of any complex disease or phenotype.)\n\n“there was no particular forward genetics contribution that was the important” – should say “the most important”?\n\n“quantifiable traits” should be “quantitative traits”\n\n“in their view, forward genetics is the…” should be “in their view, contemporary forward genetics comprises….”\n\n“Forward genetics is remains…” should be “Forward genetics remains…”\n\n“Therefore, more sophisticated human diseases models…” should be “…more sophisticated models of human diseases….”\n\n“In addition, a wide spectrum of mutations is possible using mutagens that can create a variety of alleles…” This sentence omits natural alleles that also comprise a wide variety of non-lethal yet sometimes large-effect mutations on phenotypes\n\nAnother advantage of forward genetics in model organisms is the detection of epistasis and the study of its biological interactions and mechanisms. Modifiers were mentioned once under the section “Mutant Production”\n\nWhile, mapping with highly diverse, outbred populations was mentioned, mapping with less diverse, yet more highly recombinant populations such as commercial outbred was omitted. These have the advantage of producing even higher resolution QTLs. Also, the use of reduced complexity crosses (RCCs) between near isogenic strains was omitted. There are several advantages to RCCs (speed, two clear genetic backgrounds to demonstrate necessity and sufficiency, etc.)\n\nThere is definitely a bias in this article toward the mutagenesis side of forward genetics (e.g., the repeated discussion/mention of “instant positional cloning” but positional cloning is not instant for QTL/GWAS studies of natural genetic and phenotypic variation. High-resolution QTLs is an advancement. Positional cloning has become more precise with WGS as one can precisely select a panel or markers to monitor recombination events for fine mapping/cloning\n\nIn my opinion, no specific concrete examples were elaborated upon in any level of depth to make the case that forward genetics in model organisms is relevant and offers advantages over discovery based genetics in humans. I applaud the effort behind arranging this panel and summarizing the discussion but I think there is room for making a stronger case for forward genetics in model organisms than currently stands. Perhaps this brief article is not the venue for achieving this goal as it seems to represent what was actually discussed at the panel rather than what could have been discussed or what should have been discussed in greater detail.\n\nIs the topic of the opinion article discussed accurately in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nAre arguments sufficiently supported by evidence from the published literature? Partly\n\nAre the conclusions drawn balanced and justified on the basis of the presented arguments? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-456
|
https://f1000research.com/articles/10-455/v1
|
08 Jun 21
|
{
"type": "Study Protocol",
"title": "Development of a checklist to detect errors in meta-analyses in systematic reviews of interventions: study protocol",
"authors": [
"Raju Kanukula",
"Matthew J. Page",
"Kerry Dwan",
"Simon L. Turner",
"Elizabeth Loder",
"Evan Mayo-Wilson",
"Tianjing Li",
"Adya Misra",
"Steve McDonald",
"Andrew B. Forbes",
"Joanne E. McKenzie",
"Raju Kanukula",
"Matthew J. Page",
"Kerry Dwan",
"Simon L. Turner",
"Elizabeth Loder",
"Evan Mayo-Wilson",
"Tianjing Li",
"Adya Misra",
"Steve McDonald",
"Andrew B. Forbes"
],
"abstract": "Background: Systematic reviews underpin clinical practice and policies that guide healthcare decisions. A core component of many systematic reviews is meta-analysis, which is a statistical synthesis of results across studies. Errors in the conduct and interpretation of meta-analysis can lead to incorrect conclusions regarding the benefits and harms of interventions; and studies have shown that these errors are common. Enabling peer reviewers to better detect errors in meta-analysis through the use of a checklist provides an opportunity for these errors to be rectified before publication. To our knowledge, no such checklist exists. Objective: To develop and evaluate a checklist to detect errors in pairwise meta-analyses in systematic reviews of interventions. Methods: We will undertake a four-step process to develop the checklist. First, we will undertake a systematic review of studies that have evaluated errors in the conduct and interpretation of meta-analysis to generate a bank of items to consider for the checklist. Second, we will undertake a survey of systematic review methodologists and statisticians to seek their views on which items, of the bank of items generated in step 1, are most important to include in the checklist. Third, we will hold a virtual meeting to agree upon which items to include in the checklist. Fourth, before finalising the checklist, we will pilot with editors and peer reviewers of journals. Conclusion: The developed checklist is intended to help journal editors and peer reviewers identify errors in the application and interpretation of meta-analyses in systematic reviews. Fewer errors in the conduct and improved interpretation will lead to more accurate review findings and conclusions to inform clinical practice.",
"keywords": [
"systematic review",
"meta-analysis",
"errors",
"checklist",
"reporting guideline",
"statistical issues",
"synthesis",
"pair-wise meta-analysis"
],
"content": "1. Introduction\n\nSystematic reviews (SRs) frequently underpin clinical practice guidelines and policies that guide healthcare decisions. A core component of many SRs is meta-analysis, a statistical technique used to synthesise study effect estimates from studies addressing similar questions, yielding a quantitative summary.1 Extensions to meta-analysis (e.g. meta-regression, subgroup analysis) allow for investigation of factors that may explain variation of results across studies. These methods have the potential to provide valuable insights for healthcare decision-making; however, they are reliant on the methods being appropriately applied and interpreted.\n\nMany errors can arise when conducting meta-analysis. For example, when meta-analysing continuous outcomes, calculations may be incorrect if standard errors are confused with standard deviations. When data are included from multi-arm trials, there is the risk that participants might be counted more than once when multiple comparisons from these trials are eligible for inclusion in the same meta-analysis. For example, from a three-arm trial of paroxetine, fluoxetine, and placebo, two comparisons would be eligible for a meta-analysis of ‘antidepressants versus placebo’ (i.e., ‘paroxetine versus placebo’ and ‘fluoxetine versus placebo’). When dealing with non-standard randomized trials – such as crossover trials, cluster-randomized trials, or split-body trials – there is a risk that variances of the effect estimates in the meta-analysis do not appropriately account for the correlation in observations induced by these designs.2–5 Such errors can lead to studies receiving the incorrect weight in the meta-analysis with potential consequent impact on the combined estimate of intervention effect and its confidence interval, and other statistics, such as the estimated heterogeneity variance and measures of inconsistency. In some circumstances, these errors will lead to a different interpretation of the findings and review conclusions.6\n\nStatistical errors have been observed frequently in published SRs. For example, a study including 42 reviews from the Cochrane Cystic Fibrosis and Genetic Disorders Group found that nearly half of the SRs had at least one error (e.g., used standard error instead of standard deviation; calculated standard deviations incorrectly from the standard error given in the report; entered median instead of mean).7 Another study in which the authors re-extracted the data from two randomly selected trials included in each of 27 meta-analyses, found errors in how the meta-analyst entered data for at least one of the two trials in 17 (63%) of the meta-analyses.6 Furthermore, some published meta-analyses papers have been retracted because of errors in analyses and error in results and/or conclusions.8–10\n\nResearch has shown that errors in the interpretation of statistical analyses in reviews are also common. For example, of 110 SRs indexed in MEDLINE® in 2014, 62 used the random-effects model, but 57 (92%) incorrectly interpreted the meta-analytic effect as the best estimate of a common intervention effect across studies, rather than as the average of the intervention effects across studies. In 42 of the 110 meta-analyses, a subgroup analysis was undertaken, but the findings were not interpreted with respect to a test for interaction in 29/42 (69%), and in 11/42 (26%), a claim of a subgroup difference was made based on a statistically significant effect in one group and not the other.11 Furthermore, the potential for confounding by other factors as a possible explanation for observed subgroup effects, was not raised in any of the SRs.11,12\n\nMany strategies have been proposed to improve the conduct of meta-analysis (thus lessening the chance of errors occurring) and the interpretation of findings. These include, for example, textbooks,13–15 training on meta-analysis methods, connection with support systems (e.g., Cochrane’s TaskExchange), and the inclusion of statisticians on review teams. However, even with these strategies, errors will still occur. A possible additional strategy is to enable peer reviewers to better detect possible errors in meta-analyses.\n\nThe peer-review process is regarded as a valuable approach for helping peer reviewers and journal editors to judge the quality, critically appraise and finally accept or reject the submitted manuscripts for publication.16 Researchers have explored the impact of checklists to guide peer reviewers in assessing the completeness of reporting of submitted manuscripts, and have found some evidence that these are effective.17–19 For example, training early career researchers to use the COBPeer tool (which is an online CONSORT-based peer-review tool assessing nine domains: the eight most important CONSORT domains and a switch in primary outcome(s)) helped them detect inadequate reporting in randomized trials compared to the usual review process.17,20 To our knowledge, no such checklist has been developed to detect statistical errors in meta-analyses.\n\nAim: To develop and evaluate a checklist to detect conduct and interpretation errors in pairwise meta-analyses in systematic reviews of interventions.\n\n\n2. Defining the concept of statistical errors\n\nThe notion of statistical conduct and interpretation errors is not simple. Brown and colleagues21 defined errors to be “actions or conclusions that are demonstrably and unequivocally incorrect from a logical or epistemological point of view (e.g. … mathematical mistakes, statements not supported by the data, incorrect statistical procedures …)”. In this research, we will consider statistical errors to include those arising from underlying assumptions not being met, incorrect values used in the calculations, application of incorrect statistical methods, and misinterpretation of the results and statistical tests. We plan to initially group errors into categories (Section 3.2.4) and refine and revise these based on the types of errors identified through the systematic review (Section 3.2). Our focus will be on errors where it can be reasonably expected that a trained meta-analyst should have or could have known better, recognising that there is subjectivity in making this determination.21\n\n\n3. Methods\n\nA core team (RK, MJP, KD, SLT, EL, EMW, TL, AM, ABF, JEM) will lead the development of this checklist. The core team will conduct the systematic review, develop survey content and analyse survey responses, draft the checklist, coordinate piloting of the checklist, and decide the final content of the checklist. The core team consists of individuals with experience in meta-analysis methods and SR methodology, contributors of the Cochrane Handbook for Systematic Reviews of Interventions, and editors of medical journals who frequently publish SRs (BMJ, PLOS Medicine, Cochrane Database of Systematic Reviews, American Journal of Public Health, and Systematic Reviews).\n\nWe will conduct an SR of studies evaluating errors in the conduct and interpretation of pairwise meta-analysis, for the purpose of identifying types of errors, their prevalence, and to generate a bank of items to potentially be included in the checklist.\n\n3.2.1 Eligibility criteria\n\nStudies will need to meet the following eligibility criteria:\n\nInclusion criteria:\n\n• Studies evaluating types of errors (and potentially their prevalence) in the conduct and interpretation of meta-analyses (and its extensions, for example, subgroup analysis, sensitivity analysis) in SRs of interventions (irrespective of included study design);\n\n• Articles presenting a checklist or tool to evaluate the conduct of meta-analyses in SRs.\n\nExclusion criteria:\n\n• Studies evaluating the methodological or reporting quality or risk of bias in SRs using a tool that does not specifically examine statistical errors (e.g. PRISMA, AMSTAR-2, ROBIS);\n\n• Studies or checklists evaluating errors in statistical analyses in primary study designs (e.g. randomized trials and observational studies).\n\n3.2.2 Search methods\n\nWe will search MEDLINE, Embase and Scopus from inception to January 2021, without any publication type or language restrictions. The search strategies for MEDLINE and Embase combine subject heading terms and text words related to statistical errors in meta-analyses are presented in Appendix (see Extended data).22 The search was iteratively developed and tested by an experienced information specialist (SM) using a set of 10 methods articles relevant to the topic. The Scopus search closely replicates the MEDLINE search with respect to included terms and word adjacency but is limited to the following subject areas in Scopus: medicine, nursing, dentistry and health professions.\n\nWe will also search abstracts of papers and posters presented at Cochrane Colloquia since 2011 (available at https://abstracts.cochrane.org/), including the Global Evidence Summit 2017. The search strategy will be determined by assessing the relative recall of terms from eligible studies identified from searches of MEDLINE, Embase and Scopus. We will screen the reference lists and conduct a cited reference search in Web of Science of included articles and review our personal collections of reports or studies related to statistical issues in meta-analyses. In addition, we will contact organisations that produce SRs (e.g., Cochrane, Campbell Collaboration, National Institute for Health and Care Excellence), and journals that frequently publish SRs to seek any in-house checklists they are willing to share.\n\n3.2.3 Selection of studies\n\nTwo authors will screen independently all titles and abstracts according to the aforementioned eligibility criteria and retrieve the full text of any potentially relevant articles. The same authors will screen the full texts of retrieved articles. In case of any discrepancies, a senior author will adjudicate and finalise the inclusion or exclusion of any article(s).\n\n3.2.4 Data collection\n\nOnce we finalise the studies to be included, two authors will collect data independently from each article using a standardised data collection form. For studies evaluating types of errors (and potentially their prevalence), we will collect the following information: corresponding author name, email address, year of publication, journal name, objective(s), focus of error investigation (e.g., multi-arm trials, cross-over trials, cluster randomized trials), type and prevalence of errors, and recommendations provided for conducting meta-analyses. For articles presenting a checklist or tool to evaluate conduct or reporting of meta-analyses in SRs, we will collect the following information: checklist/tool name, method of checklist/tool development, number of items included in the checklist/tool and scope of the checklist/tool. In addition, we will collect all the items and response options pertinent to meta-analysis and its interpretation identified in the tools/checklists, and these will be added to our item bank.\n\nOnce we have extracted data from all articles, we will review the items in the item bank and remove any duplicate or redundant items. We will then group items into broader categories. For example, those relating to data type (e.g., continuous, binary), rare outcomes (i.e., handling of zero events in one or both arms), design of included studies (e.g. cross-over, cluster, multi-arm, non-randomised [e.g. interrupted time series, cohort]), type of analysis (meta-analysis, subgroup analysis, meta-regression, sensitivity analysis, publication bias analysis) and issues of interpretation. We will use Microsoft Excel 2016 for data management.\n\nWe will send an invitation to all SR methodologists and statisticians (identified from the Cochrane Methods community, Campbell Methods Coordinating Group, Society for Research Synthesis Methodology and other SR methodologists and statisticians known to the core team members) and SR editors and statistical editors (identified from Cochrane Review Groups, and those supporting other journals that frequently publish SRs) to complete a survey to inform the development of the checklist. The survey will ask respondents to:\n\n1) Provide their views on the most important items from the bank of items (generated from the systematic review) to include in the checklist. We will ask respondents to prioritise items that capture/identify the most common and consequential errors expected to occur in the conduct and interpretation of meta-analyses;\n\n2) Provide their views on specific signals (or ‘red flags’) that might lead them to conduct a more thorough investigation of statistical errors in reviews (e.g., size of the effect for some studies, meta-analysis methods used, I-squared value etc.).\n\nWe will ask researchers to provide rationale for their responses and to suggest additional items not listed in the survey. We will calculate frequencies of each response option for each item and specific signals. For an item or specific signal to meet consensus for discussion, one of the response options for the item or signal will need to be selected by more than 70% of survey respondents; this threshold was selected according to Sumsion 1998 et al.23\n\nFollowing the survey, the core team will hold a virtual meeting to agree upon which items to include in the statistical errors’ checklist for editors/peer reviewers, which items might trigger further investigation (by a statistical reviewer or the authors) and discuss how best to word each item. Attendees will discuss all items exceeding the 70% threshold in the survey. We will also send the items rated as important by fewer than 70% to meeting attendees prior to the meeting, to provide them with the chance of “rescuing” items for discussion at the meeting. Following the meeting, the core team will draft the checklist and an accompanying guidance document (with examples for each item).\n\nIn the first stage of piloting, two reviewers will read the draft checklist and guidance document before independently applying it to a random sample of 20 reviews; 10 from each of two previous methodological studies that collated systematic reviews. Specifically, the first methodological study includes 42 SRs of nutrition research (the ROBUST study)24 that were published between January 2018 and June 2019, and the second includes 31 SRs of interventions for arthritis, depression or anxiety (the SIM study) that were published between January 2010 and January 2012.25 The reviewers will record issues on whether the wording of items is ambiguous or difficult to interpret, and those items will be discussed by the core team and improved.\n\nIn the second stage of piloting, we will invite associate editors and peer reviewers of journals that frequently handle SR submissions to pilot the checklist and provide feedback on its usability. After collating the feedback received from the peer reviewers and editors, we will finalise the checklist and the accompanying guidance document.\n\nWe plan to publish the developed checklist and guidance document in an open-access journal. We will disseminate the checklist via presentations and workshops at relevant conferences and workshops focused on SR methodology, health technology assessment and evidence-based medicine (e.g., Cochrane Colloquia, Evidence Live, HTAi Annual Meeting, The Global Evidence Summit, G-I-N Conference), and via social media, and in a series of international webinars. We also plan to create a user-friendly, online version of the checklist and guidance document for use by journals that publish SRs and meta-analyses.\n\nThe developed checklist and related work will be published in open access journals. Associated datasets, data collection forms and analyses not included in any publication will be made publicly available via an online repository.\n\n\n4. Conclusion\n\nThe developed checklist could help journal editors and peer reviewers identify errors in the conduct and interpretation of meta-analyses in SRs. Fewer errors and improved interpretation would lead to more accurate SR findings and conclusions to inform clinical practice.\n\nStudy status: We have completed searching and screening for sections 3.2.1, 3.2.2 and 3.2.3 for systematic review.\n\n\nData availability\n\nNo underlying data are associated with this article.\n\nBridges: Search strategy for systematic review of studies evaluating errors in the conduct and interpretation of pairwise meta-analysis. Monash University. DOI: https://doi.org/10.26180/14446293.v1.22\n\nThis project contains the following extended data:\n\n- Search strategy for systematic review of studies evaluating errors in the conduct and interpretation of pairwise meta-analysis\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "References\n\nMcKenzie JE, Brennan SE: Chapter 12: Synthesizing and presenting findings using other methods. Cochrane Handbook for Systematic Reviews of Interventions. 2019: 321–47.\n\nRichardson M, Garner P, Donegan S: Cluster Randomised Trials in Cochrane Reviews: Evaluation of Methodological and Reporting Practice. PLoS One. 2016; 11(3): e0151818. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDonner A, Klar N: Issues in the meta-analysis of cluster randomized trials. Stat Med. 2002; 21(19): 2971–80. PubMed Abstract | Publisher Full Text\n\nStedman MR, Curtin F, Elbourne DR, et al.: Meta-analyses involving cross-over trials: methodological issues. Int J Epidemiol. 2011; 40(6): 1732–4. PubMed Abstract | Publisher Full Text\n\nNolan SJ, Hambleton I, Dwan K: The use and reporting of the cross-over study design in clinical trials and systematic reviews: a systematic assessment. PLoS One. 2016; 11(7): e0159014. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHrobjartsson A, Gotzsche PC: Unsubstantiated claims of large effects of placebo on pain: serious errors in meta-analysis of placebo analgesia mechanism studies. J Clin Epidemiol. 2006; 59(4): 336–8. discussion 9–41. PubMed Abstract | Publisher Full Text\n\nJones AP, Remmington T, Williamson PR, et al.: High prevalence but low impact of data extraction and reporting errors were found in Cochrane systematic reviews. J Clin Epidemiol. 2005; 58(7): 741–2. PubMed Abstract | Publisher Full Text\n\nRoba AA, Tefera M, Worku T, et al.: Retraction Note: Application of 4% chlorhexidine to the umbilical cord stump of newborn infants in lower income countries: a systematic review and meta-analysis. Matern Health Neonatol Perinatol. 2020; 6: 4. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGuo LQ, Chen Y, Mi BB, et al.: Retraction Note to: Ambient air pollution and adverse birth outcomes: a systematic review and meta-analysis. J Zhejiang Univ Sci B. 2020; 21(9): 756. PubMed Abstract | Publisher Full Text | Free Full Text\n\nEzenwa BN, Bello S, Oyenusi EE, et al.: RETRACTED: Galactogogues use Among Mothers With Preterm Births: A Systematic Review and Meta-Analysis. J Hum Lact. 2020; 36(3): NP3–NP14. PubMed Abstract | Publisher Full Text\n\nPage MJ, Altman DG, McKenzie JE, et al.: Flaws in the application and interpretation of statistical analyses in systematic reviews of therapeutic interventions were common: a cross-sectional analysis. J Clin Epidemiol. 2018; 95: 7–18. PubMed Abstract | Publisher Full Text\n\nFisher DJ, Carpenter JR, Morris TP, et al.: Meta-analytical methods to identify who benefits most from treatments: daft, deluded, or deft approach? BMJ. 2017; 356. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCooper H, Hedges LV, Valentine JC: The handbook of research synthesis and meta-analysis: Russell Sage Foundation; 2019.\n\nSchmid CH, White IR, Stijnen T: Introduction to Systematic Review and Meta-Analysis. Handbook of Meta-Analysis. 2020.\n\nHiggins JP, Thomas J, Chandler J, et al.: Cochrane handbook for systematic reviews of interventions. John Wiley & Sons; 2019.\n\nRennie D: Editorial peer review in biomedical publication: the first international congress. JAMA. 1990; 263(10): 1317. Publisher Full Text\n\nChauvin A, Ravaud P, Moher D, et al.: Accuracy in detecting inadequate research reporting by early career peer reviewers using an online CONSORT-based peer-review tool (COBPeer) versus the usual peer-review process: a cross-sectional diagnostic study. BMC Medicine. 2019; 17(1): 205. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSpeich B, Schroter S, Briel M, et al.: Impact of a short version of the CONSORT checklist for peer reviewers to improve the reporting of randomised controlled trials published in biomedical journals: study protocol for a randomised controlled trial. BMJ Open. 2020; 10(3): e035114. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBlanco D, Schroter S, Aldcroft A, et al.: Effect of an editorial intervention to improve the completeness of reporting of randomised trials: a randomised controlled trial. BMJ Open. 2020; 10(5): e036799. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChauvin A, Moher D, Altman D, et al.: A protocol of a cross-sectional study evaluating an online tool for early career peer reviewers assessing reports of randomised controlled trials. BMJ Open. 2017; 7(9): e017462. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBrown AW, Kaiser KA, Allison DB: Issues with data and analyses: Errors, underlying themes, and potential solutions. Proc Natl Acad Sci U S A. 2018; 115(11): 2563–70. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPage M, Kanukula R, McKenzie J: Search strategy for systematic review of studies evaluating errors in the conduct and interpretation of pairwise meta-analysis. Monash University. Online resource. 2021. [database on the Internet]. Publisher Full Text\n\nSumsion T: The Delphi technique: an adaptive research tool. Br J Occup Ther. 1998; 61(4): 153–6. Publisher Full Text\n\nPage MJ, Bero L, Kroeger CM, et al.: Investigation of Risk Of Bias due to Unreported and SelecTively included results in meta-analyses of nutrition research: the ROBUST study protocol. F1000Res. 2019; 8(1760): 1760. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPage MJ, Forbes A, Chau M, et al.: Investigation of bias in meta-analyses due to selective inclusion of trial effect estimates: empirical study. BMJ Open. 2016; 6(4): e011863. PubMed Abstract | Publisher Full Text | Free Full Text"
}
|
[
{
"id": "87114",
"date": "21 Jun 2021",
"name": "Ram Bajpai",
"expertise": [
"Reviewer Expertise Meta-analysis",
"Statistical analysis"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nAuthors have well prepared their systematic review protocol with clarity. I have following minor suggestions to improve the quality of this protocol.\nFrom inclusion criteria it is clear that authors will include SRs of interventions only. However, if possible, authors should elaborate on not including SR of proportions or SR of observational studies or SR of biomarkers etc. Each set of SRs will require a different type of statistical skills to perform meta-analysis. It also important to mention about whether only pharmacological intervention SRs or non- pharmacological interventions such as educational interventions etc. will also be included in this methodological systematic review.\nDid authors think that a statistician included in the author list will have any impact on error as it is possible that SRs with statistician as co-author may have less statistical errors? I think the authors have already thought about this point, however, appreciate authors reflection on this point and if they add few words in the protocol.\nIf I am not wrong, the planned survey and consensus meeting will follow Delphi survey methodology. I am wondering that authors did not mention this word explicitly or they are following some other equally useful methodology.\nI believe that authors have well refined methodology to capture statistical errors. However, in many SRs, authors wrongly choose a meta-analysis model (i.e., fixed-effect vs. random-effect) to pool study estimates and possible other statistics right. How would authors capture such errors? Please elaborate if I have missed this point.\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": "87112",
"date": "05 Jul 2021",
"name": "Therese D. Pigott",
"expertise": [
"Reviewer Expertise meta-analysis 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 work will provide an important contribution to the field, highlighting typical errors that can occur in pairwise meta-analyses of intervention effects. One question I have is the audience of the checklist. The study protocol is situated in meta-analysis for health and medical interventions. The search strategy for relevant systematic reviews for stage one of the process focuses on the health and medical literature, with only the Campbell Collaboration as a source for meta-analyses in the social sciences. If the intent of the checklist is to apply more broadly to social interventions rather than just health and medicine, then the search strategy needs to include a broader set of databases. There are relevant efforts in psychology for example (see Maasen et al. (20201)) that could also inform the checklist. I understand if the authors wish to focus this effort only on health and medicine.\n\nIn the social sciences, similar issues to those that are outlined in the protocol occur. In addition, many meta-analyses include a large number of studies, and thus key issues center on dependent effect sizes within studies and interpretation of effect size models for heterogeneity. If the authors intend the checklist to have a broader application, then these are a few issues that should be considered in the development of the checklist.\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/10-455
|
https://f1000research.com/articles/10-323/v1
|
26 Apr 21
|
{
"type": "Software Tool Article",
"title": "RNAmining: A machine learning stand-alone and web server tool for RNA coding potential prediction",
"authors": [
"Thaís A.R. Ramos",
"Nilbson R.O. Galindo",
"Raúl Arias-Carrasco",
"Cecília F. da Silva",
"Vinicius Maracaja-Coutinho",
"Thaís G. do Rêgo",
"Thaís A.R. Ramos",
"Nilbson R.O. Galindo",
"Raúl Arias-Carrasco",
"Cecília F. da Silva"
],
"abstract": "Non-coding RNAs (ncRNAs) are important players in the cellular regulation of organisms from different kingdoms. One of the key steps in ncRNAs research is the ability to distinguish coding/non-coding sequences. We applied seven machine learning algorithms (Naive Bayes, SVM, KNN, Random Forest, XGBoost, ANN and DL) through 15 model organisms from different evolutionary branches. Then, we created a stand-alone and web server tool (RNAmining) to distinguish coding and non-coding sequences, selecting the algorithm with the best performance (XGBoost). Firstly, we used coding/non-coding sequences downloaded from Ensembl (April 14th, 2020). Then, coding/non-coding sequences were balanced, had their tri-nucleotides counts analysed and we performed a normalization by the sequence length. Thus, in total we built 180 models. All the machine learning algorithms tests were performed using 10-folds cross-validation and we selected the algorithm with the best results (XGBoost) to implement at RNAmining. Best F1-scores ranged from 97.56% to 99.57% depending on the organism. Moreover, we produced a benchmarking with other tools already in literature (CPAT, CPC2, RNAcon and Transdecoder) and our results outperformed them, opening opportunities for the development of RNAmining, which is freely available at https://rnamining.integrativebioinformatics.me/.",
"keywords": [
"Machine Learning",
"non-coding RNA",
"benchmarking",
"coding potential prediction"
],
"content": "Introduction\n\nNon-coding RNAs (ncRNAs) are key functional players on different biological processes in organisms from all domains of life.1,2 Its investigation is already routine in almost every transcriptome or genome project. Dysregulations in these molecules may lead to different types of human disease, including cancers,3 neurological disorders4 and cardiovascular infirmities.5\n\nThe genome of eukaryotic6 organisms is, in general, majority composed of non-coding transcripts, with complex organisms estimated to transcribe more than 75% of their genomes.7 Besides strong evidence associating these ncRNAs to key functions in the cell, the majority are not yet associated with a functional mechanism. In a transcriptome project there exists an important step in the computational identification of ncRNAs, which is the evaluation of their potential to be translated into proteins using different bioinformatics approaches.8,9 To computationally evaluate the coding potential of a set of transcripts, available tools or algorithms normally analyse specific characteristics available in primary sequences (e.g. nucleotides counts, the existence of a trustful open reading frame).\n\nFor instance, RNAcon implements a support vector machine (SVM)-based model for the discrimination between coding and non-coding sequences.10 Coding Potential Assessment Tool (CPAT)11 assesses the coding potential through an alignment-free method, which uses a logistic regression model built based on different characteristics of the sequence open reading frame (ORF), which includes length, coverage and nucleotides compositional bias. TransDecoder identifies candidate coding transcripts based on other distinctive features from predicted ORFs (e.g. a minimum length ORF, a log-likelihood score, encapsulated ORF).12 CPC213 trained a SVM model using Fickett TESTCODE score, ORF length, ORF integrity and isoelectric point as features. The LIBSVM14 package was employed by training a SVM model using the standard radial basis function kernel (RBF kernel) with the training dataset containing 17,984 high-confident human protein-coding transcripts and 10,452 non-coding transcripts.11\n\nHere, we applied and benchmarked seven different machine learning algorithms (Random Forest, Gradient boosting (XGBoost), Naive Bayes, K-Nearest Neighbors (K-NN), SVM, Artificial Neural Network (ANN) and Deep Learning (DL)) through 15 organisms from different evolutionary branches, in order to evaluate their performance in distinguishing coding and non-coding RNA sequences. Next, we developed a stand-alone and web server tool, called RNAmining (http://rnamining.integrativebioinformatics.me/), by selecting and implementing the algorithm with the best performance in all organisms (XGBoost). RNAmining was evaluated through 24 organisms from the eukaryotic tree of life and its results outperformed publicly available tools commonly used for that purpose.\n\n\nMethods\n\nIn the classification process there is a division related to the learning paradigm, with classification algorithms divided into: (i) Symbolic, which seeks to learn by constructing symbolic representations of a concept through the analysis of examples and counterexamples (e.g. Decision Trees and Rule-based System); (ii) Statistical, which looks for statistical methods and use models to find a good approximation of the induced concept (e.g. Bayesian learning); (iii) Based on Examples (lazy systems), which aims to classify examples never seen using similar known examples, assuming that the new example will belong to the same class as the similar example (e.g. K-Nearest neighbor); (iv) Based on Optimization, which consists of maximizing (or minimizing) an objective function or finding an optimal hyperplane that best divides two classes (e.g. SVM and Neural Networks); (v) Connectionist Representation, which represents simplified mathematical constructions inspired by the biological model of the nervous system (e.g. Neural Networks). In this benchmarking, we decided to evaluate the performance of selected algorithms from each paradigm type in the coding potential prediction of RNA sequences: Random Forest, XGBoost, Naive Bayes, K-NN, SVM and Neural Networks (ANN and Convolutional Neural Networks (CNN)).\n\nAll the machine learning methods were executed using scikit-learn (Version 0.21.3),15 except for Neural Network and DL models which were implemented using Keras API with Tensorflow as backend (Version 2.3.0) and XGBoost algorithm which was executed using XGBoost Library (version 1.2.0)16 in Python Language (Version 3.8). The Random Forest model was implemented using empirical tests and the best result was selected for training the model. We considered the default parameters with the exception of the number of trees used (150 estimators) and the criterion parameter setted to 'entropy' for information gain. KNN and Naive Bayes models were trained with the default values. The SVM parameters were obtained through grid search method and the resulting model was trained with the Radial Basis Function (RBF) kernel, with the Regularization parameter (C) and Kernel coefficient (Gamma) defined in 1000 and 0.8, respectively. ANN and DL were performed with different architectures according to grid search and empirical tests. The first ANN experiment was composed of three hidden layers consisting of 32-16-8 neurons, respectively; the second ANN experiment was performed with 64-32-16-8 neurons; and the third experiment was executed with 32-32-16-8 neurons. Next, we produced four experiments with DL using 2 CNN layers, followed by 2 fully connected (dense) layers: the first experiment had 512(CNN)-512(CNN) filters and 28(Dense)-1(Dense) neurons; the second was created with 64(CNN)-64(CNN) filters and 128(Dense)-1(Dense) neurons; the third was performed with 32(CNN)-32(CNN)-128(Dense)-1(Dense) neurons; and the last was built with 128(CNN)-128(CNN)-128(Dense)-1(Dense) neurons. These layers received as input the total number of attributes (i.e. combination of tri-nucleotides counts, described in the next topics). The hyperparameters used to execute the DL and ANN approaches are made available in Extended data: Supplementary File S1.24\n\nWe compared the algorithms performances using different sets of coding and non-coding RNA sequences from Ensembl (April 14th 2020) (17) database, covering 15 organisms of distinct representative Chordata clades (Figure 1A): Anolis carolinensis (Sauria, Squamata), Chrysemys picta bellii (Sauria, Testudines), Crocodylus porosus (Archosauria, Pseudosuchia), Danio rerio (Actinopterygii, Teleostei), Eptatretus burgeri (Agnatha, Myxinidae), Gallus gallus (Archosauria, Theropoda), Homo sapiens (Placentalia), Latimeria chalumnae (Sarcopterygii, Coelacanth), Monodelphis domestica (Marsupialia), Mus musculus (Placentalia), Notechis scutatus (Sauria, Squamata), Ornithorhynchus anatinus (Monotremata), Petromyzon marinus (Agnatha, Petromyzontiformes), Sphenodon punctatus (Sauria, Rhynchocephalia), Xenopus tropicalis (Amphibia). All non-coding RNA sequences for each organism were downloaded from Ensembl transcripts. In order to obtain a balanced set of sequences (i.e. equal number of coding and non-coding), the group of coding RNAs were randomly selected in order to obtain the same number of ncRNAs for each species. Moreover, before generating the models, the sequences were normalized through their length (i.e. each tri-nucleotide count was divided by the total size of the given sequence). All sequences in FASTA format with their respective Ensembl identifiers can be retrieved at RNAmining website (https://rnamining.integrativebioinformatics.me/download).\n\nFirstly, we download the coding and non-coding sequences from Ensembl; Next, we perform the trinucleotides counts and sequence normalization. After this, we created a machine learning benchmarking within the 7 algorithms and selected the one with the best performance to be implemented in the RNAmining tool (XGBoost algorithm), which was again evaluated using sequences from 9 other different species and sets of artificially generated ones. Finally, we performed a novel benchmarking with RNAmining against the public available tools for coding potential prediction.\n\nSequences were randomly divided into training and testing datasets, using 80% of the data for training and 20% for testing. For ANN and CNN experiments, sequences were split into 60% of the data for training and 20% for validation. The testing dataset was the same used in the other machine learning algorithms. The number of sequences used for each organism for the training and test sets can be observed in Table 1. Next, we generated 180 models (i.e. one per algorithm for each organism, whereas three experiments for ANN models and four experiments for CNN models), which were further evaluated in this work.\n\nList of organisms and the total number of sequences used for testing and training both coding and non-coding RNAs. The numbers are separated into training/testing values. All sequences can be retrieved at RNAmining website (https://rnamining.integrativebioinformatics.me/download).\n\nAfter selection of the best model, it was applied and evaluated in other nine organisms (Figure 1A), including five Chordata and four phylogenetically distant species. Among the chordates, the models were tested in Carassius auratus (Actinopterygii, Teleostei), Gorilla gorilla gorilla (Placentalia), Pseudonaja textilis (Sauria, Squamata), Rattus norvegicus (Placentalia) and Terrapene carolina triunguis (Sauria, Testudines). Within non-chordates species, we evaluated the model in Arabidopsis thaliana (Plantae, Eudicots), Caenorhabditis elegans (Nematoda), Drosophila melanogaster (Insecta, Diptera) and Saccharomyces cerevisiae (Fungi, Ascomycota). Finally, it was evaluated using artificial sequences containing the same nucleotides composition of the ncRNAs for each species of the testing dataset (Table 1). Ten sets of random sequences containing the same number of ncRNAs per species were generated using MEME suite Version 5.1.1 with default parameters (18). All sequences in FASTA format can be retrieved at RNAmining website (https://rnamining.integrativebioinformatics.me/download).\n\nThe performance of all algorithms in the coding potential evaluation was compared with publicly available tools commonly employed for this purpose (RNAcon (10), CPAT (11), Transdecoder (12) and CPC2 (13)), using default parameters. It is worth noting that CPAT only made available models for H. sapiens with a coding probability (CP) cutoff of 0.364 (i.e. CP ≥ 0.364 indicates coding sequence); M. musculus with a CP cutoff of 0.44; D. melanogaster with a CP cutoff of 0.39; and D. rerio with CP cutoff 0.38. Therefore, for the other organisms we built new models using our training sets and we used the statistical method provided by the authors to calculate the cutoffs probability for coding prediction: A. carolinensis (0.4); C. picta bellii (0.57); C. porosus (0.38); E. burgeri (0.35); G. gallus (0.42); L. chalumnae (0.365); M. domestica (0.51); N. scutatus (0.15); O. anatinus (0.28); P. marinus (0.34); S. punctatus (0.18); X. tropicalis (0.25). The whole workflow of RNAmining development can be visualized in Figure 1B.\n\nThe XGBoost method was implemented using XGBoost Library (version 1.2.0) in Python Language (Version 3.8) and the models for each species were saved using pickle Python's library. The web server interface was developed using HTML and CSS. The connection within the front and back-end was implemented through Javascript. The control of files and the connection with Python's scripts was performed through PHP language. RNAmining user friendly tool and its stand-alone version can be accessed at https://rnamining.integrativebioinformatics.me/. Instructions on how to use it and a whole documentation are made available. Its source code with a Docker platform can be freely obtained at https://gitlab.com/integrativebioinformatics/RNAmining.\n\n\nResults\n\nIt is known that the algorithm performance in predictive analysis is influenced by particularities available in the genomes sequences of the organisms used in the training set (19), and it should be taken into account when developing novel tools for nucleotides coding prediction. Thus, it is necessary to test several methods to observe which ones can have a good prediction for specific species from evolutionary branches. Similar to Panwar et al. (10), we used the tri-nucleotides counts to distinguish coding and non-coding sequences. We evaluated the performance of seven machine learning algorithms using representative organisms from different branches of the Chordata clade. For that, we used a training and testing set composed by sequences from the same species. The algorithm with best performance within all evaluated organisms, according to F1-scores metric, was XGBoost, as one can see in the following: A. carolinensis (98.79); C. picta bellii (98.00); C. porosus (98.15); D. rerio (97.98); E. burgeri (97.56); G. gallus (99.24); H. sapiens (98.50); L. chalumnae (99.57); M. domestica (98.84); M. musculus (97.73); N. scutatus (96.51); O. anatinus (97.61); P. marinus (99.42); S. punctatus (99.20); X. tropicalis (99.13) (Table 2). As observed, XGBoost algorithm presented F-score values above 97.00, with the worst performance obtained for Eptatretus burgeri with a F-score of 97.56. The best performance was obtained for Petromyzon marinus with 99.42. All detailed performances with sensitivity, specificity, precision, accuracy, F1-score and the confusion matrix from each algorithm is listed in Extended data: Supplementary File S2.24 Based on these results, XGBoost was selected to be implemented in a novel web server and stand-alone tool for RNA coding potential prediction called RNAmining.\n\nF1-score for each one of the 15 species in which the algorithms were tested. Other metrics (sensitivity, specificity, precision, accuracy and the confusion matrix) used for the comparison of the algorithm’s performance were made available at the Extended data: Supplementary File S2.24\n\nTo demonstrate the generalization of the model built in our tool, we evaluated its performance using the following nine Chordata and non-Chordata organisms that were not used in our training step: A. thaliana; C. elegans; C. auratus; D. melanogaster; G. gorilla; P. textilis; R. norvegicus; S. cerevisiae; Terrapene carolina triunguis. In the training set described in the previous topic, we used sequences from representative species from amphibians, birds, mammals, fishes and reptiles. In this new experiment we executed tests using other chordates, but also covering other evolutionary groups such as plants, fungi, insects and nematodes. The F1-score obtained values varying from 86.25 to 98.10. The worst performance was when we used the training set from L. chalumnae (Sarcopterygii, Coelacanth) to predict the coding potential of known coding genes and ncRNAs from D. melanogaster (Insecta, Diptera). However, the best performance was obtained when we applied the training set from C. picta bellii (Sauria, Testudines) in coding and ncRNA sequences from Terrapene carolina triunguis (Sauria, Testudines). The F1-score for each organism, together with the respective training set evaluated, can be found in Table 3, meanwhile the confusion matrix and the other metrics can be visualized in Extended data: Supplementary File S3.24\n\nEach line comprises the model for each one of the trained species, meanwhile the columns represent the set of 9 evolutionary related and unrelated organisms in which the method was evaluated. Other metrics (sensitivity, specificity, precision, accuracy and the confusion matrix) used for the comparisons were made available at the Extended data: Supplementary File S3.24\n\nEven without using any plant in the original training set, we applied the different models to predict the coding potential of known coding and ncRNA sequences from A. thaliana (Plantae, Eudicots). The lowest F1-score that RNAmining obtained was 93.31 using a fish model (Petromyzon marinus, Agnatha, Petromyzontiformes). The best F1-score was obtained with a marsupial model (M. domestica, Marsupialia) that reached 97.40. Thus, this experiment demonstrated the efficiency of the method and the models created even when applied in organisms phylogenetically distant from those used in training.\n\nFinally, in order to show that the results obtained were not by chance, we created 10 datasets of artificial sequences containing the same number, length and nucleotides composition of the coding and ncRNA sequences from the 15 species used in our testing shown in Table 1. The F1-score mean, minimum and maximum values of the 10 datasets from each organism can be visualized in Table 5. The confusion matrix and all the other metrics (accuracy, specificity, sensitivity and precision) can be found in Extended data: Supplementary File S4.24 As we can visualize, the F1 measurement mean remained below 38.00 for all artificial sequences created for the tested organisms, with the exception of P. marinus (F1-score equals to 64.13), which still had a F1-score below to the values obtained with the other organisms tested for the coding potential prediction (Table 4).\n\nF1-score metrics for 10 datasets of artificial sequences randomly generated for each species. The mean, minimum and maximum values are displayed separated by organism. Other metrics (sensitivity, specificity, precision, accuracy and the confusion matrix) used for the comparisons were made available at the Extended data: Supplementary File S4.24\n\nNext, we compared RNAmining performance with other four tools commonly used for nucleotides coding potential prediction: CPAT, CPC2, RNAcon and Transdecoder. We used as input all coding and ncRNA sequences from the testing dataset used in the 15 species listed in Table 1. According to the F1-score metric, RNAmining outperformed all the tools in all organisms with the exception of CPAT for L. chalumnae, in which both tools presented an equal F1-score of 99.57. The comparative performance of all tools can be observed in Table 5. The detailed results regarding their accuracy, sensitivity, specificity, precision, F1-score and the confusion matrix can be found in Extended data: Supplementary File S2.24 Finally, we used the t-student test to compare the results from RNAmining and the other tools, revealing that our software presented significantly better results in performing coding potential predictions based on known coding genes and ncRNAs. The p-values obtained in these comparisons were: 0.0026 (vs CPAT); 1.57e-05 (vs CPC2); 2.69e-05 (vs RNAcon); and 2.89e-05 (vs Transdecoder).\n\nF1-score metric for CPAT, CPC2, RNAcon, Transdecorder and RNAmining, based on the predictions using models provided by each tool or generated according to their instructions. The bold numbers are the best values regarding F1-score metric. The results for other metrics were made available at the Extended data: Supplementary File S2.24\n\nRNAmining tool was made available in both stand-alone and web server versions. The tools only require the nucleotide sequences of the RNAs in which the user intends to perform the coding potential prediction in FASTA format, together with the species name in a standardized format related to the model to be used. Besides our tool presented good results even when using phylogenetically distant organisms, we recommend to always use the most closely-related species to the one the user wants to perform the predictions. Furthermore, RNAmining documentation presents all the guidelines on how to generate a model for a particular set of sequences and organisms of interest. The web interface of RNAmining tool was developed to allow users to quickly perform the coding potential prediction without the need of installing any specific program and using only a generic internet browser. The only requirement for running the tool is a FASTA file containing the nucleotide sequences and the organism model that the user wants to use, which can be selected in a drop-down menu containing all 15 organisms used in the training step (Figure 2A). There is no limit of the number of sequences, but the web server supports files up to 20Mb. For files bigger than that, we recommend using the stand-alone RNAmining tool. RNAmining will automatically classify the FASTA sequences used as input and identify which of them are coding or non-coding RNAs. Finally, as a result it offers a table with the sequences’ IDs and its classification as coding or non-coding, which can also be downloaded in tabular format, together with two separate FASTA files containing both the coding and non-coding sequences separately (Figure 2B).\n\nThe user only needs to upload the nucleotide sequences in FASTA format and select the model to be used based on the evolutionary close related species. B. Results web page screen. General report containing the list of coding and non-coding sequences in a dynamic table, in which the user can search for a particular sequence or filter only those coding or non-coding RNAs by using a free text form that will filter the results in the table dynamically. The user can download the complete table in tabular format and two FASTA files containinng the set of coding and non-coding RNAs separately.\n\n\nDiscussion\n\nThe coding potential prediction of nucleotides is a key step in the definition of the repertoire of non-coding RNAs in a genome or transcriptome project, especially when dealing with non-model organisms. Sometimes, predictive tools for the computational characterization of RNA molecules, in analyses like the prediction of specific RNA families (19) or the estimation of a network of RNA-RNA (20) or protein-RNA interactions (21), have their performance affected according to the training organism, increasing the number of false positives when applied in evolutionarily distant species. In this work, we evaluated the performances of seven different supervised machine learning algorithms, using eukaryotic species from a variety of evolutionary clades, revealing their potential to be used in the development of novel and improved computational tools for the coding potential prediction of RNA sequences. Artificial intelligence has been widely used in computational biology (22,23), but its application to characterize ncRNAs has been limited.\n\nIn this benchmarking, we opted to analyze the tri-nucleotides counting as the main feature to be evaluated for the coding potential prediction, followed by a normalization considering the sequences length (i.e. each tri-nucleotide count was divided by the total size of the given sequence). Panwar et al. (10) used nucleotides counting successfully for this purpose. They considered 40,905 non-coding RNAs from Rfam release 10.0 database and 62,473 coding RNA sequences from Human RefSeq database, divided into 50% of training and 50% of test (i.e. the training and test sets were composed of 20,453 non-coding and 31,237 coding sequences). They used the counts of mono-, di-, tri-, tetra- and penta-nucleotides and a combination of all counts using the SVM method, and showed that using tri-nucleotides counts is enough to predict the coding potential of ncRNAs with better accuracies. Our comparisons of the machine learning algorithms revealed XGBoost as the algorithm with better performance, presenting efficiency in predicting the coding potential of RNA sequences even when using the models of distantly related organisms. This latter shows the usefulness of this approach for performing coding predictions in non-model organisms.\n\nWe implemented XGBoost in RNAmining, a stand-alone and web server tool flexible to be used in genome or transcriptome projects focused in both model and non-model eukaryotic organisms. Our tool outperformed similar approaches, such as CPAT (11), CPC2 (13), RNAcon (10) and Transdecoder (12). Both versions of the software are easy to use, with the web version providing a simple report and FASTA format files that can be used in downstream analysis. It provides 15 models generated from eukaryotic from different evolutionary clades. Other models can be generated by the user using the stand-alone version, which can be used with simple command line operations. These features facilitate its usage for experienced users and, especially, for those without any programming experience, which can easily perform large-scale predictions of the coding potential of nucleotide sequences in both genome or transcriptome initiatives.\n\n\nConclusions\n\n\n\n• We used pattern recognition approaches to investigate the coding potential prediction of RNAs, using 64 features (all combinations of tri-nucleotides counts).\n\n• We performed a benchmarking from seven machine learning algorithms (Naive Bayes, SVM, KNN, Random Forest, XGBoost, ANN and DL), through 15 model organisms from different evolutionary branches and implemented the best one (XGBoost) in a novel tool (RNAmining).\n\n• RNAmining is a user-friendly coding potential prediction web tool that performs XGBoost algorithm to predict the coding potential of RNA sequences.\n\n• A comprehensive analysis using data from 15 organisms revealed that RNAmining outperformed other tools available in literature (CPAT, CPC2, RNAcon and Transdecoder).\n\n\nData availability\n\nEnsembl is an open access genome browser for vertebrate genomes in the Ensembl website (https://www.ensembl.org/index.html).\n\nRNAmining is a tool for coding potential prediction which is freely available at (https://rnamining.integrativebioinformatics.me/download).\n\nZenodo: RNAmining Software Supplementary Material, http://doi.org/10.5281/zenodo.4699571.24\n\nThis project contains the following extended data:\n\n- Supplementary File S1: ANN and DL parameters\n\n- Supplementary File S2: All metrics used for the comparison of the algorithm’s performance from the 15 model organisms.\n\n- Supplementary File S3: All metrics used for the XGBoost algorithm’s performance from the 9 evolutionary related and unrelated organisms in which the method was evaluated.\n\n- Supplementary File S4: All metrics used for the XGBoost algorithm’s performance from the artificial sequences created for the tested organisms.\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\nRNAmining is available from: https://rnamining.integrativebioinformatics.me/.\n\nSource code available from: https://gitlab.com/integrativebioinformatics/RNAmining/-/tree/master/volumes/rnamining-front/assets/scripts/ and https://github.com/thaisratis/RNAmining.\n\nArchived source code as at time of publication: http://doi.org/10.5281/zenodo.4699409.25\n\nLicense: MIT",
"appendix": "Acknowledgements\n\nThe authors would like to thank Dr. Savio Torres de Farias for the helpful discussions during the preparation of this manuscript.\n\nA previous version of this article can be found on bioRXiv: https://doi.org/10.1101/2020.10.26.354357.\n\n\nReferences\n\nMattick JS: The central role of RNA in the genetic programming of complex organisms. An Acad Bras Cienc. 2010; 82: 933–939. PubMed Abstract | Publisher Full Text\n\nGelsinger DR, DiRuggiero J: The Non-Coding Regulatory RNA Revolution in Archaea. Genes. 2018; 9. PubMed Abstract | Publisher Full Text Publisher Full Text\n\nCroce CM: Causes and consequences of microRNA dysregulation in cancer. Nat Rev Genet. 2009; 10: 704–714. PubMed Abstract | Publisher Full Text Publisher Full Text\n\nSchaefer A, O’Carroll D, Tan CL, et al.: Cerebellar neurodegeneration in the absence of microRNAs. J Exp Med. 2007; 204: 1553–1558. PubMed Abstract | Publisher Full Text Publisher Full Text\n\nZhao Y, Ransom JF, Li A, et al.: Dysregulation of cardiogenesis, cardiac conduction, and cell cycle in mice lacking miRNA-1-2. Cell. 2007; 129: 303–317. PubMed Abstract | Publisher Full Text\n\nDjebali S, Davis CA, Merkel A, et al.: Landscape of transcription in human cells. Nature. 2012; 489: 101–108. PubMed Abstract | Publisher Full Text Publisher Full Text\n\nKellis M, Wold B, Snyder MP, et al.: Defining functional DNA elements in the human genome. Proc Natl Acad Sci U S A. 2014; 111: 6131–6138. PubMed Abstract | Publisher Full Text Publisher Full Text\n\nArias-Carrasco R, Vásquez-Morán Y, Nakaya HI, et al.: StructRNAfinder: an automated pipeline and web server for RNA families prediction. BMC Bioinformatics. 2018; 19: 55. PubMed Abstract | Publisher Full Text Publisher Full Text\n\nTorres F, Arias-Carrasco R, Caris-Maldonado JC, et al.: LeishDB: a database of coding gene annotation and non-coding RNAs in Leishmania braziliensis. Database. 2017; 2017. PubMed Abstract | Publisher Full Text Publisher Full Text\n\nPanwar B, Arora A, Raghava GPS: Prediction and classification of ncRNAs using structural information. BMC Genomics. 2014; 15: 127. PubMed Abstract | Publisher Full Text Publisher Full Text\n\nWang L, Park HJ, Dasari S, et al.: CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model. Nucleic Acids Res. 2013; 41: e74. PubMed Abstract | Publisher Full Text Publisher Full Text\n\nHaas BJ, Papanicolaou A, Yassour M, et al.: De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc. 2013; 8: 1494–1512. PubMed Abstract | Publisher Full Text Publisher Full Text\n\nKang Y-J, Yang D-C, Kong L, et al.: CPC2: a fast and accurate coding potential calculator based on sequence intrinsic features. Nucleic Acids Res. 2017; 45: W12–W16. PubMed Abstract | Publisher Full Text Publisher Full Text\n\nChang C-C, Lin C-J: LIBSVM. ACM Transactions on Intelligent Systems and Technology. 2011: 1–27. Publisher Full Text\n\nPedregosa F, Varoquaux G, Gramfort A, et al.: Scikit-learn: Machine Learning in Python. J Mach Learn Res. 2011; 12: 2825–2830.\n\nPython API Reference � xgboost 1.3.0-SNAPSHOT documentation.[cited 14 Oct 2020]. Reference Source\n\nZerbino DR, Achuthan P, Akanni W, et al.: Ensembl 2018. Nucleic Acids Res. 2018; 46: D754–D761. PubMed Abstract | Publisher Full Text Publisher Full Text\n\nBailey TL, Boden M, Buske FA, et al.: MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res. 2009; 37: W202–8. PubMed Abstract | Publisher Full Text Publisher Full Text\n\nAguiar RR, Ambrosio LA, Sepúlveda-Hermosilla G, et al.: miRQuest: integration of tools on a Web server for microRNA research. Genet Mol Res. 2016; 15. PubMed Abstract | Publisher Full Text\n\nSinan Uğur Umu PPG: A comprehensive benchmark of RNA–RNA interaction prediction tools for all domains of life. Bioinformatics. 2017; 33: 988. PubMed Abstract | Publisher Full Text Publisher Full Text\n\nNithin C, Mukherjee S, Bahadur RP: A non-redundant protein-RNA docking benchmark version 2.0. Proteins. 2017; 85. PubMed Abstract | Publisher Full Text\n\nde Brito DM, Maracaja-Coutinho V, de Farias ST, et al.: A Novel Method to Predict Genomic Islands Based on Mean Shift Clustering Algorithm. PLoS One. 2016; 11: e0146352. PubMed Abstract | Publisher Full Text Publisher Full Text\n\nRamos TAR, Maracaja-Coutinho V, Ortega JM, et al.: CORAZON: a web server for data normalization and unsupervised clustering based on expression profiles. BMC Res Notes. 2020; 13: 338. PubMed Abstract | Publisher Full Text Publisher Full Text\n\nRatis T, Galindo N: RNAmining Software Supplementary Material [Data set]. Zenodo. 2021. Publisher Full Text\n\nRatis T, Galindo N: thaisratis/RNAmining: RNAmining (Version v1.0.3). Zenodo. 2021, April 18. Publisher Full Text"
}
|
[
{
"id": "83973",
"date": "10 May 2021",
"name": "Gilderlanio Araújo",
"expertise": [
"Reviewer Expertise Bioinformatics. Machine Learning. Transcriptome Analysis. Population Genomics."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nAre there two different datasets of model organisms? On the abstract \"...15 organisms from different evolutionary branches...\" On the main text \"RNAmining was evaluated through 24 organisms from the eukaryotic tree of life and its results outperformed publicly available tools commonly used for that purpose.\"\n\nWhy fine-tuning SVM was performed with a grid search strategy and not Random Forest too? Provide some reasoning.\n\nWhy sequences were divided using different proportions? Provide some reasoning. \"Sequences were randomly divided into training and testing datasets, using 80% of the data for training and 20% for testing. For ANN and CNN experiments, sequences were split into 60% of the data for training and 20% for validation.\"\n\nOn the web tool, you should provide a column for prediction probability for coding and non-coding variants. The new column will improve user analysis, such as filtering for those predictions with XGboost >= 0.9.\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? Partly\n\nAre the conclusions about the tool and its performance adequately supported by the findings presented in the article? Yes",
"responses": [
{
"c_id": "6749",
"date": "08 Jun 2021",
"name": "Thaís A. R. Ramos",
"role": "Author Response",
"response": "1- The connectionist methods (e.g. Artificial Neural Networks and Convolutional Neural Networks) demand a validation dataset to adjust the model, because of the weights optimization stage and its hyperparameters. Thus, for experiments with ANN and CNN, 20% were used for validation, 60% for training (defined as 80% for the other algorithms) and another 20% for testing, in all the cases. 2- Yes, in fact we have the dataset 1 composed of 15 model organisms which were used to build the models, and the dataset 2 composed of other 9 phylogenetically related and unrelated organisms that were not used in our training, demonstrating the efficiency of the tool even when applied in species phylogenetically distant from those used in training. On the main text, we changed this sentence in the “Introduction” section to: \"Next, RNAmining was evaluated in another 9 phylogenetically related and unrelated organisms that were not used in our training, demonstrating the efficiency of the tool even when applied in species phylogenetically distant from those used in training. In total, it was evaluated through 24 organisms from the eukaryotic tree of life and its results outperformed publicly available tools commonly used for that purpose.” 3- In fact all the methods were executed with the grid search method. We made a mistake in the writing. It was modified by replacing the sentences: \"The Random Forest model was implemented using empirical tests and the best result was selected for training the model. We considered the default parameters with the exception of the number of trees used (150 estimators) and the criterion parameter setted to 'entropy' for information gain. KNN and Naive Bayes models were trained with the default values. The SVM parameters were obtained through grid search method and the resulting model was trained with the Radial Basis Function (RBF) kernel, with the Regularization parameter (C) and Kernel coefficient (Gamma) defined in 1000 and 0.8, respectively. ANN and DL were performed with different architectures according to grid search and empirical tests\" to the following: \"XGBoost, K-NN and Naive Bayes models were trained with the default values. The Random Forest and SVM parameters were obtained through grid search method, the best results using Random Forest resulted in a model generated with the default parameters, with the exception of the number of trees used (150 estimators) and the criterion parameter setted to 'entropy' for information gain. For SVM, the resulting model was trained with the Radial Basis Function (RBF) kernel, with the Regularization parameter (C) and Kernel coefficient (Gamma) defined in 1000 and 0.8, respectively. ANN and DL were performed with different architectures according to grid search and empirical tests.\" 4- Thank you for your suggestion. We considered it and provided a new column in the output file (Classification probabilities) in both web server and stand-alone versions."
}
]
},
{
"id": "84936",
"date": "25 May 2021",
"name": "Andre Yoshiaki Kashiwabara",
"expertise": [
"Reviewer Expertise Bioinformatics",
"Computational Biology",
"Machine Learning."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis paper presents RNAmining to predict the protein-coding potential of transcripts. The authors have compared many algorithms using cross-validation and selected XGBoost. The tool has the potential to be very useful. It is available online, and it is easy to use.\n\nIn recent studies, some small ORF in annotated ncRNA has validated protein-coding potential 1. How does RNAmining behave when these annotated ncRNAs that contain such small ORF challenge it?\n\nIt is important to cite RNAploc 2, BASINET 3, and CoDaN 4.\n\nI suggest plotting ROC curves when comparing classification methods.\n\nIn the abstract, the authors have described the use of cross-validation to assess the accuracy of each classification method. However, in methodology, the author explained that 80% is the training set and the other 20% is the validation set. And for CNN, and ANN this number is also different (60%/20%). It isn't clear. It will help create a figure showing the \"workflow\" of the Training/Validation/Testing part.\n\nThe standard deviation of the cross-validation can be helpful to show the stability of each classification method.\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? Partly",
"responses": [
{
"c_id": "6750",
"date": "08 Jun 2021",
"name": "Thaís A. R. Ramos",
"role": "Author Response",
"response": "1- RNAmining was trained using coding genes and ncRNAs from the Ensembl database. It evaluates the patterns in the tri-nucleotide counts in any RNA sequence (which could be an ORF or not) and, according to this, it classifies into coding and non-coding sequences. The RNAmining training was not performed with the proposal of generating a specific model for ORFs or some specific type of sequence, it works independently of this. 2- Thank you for your suggestion. We included the citations for BASiNET and CoDaN in the Introduction section of the manuscript. We were not able to find the manuscript describing RNAploc and it was not included. 3- We believe that it is possible to visualize the performance of the methods from the tables presented along the main text of the paper, as well as made available as supplementary material, since the measures used for the ROC curves construction are the same presented there. In addition, we consider that when we have too similar numbers it is easier to see the difference in a table. 4- The cross-validation method was used in the grid search method using the training dataset to validate the hyperparameters, choosing the best set of parameters. In addition, this partition method validates the hyperparameter's results through different validation sets. Therefore, it proves that our model is working and generalizing the problem. Thus, when we had the best parameters we used the test dataset (20%) to generate the final models and to calculate the metrics. The connectionist methods (e.g. Artificial Neural Networks and Convolutional Neural Networks) demand a validation dataset to adjust the model, because of the weights optimization stage and its hyperparameters. Thus, for experiments with ANN and CNN, 20% was used for validation, 60% for training (defined as 80% for the other algorithms) and 20% for testing, in all the cases. In addition, due to the complexity of these 2 algorithms, it is more common in literature to use the holdout (training/validation/test) partition method instead of cross-validation. Thereby, we modified the sentence in the abstract: \"All the machine learning algorithms tests were performed using 10-folds cross-validation...\" to \"The machine learning algorithms validations were performed using 10-fold cross-validation...\". In addition, in the section \"Training and testing datasets, model building and quality measuring for coding potential evaluation\" we changed the following sentence: \"Sequences were randomly divided into training and testing datasets, using 80% of the data for training and 20% for testing. For ANN and CNN experiments, sequences were split into 60% of the data for training and 20% for validation. The testing dataset was the same used in the other machine learning algorithms.\" to the following text: \"The cross-validation approach was applied in the grid search method, using the training dataset to validate the hyperparameters and obtain the best set of this to be used. In addition, this partition method validates the hyperparameter's results through different validation sets. Therefore, it proves that our model is working and generalizing the problem. Thus, sequences were randomly divided into training and testing datasets, using 80% of the data for training and 20% for testing. The connectionist methods (e.g. Artificial Neural Networks and Convolutional Neural Networks) demand a validation dataset to adjust the model, because of the weights optimization stage and its hyperparameters. Thus, for experiments with ANN and CNN, 20% were used for validation, 60% for training (defined as 80% for the other algorithms) and 20% for testing.The testing dataset was the same used in all machine learning algorithms.\" 5- The results shown in this paper are not obtained using cross-validation. The cross-validation method was used in the grid search method to validate the hyperparameters, choosing the best set of parameters. Thus, we can validate the hyperparameter's results through different validation sets. Therefore, it proves that our model is working and generalizing the problem. Thus, to generate the final models and to calculate the metrics, we used the test dataset (20%) with the best parameters."
}
]
}
] | 1
|
https://f1000research.com/articles/10-323
|
https://f1000research.com/articles/10-452/v1
|
08 Jun 21
|
{
"type": "Research Article",
"title": "Effects of mobile health education on sexual and reproductive health information among female school-going adolescents of rural Thailand",
"authors": [
"Premyuda Narkarat",
"Surasak Taneepanichskul",
"Ramesh Kumar",
"Ratana Somrongthong",
"Premyuda Narkarat",
"Surasak Taneepanichskul",
"Ratana Somrongthong"
],
"abstract": "Background: Adolescent pregnancy is one of the major public health issues globally, as well as in Thailand. Sexual health literacy (SHL) has been a proved effective intervention for preventing teenage pregnancy. The objective of this study was to evaluate the effects of mobile messages to improve sexual and reproductive health literacy among secondary school female students. Methods: A comparative cross-sectional study with pre–post design was conducted in two secondary schools of rural Thailand. 128 respondents were selected through a simple random sampling method; equal number of female secondary school students were selected from each school. Health education through mobile messages on sexual and reproductive health literacy were delivered in one group while the other group was observed through routine care for 24 weeks. Baseline (pre) and endline (post) measurement was taken to compare the effects of mobile messages. Study was ethically approved by the institutional review board of Chulalongkorn University, Thailand. Results: Both groups were same at baseline and found statistically non-significant (p>0.05). After the 24-week health education program, the mean scores of health education groups was found statistically significant (p<0.05), while the mean score in observed group did not show any statistical change (p>0.05) . Level of sexual health literacy scores among female students in the health education group was found statistically significant (p<0.05) in all four domains. While, the observation group was remained same at both measurements pre and post (p=0.521). Conclusion: The study concluded that the mobile messages have proved an effective information method for sexual and reproductive health information among female secondary students of rural Thailand.",
"keywords": [
"Sexual Health",
"Reproductive Health Literacy",
"teenage pregnancy",
"sex education",
"mobile health",
"effective health education."
],
"content": "Introduction\n\nAdolescent pregnancy is a well-known reproductive health problem in the teenage population of Thailand. Moreover, this age group is more prone to pregnancy due to their active sexual and biological health.1 Studies have found that 41% of adolescents were sexually active, and about 20% were engaged in risky sexual behaviors.1,2 The reported data showed that, annually, about 47 childbirths occurs in 1,000 adolescent mothers in the world.3 The United Nations Children's Fund data from Thailand, 2016–2017, found that the prevalence of adolescent pregnancy in the age group of 15–19 years was 51%.4 Moreover, other sources also revealed that the birth rates among adolescents aged 15–19 years during in 2013, 2014 and 2015 was 51.1, 47.9 and 44.8 per 1,000 adolescents women, respectively.5,6 In 2018, the childbearing rate among adolescents aged 10–19 years increased to 12.9%, which is an alarming signal for policy makers in sexual and reproductive health in the country.7 Hence, the situation of adolescent pregnancy has become a predominant problem in Thailand that needs urgent interventions.8 Moreover, it has been observed through the evidence that the this number of adolescent pregnancy is more in the southern part of Thailand including Chumpon province, Krabi province, and Nakhon Si Thammarat province.9 This problem of adolescent pregnancy has not yet been resolved. Moreover, proper information and knowledge for adolescents on sexual health literacy, early aged pregnancy, sexually transmitted diseases (STD), childbearing information and care are highly needed.10\n\nSexual health literacy is very effective approach for improving an individual's cognitive and social skills that result in developing a positive behavior.11 Sexual health literacy implies the achievement of knowledge levels, personal skills, and confidence to take action for personal and community health improvement by changing personal lifestyles and living conditions. Improving adolescents' access for sexual and reproductive health information, and their capacity to use it effectively, sexual health literacy should be provided and tested among the younger population of Thailand. Therefore, this study was conducted to evaluate the effects of mobile messages to improve sexual health literacy among secondary School female students of rural Thailand.\n\n\nMethods\n\nA comparative cross-sectional study with pre–post design was conducted at two secondary Schools of Nakhon Si Thammarat and Krabi provinces of southern Thailand from February–July 2020. Secondary school female students were the respondents in this study. One school was randomly selected as a group with health education and other school as the observation group.\n\nThe sample size was calculated using 80% power, 0.05 alpha with 10% difference, and 128 students were selected for this study. An equal number of 64 female students were randomly selected from each school and allocated for both groups.\n\nData collectors were trained on how use the data collection tool, and briefed on the study prior to starting the study. The survey technique was face-to-face interviews. The process took approximately 30 minutes for each participant. The internal consistency of the questionnaires was measured through Cronbach alpha (0.9) was used to collect sociodemographic information and sexual health literacy as per the objectives.12 Health education group was given; 24-week program consisted of a weekly sexual health education animation on Facebook and a LINE application message on the importance of sexual health was given. The eight-week sexual health education topics were delivered once a week for 1.5 minutes through the LINE application. All the selected intervention participants gave responses via Facebook twice a week for up to 24 weeks. Female secondary school students received three LINE messages each week, sent in the evening hours. They continued receiving such messages from recruitment (at the first week of the section education animation on Facebook period intervention) to 24 weeks at the end of the intervention. A total of 72 LINE messages were developed and three line messages were sent per week. Furthermore, the activities included the presented infographic which the participants received for each topic of animation. The contents were the same as the knowledge on Facebook's contents. The control group received only the routine education. Weekly messages were sent for four weeks' time on situation of unintended pregnancy and contraception for accessing, understanding the actual situation, appraising the contexts of this problem and finally applying this problem in real life. A complete information with different pictures and real-life examples on sexual health were also shared with the respondents. Participants were briefed that they should contact a free help line to get more information in this regard.\n\nData were analyzed using the Statistical Package for Social Science (IBM SPSS Statistics, RRID:SCR_019096) Software version 22 licensed for Chulalongkorn University; JASP (RRID:SCR_015823) is an open access alternative to SPSS. The sexual health literacy (SHL) score was calculated by using the formula “Index - score = (mean–minimal value of mean)×(50/3)”, scaled by four levels: inadequate: 0–25; problematic: >25–33; sufficient: >33–42; and excellent: >42–50. Both the formula and the scales were adopted from the European Health Literacy Survey (HLS-EU-Q47) method.13 The homogeneity of baseline characteristics was analyzed by using Chi-squared test for nominal data. In inferential statistics, one-way ANOVA repeated measurement was used for comparison of mean changes for all time points within intervention and control groups. The pairwise comparison of one-way ANOVA repeated measurement was used for intervention and control groups at different times of measurement. The independent t-test was used to compare the change between intervention group and control group for all time points. The level of significance was set at a p-value < 0.05 for all statistical analyses.\n\nThis study was approved by the Research Ethics Review Committee for Research Involving Human Research Participants, Health Sciences Group, Chulalongkorn University (COA No. 252.2/62). Data was collected from the respondents after taking the written informed consent from their parents. Administration approval was taken from the head of both schools.\n\n\nResults\n\nSociodemographic characteristics of the respondents of both the health education and observation groups are explained in Table 1. The comparison of general characteristics between the two groups were not different in terms of grade point average, age, allowance, and parent's marital status. Most of the female students were 14-year-old students of grade 8, and obtained grade point average over 3.0. The characteristics between two groups were not statistically different in term of grade point average (p = 0.439), age (p = 0.312), monthly income (p = 0.220), living condition (p = 0.410), and their parent's marital status (p = 0.465). Hence, both groups have similar socio-demographic information selected for the study.\n\na Value are mean ± SD.\n\nb P-value resulted from the Independent t-test.\n\nc P-value resulted from the Chi-square-test.\n\nThe level of sexual health literacy scores calculated as per index score mentioned in the method section among secondary school female students of both groups shows statistical significant difference in mean, SD and range (p = 0.000) after the health education. Group with health education was observed with significant changes with domains like; sufficient (76%), problematic (22%) and inadequate only (2%). However, the observation group remained the same without any change. The health education group reported only 1 (2%) participant with inadequate but on other hand, observation group showed all their participants with inadequate sexual health literacy group (Table 2).\n\n* Significant at 0.05 level.\n\nBoth groups were compared through average mean score measured by calculation of all four domains like: accessing, understanding, appraising and applying. The observation group remained the same at both measurements: pre and post (p = 0.521). However, the health education group showed statistically significant differences in all four domains (p = 0.000). This shows that the health education group has received positive information as compared to observation group that remained same (Table 3).\n\nThe magnitude of change in the mean score of sexual health literacy scores was significantly higher in the health education group than the observation group (Figure 1).\n\n\nDiscussion\n\nStudents with good educational record perceived health education messages in better way as compared to those who had poor academics performance. This is consistent with a study showed that adolescents who attended school in urban setting had significantly higher score on sexual health literacy and knowledge.12,13 Female adolescents who are in the middle of psychosocial development phases, they undergo various changes in terms of their physical, cognitive, emotional, and sexual development at this stage.14 These changes can lead to major risk factors for premarital sexual behaviour, adolescent pregnancy, abortion, and sexually transmitted infections. Health literacy is also effected by factors such as education, ethnicity, gender, age, profession, income, culture, language, and social support.15,16 However, this study focused on several variables including age, grade point average, average allowance, parent's marital status, and living with parents that also indirectly affected the sexual and reproductive health of the respondents. This can be assumed that students who are performing well in school may have higher knowledge and understanding toward sexual health literacy.\n\nIt was found that the measurement of the sexual health literacy scores (index) of the health education group in the baseline and endline had increased respectively through duration of the health education. There were statistically significant changes of the overall index scores before and after the health education program of the health education group. These findings are consistent with a study conducted on sex education program and prevention among grade 8 female students, where it was found that the experimental group had significantly higher levels of knowledge about preventing sexually transmitted disease and unwanted pregnancy, attitudes towards sexual behavior, self-efficacy in prevention of undesirable sexual behaviors, self-esteem, and sexual behaviors. This can be explained by the score of female students who received program information that was relevant to sexual health literacy which is consistent with accessing, understanding, appraising, and applying. Comparison of sexual health literacy scores (index) of the health education and observation groups at different time of measurement showed that the health education group's sexual health literacy scores had changed as compared to baseline. However, the observation group's sexual health literacy scores did not change and remained same in both pre and post measurements. This can be explained by that the observation group did not receive the program; moreover, people can improve their literacy skills through intensive health education. The mean scores in the comparison group gradually declined in all four domains. The increasing trend in scores from the baseline to endline can be explained by the health education activities that comprised all four domains of sexual health literacy. Moreover, the health education group received health education through social media model plus line messages. In addition, the program designed was based on information, motivation and behavioral skills health education that is relevant to sexual health literacy and cover assessing, understanding, appraising and applying in display of info-graphic and animations. Participants randomly received rewards when joining the activities through LINE. This is similar to the health education study which found that the mean scores of health literacy were higher than those in the observation group after receiving the Sex Must Safe Program, the health education program, which included all the elements of health literacy.16\n\n\nConclusion\n\nThis study concluded that the mobile messages are proved to be effective among adolescents to increase their sexual and reproductive health literacy and this could be replicated in similar settings of the country to promote sexual and reproductive health and control the teenage pregnancy issues in the country.\n\n\nLimitations and recommendations\n\nThe sample size of this study was small and population in the study was secondary school female students only. The areas of the study were purposively selected; hence the results of the study may not be generalizable to other locations and population. This Social Media Model should be recommended to policy makers in order to be applied in the prevailing situation. Implementation and modification of the Social Media Model's contents should be performed by relevant government authorities in order to be applicable for general population; especially for a rapid observation and prevention of teenage pregnancy. Limited time of measurements in the intervention group could have an effect on the knowledge of the participants in medium or long term knowledge, hence this study focuses on a short-term evaluation.\n\n\nData availability\n\nOpen Science Framework: Underlying data for ‘Effects of mobile health education on sexual and reproductive health information among female school-going adolescents of rural Thailand’. http://www.doi.org/10.17605/OSF.IO/WPUCZ\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\nPN conceived the study design and ST supervised the data collection. RK, did the data analyses and drafted the paper. RS conducted the critical review and added the intellectual content to the paper. All authors read and approved the final draft.",
"appendix": "Acknowledgements\n\nThe authors would like to express their gratitude for the support and help which is funded by The 90TH Anniversary of Chulalongkorn University Scholarship and third author would like to acknowledge the support by Ratchadapisek Somphot Fund for Postdoctoral Fellowship, Chulalongkorn University Thailand.\n\n\nReferences\n\nHansen L, Mann J, McMahon S, et al.: Sexual Health. BMC women's health. 2004; 4(1): S24–S. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFleary SA, Joseph P, Pappagianopoulos JE: Adolescent health literacy and health behaviors: A systematic review. J Adolescence. 2018; 62: 116–27. PubMed Abstract | Publisher Full Text\n\nWHO: Preventing early pregnancy and poor reproductive outcomes among adolescents in developing countries. Geneva: WHO; 2011.\n\nNational Statistical Office of Thailand: Thailand Multiple Indicator Cluster Survey 2019, Report of 17 Selected Provinces. Bangkok, Thailand: National Statistical Office of Thailand; 2019.\n\nArnott G, Sheehy G, Chinthakanan O, et al.: Exploring Legal Restrictions, Regulatory Reform, and Geographic Disparities in Abortion Access in Thailand. Health Hum Rights. 2017; 19(1): 187–96. PubMed Abstract | Free Full Text\n\nBureau of Reproductive Health: Statistics on adolescent births. Department of Health, Ministry of Public Health. Thailand; 2015.\n\nBureau of Reproductive Health: Statistics on adolescent births. Department of Health, Ministry of Public Health. Thailand; 2018.\n\nPojanapotha P, Singhakant S, Kaewpornsawan T, et al.: Attitudes and sex education associated with sexual behavior in Thai male students in Bangkok. J Public Health and Dev. 2017; 47(1).\n\nSukrat B, Okascharoen C, Rattanasiri S, et al.: Estimation of the adolescent pregnancy rate in Thailand 2008–2013: an application of capture-recapture method. BMC Pregnancy Childbirth. 2020; 20: 120. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAsavapiriyanont S, Chaovarindr U, Kaoien S, et al.: Prevalence of Sexually Transmitted Infection in Teenage Pregnancy in Rajavithi Hospital, Thailand. J Med Assoc Thai. 2016; 99(2): S153–60. PubMed Abstract\n\nNeedham HE, Wiemann CM, Tortolero SR, et al.: Relationship between health literacy, reading comprehension, and risk for sexually transmitted infections in young women. J Adolescent Health. 2010; 46: 506–8. PubMed Abstract | Publisher Full Text\n\nVongxay V, Albers F, Thongmixay S, et al.: Sexual and reproductive health literacy of school adolescents in Lao PDR. PLoS One. 2019; 14(1): e0209675. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPsaki SR, Soler-Hampejsek E, Saha J, et al.: The Effects of Adolescent Childbearing on Literacy and Numeracy in Bangladesh, Malawi, and Zambia. Demography. 2019; 56: 1899–929. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKar SK, Choudhury A, Singh AP: Understanding normal development of adolescent sexuality: A bumpy ride. J Hum Reprod Sci. 2015; 8(2): 70–4. PubMed Abstract | Publisher Full Text | Free Full Text\n\nNutbeam D: The evolving concept of health literacy. Soc Sci Med. 2008; 67(12): 2072–8. PubMed Abstract | Publisher Full Text\n\nThongnopakun S, Pumpaibool T, Somrongthong R: The association of sociodemographic characteristics and sexual risk behaviors with health literacy toward behaviors for preventing unintended pregnancy among university students. J Multidiscip Healthc. 2018; 11: 149–56. PubMed Abstract | Publisher Full Text | Free Full Text"
}
|
[
{
"id": "87018",
"date": "15 Jun 2021",
"name": "Abdelazeem Mohamed Algammal",
"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 excellent academic research study aimed to evaluate the effects of mobile messages to improve sexual and reproductive health literacy among secondary school female students in Thailand. The aims, objectives and study design including sample size and data collection methods are appropriate and sufficiently explained by the authors. The authors have cited the local and contextual literature and well justified their findings in discussion part. Ethical considerations, a written consent was taken from the parents that is an important element of this study. However, considering the importance of the topic under study, I would suggest the investigators need to provide more details on the recruitment of the respondents. Additionally, the manuscript should be revised for English editing and grammar mistakes.\nComments:\nTitle: I think the work would benefit from the title that contains the main conclusion of the study (should be derived from the conclusion), please modify the title.\n\nAbstract: Please, highlight the main conclusion of the study.\n\nMethods: Please, add more details about the study design with specific references.\n\nResults: Good presentation.\n\nDiscussion: The authors are advised to illustrate the real impact of their findings without the repetition of results.\n\nConclusion: Should be rephrased to be sound better. A real conclusion should focus on the question or claim you articulated in your study, whose resolution has been the main objective of your paper? That question now needs to be re-invoked and definitively answered. More still, you need to leave your reader with a higher level of insight into your topic.\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": "87017",
"date": "09 Jul 2021",
"name": "Abdul Wali Khan",
"expertise": [
"Reviewer Expertise MSPH",
"PhD (Public Health)"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors have conducted study on a very important public health area. I reviewed the article and have made the following observations as part of my review:\nIn the title, please mention the place of study in Rural Thailand.\n\nIn the Abstract also mention the place of study in both the objectives and methodology sections.\n\nSome more literature especially about explanation of adolescence...as risk group; and also on effects of sexual literacy on adolescence and as well as on pregnancy's in this group need to be added.\n\nIn the Methods section, study design i.e. pre-post design is not clear. It should be further elaborated. It is stated that school was randomly selected...it should be explained...how this was selected from how many schools. It is not clear how the study participants were selected inside the school. Please explain it.\n\nIn the Results section, in the description also mention the exact number with percentages. Also explain the captions in Figure 1 as well as the tables. If you have bar-charts, could be incorporated in the Result Section.\n\nIn the Discussion section, individual findings of the study need to compared with the similar findings of the relevant studies (especially 2nd Paragraph of the Discussion).\nThe above changes need to be made before indexing. The authors have conducted study on a very important public health area.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-452
|
https://f1000research.com/articles/9-124/v1
|
19 Feb 20
|
{
"type": "Method Article",
"title": "An unsupervised learning method for reconstructing cell spatial organization with application to the DREAM Single Cell Transcriptomics Challenge",
"authors": [
"Yang Chen",
"Disheng Mao",
"Yuping Zhang",
"Zhengqing Ouyang",
"Yang Chen",
"Disheng Mao",
"Yuping Zhang"
],
"abstract": "Single cell RNA sequencing (scRNA-seq) data analysis is important for building a global transcription landscape of all cell types in tissues, tracing cell lineages, and reconstructing cell spatial organizations. In this article, we propose an unsupervised learning method to predict spatial positions and gene expression of individual cells in Drosophila embryos using a small number of driver genes. Specifically, we develop a two-stage clustering approach, and compute a probability matrix of the spatial positions of single cells. This method is applied to dataset in the DREAM Single Cell Transcriptomics Challenge. The comparison with the “gold standard” suggests that our method is effective in reconstructing the cell positions and gene expression patterns in spatial tissues.",
"keywords": [
"Spatial organization",
"single cell RNA-seq",
"Drosophila embryo",
"clustering",
"DREAM challenge"
],
"content": "Introduction\n\nThe development of single cell RNA sequencing (scRNA-seq) has provided a powerful solution for building a global transcription landscape of all cell types in tissues, finding new cell types, cell lineage tracing, spatial reconstruction, and combining with other omics1–4. The single cell is originally made from dissociated tissues without spatial information, and spatial gene expression pattern is unknown. In situ hybridization (ISH) and its variants can detect the spatial information of mRNA transcripts and produce gene expression reference atlas. Using enough marker genes, users can reconstruct the spatial position of single cell RNA-seq data by combing the ISH reference atlas3–7. Some works have also combined sequential fluorescence in situ hybridization (seqFISH) and multiplexed error robust fluorescence in situ hybridization (MERFISH) with scRNA-seq data to map cell types to the reference atlas8–10.\n\nRecent methods have successfully mapped cells from scRNA-seq data to the spatial positions using dozens of landmark genes3–7. Nikos et al. developed a DistMap method for mapping the ~1300 Drosophila embryo cells into ~3000 bins in the spatial position using 84 marker genes3. Satija4 et al. mapped 851 cells of zebrafish embryo into 64 bins in spatial embryo using 47 genes. Kaia et al. computed the correspondence score and mapped 139 cells into a Platynereis dumerilii brain using a set of 98 genes5. Andreas et al. reconstructed spatial single enterocytes along the villus axis in 1-D space using 50 bottom and top landmark genes for 1383 cells6. Mor et al. proposed novoSpaRc for spatial mapping of the scRNA-seq cells into an existing reference atlas to infer spatial gene expression7. In these methods, the dimension and resolution of the spatial region, as well as the number of marker genes, are key factors to affect the recovery of the spatial position.\n\nThe DREAM Single Cell Transcriptomics Challenge aims to develop new algorithms to find embryo spatial pattern. Participating teams are asked to predict the positions in the embryo of 1297 cells using the expression pattern from 60 (sub challenge 1), 40 (sub challenge 2), and 20 (sub challenge 3) driver genes from in situ hybridization data. The challenge is different from the published methods as it endeavors to use less marker genes to infer the spatial locations of cells.\n\nIn this article, we introduce an unsupervised learning approach for the three challenges, and validate the results using the “gold standard” method derived from DistMap which uses 84 genes. The paper is organized as follows: Methods, we briefly describe the solutions for all three sub-challenges; Results, we present results of three sub-challenges on the data of the DREAM Single Cell Transcriptomics Challenge; finally, we discuss our results and summarize our work.\n\n\nMethods\n\nThe dataset is from Drosophila embryos. The scRNA-seq dataset is from ~1000 handpicked stage 6 fly embryos using Drop-seq11. It contains both raw and normalized UMI counts with 1297 cells and 8924 genes per cell. A total of 84 driver genes are used. In situ hybridization expression patterns are from the Berkeley Drosophila Transcription Network Project (BDNTP). The BDNTP reference atlas are binarized. The bin number of one half of the embryo is 3039. The spatial coordinates of these bins are also specified. The dataset files can be downloaded from the DREAM Single Cell Transcriptomics Challenge after registration with Synapse free of charge (https://www.synapse.org/#!Synapse:syn16782360).\n\nWe directly use the normalized scRNA-seq data, the in situ matrix and the geometry of the embryo. The gene names “E.spl.m5.HLH” and “Blimp.1” are replaced by “E(spl)m5-HLH” and “Blimp-1”.\n\nWe use a hierarchical clustering method to select 60, 40, and 20 driver genes from the 84 genes based on the normalized scRNA-seq data.\n\nBased on the belief that the scRNA-seq gene expression pattern is similar to the driver genes’ pattern, we propose to select the essential driver genes based on the information provided by scRNA-seq data. Namely, if two genes have high correlation in the scRNA-seq data, we assume the same pattern happens in the in situ matrix. Therefore, we choose only one of them without losing too much of the information. To find the correlated genes, we perform hierarchical clustering on the normalized scRNA-seq data to separate all 84 genes into 60 clusters (with the Euclidean distance and the Mcquitty linkage). The Mcquitty linkage gives more weights for objects in small clusters than those in large clusters in calculating the distance between two clusters. Thus, it is suitable for situations with many small clusters. Since the numbers of clusters are fairly large in the sub-challenge 1 and 2, we opt to use the Mcquitty linkage for distance calculation. In sub-challenge 3, since the total number of clusters is shrunk to 20, which is smaller than sub-challenge 1 and 2, we choose to use the ward linkage in the hierarchical clustering part to obtain larger-sized clusters from the data. After this step, the gene selection process remains the same as sub-challenge 1 and 2.\n\nAfter getting the clusters, we pick the most representative gene of each cluster by calculating the distance between each member gene and the cluster center based on the Euclidean distance and selecting the closest one.\n\nWe perform binarization on the normalized scRNA-seq data for the selected genes based on the “binarizeSingleCellData()” function in DistMap (https://github.com/rajewsky-lab/distmap). The details of binarization is as follows: for each quantile threshold, we perform binarization on the scRNA-seq data for each gene. If the gene expression value is larger than the quantile gene expression value, it will be set as 1, otherwise it is 0. Then we compute the difference between the correlation matrix of binarized scRNA-seq data and the correlation matrix of in situ matrix based on the root-mean-square error. Last, we select the quantile threshold which has the smallest difference to perform binarization for scRNA-seq data.\n\nGiven the binarized scRNA-seq data and in situ matrix, we calculate the probability matrix between cells and bins based on the selected driver genes. Here, we assume the selected driver gene number as ng. The probability pij of a cell ci (i∈[1,1297]) originating from the bin bj (j∈[1,3039]) can be expressed as follows.\n\n\n\nnsij is the number of the same gene expression value (0 or 1) in the two binarized vectors of the scRNA-seq data and the in situ matrix for cell ci and bin bj.\n\nThe probability of a cell originating from a bin is determined by the gene expression in the bin and cell. More genes can improve the prediction of cell position. The bins with the higher probability are possibly the potential cell position. For sub-challenges 1–3, we follow the same process shown in Figure 1. To make the results more stable, we select enough bins (see below) based on the probability values. Then we use clustering to determine a more stable cell position.\n\nTo select the potential bins for predicting cell position, we check the distribution of the maximum values in the probability matrix for the bins (Figure 2). Then we use the third quartile of probability values to select the top bins in sub challenge 1 when using 60 driver genes. We use the first quartile of probability values in sub challenge 2 when using 40 driver genes. And we use all bins in sub challenge 3 when using 20 driver genes. If the number of selected bins is 0, the bin which has the maximum probability will be the predicted position. If the number of selected bins is larger than 100, then only the top 100 bins will be kept based on the probability.\n\nTo check the effect of threshold on the prediction results, we test our method under different thresholds as shown in Figure 4 (b)–(d).\n\nFor high probability bins, we need to perform clustering to select the cluster which has the maximum sum of probability as cell position. Here, we use hierarchical clustering on the selected bins. The cluster number is determined by the silhouette score, which measures the average distance of a point to other points in its cluster compared to the smallest average distance to other clusters. The silhouette score ranges from -1 to +1. The higher the silhouette score, the closer the point is closer to its own cluster and the farer it is away from other clusters.\n\nWe use the average silhouette score across all points to select the clustering number. We use NbClust package12 to perform hierarchical clustering with the “centroid” method. Based on the silhouette score, we obtain the best clustering number. Then we compare the sums of probabilities of all clusters, and select the cluster which has the maximum sum of probabilities. We use the selected cluster center as a reference point to select 10 nearest bins as the top 10 most possible cell positions.\n\nTo evaluate the performance of our method, we use the three performance scores in the DREAM challenge (https://www.synapse.org/#!Synapse:syn17091286, https://github.com/dream-sctc/Scoring/blob/master/dream_scoring_clean.R). The first scoring metric is the primary score to estimate the precision of the assignment for the single cells. The second scoring metric is the average of the relative assignment metrics over all the single cells which is used when the first scores are equal for two methods. The third scoring metric is comparing prediction of gene patterns.\n\nAmbiguous cells: If the predicted top 1 and top 2 positions are the same in the DistMap results, the prediction position will be ambiguous, and the cell will not be computed in the score 1–3. In this challenge, the number of ambiguous cells derived from DistMap are 287.\n\n\nResults\n\nWe calculated the sums of gene expression values in the in situ matrix for all selected driver genes for all 3039 bins. As Figure 3(a) shows, each bin has at least one gene expressed in the in situ matrix. It suggests that our selected driver genes can cover all bins. As the gene number decreases, the frequency of gene expression in each bin decreases. We also compared the overlapped genes in Figure 3(b). Among the 40 driver genes of the sub challenge 2, only one driver gene is not in the selected 60 driver genes of the sub challenge 1. Similarly, only 2 driver genes of the sub challenge 3 are not in the selected 60 driver genes. It suggests our method is consistent in selecting different number of driver genes.\n\n(a) The frequency of gene expression in each bin in the in situ matrix in different selected driver genes scenarios. (b) The overlaps among the selected genes from the three sub challenges.\n\nWe used the score 1–3 to evaluate our method under the different selected driver genes scenarios. Figure 4(a) shows the scores of our submitted results for the sub-challenge 1, 2, 3. The blue bar is the score for the gold standard method using 84 driver genes from DistMap. For score 1, our method is close to the gold standard in sub challenge 1 when using 60 driver genes. The results of our method in sub challenge 2, 3 shows a larger difference. For score 2, our method shows high scores when using 60 and 40 driver genes. Score 2 is the average relative precision for all cells. It suggests that our method is robust for predicting the right position. The score 3 shows a small difference in our method when using 60 and 40 driver genes. Figure 4(b)-(d) shows the consistency of the score 1–3 over a range of thresholds in the different numbers of driver genes scenarios. Hence, Figure 4 shows that our method can obtain a close performance to the gold standard when using 60 driver genes.\n\n(a) Comparing the score 1, 2, 3 for sub challenge 1 (60 driver genes), 2 (40 driver genes) and 3 (20 driver genes) with the gold standard (84 driver genes). (b–d) Comparing the score 1, 2, 3 using different thresholds for (b) sub challenge 1; (c) sub challenge 2; (d) sub challenge 3. (The numbers are rounded for visualization.)\n\nAs shown in Figure 5, the spatial gene expression prediction accuracy is represented by MCC correlation between the predicted cell position in the in situ matrix and the binarized scRNA-seq data for each driver gene. Score 3 is based on the MCC correlation for each driver gene used in each sub challenge. Corresponding to Figure 4(a), the MCC between the DistMap (84) and our method (60 or 40) for each driver gene in sub challenges 1 and 2 are very close. In sub challenge 3, the MCC of gene “dpn”, “erm”, “ftz”, “h” from our method are much lower than DistMap. It is consistent to the lower score 3 in sub challenge 3.\n\nComparing the spatial gene expression between DistMap (84) with our method using (a) 60 genes in sub challenge 1; (b) 40 genes in sub challenge 2; (c) 20 genes in sub challenge 3.\n\n\nConclusion\n\nWe described our method and its performance using 60, 40 and 20 driver genes by comparing with the gold standard (DistMap results). In sub challenge 1, our results shows a close performance to the gold standard. In sub challenges 2 and 3, when using 40 and 20 driver genes, the score 1 decreases and score 3 is still close to the gold standard. It suggests our method can predict cell positions using 60 genes and predict gene expression patterns using less genes. We tested the threshold for selecting top bins (Figure 4(b)–(d)): the results suggest that our method can achieve even better results when using the maximum threshold for sub challenges 1, 2, and 3.\n\n\nData availability\n\nThe dataset associated with the DREAM Single Cell Transcriptomics Challenge is available for registered participants at https://www.synapse.org/#!Synapse:syn16782360 and https://www.synapse.org/#!Synapse:syn18632189. Due to sharing protocol of Synapse, users should register in Synapse (free of charge; https://www.synapse.org/) using their email address, and agree to the dataset conditions of use. Once registered, users can download the files.\n\nSynapse: SCTC Challenge zho_team Submission. Code and results underlying this article, https://doi.org/10.7303/syn1705643513.\n\n\nSoftware availability\n\nSource code implementation for the method presented in this article and used in the DREAM Single Cell Transcriptomics Challenge is available from: https://github.com/ouyang-lab/SCTC-Challenge-zho_team. Scoring scripts are available from: https://github.com/dream-sctc/Scoring/blob/master/dream_scoring_clean.R.\n\nArchived source code as at time of publication: https://doi.org/10.5281/zenodo.359253214\n\nLicense: GLP 3.0",
"appendix": "Acknowledgements\n\nData used in this publication were generated by Prof. Dr. Nikolaus Rajewsky, Max Delbrück at the Center for Molecular Medicine, and these results were obtained as part of the DREAM Single Cell Transcriptomics Challenge project through Synapse ID (syn15665609). We thank Pablo Meyer and Jovan Tanevski for providing the documents, code and suggestions for score 1–3.\n\n\nReferences\n\nStuart T, Satija R: Integrative single-cell analysis. Nat Rev Genet. 2019; 20(5): 257–272. PubMed Abstract | Publisher Full Text\n\nFarrell JA, Wang Y, Riesenfeld SJ, et al.: Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis. Science. 2018; 360(6392): pii: eaar3131. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKaraiskos N, Wahle P, Alles J, et al.: The Drosophila embryo at single-cell transcriptome resolution. Science. 2017; 358(6360): 194–199. PubMed Abstract | Publisher Full Text\n\nSatija R, Farrell JA, Gennert D, et al.: Spatial reconstruction of single-cell gene expression data. Nat Biotechnol. 2015; 33(5): 495–502. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAchim K, Pettit JB, Saraiva LR, et al.: High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin. Nat Biotechnol. 2015; 33(5): 503–9. PubMed Abstract | Publisher Full Text\n\nMoor AE, Harnik Y, Ben-Moshe S, et al.: Spatial reconstruction of single enterocytes uncovers broad zonation along the intestinal villus axis. Cell. 2018; 175(4): 1156–1167.e15. PubMed Abstract | Publisher Full Text\n\nNitzan M, Karaiskos N, Friedman N, et al.: Charting a tissue from single-cell transcriptomes. bioRxiv. 2018; 456350. Publisher Full Text\n\nShah S, Lubeck E, Zhou W, et al.: In situ transcription profiling of single cells reveals spatial organization of cells in the mouse hippocampus. Neuron. 2016; 92(2): 342–357. PubMed Abstract | Publisher Full Text | Free Full Text\n\nZhu Q, Shah S, Dries R, et al.: Identification of spatially associated subpopulations by combining scRNAseq and sequential fluorescence in situ hybridization data. Nat Biotechnol. 2018; 36: 1183–1190. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMoffitt JR, Bambah-Mukku D, Eichhorn SW, et al.: Molecular, spatial, and functional single-cell profiling of the hypothalamic preoptic region. Science. 2018; 362(6416): pii: eaau5324. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMacosko EZ, Basu A, Satija R, et al.: Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets. Cell. 2015; 161(5): 1202–1214. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCharrad M, Ghazzali N, Boiteau V, et al.: NbClust: An R Package for Determining the Relevant Number of Clusters in a Data Set. J Stat Softw. 2014; 61(6): 1–36. Publisher Full Text\n\nChen Y, Mao D, Zhang Y, et al.: SCTC Challenge zho_team Submission. Synapse [dataset]. 2019. http://www.doi.org/10.7303/syn17056435\n\nyancychy: ouyang-lab/SCTC-Challenge-zho_team v0.1 (Version v0.1). Zenodo. 2019. http://www.doi.org/10.5281/zenodo.3592532"
}
|
[
{
"id": "69520",
"date": "02 Sep 2020",
"name": "Xianwen Ren",
"expertise": [
"Reviewer Expertise Bioinformatics"
],
"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\nReconstructing the spatial information of single cells from single-cell RNA-seq data is a pivotal question to further release the revolutionary power of the scRNA-seq technology. Here the authors propose a computational method to infer the spatial positions of single cells of Drosophila embryos based on scRNA-seq data and a reference spatial map based on in situ hybridization of 84 driver genes. While the method is finely tuned for this specific scientific question, some concerns exist.\nFirst, the title is misleading. The authors claimed \"an unsupervised learning method\". This is not valid because this method uses the reference spatial map of Drosophila embryos. Unless the method only uses the scRNA-seq data, it cannot be claimed \"an unsupervised learning method\".\n\nSecond, the current method has only been evaluated on one dataset. More independent evaluations should be added to demonstrate the generalizing capacity of this method.\nOverall, this manuscript addresses an important scientific question. But the method needs more justifications and evidence to demonstrate its novelty and power.\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? No source data required\n\nAre the conclusions about the method and its performance adequately supported by the findings presented in the article? Partly",
"responses": [
{
"c_id": "6282",
"date": "07 Jun 2021",
"name": "Zhengqing Ouyang",
"role": "Author Response",
"response": "Point-by-point response to the comments of Reviewer 1 Reviewer 1 Reconstructing the spatial information of single cells from single-cell RNA-seq data is a pivotal question to further release the revolutionary power of the scRNA-seq technology. Here the authors propose a computational method to infer the spatial positions of single cells of Drosophila embryos based on scRNA-seq data and a reference spatial map based on in situ hybridization of 84 driver genes. While the method is finely tuned for this specific scientific question, some concerns exist. 1. First, the title is misleading. The authors claimed \"an unsupervised learning method\". This is not valid because this method uses the reference spatial map of Drosophila embryos. Unless the method only uses the scRNA-seq data, it cannot be claimed \"an unsupervised learning method\". We thank the reviewer for the comments. To clarify, we used unsupervised hierarchical clustering for gene selection. Based on the selected genes, we predicted the spatial position of each individual cell. Unsupervised and supervised gene selection approaches are used by the methods in the DREAM Single Cell Transcriptomics Challenge for predicting cell spatial position. Table S2 of the consortium paper (Gene selection for optimal prediction of cell position in tissues from single-cell transcriptomics data, Life Sci Alliance. 2020 Nov; 3(11): e202000867) listed the top performing methods (included ours) using either unsupervised or supervised gene selection. 2.Second, the current method has only been evaluated on one dataset. More independent evaluations should be added to demonstrate the generalizing capacity of this method. We thank the reviewer for the constructive comments. The results of our method (Zho_team) and other top performing methods have been systematically and independently evaluated on the Drosophila embryo dataset in the DREAM Single Cell Transcriptomics Challenge (https://www.synapse.org/#!Synapse:syn15665609/wiki/583234) and in the consortium paper aforementioned. Our manuscript, collected in the F1000Research DREAM Challenges Gateway (https://f1000research.com/gateways/dreamchallenges/singlecelltranscriptomics), is focused on describing the details of our method used in the DREAM Challenge. To avoid ambiguity, in the revised manuscript, we changed the title of our manuscript to “Unsupervised gene selection for predicting cell spatial positions in the Drosophila embryo”. Overall, this manuscript addresses an important scientific question. But the method needs more justifications and evidence to demonstrate its novelty and power. We thank the reviewer for the comments. Our method is the only one that uses unsupervised hierarchical clustering for gene selection among the top performing methods as described in Table S2 of the DREAM Challenge consortium paper mentioned above. The power has been systematically demonstrated in our manuscript as well as the consortium paper using independent measurements and comprehensive comparisons."
},
{
"c_id": "6802",
"date": "17 Jun 2021",
"name": "Xianwen Ren",
"role": "Reviewer Response",
"response": "The authors have clarified my concerns."
}
]
},
{
"id": "70705",
"date": "23 Sep 2020",
"name": "Mark S. Cembrowski",
"expertise": [
"Reviewer Expertise Transcriptomics"
],
"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 manuscript, the authors describe an approach to infer spatial gene expression using scRNA-seq data. The authors aimed to identify spatial expression of cell clusters using 20, 40 or 60 marker genes, and compared to the “gold standard” Distmap method using 84 marker genes.\nThe authors begin to explain the rationale of the manuscript by describing the concept of the DREAM challenge, which aims to introduce novel computational techniques to map spatial gene expression using transcriptomic data. Since the DREAM challenge aims to implement novel methods, it is imperative to introduce and carefully compare common methods with the novel proposed approach, which was underdeveloped by the authors. As an example, the “gold standard” method is mentioned several times, though it is not clear what exactly the “gold standard” is or how well-controlled it is. As another key example, a discussion of any kind is completely missing.\nThe design of figures for a manuscript should be chosen to clearly emphasize the main points of the data. Here, the figures are difficult to interpret because key information and description is missing (e.g., legends are too brief, axis labels are missing, subplot headings are redundant, figure design is inconsistent). In addition, the design and presentation of the figures seem unmotivated and thereby difficult for the reader to see the importance of any particular data or easily draw conclusions from the results. In addition, consistent colour schemes and designs would help the reader to follow the manuscript and understand the results.\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? Yes\n\nAre the conclusions about the method and its performance adequately supported by the findings presented in the article? No",
"responses": [
{
"c_id": "6283",
"date": "07 Jun 2021",
"name": "Zhengqing Ouyang",
"role": "Author Response",
"response": "Point-by-point response to the comments of Reviewer 2 Reviewer 2 In this manuscript, the authors describe an approach to infer spatial gene expression using scRNA-seq data. The authors aimed to identify spatial expression of cell clusters using 20, 40 or 60 marker genes, and compared to the “gold standard” Distmap method using 84 marker genes. The authors begin to explain the rationale of the manuscript by describing the concept of the DREAM challenge, which aims to introduce novel computational techniques to map spatial gene expression using transcriptomic data. Since the DREAM challenge aims to implement novel methods, it is imperative to introduce and carefully compare common methods with the novel proposed approach, which was underdeveloped by the authors. As an example, the “gold standard” method is mentioned several times, though it is not clear what exactly the “gold standard” is or how well-controlled it is. As another key example, a discussion of any kind is completely missing. We thank the reviewer for the constructive comments. The “gold standard” is generated by DistMap, which is the best available single cell position reference used in the DREAM Challenge. DistMap determines single cell position by searching the maximum similarity for cells and spatial bins using the in situ expression of 84 driver genes in the Berkeley Drosophila Transcription Network Project (BDNTP). It is shown that the 84 driver gens are sufficient to uniquely and individually label most of the 1,297 cells (Karaiskos, et al. 2017). Thus, it is used in the DREAM Challenge to assess the performance of methods using smaller numbers (60, 40, and 20) of driver genes. In the revised manuscript, we changed “gold standard” to “silver standard”, as the cell positions generated by DistMap are not experimentally validated. We added the description of the DistMap “silver standard” in the Method section. We also added more introductions to the common methods for the cell position prediction from single cell transcriptome data in the Introduction section. We described the limitation of current methods and explain the motivation to study how the driver gene selection affecting the prediction of cell spatial position. The comparisons of our methods (Zho_team) and other top performing methods have been described in the DREAM Single Cell Transcriptomics Challenge consortium paper (Gene selection for optimal prediction of cell position in tissues from single-cell transcriptomics data, Life Sci Alliance. 2020 Nov; 3(11): e202000867). Our manuscript is focused on describing the details of our method used in the DREAM Challenge. We also expanded the Discussion section of our manuscript. In addition to summarizing our method and results, we also pointed that gene-gene correlation and spatial correlation are useful information for spatial cell position and gene expression prediction. The design of figures for a manuscript should be chosen to clearly emphasize the main points of the data. Here, the figures are difficult to interpret because key information and description is missing (e.g., legends are too brief, axis labels are missing, subplot headings are redundant, figure design is inconsistent). In addition, the design and presentation of the figures seem unmotivated and thereby difficult for the reader to see the importance of any particular data or easily draw conclusions from the results. In addition, consistent colour schemes and designs would help the reader to follow the manuscript and understand the results. We thank the reviewer for the constructive comments. In the revised manuscript, we improved all figures and legends. We enlarged the font sizes for all figures. In Figure 1, we clarified the whole workflow to display the motivation of our method. In Figure 2, we changed it to display the number of bins with high similarity values (> 0.8) in the similarity matrix for each cell when the number of driver genes is 60, 40, or 20. In Figure 3, we enlarged the font size and added more information in the figure labels. In Figure 4, we enlarged the font size. In figure 5, we changed it to the comparison of the Pearson correlation of predicted gene expression from DistMap (using 84 driver genes) and our method (using 60, 40, or 20 genes)."
}
]
}
] | 1
|
https://f1000research.com/articles/9-124
|
https://f1000research.com/articles/9-1108/v1
|
09 Sep 20
|
{
"type": "Research Article",
"title": "Iron overload parameters and early detection of cardiac disease among Egyptian children and young adults with β-thalassaemia major and sickle cell disease: a cross-sectional study",
"authors": [
"Khaled Salama",
"Amina Abdelsalam",
"Hadeel Seif Eldin",
"Eman Youness",
"Yasmeen Selim",
"Christine Salama",
"Gehad Hassanein",
"Mohamed Samir",
"Hanan Zekri",
"Khaled Salama",
"Amina Abdelsalam",
"Hadeel Seif Eldin",
"Eman Youness",
"Christine Salama",
"Gehad Hassanein",
"Mohamed Samir",
"Hanan Zekri"
],
"abstract": "Background: Cardiac, hepatic and pancreatic T2* measured by magnetic resonance imaging (MRI) has been proven to be an accurate and non-invasive method for measuring iron overload in iron overload conditions. There is accumulating evidence that pancreatic iron can predict cardiac iron in young children because the pancreas loads earlier than the heart. The aim of our study was to investigate cardiac function and cardiac iron and their relation to pancreatic iron among patients with β-thalassaemia major (βTM) and sickle cell disease (SCD). Methods: 40 βTM and 20 transfusion-dependant SCD patients were included along with 60 healthy age-matched controls. Echocardiography and Tissue Doppler Imaging were performed for all subjects as well as the control group. Hepatic, cardiac and pancreatic iron overload in cases were assessed by MRI T2*. Results: The study group consisted of 40 βTM and 20 transfusion dependant SCD patients with mean age 13.7 years and mean frequency of transfusion/year 12. Mean cardiac T2* was 32.9 ms and mean myocardial iron concentration was 0.7 mg/g; One patient had cardiac iron overload of moderate severity. Mean pancreatic T2* was 22.3 ms with 20 patients having mild pancreatic iron overload. Pancreatic T2* correlated positively with main pulmonary artery diameter (p=0.046), peak late diastolic velocity at septal mitral annulus (p=0.038), peak early diastolic velocity at tricuspid annulus (p=0.001) and mitral annular plane systolic excursion (p=0.01); and negatively with end systolic pulmonary artery pressure (p=0.007). We couldn’t test the predictability of pancreatic T2* in relation to cardiac T2* as only one patient had cardiac T2*<20 ms. Conclusion: Assessment of pancreatic T2* in multi-transfused patients with βTM and SCD can predict myocardial dysfunction. No direct relation between pancreatic iron and cardiac siderosis was detected.",
"keywords": [
"Iron overload",
"pancreatic iron",
"Thalassemia major",
"Sickle cell disease",
"Tissue Doppler Imaging"
],
"content": "Introduction\n\nThe hallmark of chronic hemolytic anemias (CHAs) is premature destruction of erythrocytes1. In Egypt, the common forms of inherited CHAs include β-thalassemia major (βTM) and sickle cell disease (SCD)2. The main lines of therapy is blood transfusion and iron chelation. Quality of life and life expectancy have markedly improved since the introduction of oral iron chelators. Nevertheless, death from cardiomyopathy and heart failure in these patients remains high, possibly because of cardiac damage induced by labile plasma iron3 or oxidative stress4.\n\nConsequently, it is important to detect silent cardiac dysfunction early before the development of symptomatic heart disease5. Currently, several methods have been used in clinical studies for the determination of cardiac affection in iron overload conditions. Meanwhile, their uses are limited in βTM and SCD patients due to controversy on their reliability as well as their high cost. The aim of this study was to detect cardiac functions and cardiac iron and their relation to pancreatic iron in multi-transfused Egyptian patients with βTM and SCD.\n\n\nMethods\n\n40 βTM and 20 SCD patients aged ≥7 years with the onset of regular transfusions before the age of 2 years and receiving regular transfusions (≥ 3 transfusions per year with total volume ranging from 100 to 150 cc/kg/year according to Gale et al., 2011)6 following up at the hematology outpatient clinic, Cairo University Children’s Hospital, Cairo, Egypt during the study period (from June, 2017 to June, 2018) were enrolled in the study.\n\nPatients with congenital or acquired heart diseases, hypertension, heart failure, cardiac drug usage, known risk factors for secondary pulmonary hypertension, acute febrile illness at enrollment or those with contraindications or inability to undergo magnetic resonance imaging (MRI) without sedation were excluded.\n\nIn addition, 60 healthy subjects with the same age and gender referred to our hospital for routine checkup were selected as the control group.\n\nDemographics, transfusion history, and information concerning iron chelation and therapy were obtained by through patient interview during routine check-ups and chart review. Labs, including complete blood picture with blood indices, reticulocytic count and serum ferritin, were performed as routine labs done during check-ups.\n\nThe study was approved by the ethics and scientific research committee of Cairo University, Faculty of Medicine (ethical clearance number, I-060317) and the study was conducted in accordance with Cairo University’s laws for human research. Written informed consent was obtained from participants and parent/guardians in the case of children <18 years. Assent was obtained in addition from children <18 years.\n\nAll patients were scheduled for cardiac, hepatic and pancreatic MRI T2* at the Radiology Department, using a Philips Achiva, Netherland (1.5 Tesla) superconducting magnet with a Torso XL coil.\n\nScans were synchronized to the cardiac cycle using standard electrocardiogram gating. We then took a single 10 mm-thick short axis, mid ventricular slice positioned half way between the base and the apex of the left ventricle with repition time (TR) 20 ms and multiple echo times (TEs) (2.4, 4.6, 6.8, 9.1 and 11.3ms). Flip angle 30 and field of view (FOV) 320 mm. A fitting curve algorithm using a monoexponential decay with a constant offset (S=S0e-TE.R2*+C; S is the signal intensity, S0 is the signal intensity at TE=0 ms, and C is a constant) was applied to determine the T2* value. Results of cardiac T2* and myocardial iron concentration (MIC) measurements were considered as discontinuous variables and were classified as follows: normal iron concentration (T2* >20, MIC < 1.16 mg/g), light (T2* 15–20, MIC 1.16- 1.65 mg/g), moderate (T2* 10–15, MIC 1.65- 2.71 mg/g) and severe (T2* <10, MIC > 2.71 mg/g)7.\n\nThe liver T2* was measured by imaging a single trans-axial slice (10 mm) through the center of the liver. The pancreas T2* was measured by imaging a single trans-axial slice (10 mm) through the head of the pancreas with TR 20 ms and multiple TEs (2.4, 4.6, 6.8, 9.1 and 11.3ms) as well as through the body and mean region of interest was taken. Results of hepatic and pancreatic T2* measurements were considered as discontinuous variables and were classified as follows: normal iron concentration (T2* >11.4, liver iron concentration (LIC) < 2 mg/g), light (T2* 3.8–11.4, LIC 2.0- 7.0 mg/g), moderate (T2* 1.8–3.8, LIC 7.0–15.0 mg/g) and severe (T2* <1.8, LIC > 15 mg/g)8.\n\nTrans-thoracic two dimensional (2D) guided (M mode) and doppler echocardiogram were performed with a Hewlett-Packard 5500 SONOS ultrasonic machine phased array sector scanner with the 4 and 8 MHZ probes according to age. M-mode, 2D and doppler echocardiographic parameters were averaged over three cardiac cycles and all echocardiographic measurements were performed according to the guidelines for performance of echocardiogram by American Society of Echocardiography9. Tissue Doppler Imaging was performed for all patients and 60 – age and sex-matched – healthy subjects as a control group. Systolic function was assessed through measuring peak systolic (S’) myocardial velocities at both the septal and lateral mitral and free-wall tricuspid annulus. Diastolic function was assessed through measuring peak early diastolic (E’) and peak late diastolic (A’) myocardial velocities at both the septal and lateral mitral and free-wall tricuspid annulus. The ratio of E to E’ velocity (E/E’) was computed as a surrogate of LV filling pressure10.\n\nThe statistical package SPSS version 25 was used for data analysis. Mean, SD, and range were used for describing quantitative variables. The χ2 test was used to compare qualitative variables between groups. The t-test was used to compare quantitative variables in parametric data. The Mann-Whitney test was used instead of the t-test for nonparametric data. Univariate correlations among the biological markers of iron metabolism and MRI LIC will be studied with Spearman’s rank-order correlation coefficient. Receiver-operator characteristic (ROC) curves will be used to analyze the capacity of serum ferritin to predict MRI-based hepatic iron overload, and to identify optimal test and threshold values. P-values <0.05 was considered significant and P values <0.01 were considered highly significant.\n\n\nResults\n\nIn total, 40 βTM, 20 SCD and 60-age and sex matched subjects were included in the study. The study group consisted of 33 (55%) men and 27 (45%) women. Their mean age was 13.7 (±4.4) years and mean age at diagnosis was 12.4 (±8.6) months. A total of 40 (66.7%) patients were splenectomised (33 with βTM and 7 with SCD), and 58 patients (96.7%) were receiving a chelator (39 βTM; 19 SCD; p=0.6) for a duration ranging from 6 to 120 month (median 48 months). Assessment of the iron overload status of the studied patients revealed that 34 (56.7%) patients had average serum ferritin exceeding 2500 ng/ml, 10 (16.7%) had LIC ≥7 mg Fe/g dry liver weight (dw), 20 patients (33.3%) showed mild pancreatic iron overload and only one patient had evidence of cardiac iron overload of moderate severity (Figure 1). Other demographic and laboratory data are illustrated in Table 1.\n\na) Calculated myocardial T2* equals 13.3 ms and myocardial iron concentration equals 1.91 mg/g (moderate cardiac iron overload). b) Calculated hepatic T2* equals 26.5 ms and liver iron concerntration equals 0.60 mg /g (no hepatic iron overload). c) Calculated pancreatic T2* equals 40 ms (no pancreatic iron overload). Conclusion: The patient has moderate cardiac iron overload, normal hepatic and pancreatic iron concentration.\n\nData are expressed as mean±SD (range).\n\n*Statistically significant, ms=milliseecond, SD=Standard deviation.\n\nInvestigating the relation between different iron overload parameters revealed that serum ferritin correlated negatively with pancreatic T2* and positively with LIC. We divided our patients into two groups according to LIC, normal <7 or overload >7 (LIC is our gold standard), and this was plotted against pancreatic T2* using ROC curve. We found that area under the curve of pancreatic T2* was 0.851 (95% CI: 0.757–0.945). The sensitivity of pancreatic T2* in predicting LIC was 82% and specificity was 80% at a cutoff value ≥10.1 (Figure 2). We failed to test the predictability pancreatic T2* in relation to cardiac T2* as nearly all patients have cardiac T2 > 20 and only. One patient has cardiac T2 < 20. ROC curve analysis couldn’t be done.\n\nEchocardiographic assessments of the studied βTM and SCD patients were compared to the control group and the results are illustrated in Table 2. Mitral E/A ratio >2 was found in 18 (30%) patients indicating diastolic dysfunction of restrictive pattern. None of our patients had a mitral E/A ratio <1 denoting that none of them had diastolic dysfunction of impaired relaxation pattern. Statistically significant differences between patients and controls were detected in late diastolic myocardial velocities (A) and systolic myocardial velocities (S) at the basal mitral annulus of the lateral and septal walls being higher in patients than controls. Also peak systolic velocity at the tricuspid annulus of patients was significantly higher than controls (Table 2).\n\nData are expressed as mean±SD (range).\n\n*Statistically significant, ms=milliseecond, βTM=Beta thalassemia major, SCD=Sickle cell disease, LIC=Liver iron concentration, MIC=Myocardial iron concentration, SD=Standard deviation.FS=Fractional shortening, EF=Ejection fraction, Mitral E/A=Ratio of the peak velocity of early diastolic transmitral flow to the peak velocity of the late diastolic transmitral flow, TAPSE=Tricuspid annular plain systolic excursion, MAPSE=Mitral annular plane systolic excursion, ESPAP=End systolic pulmonary artery pressure, Mitral E/ E'= Ratio of the peak velocity of early diastolic transmitral flow to early diastolic mitral annular velocity, Mitral E/A=Ratio of the peak velocity of early diastolic transmitral flow to the peak velocity of the late diastolic transmitral flow S'=Peak systolic velocity, E'=Peak early diastolic velocity, A'=Peak late diastolic velocity.\n\nWe divided our patients according to grade of pancreatic iron; group (n=40) with normal pancreatic iron and group (n=20) with pancreatic iron overload. The pancreatic iron overload group showed higher LIC, higher end systolic pulmonary artery pressure (ESPAP) and lower tricuspid annulus peak early diastolic velocity compared to the group with normal pancreatic iron (Table 3).\n\n*Statistically significant, LIC=Liver iron concentration, MIC=Myocardial iron concentration, FS=Fractional shortening, EF=Ejection fraction, ESPAP=End systolic pulmonary artery pressure, S'=Peak systolic velocity, E'=Peak early diastolic velocity, A'=Peak late diastolic velocity.\n\nPancreatic T2* correlated positively with peak late diastolic velocity at septal mitral annulus, peak early diastolic velocity at tricuspid annulus and mitral annular plane systolic excursion (MAPSE). It correlated negatively with main pulmonary artery diameter (MPA) and ESPAP (Table 4).\n\nLVEDD=Left ventricular end diastolic diameter, LVESD=Left ventricular end systolic diameter, FS=Fractional shortening, EF= Ejection fraction, RVDd=Right ventricular dimension at end diastole, LA/Ao=Ratio of the left atrial dimension to the aortic annulus dimension, MPA=Main pulmonary artery, ESPAP=End systolic pulmonary artery pressure, S'=Peak systolic velocity, E'=Peak early diastolic velocity, A'=Peak late diastolic velocity, TAPSE= Tricuspid annular plain systolic excursion, MAPSE=Mitral annular plane systolic excursion, Mitral E/A=Ratio of the peak velocity of early diastolic transmitral flow to the peak velocity of the late diastolic transmitral flow, R= Spearman correlation coefficient.\n\nThere was a significant negative correlation between LIC and right ventricular dimension at end diastole (RVDd) as well as the following Tissue Doppler parameters: peak systolic velocity at lateral and septal mitral annulus, peak late diastolic velocity at septal mitral annulus and peak early diastolic velocity at tricuspid annulus (Table 4).\n\n\nDiscussion\n\nThe aim of this study was to investigate cardiac functions and cardiac iron and their relation to pancreatic iron among Egyptian patients with βTM and SCD.\n\nCardiac iron overload occurs earlier than pancreatic iron overload, therefore pancreatic iron can predict cardiac iron in young children11. Because the pancreas takes up non-transferrin bound iron, generating reactive oxygen specie of the heart, but earlier, it can be used as an early and strong marker of prospective risk of cardiac siderosis, with a 100% negative predictive value for cardiac iron accumulation12. Unfortunately, we failed to test the predictability of pancreatic T2* in relation to cardiac T2* in our study as nearly all of our patients had normal cardiac T2* and only one patient was cardiac iron loaded. In spite of the extensive involvement of the liver and pancreas among our patients, almost absence of cardiac iron loading (n=1) was striking. Several factors affect the transport, storage and removal of iron in the different organs in iron overload conditions leading to the heterogenous distribution of storage iron in each organ measured by MRI T2*13. Genetic background of thalassemic patients in Egypt might be implicated for the low prevalence of cardiac iron loading in our population in spite of very high serum ferritin and high LIC14. In another study in Alexandria University performed on thalassemic patients, only 8.7% of cases were cardiac iron loaded15. Similarly in SCD patients, Elalfy et al. found that cardiac siderosis was absent in transfusion dependant SCD patients with minimal or no pancreatic and moderate to severe hepatic iron loading16.\n\nOur results disagree with a study carried out on 131 βTM patients that reported increased cardiac iron in almost one third of patients and increased pancreatic iron in more than 70% of patients with good correlation between pancreatic and cardiac iron (r2= 0.52), with the pancreas loading a decade earlier than the heart11. This difference might be explained by the smaller sample size, the design of our study, as well as the younger age group of our patients.\n\nDespite the absence of cardiac iron deposition, there was significant difference between cases and controls (p<0.0001) in diastolic indices of LV (Trans-mitral E/A ratio) and mitral E/A ratio >2 was found in 30% indicating diastolic dysfunction of restrictive pattern. None of our patients had diastolic dysfunction of impaired relaxation pattern.\n\nThe diagnosis of subclinical LV systolic dysfunction can be detected by assessing MAPSE. MAPSE was significantly reduced in patients with chronic heart failure, with a good correlation between MAPSE and EF17–19. Among our patients the mean MAPSE was comparable between SCD and controls and was higher in βTM patients (p=0.019) when compared to SCD and controls. This indicates an absence of subclinical LV systolic dysfunction in our studied patients.\n\nUp to one third of our patients had ESPAP ≥35 mmHg. Moreover, both βTM and SCD groups had significantly higher ESPAP than controls (p<0.0001). At the time of enrollment 66.7% patients had been splenectomized, also βTM patients had a higher platelet count; both factors could contribute to the higher ESPAP in thalassemia patients. This was in agreement with previous studies that reported splenectomy as one of the main risk factors of cardiac disease in such a group of patients20,21.\n\nComparing the myocardial velocity measurements of cases with controls; there were significant differences in late diastolic (A’) and systolic myocardial velocities (S’) at the basal mitral annulus of the lateral and septal walls (p<0.0001, p=0.005, p=0.031 and p=0.004 respectively) being higher in patients than controls. Also peak systolic velocity (S’) at the tricuspid annulus of patients was significantly higher than controls. These findings may be due to the chronic anemia and high cardiac output, which dominate the picture in children unlike other studies that reported that tissue Doppler systolic velocity was significantly lower in the βTM group compared to controls22.\n\nMinimal preliminary data have postulated a correlation between pancreatic iron overload and cardiac function in βTM and SCD patients. Our data revealed that pancreatic T2* correlated positively with peak late diastolic velocity at septal mitral annulus (r=0.269, p=0.038) and peak early diastolic velocity at tricuspid annulus (r=0.430, p=0.001); which means that pancreatic iron overloaded patients had some degree of left and right ventricular diastolic dysfunction respectively, though not yet cardiac loaded. Also patients with pancreatic iron overload had a higher ESPAP compared to those with normal pancreatic T2* (p=0.046), pancreatic T2* showed a weak negative correlation with ESPAP (r=-0.343, p=0.007) and with main pulmonary artery diameter (MPA) (r=-0.259, p=0.046). This means that pancreatic iron load might serve as a good indicator of the risk of developing pulmonary hypertension in βTM and SCD patients even before frank cardiac iron loading and before appearance of cardiac symptoms as well. Searching the literature, similar correlations between pancreatic T2* and the development of pulmonary hypertension and diastolic dysfunction could not yet be found. But Pepe et al., in their study on a large cohort of βTM patients, reported that pancreatic iron was correlated to the LV EF, but not to the RV EF23.\n\n\nConclusion\n\nMulti-transfused SCD and βTM patients with iron overload showed more iron deposition in the liver, followed by the pancreas with relative sparing of the heart. Assessment of pancreatic T2* in multi-transfused children and young adults with SCD and βTM can predict myocardial dysfunction detected by Tissue Doppler Imaging in the absence of abnormal indices of global ventricular dysfunction or even the appearance of symptoms and signs of overt heart failure. In fact, pancreatic T2* should be considered as an additional tool to LIC and cardiac T2 * for evaluation and monitoring of young children with βTM and SCD at risk of iron overload. Tissue Doppler echocardiography should be applied in cardiac assessment among patients with chronic hemolytic anemia and should be performed at regular intervals.\n\n\nData availability\n\nOpen Science Framework: Iron overload parameters and early detection of cardiac disease among Egyptian children and young adults with β-thalassaemia major and sickle cell disease: a cross-sectional study, https://doi.org/10.17605/OSF.IO/58Q3D24.\n\nData are available under the terms of the Creative Commons Zero \"No rights reserved\" data waiver (CC0 1.0 Public domain dedication).",
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PubMed Abstract | Publisher Full Text\n\nGale RP, Barosi G, Barbui T, et al.: What are RBC-transfusion-dependence and -independence?. Leuk Res. 2011; 35(1): 8–11. PubMed Abstract | Publisher Full Text\n\nCarpenter JP, He T, Kirk P, et al.: On T2* Magnetic Resonance and Cardiac Iron Clinical Perspective. Circulation. 2011; 123(14): 1519–1528. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHankins JS, McCarville MB, Loeffler RB, et al.: R2* magnetic resonance imaging of the liver in patients with iron overload. Blood. 2009; 113(20): 4853–5. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLai WW, Geva T, Shirali GS, et al.: Task Force of the Pediatric Council of the American Society of Echocardiography.Guidelines and standards for performance of a pediatric Echocardiogram: A Report From the Task Force of the Pediatric Council of the American Society of Echocardiography. J Am Soc Echocardiogr. 2006; 19(12): 1413–1430. PubMed Abstract | Publisher Full Text\n\nPark JH, Marwick TH: Use and limitations of E/e’ to assess left ventricular filling pressure by Echocardiography. J Cardiovasc Ultrasound. 2011; 19(4): 169–173. PubMed Abstract | Publisher Full Text | Free Full Text\n\nNoetzli LJ, Papudesi J, Coates TD, et al.: Pancreatic iron loading predicts cardiac iron loading in thalassemia major. Blood. 2009; 114(19): 4021–6. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWood JC: Use of magnetic resonance imaging to monitor iron overload. Hematol Oncol Clin North Am. 2014; 28(4): 747–764. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPapakonstantinou O, Alexopoulou E, Economopoulos N, et al.: Assessment of iron distribution between liver, spleen, pancreas, bone marrow, and myocardium by means of r2 relaxometry with mri in patients with β-thalassemia major. J Magn Reson Imaging. 2009; 29(4): 853–9. PubMed Abstract | Publisher Full Text\n\nEl Beshlawy A, El Tagui M, Hamdy M, et al.: Low prevalence of cardiac siderosis in heavily iron loaded Egyptian thalassemia major patients. Ann Hematol. 2014; 93(3): 375–9. PubMed Abstract | Publisher Full Text\n\nElfawal SK, Emara DM, Shehata AA: Assessment of hepatic and cardiac iron overload in thalassemia patients by magnetic resonance imaging: Our experience in Alexandria University. The Egyptian Journal of Radiology and Nuclear Medicine. 2018; 49: 323–328. Publisher Full Text\n\nElalfy MS, Allam K, Ibrahim A, et al.: Pancreatic Iron Deposition Following the Role of Iron Loading Among Transfusion Dependent Sickle Cell Disease Egyptian Children and Young Adults. Blood. 2019; 134(Supplement_1): 4828. Publisher Full Text\n\nAlam M, Hoglund C, Thorstrand C, et al.: Atrioventricular plane displacement in severe congestive heart failure following dilated cardiomyopathy or myocardial infarction. J Intern Med. 1990; 228(6): 569–75. PubMed Abstract | Publisher Full Text\n\nMatos J, Kronzon I, Panagopoulos G, et al.: Mitral annular plane systolic excursion as a surrogate for left ventricular ejection fraction. J Am Soc Echocardiogr. 2012; 25(9): 969–74. PubMed Abstract | Publisher Full Text\n\nTaşolar H, Mete T, Çetin M, et al.: Mitral annular plane systolic excursion in the assessment of left ventricular diastolic dysfunction in obese adults. Anatol J Cardiol. 2015; 15(7): 558–64. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBelhoul KM, Bakir ML, Saned MS, et al.: Serum ferritin levels and endocrinopathy in medically treated patients with β thalassemia major. Ann Hematol. 2012; 91(7): 1107–14. PubMed Abstract | Publisher Full Text\n\nDerchi G, Dessì C, Bina P, et al.: Risk factors for heart disease in transfusion-dependent thalassemia: serum ferritin revisited. Intern Emerg Med. 2019; 14(3): 365–370. PubMed Abstract | Publisher Full Text\n\nAbdelmoktader AM, Azer HY: Usefulness of pulsed wave tissue doppler imaging in assessment of left ventricular functions in children with beta-thalassemia major. Indian J Pediatr. 2013; 80(9): 721–725. PubMed Abstract | Publisher Full Text\n\nPepe A, Pistoia L, Giunta N, et al.: The strong link between pancreas and heart in thalassemia major. European Heart Journal. 2018; 39(suppl_1): 3706. Publisher Full Text\n\nselim YMM: Iron overload parameters and early detection of cardiac disease among Egyptian children and young adults with β-thalassaemia major and sickle cell disease: a cross-sectional study. 2020. http://www.doi.org/10.17605/OSF.IO/58Q3D"
}
|
[
{
"id": "71231",
"date": "21 Sep 2020",
"name": "Emanuele Angelucci",
"expertise": [
"Reviewer Expertise Iron overload and iron toxicity. Hemopoietic cell transplantation."
],
"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 reviewed the document from my Egyptian colleagues with great interest. This paper is well written and addresses an important topic which is the clinical damage by iron overload and the efficacy of iron chelation therapy in a population of young children in the southern Mediterranean area.\n\nThe article is clear and of relevance also because the population described is rarely seen in industrialized countries and consequently today rarely described in international medical journals.\nFurthermore, modern diagnostic technology is applied in a young hemoglobinopathy population suffering from severe iron-overloaded (probably inadequately chelated). Of relevance the conclusions are supported by an adequate (# 60) and well-studied age-matched control group.\n\nAlthough the main goal is, as expected, partially not achieved (correlation between pancreatic-hepatic iron with cardiac iron), there are several important conclusions from this article: Pancreatic iron concentration and liver iron concentration are good predictors of early cardiac function impairment. Very important: Cardiac function begins to deteriorate long before cardiac iron deposition is manifest by T2 * MRI even in a population of young children (mean age 13 years): this observation once again underlines the need for a regular (even intensive) iron chelation since initial stages of transfusion dependence. Correctly the authors use liver iron concentration as the standard for iron overload throughout the body1.\n\nTo improve paper readability, I suggest the following:\n\nPlease clarify the definition of transfusion dependence (methods first paragraph). Few data are reported twice (methods and results; results and discussion). This is not necessary. The technical details of MRI and cardiac ultrasound are not needed. They can simply be referenced. Please be consistent with the definition of liver iron concentration (page 3: liver and pancreas T2 * versus second paragraph results). Liver iron concentration <2 mg / g dw is normal, liver iron concentration between 2 and 7 mg / g dw is mild overload. Figure 1 is unnecessary and can be deleted. Likewise, Tables 1 and 4 can be omitted. Table 5: missing caption. The discussion can be shortened. I don't understand reference no. 24. Include demographic details of the control population (age, gender, etc.).\n\nAs a further question: Did the authors observe any difference between thalassemia and sickle cell disease?\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": "72131",
"date": "20 Oct 2020",
"name": "Hadi Darvishi-Khezri",
"expertise": [
"Reviewer Expertise Thalassemia",
"Clinical Science",
"Critical Care"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe article has been reviewed. The study meticulously investigated pancreatic, cardiac and liver iron loading, as well as cardiac dysfunctions among transfusion-dependent β-thalassaemia and sickle cell patients. The researchers tried to reveal the correlation between pancreatic iron loading with cardiac and liver iron siderosis and also cardiac dysfunction. Although the results of study are intriguing, several flaws still remain in the paper.\nTitle\nThe title of article is not completely matched with the aim of study.\n\nThe term of cardiac disease used in the title is rather wide. It would be better that more specific term would be chosen for the title of study.\n\nAbstract\nThe first sentence of the result and method in the Abstract is similar, and a repetition as well (40 βTM and 20 transfusion-dependent SCD patients).\n\nThe last sentence in the Abstract part reflects the results of the relationship between pancreatic T2* values and cardiac iron loading, which is not present in the aim of the study.\n\nThe results of cardiac function were not reflected as part of results in the Abstract.\n\nIt would be better the correlation coefficients (r) in the Abstract would be reported.\n\nThe study did not assess the prediction of cardiac dysfunctions by pancreatic T2* values. So, a more appropriate substitutional sentence for the conclusion is “There was a relationship between pancreatic iron siderosis with cardiac dysfunction in these patients”.\nIntroduction\nThe authors stated that the aim of the study is to investigate 1. Cardiac function 2. Cardiac iron loading 3. Their relation to pancreatic iron loading in patients with β-thalassemia major and sickle cell disease (mentioned in the Abstract, Introduction and Discussion sections). However, it seems that the study was established to assess the relationships between pancreatic T2* values and pancreatic iron loading with cardiac dysfunctions and liver and cardiac iron siderosis, not a prediction analyses.\n\nThe last sentence in the first paragraph of the Introduction section is vague.\nMethod\n\nThe logic for calculating sample size is missed in this study. The calculation of sample size or a power analysis is necessary.\n\nWhether the healthy controls has been matched based on age and sex or only age? The first sentence of the Results section in the Abstract part and the main text of the article is different.\n\nUsually serum ferritin levels of greater than 2000 ng/mL is considered as iron overload in transfusion dependent thalassemia [1]. Hyperferritinemia in non-transfusion dependent thalassemia is a serum ferritin higher than 800 ng/mL [2].\nResults\nThe number (%) of myocardial dysfunctions (systolic and diastolic), pancreatic, cardiac and liver iron siderosis were not clearly reported in the article.\n\nThe authors could have used odds ratio to show the relationship between pancreatic T2* values with cardiac dysfunction, as well as the strength of the relationship.\n\nThe categorization of patients based on LIC should have been placed in the Method section.\n\nIn the second paragraph, the results related to the prediction of liver siderosis by pancreatic T2* values is not reflected in the aim of study.\n\nFigure 2 is not so meaningful.\n\nBased on the title of Table 3, LIC reported in Table 3 does not belongs to cardiac function.\n\nI expected to see the status of cardiac and liver MRIs according to pancreatic iron siderosis.\n\nThe majority of correlations between pancreatic T2*, LIC and serum ferritin with cardiac indices measured by trans thoracic and tissue Doppler echocardiography were weak (correlation coefficient < 0.4). The correlation of LIC and peak late diastolic (A') was detected as a moderate strength of relationship (r = 0.423). The intensity of correlation between pancreatic T2* with E' was also moderate (r = 0.43).\n\nDiscussion\nThe aim of the study should have been mentioned at the end of the Introduction part instead of at the beginning of the Discussion section.\n\nThere is a disparate concept in the paper about the time of pancreatic and cardiac iron loading. In the Abstract it is written: “There is accumulating evidence that pancreatic iron can predict cardiac iron in young children because the pancreas loads earlier than the heart”. Conversely, in the second paragraph of the Discussion part it is written: “Cardiac iron overload occurs earlier than pancreatic iron overload, therefore pancreatic iron can predict cardiac iron in young children”.\n\nWording and writing in the Discussion part is similar to the Results section. To some extent, the Discussion part is the repetition of the results section. Discussion should be the interpretation of the results and a comparison with other studies.\n\nThere have been some limitations in this study, which is absent in the paper. The population of the study is heterogeneous, comprising with β-thalassemia major and sickle cell disease. As you can see, the difference of pancreatic T2* values between two groups (βTM and SCD patients) shown in Table 1 is significant. In addition, I expected to see several recommendations to make a contribution to set up future studies.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": [
{
"c_id": "6611",
"date": "07 Jun 2021",
"name": "yasmeen selim",
"role": "Author Response",
"response": "Title The title of article is not completely matched with the aim of study You are right dear sir/I am going to modify the title The term of cardiac disease used in the title is rather wide. It would be better that more specific term would be chosen for the title of study I am going to change the term cardiac disease to a more specific term Abstract The first sentence of the result and method in the Abstract is similar, and a repetition as well (40 βTM and 20 transfusion-dependent SCD patients) I am going to change this sentence The last sentence in the Abstract part reflects the results of the relationship between pancreatic T2* values and cardiac iron loading, which is not present in the aim of the study The aim of our study was to investigate cardiac function and cardiac iron and their relation to pancreatic iron among patients with β-thalassaemia major (βTM) and sickle cell disease (SCD), So the last sentence in the Abstract part that reflects the results of the relationship between pancreatic T2* values and cardiac iron loading is actually mentioned in the aim of the study The results of cardiac function were not reflected as part of results in the Abstract The results of cardiac function were not reflected as part of results in the Abstract as we were restricted by the number of word count of the abstract so we only included the positive correlations with pancreatic T2 It would be better the correlation coefficients (r) in the Abstract would be reported I will add the r value The study did not assess the prediction of cardiac dysfunctions by pancreatic T2* values. So, a more appropriate substitutional sentence for the conclusion is “There was a relationship between pancreatic iron siderosis with cardiac dysfunction in these patients” I will change this sentence in the conclusion Introduction The authors stated that the aim of the study is to investigate 1. Cardiac function 2. Cardiac iron loading 3. Their relation to pancreatic iron loading in patients with β-thalassemia major and sickle cell disease (mentioned in the Abstract, Introduction and Discussion sections). However, it seems that the study was established to assess the relationships between pancreatic T2* values and pancreatic iron loading with cardiac dysfunctions and liver and cardiac iron siderosis, not a prediction analyses. I am going to edit this part The last sentence in the first paragraph of the Introduction section is vague I am going to replace the last sentence in the first paragraph of the Introduction by a more understandable one Methods Whether the healthy controls has been matched based on age and sex or only age? The first sentence of the Results section in the Abstract part and the main text of the article is different Healthy controls were both age and sex matched, It is just a typing error I will fix it Usually serum ferritin levels of greater than 2000 ng/mL is considered as iron overload in transfusion dependent thalassemia [1]. Hyperferritinemia in non-transfusion dependent thalassemia is a serum ferritin higher than 800 ng/mL [2] The estimation of serum ferritin levels is the most commonly employed test to evaluate iron overload in Beta Thalassemia Major. A target ferritin of approximately 1000 ng/ml is generally recommended standard practice in thalassaemia major (TIF Guidelines, 2000) and other forms of iron overload resulting from blood transfusion. When the serum ferritin level reaches 1000 ng/ml (usually after 10th to 12th transfusion), it is generally taken as the point to initiate iron chelation therapy. Results The number (%) of myocardial dysfunctions (systolic and diastolic), pancreatic, cardiac and liver iron siderosis were not clearly reported in the article The Hepatic, Cardiac and pancreatic iron loading data are illustrate din table 1 and myocardial dysfunction data are illustrated in the third paragraph in results and table 2 The categorization of patients based on LIC should have been placed in the Method section Categorization of patients based on LIC will be added in methods section In the second paragraph, the results related to the prediction of liver siderosis by pancreatic T2* values is not reflected in the aim of study The results related to the prediction of liver siderosis by pancreatic T2* values is not reflected in the aim of study as this was a secondary outcome not our primary one Figure 2 is not so meaningful Figure 2 is based on the secondary outcome that we found Based on the title of Table 3, LIC reported in Table 3 does not belongs to cardiac function I will change the title of table 3 The majority of correlations between pancreatic T2*, LIC and serum ferritin with cardiac indices measured by trans thoracic and tissue Doppler echocardiography were weak (correlation coefficient < 0.4). The correlation of LIC and peak late diastolic (A') was detected as a moderate strength of relationship (r = 0.423). The intensity of correlation between pancreatic T2* with E' was also moderate (r = 0.43) Though the correlations are weak but there still exist a correlation and this is actually what we found Discussion The aim of the study should have been mentioned at the end of the Introduction part instead of at the beginning of the Discussion section I will remove this part There is a disparate concept in the paper about the time of pancreatic and cardiac iron loading. In the Abstract it is written: “There is accumulating evidence that pancreatic iron can predict cardiac iron in young children because the pancreas loads earlier than the heart”. Conversely, in the second paragraph of the Discussion part it is written: “Cardiac iron overload occurs earlier than pancreatic iron overload, therefore pancreatic iron can predict cardiac iron in young children” I am going to edit this part regarding Cardiac iron overload occurs earlier than pancreatic iron overload, therefore pancreatic iron can predict cardiac iron in young children as it is really contradictory There have been some limitations in this study, which is absent in the paper. The population of the study is heterogeneous, comprising with β-thalassemia major and sickle cell disease. As you can see, the difference of pancreatic T2* values between two groups (βTM and SCD patients) shown in Table 1 is significant. In addition, I expected to see several recommendations to make a contribution to set up future studies I will add some recommendations as suggested"
}
]
}
] | 1
|
https://f1000research.com/articles/9-1108
|
https://f1000research.com/articles/10-451/v1
|
07 Jun 21
|
{
"type": "Research Article",
"title": "Formulation and characterisation of alginate hydrocolloid film dressing loaded with gallic acid for potential chronic wound healing",
"authors": [
"Jhing-Ee Gan",
"Chai-Yee Chin",
"Jhing-Ee Gan"
],
"abstract": "Background: A dramatic growth in the prevalence of chronic wounds due to diabetes has represented serious global health care and economic issues. Hence, there is an imperative need to develop an effective and affordable wound dressing for chronic wounds. Recent research has featured the potential of bioactive compound gallic acid (GA) in the context of wound recovery due to their safety and comparatively low cost. However, there is a scarcity of research that focuses on formulating GA into a stable and functional hydrocolloid film dressing. Thus, this present study aimed to formulate and characterise GA-loaded alginate-based hydrocolloid film dressing which is potentially used as low to medium suppurating chronic wound treatment. Methods: The hydrocolloid composite films were pre-formulated by blending sodium alginate (SA) with different combinations of polymers. The hydrocolloid films were developed using solvent-casting method and the most satisfactory film formulation was further incorporated with various GA concentrations (0.1%, 0.5% and 1%). The drug-loaded films were then characterised for their physicochemical properties to assess their potential use as drug delivery systems for chronic wound treatment. Results: In the pre-formulation studies, sodium alginate-pectin (SA-PC) based hydrocolloid film was found to be the most satisfactory, for being homogenous and retaining smoothness on surface along with satisfactory film flexibility. The SA-PC film was chosen for further loading with GA in 0.1%, 0.5% and 1%. The characterisation studies revealed that all GA-loaded films possess superior wound dressing properties of acidic pH range (3.97-4.04), moderate viscosity (1600 mPa-s-3198 mPa-s), optimal moisture vapor transmission rate (1195 g/m2/day, 1237g/m2/day and 1112 g/m2/day), slower moisture absorption and film expansion rate and no chemical interaction between the GA and polymers under FTIR analysis. Conclusion: An SA-PC hydrocolloid film incorporated with gallic acid as a potentially applicable wound dressing for low to medium suppurating chronic wounds was successfully developed.",
"keywords": [
"Alginate",
"pectin",
"gallic acid",
"wound dressing",
"hydrocolloid film"
],
"content": "Introduction\n\nDelayed wound healing that leads to chronic diabetic foot ulcers (DFU) and lower limb complications are the most devastating complications of diabetes which has impacted 40 to 60 million people worldwide (International Diabetes Federation, 2019). In the year of 2001, the United States (US) healthcare system reported an expenditure of 10.9 billion USD in management and treatment of DFU. The expenditure of wound management for individuals with diabetes and foot ulcer are 5.4 times higher in the year of the first event and 2.6 times higher in the year of the second event as compared to individuals with diabetes but without foot ulcers. DFU can lead to serious infection, gangrene, foot amputation and even death if proper care and attention was not given. Wound healing treatment is more challenging specifically in persons with DFU as the delayed wound healing is contributed by multiple mechanisms such as the reduced response of cells and growth factors resulting in reduced peripheral flow of blood and local angiogenesis. Therefore, wound care is a crucial component of DFU management (Brem & Tomic-Canic, 2007).\n\nAmong the plethora of modern wound dressings present in the marketplace nowadays, moisture-retentive dressings such as hydrocolloid films have advanced to become a famous wound healing modality for moist wound management. Upon contact with the wound exudate, this matrix converted to a gel sheet from a dry dressing to create moist surroundings around the wound area to facilitate the proliferation and migration of dermal fibroblasts as well as to advance collagen synthesis which is beneficial in reducing the formation of scar (Moura et al., 2013). Sodium alginate (SA) is a hydrophilic soluble salt of alginic acid, which is a polysaccharide that exists in the cell wall of brown algae. It possesses good film fabrication properties and is widely used as a controlled release medium in delivering drugs with its ability to expand itself upon water absorption. Pectin (PC), a linear polysaccharide which has been explored extensively for film dressings application due to several advantages in wound healing discovered namely, its (1) hydrophilicity, which facilitates exudate removal in wounds by reacting with the wound fluid to create a gel with soft texture over the wound site, (2) role as binding agent when added to wounds to safeguard the growth factors from degradation hence promote new cell generation, and (3) ability to retain an acidic environment of the wound to prevent any microbial growth (Munarin et al., 2012). Given their safety and relatively affordability, there has been a gradually increasing interest in using bioactive plant compound in the context of wound healing. One such extract is gallic acid (GA), which is a natural phenolic compound found in the fruits, leaves, and wildflowers (Badharu et al., 2015). GA had been well demonstrated for antioxidant, analgesic, anti-inflammatory, including anti-diabetic properties. Singh et al. (2019) and Kaparekar et al. (2020) have noted an improved wound contraction as well as a reduction in duration of re-epithelialization of the excision wound with the use of GA. In short, all the beneficial features that GA possess to support its advancement into a practical wound recovery agent. This present study aimed to formulate and characterise GA-loaded alginate (SA) based hydrocolloid film dressing which is potentially used as low to medium suppurating chronic wound treatment.\n\n\nMethods\n\nGallic acid 97.5-102.5% (CAS No. 149-91-7, MW: 170.12g/mol), sodium carboxymethylcellulose (CAS No. 9004-32-4) and Pluronic F-127 (CAS No. 9003-11-6) were supplied by Sigma Aldrich (USA). Sodium Alginate (CAS No. 9005-38-3, MW~ 20-40 kDa) was procured from Fisher Scientific (UK), whereas pectin pure (CAS No. 9005-69-5, >99.0%) was supplied by Sime Scientific.\n\nFive (5) different combinations of polymers were used in the pre-formulation of blank hydrocolloid film which include: sodium alginate (SA), pectin (PC), sodium carboxymethylcellulose (NaCMC), chitosan (CS) and Pluronic F-127 (PF127) presented in Table 1. The blank hydrocolloid films were solvent-casted by filling the uniform gel slurry (20g) into petri dishes (d = 90 mm) then dried in the oven (39 ± 3°C) for 24 h. After the preliminary evaluation, GA was loaded into the sodium alginate pectin (SA-PC) composite film to produce the drug-loaded film as summarized in Table 2. Formulation of GA-loaded films with the strength of 0.1, 0.5 and 1.0% w/v were based on literature review and formulation suitability. The dried film was stored in desiccators to prevent it from reacting with moisture from humidity.\n\n* Abbreviations: SA- Sodium alginate, PC-Pectin, NaCMC-Sodium carboxymethylcellulose, CS-Chitosan, PF127-Pluronic F-127.\n\nThe morphology of film samples was examined under a polarized microscope built with a camera. The films were put on top of a glass slide with the slip covered before viewing under the microscope at a magnification of 4x. The snapshots of the magnified film were captured under bright and polarized light.\n\nDigital pH meter (Sartorius pH meter, Germany) was used to determine the acidity properties of polymers (before drying). The viscosity of polymers (before drying) was determined by using a rheometer (Brookfield DV2T Viscometer, USA). Gel samples were sheared continuously at a rate of 100 rpm for I min with spindle LV-4 (64) or 200rpm for one min with spindle LV-3 (63).\n\nFourier transform infrared (FTIR) analysis was executed with a spectrophotometer (Perkin Elmer Spectrum 100 FTIR Spectrometer, USA) equipped with an attenuated total reflection (ATR) assembly. The FTIR spectra of the pure gallic acid, SA, PC and drug-loaded films were recorded.\n\nThe films (diameter = 13mm) fitted over the brim of 20 mL clear glass vials with dry silica beads (2 g). The vials containing the film with dry silica beads, were weighed as 0 h and kept in a moist chamber at an RH of 88 ± 2% at 33°C. The vial was taken out from the desiccator to perform weighing at every 1 h interval for the first subsequent eight hours then followed by the 24th hour. The weight gained for respective hours were reported and repeated in triplicate to obtain the average values. The MVTR was calculated by using Eq. (1):\n\nwhere, W is the weight that is gained by desiccant over 24 h, and S is the exposed surface area of the film (m2); MVTR expressed in units as g/m2/day.\n\nThe film samples (diameter = 22mm) kept in desiccators with silica beads overnight to retain their dryness. Weighing boats (small) were weighed and labeled accordingly with the film samples. Its initial weight at 0th hour was regarded as zero weight gained. The trimmed films were transferred into a moist chamber (RH 88 ± 2%). Weighing boats with the film samples were then weighed again at the 24th hour as final weight gained. The moisture absorption was obtained using Eq. (2):\n\nwhere, Wt is the weight of film samples after 24 h, and Wo is the weight of film sample before inserted into the moist chamber.\n\nFilm swelling was studied using a gelatin model adapted from a previously established protocol by Chin et al. (2018). The films (diameter = 22 mm) placed at the center of gelatin gel contained in petri dishes. The diameter of films was measured using vernier calipers at the beginning of the experiment as 0 h. Next, the differences in film expansion were reported at a predetermined time interval of every 1 h in the subsequent first 8 hours and after the 24 hours. Each measurement of film was carried out three times and the average values of expansion ratio was calculated with the Eq. (3):\n\nwhere Dt is the diameter of film after expansion and Do is the diameter of film before expansion.\n\n\nResults\n\nAll the gel samples were sheared continuously at a rate of 100 rpm for 1 min with spindle LV-4 (64) except the asterisks (*) represent gel samples that sheared continuously at a rate of 200 rpm for one min with spindle LV-3 (63).\n\n\nDiscussion\n\nPre-formulation study is an essential preliminary study to ensure the successful establishment of an optimum drug delivery system prior to formulation of a novel modality for wound healing. The SA-PC composite films appeared as translucent, smooth texture without air bubbles when viewed under bright light microscope along with adequate flexibility in texture. Films formulated with SA and PC alone, also shown as translucent with slightly uneven surface and has a reduced flexibility in nature as compared to SA-PC composite films (Figure 1A). All in all, SA-PC films were identified as the most satisfactory film and selected for further loading with GA of various strengths (0.1%, 0.5%, 1.0% w/v) and were continued for characterisation studies. All the films showed homogenous and smooth surface without any visible bumps, flaws or cracks when viewed under the microscope hence indicating excellent compatibility between GA and SA-PC polymers (Figure 1B).\n\nMacroscopic and microscopic images of (A) SA, PC and blank SA-PC hydrocolloid films and (B) Gallic acid-loaded films of various strengths (SA-PC-GA 0.1%, 0.5% and 1.0% w/v) taken on physical examination and under brightfield microscope at 4× magnification.\n\nAll the hydrocolloid gel slurry had exhibited acidic pH values, as shown in Table 3, except for the formulations produced with chitosan which are the NaCMC-CS and SA-CS. All the polymeric gels formulated using PC polymer generally displayed a slightly lower pH value range (3.56-5.23) than the other combination of polymers having pH value range (6.18-8.19), with PC polymer alone having the lowest pH value of 3.74. All the mixtures of SA-PC polymeric gel loaded with GA also exhibited acidic properties with pH value range (3.97-4.04) as shown in Table 4. Therefore, hydrocolloid film with slight acidic properties formulated in this study might promote wound recovery attributed to the role of pH in affecting the phases of wound repair.\n\nThe viscosity of hydrocolloid film is crucial as it determines the formulation stability and efficacy in terms of drug release (Matthews et. al, 2006). Polymeric gel of PC, SA-CS, PC-CS, PF-127, SA-PFl27 PC-PFl27 possess a viscosity value ranging from 58 to 726 mPa-s which is too low for the formulated film to retain on wound area for sufficient time for wound healing. On the contrary, SA polymeric gel possesses a high viscosity value of 5396 mPa-s, hence causing the formulated film to have less flexibility. The formulated NaCMC hydrocolloid gel possesses overly high viscosity above 6000 mPa-s and tend to produce excessively hard texture films. Therefore, SA-PC with moderately high viscosity value of 1974 mPa-s has been selected to further incorporation with GA. All GA-loaded SA-PC hydrocolloid films were displayed high viscosity and the viscosity increased from 1600, 2300 to 3198 mPa-s as the concentration of drug incorporated increases. Zaman et al. (2011) also presented the findings that the greater the viscosity of a developed film, the better it is to maintain the integrity as a drug delivery system.\n\nFTIR was conducted to identify any chemical interactions and investigate the compatibility between GA with the polymers within the film. The FTIR spectra of blank and GA-loaded films are shown in Figure 2A & 2B. GA characteristic peaks at 3280 and 3493 cm-1 suggested to be the aromatic and carboxylic O—H stretching, the hydroxyl groups (—OH) present in positions three, four, and five of the aromatic rings. Bands at 1695 cm-1 are for the C=O stretching of carboxylic acid whereas bands at 1540 and 1468 cm-1 areas corresponding to C=C aromatic stretching vibration. The FTIR spectra of SA-PC-GA films exhibited characteristic peaks of individual polymers of SA and PC, as well as the presence of the prominent peaks of GA. Moreover, the FTIR spectra of drug-free and GA-loaded films did not display any major distinction from each other, indicating the lack of obvious chemical interaction occurred between the polymers and the drug. In short, the bioactive constituent did not lose its activity when loaded into the films by blending with SA‐PC polymers.\n\n* Abbreviations: SA, sodium alginate; PC, pectin; GA, gallic acid.\n\nA desirable wound dressing should provide an optimal moisture vapor transmission rate (MVTR) which is crucial for creating a moist environment to advance wound recovery (Bajpai et al., 2014). According to Gupta et al. (2010), MVTR for normal skin is 204 g/m2/day whereas for wounded skin, it can range from 279 to 5138 g/m2/day. As shown in Figure 3A, the MVTR for all the formulated films (0.1%, 0.5% and 1.0% w/v SA-PC-GA) were reported to fit within the range for injured skin, which is 1195, 1237 and 1112 g/m2/day with no significant differences (p>0.05) between the films and blank SA-PC film. It has also been revealed that the moisture vapor gained per area of films has increased gradually over the first 8 h of experiment to facilitate an optimum gaseous exchange for wound healing. This is in accordance with the findings reported by Xu et al. (2016) that the MVTR within ≤ 2028 g/m2/day is appropriate to create a moist wound bed. In short, all the formulated films loaded with GA able to maintain sufficiently high MVTR for accelerating epithelialization process at injured wound area (Tan et al., 2020). The moisture absorption ratio of GA loaded hydrocolloid films ranged from 73.05-76.87%, as displayed in Figure 3B with no significant difference (p > 0.05). The absorption of moisture by the films could be assignable to the constituents that made up the film, for instance glycerol. As reported by Rusli (2017), glycerol is capable of increasing the moisture absorption ability to a certain extent and causing an increment in thickness by film swelling. Therefore, it can be deduced that the GA-loaded films with a lower percentage of moisture absorption is more favorable for low to medium exudative wounds.\n\nThe swelling study was assessed to investigate the expansion rate of the hydrocolloid film dressing under exudative wound condition. As displayed in Figure 3C, the SA-PC-GA 0.1% hydrocolloid film presented with the highest hydration and expansion rate in the first 4 h. The film expansion ratio was presumed to be related to the viscosity profile of the formulated films, as reported by Thu et al. (2012). Since SA-PC-GA 0.1% w/v hydrocolloid film is having the least viscosity, it swells upon moisture uptake more rapidly and loses its circular shape quicker. The film expansion ratio was observed to be slower in SA-PC-GA 0.5% w/v and followed by SA-PC-GA 1.0% w/v hydrocolloid film, which is having the lowest expansion ratio. All the hydrocolloid films attained a nearly plateau state after 8 h, where they became highly viscous and could not expand further. In short, a wound dressing that can maintain its shape and structure for a prolonged period of application is desirable for highly exudative wounds. From this present study, it was postulated that SA-PC-GA 0.1% w/v hydrocolloid film is more suitable to be used for low suppurating wounds or shorter-term application. On the other hand, SA-PC-GA 1.0% w/v hydrocolloid film may be particularly useful in medium to heavy exudative wounds or longer-term application owing to its high-water retention capacity.\n\n\nConclusion\n\nIn this present study, the GA-loaded hydrocolloid films exhibited ideal wound dressing properties of (1) acidic pH, (2) moderate viscosity, (3) absence of chemical interaction between drug and polymer excipients, (4) optimal MVTR, (5) lower moisture absorption, and (6) film expansion rate, thus suggesting its potential use as a wound dressing for low to medium suppurating wounds. Future investigations which focus on the in vivo performance of gallic acid loaded film formulations are necessary to establish its safety and efficacy profile as a chronic wound healing application.\n\n\nData availability\n\nHarvard Dataverse: Formulation and Characterisation of Alginate Hydrocolloid Film Dressing Loaded with Gallic Acid for Potential Chronic Wound Healing. https://doi.org/10.7910/DVN/1AIBEU (Gan and Chin, 2021) This project contains the following underlying data:\n\n- Moisture Absorption Studies.csv\n\n- Moisture Vapour Transmission Rate Studies.csv\n\n- Swelling Studies.csv\n\n- Microscopy images for all drug-free films and GA loaded hydrocolloid films\n\n- pH and viscosity readings for all drug-free polymeric gels\n\n- pH and viscosity readings for all GA-loaded polymeric gels\n\n- Pure gallic acid FTIR image\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).",
"appendix": "Acknowledgements\n\nThe authors would like to express the deepest gratitude to the Taylor’s Faculty Health and Medical Sciences laboratory staffs who have shown support towards the successful completion of this research. This manuscript is not submitted nor being considered for publication elsewhere but has been partly presented as oral presentation in 1st International Conference of MEDICAL GOES PUBLIC (ICON-MEGOPIC2021), held in Kuala Lumpur, Malaysia, 2021.\n\n\nReferences\n\nBadhani B, Sharma N, Kakkar R: Gallic acid: A versatile antioxidant with promising therapeutic and industrial applications. Rsc Advances . 2015; 5(35): 27540–27557. Publisher Full Text\n\nBajpai M, Bajpai SK, Gautam D: Investigation of Regenerated Cellulose/Poly (acrylic acid) Composite Films for Potential Wound Healing Applications: A Preliminary Study. J Appl Chemistry . 2014; 2014: 1–9. Publisher Full Text\n\nBoateng JS, Stevens HN, Eccleston GM, et al.: Development and mechanical characterization of solvent-cast polymeric films as potential drug delivery systems to mucosa! surfaces. Drug Dev Ind Pharm . 2009; 35(8): 986–996. PubMed Abstract | Publisher Full Text\n\nBrem H, Tomic-Canic M: Cellular and molecular basis of wound healing in diabetes. J Clin Invest. 2007; 117(5): I219–1222. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChin C-Y, Jalil J, Ng PY, et al.: Development and formulation of Moringa oleifera standardised leaf extract film dressing for wound healing application. J Ethnopharmacol. 2018; 212, 188–199. PubMed Abstract | Publisher Full Text\n\nGan JE, Chin CY: Formulation and Characterisation of Alginate Hydrocolloid Film Dressing Loaded with Gallic Acid for Potential Chronic Wound Healing. Harvard Dataverse . 2021; V2. Publisher Full Text\n\nGupta B, Agarwal R, Alam MS: Textile-based smart wound dressings.2010. Reference Source\n\nInternational Diabetes Federation: IDF Diabetes Atlas, 9th edn. Brussels, Belgium: 2019. Reference Source\n\nKaparekar PS, Pathmanapan S, Anandasadagopan SK: Polymeric scaffold of Gallic acid loaded chitosan nanoparticles infused with collagen-fibrin for wound dressing application. Int J Biol Macromol. 2020; 165: 930–947.\n\nMoura LI, Dias AM, Carvalho E, de Sousa HC: Recent advances on the development of wound dressings for diabetic foot ulcer treatment—a review. Acta Biomater. 2013; 9(7): 7093–7114.\n\nMunarin F, Tanzi MC, Petrini P: Advances in biomedical applications of pectin gels. Int J Biol Macromol. 2012; 51(4): 681–689. PubMed Abstract | Publisher Full Text\n\nRezvanian M, Amin MCIM, Ng S-F: Development and physicochemical characterization of alginate composite film loaded with simvastatin as a potential wound dressing. Carbohydr Polym. 2016; 137: 295–304. PubMed Abstract | Publisher Full Text\n\nRusli A: Physical and mechanical properties of agar based edible film with glycerol plasticizer.2017. Publisher Full Text\n\nSingh K, Sinha M, Pal D, et al.: Cutaneous Epithelial to Mesenchymal Transition Activator ZEB1 Regulates Wound Angiogenesis and Closure in a Glycemic Status—Dependent Manner. Diabetes 2019; 68(11): 2175–2190.\n\nTan WS, Arulselvan P, Ng S-F, et al.: Healing Effect of Vicenin-2 (VCN-2) on Human Dermal Fibroblast (HOF) and Development VC-2 Hydrocolloid Film Based on Alginate as Potential Wound Dressing. Biomed Res Int. . 2020; 2020: 4730858. PubMed Abstract | Publisher Full Text | Free Full Text\n\nThanikachalam T, Selvaraj TKR, Ayyappan M, et al.: Gap closure of different shape wounds: in vitro and in vivo experimental models in the presence of engineered protein adhesive hydrogel. J Tissue Eng Regen Med . 2019; 13(2): 174–178. PubMed Abstract | Publisher Full Text\n\nThu H-E, Zulfakar MH, Ng S-F: Alginate based bilayer hydrocolloid films as potential slow-release modem wound dressing. Int J Pharm . 2012; 434(1-2): 375–383. PubMed Abstract | Publisher Full Text\n\nXu R, Xia H, He W, et al.: Controlled water vapor transmission rate promotes wound-healing via wound re-epithelialization and contraction enhancement. Sci Rep. 2016; 6(1): 1–12.\n\nYang DJ, Moh SH, Son DH, et al.: Gallic Acid Promotes Wound Healing in Normal and Hyperglucidic Conditions. Molecules (Basel, Switzerland). 2016; 21(7). PubMed Abstract | Publisher Full Text | Free Full Text\n\nZaman HU, Islam JMM, Khan MA, et al.: Physico-mechanical properties of wound dressing material and its biomedical application. J Mech Behav Biomed Mater . 2011; 4(7): 1369–1375. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "86942",
"date": "21 Jun 2021",
"name": "Pijush Kumar Paul",
"expertise": [
"Reviewer Expertise Drug delivery",
"polymer"
],
"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 study of formulation and characterization of gallic acid-loaded alginate-based hydrocolloid film dressing for chronic wound treatment.\nComments The manuscript is well written however, additional proofreading of the manuscript’s English grammar could enhance the clarity of the paper.\nThis manuscript does not do justice to the previous work. The review concerning the recent trends on wound management has not been cited.\nE.g., Okur, M. E., Karantas, I. D., Şenyiğit, Z., Üstündağ Okur, N., & Siafaka, P. I. (2020). Recent trends on wound management: New therapeutic choices based on polymeric carriers. Asian journal of pharmaceutical sciences, 15(6), 661–6841.\nThe source of pectin should be written clearly including the country of origin. The source of chitosan is not mentioned in the materials section.\nThere should be error bar in the figure 3.\nThere are a few typos in the manuscript.\nE.g., on page 3, there will be 1 instead of I in the last line of pH study and viscosity profile of method section and there will be space between 200 and rpm. There will be space between 22 and mm in the first line of moisture absorption. In addition, there should be h instead of hour in the same paragraph.\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": "86941",
"date": "25 Jun 2021",
"name": "Azad Abdul Kalam",
"expertise": [
"Reviewer Expertise My area of research is natural drug product development",
"advanced drug delivery system or develop drug delivery carrier."
],
"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 am very happy to announce that this invited research paper has been completed in a very fluent language and in a proper manner. I read the research paper very carefully and realized that the research has practical application and novelty which enables the reader and other researchers to take their research work one step further and get the right direction.\nEven then I came to realize that the research work could be much more informative and meaningful if the author's will able to include drug (GA) entrapment and release study data. Thank you so much.\nThe work clearly and accurately presented, and the authors have cited the recent published literature.\n\nI have found this study in appropriate design with its academic merit.\n\nAuthors have described with sufficient details of methods and analysis provided to allow replication by other researchers for further investigation.\n\nI noticed that the statistical analysis and its interpretation is appropriate and scientific manner.\n\nIn these current results described by authors data underlying the results available to ensure full reproducibility.\n\nThe conclusions drawn adequately supported by the results presented in this manuscript.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-451
|
https://f1000research.com/articles/10-449/v1
|
07 Jun 21
|
{
"type": "Research Article",
"title": "Prevalence of urinary tract infections and antibiogram of uropathogens isolated from children under five attending Bagamoyo District Hospital in Tanzania: A cross-sectional study",
"authors": [
"Raphael Z. Sangeda",
"Franco Paul",
"Deus M. Mtweve",
"Franco Paul",
"Deus M. Mtweve"
],
"abstract": "Background: Urinary tract infection (UTI) is a common condition in children that recurs frequently. This study aimed to determine the prevalence of UTIs among children under five attending Bagamoyo District Hospital and determine its association with nutritional status. Methods: This was a cross-sectional study that enrolled 214 children under five years old attending Bagamoyo District Hospital in Tanzania. Midstream urine was collected in sterile conditions and bottles. Samples were transported to the laboratory to isolate bacteria using cysteine lactose electrolyte deficient (CLED) agar. Identification was undertaken using Gram staining, single iron agar test, sulfide-indole motility (SIM) test, and catalase and oxidase tests. A susceptibility test was done using the disc diffusion method. Anthropometric measurements were employed to assess malnutrition status and body mass index was determined using each child's weight and height. Results: Of the 214 children under five enrolled in the study, 123 (57.4%) were girls and 91 (42.6%) were boys. A total of 35 children were confirmed UTI-positive, making the prevalence 16.4%. Of positive children, 17 (7.9%) were girls and 18 (8.4%) were boys. The UTI prevalence was higher in boys than in girls but not statistically significant (p=0.244). Among the isolated uropathogens, Escherichia coli were common bacteria accounting for 65.7% of all isolates. The rate of other uropathogens isolated was Klebsiella spp. (17.1%), Pseudomonas spp. Proteus spp (11.4%) and (2.9%) and Staphylococci spp. (2.9%). The antibiogram of the isolated bacterial uropathogens showed high in-vitro resistance ranging from 90-95% to erythromycin, trimethoprim-sulfamethoxazole and ampicillin. Conclusion: The prevalence of UTI for children under five was 16.4%. The most common causative agent of UTI was Escherichia coli. There was no association between UTI status and malnutrition status of the children. High resistance to antibiotics calls for antimicrobial stewardship and surveillance to preserve antibiotics' effectiveness in treating uropathogens.",
"keywords": [
"UTI",
"Prevalence",
"children under five",
"antibiogram",
"Bagamoyo",
"Tanzania"
],
"content": "Introduction\n\nUrinary tract infection (UTI) is common in children and tends to recur frequently. UTI is ranked the second most prevalent infection after upper respiratory tract infection in children1,2. The recurrence of UTI is more widespread in girls than in boys3,4. About 30% of children under five suffer from recurrent UTI within the first twelve months after the first occurrence5. If not treated, UTI may lead to pyelonephritis and acute morbidity when associated with abnormalities like vesicoureteral and reflux nephropathy in children. In the long run, UTI may result in parenchymal scarring, hypertension, decreased renal function and renal scarring6,7. For that reason, UTI is a significant contributor to mortality and morbidity in children. However, when recognized and appropriately managed, renal sequelae are rare.\n\nUTI occurs in 2.4-2.8% of children in the United States annually8. The incidence of UTIs is mostly influenced by the host factors such as age and gender. Other risk factors are congenital genitourinary conditions, immature host defenses, lack of circumcision in boys, malnutrition, social status, prior history of UTI, instrumentation, the existence of abnormal urinary tract and the extent of virulence of the etiological agent7,9–11. In both boys and girls, the prevalence of UTI is high in the first twelve months of life and decreases after that5. Shaikh and colleagues reported a UTI prevalence of 7.0% in infants with fever12. In febrile infants aged 0–2 months, UTI prevalence in girls and uncircumcised boys was 5% and 20%, respectively12. In the first six months, the risk of UTI was 10 to 12 higher in uncircumcised boys7. Estimates show that about 7.8% of girls and 1.7% of boys develop UTI by the age of seven. At sixteen years of age, 11.3% of girls and 3.6% of boys may suffer from UTI7.\n\nA prompt diagnosis and appropriate treatment are essential to reduce the morbidity and sequelae following a UTI13. However, diagnosis of UTI in children under two years is usually confounded by the non-specific signs and symptoms of UTI9. Children with uncomplicated UTI may respond to amoxicillin, sulphonamides, trimethoprim-sulfamethoxazole or cephalosporins, concentrating in the lower urinary tract14. Several studies show similar efficacy among the oral and intravenous antibiotics for UTI treatment15. However, studies in high-income countries suggest that UTI causative bacteria increase acquiring resistance to commonly used antibiotics, such as trimethoprim-sulfamethoxazole16,17.\n\nGram-negative organisms highly contribute to the proportion of uropathogens isolated from children with UTI6,18. Escherichia coli accounts for up to 90% of infections6. Other uropathogens commonly isolated in UTI include Klebsiella pneumoniae, Proteus mirabilis, Citrobacter, Pseudomonas aeruginosa, Enterobacter aerogenes, Enterococcus species and Serratia species18. Proteus mirabilis is more commonly found in boys compared to girls19. Streptococcus agalactiae is commonly isolated from newborns20. Staphylococcus saprophyticus is isolated in sexually active female adolescents and contributes to 15% of UTI cases21.\n\nMalnutrition is a major risk factor for child mortality and adult ill-health. Malnutrition could increase the risk of serious infections22. Malnutrition is still a problem Bagamoyo district in Tanzania due to poor living conditions among people living within and around Bagamoyo23. The living condition may predispose an individual to acquire a UTI. However, the association between malnutrition and the acquisition of UTI has not been studied in this setting. This study was undertaken to determine the prevalence of UTI, antibiotic susceptibility testing of uropathogens and assess the association between UTI acquisition and nutritional status among children under five attending Bagamoyo District Hospital in Tanzania.\n\n\nMethods\n\nThis was a cross-sectional study enrolling symptomatic and asymptomatic children under five attending Bagamoyo District Hospital in Tanzania. The inclusion criteria were age range 12 months to 59 months. The study was conducted from April to July 2017. Convenience sampling was used whereby 214 children under five were recruited to participate in the study. The exclusion criteria were children who had recently taken antibiotics, children who were diabetic or HIV positive, and those out of the inclusion age range.\n\nThe sample size (n) was calculated according to the formula24 n = z2 * p * (1 - p) / e2, where: z = 1.96 for a confidence level (α) of 95%, p = prevalence and e = margin of error.\n\nAccording to a study conducted in Tanzania, the prevalence of UTI in children was 16.825, thus making p = 0.168 and taking e = 0.05. The sample size obtained was 214.\n\nEthical clearance for this study was granted by the Muhimbili University of Health and Allied Sciences Ethics Review Board number 2017-02-20/AEC/Vol XII/59. The parents or guardians permitted their child to participate in the research study following reading and approving the study information provided by the researcher, and parents or guardians signed the consent on behalf of their child. The parents and guardians were informed and consented to the publication of this manuscript.\n\nMid-stream urine samples were collected from the children attending Bagamoyo District Hospital using the widely recommended urine sampling method in children under five, where guardians were instructed to collect a urine sample in sterile conditions26. Therefore, when the container was one-third complete, the lid was closed and clean catch mid-stream urine samples in sterile containers were transported immediately to the Pharmaceutical Microbiology laboratory for analysis. During transportation, the temperature of 4-8°C was maintained in a cool box containing ice blocks to control microorganism growth27.\n\nA semi-structured questionnaire (see Extended data28), was given to parents or guardians of children under five eligible to participate in this study. The questionnaire collected information about age, gender, type of meal frequently given, and the number of meals per day. We also used the questionnaire to capture height and weight of the children attending the clinic at Bagamoyo District Hospital. Body mass index (BMI) was calculated.\n\nIsolation of bacterial pathogens from urinary samples was carried out using a calibrated loop method in which a sterile standard loop was used to pick 50µL of urine. A loopful urine sample was plated on cysteine lactose electrolyte deficient (CLED) agar. The inoculated plate was incubated at 37°C overnight. The numbers of isolated bacterial colonies were counted as the colony unit to estimate bacterial load/mL of the urine sample. Any sample specimen that contained a bacterial load of ≥105cfu/ml on the calculation of urine samples using a microscope was considered positive for UTI29.\n\nAfter 24 hours of incubation of the sample on cysteine lactose electrolyte deficient agar (CLED), the growth of bacterial uropathogens in plates was considered positive. The appearance of colonies was observed and recorded. For non-pure bacterial growth, following the use of a sterilized and calibrated loop, a single colony of the pure colony was picked and sub-cultured on MacConkey's agar and incubated at 37°C. After the overnight incubation at 37°C, the bacterial growth appearance, including color and morphology, was observed and recorded30.\n\nBacteria were identified using the Gram stain test, Kliger's iron agar (KIA), sulfide, indole, motility (SIM) media, catalase and oxidase test31.\n\nThe identified uropathogens were subcultured two times before being used for antibiotic susceptibility tests. Antibiotic susceptibility testing was performed as recommended by the Clinical Laboratory Standards Institute guidelines32. The method adopted was Kirby Bauer's discs diffusion assay33. Mueller Hinton agar was used as media for performing antibiotic susceptibility tests.\n\nThe antibiotic disc was placed onto the media along the parallel lines separating the standard organism and test organism; seven antibiotic discs were tested against the isolated uropathogens. The seven antibiotic discs tested included amoxicillin-clavulanate acid (20/10µg), ceftriaxone (45µg), ampicillin (25µg), erythromycin (15µg), nalidixic (30µg), trimethoprim-sulfamethoxazole (1.25/23.75µg) and nitrofurantoin (30µg). After overnight incubation, the zone of inhibition of each tested antibiotic disc (6mm disc) was measured using a measuring scale33.\n\nThe zone of inhibition's measured diameter was interpreted into resistant, intermediate and sensitive as per the National Committee for Clinical Laboratory Standards (NCCLS)32.\n\nQuality control and review of the collected data were ascertained to remove any errors. Demographic data were available for all participants. For participants who tested negative for urinary tract infection, the corresponding laboratory variables were marked as 'NA; to indicate that data was not applicable in the dataset. The cleaned data was entered into the Statistical Package for Social Scientists (SPSS version 20) computer program and subjected to analysis. The data was analyzed to provide frequency tables. The Pearson chi-square test was employed to determine the association between the demographic data and UTI status, taking a P-value < 0.05 as a significant cutoff at a 95% confidence interval.\n\n\nResults\n\nA total of 214 urine samples were obtained from children aged between 12 months and 59 months who visited Bagamoyo District Hospital (see Underlying data28), including 123 females and 91 males (Table 1). Demographic data were available for all the 214 participants, while the laboratory analysis was only done for the 35 samples that tested positive for urinary tract infection.\n\nThe mean age was 27.1 months. The majority of the children (37.8%) were in the age range 13-24 months, followed by 37.3% in the age range 25-36 months (Table 1).\n\nThe prevalence rate of UTI among children attending Bagamoyo District Hospital was 16.4% (Table 2).\n\nThe most common causative agent of UTI in children attending Bagamoyo district was E. coli (65.7%), followed by Klebsiella spp (17.1%) (Table 3).\n\nA proportion of 94.3% of the five uropathogens was resistant to ampicillin, followed by erythromycin and trimethoprim-sulfamethoxazole proportion of resistant isolate 94.3 and 91.4%, respectively (Figure 1).\n\nAll Proteus species (100%) were resistant to ampicillin and erythromycin (Figure 2), while for E. coli, the proportion of isolates resistant to these two antibiotics was approximately 90%.\n\n\nDiscussion\n\nUrinary tract infections (UTIs) are common causes of mortality and morbidity in children under five34. In this study, the prevalence of UTI in children attending the clinic at Bagamoyo District Hospital was 16.4%. This is comparable to the 16.8% prevalence reported in a study conducted in Muhimbili National Hospital (MNH) in Tanzania by Francis and colleagues in 201025. Also, in this study, 123 girls and 91 boys were involved. The prevalence of UTIs in girls and boys was 7.9 % and 8.4%, respectively. These results were quite different from previous studies at MNH, which are 18.8% and 15.0% for girls and boys, respectively25. A study conducted in Enugu, Nigeria, found the prevalence of UTI among children under five to be 11%35.\n\nOf all children recruited, 81 (37.8%) were aged between 13 to 24 months and 80 (37.3%) were constituting about two-thirds of the recruited children. The age range 13-24 months had the highest rate (6.5%) of UTI, followed by 25-36 months (4.2%). The rate significantly decreased with increasing age (p-value =0.05). None of the children in the age group 49-59 months tested positive for UTI.\n\nEven though our finding between girls and boys was insignificant, the high prevalence of UTIs in boys than in girls can be explained by the fact that most boys are not yet circumcised at this age. In another study, uncircumcised male infants less than three months of age had the highest baseline prevalence of UTI12. The gender of the child and the parent or guardian's employment status was not associated with UTI positivity.\n\nSimilarly, nutritional status (e.g., taking additional meals other than breastfeeding) did not affect the UTI positivity. The mean body mass index for children who were UTI positive was 20.1, which was not statistically different from the negative UTI children with a body mass index of 20.2. In the study in Enugu, Nigeria, females were more likely than males to have UTI positive status35. The lack of association between UTI and nutritional status was also found in another study in rural Africa36. However, a large meta-analysis involving more than 3000 children indicated that the children with malnutrition were more likely to suffer from UTI than the healthy controls37.\n\nThe most common causative agent of UTI in children attending Bagamoyo District Hospital was E. coli (65.7%), followed by Klebsiella spp (17.1%), Proteus spp (11.4%), Pseudomonas spp (2.9%) and Staphylococcus spp (2.9%). Similar results were reported by Aiyegoro et al., who reported Escherichia coli (57.8%) in Nigeria38. Similar results were also reported by Bahati et al., who reported that 70% of isolates were Escherichia coli conducted at Bugando Medical Center in Mwanza, Tanzania30. In Turkey, similar results were obtained39, where E. coli was the most prevalent uropathogen with an isolation rate of 64.2%. In Enugu, Nigeria, the organisms isolated from the 22 positive urine cultures were E. coli 31.8%, Staphylococcus aureus 22.7%, Klebsiella species 13.6%, Proteus species 4.55% and Pseudomonas species 4.55%35. In another study in Nigeria, the isolation rate of E. coli was 37%40, indicating higher isolation rates of E. coli in the current study.\n\nIn this study, seven antibiotics were used to study the antibiogram of uropathogens isolated from urine samples in children under five, namely amoxicillin-clavulanate, ceftriaxone, ampicillin, erythromycin, nalidixic acid, trimethoprim-sulfamethoxazole and nitrofurantoin. The overall percentage of isolates' resistance was high for ampicillin 93.4%, erythromycin 93.4%, trimethoprim-sulfamethoxazole 91.4%. The resistance was relatively less in nalidixic acid 40%, amoxicillin-clavulanate 34.3%, nitrofurantoin 34.3 and ceftriaxone 17.1%. Therefore, the isolated uropathogens showed high in-vitro resistance to ampicillin, erythromycin, and trimethoprim-sulfamethoxazole. At least 90% of five uropathogens in the 35 positive samples were resistant to these antibiotics. These resistance levels are much higher than reported in a study comprising of 17,164 urine cultures41, where the antimicrobial resistance rates were: ampicillin 36.3%, amoxicillin/clavulanic acid 24.7%, cefuroxime 16.8%, co-trimoxazole 31.1%, ciprofloxacin 14.7%, fosfomycin 14.5%, nitrofurantoin 15.6% and 3rd generation cephalosporins 9–11%41.\n\nOn focusing on the antibiogram of all 23 E. coli isolates in this study, the resistance rate to antibiotics was ampicillin 91.3%, erythromycin 91.3%, trimethoprim-sulfamethoxazole, 91.3%, nalidixic acid 39.1%, amoxicillin-clavulanate 34.8%, nitrofurantoin 30.4% and ceftriaxone 17.4%. These findings were comparable to the findings reported by Bahati et al., conducted in Mwanza Tanzania30. In another study conducted in northwestern part of Tanzania, resistance rates of E. coli were ampicillin (98.4%), trimethoprim-sulfamethoxazole (95.3%), amoxicillin-clavulanate (87.5%), cephalexin (61%), cefaclor (43.8%), gentamicin (21.9%), ceftriaxone (14%), nitrofurantoin (12.5%), ciprofloxacin (11.6%), ceftazidime (11%) and cefepime (3.1%)42. The antibiogram of E. coli was similar to that observed in a study in Turkey39.\n\n\nConclusion\n\nThe prevalence of UTIs for children under the age of five in this study was 16.4%. Escherichia coli was the most common bacteria in UTIs, followed by Klebsiella spp. There was high in-vitro antibacterial resistance to ampicillin, trimethoprim-sulfamethoxazole and erythromycin with Proteus, Pseudomonas and Klebsiella species highly resistant to these three antibiotics. There was no association found between malnutrition status and the UTI.\n\nThese findings imply that children under five attending health facilities should be evaluated for UTI. Due to high resistance patterns of erythromycin, ampicillin and trimethoprim-sulfamethoxazole, these agents' routine use for treating UTIs in children under five should be evaluated at the health care facility. These agents need to be used following susceptibility testing results. Therefore, continuous surveillance for antimicrobial stewardship and surveillance is required to curb the increasing resistance patterns of uropathogens to manage UTI and other infections successfully.\n\nOne limitation of the study is the study's cross-sectional nature, whose findings may not extrapolate to other regions in Tanzania and abroad. Nevertheless, the study sheds light on the prevalence of urinary infections, the bacteria commonly isolated, and these isolates' antibiotic sensitivity.\n\n\nData availability\n\nMendeley Data: Dataset for a cross-sectional study on the prevalence of urinary tract infections and antibiogram of uropathogens isolated from under-five children attending Bagamoyo district hospital in Tanzania - dataset. http://dx.doi.org/10.17632/ktzzsfvt79.328.\n\nThis project contains the following underlying data:\n\n- Data_uti_bagamoyo_2017_ver2.xlsx (data from questionnaire and laboratory analyses).\n\nMendeley Data: Dataset for a cross-sectional study on the prevalence of urinary tract infections and antibiogram of uropathogens isolated from under-five children attending Bagamoyo district hospital in Tanzania - dataset. http://dx.doi.org/10.17632/ktzzsfvt79.328.\n\nThis project contains the following extended data:\n\n- Questionnaire to the child parent or guardian.docx (semi-structured questionnaire).\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "References\n\nZelikovic I, Adelman RD, Nancarrow PA: Urinary Tract Infections in Children. An Update. West J Med. 1992; 157(5): 554–561. PubMed Abstract | Free Full Text\n\nFinnell SME: Urinary Tract Infection in Children: An Update. Open Urol Nephrol J. 2015; 8(Suppl 3): 92–95. Publisher Full Text\n\nMangiarotti P, Pizzini C, Fanos V: Antibiotic Prophylaxis in Children with Relapsing Urinary Tract Infections: Review. J Chemother. 2000; 12(2): 115–123. PubMed Abstract | Publisher Full Text\n\nNuutinen M, Uhari M: Recurrence and Follow-up after Urinary Tract Infection under the Age of 1 Year. Pediatr Nephrol. 2001; 16(1): 69–72. PubMed Abstract | Publisher Full Text\n\nStein R, Dogan HS, Hoebeke P, et al.: Urinary Tract Infections in Children: EAU/ESPU Guidelines. Eur Urol. 2015; 67(3): 546–558. PubMed Abstract | Publisher Full Text\n\nWang P, Djahangirian O, Wehbi E: Urinary Tract Infections and Vesicoureteral Reflux. Avery’s Dis. Newborn Tenth Ed. 2018; 31(11): 1308-1313.e2. Publisher Full Text\n\nChang SL, Shortliffe LD: Pediatric Urinary Tract Infections. Pediatr Clin North Am. 2006; 53(3): 379–400. PubMed Abstract | Publisher Full Text\n\nFreedman AL; Urologic Diseases in America Project: Urologic Diseases in North America Project: Trends in Resource Utilization for Urinary Tract Infections in Children. J Urol. 2005; 173(3): 949–954. PubMed Abstract | Publisher Full Text\n\nRemis RS, Gurwith MJ, Gurwith D, et al.: Risk Factors for Urinary Tract Infection. Am J Epidemiol. 1987; 126(4): 685–694. PubMed Abstract | Publisher Full Text\n\nSchaeffer AJ, Rajan N, Cao Q, et al.: Host Pathogenesis in Urinary Tract Infections. Int J Antimicrob Agents. 2001; 17(4): 245–251. PubMed Abstract | Publisher Full Text\n\nHailay A, Zereabruk K, Mebrahtom G, et al.: Magnitude and Its Associated Factors of Urinary Tract Infection among Adult Patients Attending Tigray Region Hospitals, Northern Ethiopia, 2019. Int J Microbiol. 2020; 2020: 8896990. PubMed Abstract | Publisher Full Text | Free Full Text\n\nShaikh N, Morone NE, Bost JE, et al.: Prevalence of Urinary Tract Infection in Childhood: A Meta-Analysis. Pediatr Infect Dis J. 2008; 27(4): 302–308. PubMed Abstract | Publisher Full Text\n\nAwais M, Rehman A, Baloch NUA, et al.: Evaluation and Management of Recurrent Urinary Tract Infections in Children: State of the Art. Expert Rev Anti Infect Ther. 2015; 13(2): 209–231. PubMed Abstract | Publisher Full Text\n\nWorld Health Organization: Urinary tract infections in infants and children in developing countries in the context of IMCI. (accessed Apr 1, 2021). Reference Source\n\nOkarska-Napierała M, Wasilewska A, Kuchar E: Urinary tract infection in children: Diagnosis, treatment, imaging - Comparison of current guidelines. J Pediatr Urol. 2017; 13(6): 567–573. PubMed Abstract | Publisher Full Text\n\nRezaei-tavirani M, Ghafourian S, Sayehmiri F, et al.: Prevalence of Cotrimoxazole Resistance Uropathogenic Bacteria in Iran: A Systematic Review and Meta-Analysis. 2018; 13(5): e63256. Publisher Full Text\n\nHrbacek J, Cermak P, Zachoval R: Current Antibiotic Resistance Trends of Uropathogens in Central Europe: Survey from a Tertiary Hospital Urology Department 2011 – 2019. Antibiotics (Basel). 2020; 9(9): 630. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFeld LG, Mattoo TK: Urinary Tract Infections and Vesicoureteral Reflux in Infants and Children. Pediatr Rev. 2010; 31(11): 451–463. PubMed Abstract | Publisher Full Text\n\nLarcombe J: Urinary Tract Infection in Children. BMJ Clin Evid. 2010; 2010: 0306. PubMed Abstract | Free Full Text\n\nClark CJ, Kennurruedy WA, Shortliffe LD: Urinary Tract Infection in Children: When to Worry. Urol Clin North Am. 2010; 37(2): 229–241. PubMed Abstract | Publisher Full Text\n\nSchlager TA: Urinary Tract Infections in Infants and Children. Microbiol Spectr. 2016; 4(5). PubMed Abstract | Publisher Full Text\n\nHuynh G, Huynh QHN, Nguyen NHT, et al.: Malnutrition among 6-59-Month-Old Children at District 2 Hospital, Ho Chi Minh City, Vietnam: Prevalence and Associated Factors. Biomed Res Int. 2019; 2019: 6921312. PubMed Abstract | Publisher Full Text | Free Full Text\n\nJuma OA, Enumah ZO, Wheatley H, et al.: Prevalence and Assessment of Malnutrition among Children Attending the Reproductive and Child Health Clinic at Bagamoyo District Hospital, Tanzania. BMC Public Health. 2016; 16(1): 1094. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCharan J, Biswas T: How to Calculate Sample Size for Different Study Designs in Medical Research? Indian J Psychol Med. 2013; 35(2): 121–6. PubMed Abstract | Free Full Text\n\nFredrick F, Francis JM, Fataki M, et al.: Aetiology, Antimicrobial Susceptibility and Predictors of Urinary Tract Infection among Febrile under-Fives at Muhimbili National Hospital, Dar Es Salaam-Tanzania. African J Microbiol Res. 2013; 7(12): 1029–1034. Reference Source\n\nClean Catch Urine Collection Guidelines for Males and Females. (accessed Apr 1, 2021). Reference Source\n\nWilson ML: General Principles of Specimen Collection and Transport. Clin Infect Dis. 1996; 22(5): 766–777. PubMed Abstract | Publisher Full Text\n\nSangeda RZ, Franco P, Mtweve DM: Dataset for a Cross-Sectional Study on the Prevalence of Urinary Tract Infections and Antibiogram of Uropathogens Isolated from under-Five Children Attending Bagamoyo District Hospital in Tanzania - Dataset. Mendeley Data. 2021. http://www.doi.org/10.17632/ktzzsfvt79.3\n\nde Toro-Peinado I, Concepción Mediavilla-Gradolph M, Tormo-Palop N, et al.: Microbiological Diagnosis of Urinary Tract Infections. Enferm Infecc Microbiol Clin. 2015; 33 Suppl 2: 34–39. PubMed Abstract | Publisher Full Text\n\nMsaki BP, Mshana SE, Hokororo A, et al.: Prevalence and Predictors of Urinary Tract Infection and Severe Malaria among Febrile Children Attending Makongoro Health Centre in Mwanza City, North-Western Tanzania. Arch Public Health. 2012; 70(1): 4. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWatson R: General Microbiology Laboratory Manual. (accessed Mar 31, 2021). Reference Source\n\nCLSI: Performance Standards for Antimicrobial Susceptibility Testing; Twenty-Fifth Informational Supplement. Document M100-S25. Wayne, PA: Clinical and Laboratory Standards Institute. 2015.\n\nBauer AW, Kirby WM, Sherris JC, et al.: Antibiotic Susceptibility Testing by a Standardized Single Disk Method. Am J Clin Pathol. 1966; 45(4): 493–496. PubMed Abstract | Publisher Full Text\n\nMasika WG, O’Meara WP, Holland TL, et al.: Contribution of Urinary Tract Infection to the Burden of Febrile Illnesses in Young Children in Rural Kenya. PLoS One. 2017; 12(3): e0174199. PubMed Abstract | Publisher Full Text | Free Full Text\n\nIbeneme CA, Oguonu T, Okafor HU, et al.: Urinary Tract Infection in Febrile under Five Children in Enugu, South Eastern Nigeria. Niger J Clin Pract. 2014; 17(5): 624–8. PubMed Abstract | Publisher Full Text\n\nReed RP, Wegerhoff FO: Urinary Tract Infection in Malnourished Rural African Children. Ann Trop Paediatr. 1995; 15(1): 21–26. PubMed Abstract | Publisher Full Text\n\nUwaezuoke SN, Ndu IK, Eze IC: The Prevalence and Risk of Urinary Tract Infection in Malnourished Children: A Systematic Review and Meta-Analysis. BMC Pediatr. 2019; 19(1): 261. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAiyegoro OA, Igbinosa OO, Ogunmwonyi IN, et al.: Incidence of Urinary Tract Infections (UTI) among Children and Adolescents in Ile-Ife Nigeria. African J Microbiol Res. 2007; 1(2): 13–19. Reference Source\n\nGunduz S, Uludağ Altun H: Antibiotic Resistance Patterns of Urinary Tract Pathogens in Turkish Children. Glob Health Res Policy. 2018; 3(1): 10. PubMed Abstract | Publisher Full Text | Free Full Text\n\nIregbu KC, Nwajiobi-Princewill PI: Urinary Tract Infections in a Tertiary Hospital in Abuja, Nigeria. African J Clin Exp Microbiol. 2013; 14(3). Publisher Full Text\n\nRodríguez-Lozano J, de Malet A, Cano ME, et al.: Antimicrobial Susceptibility of Microorganisms That Cause Urinary Tract Infections in Pediatric Patients. Enferm Infecc Microbiol Clin (Engl Ed). 2018; 36(7): 417–422. PubMed Abstract | Publisher Full Text\n\nFesto E, Kidenya BR, Hokororo A, et al.: Predictors of Urinary Tract Infection among Febrile Children Attending at Bugando Medical Centre Northwestern, Tanzania. 2011; 2(5): 1–7. Reference Source"
}
|
[
{
"id": "119583",
"date": "03 Mar 2022",
"name": "Aseer Manilal",
"expertise": [
"Reviewer Expertise Medical Microbiology"
],
"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 relates to a research manuscript entitled \"Prevalence of urinary tract infections and antibiogram of uropathogens isolated from children under five attending Bagamoyo District Hospital in Tanzania: A cross-sectional study.\" Overall, the manuscript is not well written, and should be revised with the help of native English speakers.\nTitle: It is broad, please modify the title.\n\nAbstract:\nBackground should narrate the problem existing.\n\nMethodology is incomplete; must include the sampling technique employed, techniques used for disc diffusion assay.\n\nDetails of descriptive and inferential statistics, Statistical software used. Compress the biochemical tests employed.\n\nResults; please pinpoint the most relevant results rather than incurious findings.\n\nSpeciation of major bacteria has to be done; Please write the scientific names of bacterial pathogens in the correct form all over the manuscript and in the References section (should be italic).\n\nAssociated factors have to be mentioned.\n\nSince it is a cross-sectional study, variables have to be analyzed by odds ratio and logistic regression.\n\nConclusion: Has to be revised by specifying the overall findings.\n\nIntroduction:\nIntroduction: It needs to be more informative; It is too general and shallow.\n\nClearly state the problem, causes and outcomes in the African or Tanzanian context rather than USA.\n\nResearch gap existing in the study area.\n\nUropathogens: Give a hint about the virulence factors of uropathogens and its drug resistance and eventually the complications. Factors associated with UTI in children in detail.\n\nMethodology:\nDate of the study has to precisely mentioned ie., date.\n\nWhy do the authors choose convenient sampling technique? Results couldn’t be generalize; high possibility of under or over presentation and results would be biased.\n\nInclusion criteria should be elaborated.\n\nExclusion criteria is incomplete and obscure.\n\nSample size calculation; why didn’t the authors included the non-response rate.\n\nIn this study, a total of 214 patients were evaluated in a short period. In the literature, there are well-designed studies with a larger number of cases on this subject. Why is the sample size too low?\n\nIn addition, patients should have been evaluated with at least urinary USG or uroflowmetry.\n\nSample collection parts have to be rewriten in a standard way.\n\nAdd the company, city, and country of the used bacterial media and reagents that were used in the biochemical identification of isolates. Also, enumerate all used biochemical reactions.\n\nHave you checked the data quality?\n\nAntimicrobial susceptibility testing:\nAdd the names of the antimicrobial classes of the tested antibiotics.\n\nStatistical analysis must be included, odds of ratio and logistic regression.\n\nResults:\nAre not well written.\n\nAdd this subtitle: Phenotypic characteristics of the recovered isolates.\n\nThe authors are advised to classify the tested isolates to MDR , XDR, and PDR as described by Magiorakos et al.\n\nDiscussion\nNeed substantial improvement.\n\nPlease improve the main conclusion of the manuscript.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? 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?\nNo\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
}
] | 1
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https://f1000research.com/articles/10-449
|
https://f1000research.com/articles/10-448/v1
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07 Jun 21
|
{
"type": "Software Tool Article",
"title": "scNetViz: from single cells to networks using Cytoscape",
"authors": [
"Krishna Choudhary",
"Elaine C. Meng",
"J. Javier Diaz-Mejia",
"Gary D. Bader",
"Alexander R. Pico",
"John H. Morris",
"Krishna Choudhary",
"Elaine C. Meng",
"J. Javier Diaz-Mejia",
"Gary D. Bader",
"Alexander R. Pico"
],
"abstract": "Single-cell RNA-sequencing (scRNA-seq) has revolutionized molecular biology and medicine by enabling high-throughput studies of cellular heterogeneity in diverse tissues. Applying network biology approaches to scRNA-seq data can provide useful insights into genes driving heterogeneous cell-type compositions of tissues. Here, we present scNetViz — a Cytoscape app to aid biological interpretation of cell clusters in scRNA-seq data using network analysis. scNetViz calculates the differential expression of each gene across clusters and then creates a cluster-specific gene functional interaction network between the significantly differentially expressed genes for further analysis, such as pathway enrichment analysis. To automate a complete data analysis workflow, scNetViz integrates parts of the Scanpy software, which is a popular Python package for scRNA-seq data analysis, with Cytoscape apps such as stringApp, cyPlot, and enhancedGraphics. We describe our implementation of methods for accessing data from public single cell atlas projects, differential expression analysis, visualization, and automation. scNetViz enables users to analyze data from public atlases or their own experiments, which we illustrate with two use cases. Analysis can be performed via the Cytoscape GUI or CyREST programming interface using R (RCy3) or Python (py4cytoscape).",
"keywords": [
"scRNA-seq",
"Single cell",
"Expression analysis",
"Cytoscape",
"App",
"Network biology"
],
"content": "Introduction\n\nSingle-cell RNA sequencing (scRNA-seq) has yielded significant insights into mechanisms regulating diverse biological systems.1 This technology captures transcriptome-wide expression profiles of single cells, which can be used to cluster cells and identify the biological features that distinguish the clusters.2 With continued technological advances and cost efficiencies, scRNA-seq is becoming increasingly common and new data are being generated at a rapid pace. Global efforts such as the Human Cell Atlas,3 which aims to map a healthy human, and the EMBL-EBI Single Cell Expression Atlas,4 which organizes published datasets across multiple species and provides access to results from standardized analyses, are growing rapidly. To study cell types in scRNA-seq data, it is useful to compare cell clusters to identify cell-type-specific gene expression markers and genes associated with a phenotype.2,5 Such analysis typically provides a ranking of genes based on the statistical significance of differential expression. Besides this, applying network biology approaches can yield helpful insights for biomedical applications.6,7,8,9 In this direction, some methods enable inference of cell-type-specific regulatory networks from the experimental data.10,11,12,13 In contrast, another approach is to filter gene networks from independent experiments or public databases using single-cell data for cell-type-specific insights.7,14\n\nPublic databases such as the STRING database15 contain high-quality and well-organized information about published interaction networks. Here, we describe scNetViz— an interactive desktop Java application that harnesses the extensive network visualization and analysis capabilities of Cytoscape for single-cell data analysis.16,17 scNetViz takes a network filtering approach as mentioned above. It enables users to load their own scRNA-seq data or pull such data from public atlases, cluster cells, run differential gene expression analysis, perform dimensionality reduction of expression matrices for data visualization, generate heatmaps and violin plots of gene expression data, and examine the associated gene interaction networks from the STRING database. Below, we describe the methods implemented in scNetViz, provide two use cases to illustrate the user interface and programmatic access using R and Python, and discuss plans for future development. scNetViz enables scientists who may not be experts in scripting to explore the data and to develop biological hypotheses. Further, it provides a convenient interface for integrating gene network information with scRNA-seq datasets, which can save time for researchers.\n\n\nMethods\n\nscNetViz consists of two main components, a Java-based Cytoscape app and a web service implemented on a compute cluster at the Resource for Biocomputing, Visualization and Informatics (RBVI) at the University of California, San Francisco. In addition, the app portion uses several other Cytoscape apps, including stringApp,18 cyPlot,19 and enhancedGraphics.20\n\nThe Cytoscape app provides the following functionality:\n\n\n\n1. Acts as the graphical front-end for scNetViz, including providing various dialogs for interactive users and commands for automation uses.\n\n2. Manages all of the data that has been imported. This includes acting as a client for the Single Cell Expression Atlas4 and Human Cell Atlas3 data portal REST services as well as providing users the option to import single cell expression matrices and category data (e.g. tissue, cluster information, experimental condition, etc.) from local files.\n\n3. Calculates the differential gene expression for a chosen category (e.g. a specific clustering resolution or sample characteristic such as disease vs. non disease): a separate calculation for each group of cells (e.g. cluster) within that category vs. the set of all other cells (e.g. clusters) within that same category.\n\n4. Fetches functional association networks from STRING for the protein products of significantly differentially expressed genes.\n\n5. Interfaces with the RBVI web service described above to calculate cell plots based on UMAP21 or t-SNE.22\n\n6. Provides a Java-based implementation of t-SNE for smaller experiments (can be faster than the web service).\n\n7. Interfaces with cyPlot, a Cytoscape app that displays various plots in the Cytoscape web browser, to visualize all UMAP and t-SNE embeddings as well as volcano plots and heatmaps.\n\n8. Finally, it also interfaces with the RBVI web service to calculate clusters based on either the Louvain or Leiden algorithms as implemented in Scanpy.23\n\nThe RBVI web service component provides a simple wrapper around Scanpy that exposes REST endpoints for:\n\n\n\n1. Calculating a UMAP embedding of an scRNA-seq matrix,\n\n2. Calculating a tSNE embedding of an scRNA-seq matrix,\n\n3. Calculating a Leiden clustering of an scRNA-seq matrix,\n\n4. Calculating a Louvain clustering of an scRNA-seq matrix.\n\nMatrices are passed as compressed MatrixMarket files24 and parameters may be provided to simplify and normalize the matrix in a pre-processing step, in addition to parameters related to the appropriate algorithm.\n\nThe Cytoscape App provides the main front-end, data management, and orchestration for scNetViz. Importantly, the app also exports Cytoscape commands so that scNetViz can be used by CyREST25 packages such as RCy326 and py4cytoscape.27 Below, we discuss five of the app functions: data access, differential gene expression calculation, plot generation, network creation, and automation via R and Python. The various user interface components are all implemented in Java Swing, use the Cytoscape Java Desktop API, and are shown in the use case descriptions.\n\nscNetViz supports three types of data: cell by gene matrices (typically read in MatrixMarket format), experiment-level metadata including organism, number of cells in the experiment, and category-level metadata such as cell cluster assignments, disease state, cell type, tissue, ethnicity, which is typically in comma-separated value (CSV) format. scNetViz has a sources module, which includes submodules for each supported data source. A source module provides the tasks necessary to import data for an experiment or category, enumerates the available experiments and displays them. We have currently implemented support for three sources: EMBL-EBI’s Single Cell Expression Atlas, the Human Cell Atlas data portal, and local files. The former two are public sources and are referred to as GXA and HCA, respectively, in scNetViz commands. They provide support for browsing experiments, while the local source provides methods to read category and experiment files. Since different category data might be in a different orientation (typically clusterings files are organized with the clusters in rows and cells in columns, but cell metadata and demographics are organized with the cells in rows and categorical information in the columns), we provided the ability to read in the CSV and transpose the resulting matrix, which may be needed to feed the data to downstream analysis steps.\n\nTo import data from the two public repositories, we rely on their published REST interfaces. The Single Cell Expression Atlas provided the simplest interface as specific endpoints for the matrices, clusters, and experimental-design:\n\n• To enumerate all experiments:\n\n• To import an experiment:\n\n• To import the clusters provided:\n\n• To import the experimental design:\n\nData access from the Human Cell Atlas recently transitioned to a new data coordination platform (DCP) API. scNetViz currently uses the ”DCP1” API, and we will transition to ”DCP2” in the near future. To access the DCP1 data:\n\n• We can enumerate all experiments using the URL: https://service.azul.data.humancellatlas.org/index/projects?catalog=dcp1 but, unlike the Single Cell Expression Atlas, the Human Cell Atlas contains raw data (e.g. Fastq and BAM files) as well as calculated matrices. To restrict our enumeration to include only matrix data, we need to include a filter, which is encoded as part of the URL. We use the following filter.\n\n\n\nIt is encoded in the URL as using the ”filters” query option: https://service.azul.data.humancellatlas.org/index/projects?catalog=dcp1\\&filters={\"fileFormat\":{\"is\":[\"matrix\"]}}. This query results in a JSON file that includes metadata about each experiment and a link to the expression matrix file itself. Because in the Human Cell Atlas a single ”Project” may include multiple matrices, one for each tissue or organ that was investigated, we split those projects into independent experiments.\n\n• To load the experiment data, we follow the URL provided by the experiment-level metadata. The result is a zip file that contains the matrix itself in MatrixMarket format, the gene identifiers, and a file that contains both the cell barcodes and categorical data for each cell.\n\nAs shown below, the key function of scNetViz is to calculate the differential expression of each gene across categories and then use the highly differentially expressed genes (possible marker genes) to construct a gene functional interaction network. We calculate differential gene expression using Mann-Whitney U test and represent it as the log2(fold change) where fold change is the ratio of the mean expression of a gene in a single group within a category vs. the mean expression of that gene in the comparison set of all other groups within that same category. For example, if the chosen category is a clustering with K=5 classes, then each of the five classes is one group within the category. We provide two cutoff values to reduce noise in the resulting gene interaction network. First, a gene must be expressed in at least 10% of the cells in the group or 10% of the cells in the set of all other groups in the category. Second, we have a minimum log2(fold change) cutoff that drops any changes that are beneath that threshold. All of this data is provided in a table that is created and provided to the user.\n\nAll of the plots provided by scNetViz are generated by the cyPlot Cytoscape App.19 cyPlot uses the built-in Cytoscape web browser and the plotly.js Javascript library to display plots. All of the data is passed to cyPlot using its automation interface. For example, below is the scNetViz method to create a violin plot.\n\n\n\nAll of the arguments in the above code chunk are JSON strings that are consumed by cyPlot and passed on to the plotly.js library for display.\n\nOnce the calculation of differential expression is complete, scNetViz can create networks to show the functional interactions among the proteins encoded by the differentially expressed genes. This proceeds in two steps. First, the STRING network of a user-specified number (default 200) of top differentially expressed genes for each group within the category is created by using the Cytoscape automation interface of the stringApp. The method that does this is:\n\n\n\nThis creates the argument map and then calls the executeCommand method, which is a wrapper method that we implemented around the Cytoscape org.cytoscape.command.CommandExecutorTaskFactory. The stringApp queries STRING and creates the network. The second part of the process extracts significantly differentially expressed genes in a single group from the network that contains the top differentially expressed genes in a category. This is done using the Cytoscape API to create subnetworks and provide styles that color nodes based on their differential expression in a given group.\n\nSimilar to the automation functionality that scNetViz uses, described above, scNetViz provides its own automation commands, useful for scripts to control scNetViz operations. The following is a list of available commands (details available in the Swagger documentation (Help → Automation → CyREST Command API)).\n\n\n\nList of scNetViz Commands\n\n\n\nAs an example workflow, one might execute the following commands:\n\n\n\nAs discussed above, the web service component is primarily a wrapper around Scanpy that exposes a limited set of the Scanpy functionality appropriate to the needs of scNetViz. In each case, the web service collects the data and arguments, calls Scanpy pre-processing routines as appropriate, and then calls the Scanpy implementation of the algorithm. By default, the matrix will be normalized, log-transformed, restricted to only the most variable genes, and scaled. The default minimum of 100 genes/cell and a minimum of at least 1 cell for each gene are also used. The parameters to control pre-processing may be changed by opening up the Advanced pre-processing parameters section of the UMAP, t-SNE, Louvain, or Leiden dialogs, which enables the user to change any of the pre-processing defaults.\n\nThe web service implements the algorithms using the appropriate scanpy.tl methods (scanpy.tl.tsne, scanpy.tl.umap, scapy.tl.leiden, and scanpy.tl.louvain). In all cases, the matrix is pre-processed and passed to the appropriate Scanpy module. We expose the most useful parameters in each case. For UMAP, we expose the number of neighbors and the minimum distance parameters; for t-SNE, we expose the perplexity, the number of initial dimensions, the early exaggeration parameter and the learning rate. Note that if the number of initial dimensions is set to -1, a PCA will be calculated first to reduce the dimensionality of the matrix, which can improve the resulting t-SNE embedding. For Leiden and Louvain, we expose the number of neighbors to use to calculate the neighborhood graph before clustering (see scanpy.pp.neighbors). See the Scanpy documentation for a more detailed explanation of the effects of these routines and parameters.\n\nWe have prioritized providing access to the Single Cell Expression Atlas and Human Cell Atlas.3,4 Additionally, researchers can import normalized and clustered scRNA-seq data from local files. The following workflows demonstrate two use cases using either the Single Cell Expression Atlas or local files, and illustrate the utility of scNetViz in integrating network information with scRNA-seq data. Scripted versions of these workflows are also available as R Markdown documents and Jupyter notebooks, which leverage the RCy326 and py4cytoscape27 packages, respectively. They require Cytoscape (3.7.1 or later), CyREST (3.8.0 or later), and R (version 4.0 or later) or Python (version 3.6 or later). User documentation is available at: https://www.cgl.ucsf.edu/cytoscape/scNetViz/index.shtml. Downloadable notebooks of these workflows are available in R and Python at http://automation.cytoscape.org.\n\nIn this example, we will browse the Single Cell Expression Atlas from within Cytoscape, explore a particular dataset, perform differential expression analysis based on one of the provided cell annotation categories, generate networks from the top differentially expressed genes for each group within the chosen category, and functionally characterize and visualize the networks.\n\n\n\n1. Click the icon in the Cytoscape toolbar. This opens the Single Cell Experiment Atlas browser. For illustration, let us select the experiment with Accession E-GEOD-81383, which contains data on three human melanoma cell lines.28 This is a dataset of 226 cells from short-term cultures of cell lines derived from subcutaneous metastases. To find this experiment, click the column header labelled Accession and search for E-GEOD-81383 in the resulting table sorted by accession numbers. Select the row with the accession number E-GEOD-81383 by clicking on it. Note that all the steps of this workflow except for functional enrichment analysis can be executed by selecting an experiment and clicking the button labeled Create Networks in the Browse interface. Default parameters for the differential expression analysis and network creation steps can be altered by clicking the gear icon.\n\n2. Click the button labeled View Data. This loads the data and opens an experiment table with three tabs.\n\n\n\nThe Categories tab lists the annotation categories of cells available in the experiment, which represent grouping of cells by cluster labels for this dataset but may represent grouping by cell types or other criteria. Throughout this manuscript, categories refers to cell annotation categories. There are two options listed under Available categories. ”Cluster” is the unsupervised grouping of cells computed by the Single Cell Experiment Atlas using the Louvain algorithm29 for a range of resolution parameters. Each value of the resolution parameter yields a different number of clusters, which is called the K value (second column of the displayed table as in Figure 1). In keeping with EBI’s practice, by default, scNetViz selects the K value corresponding to the resolution of 1 for differential analysis and visualization (indicated with a TRUE value corresponding to the selected K in the column titled sel.K; see Figure 1).30 The other columns show single cell identifiers and their cluster memberships. To get the table of differentially expressed genes press the button labeled Calculate Diff Exp. This initiates a comparison of each cluster for K=5 with other clusters.\n\nThe results are displayed in the DiffExp tab. Click the Create Networks button. This fetches protein-protein networks for the proteins encoded by genes that satisfy the Network Analysis cutoffs based on FDR (maximum false discovery rate), Log2FC (minimum absolute value of log base 2 of the fold change in expression), and Max genes (maximum number of selected proteins; see Figure 2).\n\n3. The networks are listed in the Control Panel (left side) and individually displayed in the main Cytoscape Desktop window ( Figure 3). There are six networks, one for each of the five clusters and one for all the clusters collectively. Select the part of the network that is of interest by holding down the left mouse button on the canvas background and dragging the mouse while holding down the Shift or Ctrl key (Command on Mac).\n\n4. Along the right edge of the Cytoscape window in the Results Panel, click on the STRING tab (see Figure 3). Click on the button labeled Functional Enrichment to retrieve the enriched pathways and ontology terms in the selected part of the network. The results are displayed in the STRING Enrichment tab in the Node Table at the bottom. They can be filtered for, say, pathway terms using the Filter enrichment table option located on the top left of the tab and represented with a black funnel icon.\n\nThe menu labeled New Cell Plot contains options for generating UMAP and t-SNE plots. Note that these results are for data from the Single Cell Expression Atlas release 15 (March, 2021).\n\nThe illustration shows the interaction network for genes specific to the group labeled ”Cluster 4”. Users can filter the complete network using the network analysis tools in Cytoscape. (a) A selection of the largest connected component, which is highlighted with yellow nodes and red edges. (b) Other sub-networks might also be of interest. The second-largest connected component of Cluster 4 shows enrichment of melanoma-associated terms, which is consistent with the fact that this experiment is on melanoma cell lines.\n\nIn this example, we will import normalized scRNA-seq data and cluster assignments from local files, visualize all cells in a UMAP plot, perform differential expression analysis based on one of the provided categories, visualize as a combined gene expression heat map, and generate networks for the most significantly differentially expressed genes from each group within the chosen category.\n\n\n\n1. Choose Apps → scNetViz → Load Experiment → Import from file from the menu, then browse to locate and open a zip, tar.gz, tgz, or gzip file of the three MatrixMarket files (.mtx, .mtx_cols, .mtx_rows) comprising a normalized scRNA-seq quantification dataset. These files can be obtained by normalizing standard outputs from an scRNA-seq processing software such as CellRanger.31 For illustration, we use an experiment on 329 cells at different time points of differentiation starting from human embryonic stem cells (download the normalized counts files and clustering results for accession ID E-GEOD-109979 from the Single Cell Expression Atlas32). In the dialog, select the species, which is Homo sapiens for this data.\n\n2. From the window with the experiment table, load the downloaded clustering results as category data using the Import from file option in the menu under Add Category. Alternatively, select the option for Louvain clustering or Leiden clustering from this menu to perform unsupervised clustering of the cells.\n\n3. From the Categories tab, select the row with the grouping of cells that should be highlighted on the UMAP plot. Select the UMAP option from the New Cell Plot menu. If required, change the options and press OK to view the UMAP plot ( Figure 4).\n\n4. Switch to the Categories tab on the experiment table window. Select a category by clicking its row and press Calculate Diff Exp. This switches the display to the Diff Exp tab.\n\n5. Select the Heatmap option from the View Plots menu on the Diff Exp tab. This generates a gene expression heatmap for genes that meet the filtering criteria ( Figure 5).\n\n6. Click the Create Networks button on the Diff Exp tab to fetch the protein functional interaction networks for the top genes.\n\nEach dot is a cell, and coloring is by cluster number. Note that the illustration shows results obtained from analysis with the default settings.\n\nNote that the illustration shows results obtained from analysis with the default settings.\n\n\nConclusion\n\nscNetViz is a Cytoscape app for identifying differentially expressed genes characteristic of cell clusters and displaying networks of the corresponding proteins for further analysis. This workflow aids interpretation of cell clusters from scRNA-seq and related single-cell resolution data. It provides several ways of plotting cells and gene expression data, e.g., heatmap, violin, t-SNE, and UMAP plots. We describe two use cases demonstrating its utility for integrating network information with local or public single-cell RNA sequencing data. Users can set the analysis parameters, save settings, analyze their own data or load data from public atlases, and interactively select gene sets or cell clusters for network analysis. scNetViz is highly portable to diverse computational systems via its GUI or CyREST services. It only has Cytoscape and its stringApp, cyBrowser, cyPlot and enhancedGraphics apps as dependencies. Compared with other single cell analysis tools it provides a user-friendly interface and no coding expertise is needed for its use.\n\nCurrently, scNetViz does not have options to normalize or batch-correct raw counts. To analyze their own data, users must input normalized and batch corrected data. The methods for normalization, batch correction, clustering, and differential expression analysis are under active development and benchmarking. As the standard workflow of analysis evolves, we will continue to integrate newer methods in scNetViz. For differential analysis, scNetViz only supports comparing a group of cells within a category with the set of cells in all other groups in that category combined (e.g. to identify cell-type-specific genes, or gene expression markers). In the future, we will support more general comparisons, including comparison of any two groups of cells provided or selected by the user. Future development will also enable excluding pseudogenes or other gene sets from the analysis. File formats are also evolving. For instance, the Loom format is becoming more popular. This format is not supported by scNetViz currently. As new standards are adopted for single-cell data, we will add support for them.\n\n\nSoftware availability\n\n\n\n• Software available from the Cytoscape App Store: https://apps.cytoscape.org/apps/scnetviz\n\n• Software code available from GitHub: https://github.com/RBVI/scNetViz\n\n• Archived source code at the time of publication: https://doi.org/10.5281/zenodo.4641480 33\n\n• License: Apache License, Version 2.0\n\n• Online manual: https://www.cgl.ucsf.edu/cytoscape/scNetViz/index.shtml\n\n• scNetViz Rmd and Python notebooks: http://automation.cytoscape.org\n\n\nData availability\n\nThe source data used for the use cases are available from Single Cell Expression Atlas.\n\n• Use Case #1: https://www.ebi.ac.uk/gxa/sc/experiments/E-GEOD-81383/downloads\n\n• Use Case #2: https://www.ebi.ac.uk/gxa/sc/experiments/E-GEOD-109979/downloads",
"appendix": "Acknowledgements\n\nWe thank Kristina Hanspers and Yihang Xin for testing the scNetViz Rmd and Python notebooks and providing feedback.\n\n\nReferences\n\nTanay A, Regev A: Scaling single-cell genomics from phenomenology to mechanism. Nature. 2017; 541(7637): 331–338. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLuecken MD, Theis FJ: Current best practices in single-cell RNA-seq analysis: a tutorial. Mol Syst Biol. 2019; 15(6): e8746. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRegev A, Teichmann SA, Lander ES, et al.: Science forum: the human cell atlas. Elife. 2017; 6: e27041. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPapatheodorou I, Moreno P, Manning J, et al.: Expression Atlas update: from tissues to single cells. Nucleic Acids Res. 2020; 48(D1): D77–D83. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAmezquita RA, Lun ATL, Becht E, et al.: Orchestrating single-cell analysis with Bioconductor. Nat Methods. 2020; 17(2): 137–145. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBlencowe M, Arneson D, Ding J, et al.: Network modeling of single-cell omics data: challenges, opportunities, and progresses. Emerg Top Life Sci. 2019; 3(4): 379–398. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCha J, Lee I: Single-cell network biology for resolving cellular heterogeneity in human diseases. Exp Mol Med. 2020; pages 1–11. PubMed Abstract | Publisher Full Text\n\nLee LY, Pandey AK, Maron BA, et al.: Network medicine in cardiovascular research. Cardiovasc Res. 2020. PubMed Abstract | Publisher Full Text\n\nShi H, Yan K-K, Ding L, et al.: Network approaches for dissecting the immune system. Iscience. 2020; page 101354. PubMed Abstract | Publisher Full Text | Free Full Text\n\nIacono G, Massoni-Badosa R, Heyn H: Single-cell transcriptomics unveils gene regulatory network plasticity. Genome Biol. 2019; 20(1): 110. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKamimoto K, Hoffmann CM, Morris S: CellOracle: Dissecting cell identity via network inference and in silico gene perturbation. bioRxiv. 2020. Publisher Full Text\n\nTurki T, Yh T: SCGRNs: Novel supervised inference of single-cell gene regulatory networks of complex diseases. Comput Biol Med. 2020; 118: 103656. PubMed Abstract | Publisher Full Text\n\nLi WV, Li Y: Inferring sparse gene co-expression networks from single-cell expression data. bioRxiv. 2020. Publisher Full Text\n\nMohammadi S, Davila-Velderrain J, Kellis M: Reconstruction of cell-type-specific interactomes at single-cell resolution. Cell Syst. 2019; 9(6): 559–568. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSzklarczyk D, Gable AL, Lyon D, et al.: STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res. 2019; 47(D1): D607–D613. PubMed Abstract | Publisher Full Text | Free 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; 13(11): 2498–2504. PubMed Abstract | Publisher Full Text | Free Full Text\n\nOtasek D, Morris JH, Bouças J, et al.: Cytoscape automation: empowering workflow-based network analysis. Genome Biol. 2019; 20(1): 1–15. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDoncheva NT, Morris JH, Gorodkin J, et al.: Cytoscape StringApp: network analysis and visualization of proteomics data. J Proteome Res. 2018; 18(2): 623–632. PubMed Abstract | Publisher Full Text | Free Full Text\n\nYih A, Baker L, Magee L, et al.: cyPlot: A utility to display data plots.Reference Source\n\nMorris JH, Kuchinsky A, Ferrin TE, et al.: enhancedGraphics: a Cytoscape app for enhanced node graphics. F1000Res. 2014; 3. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMcInnes L, Healy J, Melville J: Umap: Uniform manifold approximation and projection for dimension reduction. arXiv preprint arXiv:1802.03426. 2018.\n\nvan der Maaten L, Hinton G: Visualizing data using t-SNE. J Mach Learn Res. 2008; 9(Nov): 2579–2605.\n\nAlexander Wolf F, Angerer P, Theis FJ: SCANPY: large-scale single-cell gene expression data analysis. Genome Biol. 2018; 19(1): 1–5. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMatrix Market: File formats.Reference Source\n\nOno K, Muetze T, Kolishovski G, et al.: Turbocharging cytoscape access for external tools via a RESTful API. F1000Res. 2015; 4. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGustavsen JA, Pai S, Isserlin R, et al.: RCy3: network biology using cytoscape from within R. F1000Res. 2019; 8. PubMed Abstract | Publisher Full Text | Free Full Text\n\nOno K, Bouças J, Nishida K, et al.: py4cytoscape.Reference Source\n\nGerber T, Willscher E, Loeffler-Wirth H, et al.: Single cell RNA-seq of three human melanoma cell lines: Ma-Mel-123, Ma-Mel-108 and Ma-Mel-93.Reference Source\n\nBlondel VD, Guillaume J-L, Lambiotte R, et al.: Fast unfolding of communities in large networks. J Stat Mech: Theory Experiment. 2008; 2008(10): P10008. Publisher Full Text\n\nSingle Cell Expression Atlas help.Reference Source Accessed date: March 11, 2021.\n\nZheng GXY, Terry JM, Belgrader P, et al.: Massively parallel digital transcriptional profiling of single cells. Nat Commun. 2017; 8(1): 1–12. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLu J, Baccei A, da Rocha EL, et al.: Single-cell RNA-seq of human H9 cells undergoing definitive endoderm differentiation.Reference Source\n\nMorris S, Pico A, mohamedzak: RBVI/scNetViz: v1.2.0 (Version v1.2.0). Zenodo. 2021, March 26. Publisher Full Text"
}
|
[
{
"id": "86919",
"date": "26 Jul 2021",
"name": "Luca Pinello",
"expertise": [
"Reviewer Expertise Computational 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\nChoudhary et al., present scNetViz a useful Cytoscape app to perform network analysis on single-cell RNA-seq data at cluster level.\nThe manuscript is well written and clear. The software is well documented with clear examples, use cases and nice illustrative figures.\nParticularly helpful is the possibility to load datasets from several public repositories (EMBL-EBI and Human Cell Atals) with simple dedicated functions.\nSome points to consider to improve the manuscript and software:\nThe documentation regarding the installation of the software. For example on OSX it is very tricky to install and use it since Java applications that are not signed are not allowed and a warning message is displayed. This may discourage several users, so it could be helpful to have step by step and explicit instructions that cover this case and also that assume a user doesn't have yet Cytoscape installed. On Windows 10 things are much easier and I was able to install it by using the Apps-> App Manager... function.\n\nThe search text are on the window \"Single cell Expression Atlas Browser\" doesn't work properly and I was not able to select E-GEOD-8138 with this function (it doesn't scroll automatically to the correct line).\n\nI was able to reproduce the analysis for E-GEOD-81383, however the tool failed to create a network for E-CURD-3 when clicking \"Create Networks \" (the first dataset presented on the provided list). If not all the datasets are supported, it would be helpful showing to the users only the ones where it is possible to create networks and explaining why it is not possible to build networks for some datasets.\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": "7726",
"date": "19 Jan 2022",
"name": "Krishna Choudhary",
"role": "Author Response",
"response": "We thank the reviewer for their time and thoughtful comments. We have addressed all the comments below. 1. The documentation regarding the installation of the software. For example on OSX it is very tricky to install and use it since Java applications that are not signed are not allowed and a warning message is displayed. This may discourage several users, so it could be helpful to have step by step and explicit instructions that cover this case and also that assume a user doesn't have yet Cytoscape installed. On Windows 10 things are much easier and I was able to install it by using the Apps-> App Manager... function. Response: Thank you for testing the installation of scNetViz on OSX and Windows platforms. Since scNetViz is one of many Cytoscape apps featured in this app article collection, we are assuming Cytoscape installation and familiarity. We recommend users to get the latest installation instructions directly from Cytoscape.org (and that is good because the instructions may change over time). 2. The search text are on the window \"Single cell Expression Atlas Browser\" doesn't work properly and I was not able to select E-GEOD-8138 with this function (it doesn't scroll automatically to the correct line). Response: The search works by highlighting all lines that contain the search string. Since there can be multiple result lines (e.g., when searching for a species), we did not design a scroll behavior. It is working as designed. However, based on your feedback, we will work on a new feature to either scroll to the first hit or filter the table for hits in order to improve the display of search results. 3. I was able to reproduce the analysis for E-GEOD-81383, however the tool failed to create a network for E-CURD-3 when clicking \"Create Networks \" (the first dataset presented on the provided list). If not all the datasets are supported, it would be helpful showing to the users only the ones where it is possible to create networks and explaining why it is not possible to build networks for some datasets. Response: Thank you for finding this bug. We could reproduce the error. The issue is related to the species (Plasmodium falciparum) not being recognized. We have opened a bug report to characterize the issue more thoroughly in order to either fix it or detect it ahead of time (like you suggested)."
}
]
},
{
"id": "98565",
"date": "15 Nov 2021",
"name": "Kenji Kamimoto",
"expertise": [
"Reviewer Expertise Computational Biology"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors have developed scNetViz, a Cytoscape-based software for constructing and analyzing cluster-specific protein-protein interaction networks from scRNA-seq data.\nscNetViz selects genes differentially expressed in each cluster based on scRNA-seq data and constructs a cluster-specific network by filtering the universal protein-protein interaction network registered in the STRING database. The system includes all necessary steps, including data search, download, clustering, network filtering, and visualization. All these operations can be performed with the GUI, enabling easy and intuitive network analysis.\nThe installation of scNetViz by Cytoscape's App Manager is simple, and I could install scNetViz without any trouble. The use cases presented in the paper help the reader to understand the typical usage of scNetViz, and they are described clearly. The analysis with a Single Cell Expression Atlas could be conducted without any problem.\nscNetViz creates a network by filtering the STRING protein-protein interaction network database. Although this concept is described in the introduction and later sections, it is not clear from the title and abstract of the paper (version 1). Thus, the title and abstract might make the wrong impression that scNetViz can infer a de novo gene regulatory network from scRNA-seq data rather than filtering the pre-existing network. Therefore, to clarify the concept of the scNetViz paper, I would like to recommend adding descriptions of the following points in the abstract or title.\nscNetViz is a network filtering analysis, not a de novo GRN inference algorithm.\n\nscNetViz uses protein-protein interaction network analysis, and it is not another GRN analysis such as co-expression or transcriptional gene regulatory network.\n\nIs the rationale for developing the new software tool clearly explained? Yes\n\nIs the description of the software tool technically sound? Yes\n\nAre sufficient details of the code, methods and analysis (if applicable) provided to allow replication of the software development and its use by others? Yes\n\nIs sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool? Yes\n\nAre the conclusions about the tool and its performance adequately supported by the findings presented in the article? Yes",
"responses": [
{
"c_id": "7727",
"date": "19 Jan 2022",
"name": "Krishna Choudhary",
"role": "Author Response",
"response": "We thank the reviewer for their time and thoughtful comments. While the difference between de novo GRN inference and networking filtering analysis is important to understand, it may cause more confusion than clarification to highlight this unrelated algorithm in the title and abstract. Hence, we believe that this detail is best described with literature references in the introduction where more space can be given to background and contextual topics. Perhaps we can specify “protein-protein interaction networks” in a future version of the abstract."
}
]
}
] | 1
|
https://f1000research.com/articles/10-448
|
https://f1000research.com/articles/9-704/v1
|
14 Jul 20
|
{
"type": "Case Report",
"title": "Case Report: Heparin-induced thrombocytopenia in a patient with COVID-19",
"authors": [
"Ragia Aly",
"Sachin Gupta",
"Sorab Gupta",
"Balraj Singh",
"Abhinav Goyal",
"Sheila Kalathil",
"Ragia Aly",
"Sorab Gupta",
"Balraj Singh",
"Abhinav Goyal",
"Sheila Kalathil"
],
"abstract": "With the spread of the novel coronavirus disease of 2019 (COVID-19) worldwide and associated high incidence of thromboembolic complications, the use of heparin is on the rise. It therefore is crucial to identify patients with contraindications for heparin. Heparin-induced thrombocytopenia (HIT) is a life-threatening complication of exposure to heparin. We report a 66-year-old woman, who was admitted to the hospital with COVID-19 infection. Her course was complicated by pulmonary embolism and dialysis catheter thrombosis. Our patient had a known history of HIT. Treatment of this patient with heparin would have been catastrophic. The COVID-19 pandemic has overwhelmed healthcare systems and is causing a global health crisis. Nevertheless, this case serves as a reminder of the importance of making every effort to obtain thorough history and review of records of every patient.",
"keywords": [
"Heparin-induced thrombocytopenia",
"COVID- 19"
],
"content": "Introduction\n\nThe severe acute respiratory illness caused by coronavirus disease of 2019 (COVID-19) disproportionately affects elderly and patients with multiple chronic comorbid conditions, making nursing home residents particularly vulnerable1. Altered mental status is a common presentation of acute illness in this patient population, creating a challenge for obtaining an accurate medical history. In a Chinese study, 14% of patients with severe COVID-19 were noted to have impaired consciousness2. There is also an alarmingly high incidence of thromboembolic complications, including pulmonary embolism, ischemic stroke and acute limb ischemia in COVID-19 patients3. Here, we report a 66-year-old woman with a known history of heparin-induced thrombocytopenia (HIT), who was admitted to the hospital with COVID-19 infection.\n\n\nCase report\n\nA 66-year-old woman with a medical history of end-stage renal disease on hemodialysis, type II diabetes mellitus, coronary artery disease and hypertension presented to the emergency department with fever, shortness of breath, cough, vomiting and abdominal pain. Vitals signs on presentation were as follows: temperature 101.2°F; heart rate of 102; blood pressure 152/76 mm hg; respiratory rate of 22/min; and oxygen saturation 93 on room air. On exam she was somnolent and confused and unable to provide previous medical history. Nasopharyngeal swab was positive for COVID-19. The patient’s blood work was unremarkable except for elevated blood urea nitrogen of 68 mg/dl (normal range 7–20 mg/dl) and creatinine of 11.1 mg/dl (normal range 0.8–1.2 mg/dl) and low platelet count of 119 ×103/mcL (normal range, 150-400 × 103/mcL). Of note, heparin was listed on the patient’s list of allergies, without further details.\n\nThe patient was admitted and started on hydroxychloroquine 400 mg every 12 hours for two doses followed by 200 mg every 12 hours for 5 days in addition to supportive measures, including acetaminophen 650 mg as needed for fever and supplemental oxygen. The patient’s regular hemodialysis schedule was also continued during her admission. A computed tomography pulmonary angiogram Figure 1 revealed pulmonary embolism in the left lower lobe, involving segmental and proximal subsegmental arteries without right heart strain or pulmonary infarction.\n\nGiven the history of allergy to heparin, the patient’s primary care provider was contacted to obtain further medical history and to confirm her heparin allergy. It was revealed that the patient was diagnosed with HIT a few weeks previously at a different facility. The patient was started on Argatroban infusion at starting rate of 2 mcg/kg/min, and this was adjusted regularly to maintain her activated partial thromboplastin time (aPTT) between 60 and 80 seconds.\n\nThe patient was hospitalized for a total of 14 days until she recovered from the acute illness, returned to her baseline mental status and was weaned off supplemental oxygen. her platelet count improved and she was transitioned to apixaban 2.5 mg twice daily (renally adjusted dose) to complete 3 months of anticoagulation. She returned to her skilled nursing facility on discharge, physical therapy was recommended on discharge due to generalized weakness and deconditioning. The patient had a virtual visit with the outpatient hematology clinic 6 weeks after discharge; she was tolerating treatment with apixaban with no adverse effects and her dyspnea had completely resolved.\n\n\nDiscussion\n\nCOVID-19, caused by SARS-COV-2, was declared a worldwide epidemic by the World Health Organization on March 11th, 20204. COVID-19 can present with a spectrum of clinical manifestations, including fever, myalgia, cough, dyspnea, and less frequently headache, diarrhea, nausea, and vomiting. Although respiratory symptoms predominate, thrombosis can also occur. The data collected from multiple centers worldwide have shown a high incidence of thromboembolic complications in patients with COVID-19. In a cohort study done by Helms et al., 64 out of 150 patients, who developed acute respiratory distress syndrome (ARDS) secondary to SARS-COV-2 infection and were admitted to the Intensive Care Unit, developed thromboembolic complications, including pulmonary embolisms and ischemic strokes as well as circuit clotting during renal replacement therapy. The study also compared the incidence of pulmonary embolisms in patients with ARDS secondary to COVID-19 to that of patients with ARDS due to other etiologies, which was 11.7% compared to 2.1%, respectively3. In light of the available data, patients admitted to hospital with moderate to severe COVID-19 pneumonia, especially those with abnormal coagulation parameters including elevated D-Dimer levels5, are being treated with unfractionated heparin (UFH) or low molecular weight heparin (LMWH) in an effort to prevent and treat such potentially fatal complications6. Patients with severe COVID-19 infection often present with acute encephalopathy. In an observational study done by Mao et al., 36% of patients presenting with severe COVID-19 infections were encephalopathic on presentation7. Other neurological complications were also reported, including, but not limited to, encephalitis, acute myelitis, and Guillain-Barre syndrome8.\n\nHIT is one of the most serious complications related to heparin use, with a mortality rate that can reach up to 20%9. HIT is caused by autoantibody (IgG) that targets endogenous platelet factor 4 (PF4) and heparin complex. This PF4/IgG complex activates platelets and can trigger catastrophic venous and arterial thrombosis10. As the incidence of COVID-19 associated thromboembolic complication increases in patients with severe illness, the use of UFH and LMWH has increased. Consequently, it becomes crucial to identify patients with contraindications to the use of heparin.\n\nPatients with a history of HIT should avoid any forms of heparin exposure, which includes heparin flushes, heparin-bonded catheters, heparin-containing medications, such as prothrombin complex concentrates, some intravenous medication formulations, and some total parenteral nutrition preparations. With the increasing numbers of patients with severe COVID-19 pneumonia being admitted to intensive care units worldwide, the use of some of the previously mentioned heparin-containing treatments is on the rise. Patients with severe COVID-19 often present with encephalopathy and may require intubation and mechanical ventilation; both factors pose a challenge to obtaining complete medical history. Moreover, most hospitals have prohibited visitors during the pandemic, which is another barrier to obtaining history from patients’ families. A diagnosis of HIT is a serious diagnosis that must be documented accurately on patients’ medical records and be reported at every point of care transition.\n\n\nConclusion\n\nIn conclusion, we report the case of a COVID-19 patient with a history of HIT, who developed pulmonary embolism, and the patient’s management. Our case and review of literature show that health care providers should be aware of life-threatening thromboembolic events associated with COVID-19, so that prompt and appropriate intervention can be undertaken. Our case also highlights the importance of history taking and thorough review of medical records in the COVID-19 pandemic to avoid catastrophic complications.\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 the publication of the case report and any associated images was obtained from the patient.",
"appendix": "References\n\nRichardson S, Hirsch JS, Narasimhan M, et al.: Presenting Characteristics, Comorbidities, and Outcomes Among 5700 Patients Hospitalized With COVID-19 in the New York City Area. JAMA. 2020; 323(20): 2052–2059. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMao L, Jin H, Wang M, et al.: Neurological Manifestations of Hospitalized Patients with COVID-19 in Wuhan, China: a retrospective case series study. JAMA Neurol. 2020; 77(6): 1–9. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHelms J, Tacquard C, Severac F, et al.: High risk of thrombosis in patients with severe SARS-CoV-2 infection: a multicenter prospective cohort study. Intensive Care Med. 2020; 46(6): 1089–1098. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWorld Health Organization (WHO): Coronavirus disease2019 (COVID-19). Situation Report— 51. 2020. Reference Source\n\nChen N, Zhou M, Dong X, et al.: Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study. Lancet. 2020; 395(10223): 507–513. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTang N, Li D, Wang X, et al.: Abnormal coagulation parameters are associated with poor prognosis in patients with novel coronavirus pneumonia. J Thromb Haemost. 2020; 18(5): 844–847. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMao L, Jin H, Wang M, et al.: Neurologic Manifestations of Hospitalized Patients With Coronavirus Disease 2019 in Wuhan, China. JAMA Neurol. 2020; 77(6): 1–9. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAhmad I, Rathore FA: Neurological manifestations and complications of COVID-19: A literature review. J Clin Neurosci. 2020; 77: 8–12. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSalter BS, Weiner MM, Trinh MA, et al.: Heparin-Induced Thrombocytopenia: A Comprehensive Clinical Review J Am Coll Cardiol. 2016; 67(21): 2519–2532. PubMed Abstract | Publisher Full Text\n\nFranchini M: Heparin-induced thrombocytopenia: an update. Thromb J. 2005; 3: 14. PubMed Abstract | Publisher Full Text | Free Full Text"
}
|
[
{
"id": "67133",
"date": "03 Sep 2020",
"name": "Vikramaditya Dumpa",
"expertise": [
"Reviewer Expertise Hematology",
"Pediatrics"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors describe a case of an elderly woman with multiple co-morbidities affected by COVID-19. The patient had thromboembolic complications resulting from COVID-19, and with a known history of heparin-induced thrombocytopenia, received treatment with other drugs thus avoiding further complications, This is a very timely and useful case report reminding health care providers to be conscious of potential allergies to drugs being used in the management of COVID-19 patients.\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": "77377",
"date": "15 Feb 2021",
"name": "Pooja Gogia",
"expertise": [
"Reviewer Expertise Oncology",
"Hematology"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 should include more detailed case report presentation including physical examination, pertinent labs including d-dimer, troponin and inflammatory markers. Chest Xray should be included as well.\n\nThe discussion should also be more comprehensive and be focusing on treatment options in patients with Heparin induced thrombocytopenia. A brief discussion about her prior HIT diagnosis and the reason for her prior admission would be appropriate.\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? Partly\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Partly\n\nIs the case presented with sufficient detail to be useful for other practitioners? Partly",
"responses": [
{
"c_id": "6735",
"date": "07 Jun 2021",
"name": "Sachin Gupta",
"role": "Author Response",
"response": "Author comments Thanks a lot for reviewing my manuscript. I made the changes as recommended. I have included detailed case report presentation including physical examination, pertinent labs including inflammatory markers and CT PE findings. HIT management along with reason of her prior admission were also discussed in detail."
}
]
}
] | 1
|
https://f1000research.com/articles/9-704
|
https://f1000research.com/articles/9-1245/v1
|
15 Oct 20
|
{
"type": "Research Article",
"title": "Retrospective evaluation of two-year results with a filtering trabeculotomy in comparison to conventional trabeculectomy by exact matching",
"authors": [
"Alicja Strzalkowska",
"Peter Strzalkowski",
"Yousef Al Yousef",
"Jost Hillenkamp",
"Franz Grehn",
"Nils A. Loewen",
"Alicja Strzalkowska",
"Peter Strzalkowski",
"Yousef Al Yousef",
"Jost Hillenkamp",
"Franz Grehn"
],
"abstract": "Background: To compare two-year results of a filtering trabeculotomy (FTO) to conventional trabeculectomy (TE) in open-angle glaucoma by exact matching. Methods: 110 patients received an FTO and 86 a TE. FTO avoided the need for an iridectomy due to a preserved trabeculo-descemet window anterior to the scleral flap. TE employed a trabecular block excision and iridectomy. Mitomycin C was used in both. FTO and TE were exact matched by baseline intraocular pressure (IOP) and the number of glaucoma medications. Complete and qualified success (IOP ≤18 mmHg and IOP reduction ≥ 30%, with or without medication) were primary endpoints. IOP, visual acuity (BCVA), complications and intervention were secondary endpoints. Results: 44 FTO were exact matched to 44 TE. The IOP baseline in both groups was 22.5±4.7 mmHg on 3±0.9 medications. At 24 months, complete success was reached by 59% in FTO and 66% in TE, and qualified success by 59% in FTO and 71% in TE. In FTO, IOP was reduced to 12.4±4.3 mmHg at 12 months and 13.1±4.1 mmHg at 24 months. In TE, IOP was 11.3±2.2 mmHg at 12 months and 12.0±3.5 mmHg at 24 months. Medications could be reduced at 24 months to 0.6±1.3 in FTO and 0.2±0.5 in TE. There were no significant differences between the two groups in IOP, medications, complications or interventions at any point. Conclusion: Modifying aqueous flow through a limited trabeculotomy in FTO yielded clinical outcomes similar to traditional TE but allowed to avoid an iridectomy.",
"keywords": [
"trabeculectomy",
"mitomycin C",
"trabeculotomy",
"exact matching",
"open-angle glaucoma",
"iridectomy"
],
"content": "Introduction\n\nSince the first description of a guarded filtering procedure in enucleated eyes by Grant in 19581, performance of this surgery in patients in 1961 by Sugar2, popularization of the term “trabeculectomy” in 1968 by Cairns3, and introduction of mitomycin-C as an antifibrotic to make it more effective4, trabeculectomy (TE) has remained a primary surgery in the treatment of glaucoma5. Over the years, multiple modifications of this surgery have been explored to improve its effectiveness, to make outcomes more predictable and to reduce postoperative complications and need for interventions. These modifications include, among others, variations in size, localization, and thickness of the scleral-flap, different suture techniques, variable intra- and postoperative treatment with antifibrotics or a combination of these approaches with one another6.\n\nIn this study, we combined elements of deep sclerectomy7,8 and trabeculotomy9 with TE in an attempt to improve conventional outflow as well as subconjunctival aqueous humor drainage. Encouraged by a pilot study of filtering trabeculotomy (FTO) with a complete success rate of 79%10, we hypothesized that FTO had a higher success rate and lower complication rate than TE. We applied advanced statistics, exact matching11,12, to enable a highly balanced comparison of our retrospective data with two-year follow-up.\n\n\nMethods\n\nThis retrospective study was approved by the ethics committee of the University of Würzburg, Germany (#2019101601AS). Because of its retrospective nature, informed consent was waived.\n\nAll primary open angle glaucoma (POAG) patients at the University Eye Hospital Würzburg who underwent a modified FTO with mitomycin C (MMC) or TE with MMC by a single surgeon (FG) between 2007 and 2014 were analyzed. The indication for surgery was a failure to control intraocular (IOP) despite maximally tolerated medical therapy.\n\nPatients were matched by baseline IOP and the number of glaucoma medications.\n\nFrom patient records, we obtained from 2019 to 2020 the medical history, the best-corrected visual acuity assessed (BCVA [logMAR]), IOP (Goldmann tonometry [mmHg]), topical glaucoma medications (including a glaucoma medication score (GMS)13), as well as postoperative events and complications. These included hypotony with choroidals, hypotony maculopathy, flat or shallow chamber, an IOP relatively high for surgical glaucoma (above 25 mmHg), bleb leakage, a persistently flat bleb indicating absent flow, hyphema, iris incarceration and need for cataract surgery. We computed the complete and qualified success, according to the guidelines set forth by the World Glaucoma Association14. In patients who had either TE or FTO in both eyes, the first eye was chosen to be included in the study. Complete success was defined as a postoperative IOP of ≤18 mmHg with a reduction of ≥30% from baseline without glaucoma medications. Qualified success was a postoperative IOP of ≤18 mmHg with a reduction of ≥30% from the baseline, achieved with or without glaucoma medications14. Follow-up visits occurred 7 days, 1 month, 3 months, 6 months, 12 months, and 24 months after surgery.\n\nThe exclusion criteria consisted of patients aged below 18 years, glaucoma types other than open-angle glaucomas, and a history of TE, trabeculotomy or glaucoma drainage device implantation.\n\nThe eye was rotated downward with a traction suture. A 5 mm fornix-based peritomy was made at the anatomic 12 o’clock position, and a sub-tenon pocket was fashioned to accommodate a sponge soaked with MMC at a concentration of 0.2 mg/ml and 100 µl volume for 3 minutes.\n\nIn TE, a 3 mm × 4 mm half scleral thickness flap was created. A 0.8 mm × 2 mm sclerotrabecular block was excised to enter the anterior chamber, as described before10. A peripheral iridectomy was made. The scleral flap was secured with 10.0 nylon to allow visible percolation of aqueous, and the conjunctiva was closed with an interlocking running suture resulting in a diffusely forming bleb15.\n\nIn FTO, the scleral flap was sized 4 mm × 4 mm. A smaller, tongue-shaped flap was dissected underneath to unroof and create access ostia to Schlemm’s canal. This second flap was excised similar to deep sclerectomy. The canal was probed with a metal trabeculotomy probe (Mackensen, Geuder Inc., Heidelberg) on both sides while the trabeculo-descemet window at the base of the scleral flap was preserved so that no bulk aqueous outflow could occur and no iridectomy was needed. The remaining steps were identical to those in TE.\n\nPostoperative drops consisted of dexamethasone six times for the first week, which was tapered by one drop per week. Ciprofloxacin eye drops were applied four times a day for one week. All patients received 5 mg of 5-FU (0.1 cc volume) daily for a week unless IOP was below 5 mmHg or a Seidel-positive bleb leak or a corneal erosion was present. 5-FU was also given once a week for the first month during return visits using the same criteria.\n\nStatistical analyses were performed using Statistica 13.1 (StatSoft, Tulsa, Oklahoma, United States) and MedCalc (MedCalc 19.1.3, Ostend, Belgium). A total of 88 patients (1:1, FTO:TE) were matched with exact matching11,12 based on the baseline IOP and glaucoma medications.\n\nCategorical variables were described as the frequency with percentage, whereas continuous and discrete variables as mean with standard deviation (SD) or median with range. The chi-squared test or Fisher’s exact test was used for the analysis of categorical variables. Continuous variables were compared using Student’s t-test or Mann–Whitney U test, whereas discrete variables were compared using Mann-Whitney U test. The distribution of continuous variables was determined by the Shapiro-Wilk test, equality of variances by Levene’s test. Assessment of repeated measures for IOP was performed using repeated measures MANOVA and Tukey’s test, while visual acuity (logMAR) and medications were examined using the Friedman test and Wilcoxon signed-rank test. The success of treatment was expressed by a Kaplan-Meier curve and compared between treated groups using the log-rank test. The success of treatment at particular a given time point was determined by odds ratio (OR) with respective 95% confidence intervals and p-values. P-values below 0.05 were considered statistically significant.\n\n\nResults\n\nA total of 196 patients were included. The unmatched demographic data of FTO and TE had significant differences in preoperative IOP (p=0.017), glaucoma medication score (p=0.001), and pseudophakia (p=0.012). In total 88, eyes (44 in each group) could be matched as exact pairs eliminating key differences in IOP and medications. The IOP at baseline was 22.6±4.7 mmHg in FTO and 22.6±4.7 in TE while on 3.0±0.9 medications in both (Table 1). There were no significant differences between FTO and TE in gender, age, best-corrected visual acuity, type of glaucoma, or surgical side. In FTO, 13 eyes were pseudophakic compared to 3 in TE (p=0.006). Two patients in FTO had a pars plana vitrectomy and one a retinal cryopexy. In TE, there were no prior ocular surgeries other than phacoemulsification.\n\nFTO: filtering trabeculotomy; TE: trabeculectomy; BCVA: best-corrected visual acuity assessed; IOP: intraocular pressure; POAG: primary open angle glaucoma; PXG: pseudoexfoliation glaucoma; PG: pigmentary glaucoma; ALT: argon laser trabeculoplasty; SLT: selective laser trabeculoplasty; CPC: cyclophotocoagulatoin; nd:YAG: neodymium-doped yttrium aluminum garnet\n\nThere were no statistically significant inter-group differences in complete or qualified success at any time (p=0.403 for complete success; p=0.204 for qualified success at 24 months; Figure 1 and Figure 2). The complete success rate in FTO ranged from 79% at 6 to 78% at 12 months, and 59% at 24 months. In TE, it was 81%, 85%, and 66%, respectively. Similarly, IOPs of FTO and TE were not significantly different at any time (12 months: p=0.983, 24 months: p=1.000, Figure 3). At one year, the IOP had declined to 12.4±4.3 mmHg in FTO and 11.3±2.2 mmHg in TE with medications (qualified success). At two years, IOP remained at 13.1±4.1 mmHg in FTO and 12.0±3.5 mmHg in TE (qualified success), respectively. The postoperative visual acuity was not significantly different in FTO and TE at any time (p=0.894 after 12 months; p=0.443 after 24 months; Figure 4 and Figure 5).\n\nFTO: filtering trabeculotomy; TE: trabeculectomy.\n\nThere was a reduction in glaucoma medication from 3±0.9 to 0.6±1.3 in FTO and from 3±0.9 to 0.2±0.5 in TE after 24 months. There was no significant difference between the two groups in glaucoma medications at 24 months with 19% of patients in FTO and 12% of patients in TE using glaucoma drops (p=0.471, Figure 6 and Figure 7).\n\nFTO: filtering trabeculotomy; TE: trabeculectomy.\n\nFew patients required medications postoperatively.\n\nPostoperative complications in FTO included 5 eyes (12%) with a high IOP, hyphema in 5 cases (11%) and hypotony (IOP ≤ 5 mmHg16) with choroidals in 4 eyes (9%). The most common postoperative challenge in TE was a flat bleb in 6 eyes (14%), hyphema in 3 eyes (7%), high IOP in 2 eyes (5%), bleb leakage in 2 eyes (5%), and hypotony in 1 eye (2%). A total of 16, mostly reversible, complications occurred in each group (37%; Table 2).\n\nFTO: filtering trabeculotomy; TE: trabeculectomy; IOP: intraocular pressure.\n\nThe number of postoperative interventions was the same in the two groups (p=0.087). Bleb needling, conjunctival suture, and scleral flap suture were the most common interventions. There was no statistically significant difference between both groups in early or late interventions (Table 3), except 5-FU and laser suture lysis, which was performed more often in FTO.\n\n** not calculated. FTO: filtering trabeculotomy; TE: trabeculectomy; IOP: intraocular pressure\n\n\nDiscussion\n\nTE with MMC remains a primary surgery in the management of advanced glaucoma5 despite its potential for serious complications that include choroidal effusions, maculopathy, blebitis, endophthalmitis, and suprachoroidal hemorrhage17. Numerous modifications have been explored over the years to reduce the rate of these. They include a smaller scleral flap18, limbus-versus fornix-based conjunctival closure19, releasable flap sutures20,21, a combination of trabeculectomy with deep sclerectomy22, different concentrations and exposure times of MMC23 or sutureless tunnel trabeculectomy without iridectomy24. The iridectomy, which is part of traditional trabeculectomy with a trabecular block excision, can cause hyphema, inflammation, posterior synechiae, iridodialysis, and cataracts25,26. FTO addresses some of these issues by creating a more spread-out intake of aqueous humor, thereby reducing iris aspiration and avoiding the need for an iridectomy. The trabeculotomy and sclerectomy8,27,28, that are part of the FTO, were meant to remove some of the post-trabecular outflow resistance29–31.\n\nWe used matching, a nonparametric method of controlling the confounding influence of pretreatment variables in observational data32. Before matching, FTO and TE had significant differences. We have previously used coarsened exact matching, propensity score matching, and, more recently, exact matching. Coarsened exact matching applies multiple imputations to fill in missing data to not distort any relationships contained in the data while enabling the inclusion of all observed data from moderately uneven groups. Such was the case when we compared patients with a primary IOP indication to patients with a mixed indication for both cataract removal and IOP reduction33–35. Propensity score matching is helpful to compare even more divergent groups, for instance, patients undergoing tube shunt surgery with patients undergoing trabectome surgery36,37. By contrast, exact matching is well suited to compare similar pathological conditions and similar treatments, for instance, phaco-iStent or phaco-trabectome38,39. A downside of exact matching is that a certain number of datasets must be excluded from the analysis because the algorithm accepts only identical primary criteria matches. Overall, our data loss was acceptable because of the high similarity that already existed at baseline. We were able to retain a large number of eyes (about 45%) as identical pairs of preoperative IOP and medication to focus on the preeminent questions of success in IOP and medication reduction. We found that FTO was as successful as TE with a similar reduction of IOP and medications. Both had a similar intervention and complication rate, notwithstanding numerical hypotony within the first six weeks after surgery. We observed a remarkably low rate of hyphema compared to ab interno trabeculectomy40 that occurs when the IOP is at or below episcleral venous pressure allowing blood to reflux into the anterior chamber. This could indicate reduced patency of collector channels in advanced glaucoma that qualifies for filtering surgery, which has been observed ex vivo41.\n\nTrabeculotomy ab externo has been applied to adult POAG before but, compared to TE, was noted to have a lower success rate of 70% at one year, presumably due to a reapproximation or regeneration of the disrupted trabecular meshwork42. A study by Chihara et al. was in agreement with this, finding that a modified trabeculotomy ab externo lowers IOP to an average near 16 mmHg in a safe fashion43, by not as much as TEs. Ogawa et al. compared a nonpenetrating trabeculectomy with or without trabeculotomy44 using a technique that was very similar to the one applied in our study, except without MMC. Despite the absence of this antifibrotic, the authors achieved a two-year IOP of 13 mmHg, not unlike our patients.\n\nOur two-year TE results match Kirwan et al.’s multicenter study of TE with an iridectomy in 428 eyes well45. These eyes achieved an IOP of 12.4±4 mmHg and 80% did not have to use glaucoma medications anymore, slightly more than in our study population. The authors performed needling in 17% of patients, not unlike our rates, and numerical hypotony during the first six months occurred in 7.2% of patients, which is in a similar range as our 9% in FTO and 2% in TE. Leakage was observed in 14% compared to 9% in our FTO and 2% in our TE. However, Kirwan et al.’s cataract surgery rate was 31%, much higher than our 1% in both FTO and TE, which might represent a difference in practice pattern or simply easier access to this elective procedure, which is done as an outpatient surgery in the UK.\n\nIt is interesting to note that TEs in the Tube Versus Trabeculectomy (TVT) study were performed without an iridectomy46. In that study, IOP reduced from 25.6±5.3 mm Hg to 12.7±5.8 mm Hg at one year while the number of glaucoma medications declined from 3.0±1.2 to 0.5±0.947, which is also relatively similar to our results although these investigators included eyes with prior intraocular surgery, including glaucoma procedures. An early complication rate of 37% was observed by these authors, primarily consisting of a shallow or flat anterior chamber in 20% and choroidal effusions in 10%6. In another study of TE without an iridectomy by Jea et al., IOP reduced from 26.3±10.9 mmHg to 10.2±4.1 mmHg at two years48. The number of glaucoma medications decreased from 2.2±1.6 to 0.5±1.0. A complete success occurred in 76.6% at one year and 66.2% at two years, matching ours.\n\nIn all of these studies, TE was performed as an outpatient patient procedure, a practice that emerged in the late 1980s49,50 and became a standard for most types of eye surgeries and countries51–54. Even before the now-common use of antifibrotics, there was no significant difference in success or complication rates between inpatients and outpatients50, an observation that has been confirmed with antifibrotics as well53. In the country of our study, TE and FTO are only reimbursable as inpatient procedures. It has been argued that meticulous micromanagement after TE for several days may be associated with better long-term outcomes of TE. However, this hypothesis is challenged by the present study and by the findings of others49,50,53,55. One could argue that the considerably lower cataract surgery rate in our data compared to Kirwan et al.45 might indicate a higher threshold for cataract surgery. These would have typically also been done as inpatient procedures to better handle post-cataract surgery bleb care.\n\nOur study was limited by its retrospective nature and nonrandomized design. We determined that we had a testing power above 80% to detect a difference of more than 2 mmHg 1 year (alpha= 0.05), yet but no significant difference was found. Certainly, randomized controlled trials are a more sophisticated tool to reduce bias when trying to detect differences. However, given that exact matching already allows for a highly balanced comparison of retrospective data, such an effort might be difficult to justify. The indication for postoperative interventions and length of hospitalization was at the discretion of the treating physicians and was not standardized for both groups. Despite reducing confounding through the exact matching of IOP and medications, other confounding factors might have contributed to small differences in early postoperative patient management, as reflected by the fact that FTO patients received more 5-FU injections. Although these patients had a higher rate of numerical hypotony they were hospitalized for a slightly shorter time and experienced results that were not significantly different.\n\nIn conclusion, our results are largely in line with other FTO and TE outpatient studies. Combining elements from both yields reasonable two-year rates of surgical success, postoperative complications, and interventions while avoiding an iridectomy.\n\n\nData availability\n\nOpen Science Framework: Retrospective evaluation of 2-year results with a filtering trabeculotomy in comparison to conventional trabeculectomy by exact matching, https://doi.org/10.17605/OSF.IO/KDYF356.\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\nA previous version of this article is available on medRxiv: https://doi.org/10.1101/2020.01.17.20017913.\n\n\nReferences\n\nGrant WM: Further studies on facility of flow through the trabecular meshwork. AMA Arch Ophthalmol. 1958; 60(4 Part 1): 523–33. PubMed Abstract | Publisher Full Text\n\nSaul Sugar H: Experimental Trabeculectomy in Glaucoma *. Am J Ophthalmol. 1961; 51(4): 623–7.\n\nCairns JE: Trabeculectomy. Preliminary report of a new method. Am J Ophthalmol. 1968; 66(4): 673–9. PubMed Abstract | Publisher Full Text\n\nChen CW, Huang HT, Bair JS, et al.: Trabeculectomy with simultaneous topical application of mitomycin-C in refractory glaucoma. J Ocul Pharmacol. 1990; 6(3): 175–82. PubMed Abstract | Publisher Full Text\n\nSchmier JK, Covert DW, Lau EC, et al.: Trends in annual medicare expenditures for glaucoma surgical procedures from 1997 to 2006. Arch Ophthalmol. 2009; 127(7): 900–5. PubMed Abstract | Publisher Full Text\n\nGedde SJ, Herndon LW, Brandt JD, et al.: Postoperative Complications in the Tube Versus Trabeculectomy (TVT) Study During Five Years of Follow-up. Am J Ophthalmol. 2012; 153(5): 804–14.e1. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHondur A, Onol M, Hasanreisoglu B: Nonpenetrating glaucoma surgery: meta-analysis of recent results. J Glaucoma. 2008; 17(2): 139–46. PubMed Abstract | Publisher Full Text\n\nKrasnov MM: Externalization of Schlemm’s canal (sinusotomy) in glaucoma. Br J Ophthalmol. 1968; 52(2): 157–61. PubMed Abstract | Publisher Full Text | Free Full Text\n\nEsfandiari H, Taranum Basith SS, Kurup SP, et al.: Long-term surgical outcomes of ab externo trabeculotomy in the management of primary congenital glaucoma. J AAPOS. 2019. PubMed Abstract | Publisher Full Text\n\nMatlach J, Hipp M, Wagner M, et al.: A comparative study of a modified filtering trabeculotomy and conventional trabeculectomy. Clin Ophthalmol. 2015; 9: 483–92. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKing G: Exact Matching. [cited 2018 Jul 9]. Reference Source\n\nHaubold B, Börsch-Haubold A: Exact Matching. In: Haubold B, Börsch-Haubold A, editors. Bioinformatics for Evolutionary Biologists: A Problems Approach. 2017; 47–67. Publisher Full Text\n\nJacobi PC, Krieglstein GK: Trabecular aspiration. A new mode to treat pseudoexfoliation glaucoma. Invest Ophthalmol Vis Sci. 1995; 36(11): 2270–6. PubMed Abstract\n\nShaarawy T, Sherwood M, Grehn F: Guidelines on Design and Reporting of Glaucoma Surgical Trials. Kugler Publications; 2009; 83. Reference Source\n\nPfeiffer N, Grehn F: Improved suture for fornix-based conjunctival flap in filtering surgery. Int Ophthalmol. 1992; 16(4–5): 391–6. PubMed Abstract | Publisher Full Text\n\nAbbas A, Agrawal P, King AJ: Exploring literature-based definitions of hypotony following glaucoma filtration surgery and the impact on clinical outcomes. Acta Ophthalmol. 2018; 96(3): e285–9. PubMed Abstract | Publisher Full Text\n\nSchwartz K, Budenz D: Current management of glaucoma. Curr Opin Ophthalmol. 2004; 15(2): 119–26. PubMed Abstract | Publisher Full Text\n\nOphir A: Mini-trabeculectomy as initial surgery for medically uncontrolled glaucoma. Am J Ophthalmol. 2001; 132(2): 229–34. PubMed Abstract | Publisher Full Text\n\nSolus JF, Jampel HD, Tracey PA, et al.: Comparison of limbus-based and fornix-based trabeculectomy: success, bleb-related complications, and bleb morphology. Ophthalmology. 2012; 119(4): 703–11. PubMed Abstract | Publisher Full Text\n\nAykan U, Bilge AH, Akin T, et al.: Laser suture lysis or releasable sutures after trabeculectomy. J Glaucoma. 2007; 16(2): 240–5. PubMed Abstract | Publisher Full Text\n\nVuori ML, Viitanen T: “Scleral tunnel incision”-trabeculectomy with one releasable suture.. Acta Ophthalmol Scand. 2001; 79(3): 301–4. PubMed Abstract | Publisher Full Text\n\nKayikcioglu OR, Emre S, Kaya Z: Trabeculectomy combined with deep sclerectomy and scleral flap suture tension adjustment under an anterior chamber maintainer: a new modification of trabeculectomy. Int Ophthalmol. 2010; 30(3): 271–7. PubMed Abstract | Publisher Full Text\n\nBindlish R, Condon GP, Schlosser JD, et al.: Efficacy and safety of mitomycin-C in primary trabeculectomy: five-year follow-up. Ophthalmology. . 2002; 109(7): 1336–41; discussion 1341-2. PubMed Abstract | Publisher Full Text\n\nEslami Y, Mohammadi M, Khodaparast M, et al.: Sutureless tunnel trabeculectomy without peripheral iridectomy: a new modification of the conventional trabeculectomy. Int Ophthalmol. 2012; 32(5): 449–54. PubMed Abstract | Publisher Full Text\n\nde Barros DSM, Da Silva RS, Siam GA, et al.: Should an iridectomy be routinely performed as a part of trabeculectomy? Two surgeons’ clinical experience. Eye (Lond). 2009; 23(2): 362–7. PubMed Abstract | Publisher Full Text\n\nGrehn F, Müller E: [Long-term results following preventive iridectomy. A retrospective study]. Fortschr Ophthalmol. 1990; 87(3): 260–3. PubMed Abstract\n\nKrasnov MM: [SINUSOTOMY IN GLAUCOMA]. Vestn Oftalmol. 1964; 77: 37–41. PubMed Abstract\n\nGrehn F: The value of trabeculotomy in glaucoma surgery. Curr Opin Ophthalmol. 1995; 6(2): 52–60. PubMed Abstract | Publisher Full Text\n\nDvorak-Theobald G, Kirk HQ: Aqueous pathways in some cases of glaucoma. Trans Am Ophthalmol Soc. 1956; 53(1): 301–15. PubMed Abstract | Free Full Text\n\nWaxman S, Wang C, Dang Y, et al.: Structure–Function Changes of the Porcine Distal Outflow Tract in Response to Nitric Oxide. Invest Ophthalmol Vis Sci. 2018; 59(12): 4886–95. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMcDonnell F, Dismuke WM, Overby DR, et al.: Pharmacological regulation of outflow resistance distal to Schlemm’s canal. Am J Physiol Cell Physiol. 2018; 315(1): C44–51. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBlackwell M, Iacus S, King G, et al.: Cem: Coarsened Exact Matching in Stata. Stata J. 2009; 9(4): 524–46. Reference Source\n\nParikh HA, Bussel II, Schuman JS, et al.: Coarsened Exact Matching of Phaco-Trabectome to Trabectome in Phakic Patients: Lack of Additional Pressure Reduction from Phacoemulsification. PLoS One. 2016; 11(2): e0149384. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHonaker J, King G, Blackwell M, et al.: Amelia II: A program for missing data. J Stat Softw. 2011; 45(7): 1–47. Reference Source\n\nNeiweem AE, Bussel II, Schuman JS, et al.: Glaucoma Surgery Calculator: Limited Additive Effect of Phacoemulsification on Intraocular Pressure in Ab Interno Trabeculectomy. PLoS One. 2016; 11(4): e0153585. PubMed Abstract | Publisher Full Text | Free Full Text\n\nEsfandiari H, Shazly TA, Waxman SA, et al.: Similar Performance of Trabectome and Ahmed Glaucoma Devices in a Propensity Score-matched Comparison. J Glaucoma. 2018; 27(6): 490–5. PubMed Abstract | Publisher Full Text\n\nKostanyan T, Shazly T, Kaplowitz KB, et al.: Longer-term Baerveldt to Trabectome glaucoma surgery comparison using propensity score matching. Graefes Arch Clin Exp Ophthalmol. 2017; 255(12): 2423–8. PubMed Abstract | Publisher Full Text\n\nEsfandiari H, Taubenslag K, Shah P, et al.: Two-year data comparison of ab interno trabeculectomy and trabecular bypass stenting using exact matching. J Cataract Refract Surg. 2019; 45(5): 608–14. PubMed Abstract | Publisher Full Text\n\nAl Yousef Y, Strzalkowska A, Hillenkamp J, et al.: Comparison of a second-generation trabecular bypass (iStent inject) to ab interno trabeculectomy (Trabectome) by exact matching. Ophthalmology medRxiv. medRxiv; 2020. Publisher Full Text\n\nKaplowitz K, Bussel II, Honkanen R, et al.: Review and meta-analysis of ab-interno trabeculectomy outcomes. Br J Ophthalmol. 2016; 100(5): 594–600. PubMed Abstract | Publisher Full Text\n\nHann CR, Vercnocke AJ, Bentley MD, et al.: Anatomical Changes in Schlemm’s Canal and Collector Channels in Normal and Primary Open Angle Glaucoma Eyes Using Low and High Perfusion Pressures. Invest Ophthalmol Vis Sci. 2014; 55(9) PubMed Abstract | Publisher Full Text | Free Full Text\n\nLuntz MH, Livingston DG: Trabeculotomy ab externo and trabeculectomy in congenital and adult-onset glaucoma. Am J Ophthalmol. 1977; 83(2): 174–9. PubMed Abstract | Publisher Full Text\n\nChihara E, Nishida A, Kodo M, et al.: Trabeculotomy ab externo: an alternative treatment in adult patients with primary open-angle glaucoma. Ophthalmic Surg. 1993; 24(11): 735–9. PubMed Abstract\n\nOgawa T, Dake Y, Saitoh AK, et al.: Improved nonpenetrating trabeculectomy with trabeculotomy. J Glaucoma. 2001; 10(5): 429–35. PubMed Abstract | Publisher Full Text\n\nKirwan JF, Lockwood AJ, Shah P, et al.: Trabeculectomy in the 21st century: a multicenter analysis. Ophthalmology. 2013; 120(12): 2532–9. PubMed Abstract | Publisher Full Text\n\nGedde SJ, Schiffman JC, Feuer WJ, et al.: The tube versus trabeculectomy study: design and baseline characteristics of study patients. Am J Ophthalmol. 2005; 140(2): 275–87. PubMed Abstract | Publisher Full Text\n\nGedde SJ, Schiffman JC, Feuer WJ, et al.: Treatment Outcomes in the Tube Versus Trabeculectomy Study After One Year of Follow-up. Am J Ophthalmol . 2007; 143(1): 9–22.e2. PubMed Abstract | Publisher Full Text\n\nJea SY, Francis BA, Vakili G, et al.: Ab interno trabeculectomy versus trabeculectomy for open-angle glaucoma. Ophthalmology. 2012; 119(1): 36–42. PubMed Abstract | Publisher Full Text\n\nDobromyslov AN, Panina NB: [Ambulatory care of patients with (surgically treated) glaucoma]. Oftalmol Zh. 1987; (8): 505–6. PubMed Abstract\n\nBeatty S, Kheterpal S, Eagling EM, et al.: Day-case trabeculectomies: Safety and efficacy. Acta Ophthalmol Scand. 1996; 74(2): 132–4. PubMed Abstract | Publisher Full Text\n\nHolland GN, Earl DT, Wheeler NC, et al.: Results of inpatient and outpatient cataract surgery. A historical cohort comparison. Ophthalmology. 1992; 99(6): 845–52. PubMed Abstract | Publisher Full Text\n\nCastells X, Alonso J, Castilla M, et al.: Outcomes and costs of outpatient and inpatient cataract surgery. J Clin Epidemiol. 2001; 54(1): 23–9. PubMed Abstract | Publisher Full Text\n\nLleó AVP, Moratal BJ, Pinós JPR, et al.: [Safety and efficacy of outpatient glaucoma surgery]. Arch Soc Esp Oftalmol. 2000; 75(8): 535–40. PubMed Abstract\n\nWilson D, Barr CC: Outpatient and abbreviated hospitalization for vitreoretinal surgery. Ophthalmic Surg. 1990; 21(2): 119–22. PubMed Abstract\n\nCortiñas M, Martínez LL, Granados JM, et al.: [Results of an outpatient major surgery program in ophthalmology]. Arch Soc Esp Oftalmol. 2006; 81(12): 701–8. PubMed Abstract | Publisher Full Text\n\nLoewen N: Retrospective evaluation of 2-year results with a filtering trabeculotomy in comparison to conventional trabeculectomy by exact matching. 2020. http://www.doi.org/10.17605/OSF.IO/KDYF3"
}
|
[
{
"id": "73193",
"date": "30 Oct 2020",
"name": "Marc Töteberg-Harms",
"expertise": [
"Reviewer Expertise Glaucoma",
"cataract."
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors present a retrospective study comparing two surgical interventions for the management of glaucoma. The use of exact matching is a major advantage of their study design.\nIt is unclear if only one eye per patient was included and, if not, if a statistical model to account for two-eye-effect was used.\nA post-hoc power analysis could further improve this excellent paper to prove that the sample size of 44 eyes per group was sufficient to find a difference or no difference between the two study arms\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? No\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "6108",
"date": "04 Jun 2021",
"name": "Nils Loewen",
"role": "Author Response",
"response": "Manuscript No. 9:1245 (https://doi.org/10.12688/f1000research.26772.1) Title: Retrospective evaluation of two-year results with a filtering trabeculotomy in comparison to conventional trabeculectomy by exact matching Alicja Strzalkowska, Piotr Strzalkowski, Yousef Al Yousef, Jost Hillenkamp, Franz Grehn, Nils A. Loewen Authors: We appreciate the helpful comments and have provided our replies below. We trust that we could address the concerns that were raised. Marc Töteberg-Harms: The authors present a retrospective study comparing two surgical interventions for the management of glaucoma. The use of exact matching is a major advantage of their study design. It is unclear if only one eye per patient was included and, if not, if a statistical model to account for two-eye-effect was used. Authors: Thank you for pointing this out. We have updated the Method to clarify that only one eye was included per patient: “Only one eye was included per patient. If two eyes had been operated on, the first eye was chosen to take advantage of a longer history.” We added to Discussion: “In patients with surgery in both eyes, we had selected the first eye undergoing glaucoma surgery for our analysis to take advantage of a longer history with more data. This selection might have favored the eye with more severe glaucoma. However, as this occurred in both groups, a similar bias will have occurred.” Marc Töteberg-Harms: A post-hoc power analysis is missing to prove that the sample size of 44 eyes per group is sufficient to prove a difference or no difference between the two study arms. Authors: Thank you for raising this issue. We had previously written in the second last paragraph of the Discussion “We determined that we had a testing power above 80% to detect a difference of more than 2 mmHg 1 year (alpha= 0.05), yet but no significant difference was found.” We have now deleted this statement and inserted the text as described below. Our power study before commencing the study indicated that we would need 39 eyes per group to detect a difference of at least 20%. Our posthoc calculation showed that we had a power to detect a difference of 16% at 1 year and 17.6% at 2 years. We added to Methods: “Our power calculation before commencing the study indicated that we would need 39 eyes per group to detect a difference of at least 20% at a power of 80% and alpha of 0.05 (continuous endpoints, two independent sample study). We then performed a post-hoc analysis for IOP at year 1 and 2 and determined the effect size using Cohen’s d (d (.01) = very small, d (.2) = small, d (.5) = medium, d (.8) = large, d (1.2) = very large, and d (2.0) = huge [1]).” We added to Results: “The posthoc analysis showed that we could have detected an IOP difference of 16.1% at one year and an IOP difference of 17.6% at two years with a power above 80%. Cohen’s d was 0.32 at one year and 0.29 at two years, respectively, in both cases classifying as small.” Marc Töteberg-Harms: Are all the source data underlying the results available to ensure full reproducibility? - No Authors: We have made all underlying data available at Open Science Framework: Retrospective evaluation of 2-year results with a filtering trabeculotomy in comparison to conventional trabeculectomy by exact matching, https://doi.org/10.17605/OSF.IO/KDYF356. Data are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication). References 1. Sawilowsky SS (2009) New Effect Size Rules of Thumb. J Mod Appl Stat Methods 8:26"
}
]
},
{
"id": "74186",
"date": "18 Nov 2020",
"name": "Igor I. Bussel",
"expertise": [
"Reviewer Expertise Glaucoma Clinical Trials",
"Glaucoma Surgery Outcomes",
"Glaucoma Imaging",
"Glaucoma/Cataract 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\nMost glaucoma surgery clinical trials are often non-randomized, usually limited by a short duration of follow-up (<1 year), lack hypothesis, and appropriate comparison to a gold-standard. The investigators of this trial managed to overcome lack of randomization by using novel exact matching methodology. This allowed for a balanced comparison of retrospective data. FTO was compared to the gold standard, TE. It is unclear if the exact matching process created a sample bias of cases with higher success. The authors demonstrated that FTO and TE yield similar two-year rates of surgical success, postoperative complications, and interventions.\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": "73660",
"date": "08 Dec 2020",
"name": "Christian van Oterendorp",
"expertise": [
"Reviewer Expertise 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 authors present a highly controlled retrospective study comparing two glaucoma filtration surgery techniques. The statistical methods applied are sound, the presentation is well structured and transparent, the discussion is well balanced and covers the current literature.\nA few more points may be discussed:\nThe choice of the exact matching criteria. Obviously, extending the matching criteria reduces the number of available matches. But besides the criteria chosen the authors may discuss whether the inclusion of criteria directly linked to failure, such as the presence of drug related ocular surface inflammation, could have led to a further reduction of a significant confounding factor. More precisely, if a grading system for preoperative ocular surface inflammation existed, this could have been included as a matching criterion. However, given the retrospective nature of this study, such a grading might not have been available.\nDiscussion. The results suggest that both interventions may be used interchangeably. Could the authors provide arguments which speak in favour or against one or the other technique? - maybe with respect to certain details, such as:\nLens status. Should FTO be considered rather in phakic eyes as the risk for cataract development may be lower? But why was the rate of pseudophakic patients significantly higher in FTO compared to TE?\n\nSurgery time and/or need for general anaesthesia (TE faster? therefore better for local anaesthesia?).\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": []
}
] | 1
|
https://f1000research.com/articles/9-1245
|
https://f1000research.com/articles/10-68/v1
|
03 Feb 21
|
{
"type": "Brief Report",
"title": "Interactive SARS-CoV-2 mutation timemaps",
"authors": [
"René L. Warren",
"Inanc Birol",
"Inanc Birol"
],
"abstract": "As the year 2020 came to a close, several new strains have been reported of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the agent responsible for the coronavirus disease 2019 (COVID-19) pandemic that has afflicted us all this past year. However, it is difficult to comprehend the scale, in sequence space, geographical location and time, at which SARS-CoV-2 mutates and evolves in its human hosts. To get an appreciation for the rapid evolution of the coronavirus, we built interactive scalable vector graphics maps that show daily nucleotide variations in genomes from the six most populated continents compared to that of the initial, ground-zero SARS-CoV-2 isolate sequenced at the beginning of the year. Availability: The tool used to perform the reported mutation analysis results, ntEdit, is available from GitHub. Genome mutation reports are available for download from BCGSC. Mutation time maps are available from https://bcgsc.github.io/SARS2/.",
"keywords": [
"SARS-CoV-2",
"COVID-19",
"Mutation time maps",
"GISAID",
"Interactive SVG"
],
"content": "Introduction\n\nIn the last few weeks of 2020, new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mutations in the United Kingdom (UK) were reported1. Although coronavirus genome mutations have been previously discovered and announced throughout the year, including the widely discussed D614G missense change in the spike protein2,3, the latest recurring surface protein mutations to be identified (e.g. N501Y, P681H) are cause for concern. The SARS-CoV-2 viral S gene encodes a surface glycoprotein, which upon interaction with host ACE-2 receptors, makes it possible for the coronavirus to gain entry to host cells and propagate. The reported changes to its sequence may be associated with increased virulence4, infectivity3 and overall fitness5. The global response to those recent reports has been swift, with several countries shutting down air travel from the UK. This highlights the severity of the situation and the importance to track genomic variations and their predicted effects over time and space.\n\nThe rapid evolution of the SARS-CoV-2 genome in human hosts has prompted us to map all nucleotide changes that have appeared in 2020, since the first genome sequence of a COVID-19 patient isolate from the outbreak epicentre in Wuhan, China was made public6. For this, we leveraged the collaborative efforts of hundreds of institutions worldwide who have graciously shared over 260,000 SARS-CoV-2 genome sequences with the GISAID central repository since early January 20207. Our mutation time maps show the staggering number of nucleotide variants that have accumulated on the whole viral genome throughout the year, and especially since fall 2020, and in the six most populated continents. Here we present key features of these maps and how they may be of utility to researchers.\n\n\nMethods\n\nWe first downloaded all complete, high-coverage SARS- CoV-2 genomes from GISAID7 on January 23rd, 2021 (human hosts samples collected). We then ran a genome polishing pipeline, which consists of ntHits8 (v0.1.0 -b 36 -outbloom -c 1 -p seq -k 25) followed by ntEdit9 (v1.3.4 -i 5 -d 5 -m 1 -r seq_k25.bf) and required at most 0.5 GB RAM and executed in ~1 sec. per genome on a single CPU. We used the first published SARS-CoV-2 genome isolate6 (WH- Human 1 coronavirus, GenBank accession: MN908947.3) as the reference and each individual GISAID genome in turn as source of kmers to identify base variation relative to the former. The variant call format (VCF) output files from ntEdit were parsed and we tallied, for each submitted GISAID genome, the complete list of nucleotide variations. We next organized each nucleotide variant by sample collection date, continent of origin and, when applicable, evaluated its effect on the gene product that harbours the change to output an interactive scalable vector graphics (SVG) file. The script we developed to generate the maps is written in PERL and distributed under GPLv3. Users wishing to generate custom maps can download the script from Zenodo10.\n\n\nResults and discussion\n\nWe analyzed nucleotide variations over time in over 260,000 SARS-CoV-2 viral genomes, submitted to the GISAID initiative7 from around the globe, relative to that of the ground zero COVID-19 clinical isolate6. We mapped each mutation that was observed in five or more genomes each day. The 2020 calendar year from January 1st 2020 (day 1) to December 31st 2020 (day 366) is organized in a circle where each radius represents a day (1 day = 0.98 degree) and data points represent mutations along the reference genome sequence from 1 (closest to center) to 29,903 bp (near the outer rim). The size of each point is in log10 scale of the number of contributing viral genomes collected on that day that has the mutation, with colour assignments indicating the continent of origin where the mutation is observed. A mouse over each data point reveals the collection date, the nucleotide variant, the continent and associated number of contributing genome sequences (including daily sample fraction) and, when applicable, the gene product and predicted amino acid change.\n\nFrom the SARS-CoV-2 genome mutation time map (Figure 1A), we observe the first persistent mutations (≥5 genomes/day) appearing in late February 2020, including the prevalent D614G mutation in Europe on February 22nd (albeit since January in fewer samples, Figure 1B). From there, the original coronavirus genome sustained many changes overtime (5,468 distinct variants mapped in 2020 as of January 23rd, 2021), including a sizeable proportion (56.8 %) of missense mutations. It is immediately evident from Figure 1A that variations from Europe account for a larger share (71.2%) of the variants mapped. Further, there appears to be a surge in variations identified in late summer/throughout fall 2020 in this continent. This may be explained by a disproportionate number of submissions with samples originating from this jurisdiction as the second wave hit hard. Thus, caution in interpreting the map is warranted. Of note, the spike protein gene variant N501Y, observed on our maps in the UK in late September 2020 (Figure 1), is consistent with an earlier study reporting on its recurrent emergence within this time frame1. We think these maps will be of utility to researchers in their exploration of SARS-CoV-2 mutations and their predicted effect over time.\n\nntEdit was used to map nucleotide variations between the first published coronavirus isolate from Wuhan, China in early January and over 260,000 SARS-CoV-2 genomes sampled from around the globe during the 2020 coronavirus disease 2019 (COVID-19) pandemic. The maps show missense mutations arising daily (A) in the world within the whole viral genome, with the reference genome represented by the vertical axis from bases 1 to 29.9 kbp and (B) in Europe within the spike protein gene. Alternating dark/light grey vertical rectangles and associated tracks depict, starting from the center, SARS-CoV-2 genes orf1ab, S, ORF3a, E, M, ORF6, ORF7a, ORF8, N, and ORF10. Mutations identified daily are represented by circles in a given radius and are coloured by regions and sized relative to raw count (panel A) or ratio (panel B) of the daily samples. A stacked bar plot (center) shows sample count. The 2020 calendar year mutations are organized clockwise from the upper vertical. Hovering the mouse cursor over each data point reveals additional insights (not shown).\n\n\nData availability\n\nThe SARS-CoV-2 genome sequences can be accessed via the GISAID central repository. Processed single nucleotide variant (SNV) data is available from https://www.bcgsc.ca/downloads/btl/SARS-CoV-2/mutations/.\n\n\nMaps availability\n\n\n\n- Maps are available from: https://bcgsc.github.io/SARS2\n\n- SNV detection source code is available from: https://github.com/bcgsc/ntedit\n\n- Archived source code at time of publication: https://doi.org/10.5281/zenodo.446984010\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\nStudy design: RLW. Analysis: RLW. Both authors wrote the manuscript.",
"appendix": "Acknowledgements\n\nWe acknowledge Cecilia (Lingyu) Yang for her early work on SARS-CoV-2 variants.\n\n\nReferences\n\nRambaut A, et al.: Preliminary genomic characterisation of an emergent SARS-CoV-2 lineage in the UK defined by a novel set of spike mutations. Virological 2020. Reference Source\n\nDey T, et al.: Identification and computational analysis of mutations in SARS-CoV-2. Comput Biol Med 2021; 129: 104166. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKorber B, et al.: Tracking changes in SARS- CoV-2 spike: evidence that D614G increases infectivity of the COVID-19 virus. Cell 2020; 182: 812–827. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGu H, et al.: Adaptation of SARS-CoV-2 in BALB/c Mice for Testing Vaccine Efficacy Science 2020; 369: 1603–1607. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPlante JA, et al.: Spike mutation D614G alters SARS-CoV-2 fitness. Nature2020. PubMed Abstract | Publisher Full Text\n\nWu F, et al.: A new coronavirus associated with human respiratory disease in China. Nature 2020; 579: 265–269. PubMed Abstract | Publisher Full Text | Free Full Text\n\nre3data.org: GISAID; editing status. re3data.org - Registry of Research Data Repositories. 2020-02-03. Publisher Full Text\n\nMohamadi H, et al.: ntHits: de novo repeat identification of genomics data using a streaming approach. BioRxiv 2020. Publisher Full Text\n\nWarren RL, et al.: ntEdit: scalable genome sequence polishing Bioinformatics 2019; 35: 4430–4432. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWarren R, Birol I: Interactive SARS-CoV-2 mutation timemaps (Version v1.1). Zenodo 2021, January 26. Publisher Full Text"
}
|
[
{
"id": "83795",
"date": "14 May 2021",
"name": "Ingo Ebersberger",
"expertise": [
"Reviewer Expertise BioSequence-Informatics"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors present interactive mutation time maps for SARS-CoV-2, which provide a highly resolving view of when, where and how frequent a particular mutation was detected in the sampled SARS-CoV-2 genome sequences provided via GISAID. The manuscript itself is rather short. It is briefly describing the methodological approach of how the mutations have been detected and mapped to the reference genome. The combined Results and Discussion section is equally concise and comprises a description of what is seen in the interactive maps together with few example observations that can be made with these maps. The Discussion section ends with the expression of the hope that the maps presented here “will help researchers in their exploration of SARS-CoV-2 mutations and their predicted effect over time.”\nOverall, the topic that is touched in this manuscript is highly relevant, as variations of SARS-CoV-2 is something that currently is and will be of major concern in the future. Here, the graphs present a very nice access to the information that is represented by the ever-increasing amount of viral genome sequences world-wide. The data presentation is appealing, and it allows to overview the general trends of SARS-CoV-2 evolution. However, we see considerable room for (essential) improvement.\nMajor issues: The authors end the manuscript with the belief that the interactive maps will be of help for the research community working on SARS-CoV-2 variation. We miss two things here:\nFirst, it would be great if the authors show how the data provided by the maps can be used to indeed come up with new conclusions, in particular with respect to the ‘predicted effect over time’. For us, it is entirely unclear how such an analysis should be performed. Exploring the data, this is something that one nicely can do while looking at the plots, some clear signals, e.g. the fate of D614G, can also be extracted. But how to work with the data beyond this simple and straightforward ‘looking’ at the plots? Please, don’t get us wrong here, we consider looking at data a very important aspect of data analysis. Still, the sheer amount of information, which results in very dense plots with many overlapping data points, makes it, in our opinion, very hard to identify emerging variants that should be monitored right from the start. Just to give you an example: D614G is represented by a very prominent circle in the plots. What would be the authors approach to identify and monitor a novel variant, say at position 615 of the reference strain? By looking at the plots, we consider this almost impossible, since the signal will be entirely covered by the prominent mutation at position 614.\nThe analysis is presented using the “ground-zero” strain as a reference. But is this still timely? Numerous variants have now frequencies that go far beyond that of the original nucleotide at a certain position, again, for example the D614G variant. This would allow to ‘purge’ the signal of very successful variants, helping to direct the focus on emerging variants.\nWhen it comes to the website itself, we see some room for improvement:\nFirst and foremost, we think the plots are overcrowded with information. Although it is nice to see a global overview of the data across the entire genome, 365 days, and 6 continents, it is impossible (at least for me) to explore this information other than randomly clicking individual data points, as we have outlined above. we think, this approach would benefit from providing the information in more digestible data fractions. Thus far, the user can choose to focus on the spike, but not on the other proteins. It would be helpful, just as a suggestion, to focus also on variants with a certain prevalence. But we are sure that the authors will have way better ideas than our proposals here, once they specify how a user should work with the plots and the data. Looking at https://nextstrain.org, which also provides a very nice overview of SARS-CoV-2 variation, may give some hints.\n\nIt would be very convenient, if the interactive plots would be designed such that the user can toggle the information for display, instead of having to go back to the main menu and select a different display mode.\n\nTrend lines that show the prevalence of a certain variant in a certain region over time would help a lot and should be easy to implement.\n\nThe orientation of where in a genome a certain variant exists is very hard. Although the vertical bars at 12 h in the circular plot should indicate in what ORF a variant is located, this is really hard to track across the full plot. In particular, because the bar-ORF assignment is not visible.\n\nAnimation of daily variant emergence is again a nice feature. However, it is a gif and not interactive. The time lapse does not allow the user to pause, fast forward, or skip to a particular time. Moreover, x-axis labels overlap in particular for the spike. This makes the plot nice to look at, but the information that can be retrieved is only limited.\n\nGraph of weekly spike protein variant emergence is not interactive and difficult to read, as the lines overlap with each other and some have similar colors. Some functionalities could be implemented such as being able to toggle strains from the right menu, selecting a time range and continent/country, and being able to hover over to display the information. 2020 and 2021 plots have layout inconsistencies and could be merged into a single graph.\n\nThe variant emergence graph heavily competes with the information in https://nextstrain.org, which claims to be updated daily.\nIn the outermost ring, we detected a variant that is assigned to na/na. What is this supposed to mean?\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? 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": [
{
"c_id": "6670",
"date": "17 May 2021",
"name": "René Warren",
"role": "Author Response",
"response": "The authors present interactive mutation time maps for SARS-CoV-2, which provide a highly resolving view of when, where and how frequent a particular mutation was detected in the sampled SARS-CoV-2 genome sequences provided via GISAID. The manuscript itself is rather short. It is briefly describing the methodological approach of how the mutations have been detected and mapped to the reference genome. The combined Results and Discussion section is equally concise and comprises a description of what is seen in the interactive maps together with few example observations that can be made with these maps. The Discussion section ends with the expression of the hope that the maps presented here “will help researchers in their exploration of SARS-CoV-2 mutations and their predicted effect over time.” Overall, the topic that is touched in this manuscript is highly relevant, as variations of SARS-CoV-2 is something that currently is and will be of major concern in the future. Here, the graphs present a very nice access to the information that is represented by the ever-increasing amount of viral genome sequences world-wide. The data presentation is appealing, and it allows to overview the general trends of SARS-CoV-2 evolution. However, we see considerable room for (essential) improvement. We thank our Reviewers for their comments, suggestions and diligence with their extensive report. Our response can be found below, in bold face Major issues: The authors end the manuscript with the belief that the interactive maps will be of help for the research community working on SARS-CoV-2 variation. We miss two things here: First, it would be great if the authors show how the data provided by the maps can be used to indeed come up with new conclusions, in particular with respect to the ‘predicted effect over time’. For us, it is entirely unclear how such an analysis should be performed. Exploring the data, this is something that one nicely can do while looking at the plots, some clear signals, e.g. the fate of D614G, can also be extracted. But how to work with the data beyond this simple and straightforward ‘looking’ at the plots? Please, don’t get us wrong here, we consider looking at data a very important aspect of data analysis. Still, the sheer amount of information, which results in very dense plots with many overlapping data points, makes it, in our opinion, very hard to identify emerging variants that should be monitored right from the start. Just to give you an example: D614G is represented by a very prominent circle in the plots. What would be the authors approach to identify and monitor a novel variant, say at position 615 of the reference strain? By looking at the plots, we consider this almost impossible, since the signal will be entirely covered by the prominent mutation at position 614. We greatly really appreciate community feedback on the potential usefulness of this work, and not only the maps, but additional analysis we were able to provide after we submitted the paper (our Reviewers made mentioned of them below), using the wealth of information we were able to mine from the GISAID genomes (these secondary analysis results, which consists of nucleotide variants and their effect, are tallied each week from each individual SARS-CoV-2 genome). We originally built the maps to be fairly qualitative, to simply gain a [visual] appreciation for the rapid coronavirus evolution on a year scale/factoring sample regions of origin, and this is what we presented in the manuscript. In our conclusion we give an example of a mutation that is observable from the GISAID genomes, on our maps, at the time reported in published papers; Since submission, the GISAID catalogue has more than doubled in size and maps quickly became dense, as our Reviewer indicated. To help remedy the problem and make the maps more useful, we have since started to provide additional genome and spike views of variants of concerns (VOCs) and have added visualizations for 2021 (a more digestible data fraction, indicated below by our Reviewer). Another type of information that can be extracted from the maps is the speed at which mutations in VOCs have appeared and spreading in additional jurisdictions, which can be readily observed without too much effort. Our Reviewers are correct that variations in close proximity are difficult to see, which is why we provide views for the spike-encoding gene. Still, it would be difficult to differentiate between positions 614 and 615, which is why we provide the SVG-generating script such that interested parties would be able to generate custom views should they chose to (Ideally a more flexible website could help, see response below). The analysis is presented using the “ground-zero” strain as a reference. But is this still timely? Numerous variants have now frequencies that go far beyond that of the original nucleotide at a certain position, again, for example the D614G variant. This would allow to ‘purge’ the signal of very successful variants, helping to direct the focus on emerging variants. Our Reviewer is correct that the comparison is relative. When we started this project in December 2020, it made sense to use the \"ground zero\" strain genome. We could make the case for selecting another set of references to compare against, but it may lead to disagreements in scientific circles, on the base genome sequence to use. Additional maps may be produced in the future to see evolution within each VOCs, which may be an acceptable proposition. When it comes to the website itself, we see some room for improvement: First and foremost, we think the plots are overcrowded with information. Although it is nice to see a global overview of the data across the entire genome, 365 days, and 6 continents, it is impossible (at least for me) to explore this information other than randomly clicking individual data points, as we have outlined above. we think, this approach would benefit from providing the information in more digestible data fractions. Thus far, the user can choose to focus on the spike, but not on the other proteins. It would be helpful, just as a suggestion, to focus also on variants with a certain prevalence. But we are sure that the authors will have way better ideas than our proposals here, once they specify how a user should work with the plots and the data. Looking at https://nextstrain.org, which also provides a very nice overview of SARS-CoV-2 variation, may give some hints. It would be very convenient, if the interactive plots would be designed such that the user can toggle the information for display, instead of having to go back to the main menu and select a different display mode. Trend lines that show the prevalence of a certain variant in a certain region over time would help a lot and should be easy to implement. The orientation of where in a genome a certain variant exists is very hard. Although the vertical bars at 12 h in the circular plot should indicate in what ORF a variant is located, this is really hard to track across the full plot. In particular, because the bar-ORF assignment is not visible. Animation of daily variant emergence is again a nice feature. However, it is a gif and not interactive. The time lapse does not allow the user to pause, fast forward, or skip to a particular time. Moreover, x-axis labels overlap in particular for the spike. This makes the plot nice to look at, but the information that can be retrieved is only limited. Graph of weekly spike protein variant emergence is not interactive and difficult to read, as the lines overlap with each other and some have similar colors. Some functionalities could be implemented such as being able to toggle strains from the right menu, selecting a time range and continent/country, and being able to hover over to display the information. 2020 and 2021 plots have layout inconsistencies and could be merged into a single graph. The variant emergence graph heavily competes with the information in https://nextstrain.org, which claims to be updated daily. We thank our Reviewers for spending the time to navigate the website, which originally, wasn't part of the project (built as a means to share the maps). We agree that a more modern and flexible web design would help with the customization and eventual uptake of these maps. Some of the plots were added to the website for convenience, to show users what is possible to do with the extensive mutation data we are compiling for this project (and available for download here) In the outermost ring, we detected a variant that is assigned to na/na. What is this supposed to mean? These variants fall in UTR regions. Thank you for the feedback, in our next release of the maps, we will replace NA by UTR to indicate that this nucleotide variant compared to the reference is found outside coding regions. The last position indicates possible effect in the protein space, which is not applicable in this case."
}
]
},
{
"id": "85294",
"date": "17 May 2021",
"name": "Takahiko Koyama",
"expertise": [
"Reviewer Expertise Genomics",
"bioinformatics",
"oncology",
"immunology",
"virology",
"and stem cell biology."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nAuthors have developed a web based visualization tool for longitudinal evolution of SARS-CoV-2 genomes.\nAlthough they have made unique representation of longitudinal strain developments, it is not clear the utility of the tool. For instance, while concentric circle representation of daily genomes is visually appealing, it limits the duration to a year and inner part inevitably becomes crowded compared with outer area.\nLack of interactivity is also an issue. There must have been a way to magnify the area.\nFurthermore, in mutation prone loci, the dots are overlapped and not easy to see what is going on. For these reasons, utility of the tool is limited; more improvements need to be done before it gains large user base.\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? 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": [
{
"c_id": "6680",
"date": "03 Jun 2021",
"name": "René Warren",
"role": "Author Response",
"response": "Authors have developed a web based visualization tool for longitudinal evolution of SARS-CoV-2 genomes. Although they have made unique representation of longitudinal strain developments, it is not clear the utility of the tool. For instance, while concentric circle representation of daily genomes is visually appealing, it limits the duration to a year and inner part inevitably becomes crowded compared with outer area. We thank our Reviewer for the valuable insights provided and spending the time to review our work. We acknowledge limitations of the display, and we stress that our original work on this was done in December, on 200,000 GISAID genomes and one year's worth of data. Our preprint became public January 2021 and we subsequently submitted this work to F1000Research, summarizing the 2020 pandemic-associated SARS-CoV-2 variants for year 2020. A circular representation is an aesthetic choice, allowing to get a bird's eye view of the breadth of mutations. Lack of interactivity is also an issue. There must have been a way to magnify the area. This is a great suggestion. We have now added the ability to pan and zoom on each map, making the maps more interactive. Furthermore, in mutation prone loci, the dots are overlapped and not easy to see what is going on. For these reasons, utility of the tool is limited; more improvements need to be done before it gains large user base. The maps were first built to visually quantify the appreciable variability that exists in rapidly evolving SARS-CoV-2 genomes. Since, we have added spike-specific views, and variants of concerns (VOCs) to the list of maps available to the community. We also provide the tools to generate the maps, such that advanced users may customize and generate additional views of interest, as needed"
},
{
"c_id": "6758",
"date": "03 Jun 2021",
"name": "René Warren",
"role": "Author Response",
"response": "We wanted to add to our previous response to our Reviewer. Once again, we are grateful for your suggestions to improve upon interactivity of the maps. Since your Review, we have worked to improve the user experience and we list below some of the new features: Interactivity Maps are draggable. Zoom/pan. Tilt 90 degrees to make axis horizontal (this and above features implemented in a navigation wheel). Colour highlight on mutation tooltip. Gene/variant views have additional colour highlight (by region) on certain maps*. *The added functionality comes at a cost, making them sluggish when views are too dense, which is why this feature is currently only used to display individual genes/variant displays and not the whole genome Overall improvements Over 120 individual displays, all SARS-CoV-2 genes are now presented. Better discrimination of close high-frequency mutations allows more information to show through by adjusting the spot ratio (r=sqrt(freq*factor/pi) and no longer plots on a log10 in ratio mode. When same %, adjust a secondary sort such that the colour matches the first region labelled. Better grouping/sorting of overlapping points. Added ability to explore switch year from the current view 2020<->2021 and between ratio(%) and raw (#) counts without having to go to main menu and use drop-down. Thanks again for spending the time to review our work."
}
]
},
{
"id": "85512",
"date": "01 Jun 2021",
"name": "Jale Moradi",
"expertise": [
"Reviewer Expertise Medical Microbiology",
"genomics",
"immunology"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors have geographically shown the nucleotide variations for global SARS-CoV-2 sequences in a time map. The sequences have been downloaded, polished and analyzed with ntHit and ntEdit. The Wuhan-Hu-1-NC_045512/MN908947 was set as the reference sequence, then the variations output was mapped based on the sample collection time by a script written in PERL. The results have shown in two circle maps including “whole viral genome” and “spike protein gene” variations over time from January 1st 2020 as day 1 to December 31st 2020 as day 366. Each radius in these circles represents a day and each spot on this radius shows a variation. Also, the spots are shown in different colours that each colour is indicating a specific geographical region (continent or country).\nIt is a useful tool to overview the evolution of the virus since the beginning of the epidemic. Furthermore, it can be concluded which part of the genome has more variations, also, the colour appearance of the map helps us to understand approximately how many mutations there are in different regions or from which ones the mutations originated. If it were possible to identify the relevant mutation (exact mutation type) by clicking on each spot, it could help more. Also, different spots have overlaps in many parts, which would provide better information if it was possible to determine which spots this overlap includes.\nOverall, the developed script provides a useful map for viewing the pattern of virus evolution globally, although it would be more informative if the authors could improve this script to solve the mentioned issues.\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? 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": [
{
"c_id": "6757",
"date": "03 Jun 2021",
"name": "René Warren",
"role": "Author Response",
"response": "We thank our Reviewer for their support of our work and insights. We also value the suggestions, as it helps us improve upon the work and broaden the interest. We have just published a revised version of the manuscript (v2), which expands on the utility of the maps, situates them in context of other similar work, and introduces new map features to increase interactivity and overall experience. Some of the maps' new features (since original submission): Interactivity Maps are draggable. Zoom/pan. Tilt 90 degrees to make axis horizontal (this and above features implemented in a navigation wheel). Colour highlight on mutation tooltip. Gene/variant views have additional colour highlight (by region) on certain maps*. *The added functionality comes at a cost, making them sluggish when views are too dense, which is why this feature is currently only used to display individual genes/variant displays and not the whole genome Improvements: Over 120 individual displays, all SARS-CoV-2 genes are now presented. Better discrimination of close high-frequency mutations allows more information to show through by adjusting the spot ratio (r=sqrt(freq*factor/pi) and no longer plots on a log10 in ratio mode. When same %, adjust a secondary sort such that the colour matches the first region labelled. Better grouping/sorting of overlapping points. Added ability to explore switch year from the current view 2020<->2021 and between ratio(%) and raw (#) counts without having to go to main menu and use drop-down. The mutation \"spots\" are also plotted incrementally (by coordinates) and by decreasing order of frequency, allowing most mutations to interactively show (and not be obscured by overlaps). But overlaps are unavoidable with displays that are too dense, and some data points may still be out of reach, but other individual maps (eg. variant/gene levels) may provide a better visual of the most important mutations. Improvements 2), 3) and 4) in particular are in response to our Reviewer's comment on spot overlap, and calculating the ratio in such a fashion (instead of log10) enables a better resolution on close-by high-frequency mutations (such as the D614G). Most displays will show missense mutation to minimize display density, but we also offer representations by types (missense vs silent) and all-encompassing. With tooltip, the mutation type is shown as either its effect in amino acid space (eg. N501Y) or silent when the nucleotide variation has no predicted effect."
}
]
}
] | 1
|
https://f1000research.com/articles/10-68
|
https://f1000research.com/articles/10-64/v1
|
03 Feb 21
|
{
"type": "Research Article",
"title": "Association between convalescent plasma and the risk of mortality among patients with COVID-19: a meta-analysis",
"authors": [
"Shinta Oktya Wardhani",
"Jonny Karunia Fajar",
"Laksmi Wulandari",
"Gatot Soegiarto",
"Yeni Purnamasari",
"Anisa Asmiragani",
"Helnida Anggun Maliga",
"Muhammad Ilmawan",
"Gloriana Seran",
"Dheka Sapti Iskandar",
"Conchita Emiliana Ndapa",
"Viviana Hamat",
"Rafika Ajeng Wahyuni",
"Linda Oktaviana Suci Cyntia",
"Feronika Maryanti Maarang",
"Yosef Andrian Beo",
"Olivera Agnes Adar",
"Iraky Mardya Rakhmadhan",
"Emilia Tiara Shantikaratri",
"Ayu Sekarani Damana Putri",
"Rizqa Wahdini",
"Endang Pati Broto",
"Agnes Wanda Suwanto",
"Fredo Tamara",
"Aditya Indra Mahendra",
"Eden Suryoiman Winoto",
"Pratista Adi Krisna",
"Harapan Harapan",
"Shinta Oktya Wardhani",
"Laksmi Wulandari",
"Gatot Soegiarto",
"Yeni Purnamasari",
"Anisa Asmiragani",
"Helnida Anggun Maliga",
"Muhammad Ilmawan",
"Gloriana Seran",
"Dheka Sapti Iskandar",
"Conchita Emiliana Ndapa",
"Viviana Hamat",
"Rafika Ajeng Wahyuni",
"Linda Oktaviana Suci Cyntia",
"Feronika Maryanti Maarang",
"Yosef Andrian Beo",
"Olivera Agnes Adar",
"Iraky Mardya Rakhmadhan",
"Emilia Tiara Shantikaratri",
"Ayu Sekarani Damana Putri",
"Rizqa Wahdini",
"Endang Pati Broto",
"Agnes Wanda Suwanto",
"Fredo Tamara",
"Aditya Indra Mahendra",
"Eden Suryoiman Winoto",
"Pratista Adi Krisna",
"Harapan Harapan"
],
"abstract": "Background: Convalescent plasma (CCP) has been used for treating some infectious diseases; however, the efficacy of CCP in coronavirus disease 2019 (COVID-19) remains controversial. The aim of this research was to assess the efficacy of CCP as an adjunctive treatment in COVID-19 patients. Methods: Four bibliographic databases and a preprint database were searched for potentially relevant articles. Mortality rates between patients treated with standard treatment and standard treatment with CCP were compared using a Z test. Results: A total of 1,937 patients treated with CCP and 3,405 patients without CCP retrieved from 12 studies were included. The risk of mortality was 1.92-fold higher in patients without CCP compared to patients treated with CCP (OR: 1.92; 95%CI: 1.33, 2.77; p=0.0005). In severe COVID-19 sub-group analysis, we found that patients without the CCP had a 1.32 times higher risk of mortality than those treated with the CCP (OR: 1.32; 95%CI: 1.09, 1.60; p=0.0040). Conclusions: CCP, as adjunctive therapy, reduces the mortality rate among COVID-19 patients.",
"keywords": [
"convalescent plasma",
"passive immunization",
"COVID-19",
"mortality",
"outcomes"
],
"content": "Introduction\n\nThe management of coronavirus disease 2019 (COVID-19) remains challenging. While the guideline for the management of COVID-19 has been established,1-3 the mortality rate of COVID-19 remains increased over the periods.4,5 The guideline suggests that several treatments, including antiviral, hydroxychloroquine, steroid, anticoagulation, and other supportive treatments, should be used to treat patients with COVID-19.1-3 However, recent evidence from large scale studies failed to clarify the efficacy of those suggested treatments.6-8 Moreover, the findings from the World Health Organization (WHO) solidarity trials also failed to clarify the benefits of hydroxychloroquine, remdesivir, interferon regimens, and lopinavir in the management of COVID-19.8 Therefore, new approaches to COVID-19 management are required.\n\nConvalescent plasma (CCP), an immunological therapy, is suggested to have promising efficacy for managing several infectious diseases.9 CCP, a strategy of passive immunization, was first introduced by von Behring and Kitasato in 1890. Initially, it was used to manage diphtheria and other infectious diseases such as scarlet fever and pertussis.10 Moreover, due to its good efficacy, this therapy was also used for the management of Ebola, severe acute respiratory syndrome (SARS), and Middle East respiratory syndrome (MERS).11 In patients with MERS, SARS, and Ebola, the clinical improvement and reduced mortality rate were observed in patients receiving CCP than patients without CPP.12 However, the efficacy of CCP against COVID-19 is conflicting. Furthermore, previous meta-analyses resulted in inconclusive findings due to the lack of structured methodology. Therefore, a holistic meta-analysis is needed to provide insight into the clinical efficacy of CCP for the management of COVID-19.\n\n\nMethods\n\nA systematic review and meta-analysis covering the period July 2020 - December 2020 was conducted to assess the efficacy of CCP as an adjunctive treatment in COVID-19 patients. Studies from prominent bibliographic databases were searched, and the protocols followed the checklist from Preferred Reporting Items for Systematic Review and Meta-analysis (PRISMA).13\n\nRelevant articles were assessed for inclusion and exclusion criteria before the final analysis. Our analysis included articles with the following criteria: (1) observational or randomized controlled trial studies; (2) providing sufficient data of COVID-19 diagnosis methods; and (3) well-identified methodologies represented with Newcastle-Ottawa Scale (NOS). Case reports, case series, letters to the editor, reviews, commentaries, low method quality, and those with pre-post test comparison were excluded.\n\nRelevant studies in four bibliographic databases (Embase, PubMed, Web of Science, and Cochrane) and a preprint database MedRix were searched as of 2 December 2020. The searches limited to English only using Medical Subjects Heading: (“COVID-19” OR “SARS-CoV-2”) AND (“convalescent plasma” OR “serotherapy” OR “hyperimmune globulin therapy” OR “convalescent plasma treatment”). A reference list of the relevant articles was also retrieved for additional references. Information of: (1) name of the first author; (2) year of publication; (3) country of origin; (4) sample size of cases and controls, (5) CCP administration, and (6) mortality rate were collected from each article.\n\nThe quality of potential papers was assessed using the Newcastle-Ottawa Scale (NOS).14 This scoring system evaluates the sample selection, group comparison, and the outcome. The quality of the articles could be classified as low, moderate, and high quality. Articles with low quality were excluded from our analysis. The assessment was carried out by three independent investigators (MI, AAA & YP), and when there was a discrepancy among the investigators, a discussion was performed with a senior researcher (JKF).\n\nThe primary outcome measure was all causes of mortality among COVID-19 patients treated with and without CCP. The predictor variable was COVID-19 patients treated with CCP. A sub-group analysis was conducted based on the severity of COVID-19 patients treated with CCP (e.i. mild and severe).\n\nThe association between CCP and the reduction of the risk of mortality among COVID-19 patients was assessed using a Z test. Before assessing the association, the potency of bias and heterogeneity was assessed. To assess the risk of bias, an Egger test was employed to calculate tau-squared, and a p-value of less than 0.05 indicates that the potency of bias was found. A Q test was used to assess the heterogeneity among the included papers. The p-value of less than 0.10 was considered that heterogeneity across the studies was found, and the correlation was therefore determined using a random-effect model; otherwise, a fixed-effect model was employed. All analyses were carried out using Review Manager (Revman Cochrane, London, UK) version 5.3, and the cumulative calculation was presented using a forest plot.\n\n\nResults\n\nA total of 1,143 papers were identified, and 1,105 papers were excluded because they had irrelevant topics. A total of 38 papers were included for review in full-text, and 26 additional papers were excluded because of review, pre-post test model, commentary, and low-quality papers. In the final process, 12 papers were included in our analysis.15-26 The article selection flowchart is depicted in Figure 1, and the study characteristics are presented in Table 1.\n\nA total of 1,937 patients treated with CCP and 3,405 patients without CCP, collected from 12 papers, were included in our analysis. Data suggest that COVID-19 patients without the CCP had a 1.92-fold higher risk of mortality than patients treated with the CCP (OR: 1.92; 95%CI: 1.33, 2.77; p=0.0005) (Figure 2A). A sub-group analysis among severe COVID-19 patients who were treated with CCP was conducted. This sub-group consisted of nine papers with 1,458 patients treated with CCP and 2,706 patients without CCP. The data revealed a 1.32-fold higher risk of mortality in COVID-19 patients without CCP compared to patients treated with CCP (OR: 1.32; 95%CI: 1.09, 1.60; p=0.0040) (Figure 2B).\n\nA). All cases (OR: 1.92; 95%CI: 1.33, 2.77; p = 0.0005; p Egger: 0.3620; p Heterogeneity: 0.0600; I-squared: 43.00%). B). Severe COVID-19 (OR: 1.32; 95%CI: 1.09, 1.60; p = 0.0040; p Egger: 0.3790; p Heterogeneity: 0.1200; I-squared: 37.00%).\n\nThe analysis revealed evidence of heterogeneity in total case of COVID-19. Therefore, a random-effect model was applied to assess the association. In the severe COVID-19 sub-group, we found no heterogeneity, and we used a fixed-effect model to evaluate the correlation. Our analysis using an Egger test found no publication bias in both the total and the severe COVID-19 sub-group.\n\n\nDiscussion\n\nOur data suggest that CCP treatment associated with a reduction of mortality both in all cases and severe COVID-19 patients. Our current findings are consistent with the results of previous meta-analyses.27-32 The theory underlying the mechanism of CCP in COVID-19 patients remains open to controversy. Briefly, plasma transfer is the potential aspect that bridges the CCP and the reduced risk of mortality in COVID-19 patients. Plasma consists of various immunity components, including antibodies, anti-inflammatory cytokines, clotting and or anti-clotting factors, albumin, and protein C and S.33,34 It is believed that CCP in COVID-19 may modulate the immune response through antiviral effects and has immunomodulatory effects.35 Antiviral effects of CCP may occur through neutralizing antibodies, and it was reported that IgG of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and IgM SARS-CoV-2 were the primary isotype antibodies identified from COVID-19 patients treated with CCP.36 This humoral immune response may inhibit protein S of SARS-CoV-2.37 Thereafter, they may exert the protective effects against COVID-19. The immunomodulatory effects of CCP may occur through the neutralization of cytokines and complements.35,38 These effects may inhibit the overactive immune system, including cytokine storm, complement activation, and hypercoagulable state regulation.39 These mechanisms may be responsible for causing clinical improvement of COVID-19 patients. Of them, it was considered that immunoglobulin transfer is the essential factor in modulating the protective effect of CCP.40 In SARS and influenza, it was reported that immunoglobulin transfer plays a vital role in governing clinical improvement.9,11 Moreover, in MERS, the CCP administration with the titers of antibodies 1:80 provided a significant immune response, and the titers of antibodies 1:40 did not provide a similar response.41 Additionally, in Ebola, MERS, and SARS, the antibodies from the CCP may bind to the CD4 binding site on the viral envelope, and therefore may reduce the viral load and the risk of infection of the new cells.42 It was also supported by previous studies that antibody titers from CCP donors also governed the clinical improvement of COVID-19 patients treated with CCP,43,44 suggesting that antibody transfer might influence the outcomes of clinical improvement.\n\nSix meta-analyses assessing the role of CCP in COVID-19 have been reported (Table 2).27-32 However, they had some significant limitations: (a) they involved a smaller sample size. In our current study, we had a relatively larger sample size; (b) some studies did not perform meta-analysis calculations to synthesize the data27,29; (c) previous studies included several case reports and case series28,29 in which should be excluded in the meta-analysis13; (d) previous meta-analyses assessed the role of CCP in similar infectious diseases (SARS and influenza), and the results were implemented to the case of COVID-1930,31; and (e) previous meta-analyses performed a mixed calculation where the data of the case vs. control model were combined with the data of pre-post intervention models, which might provide a high risk of bias due to the final effect that might be caused by other interventions.29,32 In the present meta-analysis, we only calculated the model of the case (standard treatment and CCP) vs. control (standard treatment only) and therefore might provide a better correlation.\n\n- No calculation of data synthesis\n\n- Seven case report or case series articles were included\n\n- One study comparing the outcome between pre and post convalescent plasma.\n\n- The case is non COVID-19\n\n- Three case report or case series articles were included\n\n- The comparison was pre and post convalescent plasma.\n\n- No calculation of data synthesis\n\n- One study comparing the outcome between pre and post convalescent plasma, other studies assessing between convalescent plasma and control (Mixed calculation).\n\n- Inappropriate calculation.\n\n- The case is non COVID-19\n\nIn the present study, we emphasized that CCP provided good efficacy to reduce the risk of mortality among COVID-19 patients. Our findings might contribute to better management of COVID-19 patients, particularly to prevent the risk of mortality. It is expected that a medical council should elaborate on the standard procedures of CCP, including the dosage, donor criteria, side effects management, and post-intervention management. Since early administration of CCP provided better clinical outcomes than those with later intervention,45 the appropriate time of CCP administration should be determined, and further studies are warranted.\n\nSeveral important limitations of this study should be discussed. Some confounding factors that might govern the final outcomes were not controlled, including the immunological status, the dosage of CCP, time of intervention, donor criteria, the titers of antibodies, comorbidities, and transmission area. The majority of the included papers were retrospective studies, and therefore a further meta-analysis of randomized-controlled trials with a bigger sample size might provide a better conclusion.\n\n\nConclusion\n\nAdministration of the CCP is associated with a lower risk of mortality among COVID-19 patients compared to those without CCP, and this highlights its potency to be used for the treatment of COVID-19. However, studies are warranted to formulate the dosage, time of intervention, donor criteria, and the titers of antibodies to optimize the effects.\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: PRISMA checklist for ‘Association between convalescent plasma and the risk of mortality among patients with COVID-19: A meta-analysis’, https://doi.org/10.6084/m9.figshare.13490541.v1.46\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "Acknowledgements\n\nWe thank to Lembaga Pengelola Dana Pendidikan (LPDP) Republik Indonesia for supporting this project.\n\n\nReferences\n\nLamontagne F, Agoritsas T, Macdonald H, et al.: A living WHO guideline on drugs for covid-19. BMJ 2020; 370: m3379. PubMed Abstract | Publisher Full Text\n\nFalavigna M, Colpani V, Stein C, et al.: Guidelines for the pharmacological treatment of COVID-19. The task-force/consensus guideline of the Brazilian Association of Intensive Care Medicine, the Brazilian Society of Infectious Diseases and the Brazilian Society of Pulmonology and Tisiology. Rev Bras Ter Intensiva 2020; 32: 166–96. PubMed Abstract | Publisher Full Text | Free Full Text\n\nJin YH, Cai L, Cheng ZS, et al.: A rapid advice guideline for the diagnosis and treatment of 2019 novel coronavirus (2019-nCoV) infected pneumonia (standard version). Mil Med Res 2020; 7: 4. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBaud D, Qi X, Nielsen-Saines K, et al.: Real estimates of mortality following COVID-19 infection. Lancet Infect Dis 2020; 20: 773. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKarimullah MDH, Niazta NA, Ardining H: Venous Thromboembolism Prevention in COVID-19: A Review of Latest Evidences. Heart Science J 2020; 1: 10–14. Publisher Full Text\n\nSingh AK, Singh A, Singh R, et al.: Hydroxychloroquine in patients with COVID-19: A Systematic Review and meta-analysis. Diabetes Metab Syndr 2020; 14: 589–96. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWang Y, Zhang D, Du G, et al.: Remdesivir in adults with severe COVID-19: a randomised, double-blind, placebo-controlled, multicentre trial. Lancet 2020; 395: 1569–78. PubMed Abstract | Publisher Full Text | Free Full Text\n\nConsortium WHOSTPan H, Peto R, et al.: Repurposed Antiviral Drugs for Covid-19 - Interim WHO Solidarity Trial Results. N Engl J Med 2020. PubMed Abstract | Publisher Full Text | Free Full Text\n\nYeh KM, Chiueh TS, Siu LK, et al.: Experience of using convalescent plasma for severe acute respiratory syndrome among healthcare workers in a Taiwan hospital. J Antimicrob Chemother 2005; 56: 919–22. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKaufmann SH: Remembering Emil von Behring: from Tetanus Treatment to Antibody Cooperation with Phagocytes. mBio 2017; 8. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLiya G, Yuguang W, Jian L, et al.: Studies on viral pneumonia related to novel coronavirus SARS-CoV-2, SARS-CoV, and MERS-CoV: a literature review. APMIS 2020; 128: 423–32. PubMed Abstract | Publisher Full Text\n\nMarano G, Vaglio S, Pupella S, et al.: Convalescent plasma: new evidence for an old therapeutic tool? Blood Transfus 2016; 14: 152–7. PubMed Abstract | Publisher Full Text | Free 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. PLoS Med 2009; 6: e1000100. PubMed Abstract | Publisher Full Text | Free Full Text\n\nStang A: Critical evaluation of the Newcastle-Ottawa scale for the assessment of the quality of nonrandomized studies in meta-analyses. Eur J Epidemiol 2010; 25: 603–5. PubMed Abstract | Publisher Full Text\n\nAbolghasemi H, Eshghi P, Cheraghali AM, et al.: Clinical efficacy of convalescent plasma for treatment of COVID-19 infections: Results of a multicenter clinical study. Transfus Apher Sci 2020; 59: 102875. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAltuntas F, Ata N, Yigenoglu TN, et al.: Convalescent plasma therapy in patients with COVID-19. Transfus Apher Sci 2020; 102955. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChen B, Xia R: Early experience with convalescent plasma as immunotherapy for COVID-19 in China: Knowns and unknowns. Vox Sang 2020; 115: 507–14. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGharbharan A, Jordans CC, GeurtsvanKessel C, et al.: Convalescent Plasma for COVID-19. A randomized clinical trial. MEDRxiv 2020. Publisher Full Text\n\nHegerova L, Gooley TA, Sweerus KA, et al.: Use of convalescent plasma in hospitalized patients with COVID-19: case series. Blood 2020; 136: 759–62. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLi L, Zhang W, Hu Y, et al.: Effect of Convalescent Plasma Therapy on Time to Clinical Improvement in Patients With Severe and Life-threatening COVID-19: A Randomized Clinical Trial. JAMA 2020; 324: 460–70. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRasheed AM, Fatak DF, Hashim HA, et al.: The therapeutic potential of convalescent plasma therapy on treating critically-ill COVID-19 patients residing in respiratory care units in hospitals in Baghdad, Iraq. Infez Med 2020; 28: 357–66. PubMed Abstract\n\nSalazar E, Christensen PA, Graviss EA, et al.: Significantly Decreased Mortality in a Large Cohort of Coronavirus Disease 2019 (COVID-19) Patients Transfused Early with Convalescent Plasma Containing High-Titer Anti-Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Spike Protein IgG. Am J Pathol 2020. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSalazar E, Christensen PA, Graviss EA, et al.: Treatment of Coronavirus Disease 2019 Patients with Convalescent Plasma Reveals a Signal of Significantly Decreased Mortality. Am J Pathol 2020; 190: 2290–303. PubMed Abstract | Publisher Full Text | Free Full Text\n\nXia X, Li K, Wu L, et al.: Improved clinical symptoms and mortality among patients with severe or critical COVID-19 after convalescent plasma transfusion. Blood 2020; 136: 755–9. PubMed Abstract | Publisher Full Text | Free Full Text\n\nZeng QL, Yu ZJ, Gou JJ, et al.: Effect of Convalescent Plasma Therapy on Viral Shedding and Survival in Patients With Coronavirus Disease 2019. J Infect Dis 2020; 222: 38–43. PubMed Abstract | Free Full Text Free Full Text\n\nSimonovich VA, Burgos Pratx LD, Scibona P, et al.: A Randomized Trial of Convalescent Plasma in Covid-19 Severe Pneumonia. N Engl J Med 2020. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRajendran K, Krishnasamy N, Rangarajan J, et al.: Convalescent plasma transfusion for the treatment of COVID-19: Systematic review. J Med Virol 2020; 92: 1475–83. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRabelo-da-Ponte FD, Silvello D, Scherer JN, et al.: Convalescent Plasma Therapy in Patients With Severe or Life-Threatening COVID-19: A Metadata Analysis. J Infect Dis 2020; 222: 1575–8. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBakhtawar N, Usman M, Khan MMU: Convalescent Plasma Therapy and Its Effects On COVID-19 Patient Outcomes: A Systematic Review of Current Literature. Cureus 2020; 12: e9535. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDevasenapathy N, Ye Z, Loeb M, et al.: Efficacy and safety of convalescent plasma for severe COVID-19 based on evidence in other severe respiratory viral infections: a systematic review and meta-analysis. CMAJ 2020; 192: E745–E55. PubMed Abstract | Publisher Full Text\n\nSun M, Xu Y, He H, et al.: A potentially effective treatment for COVID-19: A systematic review and meta-analysis of convalescent plasma therapy in treating severe infectious disease. Int J Infect Dis 2020; 98: 334–46. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSarkar S, Soni KD, Khanna P: Convalescent plasma is a clutch at straws in COVID-19 management! A systematic review and meta-analysis. J Med Virol 2020. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRojas M, Rodriguez Y, Monsalve DM, et al.: Convalescent plasma in Covid-19: Possible mechanisms of action. Autoimmun Rev 2020; 19: 102554. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMudatsir M, Fajar JK, Wulandari L, et al.: Predictors of COVID-19 severity: a systematic review and meta-analysis. F1000Res 2020; 9: 1107. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAlijotas-Reig J, Esteve-Valverde E, Belizna C, et al.: Immunomodulatory therapy for the management of severe COVID-19. Beyond the anti-viral therapy: A comprehensive review. Autoimmun Rev 2020; 19: 102569. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDulipsingh L, Ibrahim D, Schaefer EJ, et al.: SARS-CoV-2 serology and virology trends in donors and recipients of convalescent plasma. Transfus Apher Sci 2020; 102922. PubMed Abstract | Publisher Full Text | Free Full Text\n\nXi Y: Convalescent plasma therapy for COVID-19: a tried-and-true old strategy? Signal Transduct Target Ther 2020; 5: 203. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFocosi D, Anderson AO, Tang JW, et al.: Convalescent Plasma Therapy for COVID-19: State of the Art. Clin Microbiol Rev 2020; 33. PubMed Abstract | Publisher Full Text | Free Full Text\n\nJaiswal V, Nasa P, Raouf M, et al.: Therapeutic plasma exchange followed by convalescent plasma transfusion in critical COVID-19-An exploratory study. Int J Infect Dis 2020; 102: 332–4. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLanghi DMJ, Santis GC, Bordin JO: COVID-19 convalescent plasma transfusion. Hematol Transfus Cell Ther 2020; 42: 113–5. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKo JH, Seok H, Cho SY, et al.: Challenges of convalescent plasma infusion therapy in Middle East respiratory coronavirus infection: a single centre experience. Antivir Ther 2018; 23: 617–22. PubMed Abstract | Publisher Full Text\n\nSchoofs T, Klein F, Braunschweig M, et al.: HIV-1 therapy with monoclonal antibody 3BNC117 elicits host immune responses against HIV-1. Science 2016; 352: 997–1001. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWu F, Liu M, Wang A, et al.: Evaluating the Association of Clinical Characteristics With Neutralizing Antibody Levels in Patients Who Have Recovered From Mild COVID-19 in Shanghai, China. JAMA Intern Med 2020; 180: 1356–62. PubMed Abstract | Publisher Full Text\n\nBradfute SB, Hurwitz I, Yingling AV, et al.: Severe Acute Respiratory Syndrome Coronavirus 2 Neutralizing Antibody Titers in Convalescent Plasma and Recipients in New Mexico: An Open Treatment Study in Patients With Coronavirus Disease 2019. J Infect Dis 2020; 222: 1620–8. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCheng Y, Wong R, Soo YO, et al.: Use of convalescent plasma therapy in SARS patients in Hong Kong. Eur J Clin Microbiol Infect Dis 2005; 24: 44–6. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFajar J: PRISMA CHECLIST for Association between convalescent plasma and the risk of mortality among patients with COVID-19: A meta-analysis. figshare 2020. Publisher Full Text"
}
|
[
{
"id": "78924",
"date": "15 Feb 2021",
"name": "Morteza Arab-Zozani",
"expertise": [
"Reviewer Expertise Health-related issues and systematic review and meta-analysis methodology."
],
"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 meta-analysis aimed to investigate the association between convalescent plasma and the risk of mortality among patients with COVID-19. This is a great area of research but, in my opinion, the manuscript needs some major revisions as follows:\nPlease indicate the name of the searched databases in the abstract section.\n\nPlease indicate the quality appraisal checklist in the abstract section.\n\nPlease indicate the method for investigating the heterogeneity and publication bias in the abstract section.\n\nPlease indicate the type of the included studies in the abstract, results, and table 1.\n\nWhat is your reason for selecting this period for your search?\n\nSearch strategy is not complete.\n\nPlease restructure the method section following the PRISMA item as you claim.\n\nThere are some problems regarding figure 1. Was there no duplicate record? It does not make much sense.\n\nIt needs to mention the type of the included studies and then we can speak about the quality appraisal checklist. it seems that NOS is not sufficient. NOS is for nonrandomized studies.\n\nPlease indicate inter-rater reliability between three raters.\n\nResult section, please add a subheading for \"study characteristics\" based on PRISMA and first write a brief and then refer to table 1. Also, add the type of the control in column control.\n\nFigure 1 has some problems. Your study is a meta-analysis. How were 11 studies included in qualitative synthesis? Which qualitative synthesis?\n\nThere is a 6 % difference between I2 for A and B, what is your rationale for selecting the fixed or random-effect model? Please provide a reference for your claim. Please add the details in the method section.\n\nPlease add the funnel plot as a supplement.\n\nPlease remove table 2 from the discussion and also discuss the added value of your study regarding the existing meta-analysis. What is the novelty of your work?\n\nThe conclusion is very optimistic. How did you come to that conclusion based solely on mortality?\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? No",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-64
|
https://f1000research.com/articles/10-426/v1
|
28 May 21
|
{
"type": "Research Article",
"title": "A review of the Cochrane COVID-19 Study Register reveals inconsistency in the choice and measurement of SARS-CoV-2 infection outcomes in prevention trials",
"authors": [
"Susanna Dodd",
"Sarah Gorst",
"Kerry Avery",
"Nicola Harman",
"Rhiannon Macefield",
"Paula Williamson",
"Jane Blazeby",
"COS-COVID-P Steering Committee",
"Sarah Gorst",
"Kerry Avery",
"Nicola Harman",
"Rhiannon Macefield",
"Paula Williamson",
"Jane Blazeby"
],
"abstract": "Background: Multiple studies are evaluating how to prevent SARS-CoV-2 infection. Interventions are wide ranging and include vaccines, prophylactic drugs, public health safety measures, and behavioural interventions. Heterogeneity in the outcomes measured and reported is leading to research waste and inefficiency, slowing worldwide identification and implementation of effective methods to prevent infection. A core outcome set (COS) for studies of interventions to prevent SARS-CoV-2 infection has recently been developed, identifying infection as a critical outcome to measure. This paper examines how SARS-CoV-2 infection outcomes are measured in registered COVID-19 prevention trials and considers how this can be improved.\nMethods: We searched the Cochrane COVID-19 Study Register to identify and review SARS-CoV-2 infection outcomes in prevention trials, including the rationale for choice of outcome measurement. We included phase 3 and 4 trials of COVID-19 prevention interventions. Early phase trials and studies relating to the transmission, treatment or management of COVID-19 were excluded.\nResults: We identified 430 entries in the register, of which 199 unique prevention trials were included across eight settings and 12 intervention types. Fifteen (8%) trials did not include any SARS-CoV-2 infection outcomes. The remaining 184 (92%) studies included a total of 268 SARS-CoV-2 infection outcomes, of which 32 (17%) did not specify how infection would be measured. Testing (i.e. formal diagnostic test) as a standalone method for determining infection was used in 57 (31%) trials, whereas defining infection by symptoms alone was used in 16 (9%) trials. All other trials (n=79, 43%) included multiple infection outcomes, defined in different ways.\nDiscussion: There is considerable variation in how SARS-CoV-2 infection is measured within and across different interventions and settings. Furthermore, few studies report the rationale for outcome selection and measurement. Better transparency and standardisation of SARS-CoV-2 infection measurement is needed for the findings from prevention trials to inform decision-making.",
"keywords": [
"SARS-CoV-2",
"infection",
"outcomes",
"outcome measurement",
"COVID-19",
"prevention",
"trials"
],
"content": "Introduction\n\nCoronavirus disease 2019 (COVID-19), resulting from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, has significant morbidity and mortality. Addressing human-to-human transmission of SARS-CoV-2 is a global research priority.1 Research to fully understand the modes of transmission of SARS-CoV-2 is ongoing. Studies to prevent the spread of SARS-CoV-2 are increasing, with more than 1000 studies registered between December 2020 and February 2021.2 Interventions are wide ranging, including public health measures such as lockdown of countries/cities, closure of schools and public places, social distancing measures and handwashing, interventions in primary and secondary care practice such as the use of personal protective equipment (PPE) and increased time for appointments/interventions, alongside the development of effective vaccines and drugs to prevent disease.\n\nEvidence is accumulating to evaluate the effectiveness of prevention interventions, but limitations in evidence synthesis have been identified because of inconsistent selection, measurement and reporting of outcomes in the studies.3–5 Whilst studies primarily focus on mitigating the risk of contracting COVID-19, they may measure other outcomes relevant to the population of interest and type of intervention, for example, educational outcomes in studies of school closures6 and tolerance/acceptability in studies of PPE use in secondary care.5 However, unnecessary heterogeneity in the outcomes measured and reported in COVID-19 prevention trials leads to research waste and inefficiency. For example, a recent commentary highlighted the rarity of randomised trials of public health interventions for COVID-19, which is likely due to the need for unattainably large sample sizes.7 Fretheim argues that underpowered trials in public health should be regarded as contributions to the larger body of evidence on COVID-19. However, for underpowered trials to be collectively assessed and synthesised in systematic reviews they need to be measuring the same outcomes.\n\nA solution to this issue is to develop a core outcome set (COS), which is defined as an agreed standardised set of outcomes that should be measured and reported, as a minimum, in all clinical research studies in a specific area of health care to address inconsistencies in outcome measurement.8 The COS-COVID-P study, in collaboration with an international and multidisciplinary committee of experts and public contributors, has developed a COS for studies of interventions to prevent SARS-CoV-2 infection. During the COS development process, online workshops were held to consider the evidence on COVID-19 prevention and the issue of outcome heterogeneity. More than 70 key international stakeholders, including clinicians, researchers, public representatives, methodologists, systematic reviewers, guideline developers, and regulatory agency representatives shared their expert opinions. Agreement on the final COS was reached in August 2020. Two outcome domains were identified as being essential to all COVID-19 prevention studies: infection and intervention-specific harms.9 How to measure these outcomes now requires consideration and led to this paper.\n\nSARS-CoV-2 infection can be measured through laboratory testing, symptom assessment or a combination of both.2 However, there is no single standalone diagnostic test nor agreement on diagnostic symptoms.10,11 Thus, there is a pressing need to consider how to assess SARS-CoV-2 infection uniformly across studies to optimise data reporting and synthesis. The aim of this study is to review SARS-CoV-2 infection outcomes in registered COVID-19 prevention trials and examine the reported rationales for choice of outcome measurement. Our intention is that this will inform optimal methods for the design of future studies.\n\n\nMethods\n\nFor the purposes of the review presented here, we searched the Cochrane COVID-19 Study Register https://covid-19.cochrane.org/ on 24 November 2020. The Cochrane COVID-19 Study Register is a freely available, annotated reference collection of primary research studies on COVID-19, including interventional, observational, diagnostic, prognostic, epidemiological and qualitative designs. The register is continually updated to support rapid evidence synthesis, and includes studies from multiple data sources including Clinicaltrials.gov, the Cochrane Central Register of Controlled Trials (CENTRAL), Embase, medRxiv, PubMed and the WHO International Clinical Trials Registry Platform (ICTRP). We restricted our Cochrane COVID-19 Study Register search results by study type (“interventional”), study design (“parallel/crossover”), intervention assignment (“randomised”) and study aim (“prevention”). The Cochrane COVID-19 Study Register defines prevention studies as those aiming to assess one or more interventions for preventing the development of a specific disease or health condition.\n\nWe included phase three and four trials of prevention interventions for COVID-19. We excluded phase one and two trials, including those that used other terms to imply that they were early phase (e.g. “explorative”), because these trials focus on safety, rather than the effectiveness of an intervention. Studies relating to the transmission, treatment or management of COVID-19 were also excluded. Studies identified from the Cochrane COVID-19 Study Register search were split equally between five experienced systematic reviewers (KA, SD, SG, NH, RM), who assessed the eligibility of their cohort of studies according to these eligibility criteria.\n\nData from eligible trials were extracted using a piloted, standardised data extraction spreadsheet, with the work split equally between five experienced systematic reviewers (KA, SD, SG, NH, RM). In cases of any ambiguity or doubt, queries were assessed by SD. Any queries were discussed with the whole team who collectively reached agreement on how to progress. The following data were extracted for each study: intervention type (e.g. drug, vaccine, behavioural), intervention (as described verbatim), setting (i.e. population of interest), SARS-CoV-2 infection outcomes (as described verbatim), SARS-CoV-2 infection outcome definition (i.e. how SARS-CoV-2 infection would be measured), whether or not the SARS-CoV-2 infection outcome was specified as being a primary or secondary outcome, and the rationale provided for SARS-CoV-2 infection outcome measurement selection. In addition, the reviewers recorded whether the study record related to a registry entry, trial protocol or the main report. If the registry entry record provided a link to a study protocol, this protocol was also reviewed, and the relevant data extracted.\n\nExtracted data were summarised according to the number of SARS-CoV-2 infection outcomes per trial. For trials that included one SARS-CoV-2 infection outcome, data were summarised according to the single outcome definition specified in each trial (i.e. testing, symptoms, testing or symptoms, testing and symptoms). For trials that included multiple SARS-CoV-2 infection outcomes, data were summarised according to each outcome definition combination. For example, some trials may have measured one SARS-CoV-2 infection outcome using testing alone, a second SARS-CoV-2 infection outcome by symptoms alone and a third SARS-CoV-2 infection outcome by testing and symptoms. In addition to analysing the data by the overarching outcome definition (e.g. testing), we also summarised the data according to the specific underlying definition. For example, a trial would be summarised as having two versions of testing if they specified that one SARS-CoV-2 infection outcome was determined by reverse-transcriptase polymerase chain reaction (RT-PCR), and another SARS-CoV-2 infection outcome was determined by serology (antibodies, seroconversion, seroprevalence). The categorisation of outcome definitions was based on the verbatim text available in the registry records. Analysis was carried out using Stata version 16.1.\n\n\nResults\n\nOur searching of the Cochrane COVID-19 Study Register returned 430 records that were screened for eligibility, of which 231 were excluded. A total of 199 unique prevention trials were identified (Figure 1).\n\nOf the 199 eligible trials, 176 (88%) had a trial registry record only. The remaining 23 trials had registry records plus a protocol (n = 15, 8%) or journal article (n = 6, 3%) or both a protocol and journal article (n = 2, 1%). Most trials examined drug prophylaxis (n = 92, 46%) or vaccine (n = 54, 27%) interventions. Other interventions included dietary supplements (n=20, 10%), behavioural/social distancing (n = 12, 6%) and PPE or other physical barriers (n = 7, 4%). Fourteen (7%) trials evaluated other interventions that included Ayurveda, homeopathy, traditional Chinese medicine, a medicinal plant, Unani, telehealth and financial support.\n\nThe trials were undertaken across eight combinations of setting and population of interest, with almost half (n = 98, 49%) in healthcare workers. Other settings included adults in the community (n = 45, 23%), high risk groups (e.g. elderly, hospitalised, or specific disease; n = 21, 11%), people in close contact with COVID-19 cases (e.g. family members; n = 16, 8%), nursing home residents and/or staff (n = 10, 5%), people with potential exposure to COVID-19 (n = 5, 3%), police (n = 3, 2%) and schools (n = 1, <1%). The characteristics of included trials are described in Table 1.\n\n1 Seven of these studies also included others in close contact with COVID cases (two of which also included high risk groups); a further two of these studies included others with potential exposure to COVID (one of which also included police).\n\n2 Or equivalent term.\n\n3 In 32 (16.1%) studies, the single COVID outcome was a non-specific term.\n\nOf the 199 trials, 15 (8%) did not include any SARS-CoV-2 infection outcomes. These 15 studies predominantly evaluated behavioural (n = 8, where interventions were ‘STOP touching your face' mindfulness online training programme; Brief informational infographic; E-E video about COVID hygiene; Mental Imagery; Digital health literacy intervention; e-learning module; Telepsychoeducation with personalized videos; combined video display and live demonstration as training methods to healthcare providers for donning and doffing PPE) or PPE/physical barrier (n = 3) interventions, with the remaining four trials evaluating social distancing, dietary supplements, a medicinal plant and homeopathy. Examples of outcomes recorded in trials that did not include a SARS-CoV-2 infection outcome included frequency of face-touching behaviour in a behavioural intervention trial12 and contamination of any part of the base clothing or exposed skin of the upper body in a PPE trial.13\n\nA total of 268 SARS-CoV-2 infection outcomes were identified across 184 (92%) trials, with infection measured as a primary outcome in 149 (81%) studies. Table 2 provides the outcome definitions recorded. We categorised outcome definitions using the verbatim text available in the registry records. In 118 (64%) trials, a single infection outcome was included. Fifty (27%) trials included two infection outcomes, 14 (8%) included three infection outcomes and two (1%) included four infection outcomes. Examples of multiple infection outcomes within the same trial are provided in Table 2. Table 3 lists the specific outcome definitions across the 184 trials.\n\n1 Note that when the same COVID outcome definition was measured at multiple time points or analysed in multiple ways (e.g. as a binary outcome AND a time to event outcome), these repetitions were considered as a single COVID outcome for the purpose of this review.\n\n2 Example of two infection outcomes: ‘Number of people turning symptomatic’ and ‘Number of people turning Covid19 positive’ (see: http://www.ctri.nic.in/Clinicaltrials/pmaindet2.php?trialid=44065).\n\n3 Example of three infection outcomes: ‘positive serology or RT-PCR for COVID-19 up until day 28’, ‘positive serology at day 28’ and ‘symptoms of COVID-19’ (see: https://clinicaltrials.gov/ct2/show/NCT04342156).\n\n4 Example of four infection outcomes: ‘Number of symptomatic infections confirmed by SARS-CoV-2 (COVID-19)’, ‘Number of asymptomatic infections confirmed by SARS-CoV-2 (COVID-19)’, ‘Severity of SARS-CoV-2 (COVID-19) infection’ and ‘Duration of symptoms of COVID-19 coronavirus infection’ (see: https://www.clinicaltrialsregister.eu/ctr-search/trial/2020-001530-35/ES).\n\n\n\n• COVID\n\n• SARS-Cov-2 infection\n\n• infected\n\n\n\n• confirmed\n\n• documented\n\n\n\n• positivity (positive disease/test)\n\n\n\n• antigen test\n\n\n\n• swab\n\n\n\n• lab confirmation\n\n\n\n• microbiologically confirmed\n\n\n\n• molecular test\n\n\n\n• RT-PCR\n\n\n\n• serology (antibodies, seroconversion, seroprevalence)\n\n\n\n• RT-PCR OR serology\n\n\n\n• test OR seroconversion\n\n\n\n• virology OR serology\n\n\n\n• molecular OR serological test\n\n\n\n• RT-PCR AND SARS-Cov-2 test\n\n\n\n• symptomatic1,2\n\n\n\n• clinical evidence\n\n\n\n• clinical disease without laboratory confirmation\n\n\n\n• confirmed via online questionnaire\n\n\n\n• confirmed OR probable\n\n\n\n• lab confirmation OR symptomatic\n\n• positive test OR symptomatic\n\n\n\n• asymptomatic OR symptomatic\n\n\n\n• microbiological test OR clinical features\n\n\n\n• RT-PCR OR symptomatic\n\n\n\n• RT-PCR OR serology OR symptomatic\n\n\n\n• molecular confirmation OR symptomatic\n\n\n\n• asymptomatic\n\n\n\n• lab confirmation AND asymptomatic\n\n\n\n• lab confirmation AND symptomatic\n\n\n\n• microbiologically confirmed AND symptomatic\n\n\n\n• microbiologically AND lab confirmed AND symptomatic\n\n\n\n• RT-PCR AND symptomatic\n\n\n\n• (RT-PCR OR serology) AND asymptomatic\n\n\n\n• (RT-PCR OR serology) AND symptomatic\n\n\n\n• (RT-PCR OR molecular test) AND symptomatic\n\n\n\n• (serology OR lab confirmed) AND symptomatic\n\n\n\n• serology AND asymptomatic\n\n\n\n• serology AND symptomatic\n\n\n\n• (serology AND symptomatic) OR RT-PCR\n\n\n\n• virologically-confirmed AND symptomatic\n\n\n\n• test AND symptomatic\n\n\n\n• molecular confirmation AND symptomatic\n\n1 Includes one study that specified individual symptoms only.\n\n2 Note that “symptomatic” includes references to clinical confirmation.\n\nForty-five (25%) trials defined infection in non-specific terms (e.g. “COVID”, “SARS-CoV-2 infection”, “infected”, “confirmed”), without specifying how infection would be/was determined (i.e. via a specific test to be undertaken or symptoms to be recorded). In 32 of these trials (17% of all included trials), the non-specific infection term was the only infection outcome listed. Figure 2 displays the number of trials with non-specific COVID outcomes by month of registration. Of the 45 trials with non-specific COVID outcomes, 23 (51%) trials were registered within the first three months (March to May 2020) of the COVID-19 outbreak being declared a global pandemic.\n\nLeft-hand axis - number of trials. Right-hand axis - % of total number of trials.\n\nTesting was the only means employed for determining infection in 57 (31%) trials, whereas relying on symptoms alone to define infection occurred in 16 (9%). All other trials included multiple infection outcomes, defined in different ways (Table 2). Where one of the infection outcomes was to be determined by testing alone (n = 96), this was most commonly by RT-PCR (n = 36, 20%) and serology (n = 22, 12%) tests. Where infection was defined on the basis of symptoms alone (e.g. symptomatic COVID-19) (n = 45), the number of symptoms and definitions varied (Tables 4 and 5). Some trials included outcomes defined by combinations of testing and/or symptoms: 13 (7%) using either testing or symptoms to determine infection; 46 (25%) specifying both testing and symptoms must be positive to define infection (e.g. RT-PCR and symptomatic).\n\nTables 6 and 7 detail the use of various SARS-CoV-2 infection outcome definitions by setting and intervention type, respectively.\n\nOf the 184 trials that included SARS-CoV-2 infection outcomes, seven provided a rationale for their choice of outcome selection and/or measurement (see Table 8). Of these seven studies, this was often to justify their specific choice of testing, with one drug prophylaxis trial explaining that “testing and criteria for diagnosis COVID-19 is likely to rapidly evolve over the course of this trial and will vary internationally”14 and a school closure trial basing outcome measures on routinely collected testing data to ensure “feasibility, facilitate speed, and limit costs”.15 A drug prophylaxis trial in healthcare workers argued that relying on symptoms consistent with infection without laboratory confirmation raises “concerns of type II error from asymptomatic participants”.16 Conversely, another drug prophylaxis trial justified the decision to use symptoms given issues of access to testing, “Given limited availability of outpatient PCR testing in many jurisdictions during our study period, particularly in April 2020, probable Covid 19 based on Covid-19-compatible symptoms was included in the composite primary endpoint”.17\n\n\n\no Confirmed positive test for COVID-19: either a laboratory test (performed according to each participating hospital’s local protocols) or a computed tomography (CT) thorax scan (based on individual radiologist interpretation and diagnosis) that confirms COVID-19 diagnosis.\n\no Confirmed negative test for COVID-19: a laboratory test (performed according to each participating hospital’s local protocols) that is negative for COVID-19 diagnosis.”\n\n\nDiscussion\n\nWe have reviewed COVID-19 prevention trials that were registered in the first nine months of the pandemic and examined in detail their rationale, selection and method of measuring SARS-CoV-2 infection. Of the 199 included trials, 268 SARS-CoV-2 infection outcomes were identified, across 184 studies. Of these, almost one fifth did not define how infection would be measured in the register entry, with the remaining studies specifying a combination of testing alone, symptoms alone, or testing and/or symptoms. Very few trials provided a rationale for the choice of how infection would be measured. The observed heterogeneity of outcome measurement of SARS-CoV-2 infection in COVID-19 prevention studies limits effective evidence synthesis and scientific comparison of interventions, which has enormous consequences for decision-making at an individual and public health level. We recommend that studies provide a rationale for choice of infection measurement and, if possible, that uniformity is agreed internationally on how to measure SARS-CoV-2 infection in trials of prevention interventions.\n\nThe heterogeneity of outcome measurement identified in the current study is not uncommon. A recent methodological systematic review revealed significant heterogeneity in the outcome measurement instruments used in trials evaluating therapeutic interventions for COVID-19, thus highlighting the need for greater consistency.18 However, such heterogeneity is not restricted to COVID-19 research studies. A multiplicity of outcome measurement instruments has recently been reported in areas such as delirium, hearing loss, chronic pelvic pain, and breast reconstruction, with studies concluding the need for consensus on outcomes and their associated measures for use in future clinical trials in these disease areas.19–22\n\nTo our knowledge, this is the first study to examine how SARS-CoV-2 infection outcomes are measured in registered COVID-19 prevention trials. However, there are some methodological limitations. Only the Cochrane COVID-19 Study Register https://covid-19.cochrane.org/ was searched to identify COVID-19 prevention trials, which may limit the number of relevant studies identified. The Cochrane register, however, is updated regularly and includes studies identified from six data sources, including ClinicalTrials.gov. Furthermore, although we did not specifically search each of the data sources, we used the trial URL provided in the Cochrane Study Register entry to access the original trial registry entry. Another limitation is the lack of detail about infection outcome definitions reported in the trial registry entries. Where readily available via links within the registry, protocols and published papers were also examined. However, due to resource limitations we did not manually search for protocols and full text papers corresponding to the trials included in this review, meaning some detail on outcome definitions may have been missed and may be readily available in trial protocols thus potentially changing the results of this study. Trialists may have a rationale for their choice of outcome measurements, but this was not included in the registry entry.\n\nThe COS-COVID-P study recommended SARS-CoV-2 infection be measured in all COVID-19 prevention trials, regardless of the intervention and setting.9 We found 92% of trials included SARS-CoV-2 infection as an outcome; however, very few reported the rationale for SARS-CoV-2 infection outcome selection and measurement. From the limited details we have regarding rationale, decisions often appear to be based on accessibility of testing and feasibility. This is understandable and will likely be due to circumstances specific to the setting and country where the trial is being conducted. Going forward, we advise trialists to be transparent about their rationale for the definition of SARS-CoV-2 infection outcomes used when registering and reporting their trials, to improve understanding of the context of their research. The trial registration should include both the rationale for outcome measurement, along with details on how infection will be analysed. In addition, we understand trialists will collect as much data as they consider relevant, but we recommend they develop a coherent statistical analysis plan (SAP) to ensure transparency and reproducibility.23\n\nIn the current review, we found two thirds of the studies evaluating behaviour interventions, such as those intended to increase handwashing or SMS text prompts to wear masks, did not include any SARS-CoV-2 infection outcomes. Trials of simple behavioural interventions may be unlikely to measure infection, as their purpose is to modify an individual’s behaviour rather than to directly prevent an individual from acquiring COVID-19. This is in contrast with those of complex interventions that include a behavioural component (e.g. donning standardised PPE versus specialised PPE; or hand washing with soap versus using alcohol wipes) where the overarching aim is still likely to be prevention of SARS-CoV-2 infection.\n\nAlongside SARS-CoV-2 infection, the COS-COVID-P study also led to the inclusion of intervention-specific harms in the COS for all COVID-19 prevention research studies.9 The current review did not examine this aspect. Determining these harm outcomes requires agreement amongst those with expertise in the specific interventions being tested. It may be that the harms are similar within certain intervention types, e.g. drug prophylaxis and vaccines. However, expert opinion will be necessary to determine the relevance of such an approach, but consistency will be important to avoid research waste and to facilitate evidence synthesis in which the results of studies of similar interventions are compared, contrasted and, where appropriate, combined. There may also be a need for COS for studies in specific settings. For example, a COS evaluating interventions for the prevention of COVID-19 transmission in care homes (COS-COVID-PCARE) is currently under development. Building on the COS-COVID-P study, the COS-COVID-PCARE study is proposing to develop a supplementary specific module for COVID-19 prevention in care homes.24\n\n\nConclusion\n\nWe have described the variation in the selection and measurement of SARS-CoV-2 infection outcomes, with illustrated examples from on-going trials across various settings and interventions. As knowledge about COVID-19 increases over time, this is leading to improvements in the design of studies and reporting. Nevertheless, our findings highlight the need for clarity, transparency and standardisation of measures of SARS-CoV-2 infection. It is now timely to highlight these issues, to improve the collection of infection data to inform key public health decisions.\n\n\nData availability\n\nUniversity of Liverpool Data Catalogue: SARS-CoV-2 infection outcomes. https://doi.org/10.17638/datacat.liverpool.ac.uk/1279.24\n\nThis project contains the following underlying data:\n\n- The dataset consists of COVID-19 prevention trials, with the following data extracted for each trial: intervention type (e.g. drug, vaccine, behavioural), intervention (as described verbatim), setting (i.e. population of interest), SARS-CoV-2 infection outcomes (as described verbatim), SARS-CoV-2 infection outcome definition (i.e. how SARS-CoV-2 infection would be measured), whether or not the SARS-CoV-2 infection outcome was specified as being a primary or secondary outcome, and the rationale provided for SARS-CoV-2 infection outcome measurement selection.\n\nData are available under the terms of the Creative Commons: Attribution 3.0 license.",
"appendix": "Acknowledgements\n\nIn addition to article authors, members of the COS-COVID-P Study Steering Committee include: Elie Akl (American University of Beirut, Lebanon); Aneel Bhangu (University of Birmingham, UK); Deborah Caldwell (University of Bristol, UK); Mike Clarke (Queen's University Belfast, UK); Jonathan Craig (Flinders University, Australia); Liang Du (Cochrane China); Adam Finn (University of Bristol, UK); Ella Flemyng (Cochrane, UK); Atle Fretheim (Norwegian Institute of Public Health, Norway); Claire Goodman (University of Hertfordshire, UK); Lars Hemkens (University of Basel, Switzerland); Tammy Hoffman (Bond University, Australia); John Ioannidis (Stanford University, USA); Martin Knapp (London School of Economics, UK); David Lalloo (Liverpool School of Tropical Medicine, UK); Susan Michie (UCL, UK); Richard Morley (Cochrane, UK); Malcolm G Semple (University of Liverpool, UK); Maureen Smith (Cochrane Consumer Network, Canada); Allison Tong (University of Sydney, Australia); Sean Tunis (Center for Evaluation of Value and Risk in Health, USA); Junhua Zhang (Tianjin University of Traditional Chinese Medicine, China).\n\n\nReferences\n\nCOVID-19 Research Priorities Identified by the Global Research Community: [cited 20-7-20]. Reference Source\n\nCochrane COVID-19 Study Register [Internet].[cited 17 February 2021]. Reference Source\n\nNussbaumer-Streit B, Mayr V, Dobrescu AI, et al.: Quarantine alone or in combination with other public health measures to control COVID-19: a rapid review. Cochrane Database Syst Rev. 2020; (9). PubMed Abstract | Publisher Full Text | Free Full Text\n\nChu DK, Akl EA, Duda S, et al.: Physical distancing, face masks, and eye protection to prevent person-to-person transmission of SARS-CoV-2 and COVID-19: a systematic review and meta-analysis. Lancet. 2020; 395(10242): 1973–87. PubMed Abstract | Publisher Full Text | Free Full Text\n\nVerbeek JH, Rajamaki B, Ijaz S, et al.: Personal protective equipment for preventing highly infectious diseases due to exposure to contaminated body fluids in healthcare staff. Cochrane Database Syst Rev. 2020; (4). PubMed Abstract | Publisher Full Text | Free Full Text\n\nKrishnaratne S, Pfadenhauer LM, Coenen M, et al.: Measures implemented in the school setting to contain the COVID-19 pandemic: a scoping review. (1469-493X (Electronic)). PubMed Abstract | Publisher Full Text\n\nWilliamson PR, Altman DG, Bagley H, et al.: The COMET Handbook: version 1.0. Trials.2017; 18(Suppl 3): 280. Epub 2017/07/07. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAvery K, Macefield R, Gorst S, et al.: Developing a core outcome set for COVID-19 prevention interventions: the COS COVID-P study. In: Collaborating in response to COVID-19: editorial and methods initiatives across Cochrane. Cochrane Database Syst Rev. 2020; 12(Suppl 1): 15–8. Publisher Full Text\n\nStegeman I, Ochodo EA, Guleid F, et al.: Routine laboratory testing to determine if a patient has COVID-19. (1469-493X (Electronic)). PubMed Abstract | Publisher Full Text | Free Full Text\n\nStruyf T, Deeks JJ, Dinnes J, et al.: Signs and symptoms to determine if a patient presenting in primary care or hospital outpatient settings has COVID-19 disease. (1469-493X (Electronic)). PubMed Abstract | Publisher Full Text | Free Full Text\n\nClinicalTrials.gov [Internet]: Identifier NCT04330352, Mindfulness-based \"STOP (Stop, Take a Breath, Observe, Proceed) Touching Your Face\" Intervention.2020 Apr 1 [cited 2020 Nov 24]. Reference Source\n\nClinicalTrials.gov [Internet]: Identifier NCT04373096, Enhanced Hood PPE to Minimize COVID-19 Transmission to Front-line Health Care Workers;2020 May 4 [cited 2020 Nov 24]. Reference Source\n\nEU Clinical Trials Register [Internet]: Identifier 2020-001448-24, Preventing Pulmonary Complications in Surgical Patients at Risk of COVID-19;2020 Apr 15 [cited 2020 Nov 24]. Reference Source\n\nFretheim AA-O, Flatø M, Steens A, et al.: COVID-19: we need randomised trials of school closures. (1470-2738 (Electronic)). PubMed Abstract | Publisher Full Text\n\nAbella BS, Jolkovsky EL, Biney BT, et al.: Efficacy and Safety of Hydroxychloroquine vs Placebo for Pre-exposure SARS-CoV-2 Prophylaxis Among Health Care Workers: A Randomized Clinical Trial. (2168-6114 (Electronic)). PubMed Abstract | Publisher Full Text | Free Full Text\n\nRajasingham R, Bangdiwala AS, Nicol MR, et al.: Hydroxychloroquine as pre-exposure prophylaxis for COVID-19 in healthcare workers: a randomized trial. LID - 10.1093/cid/ciaa1571 [doi] LID - ciaa1571. (1537-6591 (Electronic)). PubMed Abstract | Publisher Full Text | Free Full Text\n\nMathioudakis AG, Fally M, Hashad R, et al.: Outcomes Evaluated in Controlled Clinical Trials on the Management of COVID-19: A Methodological Systematic Review.2020; 10(12): 350. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRose L, Agar M, Burry L, et al.: Reporting of Outcomes and Outcome Measures in Studies of Interventions to Prevent and/or Treat Delirium in the Critically Ill: A Systematic Review.2020; 48(4): e316–e24. PubMed Abstract | Publisher Full Text\n\nGhai V, Subramanian V, Jan H, et al.: A systematic review on reported outcomes and outcome measures in female idiopathic chronic pelvic pain for the development of a core outcome set.2021; 128(4): 628–34. PubMed Abstract | Publisher Full Text\n\nHill-Feltham PR, Johansson ML, Hodgetts WE, et al.: Hearing outcome measures for conductive and mixed hearing loss treatment in adults: a scoping review. Int J Audiol. 2020: 1–7. PubMed Abstract | Publisher Full Text\n\nDavies CF, Macefield R, Avery K, et al.: Patient-Reported Outcome Measures for Post-mastectomy Breast Reconstruction: A Systematic Review of Development and Measurement Properties. Ann Surg Oncol. 2021; 28(1): 386–404. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGamble C, Krishan A, Stocken D, et al.: Guidelines for the Content of Statistical Analysis Plans in Clinical Trials. JAMA. 2017; 318(23): 2337–43. PubMed Abstract | Publisher Full Text\n\nHood K, Williamson P, Wood F, et al.: A Core Outcome Set for studies evaluating interventions for the prevention of COVID-19 transmission in care homes (COS-COVID-PCARE).Reference Source\n\nDodd S: SARS-CoV-2 infection outcomes. [Data Collection]. Data Catalogue. 2021. Publisher Full Text"
}
|
[
{
"id": "86394",
"date": "13 Jul 2021",
"name": "Natasha Tyler",
"expertise": [
"Reviewer Expertise Core outcome set 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\nSummary:\nThe authors present a systematic review to assess outcome reporting in Covid-19 infection outcome trials. They review the Cochrane COVID-19 Study Register. They found heterogeneity in the SARS-CoV-2 infection outcome measurement choices in prevention trials.\n\nIs the work clearly and accurately presented and does it cite the current literature?\nThe introduction is clearly written and accurately presented. The paper as a whole is clear and concise. As many of us are experiencing research and evidence concerning Covid become quickly outdated. I would recommend searching the Cochrane database again for a more up to date figure for reference 2 in the introduction. As the evidence moves so quickly in regards to Covid, I think it needs to be addressed in the limitations that this review concerns lots of studies that happened in a crisis period and that future studies might have better outcome/rationale reporting, and suggesting learning points from this.\nIs the study design appropriate and is the work technically sound?\nThe systematic review design is appropriate and follows the standard procedures for COS reviews. A minor concern would be the rationale component, there were only 7 reported rationale, so the research does not answer one of the key research questions/aims.\nThe aim of this study is to review SARS-CoV-2 infection outcomes in registered COVID-19 prevention trials and examine the reported rationales for choice of outcome measurement. Our intention is that this will inform optimal methods for the design of future studies.\nWhilst the authors describe how future trials can be improved through reporting rationale, there is little acknowledgement about how this research question/aim is not addressed in the results of this paper. Highlighting the limitations of using a systematic review method in this way would be beneficial and perhaps suggesting alternative methods in the discussion (i.e. stakeholder consultation) in similar research.\nMy other query would be in regards to the behavioural interventions, if you are looking at outcomes for interventions that prevent an individual from acquiring covid-19 (infection outcomes) would it not be best to remove the behaviour modification interventions from this review or present them separately, it seems to me this should have perhaps been an inclusion/exclusion criteria. I would assume this may reduce some of the heterogeneity in outcomes also.\n\nAre sufficient details of methods and analysis provided to allow replication by others?\nThe methods are detailed and analysis thorough and replicable.\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nStatistical analysis and interpretation are appropriate.\n\nAre all the source data underlying the results available to ensure full reproducibility?\nYes\n\nAre the conclusions drawn adequately supported by the results?\nConclusions are supported by the results. My only concern is that whilst the authors argue the limitations with the trials reviewed there is not much discussion about the limitations of this study, some I have mentioned above. The heterogeneity in reporting infection outcomes, could be related to studies being conducted before testing was established in many countries and acknowledging that the studies reviewed were conducted during crisis and that future studies may provide better rationale for outcomes as we move forward. Also, advice/suggestions about how trialists could improve outcome decisions in pandemic situations (when the development of adequate infection testing is developing) to improve homogeneity of outcomes would be a useful addition to the literature.\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": "261015",
"date": "16 May 2024",
"name": "Michael Samarkos",
"expertise": [
"Reviewer Expertise Infectious diseases - infection prevention & antimicrobial stewardship"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 systematic review aiming to support the need for core outcomes set (COS) development in COVID-19 prevention trials, as suggested by the COMET initiative. In general, the manuscript is clear and well-written. The authors have searched the Cochrane COVID-19 Study Register. The search methodology is clearly described; however, it is not very clear how (in terms of methodology) the authors excluded from the search results “Studies relating to the transmission, treatment or management of COVID-19”. The registry search was performed on 24 November 2020, therefore the need for an updated search is obvious. Given the changes and developments in the COVID-19 landscape, this should be a formidable task. I think that there should be a second publication, rather than an update. Results are presented clearly and meticulously. Tables are appropriate. Discussion is concise. I would only suggest that the authors should me more emphatic on how their work relates to and builds on the COS COVID-P study. The limitations of the study are discussed extensively – maybe more than they should be! In p 14/19, 2nd paragraph, the authors discuss the outcomes of studies evaluating behavioural interventions and point out that 2/3 of the studies did not use a SARS-CoV2 infection outcome. These studies, apparently, used process measures (the authors give an example of such an outcome “frequency of face-touching behaviour”) as outcomes. I wonder whether the authors could study the reported outcomes from this point of view (i.e. report how many of the study outcomes were in fact process measures). The study COS-COVID-PCARE (reference 23) has been completed and published (BMC Geriatr 22, 710 (2022). [1] therefore the authors should update the reference and rephrase the relevant paragraph at the end of the discussion. The conclusions of the study are fully supported by the results. There is a problem with the in-text citations and the respective references. Citations 8 &9 refer both to reference 8 (Cochrane Database Syst Rev. 2020; 12(Suppl 1): 15–8). As a result, citation numbers from citation 10 onwards do not correspond to the appropriate reference (they correspond to the previous reference e.g. citation 10 corresponds to reference 9 etc). Citation 24 exists twice in the text – the first occurrence corresponds to reference 23 and the second to the (correct) reference 24.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-426
|
https://f1000research.com/articles/10-425/v1
|
27 May 21
|
{
"type": "Research Article",
"title": "Epidemiology of Alzheimer’s disease and other dementias: rising global burden and forecasted trends",
"authors": [
"Syed Fahad Javaid",
"Clarissa Giebel",
"Moien AB Khan",
"Muhammad Jawad Hashim",
"Syed Fahad Javaid",
"Clarissa Giebel",
"Moien AB Khan"
],
"abstract": "Background: The burden associated with Alzheimer’s disease is recognized as one of the most pressing issues in healthcare. This study aimed to examine the global and regional burden of Alzheimer’s disease and related dementias. Methods: Epidemiological data from the latest Global Burden of Disease (GBD) dataset were analysed to determine the prevalence, incidence and mortality rates from 1990 to 2019 for 204 countries and world regions. This dataset derives estimates for health metrics by collating primary data from research studies, disease registries and government reports. Temporal forecasting was conducted using the GBD Foresight tool. Results: An estimated 0.7% of the global population has dementia, translating to 51.6 million people worldwide. The total number of persons affected has more than doubled from 1990 to 2019. Dementia metrics showed a continuous increase in prevalence, incidence, mortality, and disability adjusted life years (DALYs) rates worldwide during the last three decades. Japan has the highest prevalence (3,079 cases per 100,000), followed by Italy, Slovenia, Monaco, Greece and Germany. The prevalence is higher in high-income regions such as Western Europe compared to Asia and Africa. However, total number of affected individuals is substantial in South and East Asian regions, in particular China, Japan and India. Dementia related deaths are projected to increase from the current 2.4 million per year to 5.8 million by 2040. Women are more likely to be affected by dementia than men. Age-standardized rates have not changed indicating possible stability of risk factors. Conclusions: Alzheimer’s disease and other dementias are rising rapidly and will more than double in mortality burden over the next 20 years. The tremendous burden in high- and middle-income countries can potentially overwhelm communities and health systems. Urgent measures are needed to allocate funding and provide residential care for affected persons.",
"keywords": [
"Alzheimer’s disease",
"dementia",
"epidemiology",
"prevalence",
"mortality",
"vascular dementia",
"Lewy body disease",
"frontotemporal lobar degeneration",
"neurocognitive disorders",
"mild cognitive impairment"
],
"content": "Introduction\n\nDementia remains one of the leading causes of morbidity and mortality worldwide1. The condition exerts a profound negative impact on families, communities and health care systems alike2. The World Health Organization (WHO) estimates that there are 10 million new cases of dementia each year3. Hence, the financial implication of the condition—arising from both the direct medical and social care costs as well as the cost of informal care—is equivalent to 1.1% of the global gross domestic product (GDP)4. Those affected by dementia and their informal caregivers also face difficulties and suffer poor health outcomes that are persistent5,6. People living with dementia and their informal caregivers are more likely to be diagnosed with comorbidities and subsequently experience poorer access to health and social care services when compared to their unaffected counterparts7,8. Research also demonstrates that people living with dementia are disproportionately more likely to report a poor quality of life9. This reduced quality of life and other inequalities in outcomes are recognized to be driven by factors such as economic hardship and social isolation that are ultimately caused by the stigma associated with this condition10. Thus, those affected represent a vulnerable population group that could be better served by changes within healthcare and social services systems.\n\nThe burden associated with Alzheimer’s disease is now recognized as one of the most pressing issues in the field of public health. There is an urgent need for health care systems to identify novel and innovative solutions to meet the needs. The World Health Assembly (WHA) recently endorsed the “Global action plan on the public health response to dementia 2017–2025,” calling for renewed efforts to increase awareness, research and innovation to tackle this urgent public health issue3. However, an effective response to the challenges arising from dementia first requires an accurate understanding of the patterns of prevalence and burden of dementia11,12.\n\nThe aim of this study was to analyse the global and regional burden as well as trends and forecasts for Alzheimer’s disease and related dementias. As a unique contribution, this study assessed yearly trends using age-standardized rates to control for the effect of population aging.\n\n\nMethods\n\nBased on the aim of study, the inclusion criteria for data included prevalence, incidence, mortality rates of dementia for global, regional and national levels. Exclusion criteria included subnational data such as hospital-based records and neurological diseases other than dementia such as Parkinson’s disease and stroke. We extracted health metrics on dementia from the Global Burden of Disease (GBD) dataset. GBD is the largest and most up-to-date repository of epidemiological data for any given condition including dementia13. GBD 2019 release has data on 204 countries for 286 causes of death. The robustness of this dataset stems from its reliance on a wide range of primary sources, independent research studies, government reports, vital registration, verbal autopsies, disease registries, healthcare projects and census data. GBD 2019 utilized 990 primary data sources related dementia to develop its estimates. Based on statistical modelling from these data sources, GBD produces reliable estimates of health metrics. Furthermore, GBD incorporates modelling adjustment to address data sampling issues, missing data and variations in case definition. The methods used are compliant with Guidelines for Accurate and Transparent Health Estimates Reporting (GATHER statement).\n\nHealth metrics analysed in the present study included prevalence, incidence, mortality and disability-adjusted life years (DALY). DALY is a better measure of human suffering from a disease than prevalence or mortality, as it combines years lived with disability and the years of life lost due to premature death. Data for dementia were obtained from GBD using the Results tool. Dementia is listed under Neurological Disorders in GBD and coded as B.5.1 Alzheimer’s disease and other dementias. Data visualization was conducted in Microsoft Excel 2016 as well as the GBD Compare tool. Sub-classification of dementias such as vascular, frontotemporal and dementia with Lewy bodies was not available in this dataset. Epidemiological data on mild cognitive impairments was not included in the GBD.\n\nData were analysed using GBD analytical tools including visualizations and forecasting. These tools were utilized in order to achieve the highest fidelity. We analysed both raw and age-adjusted rates of dementia prevalence and incidence. Age-standardized rates remove the effect of population age across countries as well as over time, thus enabling inferences about intrinsic changes in dementia burden. Age of onset of dementia was inferred from age-specific incidence rates. We sought to assess whether the age of onset was decreasing over time by comparing figures from 1990 with those from 2019. Forecasting for projections for the next 20 years was achieved using the GBD Foresight tool, with the following settings: scenario: reference; uncertainty: off; rank: off; and age: all ages (unstandardized). Statistical data analysis was conducted using SPSS version 26 (IBM Inc., Armonk, NY, 2019). Paired samples t-tests were used to compare differences in prevalence rates across gender and to evaluate changes in incidence rates over from 1990 to 2019. An alpha level of 0.05 was considered statistically significant.\n\n\nResults\n\nThe global prevalence of dementia was 0.69% [uncertainty interval (UI); 0.59, 0.79] of the world population in 2019 (Table 1). The total number of persons affected has more than doubled from 1990 to 2019: increasing from 20.5 million to 51.6 million [UI; 44.2, 59.0 million] globally. The worldwide prevalence rate for all forms of dementia was 667.2 cases per 100,000 persons [UI; 572.2, 762.8]. In comparison to other major neurological diseases, the prevalence of dementia was considerably higher. For example, the prevalence of Parkinson’s disease was 110 cases, and multiple sclerosis 22.7 cases per 100,000 persons. Women were more likely to be affected by dementia than men. For instance, among persons over the age of 80, the prevalence rate among women was 20,244 per 100,000 [UI; 16,661, 34,236] compared to 14,378 per 100,000 [UI; 11,667, 17,478] in men.\n\nNotes: selected countries shown in this table (all countries were included in the analysis). Data from Global Burden of Disease, 2019. DALY, disability-adjusted life years.\n\nAcross regions, high-income Asia Pacific had the highest prevalence followed by Europe, Austrasia and North America (Figure 1). South Asia and Africa ranked the lowest in terms of prevalence of dementia. The highest prevalence rates in descending order were: Japan (3,079 cases per 100,000 population), Italy (2,269 cases per 100,000), Slovenia (1,963 cases), Monaco (1,962 cases), Greece (1,874 cases), and Germany (1,863 cases per 100,000). In terms total number persons living with dementia, China (13.1 million cases), United States (4.9 million), Japan (3.9 million), India (3.6 million) and Brazil (1.7 million) have the highest burden in the world.\n\nNotes: prevalence rates per 100,000 population by country. Red, orange and yellow shades indicate higher prevalence. Source: Global Burden of Disease, 2019.\n\nDementia metrics showed a continuous increase in prevalence, incidence, mortality, and disability adjusted life years (DALYs) rates worldwide during the 29 years of estimates from 1990 to 2019. Certain regions, such as Western Europe, showed a faster rate of rise than the global average. Japan, in particular, experienced a marked increase in prevalence rates, from 772 cases per 100,000 population in 1990 to 3,079 per 100,000 in 2019. Thus, the total number of cases continued to rise with population growth and aging.\n\nAs prevalence rates are affected by the proportion of elderly in a population, we used age-standardized rates to aid in comparisons between countries. Age standardization adjusts for any differences in underlying population age distributions. After age-standardization (to control for the effect of population aging), incidence and prevalence rates appeared to remain stable during the same period (Figure 2). Hence, there appeared to be no intrinsic increase in rates of dementia after controlling for population aging.\n\n(a) Incidence (unadjusted rates). (b) Age-standardized incidence.\n\nThe age distribution of new cases showed incidence starting from the latter half of the fifth decade of life. The age distribution of new cases of dementia has not changed since 1990 (Figure 3A). As expected, the incidence was highest at older ages (Figure 3B).\n\n(a) Prevalence (per 100 persons) by gender. p = .059, paired samples t-test, comparing prevalence in each age group for males and females. (b) Incidence (age of onset of new cases) change over three decades. p = .33, paired samples t-test, comparing incidence in each age group for 1990 and 2019.\n\nMortality rates have been rising rapidly and continuously since 1990. The global death rate due to dementia increased from 10.49 deaths per 100,000 in 1990 to 20.98 deaths per 100,000 in 2019 [UI; 5.27, 54.36]. Statistical forecasting showed a rising rate reaching 66.4 deaths per 100,000 [UI; 51.6, 85.2] by 2040. Most regions are forecasted to continue to follow this rising trend over the next 20 years. The highest death rates due to dementia are expected in Japan at 265 deaths per 100,000 population by 2040. Total deaths due to dementia are projected to increase from the current 2.4 million per year to 5.8 million by 2040 [UI; 4.5, 7.5 million].\n\n\nDiscussion\n\nThis study adds important insights on the global burden of dementia and its predicted trajectory. Based on the latest data from GBD, three key findings have emerged from our analysis. The incidence of dementias is rising especially in Western Europe and Japan. A large burden of dementia (total number of cases) was present in developing countries. When standardized for population aging, the rates are stable. These findings have considerable implications for the health and social care sectors, which need to adapt and prepare in advance to meet the rising demand.\n\nThe burden arising from Alzheimer’s disease and other dementias is acknowledged to be markedly high when compared to other non-communicable conditions affecting older age groups14. The associated burden of care correlates with the severity of dementia as the subsequent cognitive and functional decline negatively impacts the affected individual’s ability to be independent and engage in activities of daily living15,16. These factors combined with rising prevalence rates due to population growth and aging as well as the absence of curative therapies forecast a bleak picture of the future. It is not surprising that dementia has now become the focus of public health policy and research16–18.\n\nJapan depicts a grim case study of the social burden of dementia. Our analysis revealed a rapid increase in prevalence and mortality rates from 1990 to 2019, and a forecasted meteoric rise over the next two decades. The proportion of Japanese people over the age of 65 is now 26.7%19. Consequently, meeting the healthcare demands of the aging population has become a public health priority. However, the rising demand can easily overwhelm healthcare and social services capacity20. The number of residential care homes in Japan for people living with dementia remains suboptimal and the accessible care available is provided in hospital settings16–18. Hospital environments have long been considered inappropriate for long-term care of those affected. These issues raise serious concerns about how countries such as Japan and those in Western Europe will meet this ever-increasing burden of dementia, perhaps representing the greatest challenge for their current and future health care systems. On the other hand, it is important to recognize that the lower prevalence rates of dementia found in certain regions such as South Asia may arise from lack of accessible healthcare services. All forms of dementia are underdiagnosed21. Amongst other factors, the lack of accessible health care may impede timely recognition18,19.\n\nA novel finding emerging from our analysis is the stability of age-standardized rates. This implies that (apart from age) risk factors for dementia have remained constant over the last three decades. The stability of age-standardized prevalence rates over time may be a reflection of age continuing to represent the strongest predictor of dementia22. Epidemiological studies exploring the relationship between age and dementias have found that the rate of cognitive decline is 10 times greater during the last three years of life, irrespective of the country of residence22. Potential risk factors such as diabetes, hypertension, smoking, sedentary lifestyle and obesity are rising globally, and yet are not reflected in age-standardized rates of dementia. The reasons for this remain unresolved. Insights from certain studies indicate that obesity affects dementia selectively23. A national registry-based study from Denmark indicated a steady decline incidence since 200324. These results have not been consistently reported in other regions. It is possible that improvements in dietary intake, physical activity level and reductions in tobacco consumption may contribute to these remarkable trends25.\n\nThis study is subject to a few limitations. Country-level comparisons are generalizations that are susceptible to ecological bias. The GBD dataset relies on multiple sources that adopt heterogeneous methodologies including varying case definitions, which can make comparisons less robust. However, statistical modelling techniques employed by GBD adjust for these potential sources of error. At present, GBD provides the most comprehensive and current data available on the burden of dementia.\n\n\nConclusions\n\nDementia now represents one of the most pressing issues facing global public health resulting in a burden of care that profoundly impacts families, communities, and healthcare systems alike. Our findings can be used to inform policies and global health agendas that direct the allocation of resources with a need to address and support specific subgroups and regions. Research is needed to identify mild cognitive impairment and early markers of disease progression26. Future research needs to explore differences in prevalence rates of the various forms of dementia and the associated care burden. There remains an urgent need for public health initiatives that aim to promote healthier living among older populations in recognition of the many risk factors now associated with the development of dementia. Otherwise, several countries provide a stark example of the potential for healthcare systems to become overwhelmed.\n\n\nData availability\n\nThe data used in this study was obtained from the Institute of Health Metrics and Evaluation, University of Washington. http://ghdx.healthdata.org/ihme_data. The search term used was: B.5.1 Alzheimer’s disease and related dementias.\n\nData are available under the terms of the Open Data Commons Attribution License.\n\nOpen Science Foundation: Dementia. https://doi.org/10.17605/OSF.IO/DYBTM27.\n\nThis project contains the following underlying data:\n\n- Supplementary Appendix – Dementia 2019 data (numeric estimates for prevalence, incidence, mortality and DALYs)\n\nOpen Science Foundation: GATHER checklist for ‘Epidemiology of Alzheimer’s disease and other dementias: rising global burden and forecasted trends’. https://doi.org/10.17605/OSF.IO/DYBTM27.\n\nData are available under the terms of the Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0).",
"appendix": "Acknowledgments\n\nWe would like to thank the Institute of Health Metrics, Seattle, for developing the Global Burden of Disease database.\n\n\nReferences\n\nGandy S, Bartfai T, Lees GV, et al.: Midlife interventions are critical in prevention, delay, or improvement of Alzheimer’s disease and vascular cognitive impairment and dementia [version 1; peer review: 2 approved]. F1000Res. 2017; 6: 413. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWong CYT: Predictors of psychiatric rehospitalization among elderly patients [version 1; peer review: 3 approved]. F1000Res. 2015; 4: 926. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWHO: Global action plan on the public health response to dementia 2017 - 2025. WHO. World Health Organization; [cited 2020 Jun 22]. Reference Source\n\nWimo A, Guerchet M, Ali GC, et al.: The worldwide costs of dementia 2015 and comparisons with 2010. Alzheimers Dement. 2017; 13(1): 1–7. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWu YT, Clare L, Jones IR, et al.: Inequalities in living well with dementia-The impact of deprivation on well-being, quality of life and life satisfaction: Results from the improving the experience of dementia and enhancing active life study. Int J Geriatr Psychiatry. 2018; 33(12): 1736–42. PubMed Abstract | Publisher Full Text\n\nCooper C, Lodwick R, Walters K, et al.: Inequalities in receipt of mental and physical healthcare in people with dementia in the UK. Age Ageing. 2017; 46(3): 393–400. PubMed Abstract | Publisher Full Text | Free Full Text\n\nStevnsborg L, Jensen-Dahm C, Nielsen TR, et al.: Inequalities in Access to Treatment and Care for Patients with Dementia and Immigrant Background: A Danish Nationwide Study. J Alzheimers Dis. 2016; 54(2): 505–14. PubMed Abstract | Publisher Full Text\n\nBunn F, Burn AM, Goodman C, et al.: Comorbidity and dementia: a scoping review of the literature. BMC Med. 2014; 12(1): 192. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFarina N, Hicks B, Baxter K, et al.: DETERMinants of quality of life, care and costs, and consequences of INequalities in people with Dementia and their carers (DETERMIND): A protocol paper. Int J Geriatr Psychiatry. 2020; 35(3): 290–301. PubMed Abstract | Publisher Full Text\n\nWright T, O’Connor S: Reviewing challenges and gaps in European and global dementia policy. J Public Ment Health. 2018; 17(4): 157–67. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHoffman D: Alzheimer’s Disease Legislation And Policy--Now And In The Future. Health Aff (Millwood). 2014; 33(4): 561–5. PubMed Abstract | Publisher Full Text\n\nIenca M, Vayena E, Blasimme A: Big Data and Dementia: Charting the Route Ahead for Research, Ethics, and Policy. Front Med (Lausanne). 2018; 5: 13. PubMed Abstract | Publisher Full Text | Free Full Text\n\nUniversity of Washington: Institute for Health Metrics and Evaluation. [cited 2016 Nov 27]. Reference Source\n\nMelis RJF, Haaksma ML, Muniz-Terrera G: Understanding and predicting the longitudinal course of dementia. Curr Opin Psychiatry. 2019; 32(2): 123–9. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKawada T: Risk of caregiver burden in patients with three types of dementia. Int Psychogeriatr. 2019; 31(1): 153. PubMed Abstract | Publisher Full Text\n\nSudo K, Kobayashi J, Noda S, et al.: Japan’s healthcare policy for the elderly through the concepts of self-help (Ji-jo), mutual aid (Go-jo), social solidarity care (Kyo-jo), and governmental care (Ko-jo). Biosci Trends. 2018; 12(1): 7–11. PubMed Abstract | Publisher Full Text\n\nIwagami M, Tamiya N: The Long-Term Care Insurance System in Japan: Past, Present, and Future. JMA J. 2019; 2(1): 67–9. Publisher Full Text\n\nHirakawa Y, Chiang C, Aoyama A: A qualitative study on barriers to achieving high-quality, community-based integrated dementia care. J Rural Med JRM. 2017; 12(1): 28–32. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTham TY, Tran TL, Prueksaritanond S, et al.: Integrated health care systems in Asia: an urgent necessity. Clin Interv Aging. 2018; 13: 2527–38. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGeorge J, Long S, Vincent C: How can we keep patients with dementia safe in our acute hospitals? A review of challenges and solutions. J R Soc Med. 2013; 106(9): 355–61. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLang L, Clifford A, Wei L, et al.: Prevalence and determinants of undetected dementia in the community: a systematic literature review and a meta-analysis. BMJ Open. 2017; 7(2): e011146. PubMed Abstract | Publisher Full Text | Free Full Text\n\nJansen WJ, Wilson RS, Visser PJ, et al.: Age and the association of dementia-related pathology with trajectories of cognitive decline. Neurobiol Aging. 2018; 61: 138–45. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSingh‐Manoux A, Dugravot A, Shipley M, et al.: Obesity trajectories and risk of dementia: 28 years of follow-up in the Whitehall II Study. Alzheimers Dement. 2018; 14(2): 178–86. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTaudorf L, Nørgaard A, Islamoska S, et al.: Declining incidence of dementia: A national registry-based study over 20 years. Alzheimers Dement. 2019; 15(11): 1383–91. PubMed Abstract | Publisher Full Text\n\nCasaletto KB, Staffaroni AM, Wolf A, et al.: Active lifestyles moderate clinical outcomes in autosomal dominant frontotemporal degeneration. Alzheimers Dement. 2020; 16(1): 91–105. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBegcevic I, Tsolaki M, Brinc D, et al.: Neuronal pentraxin receptor-1 is a new cerebrospinal fluid biomarker of Alzheimer’s disease progression [version 1; peer review: 4 approved]. F1000Res. 2018; 7: 1012. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHashim MJ, Khan M, Javaid SF: Global epidemiology of Alzheimer’s disease and related dementias. 2021. http://www.doi.org/10.17605/OSF.IO/DYBTM"
}
|
[
{
"id": "100620",
"date": "07 Jan 2022",
"name": "Takashi Suehiro",
"expertise": [
"Reviewer Expertise Psychogeriatrics",
"neurology"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn this paper, the authors reported the global and regional burden of Alzheimer’s disease (AD) and related dementias using the data extracted from the Global Burden of Disease (GBD) 2019 dataset. The increasing number of people with dementia, regional differences in the prevalence, and the stability of age-standardized rates were described as the key findings.\nWhile the results of this paper were considered very important from the viewpoint of the future healthcare system, there are several issues and concerns.\nSeveral previous articles have already reported the epidemiology of AD and related dementias. In particular, one of the reports used the GBD 2016 dataset1. The authors may want to consider revising the title to specify that this study used the GBD 2019 data.\n\nIn the introduction section, the authors need to refer to the previous articles about the epidemiology of dementia and put more emphasis on the added values of this study. The authors considered that the assessment of yearly trends with the age-standardized rates was the unique approach, and the reviewer agrees with the idea. To clarify the strength of the study, the authors should describe the reasons why the control of the population-aging effect is important.\n\nWhile the authors referred to the death rates relating to dementia, the age-standardized death rates were not assessed. Because the death rates can be influenced by the population aging as well as the prevalence rate, the age-standardized death rates would also be assessed.\n\nBecause the age-standardized prevalence ratio is one of the important findings, the method of age standardization should be explained in the methods section.\n\nAlthough the estimated mortality rates in the point of 2040 were described in the results section, those estimations are not the main outcome of this article and could be addressed in the discussion.\n\nIn Figure 3B, the legend needs an explanation of the “age group”.\n\nThere was no discussion about the statistical comparison of the prevalence rates across the gender. The authors should address this point in the discussion section.\n\nWhile the suggestion that age-standardized prevalence might be stable over the last thirty years was interesting, the statistical assessment was not conducted about this part and it was purely speculative. The reviewer thinks the statistical comparison of age-standardized prevalence between 1990 and 2019 should be included.\n\nThe sentence in the discussion section, “Potential risk factors such as diabetes, hypertension, smoking, sedentary lifestyle and obesity are rising globally, and yet are not reflected in age-standardized rates of dementia” was interesting. It would be more convincing if the concrete data or references about the increase in the incidence rate of the risk factors are added.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-425
|
https://f1000research.com/articles/10-424/v1
|
27 May 21
|
{
"type": "Research Article",
"title": "The city emptied and the homes and hospitals turned into 'the world'. A sociological approach",
"authors": [
"Juan Coca",
"Juan A. Roche Cárcel",
"Juan A. Roche Cárcel"
],
"abstract": "Background: The coronavirus pandemic has generated social measures in order to contend virus expansion, and deaths. One of the most important political norms in the first wave was the domestic enclosure. This measure generates social, psychological and personal problems. Objective: The aim of this paper is to analyze the social impact of this home confinement through the study of journalistic images. Methods: We use a set of images selected previously according our epistemic necessities. Results: The results show that the fundamental elements of the current life were questioned. In fact, social space, and the own society had collapsed. Also, the enclosure of Spanish populations has been accompanied by the intensification of the individualism, but also has generated an increase of the ideal of communitas. Conclusions: Coronavirus enclosure has produced that the cities have emptied, and the houses and hospitals, were the last refuge of society. This phenomenon has generated that population has been accompanied by the paradox intensification of social relationships.",
"keywords": [
"Frame visual",
"social enclosure",
"cities emptied",
"hospitals",
"houses",
"social paradox",
"COVID-19",
"social interrelations."
],
"content": "Introduction\n\nThe dramatic situation faced by Spain as one of the countries most strongly hit by COVID-19 (regarding both the number of deaths and that of variants of the virus) led the Spanish government to declare a “state of emergency,” a legal and constitutional figure meant to suppress multiple rights of citizens in order to preserve their health and safety. This remained in force between March 14th and May 18th 2020 during the first phase. In accordance with our starting hypothesis that will be eventually confirmed or rejected on the following pages, the aforesaid state of emergency has important consequences in at least three respects. Firstly, cities —amongst them Alicante— became deserted, which in turn meant that due to the complete absence of action and social relationships, the lack of a political agora, and the forced social distancing between bodies together with their confinement inside homes, society was somehow emptied too. Secondly, as a result of the above, both homes and hospitals have expanded their traditional functions and transformed into a real “world” where the usual activities as well as new ones are carried out. In this confinement situation, the population perceives hospitals as the only ones with capacity to save people. For this reason, the traditional activity of hospitals is collectively perceived as more relevant, more “real” and closer to the community. And, thirdly, such a transformation has gone hand in hand with a strengthening of individualism and, paradoxically, of the communitas too. We know that individualization has played an important role in both classical and modern sociology. Indeed, sociological theories start from the importance of people’s choice. Faced with social reality, individuals can make the choice to separate themselves or to draw closer to others. In other words, both characteristics of the Society of Individualization1-7 and others typically associated with the Society of Separativity8 and the communitas9 have been simultaneously reinforced.\n\n\nMethods\n\nOur implementation of the starting hypothesis described above will rely not only on two perspectives of sociology but also on two basic methods aimed at analyzing the content of the photographs taken by the Alicante-born photojournalist Rafa Arjones, which will be discussed in this research. The first key reference for our work - Weberian Comprehensive or Interpretative Sociology,10,11 according to which both the social world and the relationships that it generates are meaningful — was chosen in the hope that, through “correspondence in meaning” or “elective affinities,” it could help us identify the common links between the different cognitive dimensions —aesthetic, ethical, economic, political, religious, and social— that modernity has fragmented and, more specifically, the physical and socially constructed reality inside which Alicante developed throughout the COVID-19 lockdown. The second main topic behind our approach can be found in Visual Sociology, which mainly focuses on two issues: analyzing the image in its various forms; and using this analysis to collect data about social reality. Both dimensions converge on the ultimate goal of this subdiscipline, namely, the production of social knowledge through images.12 It should be noted, though, that Social Sciences have historically tended to privilege written sources, thus marginalizing or even excluding others such as sound and visual sources. More precisely, the latter “have been rejected either as mere ‘data’ or as simple ‘research instruments’”.13 Notwithstanding the above, Visual Sociology takes advantage of certain excellent sociological antecedents.14-17 Furthermore, as stated by Eduardo Bericat,18 numerous studies have revolved around the Sociology of Photography. Examples close to our research project include the works of Bruce Jackson —life in prison (1977, 1978)—; Douglas Harper —the vagabonds (1978)—; Lewis Wickes Hine —a sociologist and photographer who called his works “photointerpretations” (from working children in the United States (1908))—; and John Grady —the segregation of the black race (2007)—.13,18 This subdiscipline is currently experiencing a new rebirth, with researchers more experienced in new technologies.10 This sociological tradition which links photography and sociology —both of them modalities to explore the social — has included, on the one hand, three perspectives when reading any photograph (according to H. Becker): journalistic; documentary; and Visual-Sociology-inspired.19 On the other hand, two great approaches have emerged in Visual Sociology: working with or on already-taken photographs. The first case refers to the incorporation of that practice by the actual research team, either working from the photographs or creating them. Photography thus plays a relevant role in the research process itself, albeit changing its consideration: as a secondary source (insofar as the purposes sought with the photographs used had nothing to do with the research process, e.g. giving rise to a collection, a fund or an archive); or as a primary source, because the former are original observations made for or through relevant research studies.13,20 This article belongs within the sociological work on photojournalistic images, since it discusses work on photographs from a documentary repertoire, in this case of a professional nature, as is the case with the Spanish press. In any case, the photographs under analysis raise a special sociological interest when regarded in terms of self-presentation and approached on the basis of the actual conception that a society has of itself at a given moment, or expressed differently, of how that society imagines itself.21 More specifically, these images were taken — as seen below — by the photojournalist Rafa Arjones, while the state of emergency remained in force (during stage 0). Finally, the following additional considerations about photography should be borne in mind:\n\n1. Photography and Sociology have contemporaneity in common;22 2. Photographic images are “index” i.e. a trace verifying the existence of real phenomena for which these images are references;23 3. The emotional component of photography always outweighs that of any written text and consequently helps humanize social problems that lonely and uprooted people go through.24 In other words, a photograph allows its viewers to see those underprivileged persons as individual human beings who suffer and fight and no longer as impersonal generalized abstractions; 4. The interpretation of photographic images cannot cease to be historical, insofar as it depends on the prior knowledge about the situation and considering that several years elapse before the analysis25 and the publication of dozens of works; 5. Photography provides an alternative discourse on the pandemic experience, on this occasion from the perspective of an experienced photojournalist;26 6. As a tool for social analysis, photography largely helps in the construction of social reality;27 7. Since photojournalists are the ones who have to produce clear, self-explanatory and descriptive images than can appear on the pages of media,19 their photographs become a first-rate social document. Photojournalists additionally serve as an essential source of information through which the extreme situations undergone by human beings during the lockdown can be given an affective touch.\n\nThe search for meaning leads us to perform a qualitative or content analysis28,29 materialized through heuristics or hermeneutics and the combination of three visual methods. The “heuristic or interpretive method” comes from social hermeneutics, a particularly useful science when it comes to comprehensive sociology, insofar as interpretation constitutes its central problem.30 Certainly, what social hermeneutics helps interpret is the things themselves —though seen in their own context:31 with the aim of finding the deep keys to photographic images, or expressed differently, of revealing their inner meaning from the external ideological discourse.32 Ideology is a system of ideas, values, and precepts which organize or legitimize the actions of individuals or groups, whereas discourse can be described as an action and social interaction mode located in social contexts, i.e. both discourse itself and its mental dimensions (e.g. its meanings) form part of specific situations and social structures.33 The three audiovisual methods involved here are: Panofsky’s “iconological —or iconographic— analysis”,34,35 which in fact has a long sociological tradition; and K. Mannheim’s “documentary method”,36 which deals with the social information supplied by images; and “visual framing,” which visually situates reality and contextualizes information.25,29,37 In short, this connection facilitates an interaction between three levels of reality, namely: the world (the city, the houses, the hospitals and the objects); photography; and the photojournalist’s intention. The photographs reflecting the emptiness of Alicante will be analyzed with regard to those three levels, although bearing in mind that, despite not being the complete reality, the photographs under examination do represent a plausible approximation to the existing reality and convey a clear ontological, ethical, political, aesthetic and sociological content.\n\nIt should be highlighted that the 13 selected photographs were taken by the photojournalist Rafa Arjones (Figure 1), who has been a professional photographer since 1987 and belongs to a family of photojournalists from Galicia that settled down in Alicante (with a population of 330,000 inhabitants and the capital of a dynamic province located in Southeast Spain). Arjones works for Información, Alicante’s most read newspaper and arguably one of the most outstanding within the Prensa Ibérica Group — the largest journalistic holding in Spain — and he also graduated with a degree in Photography and Visual Arts at Elche’s Miguel Hernández University (Alicante, Spain), in addition to which he studied audiovisual journalism, and was awarded with the Fotopres Prize by Fundaciò La Caixa in 1987. In order to select the photographs, we accessed Información’s newspaper and periodicals library, where we consulted and read all the newspapers published (66) in the period comprised between March 14th and May 18th, 2020 (corresponding to the first state of emergency). To be more precise, incorporating the keyword “Rafa Arjones” allowed us to obtain a total of 420 entries where his photographs were published. Nevertheless, those entries included many repeated images, because they had been published on several dates and/or in different regional versions of the periodicals (eg. Alicante, Elche, Alcoi, Vega Baja) to complement the corresponding articles. Furthermore, these images collected from Información were contrasted with those kept in the photojournalist’s own archive, which provided us with 102 images that, according to him, were the best and most representative of his professional career. He organized them by themes which revolved around the following concepts: “Empty city” (9), “Solidarity” (28), “Lockdown Surveillance” (7), “UME (Spanish Military Emergency Unit])” (5), “Rich Neighborhood-Poor Neighborhood” (11), “Reporters on the street” (6), “Disinfection” (5), “Healthcare Staff” (11), “Lockdown” (13), and “Queues in the supermarket” (7). Our final selection therefore includes 13 images (approximately 12.7 percent of the total) which, in our view, can be classified as representative and significant both in relation to the topics being studied and concerning Arjones’s way of thinking, as well as the events of the lockdown. Nonetheless, in order to achieve our aims, we paid attention not only to the general context of the pandemic — its main characteristics and effects — but also to the captions and to the written information offered by the journalist together with the image itself. Despite all our efforts, we are fully aware that the chosen corpus — as it usually happens — is undoubtedly small and, consequently, arbitrary. However, we strived to ensure that the selection included representative and meaningful images, or different expressions, and that they portrayed the most important issues and values with which Arjones observed Alicante’s urban reality and that, in parallel, they reflected in the most objective way possible the real circumstances in which the photographer worked during that period. Therefore, these 13 photographs lie at a crossroads between the photographer’s subjectivity and the objective goal of showing the historical reality of a city like Alicante during the lockdown. This article is accordingly framed within Weber’s Comprehensive or Interpretive Sociology, which regards the social world and the relationships generated by it as being meaningful. It also draws on applying the postulates of Visual Sociology to photojournalistic images taken during the lockdown. And last but not least, it takes into account that these journalistic photographs are social documents that grant what Weber refers to as “social schemes or types” and which, despite not exactly being the reality determined by coronavirus, allow us to better understand that specific reality.\n\nThis figure has been reproduced with kind permission of the author.\n\n\nResults and discussion\n\nCOVID-19 has expanded globally and transnationally38 because globalization, its networked structure or order and its multiple flows, along with urban and territorial organization, have favored its dramatic spread. In fact, people not only inhabit densely populated areas and live in multi-family buildings but also use public transport on a massive scale, all of which has largely increased the proximity of bodies. That is why the measures adopted by different states to “protect” their citizens against the risk of death have made 2020 a year that we are experiencing as an “historic” period with wide-ranging and unpredictable social, cultural, economic, environmental, ethical, and political consequences that especially affect individual and social bodies. No wonder this pandemic is a “disaster,”, a “catastrophe”,38 a strange crisis which redefines uncertainty and risk, while disrupting daily life and its rhythms and directly reminding us of the congenital human fragility.39 What is more, it amplifies this already unstable situation, insofar as nobody knows for sure where the pathogen came from. To complicate matters even further, this unprecedented and complex situation has not only stressed or collapsed public health systems but also interrupted or paralyzed economic activity all over the world.38 Moreover, the merciless attack of the virus has forced nations to implement extraordinary measures pursuant to legislations, such as permitting the declaration of a “state of emergency”, which has curtailed basic human rights of citizens, amongst them: going shopping; demonstrating; attending events or participating in public activities; socializing; enjoying the open air; doing sport or meeting and hugging their loved ones. Alongside all of the above, the coronavirus crisis has placed science at the center of public space;40 to such an extent that nations have adapted — at different speeds and with various levels of intensity — to different means that seemed useful to them in these circumstances: technical, scientific, and medical rationality, which even outplayed the hitherto dominant economic rationality, albeit only in the short term. At present, the prevalence is of measures such as social distancing, covering one’s mouth and nose, mass reclusion and care taken with hygiene. It might appear that, more than ever before, Society has become the space and time of rationality, order and security, whereas Nature would instead represent chaos, uncertainty and insecurity. However, it should also be borne in mind that the most recent coronavirus (SARS-CoV-2) is a product of the interaction between wild animals and human society.38 Furthermore, it has both natural and social dimensions while simultaneously constituting a biological and social phenomenon41 which is both chaotic and orderly, since it has generated pathogens — by Nature — that determine social norms and actions. That explains why 2020 is witnessing an intensified version of the old Western fight between Nature and Society, Culture and Civilization,42 the only difference being that, for the first time in centuries, the latter three dimensions seem to be on the defensive and Nature is waging a fierce counterattack. While we wait for the final outcome, at the moment, Society has diminished in many respects and Nature, or at least a part of it, has grown rapidly.\n\nThe current global pandemic has strongly affected Spain, one of the countries with the highest incidence of coronavirus as well as the highest associated mortality rates in the world: 27,709 deaths and 231,606 infected throughout the state of emergency in its home confinement phase (from March 14 to May 4, 2020). Although a variety of reasons may account for these particular conditions, Spain’s social and cultural context, built around interpersonal relationships where sociability, proximity, physical affection, and intergenerational family structures prevail, arises as a key factor. Bearing that in mind, the Spanish government’s decision to implement social distancing through home confinement as the main strategy to protect its citizens comes as no surprise.38 This has had manifold consequences. Above all, the country has been silenced and the streets, squares, gardens, and stadiums, as well as the cultural and entertainment venues of the cities — including Alicante — are suddenly empty and completely deprived of any activity: no walkers, no music, no cars, no cinemas, no shopping centers, no beaches, and the usual social activities have been cancelled or modified in line with new government guidelines. In effect, social, cultural, and spiritual interrelations have deteriorated due to the social distancing of bodies, the confinement inside homes, and the cancellation not only of every kind of public cultural and sporting event — except for TV remakes and the artistic spontaneous activities meant to show solidarity on social media and on private balconies — but also of religious and political ceremonies. In turn, personal homes and hospitals have transmuted into a “Home-World”.43 This is the result of a process in which the social universe has been placed within its four walls. Expressed another way, social, family and other relationships have been overlapped with the public activities of the so-called “home office”. In addition, family life has been reshaped through the organization of online virtual gatherings and the transformation of the living room or the bedroom into a virtual classroom.44 Furthermore, the healthcare staff in hospitals not only had to care for the basic needs of the isolated patients but also helped them emotionally. The population has additionally been forced to share their day-to-day life together more intensely, even if it is through the Internet, arranging both family and social life around social media such as Instagram, Facebook or TikTok and popular messaging or communication-oriented applications such as Whatsapp, Zoom or Google Meet.45,46 This digitization of society has made social interrelations become more virtual and therefore less carnal than ever before. Moreover, certain emotions strongly arise in this context which, albeit lived in “isolation,” are shared in the households, from balcony to balcony, from call to call, from video to video, and from whatsapp to whatsapp. More specifically, what we all communicate in these spaces of shelter — homes, hospitals, and social networks — is ambivalent. On the one hand, people lay more emphasis on sharing their day-to-day routine as well as on the implicitly associated emotions, e.g. love, play, smiles, happiness or solidarity, the last of which has visibly materialized through the active mobilization of civil society to help those who needed it most in this crisis situation as well as through the intergenerational volunteerism initiatives undertaken in many towns and cities.45 Likewise, expressions of gratitude and affection are being addressed to the new heroes of society, those everyday beings without whom chaos and tragedy would have taken over, namely: doctors, nurses, the police, the military, undertakers, drivers, transporters, pilots, supermarket cashiers, pharmacists and pharmacy assistants, and journalists. Nevertheless, alongside positive emotions, other negative ones have also developed such as fear, anguish, rancor, conflicts, gender and childhood violence — at home or on social media — combined with expressions of fear and racism, the unstoppable growth of Fake News, the revival of latent feelings of hatred and resentment, the exacerbation of political differences and the consequent social polarization.\n\n\nThe images that reflect the emptying of Alicante and the emergence of the “Home-World” and the “Hospital-World”\n\nFigure 2 shows a tree-lined walk of a central street in Alicante with a perspective towards the commercial area of Maisonnave Avenue, where you can find El Corte Inglés (department store) and numerous stores in which products such as clothes, shoes, perfumes or jewellery, amongst others, are sold. The photograph is taken in the middle of the day, without any passers-by and with no cars moving around. The photographer neatly captures the symmetry of the whole area, with two lampposts and two trees visible on both sides and, in the center of a stone balustrade, there are two sorts of jambs resembling a door which open in parallel to the walk. On one of the lampposts, some advertising banners are being blown by the wind. In front of them, exactly in the center of this geometric composition, there is a zebra crossing with parallel horizontal white stripes which, despite breaking the verticality of the other urban objects, gives continuity to the linear axis of the walk at the same time. The words “PARA-MIRA-CRUZA” (STOP-LOOK-CROSS) can easily be seen written on two of those stripes written in capital letters. The advertising has become useless, since there is no one around who can see those banners, as has the commercial street, insofar as its businesses are closed and consumers have disappeared too. The economy finds itself at a standstill, the same as the urban dynamics, activity, and social interrelations. In short, this space has undergone a minimization process, ceasing to be understood as a culturally affective and symbolic space,47 and time has come to a standstill around it. On the other hand, the vertical and horizontal coordinates along which social life flows, as well as the norms dictating it, have suddenly become outdated, as they do not seem to be valid for the current circumstances brought about by the pandemic: the absence of individuals who could comply with them turns those rules into ineffective regulations whose existence is absurd.\n\nPeople remain, therefore, in their homes. This figure has been reproduced with kind permission of the author.\n\nIn front of the horizontal facade of a supermarket, there is a long line of people waiting to enter and do their shopping whilst complying with the social distancing rules (Figure 3). Most of them have a shopping trolley, two of them an umbrella, and another one a hooded anorak; some are looking at the person standing in front of them, whereas others gaze at the camera lens. An empty zebra crossing stands out in the center of the photograph, and across the street, there is a stop sign and a green light to signal the non-existent cars. Leafless trees arranged along the same sidewalk occupied by the future buyers, all of whom are standing, and lower iron pylons around the zebra crossing, together with lampposts and traffic signs, all of them in a vertical position, complete the main scene. Finally, on the right of the zebra crossing, and seemingly unwilling to cross it, a woman with a shopping trolley with her back to the viewers takes a shortcut towards the line. The citizens standing still on the wall are organized following a calculated and orderly arrangement which is coherently reinforced by the vertical and horizontal lines of all the other objects in the photograph. Thus, the usually chaotic movement of city dwellers has been replaced by a group of paralyzed individuals whose apparent lifelessness makes them look like any other inert object. In fact, these people now form a motionless part of the townscape — exactly like the lampposts, the pylons, and the leafless trees — as if coronavirus had absorbed their social, and also to a certain extent their individual body energy, which only manifests itself in the different stances or ways of waiting. Attention should likewise be paid to the touch of chaos and individual “indiscipline” transmitted by the walking woman who has chosen not to go across the zebra crossing in the normal way.\n\nPeople are seen waiting to be able to buy and keeping the presribed safe distance. In those moments, when it was possible to go out to the street, waiting becomes one of the main moments in which there is a certain social relationship. This figure has been reproduced with kind permission of the author.\n\nThe eight municipal policemen in Figure 4 are also arranged in order, and separated pursuant to social distancing rules, in the middle of the day. What is more, they try to ensure that confinement regulations are being abided by and, more precisely, that the cars on the road have the corresponding authorization to circulate. The first of these policemen on the left of the photograph, has stopped a vehicle, probably to check whether the driver has such an authorization or not. As the case may be, the driver will be allowed to continue, warned that the quarantine is not being complied with or even fined for the possible infringement committed. Both the diagonal line on the road and the one formed by the standing officers seem to head towards a city street that the vehicles are coming from; hence why all the policemen are looking in that direction instead of paying attention to what is happening on the opposite side of the same street. As attested by this photograph, COVID-19’s virulence has made it necessary to apply social surveillance and control measures, since what is really at stake is survival through the maintenance of social institutions, especially economic, health and democratic ones. The problem with this virus precisely lies in the fact that it attacks not only the regulated social organization and its dynamics, but also the density of contacts, affections, and interrelations, as well as our individual biology. To counter this, and following scientists’ advice, the government has imposed discipline on physical bodies to prevent them from coming into contact and to encourage society as a whole to apply self-control and energy-restriction measures, ultimately seeking to prevent the virus from being fed and accordingly allowed to spread freely. Two questions may be posed in this regard, though: (a) is the problem being addressed head-on (the policemen are looking in a single direction)? and (b) has society not been reduced to a certain extent as a result of this?\n\nThis figure has been reproduced with kind permission of the author.\n\nThe popular Explanada, Esplanade, in Alicante, usually full of people, wandering passers-by, families, children, seniors and tourists, is now empty (Figure 5) despite the fact that it is daytime. We can only see, right in the center of the composition, a private company worker wearing a yellow protective suit, a mask, and gloves who is fumigating. Although he is standing, his position is perpendicular to the orientation of the walkway, marked by the linear and vertical arrangement of the palm trees, with which he also contrasts due to the horizontality of the device in his hand. The geometric coordinates that represent order in society are once again subverted by the situation, which in turn alters the function normally associated with a walkway like this one. Why fumigate if nobody is strolling in the area and there will be no one for weeks to come either? And, more importantly, will the amount of chemical dumped onto the street be effective and sufficient to destroy the virus in such an open space? Do these actions not appear to reflect the state of confusion in which this situation has immersed us, our scarce knowledge about the pandemic or about what really needs to be done in order to fight it? On the other hand, this worker’s loneliness becomes evident, since he is now the only inhabitant of this city, an anonymous tragic hero — we cannot see his face — who risks his life to keep the city clean, without knowing for sure if his effort will eventually turn out to be useful or useless. Figure 6 also shows the individuality of the young woman portrayed in the foreground, dressed in a yellow protective suit that covers her hair and wearing an anti-pollution mask as well as protective glasses. Behind them, we can see her large dark eyes wide open and looking directly into the camera, seriously scrutinizing or expressing her state of mind and/or the gravity of the situation. The skin allergy on her face, above her nose, most probably caused by (wearing) the mask, might also be a psychosomatic effect of the stress she is experiencing. It should also be highlighted that her mask resembles those used by soliders in war to protect themselves against polluting gases, the only difference being that our enemies are not other human beings now; we are waging a hand-to-hand combat against nature, embodied in the virus. In any case, its harmful effects can hardly be denied, insofar as COVID-19 affects not only the health of bodies but also that of minds. The next photograph (Figure 7) shows three UME (Military Emergency Unit) soldiers wearing their military outfits, masks that cover their faces completely, and gloves. In this case, they are disinfecting an educational center, but it might as well have been a private residence (it should be remembered that in Spain there are a number of old people’s homes managed by the State and the regional governments) or an airport. Rather than individuals — defined by faces with unique features — and human bodies, what we see is uniforms indicative of their social condition, social roles, and anonymous heroes who are working for the benefit of public health, putting their own lives at risk.\n\nThe lack of knowledge about SARS-CoV-2 led the authorities to implement various measures without knowing their real effectiveness. Subsequent rapid advances in knowledge led to social confusion about these decisions. This figure has been reproduced with kind permission of the author.\n\nThis figure has been reproduced with kind permission of the author.\n\nWhat it can be seen are uniforms that indicate their status and social role. The involvement of the military in the protection processes generated a certain identification of the military with the heroes. This figure has been reproduced with kind permission of the author.\n\nFigure 8 shows the facades of two buildings in the Santa Cruz neighborhood — a typical area of Alicante’s historical center — and, more specifically, four balconies adorned with the Spanish flag, three of the balconies are adorned with the black outfits of the Holy Week brotherhood and are occupied by five people — three men, one woman, and a little girl — dressed in the same color and outfit. All these inhabitants of the neighborhood whose black color stands out from the white or light-colored walls seem serious, including the young girl, and appear indifferent to one another, even those who share the same balcony and must be relatives. The mother, on the other hand, makes a gesture to approach her daughter, who barely peeks through the railing and over the ritual garment while attentively looking at the street. No one occupies the fourth balcony, and there is no hanging black outfit either, although the window ajar suggests that its owners might be inside. Finally, a tile with the body of Christ can be seen on the white front of the left hand-side building. The presence of Christ, added to the scene with the dark ritual costumes on the balconies along with the ritual and festive clothing of the neighborhood inhabitants, constitutes a physical embodiment of the festivity both in the actual buildings and in those who inhabit them. Truth be said, though, the sad faces express the emotional frustration for the inability to parade, with fervour and full of an “effervescent”, “emotional” and “integrating” energy, the paso (scene/image) of the Reclining Christ through the streets of Santa Cruz. In fact, the people in the housing blocks do not seem to care about one another, all of them absorbed in their own disillusionment or bewilderment, and indifferent to whatever their next door neighbours may be doing and experiencing emotionally. Meanwhile, the neighbourhood is empty; nobody stands outside the houses, there are neither women nor men, children, elderly people nor tourists, which means that the festivity has been left hanging from the balconies due to the impossibility to descend and parade down the street.\n\nThe pandemic also increased certain patriotic spirit. After all, it was a symbolic war against the virus. This figure has been reproduced with kind permission of the author.\n\nThe interpersonal relationships in the building in Figure 9 are very different. Some people occupy the balcony on three of the floors. On the lower balcony, we can see a young couple somewhat separated from each other, whose bodies do not touch; he is looking at his mobile phone while she observes the street. The balcony on the flat above them shows a girl and a man whose distorted body is turned upwards while he leans on the window frame. He is chatting happily with the couple on the top floor, as suggested by the smile of the woman who directs her gaze downwards. A poster with a rainbow drawn on it is glued to the windowpane by her side. These social interrelations which seem temporary and somewhat forced, coexist with those of indifference or self-absorption represented by the couple on the bottom floor. Furthermore, the rectangular space of each terrace, together with their glazing and awnings, separate the respective flats which despite being arranged one on top of the other, are autonomous. This is reinforced by the fact that they are not at street level, but above it, which keeps residents far from the normal daily urban pulse. Furthermore, the space where these flats are located represents the edge of the construction, the limit between the inside and the outside, between the society of individualization and the family, between intimacy and the expression both of emotions and of social interrelations with other people, and between the household and the street. For this reason, every day at 8:00 p.m, they ritually applaud the professionals who are risking their lives, greet other neighbours, show their attachment to traditions, participate in some cultural activities or call on the population — as denoted by the rainbow which has become synonymous with the healthcare profession during this crisis — to become aware of the need to stay at home for the sake of collective health and to be hopeful that they will successfully overcome the critical situation in which they find themselves.\n\nThe image shows how people talked from their balconies when they were unable to go out into the street. This figure has been reproduced with kind permission of the author.\n\nOn the landing inside a block of apartments in Figure 10, a young man wearing a face mask and a short-sleeved shirt is seen in the foreground as he turns his head to look at the photographer and tell him what is happening there. On the same floor, a very long horizontal corridor opens in which the flat doors are separated by openings and handrails and where someone else can be seen, blurred and distant, in the background. Downstairs, there are two elderly people, one in underwear or swimming trunks and shirtless — he carries his shirt in one hand and his cell phone in the other — and a woman leaning against the door of her home wearing a housecoat. Both look at the camera too, and the older man seems to show, amusingly opening his hands, how he is dressed, or undressed. The segmentation between neighbours in the design of this building follows a horizontal pattern organized around the openings and metallic handrails, in such a way that the flats are separated not only by their inner walls but also by the architectural elements of the corridor, without forgetting the invisible virus that also forces them to stay apart. In the scene, the main three protagonists seem to establish a communication between accomplices: the young man prefers to look at the photographer and, the same as the older man, speaks to him, while his wife observes the photographer with an expression situated between amusement and amazement. Finally, the person in the background is so far away that he remains totally unaware of what is going on a few meters away. On the other hand, the neighbours are outside their houses, in the corridor, albeit dressed as if they were inside their homes or on the beach, which attests to the confusion between what is inside and outside, what is intimacy and “extimacy” and, in short, what it means to be imprisoned — reflected in the numerous bars of the banister — to be safe or to be free to run risks.\n\nPeople seek to promote social interaction as a reaction to a mechanism that was intended to promote a degree of temporary social isolation. This figure has been reproduced with kind permission of the author.\n\nA narrow room (Figure 11) in an retirement home on whose white wall we can find a large crucifix and a window with its closed white curtains that prevent us from seeing the outside, although a sifted light manages to come in. This relatively dim room is almost entirely occupied, with hardly any space left, by three healthcare professionals wearing white protective suits, a mask and gloves, who are about to transfer an elderly woman to the hospital, who also wears a mask and sits on a folding chair. Is she infected with coronavirus? In such a small and unventilated space, it is easy for the virus to flood the room and infect its occupants, without the dark cross being able to do anything about it, other than announce the proximity of a possible future death. In nursing homes it is usual for one or two people to be responsible for cleaning the residents’ rooms. In contrast, the photo shows three people cleaning the room. This generates a symbolic process of transformation of social environments into biomedical ones. It also shows the commitment of public institutions to public health. In fact, during the strict confinement, the authorities sent external staff to the nursing homes in order to protect the most vulnerable. Figure 12 shows a hospital room with equipment and six people, five of whom are healthcare workers wearing suits, masks and gloves, and the other, someone lying on a stretcher almost completely covered by a sheet, so that only one leg can be seen. The hyper-protective behaviour of the healthcare professionals clearly suggests that the patient is infected with COVID-19, whereas their different gestures and bodies denote action and concentration. On the left side of the picture a standing healthcare worker can be seen. Despite apparently observing the scene calmly and motionless, her leg is advancing in a way which reveals that she may approach the patient or move towards any of the machines or objects in the room immediately. Time to act is compressed, minute by minute, although chaos, urgency, accelerated body movements and the flow from life to death unfold in a context of heightened uncertainty. In Figure 13 we can see a motley group of nurses, doctors, cleaners and service staff, as well as local police in their uniforms, mixed amongst one another, at the door of a hospital. Most of them are raising their hands to draw attention to the dramatic situation that they are living through or applauding as they look to the camera, with the exception of some policemen with their backs on the spectators who are looking at the healthcare staff and applaud them by way of a heartfelt tribute. The photography transmits great dynamism and, despite the absence of joy in the group, there is a strong emotional energy as well as a powerful conviction that they are doing the right thing and, more importantly, a will to do whatever it takes both ethically and based on solidarity to help anyone who may need it. Moreover, by standing so close, without any social distancing, they demonstrate the inseparable unity and huge strength of this group and, in short, make it clear that the only possible way to cope with all this is working side by side, joining hands, bodies and brains.\n\nIn the picture you can see how a small room was occupied by several people in order to clean and keep the sanitary situation under control. In the process, the social space becomes (symbolically) an alternative “health centre”. This figure has been reproduced with kind permission of the author.\n\nLack of knowledge about the virus leads to an increase in health measures. This is in addition to the numerous cases of people affected by respiratory problems. In this image, hyper-protective behavior of the healthcare professionals clearly suggests that the patient is infected with COVID-19. This figure has been reproduced with kind permission of the author.\n\nIn response to this phenomenon, hospital workers would go out to the hospital gates to clap and express their gratitude to the population for its social behaviour. This figure has been reproduced with kind permission of the author.\n\n\nConclusion\n\nIn our view, the analysis of the photographs taken by the photojournalist Rafa Arjones has allowed us to confirm the three key consequences of the COVID-19 lockdown in Alicante. The first one, that the city was deserted, its streets uninhabited, its stores and promenades closed, without any vehicles or pedestrians (Figure 2). The people who could leave their homes did so only to buy the essentials to eat (Figure 3); the lonely ones took to the streets to work e.g police (Figure 4), fumigators (Figure 5 and Figure 6), the military (Figure 7), healthcare staff (Figures 11, 12 and 13), drivers, pharmacy and shop assistants, sweepers all became heroes who risked their lives to decontaminate, to attend to the sick, to ensure safety or to maintain the essential services. The Alicante-born photojournalist’s carefully taken images likewise emphasize a neat geometry framed within two coordinates — horizontal and vertical — and a central axis of the composition around which the portrayed objects and persons are distributed (Figures 1, 2, 4, 8 and 9). He does so because one of his discourses refers to how the critical situation triggered by the pandemic has disrupted the social order and the norms guaranteeing it which that geometry represents. It is as if questioning the coordinates and axis that sustain current life social space had resulted in a collapse of society itself. In fact, its content has been radically altered, since social interrelations, the economic dynamics, urban vitality, affections and the contact between bodies, together with the energy which renews the citizens’ pulse, have been minimized, thus emptying society. At the same time, control and surveillance have increased with the aim of keeping us safe (Figure 3). Therefore, representative democracy has somehow entered “quarantine”48 and has been partially emptied as well.\n\nThe streets have been emptied while homes and hospitals — society’s last shelter — have been filled, expanding their traditional functions to become a more or less safe “world” where both the usual activities and new ones can take place. Thus, the rituals (Figure 7), the manifestations of solidarity, and the conversations that used to form part of street life now develop in balconies or corridors (Figures 7, 8 and 9), narrow, enclosed, and segmented areas where the new forms of loneliness, self-absorption, estrangement and lack of affection also become visible. Hospitals (Figures 10 and 11) have in turn assumed new rituals of empathy, providing social cement and loving care for the sick, and their staff have acted as a true family for patients during these times of loneliness and forced isolation. The photojournalist has successfully captured human emotions typical of such a critical situation in homes or hospitals, amongst them the disappointment due to the impossibility to enjoy parties and rituals (Figure 7), the seriousness (Figures 5, 7, 8 and 12), the estrangement and uncertainty associated with this situation, the tension, the concentration (Figures 10 and 11), the empathy, the solidarity, and the firm will to protect loved ones and to look after the most vulnerable people. As for the street, it has lost almost all of its traditional functions, while the balcony (Figures 7 and 8), the corridor (Figure 9) or the hospital door (Figure 12) have assumed its competences to a large extent. For this reason, they have been transformed into a space of communication or isolation, of ritual, of solidarity, and of externalization or containment of emotions. They have become a new liminal space used in the three successive phases — separation, marginality, and aggregation49 — or moments of transit that characterize the rites of passage of ancient societies.50 They now constitute the door jambs through which citizens confusingly go from the inside to the outside, from the public to the private, from the normality of the past to the uncertainty of the future, from vitality to the death of the social, perhaps so that — the same as in rites of passage — a regeneration takes place and a new stage can begin.\n\nThe confinement of the population has been accompanied by an increased individualism and, paradoxically, by a reinforcement of the ideal of communitas. The first happens because city streets have been emptied of crowds and only lonely citizens who work (Figures 4 and 5) or go shopping (Figure 2) move through them and, although they form lines (Figures 2 and 3), they maintain their social distancing, which means that they are autonomous and independent, with their thoughts, their bodies, and their emotions kept to themselves and completely ignoring those of other people. Even the brotherhood members who traditionally share the celebration of the Holy Week are now isolated in their homes, the only trace left of that collective fusion being a black outfit and a flag which helps them to express their inconsolable frustration (7). Patients, for their part, have become more “pathogenic” (Figures 10 and 11), as they are isolated and, despite being surrounded by several professionals who do their best to look after them and preserve their health, the fragility of their bodies has intensified to such an extent that one leg (Figure 11) is no longer capable of walking, but to remain prostrate. Consequently, this leg has become a sign of the extreme fragility of the helpless members of the communitas. To this it should be highlighted that in the worst case scenario, many patients will die (Figure 10) a doubly lonely death because, in addition to dying alone, they will pass away without the company of their loved ones. The architecture of dwellings and buildings, which intrinsically encourages fragmentation, segmentation, and social distance (Figures 8 and 9), can now further strengthen the isolation of its inhabitants, locked inside their homes, separated from one another by corridors, balconies, handrails, openings, and different heights, and also from the street, because they find themselves at a higher level that keeps them far from the daily urban pulse. In short, despite the increased individualism, it takes on a less substantial character and remains closer to the inert townscape objects. In any case, if individualism — and with it the society of individualization and separativity — has seen the birth of new defining aspects, so has the community ideal. Inside homes, mobiles phones and computers (Figures 8 and 9) have become the only means to communicate with our loved ones, friends, and relatives locked in their homes too. Family members have shared life more than ever before, and neighbours have forced themselves to chat with one another (Figure 8). In hospitals (Figures 10 and 11), the bustle, the feverish dynamics, the heart rate, the vital intensity, the effervescent energy, the merging emotions, the empathy, and solidarity have been complemented by the strong will to help others and to leave this situation behind together. Consequently, the ethics of neighbourliness and fraternity to which Max Weber51 referred has been renewed in some of its aspects. However, this ideal of communitas arises from absence and emptiness and can therefore not escape a certain void feeling, without forgetting that it has reached a greater pathos which used to characterize the temporary religious ritual, which is now normalized and metamorphosed into daily life.\n\n\nData availability statement\n\nNo data are associated with this article.",
"appendix": "References\n\nBeck U: La sociedad del riesgo global. Madrid: Siglo XXI; 2006.\n\nBeck U, Bech-Gernsheim E: La individualización. El individualismo institucionalizado y sus consecuencias sociales y políticas. Barcelona: Paidós; 2016.\n\nBeck U: The Metamorphosis of the World: How Climate Change Is Transforming Our Concept of the World. Cambridge, UK: Polity; 2016.\n\nBeck U: Risk Society: Towards a New Modernity. London-NY: SAGE; 1992.\n\nLash S: Sociología del posmodernismo. Buenos Aires: Amorrortu; 2007.\n\nBauman Z: Modernidad líquida. Buenos Aires: FCE; 2003.\n\nBauman Z: Vida líquida. Barcelona: Paidós; 2006.\n\nScheff T: What's love got to do with it? The social-emotional world of pop songs.London-New York: Routledge; 2016.\n\nTönnies F: Community and Civil Society. Cambridge: Cambridge University Press; 2001.\n\nWeber M: Basic concepts in Sociology. New York: Philosophical Library Inc; 1962.\n\nGonzález García JM: Sociología e iconología. 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Madrid: Centro de Investigaciones Sociológicas; 2012b.\n\nBericat Alastuey E: Ciencias Sociales y cultura audiovisual: El conocimiento de la fotografía. In: Roche Cárcel JA (Ed.) La sociología como una de las bellas artes. Barcelona: Anthropos; 2012a; 201–224.\n\nFaccioli P, Losacco G: Manuale di sociologia visuale. Milano: Franco Angeli; 2003.\n\nAppadurai A: Mondialisation, Recherche, Imagination. RISS/ISSJ. 1999; 160: 257–268.\n\nHarper D: Visual sociology: Expanding sociological vision. Am Sociol. 1988; 19(1): 54–70. Publisher Full Text\n\nAmezaga BR: Las imágenes como fenómeno cultural: una necesaria mirada en etapas para abordar los retos actuales. Historia y Memoria de la Educación. 2019; (10): 17–49.\n\nLópez Del Ramo J, Humanes ML: Análisis de contenido de la representación fotográfica de la crisis de los refugiados sirios y su incidencia en el framing visual. Scire. 2016; 22(2): 87–97.\n\nDe Andrés S, Nos-Aldás E, García-Matilla A: La imagen transformadora. El poder de cambio social de una fotografía: la muerte de Aylan. Comunicar. Revista Científica de Educomunicación. 2016; 47XXIV: 29–37.\n\nAguilar MJ: Usos y aplicaciones de la Sociología Visual en el ámbito de las migraciones y la construcción de una ciudadanía intercultural. Tejuelo. 2011; 12: 100–135.\n\nDe Miguel JM, Ponce De Leon O: Para una Sociología de la fotografía. REIS. 1998; 84(/98): 83–124.\n\nAbreu C: El análisis cualitativo de la foto de prensa. Revista Latinoamericana de Comunicación Social. 2004; 57: 1–5.\n\nMuñiz C, et al.: Imágenes de la inmigración a través de la fotografía de prensa. Un análisis de contenido. Comunicación y sociedad. 2006; XIX(/1): 103–128.\n\nRicoeur P: Hermenéutica y acción. De la hermenéutica del texto a la hermenéutica de la acción. Buenos Aires: Prometeo; 2008.\n\nBeltrán M: Dramaturgia y hermenéutica: para entender la realidad social. Madrid: Centro de Investigaciones Sociológicas; 2016.\n\nGrondin J: A la escucha del sentido: conversaciones con Marc-Antoine Vallée. Barcelona: Herder; 2014.\n\nVan Dijk TA: Ideología. Una aproximación multidisciplinaria. Gedisa: Barcelona; 1998.\n\nPanofsky E: Studies in iconology. Humanistic Themes In the Art of the Renaissance. Boulder-Oxford: Westview Press; 1972.\n\nPanofsky E: Meaning in the Visual Arts. Chicago: The University of Chicago Press; 1983.\n\nBarboza Martínez A: Las imágenes como objeto y técnica de análisis en la Sociología: el método de la interpretación documental. In: Roche Cárcel JA, Oliver Narbona M (eds.), Cultura y globalización. Entre el conflicto y el diálogo, Alicante: Publicaciones de la Universidad de Alicante; 2005; 347–366.\n\nCarter MJ: The Hermeneutics of Frames and Framing: An Examination of the Media’s Construction of Reality. SAGE Open. 2013. Publisher Full Text\n\nLavell A, Mansilla E, Maskrey A, et al.: La construcción social de la pandemia COVID-19: desastre, acumulación de riesgos y políticas públicas. La Red (Red de Esudios Sociales en Prevención de Desastres en América Latina). 2020. Reference Source\n\nGarcía-Lastra M: Crisis, pandemia y fragilidades: reflexiones desde un “balcón sociológico”. Revista de Sociología de la Educación-RASE. 2020; 13(2): 140–144.\n\nPleyers G: Global Sociology in Times of Coronavirus. Belgium: Université Catholique de Louvain); 2020.\n\nEsquinas MF: Sociología y Ciencias Sociales en tiempos de crisis pandémica. Revista de Sociología de la Educación-RASE. 2020; 13(2): 105–113.\n\nHorkheimer M, Adorno T: Dialectic of enlightenment: philosophical fragments. Stanford: Stanford University Press; 2002.\n\nAugé M: Pour une anthropologie de la mobilité. Paris: Payot and Rivages, coll. Manuels Payot; 2009.\n\nAlcalá FG: Conjurar el miedo: El concepto Hogar–Mundo derivado de la pandemia COVID-19. Revista Latinoamericana de Investigación Social. 2020; 3(1): 2–26.\n\nRivero SC: Sociología de las relaciones familiares e intergeneracionales en periodo pandémico. In: Vázquez Atochero A, Rivero SC (eds.) Reflexiones desconfinadas para la era posCOVID-19. Badajoz: AnthropiQa; 2020; 105–134.\n\nPulido CM, Villarejo-Carballido B, Redondo-Sama G, et al.: COVID-19 infodemic: More retweets for science-based information on coronavirus than for false information. Int Sociol. 2020; 35(4): 377–392.\n\nMaderuelo J: La Idea de Espacio. Madrid: Akal; 2008.\n\nIglesias RLB, Alonso AI: Democracias en cuarentena: respuestas políticas a COVID-19 y el futuro de la democracia. Revista Española de Sociología. 2020; 29(3): 703–714.\n\nBauman Z, Leoncini T: Generación líquida. Transformaciones en la era 3.0. Barcelona: Paidós; 2018.\n\nBalandier G: El desorden. La teoría del caos y las ciencias sociales. Barcelona: GEDISA; 2014.\n\nBellah R: La religión en la evolución humana. Del Paleolítico a la era axial. Madrid: CIS; 2017."
}
|
[
{
"id": "86294",
"date": "01 Jun 2021",
"name": "Francesca Randazzo Eisemann",
"expertise": [
"Reviewer Expertise Social Imaginaries",
"Qualitative research",
"Gender",
"Microsociology",
"Garifunas"
],
"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 sociological approach is enriched by iconological analysis and the visual frame. The authors put into value the content of the photographs that mark a concrete experience related to COVID pandemics. It is both an important academic and ethnographic testimony.\nThe literature cited corresponds to in vogue sociology theoreticians and visual analysis.\n\nThe design is adapted to the scientific article model.\n\nQualitative data is provided and illustrates the purpose of the article.\n\nOne of the most interesting conclusions is the disruption of the social order translated into geometrical terms, specifically the collapse of coordinates and axis of social life.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
},
{
"id": "86292",
"date": "04 Jun 2021",
"name": "Mauro Guilherme Pinheiro Koury",
"expertise": [
"Reviewer Expertise Anthropology of Emotions",
"Urban Anthropology",
"Anthropological Theory",
"Visual Anthropology"
],
"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 'The city emptied and the homes and hospitals turned into 'the world'. A sociological approach' is an instigating study about the daily life lived during an extreme situation, in the COVID-19 worldwide pandemic. Its thematic universe is located in the city of Alicante, Spain, and comprises the changes in the daily lives of a population in the dark times of the pandemic. The authors use visual sociology as a theoretical-methodological resource, in which they figure everyday situations, places of belonging, and conflicting and tense institutional spaces where tomorrow - hope - becomes an unattainable and anguished dream, on the one hand. On the other, an illusioned possibility of a tomorrow, if it arrives, with profound changes in sociability between people and construction of a new - and better - world.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
},
{
"id": "86291",
"date": "09 Jun 2021",
"name": "Pedro Lisdero",
"expertise": [
"Reviewer Expertise Sociology",
"Visual Sociology",
"Creative Methodologies."
],
"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\nThrough the analysis of journalistic images, the authors investigate the impact of home confinement around the COVID-19 pandemic in Spain. The \"images\" are used as an anticipatory formulation of meaning to interpret some relevant signs of social relations in times of pandemic. The article highlights an interesting theoretical-methodological construction that makes it possible to recover the power of \"the visual\" in the understanding of \"society\". From some virtuous crossroads between \"iconological analysis, the documentary method, and the visual frame\", images are understood beyond a mere vehicle for research, to unravel what they show from a non-translatable language about social reality. Thus, the images of Alicante (by photojournalist Rafa Arjones), analysed from their capacity to \"show\" the meanings constructed around the \"Home-World\" and the \"Hospital-World\", constitute a \"message\" (sensu Melucci) about the re-structuring of the processes of individualism and \"communitas\" that traverse Spanish society. These tendencies converge in a paradox \"visualised\" on the basis of pandemic confinement, reinforcing the productivity of \"the gaze\" proposed by the authors, and opening up questions about the processes of social structuring underway.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-424
|
https://f1000research.com/articles/9-1305/v1
|
06 Nov 20
|
{
"type": "Research Article",
"title": "Using agricultural metadata: a novel investigation of trends in sowing date in on-farm research trials using the Online Farm Trials database",
"authors": [
"Judi Walters",
"Kate Light",
"Nathan Robinson",
"Kate Light",
"Nathan Robinson"
],
"abstract": "Background: A growing ability and interest in the collection of data, together with the development and adoption of the FAIR guiding principles, has increased the amount of data available in many disciplines. This has given rise to an urgent need for robust metadata. Within the Australian grains industry, data from over thousands of on-farm research trials (Trial Projects) have been made available via the Online Farm Trials (OFT) website. OFT Trial Project metadata were developed as filters to refine front-end database searches, but could also be used as a dataset to investigate trends in metadata elements. Australian grains crops are being sown earlier, but whether on-farm research trials reflect this change is currently unknown. Methods: We investigated whether OFT Trial Project metadata could be used to detect trends in sowing dates of on-farm crop research trials across Australia, testing the hypothesis that research trials are being sown earlier in line with local farming practices. The investigation included 15 autumn-sown, winter crop species listed in the database, with trial records from 1993 to 2019. Results: Our analyses showed that (i) OFT Trial Project metadata can be used as a dataset to detect trends in sowing date; and (ii) cropping research trials are being sown earlier in Victoria and Western Australia, but no trend exists within the other states. Discussion/Conclusion: Our findings show that OFT Trial Project metadata can be used to detect trends in crop sowing date, suggesting that metadata could also be used to detect trends in other metadata elements such as harvest date. Because OFT is a national database of research trials, further assessment of metadata may uncover important agronomic, cultural or economic trends within or across the Australian cropping regions. New information could then be used to lead practice change and increase productivity within the Australian grains industry.",
"keywords": [
"metadata",
"FAIR",
"grains",
"crop",
"sowing timing",
"wheat",
"barley",
"canola"
],
"content": "Introduction\n\nThe amount of digital data being generated around the world every day is truly massive. More data were generated between 2015 and 2017 than in the whole length of human history before that (Marr, 2015). It is expected that the entire digital universe is expected to reach 44 zettabytes1 by 2020 and by 2025, it’s estimated that 463 exabytes2 of data will be created globally each day (Desjardins, 2019). The sheer volume of data being produced means that excellent data management is essential (Harper et al., 2018). However, it has been estimated that between 80 and 93% of data are held on personal computers or in offline repositories (Babcock, 2015), where they are left in the ‘dark’, and are of limited use (Sadiq, 2016). There are increasing calls for data to be made more widely available for maximum use, as well as the view that research funded by taxpayers should be more readily accessible (Stow et al., 2018). Research data is no longer just ‘nice to have’: such data underpin decisions about health, development of public policy, innovation, profitability and environmental sustainability (Barbour, 2019).\n\nFor data to be used they need to be brought out of the ‘dark’ and into the ‘light’. That is, they need to be findable. Making data findable is the first step in the ‘FAIR Guiding Principles’ (i.e. Findable, Accessible, Interoperable and Reusable) for scientific data management and stewardship (Wilkinson et al., 2016), and for data to begin to be considered ‘findable’ they must first be available in digital formation in an online platform (i.e. on the internet). Once online, data are made more findable by having rich metadata. The term ‘metadata’ generally refers to ‘information about information’, or ‘data about data’ (Brand et al., 2003), and there are increasing calls for metadata to be treated as equally important as the objects they describe (de Waard & Kircz, 2003). However, metadata records vary greatly in their richness; that is, how much or little of the data is described and captured in the metadata record, where generally the ‘richer the metadata record, the greater the possibilities’ (Brand et al., 2003).\n\nThe term ‘metadata’ can mean different things within different settings, and there are many different ways that metadata can be classified. The ‘Metadata, Encoding and Transmission Standard’ (METS) divides metadata into three broad categories: ‘descriptive’, ‘structural’ and ‘administrative’ (Davenhall, 2011). Of these, descriptive metadata elements are the most commonly used in outward-facing online searches. For example, putting ‘keywords’ into a search engine such as Google allows sources of online information to be identified and selected as appropriate. Thus, the richer the metadata applied to a data source, the more findable the data becomes.\n\nThe creation and use of meaningful metadata are now recognised as crucial elements in providing value-added services (Simek et al., 2013). Metadata are increasingly being used to detect trends and obtain insights into social, economic and political interactions (Oh & Park, 2018; Conte et al., 2012; Lazer et al., 2009). For example, many scientific publications have reported use of Google Trends to identify changes in people’s search behaviour as indicators of changing interest in a topic (Kampf et al., 2015), measures of public health (e.g. Cook et al., 2011), economics (Kristoufek, 2015) and environmental events (Cha & Stow, 2015). Such studies have typically relied upon metadata from internet usage or high-throughput data; however, trend detection can be conducted on other types of metadata. For example, metadata from weather stations have been used to detect changepoints that indicate events such as gauge changes or station relocation (Li & Lund, 2015).\n\nTo maximise use once a data source has been found, the data also need to be accessible. Making data ‘accessible’ is the second step in the FAIR Guiding Principles, meaning that people seeking to use the data can access them at the defined time and by the defined method (Luque, 2019). Further, there are increasing calls to make research data and findings ‘open’, meaning that data can be ‘used, reused and redistributed freely by any person, and that are subject, at most, to the requirement of attribution and to be shared in the same manner in which they appear’ (Dietrich et al., 2015). This is especially the case for projects that are publicly funded (Chugh & Howah, 2019). Thus, the process of and results from experimental research should be open, transparent, reproducible and testable (Davenhall, 2011). Science funders, publishers and governmental agencies now often require data management and stewardship plans for data that are generated in publicly funded research projects (Wilkinson et al., 2016). These typically state that data should be published under an ‘open access’ (OA) model. OA is a set of principles and practices through which research outputs are distributed online, free of cost or other access barriers (Suber, 2004).\n\nMany types of data and information lend themselves well to OA. For example, many scholarly publishers now provide authors with the opportunity to make the research manuscripts available through OA publishing models, and application of licenses such as those by Creative Commons promote sharing of research outputs. For some types of experimental and research data – particularly those from laboratory-based or sensor-driven experiments – there are a number of well-curated, deeply integrated, special-purpose open data repositories such as Genbank (Benson et al., 2013), the Worldwide Protein Data Bank (Berman et al., 2003), and UniProt (The Uniprot Consortium, 2019). A number of ‘general-purpose’ repositories such as Figshare and DataHub, have also been developed, but not all research data or data types can be captured by or submitted to these repositories, and searching repositories that hold such disparate data is often problematic. Indeed, many potentially valuable datasets emerging from traditional, low-throughput research trials don’t fit well into these repositories (Subramaniam, 2004).\n\nThe use of agricultural trial data has enormous potential to improve cropping and management practices (Hyman et al., 2017). Serra da Cruz & do Nascimento (2019) identified a number of difficulties in data-driven research projects in agriculture, including a lack of appropriate infrastructure to store and preserve data and difficulty in sharing datasets. Harper et al. (2018) asserted that ‘the future of agricultural research depends on data’, and that ‘the sheer volume of agricultural biological data being produced today makes excellent data management essential’. These authors also suggest that the ‘value of data increases exponentially when they are properly stored, described, integrated and shared, so they can be easily utilized in future analyses’.\n\nWithin the grains and cropping sector in Australia, many thousands of field-based and on-farm research trials have been conducted by grower and farming systems groups, government researchers, universities and private industry groups with the aim of improving the profitability and sustainability of Australian grain production (Wills et al., 2019). However, the results from much of this work is traditionally retained ‘in house’ – on personal computers or institutional and private websites (Serra da Cruz & do Nascimento, 2019) that can be accessed only via subscription or membership status. The data are thus neither findable nor accessible, so the potential value from the re-use of research findings is not being realised. Further, many research topics are being duplicated in both time and space, resulting in wasted time, effort and funding investment (Sexton et al., 2019).\n\nIdentification of this urgent need for greater dissemination of research trial data and findings within the Australian grains research community led to the development of Online Farm Trials (OFT) – an open online database that provides open access to on-farm or field-based cropping research trial data and information. Hosting past and present research trials undertaken and contributed by a range of contributors throughout Australia, OFT is a source of knowledge and information to support decision making, practice change and improvements in farm profitability and sustainability.\n\nOFT can be considered as a ‘biocurator’ (Harper et al., 2018), striving to present ‘accessible, accurate and comprehensive representation of biological knowledge’. Biocuration is the process of ‘selecting and integrating biological knowledge, data and metadata within a structured database so that it can be accessible, understandable and reusable by the research community’ (Harper et al., 2018). Data and metadata are taken from trial reports to form the basis of the Trial Projects, which are integrated with other data, including SILO and Bureau of Meteorology weather data and the Soil and Landscape Grid of Australia to deliver a value-added product to database users. OFT Trial Project metadata can be considered as ‘descriptive’, providing information about the basic parameters of each research trial project within the database. The online fields into which mandatory metadata are entered on the OFT website are Trial project code, Trial project title, Growing season year, Trial site, Crop type, Trial type, Trial design and Treatment type. These fields have been defined as the minimum information metadata elements required for the creation of a Trial Project in the OFT database. On-farm crop research trials typically follow the basic scientific procedure whereby experiments are conducted under controlled, documented conditions, and the results are used to determine the best inputs to achieve the desired outputs. However, this may not be the case for demonstration trials, and scientific publishing standards have not generally been applied within the on-farm research activities in the past, so legacy trial reports do not always contain all the required information to generate searchable metadata within OFT (Robinson et al., 2019).\n\n\nSowing timing\n\nSowing time is critical in determining crop yield, so getting the right sowing timing for a crop is one of the most useful ways of maximising grain yield in dryland agriculture (Sharma et al., 2008). It is generally acknowledged within the Australian grains industry that crops are being sown earlier than in the past (GRDC, 2011), and it could be expected that cropping research trials would be designed to follow the same practices as those being employed within the general industry to ensure results data are relevant to what growers are doing in their paddocks. However, Stephens & Lyons (1998) suggested that is not always the case, and, to the best of our knowledge, investigations into their claim have not yet been reported.\n\nIn the first study of its kind in the grains industry, we investigated whether OFT Trial Project metadata can be used as a dataset to detect trends; testing the hypothesis that research trial sowing dates reflect district practice in grains cropping management (i.e. sowing date moving earlier in the year within the study period).\n\n\nMethods\n\nAt the time of analysis (18 December 2019), there were 11,458 Trial Projects (i.e. site × growing year × crop type combinations) in the OFT database. These included both published and unpublished trials. Of these, 3634 (30.72%) contained a sowing date (SD) in the available metadata field. Where multiple dates were available (i.e. ‘time of sowing’ trials), the earliest date was used to provide the broadest range of dates being trialled by researchers and to corresponded with the first date used in trials with only a single sowing date. Trial Projects that met the following criteria were included in the analysis of sowing date:\n\n1. winter crop species; specifically, barley, canola, chickpeas, faba beans, field peas, kaspa peas, lentils, linseed, lucerne, lupins, mustard, oats, triticale, vetch and wheat; and\n\n2. sown in an ‘autumn’ period; specifically, between 1 March and 31 July.\n\nThe winter crop species selected were those that (i) were contained in records in the OFT database, and (ii) rely on an autumn rainfall ‘break’ to germinate, so would traditionally be sown within a specific ‘sowing window’ aimed at achieving optimal growth and yield. The period between 1 March and 31 July incorporates the broadest possible sowing window for these crop species.\n\nThe remaining 3067 Trial Projects were included in the metadata export. The export was saved as an MS Excel spreadsheet, and contained data for ‘Sow date’, ‘Crop type(s)’, ‘Growing season year(s)’ and ‘Trial site(s)’ (i.e. trial location) from the OFT database. Sowing dates were converted from calendar dates to Julian days, the frequency of dates was assessed to determine whether they were normally distributed. All data were found to display a normal distribution, so no data cleaning was required.\n\nTrial Projects sites were located on a map of Australia to show the spatial distribution of trials. Trials in the export were then classified by state (i.e. New South Wales (NSW), Queensland (Qld), South Australia (SA), Tasmania (Tas.), Victoria (Vic.) and Western Australia (WA)) and by crop type (species). There were a limited number of Trial Projects for crop types other than wheat, barley and canola, so data assessments focussed on the six states × three crop types (wheat, barley, canola) and an ‘all crops’ category including all crop types listed above. A total of 24 combinations were generated for analysis.\n\nTo determine the minimum number of Trial Projects needed in each state × crop type combination to provide a margin of error (MOE) required for a 95% confidence interval (CI), we calculated the standard deviation of SD across the years on record, then used the following equation to calculate μ, where μ is the sample size of n ≥ (z*σ/MOE)2; z* = 1.96 (value corresponding to CI of 95%) and σ is standard deviation of the population. The standard deviation of the sample was 19.5 days, and we selected a MOE of 7 days. From this, a sample size of >29.8 days was calculated. Thus, in the analyses, we included only state × crop type combinations with >30 Trial Projects. SDs were averaged for each year within the remaining state × crop type combination. Ordinary least squares regression plots of SD versus year were created for each of the state × crop type combinations. Linear regression analysis was conducted in StatPlus:macLE build 7.1.1.0 to investigate the relationship between SD and year. The effect of the resultant coefficient of determination (R2) values were considered following Moore et al. (2013):\n\nR2 < 0.3 = none or very weak,\n\nR2 such that 0.3 < r < 0.5 = weak,\n\nR2 such that 0.5 < r < 0.7 = moderate, and\n\nR2 > 0.7 = strong.\n\nPlots of residuals versus fitted values were created for each regression to check validity of the assumption of normality in the data. One-way analysis of variance (ANOVA) was used to test the overall significance of the regressions via Student’s t-tests. The significance of results was considered: P < 0.001, highly significant; P < 0.01, moderately significant; and P < 0.05, significant; P > 0.05, not significant. Plots of residuals demonstrated that the assumption of normality was validated for all regression plots (data not shown).\n\nThe sowing date of trials that formed the National Variety Trials (NVT) between 2010 and 2019 were also investigated. An NVT dataset of 6084 trials meeting the same requirements for SD and crop type as utilised above was investigated following the same protocol as specified for the OFT dataset.\n\n\nResults and discussion\n\nMetadata is critical to increase the findability of digital information, but it can also be used to detect trends and thus make predictions. Here we used Trial Project metadata from the OFT database as a stand-alone dataset to investigate possible trends in sowing date (SD) of on-farm research trials from across Australia from 1993 to 2019, which was the year range resulting from analysis of the database. The primary purpose of our analysis was to determine if a dataset such as this could be interrogated to provide insights into agricultural trends. In-depth discussions of any agronomic or other factors that could explain specific trends are beyond the scope of the current study.\n\nThe 3067 Trial Projects identified and used in the analysis covered a broad spatial spread of trial sites (Figure 1) with a similar number of research trials having been conducted in each year across the study period. Our results show that OFT Trial Project metadata can be used to detect trends in SD when sufficient data are accessible. The median SD for all Trial Projects included in the analysis was 140.4 Julian days, which equates to 20 May in a non-leap year (19 May in leap years). The frequency of SDs between designed dates (1 March to 31 July) followed a normal distribution (data not shown), with a standard deviation of 19.5 days. The calculated sample size needed for analysis within each state × crop type combination was 30 Trial Projects, and for the state × crop type combinations that met these criteria, there was only a weak relationship (R2 = 0.25) between the number of SD data points and the R2 value of the SD vs year plot, suggesting that 30 data points was sufficient to detect a trend where it existed, and a larger sample size beyond this did not necessarily lead to better trend detection. Similarly, the relationship between the number of years in a state × crop type combination and R2 value of the SD vs year plot was also weak (R2 = 0.44), suggesting that a greater span did not always lead to a stronger trend.\n\nOf the 11,458 Trial Projects in the OFT database at the time of analysis, only 3067 contained a record of sowing date (SD) and met the crop-type (i.e. winter crops, see ‘Materials and methods’) and date criteria (i.e. sown between 1 March and 31 July). At the present time, the SD metadata element field in OFT is highly recommended, but is not mandatory because the bulk of Trial Projects in OFT are legacy trials, many of which did not contain a record of SD, or sowing was recorded simply as a period such as ‘late autumn’ or ‘mid-June’, rather than a specific calendar date. These factors limited the number of Trial Projects that could be included in the analyses, and this demonstrates that (i) a record of the SD should be considered mandatory for the reporting of future research trials; (ii) it would be useful for SD to be a mandatory field for current and future Trial Projects from more recent research, and (iii) the format of the date should include a specific date to be references to the Gregorian calendar, which can be converted to a single Julian day if required. Furthermore, we suggest that an international standard should be used to report the date in OFT to increase clarity and interoperability of data. For example, the ISO 8601 standard requires that date and time values are ordered from the largest to smallest unit of time starting with year, month and day, separated by hyphens, e.g. 2020/08/04, meaning the 4th of August 2020.\n\nAnalyses of metadata in the OFT database showed that changes in research trial sowing dates over time have differed between the states and crops within the regional cropping areas of Australia. In general, our results suggest that research trial sowing dates in Vic. and WA have been moving earlier each year across the study period (Table 1), but dates in the other states (SA, NSW and Tas.) do not seem to have changed markedly in the last ~25 years (since ~1993).\n\n(NSW = New South Wales; Qld = Queensland; SA = South Australia; Tas. = Tasmania; Vic. = Victoria; WA = Western Australia).\n\nACrops were sown in ‘autumn’, between 1 March and 31 July.\n\nBThe category of ‘all crops’ included barley, canola, chickpeas, faba beans, field peas, lentils, linseed, lucerne, lupins, mustard, oats, kaspa peas, triticale, vetch and wheat.\n\nSimilar trends were undetected in the NVT dataset investigated. No state × crop type combinations had significant changes in SD across years. This is most likely due to the fact that NVT trials are required to be sown during a mandated (specified in trial contracts) sowing window that is deemed appropriate for the crop variety and specific location. SD is therefore predetermined, and is not an independent variable for NVT trials.\n\nOne complication in comparing reports of SD lies in the definition of the ‘time of sowing’ (TOS, or ‘sowing date’). Flohr et al. (2018) define TOS as ‘the calendar date at which seeds become imbibed and begin the process of germination. For instance, this could be the date on which they are planted into a moist seed bed, or the date on which they receive rainfall/irrigation after being sown into a dry seed bed’. However, we suspect that most reports do not apply this definition, but rather, simply use the date on which the seeds were planted regardless of whether they were dry-sown or how long after the first significant rain (or ‘break’) occurred.\n\nAnother complication arises from the observation that choice of sowing date for a crop on a farm is influenced by many factors including climate (especially rainfall events), the size of the cropping enterprise, the equipment and labour available, the tillage method and other management tools to be employed, the crop type and variety to be sown. For research trials, many of these factors are negated, but other limitations may influence the date chosen for sowing. For example, availability of funding, equipment and staff, as well as access to the trial site may play a role in determining the sowing date of a trial. However, these influences are probably usually minor, so likely insufficient to change the desired date significantly. Thus, the SD of a research trial is usually the function of a single establishment date, whereas a sowing schedule on a farm may take anywhere from several days up to a month depending on the size of the area being planted (Hunt et al., 2019) due to constraints on the availability of machinery and labour (Fletcher et al., 2016a). In practice, the SD of a research trial can be considered as a distinct entity as the entire trial is usually planted on one day. We suggest it should be compared with the midpoint of farm sowing dates reported elsewhere, which is considered as a good mean measure of whether crops are sown early or late (Stephens & Lyons, 1998).\n\nThe sowing date for cropping research trials for WA SDs, with trials in ‘all crops’ moving earlier by around 1.9 days per year between 1998 and 2018; and wheat, barley and canola trials in WA were sown about 1.7, 2.1 and 2.3 days earlier each year, respectively, for the year analysed in each of these crop species (Figure 2; Table 2).\n\nThe category of ‘all crops’ included barley, canola, chickpeas, faba beans, field peas, lentils, linseed, lucerne, lupins, mustard, oats, kaspa peas, triticale, vetch and wheat. Blue line indicates predicted SD, dashed red lines indicate 95% confidence intervals, and green dashed lines indicate 95% prediction intervals.\n\nA‘All crops’ included barley, canola, chickpeas, faba beans, field peas, lentils, linseed, lucerne, lupins, mustard, oats, kaspa peas, triticale, vetch and wheat.\n\nThese findings correspond with multiple reports of earlier sowing of crops in general farming practices in WA. Fletcher et al. (2016a); Fletcher et al. (2016b) reported that field records from seven farms in WA showed sowing of the first cereal crop (wheat or barley) on-farm had advanced markedly in recent years, and was most prominent from 2010 to 2014. The sowing date moved from late May to late April at most sites (although the actual pattern of change was notably different at the seven sites included in the report; see Figure 1 in Fletcher et al. (2016b)) and was likely impacted by changes in management and agronomical practices, including adoption of no-till methods and herbicide resistant crop varieties (Fletcher et al., 2019). This work was based on the report by Stephens & Lyons (1998), who reported that sowing dates of wheat in WA had moved earlier by 1.2 days per year between 1977 and 1990, and confirmed that sowing dates continued to move earlier from around 1995 to 2015. Flohr et al. (2018) also confirmed the general shift, reporting that wheat sowing date records from the Yield Prophet database (the online commercialised version of the crop production models APSIM) in WA show a shift of around 1.3 days/year over the 10-year period from 2008 to 2015. Farre et al. (2019) asserted that trends in earlier sowing in WA over the last decade also apply to canola crops, and used APSIM-canola simulations to establish the optimum sowing window to maximise grain yield for different locations in WA. A report by DPIRD WA (2019) also noted that ‘in the last decade there has been a trend toward earlier sowing of canola by Western Australian growers’.\n\nResults from the OFT metadata analysis show that sowing of crops in WA research trials reflect the trends seen in general practice in this cropping district, and extends the current knowledge to show that the trend is continuing past 2015, at least as far as 2018, and possibly beyond.\n\nIn Vic., the SD for cropping research trials for ‘all crops’ moved earlier by around 1.3 days per year between 1993 and 2018; wheat, barley and canola trials in Vic. were sown approximately 1.9, 1.6 and 1.6 days earlier each year for the years analysed for each of these crop types (Figure 2; Table 2).. This result is similar to the data from the Yield Prophet database showing a rate of change of 2 days/year between 2008 and 2015 for wheat in Victoria (Flohr et al., 2018). However, it differs from findings of Stephens & Lyons (1998), whose survey work showed no change in sowing date in the state between 1977 and 1990. These authors note that their data were based on only five survey responses (the least number of any state), so ‘little confidence can be placed on the results’. The OFT metadata suggests that sowing of research trials in Vic. has moved forwards during the study period, in a similar fashion to WA, and thus reflect general practice in cropping across the state.\n\nWe detected weak trends in SD in three of the state × crop type combinations in these states: NSW barley R2 = 0.3771, SA ‘all crops’ R2 = 0.3405 and SA barley R2 = 0.3497. R2 values for all other NSW, Qld, SA and Tas. state × crop type combinations were very weak (< 0.3771), suggesting no clear or consistent relationship between SD and year.\n\nThese results differ from those of Stephens & Lyons (1998), who reported that ‘during the 1980s, sowing progressed a day earlier each year at a national scale’. For NSW; however, they note that there were large standard deviations in sowing (wheat) midpoints (see their Figure 4), averaging 21.2 days. Flohr et al. (2018) used simulations to show NSW wheat crops were planted 1.1 days/year earlier between 2008 and 2015, but note that southern NSW had the lowest number of fields subscribed to Yield Prophet and that there is a very broad sowing window in this environment. These authors reported sowing of wheat crops in SA has moved 1.3 days/year earlier in the same period. Maitland (2013) reported in the South Australian No Till Farmers Association (SANTFA) newsletter that ‘in recent years, farmers have sown crops earlier in the season’; however, this report contains no data, and thus provides little evidence on which to base further analyses. No published data could be found for Qld or Tas.\n\nThere are several possibilities that could explain why we detected no strong trends in SD in OFT metadata for NSW, Qld, SA and Tas. First, reports of earlier sowing of crops in paddocks may be anecdotal or outdated, and crops were not actually sown earlier in these areas during the period included in our analyses. Stephens & Lyons (1998) surveyed wheat farmers undertaken between 1978 and 1990, which is several years before the earliest record used in our analyses, and almost 20 years before the bulk of the data used here. These authors noted that the national trend towards reduced or minimum tillage techniques coincided with their reported earlier sowing dates, so it is possible that once any farmers who were adopting these different management methods had done so, sowing dates ceased to move any further forwards. The only other reports providing data regarding sowing trends in these states were from the Yield Prophet database, so are for wheat only and derived from simulations rather than measured data. Thus, it is possible that sowing dates for crops in NSW, Qld, SA and Tas. have not changed significantly in the years included in our analyses.\n\nA second possible reason why no notable trends between SD and year were detected for NSW, Qld, SA or Tas., is that research trial SDs in these areas may not reflect general practice in the region, so in fact have not been sown earlier across the study period even if farmers were sowing crops earlier. If the main reason why farmers are sowing crops earlier is increased farm size, then the need for earlier sowing is negated in research trials, meaning they are simply not sown earlier.\n\nThird, it may be that trends in SD exist only within smaller geographic regions within each state, and so have been masked by separate agro-ecological zones. Sowing dates are known to be strongly influenced by geographical regions (NSW DPI, 2019), driven by variation in a plethora of environmental variables such as rainfall (particularly in autumn; Bloomfield et al., 2018), spring temperatures and frost risk (Hunt et al., 2019). Large-scale rainfall anomalies have been cited as a driving factor for sowing dates, especially in states with a distinct Mediterranean climate (Stephens & Lyons, 1998). Frost risk was recently reported to vary considerably across the northern grains region, and manipulation of sowing time was identified as one way to minimise yield losses (in chickpeas) due to frost (Chauhan & Ryan, 2020). There are likely many reasons that have contributed to this change but investigations into and discussion of the agronomic factors driving earlier sowing are beyond the scope of the current investigation. However, our work demonstrates that OFT provides a useful source of information, and could be used to investigate trends within, for example, different agro-environmental zones or across different rainfall gradients.\n\nThe OFT database currently provides for the inclusion of exact and accurate geolocation of a trial in the form of latitude and longitude. If entered, this information can be displayed or, for privacy reasons, hidden from the public view at the request of the contributor. Whether hidden or displayed, it can be used to accurately geo-locate a trial site for which climatic variables can be derived for use in analyses. However, few legacy reports contain accurate location information, and even where it may be available, the information is not always entered into the database because it is an optional field. Accurate geo-location (e.g. measurements made via a global positioning system (GPS) could be useful in future analyses, and the location of research trials should be recorded and entered into the database.\n\nThe present process of Trial Project creation in OFT is one of manual biocuration, and requires a multidisciplinary effort involving subject area experts, software and technical developers, researchers and project staff. The process of manual biocuration typically involves reading of the trial report and entering data manually into the database. It requires a good understanding of both the research work being entered as well as the functional capacity of the database itself. The original Trial Project entry process for OFT was conducted via a spreadsheet import process, which was managed in-house. Once an upload of projects was completed, the contributor was notified and asked to check that the information had been entered and represented correctly before it was published to the live site (online). However, this process was labour-intensive and slow, and required members of the OFT team to facilitate data entry and publication, so an ‘administration’ centre was developed to allow contributors to enter their data directly to the OFT database without input from the in-house OFT team. This made it easier for contributors to enter data and removed the need for double-handling of trials, however, it simultaneously introduced the problem of quality control. Without the need for Trial Projects to be checked by a member of the OFT team before being published, entry of non-mandatory metadata had not been monitored. Harper et al. (2018) note that manual biocuration is perhaps the best way to curate data, but no database has enough resources to curate all data manually. Investments into the Australian grains industry have been recognised as critical drivers for achieving future productivity gains essential for the sustainability and profitability of cropping enterprises (Walters et al., 2018), so it will be important to evaluate the benefits against the costs of collecting more metadata within the context of ongoing OFT database curation and quality control. There is generally a time investment required to collect metadata, and it is recognised that enriching existing metadata records can be ‘difficult and time consuming’ (Kemp et al., 2018), so recognition of the trade-off remains an important consideration in the collection of metadata for OFT Trial Projects.\n\nFor wheat in particular, the trend of earlier sowing dates may have been facilitated by an increase in use of winter wheat varieties investigated in these areas, as the trend towards earlier sowing is reported to have resulted in the planting of more longer-season varieties and less shorter-season varieties (Hamblin & Kyneur, 1993; Stephens, 1995). There is currently no metadata field for variety in OFT, thus, the possible role of varietal-driven differences in sowing date trends could not be accounted for in our analyses. Future development of OFT Trial Project metadata to include variety could be highly beneficial in understanding the role of variety in sowing date trends across the different Australian cropping regions.\n\nIn our analyses we used simple linear regression, and results suggest that in some areas, research trial crops are continuing to be sown earlier (up to the end of analyses, which was ~2018–19). Simulation studies of wheat in WA suggest that the optimal flowering period (and by extension, sowing date) may move earlier by as much as 29 days under a drier climate (Chen et al., 2020). This raises the question of how much earlier can crops be planted before the advantage is negated, i.e. how many more years will the current trends persist, and what will be the best way to continue to monitor ongoing shifts in sowing dates in the future to allow for the expected effects of ongoing climate change on crop phenology (Kukal & Imrak, 2018)? As Trial Projects from current and future research trials are added to the OFT database, further analyses may show further changes in SD trends, and these could be useful in predicting sowing dates to be used during the planning of future research trials. Further, the question of whether earlier sowing in research trials has led to the expected benefits in terms of crop yield has yet to be investigated. At the present time, there is much information in OFT that is not captured in metadata fields, but future development to improve the richness of the metadata would enable these questions, and many others, to be investigated using Trial Project metadata from the OFT database.\n\nTrial Project metadata from the OFT database is unique in that it can be used in two distinct ways: as filters for online searches of the database; and as a stand-along dataset that can be interrogated to detect trends in recorded fields. Using OFT Trial Project metadata as a dataset we demonstrated that sowing dates of on-farm research trials for ‘all crops’, barley, canola and wheat have moved earlier by 1.3–2.3 days per year from 1993 to 2018 in Vic. and WA. Trends in SD in the other cropping states in Australia were either weak or very weak, suggesting research trials in these areas have not been sown earlier during the study period (1993–2018). To help improve OFT Trial Project metadata for future data discoveries, we recommend that future projects include sowing date as a mandatory field. Numerous other research questions could be investigated using OFT Trial Project metadata, and our work shows that the database provides an effective way for users to access, search, filter and re-use on-farm trials to help improve sustainability and profitability of Australian grains research.\n\nFigshare: Dataset 1: Online Farm Trials Sowing Date Metadata export 18 December 2019 https://doi.org/10.6084/m9.figshare.12895103.v2 (Walters, 2020a).\n\nThis project contains the following underlying data:\n\nfigshare_Dataset 1_Online Farm Trials.xlsx. This dataset was compiled from the Online Farm Trials metadata export on 18 December 2019. It shows the autumn sowing dates (limited to those between 1 March and 31 July) of various crop types across cropping states within Australia between 1993 and 2018. The 'all crops' categories includes barley, canola, chickpeas, faba beans, field peas, lentils, linseed, lucerne, lupins, mustard, oats, kaspa peas, triticale, vetch and wheat.\n\nFigshare: Dataset 2: Online Farm Trials spatial spread of trial sites export 18 December 2019 https://doi.org/10.6084/m9.figshare.12932732.v1 Walters (2020b).\n\nThis project contains the following underlying data:\n\nfigshare_Dataset 2_Online Farm Trials.xlsx. This dataset was compiled from the Online Farm Trials export on 18 December 2019. It shows the autumn sowing dates (limited to those between 1 March and 31 July) of various crop types across cropping states within Australia between 1993 and 2018. The data were used to generate a map showing trial site locations within Australia.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International (CC BY 4.0) Licence.\n\nReaders are also encouraged to visit the Online Farm Trials website where metadata and other information on grain-based trials from across Australia can be accessed (www.farmtrials.com.au).",
"appendix": "Acknowledgements\n\nOnline Farm Trials is a collaboration between the Grains Research and Development Corporation (GRDC) and the Centre for eResearch and Digital Innovation (CeRDI) at Federation University Australia (FedUni). The authors thank all contributors who have provided trial research for the Online Farm Trials project; GRDC; members of the OFT team – especially Paul Feely and Jude Channon; and the Senior Management Team at the CeRDI. We also thank John Rivers (GRDC) for comments on an earlier version of this manuscript, and the GRDC NVT Program.\n\n\nFootnotes\n\n1A zettabyte is 1 × 10007 bytes.\n\n2 An exabyte is 1 × 10004 bytes.\n\n\nReferences\n\nBabcock C: IBM Cognitive Colloquium spotlights uncovering dark data. 2015; (accessed 4 May 2020). Reference Source\n\nBarbour V: The future of academic publishing: disruption, opportunity and a new ecosystem. Med J Aust. 2019; 211(4): 151–152.e1. 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Computational social science. Science. 2009; 323(5915): 721–723. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLi Y, Lund R: Multiple changepoint detection using metadata. J Clim. 2015; 28(10): 4199–4126. Publisher Full Text\n\nLuque C: Open data and FAIR data: Differences and similarities. 2019; (accessed 26 August 2020). Reference Source\n\nMaitland K: Time of sowing key to yield and profit. The Cutting Edge. Summer 2013. South Australian No Till Farmers Association (SANTFA). 2013; (accessed 5 August 2020). Reference Source\n\nMarr B: Big data: 20 mind-boggling facts everyone must read. 2015; (accessed 6 May 2020). Reference Source\n\nMoore DS, Notz WI, Flinger MA: The basic practice of statistics. (6th edn) (H. Freeman Y& Co.: New York). 2013. Reference Source\n\nNSW DPI: Winter crop variety sowing guide 2019. (NSW Government: Sydney, NSW Australia). 2019. Reference Source\n\nOh J, Park ON: Topics and trends in metadata research. J Inf Sci Theor Pract. 2018; 6(4): 39–53. Publisher Full Text\n\nRobinson NJ, Dahlhaus P, Feely P, et al.: Online Farm Trials (OFT) – the past, present and future. In: Cells to satellites. Proceedings of the 19th Australian Society of Agronomy Conference. 25–29 August 2019, Wagga Wagga, NSW, Australia. (Ed. J Pratley). 2019; (accessed 7 August 2020). Reference Source\n\nSadiq S: Use it or lose it: the search for enlightenment in dark data. 2016; (accessed 6 May 2020). Reference Source\n\nSerra da Cruz S, do Nascimento JAP: Towards integration of data-driven agronomic experiments with data provenance. Comput Electron Agric. 2019; 161: 14–28. Publisher Full Text\n\nSexton A, Murphy A, Wills B, et al.: Online Farm Trials (OFT) Impact research: eResearch (Second Wave) extended timeframe research study. Centre for eResearch and Digital Innovation, Federation University Australia (Ballarat). 2019. Reference Source\n\nSharma DL, D’Antuono MF, Anderson WK, et al.: Variability of optimum sowing time for wheat yield in Western Australia. Aust J Agric Res. 2008; 59(10): 958–970. Publisher Full Text\n\nŠimek P, Vaněk J, Jarolímek J, et al.: Using metadata formats and AGROVOC thesaurus for data description in the agrarian sector. Plant Soil Environ. 2013; 59(8): 378–384. Publisher Full Text\n\nStephens DJ: Crop yield forecasting over large areas in Australia. PhD thesis, Murdoch University, Perth, WA Australia. 1995. Reference Source\n\nStephens DJ, Lyons TJ: Variability and trends in sowing dates across the Australian wheatbelt. Aust J Agric Res. 1998; 49: 1111–1118. Publisher Full Text\n\nStow CA, Webster KE, Wagner T, et al.: Small values in big data: The continuing need for appropriate metadata. Ecol Inform. 2018; 45: 26–30. Publisher Full Text\n\nSubramaniam S: Bioinformatics and computational systems biology: at the cross roads of biology, engineering and computation. In: The 26th annual international conference of the IEEE engineering in medicine and biology society. San Francisco, CA, USA. Conf Proc IEEE Eng Med Biol Soc. 2004; 2004: 5458. PubMed Abstract | Publisher Full Text\n\nSuber P: Open access overview. 2004; (accessed 17 September 2020). Reference Source\n\nUniprot Consortium: UniProt: a worldwide hub of protein knowledge. Nucleic Acids Res. 2019; 47(D1): D506–D515. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWalters J: Dataset 1: Online Farm Trials sowing date metadata export 18 December 2019. figshare. Dataset. 2020a. http://www.doi.org/10.6084/m9.figshare.12895103.v2\n\nWalters J: Dataset 2: Online Farm Trials spatial spread of trial sites export 18 December 2019. figshare. Dataset. 2020b. http://www.doi.org/10.6084/m9.figshare.12932732.v1\n\nWalters J, Milne R, Thompson H: Online Farm Trials: a national web-based information source for Australian grains research, development and extension. Rural Extension and Innovation Systems Journal. 2018; 14(1): 117–123. Reference Source\n\nWilkinson MD, 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 | Free Full Text\n\nWills B, Parker J, Robinson N, et al.: Improving the FAIRness of Australia’s grains research sector data. In: Proceedings of the 2019 Agronomy Australia Conference. August 2019, Wagga Wagga, Australi. 2019; 25–29. Reference Source"
}
|
[
{
"id": "74582",
"date": "10 Dec 2020",
"name": "Daoud Urdu",
"expertise": [
"Reviewer Expertise Information Modelling",
"Systems Analysis",
"Digital Innovation"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 explore the possibility of using and analyzing metadata in order to tackle overarching agricultural challenges like yield prediction. By applying statistical methods for a specific question, the value of metadata is presented. Different literature has been studied and categorized as part of the introduction. However, the interrelation between these data categories and FAIR could be more clear in the introduction part. Also, the objective could be stated more clearly.\n\nFurthermore, the reviewers think that the statistical part could be reviewed by someone with a more statistical background.\n\nIn the context of FAIR – This paper seems to contribute to the Accessibility part. However, this could be stated more explicitly. The other characters (F, I, and R) in the abbreviation could also get some more attention.\n\nWith regard to standardization – what is the role of data modelling and information modelling? What does the study contribute to the interoperability part of FAIR? Is ISO8601 the only relevant standard?\n\nTwo figures 3067 and 3034 were used. This brought a slight confusion.\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? Partly\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "6682",
"date": "26 May 2021",
"name": "Judi Walters",
"role": "Author Response",
"response": "The Introduction of this paper introduces the category of digital data and links the amount of digital data being produced with the need for it to be both ‘findable’ and ‘accessible’ to be of increased use. The role of metadata in making digital data more findable is then discussed. The accessibility of data is then also discussed in the context of open access publishing models. The other components of the FAIR guiding principles (i.e. interoperability and reusability) are not discussed in detail as they were considered outside the scope of the current work: constituting another entire conversation in their own right. For this reason, we have chosen to leave the text as it stands. The reviewer requested that the objective be stated more clearly, so we changed the wording in the second paragraph under ‘Sowing timing’ to clarify. We note the reviewer’s comment that the statistical part could be reviewed by someone with a more statistical background, and confirm that we did consult a statistician at Federation University during the analysis phase of the research. We were advised that further analysis techniques would not add to the main objective of the work: to demonstrate that metadata can be used to detect trends, rather than to apply highly-sophisticated statistical methods to prove or disprove a specific hypothesis, which, we agree, would necessitate greater statistical rigour if that had been our objective. Because statistical complexity was unnecessary to demonstrate the information we were trying to convey we did not attempt to complicate the data with extra analysis. The reviewer is correct that “In the context of FAIR – this paper seems to contribute to the Accessibility part”, so we have highlighted this further by adding a sentence to this effect at the beginning of the Conclusions. As stated above, the I and R components are not given greater attention because we consider them to be separate discussions, beyond the scope included here. The reviewer asked what is the role of data modelling and information modelling? The reviewer asked “What does the study contribute to the interoperability part of FAIR?”. We reiterate that the study was not attempting to focus on Interoperability, and that the comment regarding the ISO 8601 was given as an example of what could be implemented in the future to increase interoperability of OFT Trial Projects. The ISO standard mentioned is not the only relevant standard but is provided as an example only. The reviewer’s comment regarding ‘slight confusion’ around the numbers 3067 and 3034 was investigated, and we suspect the reviewer was referring to ‘3634’ rather than ‘3034’. For clarification, 3634 refers to the number of Trial Projects containing sowing date in the metadata field, and this number was reduced to 3067 by the limits set on the sowing window (1 March to 31 July)."
}
]
},
{
"id": "82540",
"date": "04 May 2021",
"name": "James Hunt",
"expertise": [
"Reviewer Expertise Agronomy",
"crop physiology",
"farming systems"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis manuscript describes a study in which metadata from the Online Farm Trials website were used to detect changes over time in trial management, specifically sowing date. The analysed results are compared to published data relating to grower sowing date and the differences at a state level and possible causes are discussed. This exercise is used as an example of how agricultural metadata can be used to detect trends in management practice.\nThe manuscript is well written and well prepared and will be of interest to agricultural researchers.\nIt should be noted that grower time of sowing data are available in the following peer reviewed references, which are stronger sources of evidence than the GRDC fact sheet that is cited under the heading ‘Sowing timing’.\nFlohr, BM, Hunt, JR, Kirkegaard, JA, Evans, JR, Trevaskis, B, Zwart, A, Swan, A, Fletcher, AL, Rheinheimer, B (2018) Fast winter wheat phenology can stabilise flowering date and maximise grain yield in semi-arid Mediterranean and temperate environments. Field Crops Research 223, 12-25.1\nAnderson, WK, Stephens, D, Siddique, KHM (2016) Dryland Agriculture in Australia: Experiences and Innovations. In 'Innovations in Dryland Agriculture.' (Eds M Farooq, KHM Siddique.) pp. 299-319. (Springer International Publishing: Cham)2\n[I note the Flohr et al. (2018) reference is cited later in the manuscript]\nBoth references use the same data source (the Yield Prophet® database, see Hochman, Z, van Rees, H, Carberry, PS, Hunt, JR, McCown, RL, Gartmann, A, Holzworth, D, van Rees, S, Dalgliesh, NP, Long, W, Peake, AS, Poulton, PL, McClelland, T (2009) Re-inventing model-based decision support with Australian dryland farmers. 4. Yield Prophet® helps farmers monitor and manage crops in a variable climate. Crop and Pasture Science 60, 1057-1070.).3 The Anderson et al. (2016) reference also uses the Stephens & Lyons (1998) data. The Flohr et al. (2018) reference breaks the trends down to a state level which would make a useful comparison to this study.\nCrop types – ‘Kaspa’ is a cultivar of field pea, not a distinct species, and experiments with this cultivar can be included in the field pea category.\nNormality of data - do you mean no data transformations were required (rather than data cleaning, which implies removal of data)?\nI don’t think the definition provided by Flohr et al. (2018) re imbibed seeds provides a problem for his study because growers are sowing earlier regardless of the timing of rainfall (i.e. ‘dry’ sowing). See;\nFletcher, AL, Robertson, MJ, Abrecht, DG, Sharma, DL, Holzworth, DP (2015) Dry sowing increases farm level wheat yields but not production risks in a Mediterranean environment. Agricultural Systems 136, 114-124.4\nFletcher, A, Lawes, R, Weeks, C (2016) Crop area increases drive earlier and dry sowing in Western Australia: implications for farming systems. Crop and Pasture Science 67, 1268-1280.#5\nFletcher, A, Flohr, BM, Harris, F (2019) Evolution of early sowing systems in southern Australia. In 'Australian Agriculture in 2020: From Conservation to Automation.' (Eds J Pratley, JA Kirkegaard.) pp. 291-305. (Agronomy Australia and Charles Sturt University: Wagga Wagga)\nIt would be worth noting that rainfall of sufficient magnitude to germinate seed (the ‘autumn break’) is arriving later and that this could be having an effect on results. See;\nFlohr, BM, Ouzman, J, McBeath, TM, Rebetzke, GJ, Kirkegaard, JA, Llewellyn, RS (2021) Redefining the link between rainfall and crop establishment in dryland cropping systems. Agricultural Systems 190, 103105.6\nPook, M, Lisson, S, Risbey, J, Ummenhofer, CC, McIntosh, P, Rebbeck, M (2009) The autumn break for cropping in southeast Australia: trends, synoptic influences and impacts on wheat yield. International Journal of Climatology 29, 2012-2026.7\nIn the paragraph headed ‘Other states’, the statement that Flohr et al. (2018) used simulation to show NSW wheat crops were planted 1.1 days/year earlier between 2008 and 2015 is incorrect. The reported shift in sowing dates are actual dates entered by growers into Yield Prophet® i.e. they are actual grower sowing dates, not simulated.\nLikewise in the paragraph headed ‘Trend detection’ the following statement is incorrect:\n“The only other reports providing data regarding sowing trends in these states were from the Yield Prophet database, so are for wheat only and derived from simulations rather than measured data.”\nThese data ARE measured observations, not simulated. This misinterpretation needs to be corrected. Albeit the sample of growers in the Yield Prophet database is biased toward early adopters of technology.\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": [
{
"c_id": "6683",
"date": "26 May 2021",
"name": "Judi Walters",
"role": "Author Response",
"response": "We agree with the reviewer’s suggestion that reference to grower time of sowing data available in Flohr et al, (2018) and Anderson et al. (2016) provide stronger sources of evidence than the GRDC fact sheet that is cited under the heading ‘Sowing timing’, so have added in-text citations to these references alongside that of the GRDC fact sheet. We note that the crop type ‘Kaspa’ is a cultivar of ‘Field pea’, rather than a distinct species, but because the OFT database separates these we have decided to keep them separate in this work. The reviewer asked in relation to ‘normality of data’ whether we mean no data transformations were required (rather than data cleaning, which implies removal of data): we confirm no data transformations were performed, neither were any data removed other than as described in the ‘Materials and methods’. We note the comment regarding the definition provided by Flohr et al. (2018) re imbibed seeds not providing a problem for his study because growers are sowing earlier regardless of the timing of rainfall (i.e. ‘dry’ sowing), so have retained the text and added a further comment including reference to Fletcher et al. (2015, 2016a, 2019). We have also noted that rainfall of sufficient magnitude to germinate seed (the ‘autumn break’) is arriving later and that this could be having an effect on results; including reference to Pook et al. (2009) and Flohr et al. (2021) as suggested. We have corrected the error in the paragraph headed ‘Other states’, stating that Flohr et al. (2018) used simulation to show NSW wheat crops were planted 1.1 days/year earlier between 2008 and 2015, now saying that the reported shift in sowing dates are actual dates not simulated data. The paragraph headed ‘Trend detection’ has also been corrected to reflect that ‘actual’ rather than ‘simulated’ nature of data from previous reports, and include a note from the reviewer (pers. comm.) that “the sample of growers in the Yield Prophet database is biased toward early adopters of technology”."
}
]
},
{
"id": "82422",
"date": "04 May 2021",
"name": "Medha Devare",
"expertise": [
"Reviewer Expertise agronomic research for development",
"data management",
"OA",
"FAIR",
"responsible data",
"semantic web"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 possibility of analyzing metadata to detect trends in agricultural data - using sowing data in on-farm research trials from 1993 to 2019 as a use case to assess if metadata analysis can unearth trends in sowing date.\n\nThe authors cite FAIR, but in fact, there is nothing in this paper on interoperability and very little on accessibility or reusability - this work is primarily about the value of specifying metadata fields beyond the generic typically requested in standard metadata schemas. However, I wonder how realistic this is - how many fields can be reasonably added to metadata schemas? Aren't NLP and text mining techniques able to get at information to inform this sort of analysis without adding fields to metadata schemas? Data can be richly mined if interoperability using controlled vocabularies or ontologies to describe data variables is implemented by design, surely?\nNonetheless, this work is interesting and could provide a bit more impetus to improve annotations of research data. It would be good to see more discussion around the possibilities, and how such derivable value could address challenges. I'd focus less on FAIR since this work doesn't really address all aspects of FAIR.\nOFT seems like an interesting resource, but I was unable to export data that was open - and not all of the data in the db is - so that needs to be better clarified in the paper. I wanted to see more on the metadata schema used, the decisions that went into this, how it was received by researchers/data managers, etc. I would suggest a bit of a rewrite to explore these angles, leading into the particular use cases - which are good.\nOne nitpicky point: The authors say \"More data were generated between 2015 and 2017 than in the whole length of human history before that (Marr, 2015)\" Presumably Marr was predicting more data being generated... in 2015, and not stating that it was so!\nI also don't quite get the 3067 and 3634 numbers in the methods - and how they relate to the 11,458 projects. I also don't understand why the notion of \"trial project\" is needed - it is confusing. Aren't these just all trials that meet the filters of site, growing year, and crop type?\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "6684",
"date": "26 May 2021",
"name": "Judi Walters",
"role": "Author Response",
"response": "We note the reviewer’s comment that there is “ nothing in this paper on interoperability and very little on accessibility or reusability [and that] this work is primarily about the value of specifying metadata fields beyond the generic typically requested in standard metadata schemas”. This is a reasonable comment with which we do not disagree, but would add that the paper does not claim to discuss all elements of FAIR. Rather, it mentions FAIR to place the discussions around the benefits of the OFT database in a broader context of the publication and re-use of research data. Then, the paper highlights the value of using the metadata fields used in OFT as a way to search for information, much like a bibliographic database of research papers. The reviewer asked “how many fields can be reasonably added to metadata schemas?” and suggest that “NLP and text mining techniques able to get at information to inform this sort of analysis without adding fields to metadata schemas?” We suggest that, although some researchers may be able and willing to go to the lengths required to using text mining techniques to locate information, there are many researchers (particularly in the agricultural sciences), agronomists, and grain growers, for whom this type of searching would not be possible. Hence, the value of the simple, easy, and freely-accessible searches made available via OFT. The observation that “[d]ata can be richly mined if interoperability using controlled vocabularies or ontologies to describe data variables is implemented by design, surely?” is true, and work in progress may mean that OFT adopts a controlled vocabulary to increase interoperability in the future. We have included some changes in response to other reviewers, so hope this satisfies the suggestion for further discussion around research data annotation/use. Without further clarification we are unable to determine the reasons why the reviewer was unable to “open export data”, and suggest that contact be made with the OFT team via email (oft@farmtrials.com.au) to get support because all exports in the database should be retrievable with sufficient internet capabilities. It was decided to avoid further discussion of the metadata schema used because further development under the current funding contract is expected to explore this aspect of OFT in the near future, and subsequent publications would be better to address this topic in greater depth. We thank the reviewer for picking up the extrapolation error when that we said \"More data were generated between 2015 and 2017 than in the whole length of human history before that” and given the citation was Marr (2015) presumed that Marr was predicting more data being generated. We checked the reference and note that Marr wrote “The data volumes are exploding, more data has been created in the past two years than in the entire previous history of the human race”, so we have corrected the text to reflect this. To clarify the numbers “3067 and 3634” in the “Methods”: of the total number of trial projects in the OFT database at the time of investigation (i.e. 11,458), 3634 trial projects had data available for sowing date (SD). Of the 3634 trial projects that had SD available (and could therefore be included in the investigation), 567 trial projects had SDs that were outside the dates considered reasonable for an ‘autumn’ sowing period (i.e. not between 1 March and 31 July), so that left 3067 trial projects available for the investigation. The concept of a ‘trial project’ is unique to OFT and was so named to define a database entry for a site x growing year x crop type combination. The institution of ‘trial projects’ was necessary so that an individual piece of research work that spanned a multiple of any one of these factors could be entered in the system with adequate metadata so it could be located via a metadata search."
}
]
}
] | 1
|
https://f1000research.com/articles/9-1305
|
https://f1000research.com/articles/8-1899/v1
|
11 Nov 19
|
{
"type": "Research Article",
"title": "Australian state influenza notifications and school closures in 2019",
"authors": [
"Anna Mae Scott",
"Mina Bakhit",
"Justin Clark",
"Melanie Vermeulen",
"Mark Jones",
"David Looke",
"Chris Del Mar",
"Paul P Glasziou",
"Mina Bakhit",
"Justin Clark",
"Melanie Vermeulen",
"Mark Jones",
"David Looke",
"Chris Del Mar",
"Paul P Glasziou"
],
"abstract": "Background: The impact of school holidays on influenza rates has been sparsely documented in Australia. In 2019, the early winter influenza season coincided with mid-year school breaks, enabling us the unusual opportunity to examine how influenza incidence changed during school closure dates. Methods: The weekly influenza data from five Australian state and one territory health departments for the period of week 19 (mid-May) to week 35 (early September) 2019 were compared to each state’s public school closure dates. We used segmented regression to model the weekly counts and a negative binomial distribution to account for overdispersion due to autocorrelation. The models’ goodness-of-fit was assessed by plots of observed versus expected counts, plots of residuals versus predicted values, and Pearson’s Chi-square test. The main exposure was the July two-week school vacation period, using a lag of one week. The effect is estimated as a percent change in incidence level, and in slope. We also dichotomized the change in weekly counts into decreases versus increases (or no change). The proportion of decreases were then compared for each of three periods (pre-vacation, vacation, post-vacation) using Fishers exact test. Results: School holidays were associated with significant declines in influenza incidence. The models showed acceptable goodness-of-fit. The numbers and percentages of decreases in weekly influenza counts from the previous week for all states combined were: 19 (33%) pre-vacation; 11 (92%) decreases during the vacation; and 19 (59%) decreases post-vacation (P=0.0002). The first decline during school holidays is seen in the school aged (5-19 years) population, with the declines in the adult and infant populations being smaller and following a week later. Conclusions: Given the significant and rapid reductions in incidence, these results have important public health implications. Closure or extension of holiday periods could be an emergency option for state governments.",
"keywords": [
"Influenza",
"influenza epidemic",
"child",
"adolescent",
"school closure",
"school holidays",
"absenteeism"
],
"content": "Introduction\n\nIn 2009, the United Kingdom experienced a summer influenza pandemic, with the National Health Service resorting to pharmacy dispensed oseltamivir to slow the growth. However, when schools closed in August for the six-week summer break, the epidemic dropped to almost zero within a few weeks1. This was an extreme example of an association that has been documented in other countries, though generally for shorter closures2–4. A 2013 review of both deliberate and non-deliberate school closures concluded that even without co-interventions, closure of schools could reduce flu transmission during an outbreak3,5.\n\nThe association of school closure and influenza rates has been only sparsely documented in Australia, partly because school holidays generally fall outside the peak influenza period. However, 2019 saw an early epidemic of influenza in Australia with rates around five times normal for the May-July period, with consequent hospitalisation and deaths also increased. Because of the early high rates, winter influenza in 2019 also coincided with the mid-year school breaks, which appeared to be associated with a dip in influenza incidence.\n\nTo explore any relationship between the holiday school closure and influenza cases, we examined the relationship between changes in influenza incidence with the school closure dates in 2019 using the different holiday dates that apply in the Australian states and territories.\n\n\nMethods\n\nInfluenza is a notifiable disease in all Australian states and territories6. We collected influenza data notified weekly to state and territory health departments, for the period of week 19 (mid-May) to week 35 (early September) 2019, which corresponds to the flu season in Australia.\n\nWe included data from five states (New South Wales, Queensland, Victoria, South Australia, Western Australia) and one territory (Australian Capital Territory); we excluded data from one state (Tasmania) and one territory (Northern Territory) due to paucity of available data and small population sizes.\n\nStates and territories differ in how they collect and report data on flu cases. New South Wales7 and Queensland8 report the number of samples that test positive for Influenza A and B (lab-confirmed); Australian Capital Territory9 reports the number of influenza (lab) notifications to the state; and Western Australia10, Victoria11 and South Australia12 report the number of lab-confirmed influenza cases (strains unspecified).\n\nWe collected flu data as it was reported by each jurisdiction. We collected data on public school closures between week 19 and week 35 from each state or territory’s education department website.\n\nWeekly, numerical flu data were available from reports produced by the Health Departments in New South Wales, Queensland, Western Australia, Victoria, and Australian Capital Territory. For South Australia, the number of lab-confirmed influenza cases for weeks 19–24 were extracted from a figure (using webplotdigitiser13) since weekly numerical data were available only for weeks 25–35. Data on school holidays were extracted from each state or territory’s website. Raw data are provided (see Data availability section)14.\n\nDue to differences in the population numbers of each state and territory, differences in the methods of data collection, and insufficient number of states to reliably fit a random effects model, analysis was conducted separately by state.\n\nWe used segmented regression15 to model the weekly counts and specified a negative binomial distribution to account for overdispersion due to autocorrelation. Explanatory factors included the linear effect of week (slope), initial effect of vacation (change in level), change in linear effect of week after start of vacation (change in slope), initial effect of returning to school, and change in linear effect of week after school return (Appendix 2, Extended data)16. Goodness-of-fit of the models was assessed by plots of observed versus expected counts, plots of residuals versus predicted values, and Pearson’s Chi-square test. The main exposure for our analysis was the July school vacation period of two weeks. Due to the delay from exposure to the virus to confirmation of infection status, we included a lag of one week17. The effect of school vacation is reported as a percentage change in level (with 95% confidence interval) as well as a percentage change in slope (with 95% confidence interval). We hypothesized that the vacation period (lagged by one week) would lead to reductions in weekly counts of influenza cases.\n\nIn a separate analysis, for each state, we calculated the change in weekly counts from the previous week and dichotomized into decreases versus increases (or no change). For example, a change from 100 influenza cases in the previous week to 50 influenza cases in the current week would be classified as a decrease. The proportion of decreases were then compared for each of three periods (pre-vacation, vacation, post-vacation) using Fishers exact test.\n\nStatistical analysis was conducted using SAS University Edition 9.4 for Windows.\n\n\nResults\n\nFigure 1 shows the rates of influenza for the included states and territory. Figures for each individual state or territory are provided in Appendix 3, Extended data16.\n\nNSW, New South Wales; QLD, Queensland; WA, Western Australia; ACT, Australian Capital Territory; VIC, Victoria; SA, Southern Australia.\n\nThe estimates for the initial effect and the subsequent slopes (Table 1) show significant declines for all states except South Australia, which had already passed its peak by the time of the school holidays (Appendix 3, Extended data)16. The models showed acceptable goodness-of-fit (Appendix 4, Extended data)16 with Pearson’s Chi-square tests all indicating insufficient evidence of lack of fit (P>0.05).\n\n*Compared to pre-vacation period.\n\nNSW, New South Wales; QLD, Queensland; VIC, Victoria; WA, Western Australia; SA, South Australia; ACT, Australian Capital Territory.\n\nFor the analysis of changes in weekly influenza counts from the previous week (as described in the statistical methods section, third paragraph) for all states combined, there were 19 (33%) decreases pre-vacation; 11 (92%) decreases during the vacation; and 19 (59%) decreases post-vacation (P=0.0002).\n\nThe data on influenza rates by age group (Figure 2) show the first decline during school holidays is seen in the school aged (5–19 years) population, with the decline in the adult (20–64 years) population being smaller and following a further week later, and with even smaller and delayed drops in the infant (1–4) and elderly (65+ years) age groups. We did not have access to the state specific age bands, and hence have indicated the school closure dates with the largest population groups.\n\n\nDiscussion\n\nThe 2019 Australia influenza notification data show a significant association between school holidays and declines in influenza incidence in most states in Australia. We also found the earliest and largest declines in influenza incidence were in the school aged group (5–19 years), with still later and smaller declines in the adult group (20–64), and least impact on the preschool and over 65’s.\n\nOur findings are consistent with previous reports3 of school closure for both usual holiday periods and emergency closure for epidemics.\n\nThe size of the declines is also consistent with those predicted by models of transmission for school closures18. Some states experienced a rebound within weeks of school restarting whereas others saw a continued decline. We do not have a simple explanation for this difference.\n\nThe association of school closure with declines in influenza has several potential explanations besides a causal effect. First, cases of influenza might be underreported because of delayed presentation or non-presentation during the school holiday period, for example, because with parents able to care for them they do not attend for medical certificates. However, if this were true, we would expect to see an immediate restart after school returns, which is not the case. Second, it could be because of other societal changes, such as parents also being on holiday and hence less transmission at work. However, if this were true, we would expect to see a simultaneous reduction in both child and adult cases. A final issue is that, even if reduction in incidence is real, it not clear whether there is a net annual decrease or merely a delay in total annual cases.\n\nThere are some limitations to both our data and the analysis. Good quality, numerical weekly flu data were unavailable for all states – e.g., South Australia reports its data as a mix of figures and numbers. This may have introduced some errors into the accuracy of the numbers for those states. We contacted the Australian National Notifiable Diseases Surveillance System, which coordinates the national surveillance of influenza in Australia, to obtain raw data for each state and territory. However, the raw data underlying the notifications for 2019 will not be available for release until July 2020. There is also likely to be differences in the accuracy of different states’ data, due to the different methods of collection. For the analysis, we used a lag of one week to allow for the delay from exposure to the virus to confirmation of infection status17. In a sensitivity analysis we refitted the model without a lag and produced consistent results (Appendix 5, Extended data)16.\n\nGiven the size of the effect, these results have important public health implications as no other intervention has comparable effects. Hence closure or extension of holiday periods could be an emergency option for state governments. In addition to encouraging flu vaccination, the Centres for Disease Control has a number of suggestions in their guidance, such as encouraging students and staff to stay home when sick, liberalising sickness policies during epidemics, encouraging respiratory etiquette, encouraging hand hygiene, regular cleaning of shared surfaces such as door handles and faucets, and providing a “sick room” to quarantine students with flu-like illnesses19. An additional strategy is to consider face masks, which, with hand hygiene, appear to substantially reduce transmission. All these strategies would need to be triggered by health departments to schools at an appropriate point in an epidemic or pandemic.\n\n\nData availability\n\nBond University Research Portal: Australian state influenza notifications and school closures in 2019: Appendix 1 – Underlying data. https://doi.org/10.26139/5c47ae4cd8e1614\n\nBond University Research Portal: Australian state influenza notifications and school closures in 2019: Appendix 2–5 – Extended data. https://doi.org/10.4225/57/555d781f8f2a316\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 like thank Nancy Glasziou for pointing out the potential of school closure, and for comments on the manuscript.\n\n\nReferences\n\nHealth Protection Agency: Weekly pandemic flue media update: 17 December 2009. 2009; [Accessed: 18 October 2019]. Reference Source\n\nEwing A, Lee EC, Viboud C, et al.: Contact, Travel, and Transmission: The Impact of Winter Holidays on Influenza Dynamics in the United States. J Infect Dis. 2017; 215(5): 732–739. PubMed Abstract | Publisher Full Text | Free Full Text\n\nJackson C, Vynnycky E, Hawker J, et al.: School closures and influenza: systematic review of epidemiological studies. BMJ Open. 2013; 3(2): pii: e002149. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLuca GD, Kerckhove KV, Coletti P, et al.: The impact of regular school closure on seasonal influenza epidemics: a data-driven spatial transmission model for Belgium. BMC Infect Dis. 2018; 18(1): 29. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBin Nafisah S, Alamery AH, Al Nafesa A, et al.: School closure during novel influenza: A systematic review. J Infect Public Health. 2018; 11(5): 657–661. PubMed Abstract | Publisher Full Text\n\nAustralian Government: Australian national notifiable diseases and case definitions. 2019; [Accessed: 20 September 2019]. Reference Source\n\nNew South Wales Dept of Health: Influenza Surveillance Report. 2019; [Accessed: 20 September 2019]. Reference Source\n\nQueensland Health: Influenza surveillance reporting. 2019; [Accessed: 20 September 2019]. Reference Source\n\nACT Government Department of Health: Flu in the ACT. 2019; [Accessed: 20 September 2019]. Reference Source\n\nGovernment of Western Australia Dept of Health: Virus WAtch. 2019; [Accessed: 20 September 2019]. Reference Source\n\nVictoria Department of Health: Seasonal Influenza Reports for 2019. 2019; [Accessed: 20 September 2019]. Reference Source\n\nSouth Australia Health: Surveillance of notifiable conditions. 2019; [Accessed: 20 September 2019]. Reference Source\n\nRohatgi A: WebPlotDigitizer (Version 4.2). 2019; [Accessed: 25 September 2019]. Reference Source\n\nScott A, Bakhit M, Clark J, et al.: Australian state influenza notifications and school closures in 2019: Appendix 1 – Underlying data. Bond University. Scott_et_al_Australian_state_influenza_notifications_and_school_closures_in_ 2019_Appendix_ 1_Underlying_data(.xlsx), 2019. http://www.doi.org/10.26139/5c47ae4cd8e16\n\nGebski V, Ellingson K, Edwards J, et al.: Modelling interrupted time series to evaluate prevention and control of infection in healthcare. Epidemiol Infect. 2012; 140(12): 2131–41. PubMed Abstract | Publisher Full Text\n\nScott A, Bakhit M, Clark J, et al.: Australian state influenza notifications and school closures in 2019: Appendix 2-5 – Extended data. Bond University. Appendix_ 2_ 5_Extended_data(.pdf), 2019. http://www.doi.org/10.4225/57/555d781f8f2a3\n\nCenters for Disease Control and Prevention: Seasonal Influenza (Flu): How Flu Spreads. 2019a; [Accessed: 25 September 2019]. Reference Source\n\nJackson C, Mangtani P, Hawker J, et al.: The effects of school closures on influenza outbreaks and pandemics: systematic review of simulation studies. PLoS One. 2014; 9(5): e97297. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCenters for Disease Control and Prevention: Guidance for School Administrators to Help Reduce the Spread of Seasonal Influenza in K-12 Schools. 2019b; [Accessed: 25 September 2019]. Reference Source"
}
|
[
{
"id": "57787",
"date": "16 Jan 2020",
"name": "Casey Zipfel",
"expertise": [
"Reviewer Expertise Modeling social and spatio-temporal dynamics of infectious disease",
"with specific experience in seasonal influenza."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nSummary: Australia’s influenza season does not typically coincide with school holidays. However, in 2019, the influenza season occurred earlier than usual, allowing the opportunity to evaluate the impacts of school closure on influenza dynamics in Australia. In this article, the authors present state and territory-level influenza data by week, and perform segmented regression, comparing influenza incidence before and after the school holiday. They also count weekly increases and decreases before, during, and after the school holiday, and show age-based dynamics. This article asks an important question of public health relevance to non-pharmaceutical interventions in a setting where it has not been previously investigated in a concise manner. However, this article could be strengthened through additional framing, increased statistical rigor, and more nuanced interpretation.\n\nComments:\nThe introduction leaves several unanswered questions that would help to more clearly identify the importance of the study. The relationship between school closure and influenza dynamics has been explored in a number of previous papers, with both epidemiological data and mechanistic models. Thus, it is unclear to me why is it important to consider this relationship in Australia, specifically. Do the authors have hypotheses regarding trends or mechanisms that might be different from other countries? Is it important for public health planning? This question seems especially salient to me since school closures and the influenza season in Australia do not typically coincide, so these epidemiological trends may not be typical for Australia.\n\nThe article concludes that there is a significant reduction in influenza in most states in Australia based on the results of segmented regression comparing influenza incidence level and slope before and after the holiday period. I am not totally convinced by this conclusion, as Table 1 shows that the change in level is not significant for Victoria, Australian Capital Territory, and Southern Australia, and the change in slope is not significant for Queensland, Victoria, Western Australia, and Southern Australia. This is contrary to the section of the results that states that “the estimates for the initial effect and the subsequent slope show significant declines for all states except South Australia”. These results could be more carefully interpreted. This would give rise to an interesting question: what are the differences between the states/territories that result in different dynamics?\n\nI think this article could be strengthened with a more robust time series modeling approach, like ARIMA modeling. This would be particularly useful because the predicted vs. residual plot in Appendix 4 appears to indicate heteroskedasticity in the data. Including model terms in a time series model could handle this issue, as well as temporal autocorrelation.\n\nThe results also provide the percent of weeks in the pre-vacation, during-vacation, and post-vacation period in which there is a weekly decrease in influenza incidence, indicating that there is a higher proportion of decreases in the during and post-vacation period. However, the pre-vacation period seems to include all of the early part of the season. If there were numerous decreases in this time period, then the onset of the influenza season would not have occurred. Thus, this finding may be a bit circular.\n\nIt would be useful to compare this influenza season, which co-occurs with the holiday period, with another influenza season that does not co-occur with the holiday period, as a control. This could help to isolate the impact of school closure on influenza dynamics.\n\nThe authors specify mid-May to early September as their study period. However, it’s unclear what total population and age-specific dynamics looked like post week 35. Past studies have shown that school holidays simply delay dynamics so that the epidemic wave recovers to pre-holiday rates after the holiday. I would be curious if this is the case here.\n\nIn the model, a one-week lag was assumed. Is there evidence about care-seeking and influenza surveillance/reporting to support this? The discussion mentions a sensitivity analysis performed with no lag, but I wonder if the lag could be longer due to a combination of delay to seeking healthcare and delay in reporting.\n\nThe fourth paragraph of the discussion comments on the possible causes of the association between school closure and influenza. This paragraph rules out several possible explanations but does not then provide a plausible explanation.\nMinor comments:\nA y-axis label on Figure 1 and Figure 2 would be helpful. The Figure 1 caption says it is the influenza rate, so I assume it is influenza cases per week, but this could be clearer.\n\nIs the x-axis in Figure 2 the week number? It would be easier to interpret if it was put into the same units as Figure 1, with dates instead of week counts.\n\nDoes Figure 2 include cases for all of the states and territories combined?\n\nIn Table 1, it is unclear whether the changes described (in both slope and level) are comparing the during-vacation period or the post-vacation period to the pre-vacation period. The observed and predicted plots in Appendix 3 appear to show 3 different segments fit for each of these periods, but it is unclear what change is reported in Table 1.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "5966",
"date": "08 Oct 2020",
"name": "Anna Scott",
"role": "Author Response",
"response": "Thank you very much for your comments. We provide our responses to each comment below: We have added to the introduction the following: \"Since each country’s school system differs in features such as age range, classroom structure and sizes, and class mixing, we thought it important to document the size of any impact in Australia. Furthermore, the variation by states, and the ability to examine delay to changes in the non-school population would extend the range of sub-questions we could address.\" We agree, and have revised our interpretation of the results. We are unfamiliar with ARIMA modelling, but generally prefer simpler approaches. Our main purpose for the statistical analysis is to test hypotheses for each state on whether the school closures have resulted in changes in levels and/or changes in slopes with regards to influenza cases. The goodness-of-fit measures suggest the regression models provide adequate fit hence we believe our results are valid. We agree, and have removed this analysis from the manuscript. Unfortunately we were unable to formally compare as the previous years’ raw numbers are not readily available. We have included the lack of control group as a limitation of the study, and provided a reference to a Government document comparing the trend from 2019 to years going back to 2013. We have included 1 additional month of data – up until the start of the October school holiday period. A lag of 2 weeks would only be plausible if a person being exposed to influenza on the last week of school prior to the vacation would generally be reported at least 2 weeks and 3 days later. Given “symptoms can begin about 2 days (but can range from 1 to 4 days) after the virus enters the body” this delay seems unrealistic. We agree, and have added the following: \"Hence, the most likely remaining explanation seems to be causal reduction in transmission from school holidays.\" Comments: 9-12. We have revised the Figures and Tables to address these comments."
}
]
},
{
"id": "66760",
"date": "27 Jul 2020",
"name": "Núria Torner",
"expertise": [
"Reviewer Expertise Surveillance",
"prevention and control of infectious disease outbreaks",
"with specific experience in seasonal influenza."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nSeasonal Influenza Surveillance deploying epidemiological and virological data on patients with influenza virus infection is a global task performed in coordination with WHO requirements. These include sentinel surveillance and hospital surveillance for severe cases of laboratory confirmed influenza. Even though influenza has been studied in depth, there are still some issues that need to be addressed, at least to encourage increase in vaccine uptake and recommendations.\nThere are several issues that are not clear and being this a point observation of just one season, inference is not sound enough to ascertain as evidence. Comparison with previous seasons would be desirable.\nComments:\nOne highly contrasted issue is the amplification that children trigger as to transmission of infection to their siblings and household members from the school setting. And this might be prevented by vaccination. (Basta et al. 2009)1. So this is not new but it might be relevant for Australia to implement preventive measures, if so this should be stated.\n\nDuring epidemic periods transmission is high and the number of syndromic cases make laboratory confirmation out of range of heath systems. Is this so in Australia? As stated in data sources only laboratory confirmed cases are taken into account for reporting: States and territories differ in how they collect and report data on flu cases. New South Wales7 and Queensland8 report the number of samples that test positive for Influenza A and B (lab-confirmed); Australian Capital Territory9 reports the number of influenza (lab) notifications to the state; and Western Australia10, Victoria11 and South Australia12 report the number of lab-confirmed influenza cases (strains unspecified).\nWhat is the difference between the three (besides type identification)? Positive for Influenza A and B (lab-confirmed); number of influenza (lab) notifications; and number of lab-confirmed influenza cases (strains unspecified). Do the authors mean type and subtype by strain? Or does it make reference to the strain type? Type A Subtype A H1N1 Strain: A/Brisbane/59/2007 (H1N1) Use the correct term.\n\nThere is also the climate factor to be taken into account. Do all regions included in the study have the same temperature, humidity range? Some differences in decrease of transmission could also be due to a lesser degree of transmission such as in Victoria and Southern Australia for example. Did this particular season have a different climatology that made it coincide with the school holiday period?\n\nThe results of the pre-school closure period refer to the baseline epidemic burden of disease, if so then there is a decline before school closure? By the way, the term school closure can be misleading as to a containment preventive measure that can be implemented to stop transmission and what is referred to in the study should be specific to school holiday closure. What has happened in other epidemic seasons should be included to be able to compare and strengthen the results obtained.\n\nIn the introduction first line: A pandemic is global, so it wasn’t just the UK that was affected. As a matter of fact school closure emerged as one of the non-pharmaceutical strategies during that pandemic and has been implemented in the present COVID-19 pandemic. Sentence should be rephrased.\nThe authors findings could be in the same line as Eames (2013)2 who stated that allowing some flexibility in holiday timing would provide maximum health benefit from the holiday period, yet this is difficult to carry out because of the different social and labor implications it has for schools, parents, and care givers. Was this the aim of the study?\n\nIn the conclusions the authors state that: no other intervention has comparable effects. There is no comparison in the study to other non-pharmaceutical mitigation measures. Can you include a reference to this statement?\nMinor comments:\nInclude label on Figure 1, are they number of cases in total for all states or incidence rates? Please complete.\n\nWhy does Fig 1 have dates in the x-axis and Figure 2 the week number? Why different, they should be the same.\n\nIs the work clearly and accurately presented and does it cite the current literature? No\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": [
{
"c_id": "5967",
"date": "08 Oct 2020",
"name": "Anna Scott",
"role": "Author Response",
"response": "Thank you very much for your comments. We provide our responses below: We agree that a multi-year comparison would be preferable. However, for 2020, the number of flu infections is atypical (because of COVID), and for years prior to 2019, raw data is very difficult to obtain as it requires multiple data access applications to the individual states and to the Commonwealth. We have included the lack of control group as a limitation of the study, and provided a reference to a Government document comparing the trend from 2019 to years going back to 2013. Thank you for providing this reference. We added the following sentence to the Discussion: \"Vaccinating children against influenza has also been shown to substantially reduce influenza attack rates in both children and adults (Basta et al 2009).\" The relatively small size of the Australian population (approximately 25 million) makes laboratory confirmation a bit easier than in many other, more populous countries (e.g. in Europe, North America, South America). As we note in the methods section, we report lab-confirmed cases. States/territories report influenzas a bit differently from each other. States of NSW and QLD report influenza A and influenza B only. ACT reports influenza A, influenza B, and coinfections with influenza A and B. The remaining states report lab-confirmed influenzas but do not specify strains. We have made this clearer in the text. The temperatures were 1.6 deg above the long-term average, in line with global warming but with no unusual anomaly in July 2019 (http://www.bom.gov.au/climate/mwr/aus/mwr-aus-201907.pdf). We do not have humidity data, but rainfall was lower than usual, suggesting lower humidity. There was no decline before school closure – as Figure 1 shows, the decline only occurs within the grey boxes (the holiday periods). Any apparent decline – e.g. NSW – is because we have joined the dots of the weekly reported numbers. We have modified the title, and edited the body of the manuscript to refer to school holiday closures, to make this clearer. We have replaced the term 'pandemic' with the term 'epidemic' in the first line of the introduction. Eames' study used modelling to estimate a counterfactual: what would have happened if the UK had NOT closed the schools during the 2009 epidemic - and found the epidemic would have been much worse than it was. We estimated what happened with the actual school holiday closure in Australia - and found the influenza incidence decreased. Our study and Eames study are therefore consistent. We have added this point to the discussion section. We added references to the newly updated Cochrane review by Tom Jefferson, on physical interventions to reduce the spread of respiratory viruses. They are cases - we edited the figure and its title to clarify this. We edited the figures so they both refer to dates for consistency."
}
]
}
] | 1
|
https://f1000research.com/articles/8-1899
|
https://f1000research.com/articles/10-420/v1
|
26 May 21
|
{
"type": "Research Article",
"title": "Health-Related Quality Of Life, Uncertainty, and Anxiety among Patients with Chronic Obstructive Pulmonary Disease",
"authors": [
"Nazih Abu Tabar",
"Mohammad Al Qadire",
"Imad Thultheen",
"Jafar Alshraideh",
"Nazih Abu Tabar",
"Mohammad Al Qadire",
"Imad Thultheen"
],
"abstract": "Patients’ with Chronic Obstructive Pulmonary Disease suffer from serious respiratory symptoms that increase anxiety, stress, and uncertainty, and affect quality of life. The aim of this study was to assess level of anxiety, uncertainty, and health related quality of life (HRQoL) among COPD patients in Jordan. Correlational cross-sectional survey design was used to collect data from 153 COPD patients. The study was conducted at pulmonary clinics in three major referral hospitals in Jordan that provide care for COPD patients from different parts of the country. To assess HRQoL, St. George Respiratory Questionnaire was completed. Uncertainty and anxiety level was measured by Mishel's uncertainty of illness scale and state anxiety inventory respectively. The mean age of participants was 66.8 (SD= 10.3) and most participants were males (94.1%) with. The mean score of HRQoL was 57.9 (SD = 20.5). The mean score of participants’ level of anxiety was 38.1 (SD = 11.1). The mean score of uncertainty was 66.1 (SD= 11.1). There is a statistically significant positive relationship between HRQoL and anxiety (r =.433, p< .01), and uncertainty (r=.483, p<.01). Increased anxiety and uncertainty among COPD patients was associated with low HRQoL. Health care providers need to pay attention the effect of anxiety and uncertainty on COPD patients’ quality of life and institute appropriate management.",
"keywords": [
"COPD",
"St. George Respiratory Questionnaire",
"Jordan",
"Anxiety",
"quality of life",
"uncertainty"
],
"content": "Introduction\n\nChronic obstructive pulmonary disease (COPD) is one of the chronic irreversible respiratory diseases which result in comorbidities and a high number of annual deaths1 leading to the increased burden of chronic diseases worldwide.2 The burden associated with COPD is increasing as the percentage of smokers is increasing, with most deaths occur within the developing countries.3,4 COPD remains the most prevalent of chronic respiratory diseases globally among men and women, with an overall prevalence of 5.9% in 2017.2 It is estimated that 3.6% of the population in the Middle East have been diagnosed with COPD and the figure reaches 11% among Jordanian male smokers.5,6 COPD and related symptoms are associated with increased anxiety and uncertainty that affect health-related quality of life (HRQoL).7\n\nHRQoL is an important outcome that should be evaluated among COPD patients. It is continuously changing as patients progress from one stage to another during the disease trajectory.8 Several factors were found to negatively affect quality of life, including disease symptoms, such as difficulty in breathing, cough, compromised physical status, anxiety, and uncertainty.7,9–11 Psychological distress is significantly correlated with COPD severity and poorer quality of life. Several studies have reported that patients with COPD have a higher prevalence of anxiety (21–96%) compared with the general population (20%).12–14 In addition, most of the patients diagnosed with moderate-to-severe COPD reported severe breathlessness, which is worsened with the experience of anxiety or depression. This may increase the frequency and severity of breathing symptoms, number of readmissions, and mortality.14–16 Further, several studies reported that anxiety was a predictor of low mean of total score of HRQoL.17–21 In Jordan, high prevalence of anxiety and depression, and poor quality of life were found among COPD patients and their partners.17\n\nIllness-related uncertainty is all about the patients’ inability to comprehend the process underpin their disease and being unable to expect the events associated with it.22 Two studies have shown that greater uncertainty is associated with anxiety, impaired HRQoL, and fatigue,23,24 and another has shown that it impairs self-expectancy and resulted in maladaptation with the disease.25 In a longitudinal study that was conducted to examine relationship between uncertainty and complexity of COPD patient outcomes, it was found that depression and anxiety were associated with an increased frequency of breathlessness and poor quality of life.26 Limited studies have discussed uncertainty from COPD patients’ perspectives and its impact on HRQoL specifically.27 Assessing uncertainty and anxiety and their effect on HRQoL among COPD patients would aid the effort of symptoms management among such patients. Thus, the aim of the study was to assess level of anxiety, uncertainty, and HRQoL among COPD patients in Jordan; and explore the relationships between these variables.\n\n\nMethods\n\nA correlational design using a cross-sectional survey method was used. The sample size was estimated based on generic correlation test with a power of 80, 0.05 alpha, and a medium effect size (0.3). The minimum sample required was 82, however a sample of 153 COPD patients was included. Patients were included if they were 40 years and older and agreed to participate. Patients with primary diagnosis of bronchial asthma, bronchiectasis, and chronic obstructive asthma were excluded. The study was conducted at pulmonary clinics in three major referral hospitals in the capital, Amman. These clinics usually provide care for COPD patients from different parts of the country. Medical care and follow up is provided mainly by pulmonary medicine specialists in these clinics. Ethical approval to conduct the study was obtained from Institutional Review Board of the involved hospitals (IRB reference, 90/2019/724). Patients’ participation was voluntary and based on informed written consent.\n\nData were collected by one researcher for all patients using standardised structure interview in the period from July 2019 to January 2020. The data collection questionnaire included: sociodemographic and clinical characteristics part, HRQoL Questionnaire, State-Trait Anxiety Inventory, and Mishel’s Uncertainty of Illness Scale. Data were collected using a structured interview format by one trained researcher for all patients.\n\nRespiratory HRQoL Questionnaire-C version\n\nThe Arabic version28 of the St. George’s Respiratory Questionnaire, C version (SGRQ-C), was used to measure HRQoL among patients with respiratory disease like COPD and asthma.29 The original SGRQ-C contains 17 items and three subscales that are: symptoms (items 1 to 8), activity-related (items 11 and 15), and impact-related (items 9, 10, 12 to 14, 16 and 17). Higher scores in the total SGRQ-C and sub-scales indicate a decrease in quality of life. The scale’s validity and reliability was established.30 Cronbach’s alpha internal consistency of the scale was 0.95 and the long-term test–retest reliability ranged from 0.70 to 0.86.28,30–32 The internal consistency (Cronbach’s alpha) of the Arabic version of SGRQ-C in this study was 0.83.\n\nMishel’s uncertainty of illness scale\n\nMishel’s uncertainty of illness scale (MUIS) was used to assess uncertainty related to disease trajectory. It consists of a 23-items using a five-point Likert scale (strongly agree to strongly disagree). The level of illness uncertainty increased as the total score increased. The uncertainty total score also can be divided into three levels: mild (23–53), moderate (54–84), and high (≥85).33 The scale has a Cronbach alpha of 0.74–0.92.22,24 The Arabic version34 was used in the study. Internal consistency (Cronbach’s alpha) of the Arabic version of MUIS-C in this study was 0.86.\n\nState- Trait Anxiety Inventory (SAI)\n\nThe SAI35 consists of 20 self-reported items that measure patients’ situational anxiety levels. The SAI has responses 1–4 where one means “not at all”, two “somewhat”, three “moderately so”, and four “very much so”. The total scores can range 20–80: a higher total score indicates increased level of anxiety.35 The Cronbach’s alpha coefficient for the STAI was 0.92.35 The internal consistency (Cronbach’s alpha) of the Arabic version of SAI in this study was 0.94. Permission to use the SAI was obtained from the copyright holder Mind Garden, Inc.36\n\nThe Statistical Package for Social Science (IBM SPSS Statistics, RRID:SCR_019096) version 2337 for Windows was used for data analysis. Mean, frequency, standard deviation, minimum, and maximum were used to summarize study variables. The Pearson correlation coefficient was used to explore the relationship between HRQoL and other variables.\n\n\nResults\n\nA total of 153 patients completed the study with no missing data. The mean (SD) age of participants was 66.8 (10.3) years. There were 144 (94.1%) male participants. 77 (50.3%) of participants were current smokers, and 68 (44.4%) were ex-smokers. Sociodemographic characteristics of participants are presented in Table 1.\n\n* in the 146 current or past smokers.\n\n** in the 77 current smokers.\n\nThe mean (SD) score of the SGRQ-C which represent the HRQoL was 57.9 (20.5) with a range of 6–92. The highest subscale scores were for the activity domain: 74.6 (21.9); and the lowest score was for the symptom’s domain: 43.8 (25.0). The results indicate that the level of HRQoL among patients with COPD in this study was reduced across all domains of HRQoL measurement.\n\nThe mean (SD) total score of the patients’ anxiety level was 38.1 (11.1), ranging 23–73, which indicates that the level of patients’ anxiety was moderate. The higher anxiety means (2.36, 2.36, 2.28, 2.25, and 2.18) were with items 15, 16, 10, 5, and 11, respectively, which are related to the positive response of patients feeling; and the lower anxiety means (1.33, 1.41, 1.41, 1.45, and 1.50) were with items 9, 17, 18, 13, and 3, respectively, which are related to the negative response of patients feeling. The mean responses to each item on the SAI scale are presented in Table 2.\n\n\n\n1. I feel calm\n\n\n\n2. I feel secure\n\n\n\n3. I am tense\n\n\n\n4. I feel strained\n\n\n\n5. I feel at ease\n\n\n\n6. I feel upset\n\n\n\n7. I am presently worrying over possible misfortunes\n\n\n\n8. I feel satisfied\n\n\n\n9. I feel frightened\n\n\n\n10. I feel comfortable\n\n\n\n11. I feel self-confident\n\n\n\n12. I feel nervous\n\n\n\n13. I am jittery\n\n\n\n14. I feel indecisive\n\n\n\n15. I am relaxed\n\n\n\n16. I feel content\n\n\n\n17. I am worried\n\n\n\n18. I feel confused\n\n\n\n19. I feel steady\n\n\n\n20. I feel pleasant\n\nThe mean (SD) total score of uncertainty was 66.1 (11.1) and ranged 31–94. According to the score categories proposed by,33 the mean score of 66.1 in the current study indicates that the average patients’ uncertainty was moderate. The higher uncertainties (3.8, 3.7, and 3.7) were with items 13, 18, and 7, respectively, which are related to the ambiguity (cues about state of illness), and the lower uncertainties (1.8 and 2.1) were with items 8 and 6, respectively, which are related to the complexity (cues about treatment). Patient responses for the MUIS-C scale are presented in Table 3.\n\n\n\n1. I do not know what is wrong with me.\n\n\n\n2. I have a lot of questions without answers.\n\n\n\n3. I am unsure if my illness is getting better or worse.\n\n\n\n4. It is unclear how bad my pain will be.\n\n\n\n5. The explanations they give about my condition seem hazy to me.\n\n\n\n6. The purpose of each treatment is clear to me.\n\n\n\n7. My symptoms continue to change unpredictably.\n\n\n\n8. I understand everything explained to me.\n\n\n\n9. The doctors say things to me that could have many meanings.\n\n\n\n10. My treatment is too complex to figure out.\n\n\n\n11. It is difficult to know if the treatments or medications I am getting are helping.\n\n\n\n12. Because of the unpredictability of my illness, I cannot plan for the future.\n\n\n\n13. The course of my illness keeps changing. I have good and bad days.\n\n\n\n14. I have been given many differing opinions about what is wrong with me.\n\n\n\n15. It is not clear what is going to happen to me.\n\n\n\n16. The results of my test are inconsistent.\n\n\n\n17. The effectiveness of the treatment is undetermined.\n\n\n\n18. Because of the treatment, what I can do and cannot do keeps changing.\n\n\n\n19. I’m certain they will not find anything else wrong with me.\n\n\n\n20. The treatment I am receiving has a known probability of success.\n\n\n\n21. They have not given me a specific diagnosis.\n\n\n\n22. The seriousness of my illness has been determined.\n\n\n\n23. The doctors and nurses use everyday language so I can understand what they are saying.\n\nThe Pearson correlation was utilized to test the relationship between the total HRQoL score and perceived anxiety score and the total uncertainty score. The results revealed the presence of a statistically significant positive relationship between HRQoL and anxiety (r = 0.433, p < 0.01), and uncertainty (r = 0.483, p < 0.01). The correlations between total HRQoL and subscales, with perceived anxiety and uncertainty are presented in Table 4.\n\n\nDiscussion\n\nIn this study, more than one-third of the Jordanian patients reported a moderate level of anxiety. Our finding of anxiety level was in line with the findings of a systematic review which indicated that anxiety was prevalent among COPD patients and the anxiety level was moderate in several studies.38 Anxiety is considered one of the comorbidities associated with physical and psychological discomfort.39 Anxiety can become severe and prolonged and cause significant disruption for patients’ daily functioning and socialization.40 It has been acknowledged that anxiety could increase COPD severity and interfere with patients’ daily life activities and then resulted in a poor quality of life.14–16 Anxiety doubles the likelihood of having limited daily living activity, exercise intolerance, and severe and frequent symptoms in COPD patients. The results of the current study are in line with the previous literature that found patients with a significant increase in the levels of anxiety are more likely to have poor HRQoL.18,19,21 Anxiety disorders are disabling and, unless adequately treated, can become chronic, lower self-esteem, predispose to suicidal ideation, and increase the risk of hospitalization and ultimate worsen HRQoL. Healthcare providers should assess the level of anxiety on each patient’s visit and should promote interventions that can lower patient’s anxiety level.\n\nThe results of the study showed that Jordanian patients with COPD have experienced a moderate level of uncertainty concerning their disease and its management. This was consistent with the literature.23,24,34,41,42 Uncertainty among COPD patients has been limitedly investigated.23,43 This study provides information about the experience of uncertainty among Jordanian COPD, and its relationships with anxiety and HRQoL. The current evidence showed that patients had relatively high levels of uncertainty and it affected their disease-related outcome. Indeed, Jordanian patients diagnosed with COPD reported a high level of uncertainty in most of the uncertainty items scale. For those patients, the uncertainty might generate some negative emotions including anxiety, unexpected feeling, frustrations, and nervousness behavior by delaying treatment plans and strategies; the treatment itself; the decision-making process; the patient's response to the therapy or complications; and ultimately the patients' overall HRQoL might also be compromised. The findings in our study are consistent with a study conducted by.26 When disease-related symptoms are not adequately managed, uncertainty feeling increased combined with apprehension about disease perception and management.34,44 Jiang and He23 reported that COPD used cognitive adaptation to the feeling of uncertainty. The cognitive–behavioral intervention is a useful example in strengthening health education and psychological support to decrease the uncertainty in illness, increase the quality of life, and for better coping among COPD patients with their disease problems.23,43 The adoption of such programs among Jordanian COPD patients would add more benefit in enhancing their quality of life and improve disease outcomes.\n\nJordanian patients with COPD reported poor HRQoL. This finding was consistent with the results from two previous studies.45,46 Also, the study was consistent with other studies conducted in different global countries, indicating that dyspnea, cough, and fatigue were the most burden symptoms affecting HRQoL.47–50 This result can be related to several factors: activity domains had the highest scores indicated the leading cause of poor quality of life is the factors related to the severity of the disease and level of activity. Also, the fact that most patients in this study were older people, their level of education from illiterate up to the primary, not employed, types of their work and having severe disease stages and being anxious and uncertain. Inconsistent with our findings, Sharma and Joshi51 found that subscales' psychological and social domains had the highest scores.\n\nThe present study revealed the significant correlation between the perceived anxiety and HRQoL. The result was in the lines with the previous literature17,18,20,21 that revealed COPD patients with anxiety had a poor HRQoL and anxiety was the determinant of low HRQoL score. Studies conducted by Borge et al.;12 Chen et al.;52 and Lim et al.53 reported a strong positive correlation between anxiety and HRQoL among COPD patients. The results of the present study indicated that a higher uncertainty score was correlated with poorer HRQoL. This might be because patients lack knowledge of the disease, noncompliance to treatment, and having vagueness about the disease's progress. Hoth et al.26 suggested that social support might help in reducing uncertainty and improving quality of life. Therefore, it is necessary to reinforce social support for COPD patients to improve their coping strategies and social adaptability to improve their quality of life.\n\n\nConclusions\n\nPatients with COPD participated in the study in general have low quality of life, significant level of anxiety and uncertainty. The findings suggest that anxiety and uncertainty are correlated with poorer HRQoL among COPD patients. Healthcare providers need to pay more attention to assess anxiety and uncertainty components on a regular basis among COPD patients and institute appropriate management.",
"appendix": "Acknowledgements\n\nThe researchers would like to thank all patients who participated in this study. Also, the authors acknowledge the support provided by the University of Jordan in facilitating access to research materials, as well as to the target hospitals.\n\n\nConsent\n\nWritten informed consent of the participants was obtained from the participants.\n\n\nReferences\n\nWHO: Chronic respiratory diseases.2020 [cited 2020 May 22, 2020]. Date accessed: May 22, 2020. Reference Source\n\nSoriano JB, Kendrick PJ, Paulson KR, et al.: Prevalence and attributable health burden of chronic respiratory diseases: 1990–2017: a systematic analysis for the Global Burden of Disease Study 2017. Lancet Respir Med. 2020; 8(6): 585–596. PubMed Abstract | Publisher Full Text | Free Full Text\n\nQuaderi SA, Hurst JR: The unmet global burden of COPD. Glob Health Epidemiol Genom. 2018; 3: 1–3. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWHO: COPD: Definition.2019. 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Publisher Full Text\n\nAl-Moamary MS, Al-Hajjaj MS, Tamim HM, et al.: The reliability of an Arabic translation of the chronic obstructive pulmonary disease assessment test. Saudi Med J. 2011; 32(10): 1028–1033. PubMed Abstract\n\nBarr JT, Schumacher GE, Freeman S, et al.: American Translation, Modification, and Validation of the St. George's Respiratory Questionnaire. Clin Ther. 2000; 22(9): 1121–1145. PubMed Abstract | Publisher Full Text\n\nMcCormick KM: A concept analysis of uncertainty in illness. J Nurs Scholarsh. 2002; 34(2): 127–131. PubMed Abstract | Publisher Full Text\n\nSubih M, Al-Kalaldeh M, Salami I, et al.: Predictors of uncertainty among postdischarge coronary artery bypass graft patients in Jordan. J Vasc Nurs. 2018; 36(2): 85–90. PubMed Abstract | Publisher Full Text\n\nSpielberger CD: State-Trait anxiety inventory. The Corsini encyclopedia of psychology. 2010: 1–1.\n\nGarden. Mind Garden, Inc: 1983. 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PubMed Abstract | Publisher Full Text | Free Full Text\n\nBailey DE Jr, Wallace M, Latini DM, et al.: Measuring illness uncertainty in men undergoing active surveillance for prostate cancer. Appl Nurs Res. 2011; 24(4): 193–199. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMishel MH, Germino BB, Gil KM, et al.: Benefits from an uncertainty management intervention for African–American and Caucasian older long-term breast cancer survivors. Psychooncology: J Psychol, Soc Behav Dimensions Cancer. 2005; 14(11): 962–978. PubMed Abstract | Publisher Full Text\n\nSmall SP, Graydon JE: Uncertainty in hospitalized patients with chronic obstructive pulmonary disease. Int J Nurs Stud. 1993; 30(3): 239–246. PubMed Abstract | Publisher Full Text\n\nSchulz PS, Zimmerman L, Pozehl B, et al.: Symptom management strategies used by elderly patients after coronary artery bypass surgery. Appl Nurs Res. 2011; 24(2): 65–73. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFarag TS, Sobh ESM, Elsawy SB, et al.: Evaluation of health-related quality of life in patients with chronic obstructive pulmonary disease. Egypt J Bronchol. 2018; 12(3): 288–294. Publisher Full Text\n\nZamzam MA, Azab NY, El Wahsh RA, et al.: Quality of life in COPD patients. Egypt J Chest Dis Tuberculosis. 2012; 61: 281–289. Publisher Full Text\n\nBakas T, McLennon SM, Carpenter JS, et al.: Systematic review of health-related quality of life models. Health Qual Life Outcomes. 2012; 10: 134–134. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGhilley VP, Bhadoria DP, Pandit S: Correntional study of the health-related quality of life, chronic obstructive airway disease in Northern India, New Delhi. Int J Adv Med. 2018; 5(3): 705. Publisher Full Text\n\nPati S, Swain S, Patel SK, et al.: An assessment of health-related quality of life among patients with chronic obstructive pulmonary diseases attending a tertiary care hospital in Bhubaneswar City, India. J Family Med Prim Care. 2018; 7: 1047–1053. PubMed Abstract | Publisher Full Text | Free Full Text\n\nShah AM, Shah RB, Kachoria S: Health-related quality of life and associated factors in patients with chronic obstructive pulmonary disease. J Thorac Dis. 2019; 35(5): 241–249. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSharma K, Joshi S: Quality of life of patients with chronic obstructive pulmonary disease in Chitwan, Nepal: a pilot study report. Int J Med Sci Public Health. 2015; 4: 1235–1241. Publisher Full Text\n\nChen YW, Camp PG, Coxson HO, et al.: A Comparison of Pain, Fatigue, Dyspnea and their Impact on Quality of Life in Pulmonary Rehabilitation Participants with Chronic Obstructive Pulmonary Disease. COPD: J Chronic Obstructive Pulmonary Dis. 2018; 15: 65–72. PubMed Abstract | Publisher Full Text\n\nLim KE, Kim SR, Kim HK, et al.: Symptom clusters and quality of life in subjects with COPD. Respir Care. 2017; 62(9): 1203–1211. PubMed Abstract | Publisher Full Text\n\nAbu Tabar N, Al Qadire M, Thultheen I, et al.: Underlying data for 'Health-related quality of life, uncertainty, and anxiety among patients with chronic obstructive pulmonary disease'.Publisher Full Text"
}
|
[
{
"id": "87506",
"date": "29 Jun 2021",
"name": "Nabeel Al-Yateem",
"expertise": [
"Reviewer Expertise Nursing"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn general, the study description is very good. It is easy to read and follow. The study topic is important, and it has even more importance given the context of where it was conducted. In Jordan, the prevalence of COPD is high, as the authors truly reported. Therefore, more focus on the context of the study (i.e. in Jordan) would have been very beneficial as it would reinforce the importance of the study, and inform the reader about the current situation about COPD management and how this study would contribute to its improvement. This is also important given that in the Introduction, the authors cite a study conducted in Jordan that has addressed a similar topic (i.e. anxiety and depression, and quality of life among COPD patients and their partners).\nThe Methods used in the study are quantitative, cross-sectional, and correlational design. It utilized known valid and reliable questionnaires. Given the stated aim of the study to “assess level of anxiety, uncertainty, and HRQoL among COPD patients in Jordan; and explore the relationships between these variables”, the methods and tools used seem appropriate. However, two main concerns related to the methods are:\nThe small sample size, which is 153 participants. This might be relatively low for a correlational cross-sectional study, although the authors reported using a statistical calculator to determine the sample size.\n\nAnother concern in the methodology is the use of 3 long questionnaires for the participants to complete. Also, all questionnaires are subjective in nature, it totally depends on participants' recall, perspectives, and subjective opinions.\nThe Results of the study are clear and well presented. The statistical analysis seems to be appropriate given the study aim, variables, and nature of the data collected.\nThe Discussion is also fine, it compared the results of the current study with similar international literature. It was more descriptive and less critical in some places and may have lacked a focus on the implication of the results of the study to improve current practices. Given the experience of the researchers in the healthcare system in Jordan, I wish to see more discussion on how the results of this study can be translated into care elements to improve the service provided for COPD 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?\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": "6853",
"date": "30 Jun 2021",
"name": "Jafar Alshraideh",
"role": "Author Response",
"response": "We wish to thank the reviewer for the valuable comments."
}
]
},
{
"id": "96908",
"date": "08 Nov 2021",
"name": "Abeer A. Selim",
"expertise": [
"Reviewer Expertise Psychiatric and mental health nursing"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe paper is addressing a significant research area which is quality of life and COPD along with anxiety and uncertainty.\nThe paper needs English language editing.\n\nIn the introduction, first paragraph, the authors focused on male Jordanian smokers, how about females?\n\nThe design is cross-sectional, not correlational cross-sectional.\n\nSpecify the type of COPD diseases included in the study.\n\nProvide rationales for including only 40 years old and more in the study.\n\nData collection section: this statement is redundant \"Data were collected using a structured interview format by one trained researcher for all patients\".\n\nAt the beginning of the discussion section, summarize the results, then interpret them.\n\nIn the discussion, move the following statement to the conclusion section: \"Healthcare providers should assess the level of anxiety on each patient’s visit and should promote interventions that can lower patient’s anxiety level.\"\n\n\"The findings in our study are consistent with a study conducted by.26\" - this statement is not complete.\n\nElaborate on patient's education about the disease, treatment, and prevention.\n\nAdd limitations of the study.\n\nThe paper is missing implications for practice.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "7454",
"date": "17 Nov 2021",
"name": "Jafar Alshraideh",
"role": "Author Response",
"response": "Thank you for the review and comments. We will incorporate these as applicable. Appreciate your time and efforts"
}
]
}
] | 1
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https://f1000research.com/articles/10-420
|
https://f1000research.com/articles/9-1366/v1
|
24 Nov 20
|
{
"type": "Data Note",
"title": "A dataset for the analysis of antibody response to glycan alpha-Gal in individuals with immune-mediated disorders",
"authors": [
"José de la Fuente",
"José Miguel Urra",
"Marinela Contreras",
"Iván Pacheco",
"Elisa Ferreras-Colino",
"Ernesto Doncel-Pérez",
"Isabel G. Fernández de Mera",
"Margarita Villar",
"Carmen M. Cabrera",
"Cesar Gómez Hernando",
"Eduardo Vargas Baquero",
"Javier Blanco García",
"Javier Rodríguez Gómez",
"Alberto Velayos Galán",
"Francisco Feo Brito",
"Elisa Gómez Torrijos",
"Alejandro Cabezas-Cruz",
"Christian Gortázar",
"José Miguel Urra",
"Marinela Contreras",
"Iván Pacheco",
"Elisa Ferreras-Colino",
"Ernesto Doncel-Pérez",
"Isabel G. Fernández de Mera",
"Margarita Villar",
"Carmen M. Cabrera",
"Cesar Gómez Hernando",
"Eduardo Vargas Baquero",
"Javier Blanco García",
"Javier Rodríguez Gómez",
"Alberto Velayos Galán",
"Francisco Feo Brito",
"Elisa Gómez Torrijos",
"Alejandro Cabezas-Cruz",
"Christian Gortázar"
],
"abstract": "Humans evolved by losing the capacity to synthesize the glycan Galα1-3Galβ1-(3)4GlcNAc-R (α-Gal), which resulted in the development of a protective response mediated by anti-α-Gal IgM/IgG/IgA antibodies against pathogens containing this modification on membrane proteins. As an evolutionary trade-off, humans can develop the alpha-Gal syndrome (AGS), a recently diagnosed disease mediated by anti-α-Gal IgE antibodies and associated with allergic reactions to mammalian meat consumption and tick bites. However, the anti-α-Gal antibody response may be associated with other immune-mediated disorders such as those occurring in patients with COVID-19 and Guillain-Barré syndrome (GBS). Here, we provide a dataset (209 entries) on the IgE/IgM/IgG/IgA anti-α-Gal antibody response in healthy individuals and patients diagnosed with AGS, tick-borne allergies, GBS and COVID-19. The data allows correlative analyses of the anti-α-Gal antibody response with factors such as patient and clinical characteristics, record of tick bites, blood group, age and sex. These analyses could provide insights into the role of anti-α-Gal antibody response in disease symptomatology and possible protective mechanisms.",
"keywords": [
"alpha Gal",
"immune response",
"antibody",
"allergy",
"tick",
"coronavirus",
"COVID-19",
"Guillain-Barré syndrome",
"alpha-Gal syndrome"
],
"content": "Introduction\n\nThe gene coding for α-1,3-galactosyltransferase (α1,3GT) was inactivated in old-world monkeys, an evolutionary adaptation that resulted in the production of high antibody titers against glycan Galα1-3Galβ1-(3)4GlcNAc-R (α-Gal) (Galili, 2015). Previous results showed that up to 1–5% of the circulating IgM/IgG found in healthy individuals are directed against α-Gal (Macher & Galili, 2008). Bacteria in the human gut microbiome express α1,3GT genes to produce α-Gal epitopes (Montassier et al., 2020), suggesting that natural anti-α-Gal antibodies are produced in response to gut microbiota (Bello-Gil et al., 2019; Galili et al., 1988; Mañez et al., 2001; Yilmaz et al., 2014). This evolutionary adaptation has been associated with the protective response of anti-α-Gal IgM/IgG antibodies against pathogens containing this modification on membrane proteins (Galili, 2018; Hodžić et al., 2020). In contrast, the presence of α-Gal in tick salivary glycoproteins and glycolipids (Araujo et al., 2016; Cabezas-Cruz et al., 2018; Chinuki et al., 2016; Crispell et al., 2019) and tick cement (Villar et al., 2020) induces anti-α-Gal IgE antibodies that mediate delayed anaphylaxis to mammalian meat consumption and immediate anaphylaxis to tick bites, xenotransplantation and certain drugs such as cetuximab (Cabezas-Cruz et al., 2019; Commins et al., 2009; Contreras et al., 2020; de la Fuente et al., 2019a; de la Fuente et al., 2020; Fischer et al., 2016; Levin et al., 2019; Mateos-Hernández et al., 2017; Platts-Mills et al., 2020; Steinke et al., 2015; van Nunen et al., 2007).\n\nFactors that may affect the antibody response to α-Gal include but are not limited to age, repeat consumption of certain food and meats of different origin or innards with higher α-Gal content, exposure to tick bites, ABO blood group, co-occurring disorders and exposure to cats and other pets (Cabezas-Cruz et al., 2017; Cabezas-Cruz et al., 2019; Commins, 2016; Commins et al., 2014; de la Fuente et al., 2020a; Fischer et al., 2014; Fischer et al., 2016; Morisset et al., 2012; Platts-Mills et al., 2020; Wölbing et al., 2013). Additionally, the anti-α-Gal-specific IgE response has been associated with other diseases such as atopy, coronary artery disease and atherosclerosis (Gonzalez-Quintela et al., 2014; Wilson et al., 2017; Wilson et al., 2019). Furthermore, α-Gal-mediated innate and adaptive immune response mechanisms have been associated with protection against pathogen infection in various animal models (Hodžić et al., 2020). However, little is known about the influence of anti-α-Gal immune response on immune-mediated disorders such as those occurring in patients with COVID-19 and Guillain-Barré syndrome (GBS).\n\nThese results raise questions and hypothesis regarding the role of α-Gal-mediated immune responses in disease symptomatology and possible protective mechanisms (de la Fuente et al., 2019b; de la Fuente et al., 2020b; Pacheco et al., 2020; Urra et al., 2020). Consequently, to advance in addressing these questions and hypothesis, here we provide data on the IgE/IgM/IgG/IgA anti-α-Gal antibody response in healthy individuals and patients diagnosed with AGS, tick-borne allergies, GBS and COVID-19. These data contribute to correlative analyses of the anti-α-Gal antibody response with factors such as patient and clinical characteristics, record of tick bites, blood group, age and sex. These analyses could provide insights into the role of anti-α-Gal antibody response in disease symptomatology and protection against immune-mediated disorders.\n\n\nMaterials and methods\n\nEssential methods used for the generation of the dataset (de la Fuente et al., 2020) were described in Urra et al. (2020) with additional information in Pacheco et al. (2020) and Doncel-Pérez et al. (2020).\n\nA retrospective case-control study was conducted in patients suffering from COVID-19 admitted to the University General Hospital of Ciudad Real (HGUCR), Spain from March 1 to April 15, 2020. The infection by SARS-CoV-2 was confirmed in all patients included in the study by the real-time reverse transcriptase-polymerase chain reaction (RT-PCR) assay from Abbott Laboratories (Abbott RealTime SARS-COV-2 assay, Abbott Park, Illinois, USA) from upper respiratory tract samples after hospital admission. Clinical features, as well as laboratory determinations were obtained from patient's medical records. The patients were grouped as hospital discharge, hospitalized and intensive care unit (Urra et al., 2020). Patients were hospitalized for developing a moderate-severe clinical condition with radiologically demonstrated pneumonia and failure in blood oxygen saturation. Patients with acute respiratory failure who needed mechanical ventilation support were admitted to a hospital ICU. The patients were discharged from the hospital due to the clinical and radiological improvement of pneumonia caused by the SARS-CoV-2, along with the normalization of analytical parameters indicative of inflammation, such as C-reactive protein (CRP), D-Dimer and blood cell count (Urra et al., 2020). Samples from asymptomatic COVID-19 cases with positive anti-SARS-CoV-2 IgG antibody titers but negative by RT-PCR were collected in May 22–29, 2020 and included in the dataset (Urra et al., 2020). Samples from healthy individuals (individuals without record of tick bites and allergic reactions) and patients diagnosed with tick-borne allergic reactions (AGS, anaphylaxis or urticaria) were collected prior to COVID-19 pandemic in April 2019 (Pacheco et al., 2020). The use of human peripheral blood serum samples from healthy individuals and patients diagnosed with tick-borne allergic reactions was done with their written informed consent in compliance with the Helsinki Declaration. Nursing personnel at the General University Hospital of Ciudad Real, Spain, extracted blood samples. Samples and data from patients with GBS included in this dataset were provided by the BioB-HVS, integrated into the Spanish National Biobanks Network. All samples were processed following standard operating procedures with the appropriate approval of the Ethical and Scientific Committees (Toledo Hospitable Complex 29012014-No17, University Hospital of Ciudad Real C-352 and SESCAM C-73).\n\nFor the preparation of serum samples, a sterile tube without anticoagulant was used to collect blood samples. The blood from each patient and the healthy individual was maintained in standing position at room temperature (RT) for clotting (20–30 min) and centrifuged at 1,500 × g for 20 min at RT. Serum was collected and conserved at -20°C until used for analysis.\n\nFor ELISA, high absorption capacity polystyrene microtiter plates were coated with 50 ng of BSA coated with α-Gal (BSA-α-Gal, thereafter named α-Gal; Dextra, Shinfield, UK) per well in carbonate-bicarbonate buffer (Sigma-Aldrich, St. Louis, MO, USA). After an overnight incubation at 4°C, coated plates were washed one time with 100 µl/well PBS with 0.05% Tween 20 (PBST) (Sigma-Aldrich), blocked with 100 µl/well of 1% human serum albumin (HAS) in PBST (Sigma-Aldrich) for 1 h at RT and then washed four times with 100 µl/well of PBST. Human serum samples were diluted 1:100 in PBST with 1% HAS and 100 µl/well were added into the wells of the antigen-coated plates and incubated for 1 h at 37°C. Plates were washed four times with PBST and 100 µl/well of goat anti-human immunoglobulins-peroxidase IgG (FC specific) (Cat. No. I2136), IgM (µ-chain specific) (Cat. No. I1636), and IgE (ɛ-chain specific) (Cat. No. I6284) secondary antibodies (Sigma-Aldrich) diluted 1:1000, v/v in blocking solution were added and incubated for 1 h at RT. Plates were washed four times with 100 µl/well of PBST and 100 µl/well of 3,3,´5,5-tetramethylbenzidine TMB (Promega, Madison, WI, USA) were added and incubated for 20 min at RT. Finally, the reaction was stopped with 50 µl/well of 2 N H2SO4 and the O.D. was measured in a spectrophotometer at 450 nm. The average of two technical replicates per sample was used for analysis after background (coated wells incubated with PBS and secondary antibodies) subtraction.\n\nAnti-α-Gal IgE, IgM and IgG antibody titers (O.D. at 450 nm values) were compared for each Ig by one-way ANOVA test (p < 0.05) (https://www.socscistatistics.com/tests/anova/default2.aspx) (Figure 1A and 1C). A Spearman Rho correlation analysis (p < 0.01; https://www.socscistatistics.com/tests/spearman/default2.aspx) was conducted between anti-α-Gal IgE, IgM and IgG antibody titers and age (Figure 1B).\n\nThe dataset (de la Fuente et al., 2020) was validated in studies reported by Urra et al. (2020), Pacheco et al. (2020) and Doncel-Pérez et al. (2020). Additionally, a comparative analysis was conducted between the IgE+IgM+IgG antibody response to α-Gal and blood groups (Figure 1A), age (Figure 1B) and sex (Figure 1C) in healthy individuals (n = 75) to illustrate lower antibody titers in blood group B/AB individuals as previously reported (Cabezas-Cruz et al., 2017) but no differences regarding age and sex, which have been reported before as factors affecting the antibody response to α-Gal, infection and vaccination (Buonomano et al., 1999; Giefing-Kröll et al., 2015; Wang et al., 1995).\n\nThe main limitation of the dataset is sample size for some factors (i.e. age, sex or blood group), which were not disclosed by all individuals, and anti-α-Gal IgA antibody titers that could be considered in the analysis (Mateos-Hernández et al., 2020; Urra et al., 2020).\n\nAn example of the effect of certain factors such as (A) blood group, (B) age and (C) sex on the antibody response to α-Gal in healthy individuals. Anti-α-Gal IgE, IgM and IgG antibody titers were determined by ELISA. (A, C) The ELISA O.D. at 450 nm values were compared for each Ig by one-way ANOVA test (p < 0.05). (B) A Spearman Rho correlation analysis (p < 0.01) was conducted between anti-α-Gal IgE, IgM and IgG antibody titers and age. Correlation coefficient (R2) is shown.\n\n\nData availability\n\nHarvard Dataverse: A dataset for the analysis of antibody response to glycan alpha-Gal in individuals with immune-mediated disorders. https://doi.org/10.7910/DVN/RBU2VR (de la Fuente et al., 2020).\n\nThis dataset contains characteristics and serum antibody levels of the individuals included in the study and was used in analyses reported in publications by Urra et al. (2020), Pacheco et al. (2020) and Doncel-Pérez et al. (2020).\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\nWe want to particularly acknowledge the patients, healthy volunteers and the Guillain-Barré Syndrome Collection (TOSGB) from BioB-HVS integrated into the Spanish National Biobanks Network for their collaboration in this study. We thank members of our laboratories for fruitful discussions and Almudena González García (IREC, Spain) for technical assistance. We acknowledge UCLM, Spain support to Group SaBio.\n\n\nReferences\n\nAraujo RN, Franco PF, Rodrigues H, et al.: Amblyomma sculptum tick saliva: α-Gal identification, antibody response and possible association with red meat allergy in Brazil. Int J Parasitol. 2016; 46(3): 213–220. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBello-Gil D, Audebert C, Olivera-Ardid S, et al.: The Formation of Glycan-Specific Natural Antibodies Repertoire in GalT-KO Mice Is Determined by Gut Microbiota. Front Immunol. 2019; 10: 342. 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Aging Cell. 2015; 14(3): 309–321. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHodžić A, Mateos-Hernández L, de la Fuente J, et al.: α-Gal-Based Vaccines: Advances, Opportunities, and Perspectives. Trends Parasitol. 2020; 36(12): 992–1001. PubMed Abstract | Publisher Full Text\n\nLevin M, Apostolovic D, Biedermann T, et al.: Galactose α-1,3-galactose phenotypes: Lessons from various patient populations. Ann Allergy Asthma Immunol. 2019; 122(6): 598–602. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMacher BA, Galili U: The Galalpha1,3Galbeta1,4GlcNAc-R (alpha-Gal) epitope: a carbohydrate of unique evolution and clinical relevance. Biochim Biophys Acta. 2008; 1780(2): 75–88. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMañez R, Blanco FJ, Díaz I, et al.: Removal of bowel aerobic gram-negative bacteria is more effective than immunosuppression with cyclophosphamide and steroids to decrease natural alpha-galactosyl IgG antibodies. Xenotransplantation. 2001; 8(1): 15–23. PubMed Abstract | Publisher Full Text\n\nMateos-Hernández L, Villar M, Moral A, et al.: Tick-host conflict: immunoglobulin E antibodies to tick proteins in patients with anaphylaxis to tick bite. Oncotarget. 2017; 8(13): 20630–20644. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMateos-Hernández L, Risco-Castillo V, Torres-Maravilla E, et al.: Gut Microbiota Abrogates Anti-α-Gal IgA Response in Lungs and Protects against Experimental Aspergillus Infection in Poultry. Vaccines (Basel). 2020; 8(2): 285. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMontassier E, Al-Ghalith GA, Mathé C, et al.: Distribution of Bacterial α1,3-Galactosyltransferase Genes in the Human Gut Microbiome. Front Immunol. 2020; 10: 3000. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMorisset M, Richard C, Astier C, et al.: Anaphylaxis to pork kidney is related to IgE antibodies specific for galactose-alpha-1,3-galactose. Allergy. 2012; 67(5): 699–704. PubMed Abstract | Publisher Full Text\n\nPacheco I, Fernández de Mera IG, Feo Brito F, et al.: Characterization of the anti-α-Gal antibody profile in association with Guillain-Barré syndrome, implications for tick-related allergic reactions.. Ticks and Tick-Borne Diseases, submitted. 2020.\n\nPlatts-Mills TAE, Commins SP, Biedermann T, et al.: On the cause and consequences of IgE to galactose-α-1,3-galactose: A report from the National Institute of Allergy and Infectious Diseases Workshop on Understanding IgE-Mediated Mammalian Meat Allergy. J Allergy Clin Immunol. 2020; 145(4): 1061–1071. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSteinke JW, Platts-Mills TAE, Commins SP: The alpha-gal story: lessons learned from connecting the dots. J Allergy Clin Immunol. 2015; 135(3): 589–596; quiz 597. 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PubMed Abstract | Publisher Full Text\n\nWilson JM, Schuyler AJ, Schroeder N, et al.: Galactose-α-1,3-Galactose: Atypical Food Allergen or Model IgE Hypersensitivity? Curr Allergy Asthma Rep. 2017; 17(1): 8. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWilson JM, McNamara CA, Platts-Mills TAE: IgE, α-Gal and atherosclerosis. Aging (Albany NY). 2019; 11(7): 1900–1902. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWölbing F, Fischer J, Koberle M, et al.: About the role and underlying mechanisms of cofactors in anaphylaxis. Allergy. 2013; 68(9): 1085–1092. PubMed Abstract | Publisher Full Text\n\nYilmaz B, Portugal S, Tran TM, et al.: Gut microbiota elicits a protective immune response against malaria transmission. Cell. 2014; 159(6): 1277–1289. PubMed Abstract | Publisher Full Text | Free Full Text"
}
|
[
{
"id": "75352",
"date": "04 Dec 2020",
"name": "Jacques Le Pendu",
"expertise": [
"Reviewer Expertise Glycobiology",
"Host-pathogens interactions",
"histo-blood group antigens"
],
"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 data note presents a dataset of levels of anti-alphaGal IgM, IgG and IgE in the serum of healthy individuals and of patients, including COVID-19 patients, patients with tick bites and Guillain Barré syndrome patients. The rationale and methods are clearly presented and the dataset is given in an easily accessible and convenient format.\nI would only like to see a clarification concerning the exact alphaGal-BSA antigen that was used for coating. The structure of the oligosaccharide should be given.\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": "6171",
"date": "11 Dec 2020",
"name": "Jose de la Fuente",
"role": "Author Response",
"response": "Thanks for your positive feedback to our paper. In response to your question, the alphaGal-BSA antigen used for coating the ELISA plates was Galα1-3Gal-BSA (3 atom spacer) (Product Code: NGP0203; https://www.dextrauk.com/products/neoglycoproteins/gala1-3gal-series-neoglycoproteins/product/288-gala1-3gal-bsa-3-atom-spacer)."
}
]
},
{
"id": "84326",
"date": "18 May 2021",
"name": "Tilo Biedermann",
"expertise": [
"Reviewer Expertise Immunology",
"Allergy",
"Dermatology."
],
"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 data note presented by José de la Fuente and colleagues contains α-Gal specific antibody titers of IgE, IgM, IgG isotypes in the serum and, for some individuals, IgA isotype in saliva of healthy individuals as well as patients with tick bite-associated symptoms, Guillain-Barré syndrome and COVID-19 infection, respectively. The dataset was already used in a published study by the authors correlating α-Gal specific antibodies and COVID-19 disease symptoms (Urra et al. 2020,1). Although the dataset is given in an easily accessible format (Excel sheet) and methods are adequately described, I have some major concerns in regard to the benefit of the data for other research applications which are listed below.\nThe authors validate their dataset using comparative analysis of antibody titers of healthy individuals with blood group, age and sex. What is the rational to use a summation of α-Gal IgG, IgM and IgE antibody levels for these analyses? Since different antibody isotypes are associated with certain immunological functions (effector functions mediated by Fc part of the antibody) and certain diseases are associated with certain antibody isotypes (e.g. AGS and α-Gal IgE), a summation of different antibody isotype levels is in my opinion not correct and does not provide meaningful scientific insights. Additionally, since the entries for the key characteristics are incomplete for a large proportion of the individuals included, the used comparative analysis is not generally applicable for the presented dataset and thus not appropriate for its validation.\n\nThe OD450 values and thus the titers of α-Gal specific IgE are unexpectedly high in almost half of the healthy individuals. Is there an explanation for α-Gal IgE titers in serum of healthy individuals which are as high as in AGS patients or individuals with tick-bite associated allergic reactions? Can these individuals for certain be classified as “healthy” or how can sensitization to α-Gal be explained (atopy)? In my opinion, the ELISA data presented in this manuscript requires validation due to the unexpected and controversial high titers of α-Gal specific IgE antibodies in “healthy” individuals e.g. by using α-Gal ImmunoCAP or the commercially available α-Gal IgE ELISA Kit.\n\nAs also stated by the authors as main limitation of their dataset, key characteristics such as age, sex and blood group are missing for a large proportion of the entries. This incompleteness significantly limits the benefit of the dataset for other research questions.\n\nIs the rationale for creating the dataset(s) clearly described? Yes\n\nAre the protocols appropriate and is the work technically sound? No\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": "6689",
"date": "19 May 2021",
"name": "Jose de la Fuente",
"role": "Author Response",
"response": "Thanks for your comments to our paper. In response to your comments: The data note presented by José de la Fuente and colleagues contains α-Gal specific antibody titers of IgE, IgM, IgG isotypes in the serum and, for some individuals, IgA isotype in saliva of healthy individuals as well as patients with tick bite-associated symptoms, Guillain-Barré syndrome and COVID-19 infection, respectively. The dataset was already used in a published study by the authors correlating α-Gal specific antibodies and COVID-19 disease symptoms (Urra et al. 2020,1). Although the dataset is given in an easily accessible format (Excel sheet) and methods are adequately described, I have some major concerns in regard to the benefit of the data for other research applications which are listed below. 1. The authors validate their dataset using comparative analysis of antibody titers of healthy individuals with blood group, age and sex. What is the rational to use a summation of α-Gal IgG, IgM and IgE antibody levels for these analyses? Since different antibody isotypes are associated with certain immunological functions (effector functions mediated by Fc part of the antibody) and certain diseases are associated with certain antibody isotypes (e.g. AGS and α-Gal IgE), a summation of different antibody isotype levels is in my opinion not correct and does not provide meaningful scientific insights. Additionally, since the entries for the key characteristics are incomplete for a large proportion of the individuals included, the used comparative analysis is not generally applicable for the presented dataset and thus not appropriate for its validation. Response: We agree with reviewer on the differences between antibody isotypes as disclosed in the Introduction of the paper. However, Figure 1 is only an example to illustrate the effect of some factors such as blood group, age and sex on the total antibody response to α-Gal. This is why total antibody titers for subtypes IgE, IgM and IgG were added to illustrate these correlations or the absence of it. In no case we are using these data for validation or immunologically related analyses. For this purpose, please refer to these papers published using this dataset and with analyses using different antibody isotypes: Urra JM, Ferreras-Colino E, Contreras M, Cabrera CM, Fernández de Mera IG, Villar M, Cabezas-Cruz A, Gortázar C, de la Fuente J. The antibody response to the glycan α-Gal correlates with COVID-19 disease symptoms. J Med Virol. 2021 Apr;93(4):2065-2075. doi: 10.1002/jmv.26575. Hodžić A, de la Fuente J, Cabezas-Cruz A. COVID-19 in the Developing World: Is the Immune Response to α-Gal an Overlooked Factor Mitigating the Severity of Infection? ACS Infect Dis. 2020 Dec 11;6(12):3104-3108. doi: 10.1021/acsinfecdis.0c00747. Doncel-Pérez, E., Contreras, M., Gómez Hernando, C., Vargas Baquero, E., Blanco García, J., Rodríguez Gómez, J., Velayos Galán, A., Cabezas-Cruz, A., Gortázar, C., de la Fuente, J. 2020. What is the impact of the antibody response to glycan alpha-Gal in Guillain-Barré syndrome associated with SARS-CoV-2 infection? Merit Research Journal of Medicine and Medical Sciences (MRJMMS) 8: 730-737. https://digital.csic.es/bitstream/10261/230769/1/whatinfect.pdf Pacheco I, Fernández de Mera IG, Feo Brito F, Gómez Torrijos E, Villar M, Contreras M, Lima-Barbero JF, Doncel-Pérez E, Cabezas-Cruz A, Gortázar C, de la Fuente J. Characterization of the anti-α-Gal antibody profile in association with Guillain-Barré syndrome, implications for tick-related allergic reactions. Ticks Tick Borne Dis. 2021 May;12(3):101651. doi: 10.1016/j.ttbdis.2021.101651. 2. The OD450 values and thus the titers of α-Gal specific IgE are unexpectedly high in almost half of the healthy individuals. Is there an explanation for α-Gal IgE titers in serum of healthy individuals which are as high as in AGS patients or individuals with tick-bite associated allergic reactions? Can these individuals for certain be classified as “healthy” or how can sensitization to α-Gal be explained (atopy)? In my opinion, the ELISA data presented in this manuscript requires validation due to the unexpected and controversial high titers of α-Gal specific IgE antibodies in “healthy” individuals e.g. by using α-Gal ImmunoCAP or the commercially available α-Gal IgE ELISA Kit. Response: This is an interesting observation that has been reported in other studies. However, factors such as tick bites or allergy do correlate with higher IgE antibody titers (see figure 2 in Pacheco et al. Ticks Tick Borne Dis. 2021 May;12(3):101651. doi: 10.1016/j.ttbdis.2021.101651). For the validation of the ELISA with ImmunoCAP please see Supplementary Figure A1 in this paper by Pacheco et al. with correlation analysis between different allergy-type reactions to tick bites and anti-α-Gal IgE antibody response using a Spearman Rho (rs) correlation analysis (p < 0.01) conducted between allergy-type reactions and anti-α-Gal IgE antibody titers determined by ELISA (O.D. at 450 nm) and converted to kU/l. Positive anti-α-Gal IgE levels were considered at cut-off value of 0.35 kU/l. Due to scope of Data note papers, we cannot disclose all this information in the paper, but can be referred to in the revised paper. 3. As also stated by the authors as main limitation of their dataset, key characteristics such as age, sex and blood group are missing for a large proportion of the entries. This incompleteness significantly limits the benefit of the dataset for other research questions. Response: We acknowledge these limitations of the dataset that are due to ethic issues in some of the studies. Nevertheless, we consider that this information is useful for the scientific and medical community interested in the study of the antibody response to α-Gal."
}
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}
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https://f1000research.com/articles/9-1366
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https://f1000research.com/articles/10-418/v1
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25 May 21
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{
"type": "Research Article",
"title": "Bibliographic analysis of Clinacanthus nutans papers in Scopus database (2000–2019)",
"authors": [
"Yun Jin Kim",
"Linchao Qian",
"Muhammad Shahzad Aslam",
"Yun Jin Kim",
"Linchao Qian"
],
"abstract": "Background: There has been an increasing trend in Clinacanthus nutans’ research, an important medicinal herb of Malaysia and Thailand, well known as an anti-viral, anti-cancer, and insect bite treatment. This study examines the trend in Clinacanthus nutans’ research from 2000 to 2019 and compares the contribution of research on this topic from different institutions and authors. Methods: Publications from the Scopus database were retrieved using keywords and identify top ten institutions/universities, list of prominent authors, top ten journals that published research, top five influential articles, top fifty cited papers, and global distribution of publications on Clinacanthus nutans. Microsoft Excel 2016, Wordcloud, SPSS version 26, and GunnMap 2 were used to analyse indicators. A total of 167 articles were identified from the Scopus database. All research publications were screened initially. Five articles (n=5) were removed due to the unavailability of the full-text version of the article. 162 articles were included in the final study. Results: Universiti Putra Malaysia and the Journal of Ethnopharmacology published the highest number of articles on Clinacanthus nutans. Herpes, antioxidant, phenolic, flavonoids, cancer, antimicrobial were common keywords identified using a word cloud. Over the past 20 years, the literature on Clinacanthus nutans has continuously grown, with the rate increasing after 2012. Conclusion: The prominent research on Clinacanthus nutans was based upon their identified and isolated bioactive constituents, and there is a need for more research on clinical trials.",
"keywords": [
"Clinacanthus nutans",
"Bibiolgraphic analysis",
"Scopus"
],
"content": "Abbreviations\n\nCRO: Clinical Research Organisations\n\nNKEA: National Key Economic Areas Research Grant Scheme\n\nFRGS: Fundamental Research Grant Scheme\n\nNRGS: Niche Research Grant Scheme\n\nRAGS: Research Acculturation Grant Scheme\n\nFRIM: Forest Research Institute of Malaysia\n\nMIS: Malaysian International Scholarship\n\nNSFC: National Natural Scientific Foundation of China\n\nNAFOSTED: Vietnam National Foundation for Science and Technology Development\n\nTCM: Traditional Chinese Medicine\n\n\nBackground\n\nMedicinal plants are a source of natural, semi-synthetic, or synthetic analogues with pharmacological potential and development of new therapeutic leads.1 Their potentially curative properties' chemical source is the secondary metabolites of medicinal plants.2 Traditional Chinese medicine (TCM) remedies have been used in China for centuries and often remain “different” from present Western medicine (WM), as they are still now primarily herbal mixtures.3 There is an increasing trend in identifying and isolating bioactive compounds in the poly-mixture of TCM. For example, pericarpium citri reticulatae (Rutaceae), commonly called chen pi in Chinese, as a regulating qi drug, is most frequently used in several Chinese medicine prescriptions.4\n\nClinacanthus nutans (Burm. f) Lindau (Acanthaceae) is indigenous to Southeast Asia.5 It is commonly known as Belalai Gajah (Malay) and Phaya Yo (Thai). Clinacanthus nutans used in different therapies, such as for skin rashes, snake bites, lesions caused by herpes simplex virus, diabetic myelitis, and fever.6 It is a good source of many flavonoids and phenolics.7 Several in vivo and in vitro pharmacological activities have reported. The most promising activities consist of anti-inflammatory,8 antioxidant, anti-tumour,9 anti-viral10 and antibacterial11 activities.\n\nBibliometric analyses have used previously to study the measures of quality and impact of research performed in pharmacovigilance,12 bioactive chemical constituents,13 and health-related issues such as burns,14 pressure ulcer,15 mesothelioma,16 colorectal cancer.17 It has also used to understand the impact of an important research topic. For example, Nano-medicine is one of the emerging issues in the treatment of cancer, and a bibliometric analysis was performed to understand the global trends in this field.18 The selection of the current topic is based upon the medicinal importance of Clinacanthus nutans in South East Asia.\n\nMany research articles (i.e., phytochemical, pre-clinical, in-vitro studies) published recently on Clinacanthus nutans were funded by the Ministry of Education Malaysia (MOE) under the National Key Economic Areas Research Grant Scheme (NKEA),19 the Fundamental Research Grant Scheme (FRGS),9,20 the Niche Research Grant Scheme (NRGS),21 and the Research Acculturation Grant Scheme (RAGS).22 The research funded by universities' internal grants, the natural Products Division, Forest Research Institute of Malaysia (FRIM).23 The student in Malaysia is also encouraged to study this medicinal herb under MyBRAIN24 and Malaysian International Scholarship (MIS).25 The study on the selected plant funded by other countries such as National Natural Scientific Foundation of China (NSFC),26 Vietnam National Foundation for Science and Technology Development (NAFOSTED),27 National Research Council Thailand,28 Thailand Research Fund29 and Higher Education Commission Thailand.10\n\nThis study investigated trends in Clinacanthus nutans research in recent years using the Scopus database. The researcher analysed publication outcomes from the last 20 years (2000–2019). This first attempt to use bibliographic to analyse Clinacanthus nutans-related publications aims to understand better global trends in research of one of the most well-known medicinal herb of Southeast Asia.\n\n\nMethods\n\nClinacanthus nutans was used as a keyword to search inside the Scopus database. The data collection strictly follows the Scopus database and relevant articles indexed during the given time. Other databases, such as PubMed or Web of Science, are not part of the current study. In this study, the search terms were as follows: TITLE-ABS-KEY (clinacanthus AND nutans) AND PUBYEAR > 1999 AND PUBYEAR < 2020. A flow diagram of selected articles on Clinacanthus nutans is shown in Figure 1.\n\nThe data were downloaded from the Scopus database and imported manually into Microsoft Excel 2016 (RRID:SCR_016137); Google Sheets (RRID:SCR_017679) is an open access alternative. KYJ and QLC verified the data entry and collection. The entered data consist of articles, the first author, co-authors, h-index of the first and corresponding author from Scopus. The number of Scopus citation of selected articles were part of data collection. Other data consist of the name of journal/conference, journal ranking according to Scopus (CiteScore), date of publication according to the journal website, year of paper according to Scopus, data of submission of an article, date of acceptance, number of universities/organisation contributed to that publication, name of universities/organisation contributed to that publication, journal impact factor (CiteScore) taken from Scopus, type of article, most vital topic/category, subject area, keywords, list of the significant issue addressed, number of countries, location of authors, number of pages, number of references, number of figures, number of tables, an affiliation of the corresponding author, the association of the first author, funding and department/institution/faculty.\n\nIBM SPSS Statistics 26 (RRID:SCR_019096; JASP (RRID:SCR_015823) is an open source alternative) and Microsoft Office Excel 2016 (Microsoft Corporation, Santa Rosa, California, USA) was used to analyse the characteristics of the publications. Wordclouds.com (Zygomatic, Netherlands) has been used to create a cloud of keywords. GunnMap 2 was used to create a custom world map to depict the distribution of global publications on Clinacanthus nutans.\n\n\nResults\n\nUniversiti Putra Malaysia contained the maximum number of record (n = 38), followed by University Sains Malaysia (n = 18). Table 1 shows the top 10 institutions/universities that published their research on Clinacanthus nutans.\n\nKhatib, A., from the International Islamic University Malaysia was found to be the most prominent researcher to contribute to Clinacanthus nutans (n = 11). Abas, F., was the top female researcher that contributes from Universiti Putra Malaysia, Serdang, Malaysia, on Clinacanthus nutans (n = 10). A list of the most prominent authors in studying Clinacanthus nutans is shown in Table 2.\n\nThe Journal of Ethnopharmacology (ISSN 0378-8741) has published the highest number of records on Clinacanthus nutans (n = 9), whereas BMC Complementary and Alternative Medicine (ISSN 1472-6882) were second to published (n = 8). The CiteScore (2018) of the Journal of Ethnopharmacology (3.68) was also highest among the other competing journals on this medicinal plant. Table 3 shows the top 10 journals publishing research on Clinacanthus nutans.\n\nThe authorship heat map shows some interesting facts. The number of authors has increased with time. There were few authors one of a paper in the initial years, but with time, the number of authors has increased to more than seven. This could be due to an increase in research on these medicinal herbs and increasing cross-collaboration among different institutions due to the rise in funding availability and utilisation of various resources from different universities (Figure 2).\n\nThe top influential articles published on Clinacanthus nutans are based upon bioactive constituents,30,31 anti-inflammatory property,29 anti-cancer, and antioxidant potential of the plant32 (Table 4).\n\nAnalysis of the keywords of articles published between 2000 and 2019 identified some significant interests, such as “anti-inflammatory”, “anti-cancer”, “antioxidants”, “antibacterial”, “flavonoids”, “phenolic”, “apoptosis”, and “traditional medicine”. Figure 3 illustrates the word cloud developed from the website.\n\nThe top fifty most cited papers, as of February 27, 2020, on Clinacanthus nutans were identified and are shown in Table 5.\n\nThere is an increasing trend in the number of the published article since 2012. There was a high number of citations and a low number of an articles published in 2005. This year is considered the period of initiation of research on these medicinal plants. Bioactive compounds were identified, giving a pathway to carry out further study (Figure 4).\n\nMalaysia was ranked as number one in producing papers on Clinacanthus nutans, followed by Thailand and then China. Figure 5 illustrates the global distribution of publication on Clinacanthus nutans.\n\n\nDiscussion\n\nClinacanthus nutans is one of the highly researched medicinal plants in recent years in Malaysia and Thailand. The bibliographic analysis helps to show the past trends on related topics, current research progress to identify the top researcher, institutions, and help find similar funding. Several articles published on bibliographic analysis in health-related fields.33,34 There is limited literature available on the bibliographic analysis of medicinal plants. The research identifies many phytochemical and pre-clinical studies on Clinacanthus nutans. Current research is more focused on toxicity studies35-37 before preparing for clinical trials to evaluate its health benefits on humans. Although there is an increasing trend in pre-clinical studies on Clinacanthus nutans, there is a lack of protocols or research to conduct the clinical trial. The only available registered clinical trial when search through clinicaltrials.gov had the title “prevention of mucositis in patients with head and neck cancer treated with radiotherapy”,38 which completed in March 2018. The research also identified an increasing trend in research collaboration in recent years, which could be a positive direction for developing a new drug analogue or a multi-herb combination.\n\n\nConclusion\n\nClinacanthus nutans is one of the future potentially important herbs of Southeast Asia. Malaysia and Thailand were the most significant contributors to studies on the medicinal properties or therapeutic potential. Clinical research organisations could increase research collaboration with academia to reduce the literary gap, provide financial support, especially during a pandemic such as COVID-19; fasten the process of clinical trial and growing commercialisation of medicinal herbs, especially for herbal economies such as Malaysia and Thailand.\n\n\nEthics declarations\n\nThis study was secondary analysis based on previous published studies. Ethics approval and consent to participate is not applicable.\n\n\nConsent for publication\n\nNot applicable.\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\nContributors\n\nAll authors participated in the study conception and design. MSA performed the bibliographic analysis. KYJ and QLC interpreted the data, drafted and critically revised the manuscript and approved the final version to be published. All authors had full access to all the data and took responsibility for the data integrity and data analysis accuracy.",
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J Supercrit Fluids. 2016 Oct; 116: 251–63. Publisher Full Text Reference Source\n\nUawonggul N, Chaveerach A, Thammasirirak S, et al.: Screening of plants acting against Heterometrus laoticus scorpion venom activity on fibroblast cell lysis. J Ethnopharmacol. 2006 Jan; 103(2): 201–7. PubMed Abstract | Publisher Full Text Reference Source\n\nVachirayonstien T, Promkhatkaew D, Bunjob M, et al.: Molecular evaluation of extracellular activity of medicinal herb Clinacanthus nutans against herpes simplex virus type-2. Nat Prod Res. 2010 Feb 15; 24(3): 236–45. PubMed Abstract | Publisher Full Text Reference Source\n\nChomnawang MT, Trinapakul C, Gritsanapan W: In vitro antigonococcal activity of Coscinium fenestratum stem extract. J Ethnopharmacol. 2009 Apr; 122(3): 445–9. PubMed Abstract | Publisher Full Text Reference Source\n\nThongrakard V, Tencomnao T: Modulatory effects of Thai medicinal plant extract on proinflammatory cytokines-induced apoptosis in human keratinocyte HaCat cells. African J Biotechnol. 2010; 9(31): 4999–5003.\n\nChing SM, Zakaria ZA, Paimin F, et al.: Complementary alternative medicine use among patients with type 2 diabetes mellitus in the primary care setting: a cross-sectional study in Malaysia. BMC Complement Altern Med. 2013 Dec 26; 13(1): 148. PubMed Abstract | Publisher Full Text | Free Full Text Reference Source\n\nTsai H-D, Wu J-S, Kao M-H, et al.: Clinacanthus nutans Protects Cortical Neurons Against Hypoxia-Induced Toxicity by Downregulating HDAC1/6. NeuroMolecular Med. 2016 Sep 10; 18(3): 274–82. PubMed Abstract | Publisher Full Text Reference Source\n\nAlam A, Ferdosh S, Ghafoor K, et al.: Clinacanthus nutans: A review of the medicinal uses, pharmacology and phytochemistry. Asian Pac J Trop Med. 2016 Apr; 9(4): 402–9. PubMed Abstract | Publisher Full Text Reference Source\n\nTeoh PL, Cheng AYF, Liau M, et al.: Chemical composition and cytotoxic properties of Clinacanthus nutans root extracts. Pharm Biol. 2017 Jan 8; 55(1): 394–401. PubMed Abstract | Publisher Full Text | Free Full Text Reference Source\n\nCheeptham N, Towers GHN: Light-mediated activities of some Thai medicinal plant teas. Fitoterapia. 2002 Dec; 73(7–8): 651–62. PubMed Abstract | Publisher Full Text Reference Source\n\nYam MF, Ch’ng YS, Tan CS, et al.: Vasorelaxation Study and Tri-Step Infrared Spectroscopy Analysis of Malaysian Local Herbs. J Pharmacopuncture. 2016 Jun 30; 19(2): 145–54. PubMed Abstract | Publisher Full Text | Free Full Text Reference Source\n\nRaya KB, Ahmad SH, Farhana SF, et al.: Changes in phytochemical contents in different parts of Clinacanthus nutans (Burm. f.) lindau due to storage duration. Bragantia. 2015 Aug 21; 74(4): 445–52. Publisher Full Text Reference Source\n\nArullappan S, Rajamanickam P, Thevar N, et al.: In Vitro Screening of Cytotoxic, Antimicrobial and Antioxidant Activities of Clinacanthus nutans (Acanthaceae) leaf extracts. Trop J Pharm Res. 2014 Oct 10; 13(9): 1455. Publisher Full Text http://www.ajol.info/index.php/tjpr/article/view/108729\n\nSarega N, Imam MU, Ooi D-J, et al.: Phenolic Rich Extract from Clinacanthus nutans Attenuates Hyperlipidemia-Associated Oxidative Stress in Rats. Oxid Med Cell Longev. 2016; 2016: 1–16. PubMed Abstract | Publisher Full Text | Free Full Text Reference Source\n\nMustapa AN, Martin Á, Mato RB, et al.: Extraction of phytocompounds from the medicinal plant Clinacanthus nutans Lindau by microwave-assisted extraction and supercritical carbon dioxide extraction. Ind Crops Prod. 2015 Nov; 74: 83–94. Publisher Full Text Reference Source\n\nPongmuangmul S, Phumiamorn S, Sanguansermsri P, et al.: Anti-herpes simplex virus activities of monogalactosyl diglyceride and digalactosyl diglyceride from Clinacanthus nutans, a traditional Thai herbal medicine. Asian Pac J Trop Biomed. 2016 Mar; 6(3): 192–7. Publisher Full Text Reference Source\n\nJanwitayanuchit W, Suwanborirux K, Patarapanich C, et al.: Synthesis and anti-herpes simplex viral activity of monoglycosyl diglycerides. Phytochemistry. 2003 Dec; 64(7): 1253–64. PubMed Abstract | Publisher Full Text Reference Source\n\nLe C-F, Kailaivasan TH, Chow S-C, et al.: Phytosterols isolated from Clinacanthus nutans induce immunosuppressive activity in murine cells. Int Immunopharmacol. 2017 Mar; 44: 203–10. PubMed Abstract | Publisher Full Text Reference Source\n\nSiew Y-Y, Zareisedehizadeh S, Seetoh W-G, et al.: Ethnobotanical survey of usage of fresh medicinal plants in Singapore. J Ethnopharmacol. 2014 Sep; 155(3): 1450–66. PubMed Abstract | Publisher Full Text\n\nFazil FNM, Azzimi NSM, Yahaya BH, et al.: Kinetics Extraction Modelling and Antiproliferative Activity of Clinacanthus nutans Water Extract. Sci World J. 2016; 2016: 1–7. PubMed Abstract | Publisher Full Text | Free Full Text Reference Source\n\nGhasemzadeh A, Nasiri A, Jaafar H, et al.: Changes in Phytochemical Synthesis, Chalcone Synthase Activity and Pharmaceutical Qualities of Sabah Snake Grass (Clinacanthus nutans L.) in Relation to Plant Age. Molecules. 2014 Oct 30; 19(11): 17632–48. PubMed Abstract | Publisher Full Text | Free Full Text Reference Source\n\nNarayanaswamy R, Isha A, Wai L, et al.: Molecular docking analysis of selected Clinacanthus nutans constituents as xanthine oxidase, nitric oxide synthase, human neutrophil elastase, matrix metalloproteinase 2, matrix metalloproteinase 9 and squalene synthase inhibitors. Pharmacogn Mag. 2016; 12(45): 21. PubMed Abstract | Publisher Full Text | Free Full Text Reference Source\n\nChotchoungchatchai S, Saralamp P, Jenjittikul T, et al.: Medicinal plants used with Thai Traditional Medicine in modern healthcare services: A case study in Kabchoeng Hospital, Surin Province, Thailand. J Ethnopharmacol. 2012 May; 141(1): 193–205. PubMed Abstract | Publisher Full Text\n\nYahaya R, Dash GK, Abdullah MS, et al.: Clinacanthus nutans (burm. F.) Lindau: An useful medicinal plant of south-east Asia. Int J Pharmacogn Phytochem Res. 2015; 7(6): 1244–50.\n\nTu S-F, Liu R, Cheng Y-B, et al.: Chemical Constituents and Bioactivities of Clinacanthus nutans Aerial Parts. Molecules. 2014 Dec 5; 19(12): 20382–90. PubMed Abstract | Publisher Full Text | Free Full Text http://www.mdpi.com/1420-3049/19/12/20382\n\nKongkaew C, Chaiyakunapruk N: Efficacy of Clinacanthus nutans extracts in patients with herpes infection: Systematic review and meta-analysis of randomised clinical trials. Complement Ther Med. 2011 Feb; 19(1): 47–53. PubMed Abstract | Publisher Full Text\n\nMustapa AN, Martin A, Gallego JR, et al.: Microwave-assisted extraction of polyphenols from Clinacanthus nutans Lindau medicinal plant: Energy perspective and kinetics modeling. Chem Eng Process Process Intensif. 2015 Nov; 97: 66–74. Publisher Full Text Reference Source\n\nKhoo LW, Mediani A, Zolkeflee NKZ, et al.: Phytochemical diversity of Clinacanthus nutans extracts and their bioactivity correlations elucidated by NMR based metabolomics. Phytochem Lett. 2015 Dec; 14: 123–33. Publisher Full Text Reference Source\n\nHuang D, Guo W, Gao J, et al.: Clinacanthus nutans (Burm. f.) Lindau Ethanol Extract Inhibits Hepatoma in Mice through Upregulation of the Immune Response. Molecules. 2015 Sep 18; 20(9): 17405–28. PubMed Abstract | Publisher Full Text | Free Full Text Reference Source\n\nLusia Barek M, Hasmadi M, Zaleha AZ, et al.: Effect of different drying methods on phytochemicals and antioxidant properties of unfermented and fermented teas from Sabah snake grass (Clinacanthus nutans Lind.) leaves. Int Food Res J. 2015; 22(2): 661–70.\n\nHuang D, Li Y, Cui F, et al.: Purification and characterization of a novel polysaccharide–peptide complex from Clinacanthus nutans Lindau leaves. Carbohydr Polym. 2016 Feb; 137: 701–8. PubMed Abstract | Publisher Full Text Reference Source\n\nChelyn JL, Omar MH, Mohd Yousof NSA, et al.: Analysis of Flavone C -Glycosides in the Leaves of Clinacanthus nutans (Burm. f.) Lindau by HPTLC and HPLC-UV/DAD. Sci World J. 2014; 2014(September 2015): 1–6. Reference Source\n\nWong FC, Yong AL, Ting EPS, et al.: Antioxidant, metal chelating, anti-glucosidase activities and phytochemical analysis of selected tropical medicinal plants. Iran J Pharm Res. 2014; 13(4): 1407–13. PubMed Abstract | Free Full Text\n\nLiew S-Y, Stanbridge EJ, Yusoff K, et al.: Hypoxia affects cellular responses to plant extracts. J Ethnopharmacol. 2012 Nov; 144(2): 453–6. PubMed Abstract | Publisher Full Text Reference Source\n\nShim SY, Aziana I, Khoo BY: Perspective and insight on Clinacanthus nutans Lindau in traditional medicine. Int J Integr Biol. 2013; 14(1): 7–9."
}
|
[
{
"id": "86084",
"date": "02 Jun 2021",
"name": "Aidi Ahmi",
"expertise": [
"Reviewer Expertise Bibliometric 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\nThis paper seems to have the interest to cover a bibliometric analysis of the Clinacanthus nutans over the past 20 years. However, while it has presented a few bibliometric indicators, this paper seems doesn't have a clear direction and objectives. I would suggest the aims of this paper and the research questions clearly being defined in the background section. The authors did specify that they want to analyze the trend but it seems too general.\nI'm not sure if the problem statement is clearly being defined i.e. the reason why this bibliometric analysis is important to be conducted. The literature review on the subject matters also seems not convincing.\nWhy the results of the fundings are presented in the background section?\nMethods\nI'm not sure mentioning the author names in order to do the data entry and verification is proper in this academic paper.\n\nBased on this statement: \"The entered data consist of articles, the first author, co-authors, h-index of the first and corresponding author from Scopus.\" - I'm not sure the data entry still required as most of the data downloaded from Scopus were already completed. I'm not sure if the h-index of the first and corresponding author from Scopus is necessary to be collected while it not being presented in the results. The result presented is just about the top author (in which they can be not just the first or corresponding author). I don't think the h-index of the authors is necessary as well. The h-index of the publications probably more meaningful.\n\nThese statements seem quite confusing: \"journal ranking according to Scopus (CiteScore)\" and \"journal impact factor (CiteScore)\" - I think the definition of CiteScore has been misinterpreted here.\n\nSome of the data collected and mentioned in the information extraction section seem not even been analyzed. So, what for? Some also seem not practical such as the location of authors (?), the association of the first author (?), most vital topic/category (?).\n\nNot sure why IBM SPSS Statistics 26 has been used since there is no complicated statistic has been presented in this paper.\nResults\nAll the results presented are too descriptive. There are no further interpretations or elaborations that worth as part of the contribution of this paper. The so-what question has not properly addressed for each of the results.\n\nWould be good if the analysis can be extended in order to analyze the impact of the paper based on the number of citations and h-index on the publications.\n\nFigure 4 looks quite confusing. What is the difference between yearly output and the number of published articles?\n\nThere is no legend for Figure 5. Not sure what the colours are representing.\nDiscussion\nI am not sure how the results of this paper can really \"help find similar funding\".\n\n\"Several articles published on bibliographic analysis in health-related fields\" - this is the health-related topic, of course, it will be published in this related journal.\n\nThe contribution of this paper seems not convincing enough to justify the indexing of this paper.\nConclusions\nNot sure if the conclusion is really derived from the findings.\n\nHow about the limitations of the study 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? 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?\nNo\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? No",
"responses": []
},
{
"id": "91643",
"date": "09 Sep 2021",
"name": "Samy A Azer",
"expertise": [
"Reviewer Expertise In bibliometrics analysis",
"top-cited articles",
"medical informatics",
"and medical education."
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nBibliographic analysis of Clinacanthus nutans papers in Scopus database (2000–2019) [version 1, not approved]\n\nThank you for asking me to review the above-titled manuscript. The current version is confusing, not carefully written, inaccurate, not well designed and full of bias. I have detailed comments below. If the authors respond to my comments, please kindly submit a point-by-point response letter, addressing each point raised by the reviewers, plus page and line numbers; thank you.\n\nAbstract:\nThe aims do not mention \"bibliometric analysis\"; mentioned in the title.\n\nState a research question.\n\nWhat search words were used? And when the search was carried out?\n\nState inclusion and exclusion criteria (if no space in the abstract, you must state this under methods).\n\nWhy only top 10 and then top 5? As a rule in bibliometric studies, we do not report samples; we assess the whole number of papers identified 162 papers.\n\nResults should show figures - mean ±SD, Median IQR, correlations, factor analysis and p-value. Not numbers or %.\n\nThe statement \"Five papers were removed because not available\" is not clear. If these papers were withdrawn, state this. If they were not available to you, they should be ordered and studied.\n\nThe last 4 lines in methods are part of the results, please move them. We do not know any bibliometric analysis like number of citations, type of article, number of authors, number of countries/institutes, number of grants received etc. Please read other bibliometric studies for reference.\n\nConclusions should be rewritten.\n\nIntroduction:\nWhat triggered this study? Why do we need this study?\n\nProvide more information about Clinacanthus nutans and research and uses.\n\nThe section about funding is redundant. It should be omitted or moved to the discussion. But, I wonder why the authors did not include grant funding in their assessment of the 162 papers as part of their bibliometric assessment? It should be included.\n\nState your research question.\n\nFigure 1:\nThese 5 figures that were not included, if these papers were withdrawn, state this clearly and add their details in a box. Showing names of authors, title, journal and detailed publication, and when was each withdrawn. If not withdrawn, we need we know on what bases were excluded. What was the justification?\nMethods:\nState study design. State why the Web of Science database was not searched instead of Scopus. Give justification.\n\nState the inclusion and exclusion criteria.\n\nState the bibliometric parameters and add grants/funding received.\n\nRead other papers on bibliometric studies published in BMJ and BMJ open and other top journals for reference.\n\nCitations are needed in the methods.\n\nAnalysis should include mean ±SD, Median IQR, correlation, p-value etc.\n\nResults:\nWhy was the JIF not provided?\nTable 1:\nTotal number of records is 128, while the total number of papers as per Figure 1 is 162. Where are the other missing records? Are you just interested in showing certain universities and ignoring others? But another bias is obvious when we look at Figure 5 and the authors showing Canada, the USA, Australia, India, Norway, Saudi Arabia and others involved in Clinacanthus nutans, I understand in these 162 papers. Why the universities and authors from these countries were not even mentioned in the paper or Table 1.\n\nTable 2:\nYou should include all authors who have 2 or more papers, and show the citation number, and in which was the first author or co-author. The authors must read proper papers on this area.\n\nAgain we do not give samples. If you are studying 162 papers. They all must be analysed and they should be listed in the list of references to see them and assess them as reviewers, editors, and readers. Research is about transparency, please do not give samples or do short-cuts.\nTable 3:\nCitations must be given next to the number of papers. If the number of papers is 9, you should write 9 [Reference numbers of the 9 papers].\n\nFigure 2 is not clear.\n\nTable 4:\nWhat is \"Influential\"? On what basis did you select these papers and give them that title? What is your definition of an \"Influential\" author or paper? We must see an assessment of the 162 papers not samples of 5 or 10. This table should be omitted. It also contradicts Table 5. In Table 5, Chomnawang, M.T has the highest number of citations (173), compared to Sakdarat, S. (81 citations). It is confusing and not clear how did you define \"influential\"? What are the criteria? Why were such details not explained in the method?\n\nFigure 5:\nDistribution of global publications on Clinacanthus nutans.\" - This should be explained in the methods and results, and we need to know details about papers produced by these countries. The authors should not be selective.\nDiscussion:\nShould be rewritten and improved. The whole manuscript needs an English language edit to improve grammar for clarity.\nReferences:\nThe 162 papers must be listed all in references, not samples of them. Please read other literature in bibliometric analysis for reference.\n\nIs the work clearly and accurately presented and does it cite the current literature? No\n\nIs the study design appropriate and is the work technically sound? No\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\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": []
}
] | 1
|
https://f1000research.com/articles/10-418
|
https://f1000research.com/articles/10-416/v1
|
25 May 21
|
{
"type": "Software Tool Article",
"title": "Exploiting the DepMap cancer dependency data using the depmap R package",
"authors": [
"Theo Killian",
"Laurent Gatto",
"Theo Killian"
],
"abstract": "The `depmap` package facilitates access in the R environment to the data from the DepMap project, a multi-year collaborative effort by the Broad Institute and Wellcome Sanger Institute, mapping genetic and chemical dependencies and other molecular biological measurements of over 1700 cancer cell lines. The 'depmap' package formats this data to simply the use of popular R data analysis and visualizing tools such as 'dplyr' and 'ggplot2'. In addition, the 'depmap' package utilizes 'ExperimentHub', storing versions of the DepMap data accessible from the Cloud, which may be selectively downloaded, providing a reproducible research framework to support exploiting this data. This paper describes a workflow demonstrating how to access and visualize the DepMap data in R using this package.",
"keywords": [
"depmap",
"cancer",
"Bioconductor"
],
"content": "Introduction\n\nThe consequences of genomic alterations of cancer cells on the molecular biological landscape of the cell may result in differential vulnerabilities, or “dependencies” compared to those of healthy cells. An example of genetic dependency is a gene not necessary for the survival in healthy cells, but due to perturbations of the metabolic networks caused by cancer mutations, such a gene becomes essential for the vitality of a particular cancer cell line. However, due to the complex nature of metabolic networks, the exact mechanistic nature of many genetic dependencies of cancer are not completely understood.1 A map illustrating the relationships between the genetic features of cancer and those of cancer dependencies is therefore desirable. The Cancer Dependency Map or “DepMap”, a collaborative initiative between the Broad Institute and the Wellcome Sanger Institute, aims to map genetic dependencies in a broad range of cancer cell lines. Over 1700 cancer cell lines have been selected to be tested in this effort, intended to reflect the overall distribution of various cancer diseases in the general population. The stated aim of the DepMap Project is developing a better understanding of the molecular biology of cancer and the exploiting of this knowledge to develop new therapies in precision cancer medicine.2\n\nThe DepMap initiative is, as of the date of this publication, an ongoing project, with new data releases of select datasets every 90 days. As of the 20Q4 DepMap release, 1812 human cancer cell lines have been mapped for dependencies.2 The DepMap project utilizes CRISPR gene knockout as the primary method to map genomic dependencies in cancer cell lines.2-5 The resulting genetic dependency score displayed in the DepMap data is calculated from the observed log fold change in the amount of shRNA detected in pooled cancer cell lines after gene knockout.6,7 To correct for potential off-target effects of gene knockout in overestimating dependency with CRISPR, the DepMap initiative utilized the CERES algorithm to moderate the final dependency score estimation.3 It should be noted that due to improvements in the CERES algorithm to estimate genetic dependency while accounting for CRISPR seed effects, the RNAi dependency measurements have been rendered redundant, and further data releases for RNAi dependency measurement have been discontinued as of the 19Q3 release.2,4 In addition to genomic dependency measurements of cancer cell lines, chemical dependencies were also measured by the DepMap PRISM viability screens that as of the 20Q4 release, tested 4,518 compounds against 578 cancer cell lines.2,8 A new protemic dataset was added with the 20Q2 release, providing normalized quantitative profiling of proteins of 375 cancer cell lines by mass spectrometry.9 The DepMap project has also compiled additional datasets detailing molecular biological characterization of cancer cell lines, including WES genomic copy number, Reverse Phase Protein Array (RPPA) data, TPM gene expression data for protein coding genes and genomic mutation call data. Core datasets such as CRISPR viability screens, TPM gene expression, WES copy number and genomic mutation calls are updated quarterly on a release schedule. All datasets are made publicly available under CC BY 4.0 licence.2\n\nA table of the datasets available for the depmap package (as of 20Q4 release) is displayed in Table 1.\n\nThe ‘Release’ column indicates the most recent available release.\n\nThe depmap Bioconductor package was created in order to efficiently exploit these rich datasets and to promote reproducible research, facilitated by importing the data into the R environment. The value added by the depmap Bioconductor package includes cleaning and converting all datasets to long format tibbles,10 as well as adding the unique key depmap_id for all datasets. The addition of the the unique key depmap_id aides the comparison and benchmarking of multiple molecular features and streamlines the datasets for usage of common R packages such as dplyr11 and ggplot2.12\n\nAs new DepMap datasets are continuously released on a quarterly basis, it is not feasible to include all dataset files in binary directly within the directory of the depmap R package. To keep the package lightweight, the depmap package utilizes and fully depends on the ExperimentHub package13 to store and retrieve all versions of the DepMap data (as of this publication, starting from version 19Q1 through 20Q4) in the Cloud using AWS. The depmap package contains accessor functions to directly download and cache the most current datasets from the Cloud into the local R environment. Specific datasets (such as datasets from older releases), which can be downloaded separately, if desired. The depmap package was designed to enhance reproducible research by ensuring datasets from all releases will remain available to researchers. The depmap R package is available as part of Bioconductor at: https://bioconductor.org/packages/depmap.\n\n\nUse cases\n\nDependency scores are the features of primary interest in the DepMap Project datasets. These measurements can be found in datasets crispr and rnai, which contain information on genetic dependency, as well as the dataset drug_sensitivity, which contains information pertaining to chemical dependency. The genetic dependency can be interpreted as an expression of how vital a particular gene for a given cancer cell line. For example, a highly negative dependency score is derived from a large negative log fold change in the population of cancer cells after gene knockout or knockdown, implying that a given cell line is highly dependent on that gene in maintaining metabolic function. Genes that are not essential for non-cancerous cells but display highly negative dependency scores for cancer cell lines, may be interesting candidates for research in targeted cancer medicine. In this workflow, we will describe exploring and visualizing several DepMap datasets, including those that contain information on genetic dependency.\n\nBelow, we start by loading the packages need to run this workflow.\n\n\n\nThe depmap datasets are too large to be included into a typical package, therefore these data are stored in the Cloud. There are two ways to access the depmap datasets. The first such way calls on dedicated accessor functions that download, cache and load the latest available dataset into the R workspace. Examples for all available data are shown below:\n\n\n\nAlternatively, a specific dataset (from any available release) can be accessed through Bioconductor’s ExperimentHub. The ExperimentHub() function creates an ExperimentHub object, which can be queried for specific terms of interest. The list of datasets available that correspond to the query, depmap are shown below:\n\n\n\n\n\nSpecific datasets can be downloaded, cached and loaded into the workspace as tibbles by selecting each dataset by their unique EH numbers. Shown below, datasets from the 20_Q3 release are downloaded in this way.\n\n\n\nBy importing the depmap data into the R environment, the data may be mined more effectively utilzing R data manipulation tools. For example, molecular dependency for all cell lines pertaining to soft tissue sarcomas, sorted by genes with the greatest dependency, can be accomplished with the following code, using functions from the dplyr package. Below, the crispr dataset is selected for cell lines with “SOFT_TISSUE” in the CCLE name, and displaying a list of the highest dependency scores.\n\n\n\n\n\nA brief survey of the top dependency scores identifies the gene C1orf109 among the most dependent genes found in the selected list of dependencies scores for soft tissue cancer cell lines. This gene, also known by the alias Chromosome 1 Open Reading Frame 109, codes for a poorly characterized protein which is theorized to promote cancer cell proliferation by controlling the G1 to S phase transition.14 This protein is selected as an interesting candidate target to explore and visualize the depmap data. Figure 1 displays the crispr data as a histogram showing the distribution of dependency scores for gene C1orf109. The red dotted line signifies the mean dependency score for that gene, while the blue dotted line signifies the global mean dependency score for all crispr measurements.\n\n\n\nA more complex plot of the crispr dependency data, is shown in Figure 2. Visualizing this data involves plotting the distribution of dependency scores for gene C1orf109 for each major type of cancer, while highlighting the qualitative nature of mutations of this gene in such cancer cell lines (e.g. if such mutations are damaging or conserved, etc.). Genes known to be damaging mutations for a given cancer cell line are highlighted in red, while other non-conserving mutations are highlighted in blue. Notice that the plot in Figure 1 reflects the same overall distribution in two dimensions.\n\n\n\nMany cancer phenotypes may be the result of changes in gene expression.15-17 The extensive coverage of the depmap data affords visualization of genetic expression patterns across many major types of cancer. Elevated expression of gene C1orf109 in lung cancer tissue has been reported in literature.14 Figure 3 below shows a boxplot illustrating expression values for gene C1orf109 by lineage:\n\n\n\nA relationship between elevated gene expression and genetic dependency in cancer cell lines has been reported in literature.1,7 Therefore, genes with elevated gene expression and high genetic dependency may present especially interesting research targets which may be explored through the DepMap datasets. Figure 4 shows a plot of expression versus CRISPR gene dependency for Rhabdomyosarcoma. The red vertical line represents the average gene expression for this form of cancer, while the horizontal line represents the average dependency for this cancer type.\n\n\n\n\n\nGenes with the highest depenency scores and highest TPM gene expression are found in the upper left section of the plot in Figure 4. Almost all of the genes with the highest dependency scores display above average expression.\n\n\n\n\n\nEvidence that changes in genomic copy number may also play a role in some cancer phenotypes has also been described in literature.3,18,19 This information can also be explored through the depmap datasets displaying the log genomic copy number across cancer lineages. Figure 5 shows such a plot for gene C1orf109 for each major type of cancer lineage:\n\n\n\n\nDiscussion and outlook\n\nWe hope that this package will be used by cancer researchers to dig deeper into the DepMap data and to support their research in precision oncology and developing targeted cancer therapies. Additionally, we highly encourage current and future depmap users to combine depmap data with other datasets, such as those found through the The Cancer Genome Atlas (TCGA) and the Cancer Cell Line Encyclopedia (CCLE).\n\nThe depmap R package will continue to be maintained in line with the biannual Bioconductor release schedule, in addition to quarterly releases of DepMap data.\n\nWe welcome feedback and questions from the community. We also highly appreciate contributions to the code in the form of pull requests on github.\n\n\nData availability\n\nThe depmap datasets are available through ExperimentHub. To install the depmap package, start a recent version of R and execute:\n\n\n\n\nSoftware availability\n\nThe depmap package is available from: https://doi.org/doi:10.18129/B9.bioc.depmap Source code available from: https://github.com/UCLouvain-CBIO/depmap Archived source code as at time of publication: http://doi.org/10.5281/zenodo.473994920 License: Artistic-2.\n\nAll packages used in this workflow are available from the Comprehensive R Archive Network (https://cran.r-project.org) or Bioconductor (http://bioconductor.org). The specific version numbers of R and the packages used are shown below.\n\n",
"appendix": "References\n\nTsherniak A, Vazquez F, Montgomery PG, et al.: Defining a cancer dependency map. Cell. 2017; 170(3): 564–576. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDepmap Broad: Depmap achilles 20q1 public. Cambridge, MA: Broad Institute; 2020.\n\nMeyers RM, Bryan JG, McFarland JM, et al.: Computational correction of copy number effect improves specificity of crispr–cas9 essentiality screens in cancer cells. Nat Genet. 2017; 49(12): 1779–1784. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDempster JM, Rossen J, Kazachkova M: Extracting biological insights from the project achilles genome-scale crispr screens in cancer cell lines. BioRxiv. 2019; page 720243. Publisher Full Text\n\nDempster JM, Pacini C, Pantel S, et al.: Agreement between two large pan-cancer crispr-cas9 gene dependency data sets. Nat Commun. 2019; 10(1): 1–14. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCowley GS, Weir BA, Vazquez F, et al.: Parallel genome-scale loss of function screens in 216 cancer cell lines for the identification of context-specific genetic dependencies. Sci Data. 2014; 1: 140035. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMcFarland JM, Ho ZV, Kugener G, et al.: Improved estimation of cancer dependencies from large-scale rnai screens using model-based normalization and data integration. Nat Commun. 2018; 9(1): 1–13. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCorsello SM, Nagari RT, Spangler RD, et al.: Non-oncology drugs are a source of previously unappreciated anti-cancer activity. bioRxiv. 2019; page 730119. Publisher Full Text\n\nNusinow DP, Szpyt J, Ghandi M, et al.: Quantitative proteomics of the cancer cell line encyclopedia. Cell. 2020; 180(2): 387–402. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMüller K, Wickham H: Simple data frames. R package version 1.3. 2017; 3.\n\nWickham H, Wickham MHadley: Package ‘dplyr’.2020.Reference Source\n\nWickham H: ggplot2. Wiley Interdisciplinary Reviews: Computational Statistics. 2011; 3(2): 180–185.\n\nMorgan M, Shepherd L: ExperimentHub: Client to access ExperimentHub resources. R package version 1.14.0. 2020.\n\nLiu S-S, Zheng H-X, Jiang H-D, et al.: Identification and characterization of a novel gene, c1orf109, encoding a ck2 substrate that is involved in cancer cell proliferation. J Biomed Sci. 2012; 19(1): 49. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLi X, Lalić J, Baeza-Centurion P, et al.: Changes in gene expression predictably shift and switch genetic interactions. Nat Commun. 2019; 10(1): 1–15. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHernández-Lemus E, Reyes-Gopar H, Espinal-Enríquez Jús, et al.: The many faces of gene regulation in cancer: A computational oncogenomics outlook. Genes. 2019; 10(11): 865. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFelts SJ, Tang X, Willett B, et al.: Stochastic changes in gene expression promote chaotic dysregulation of homeostasis in clonal breast tumors. Commun Biol. 2019; 2(1): 1–7. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAguirre AJ, Meyers RM, Weir BA, et al.: Genomic copy number dictates a gene-independent cell response to crispr/cas9 targeting. Cancer Discov. 2016; 6(8): 914–929. PubMed Abstract | Publisher Full Text | Free Full Text\n\nShao X, Lv N, Liao J, et al.: Copy number variation is highly correlated with differential gene expression: a pan-cancer study. BMC Med Genet. 2019; 20(1): 175. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKillian TF, Gatto L: UCLouvain-CBIO/depmap-workflow: As published in F1000Research (Version v1). Zenodo. 2021, May 6. Publisher Full Text"
}
|
[
{
"id": "86147",
"date": "11 Jun 2021",
"name": "Katharina Imkeller",
"expertise": [
"Reviewer Expertise genetic dependencies",
"immunogenetics"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe article introduces the depmap package that allows rapid access to the different datasets of the Cancer Dependency Map project. This Bioconductor package is easy to use, the code is well written and documented. Issues related to the package raised on github are addressed by the authors and the data is regularly updated. Overall this is a very useful resource for the cancer dependency research community.\nI have a few suggestions that in my opinion would improve the article and help the package become even more popular.\nIn the introduction, 2nd paragraph, the authors introduce the different types of data provided in depmap. The difference between RNAi and CRISPR screens is not clear enough. In the sentence starting with \"The resulting genetic dependency...\", shRNA should be replaced by sgRNA (single guide RNA) or gRNA (guide RNA). Also, please explain how the genetic dependency in shRNA/RNAi screens is calculated (DEMETER algorithm?). It is not clear to me what the expression \"CRISPR seed effect\" is referring to (sentence starting with \"It should be noted...\").\n\nI am wondering why the authors chose C1orf109 as an example for one of the use cases. It could be more interesting for the typical reader/user if the article illustrated another gene, for which differential genetic dependency in combination with somatic mutation can actually be observed. KRAS could be such a gene, but there are many more examples.\n\nThe figures are sometimes displayed above the code chunk that is used to generate them, which makes it difficult to follow, especially if the reader is used to Rmarkdown style. Maybe the authors could add a comment line in the respective chunks indicating \"used to generate Figure X\".\n\nSome sections of the article are difficult to read and could be easily improved by a few small modifications. I list a few examples here (not exhaustive):\n\nAbstract:\nReplace the '' and `` signs. simply -> simplify Reformulate the sentence starting with \"In addition\", because it is difficult to understand.\n\nIntroduction:\nexploiting -> exploitation/utilisation/application ? (paragraph 1). protemic -> proteomic (paragraph 2). aides -> aids (paragraph 4). reformulate sentence starting with \"Specific datasets ...\" (paragraph 5).\n\nUse cases:\nreformulate sentence starting with \"The genetic dependency ...\" (paragraph 1). cancer medicine -> cancer therapy (paragraph 1).\n\nDiscussion:\nreplace \"dig deeper into\" ? (paragraph 1). Part of the data in depmap is already derived from CCLE. Maybe specify what additional data type is available from CCLE (paragraph 1).\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? Yes\n\nAre the conclusions about the tool and its performance adequately supported by the findings presented in the article? Yes",
"responses": []
},
{
"id": "101594",
"date": "20 Dec 2021",
"name": "Ashir Borah",
"expertise": [
"Reviewer Expertise Computational biology",
"functional genomics",
"cancer target identification"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis article by Killian and Gato introduces the DepMap R package and demonstrates its application for working with DepMap data in R. This package is aimed at aiding and enhancing the reproducible analysis of DepMap datasets in R, by providing cleaned and reformatted versions of these datasets, and an easy-to-use API for importing the data into R. The authors also demonstrate the application of their package, in conjunction with commonly-used R analytical tools, for performing some common analyses of DepMap data.\nWe are excited to see the creation of such an R package to enhance the usability of the DepMap data, and the code appears to be well-written, clearly documented, and well-maintained. However, we believe most of the intended functionality of the tool is either unnecessary or not well addressed in the current implementation. In addition, some of the example analyses used to highlight the tool in the manuscript are problematic in various ways. Thus, we believe these substantial issues should be addressed before the tool will be of broader use to the community.\nIn terms of the stated goals of the DepMap R package, the authors highlight the following:\n“The value added by the depmap Bioconductor package includes cleaning and converting all datasets to long format tibbles,10 as well as adding the unique key depmap_id for all datasets.” and “The depmap package was designed to enhance reproducible research by ensuring datasets from all releases will remain available to researchers”\nWe don’t believe that there is significant ‘cleaning’ of the data being done in this package and note that all of the files being generated in quarterly DepMap data releases already include the depmap_id unique key. All of the DepMap datasets are already made available in a citable, immutable data repository (Figshare), which indeed is where the authors are sourcing (a subset of) those files. Creating an additional repository for the data, with only minor formatting changes seems to be of limited benefit. It also creates a risk of confusing users (i.e. the authors only include a subset of the files published in the DepMap releases, and if their versions of the datasets aren’t kept up-to-date users might end up using older versions of the data inadvertently).\n\nWe do agree that there is utility in creating a simple and easy-to-use API for accessing DepMap data in R, and the ability to download the data when needed, and cache locally accordingly seems useful. However, as an API there are several important limitations. First, the choice to reformat the datasets to long-form tibbles may be useful for facilitating certain analyses but is clearly a suboptimal choice for downloading and importing many of the datasets. Most of the DepMap datasets are large dense matrices, and formatting them as long-form tables increases the file sizes by > ~5x or more, which significantly impacts download and load times. Even if the authors wanted to encourage consistent use of long-form versions of the datasets it would be much more efficient to download/cache/load the datasets in their native matrix form and then create helper functions to easily/quickly convert the datasets once loaded into R (e.g. ‘pivot_longer’ from the tidyverse package). We also think it would be better for the API to access the data directly from the primary source at Figshare rather than creating an additional version on ExperimentHub. It would also be helpful to indicate the availability of other files in the DepMap data releases on Figshare that aren't included in the ExperimentHub repo so users are at least aware.\nIn terms of the manuscript itself, we also believe the example applications could be substantially improved. In particular, the main vignette highlighting the gene C1orf109 we found to be confusing and lacking clear motivation. The gene is nominally selected because it scores as a strong dependency within the ‘soft tissue’ cell lines specifically, but there is no normalization or differential comparison used, so it seems rather (also from Figure 2) that this gene is a common-essential gene, without any clear linkage to soft tissue cancers. Presumably, this gene was selected because it’s poorly characterized and could represent a novel cancer target, but the results presented don’t really support this, and are likely to create confusion. If the goal is merely to illustrate examples of using tidyverse tools to analyze depmap data, the paper would be better-suited by using well-known examples of selective cancer dependencies (e.g. BRAF dependency in BRAF mutant cancers). Similarly, other plots used to demonstrate analysis of DepMap data seem to lack clear motivation. For example, in Fig 4 the authors plot expression vs dependency across all genes and cell lines within rhabdomyosarcoma, which shows a relationship, but it’s not clear what question this is really asking or addressing. Genes that appear as dependencies in these cell lines should in general be expressed in those cell lines (otherwise they are likely false positives), but beyond this, it’s unclear what is being shown, or how it should be interpreted.\nSpecific Issues:\nIn the second paragraph the authors state “As of the 20Q4 DepMap release, 1812 human cancer cell lines have been mapped for dependencies”. This is the number of cell lines included in the sample.info metadata file, NOT the number with genetic dependencies measured. For example, the number of cell lines with CRISPR screening in the 20Q4 Achilles dataset is 789.\n\nWe don’t think it’s correct to say that RNAi has been rendered ‘redundant’ in light of large-scale CRISPR datasets, as RNAi screens are still a useful source of information that can be complementary to CRISPR screens.\n\nIt would be helpful to clarify that the package includes a subset of the available DepMap data release files. For example, the authors refer to the ‘protein-coding TPM’ expression data, which is perhaps the most commonly used file derived from DepMap RNA-Seq data. However, DepMap also provides a number of other mRNA expression datasets (e.g. all genes’ TPM, transcript level TPM, expected counts, etc.). The authors also state that “Core Datasets” are updated quarterly, though there are ~40 files updated quarterly, so it’s unclear what “Core” refers to.\n\nAlso in the second paragraph, the authors refer to ‘shRNA’ in the context of ‘gene KO’, and presumably are referring to CRISPR rather than RNAi screens (in which case the reagents are sgRNA rather than shRNA).\n\nShould mention somewhere that the RNAi dataset (DEMETER2) used is actually a combined dataset from Project Achilles, Novartis Project DRIVE, and the study by Marcotte et al.\n\nIn their example, the authors use text matching on the cell line names to filter for soft tissue cell lines. Lineage information in the cell line names has been deprecated and can be incorrect. It is important to instead use the lineage information provided in the sample info file.\n\nMinor:\nTypo in the abstract \"simply the use\" should be 'simplify the use'.\n\nWe note that as of 21Q2, DepMap CRISPR datasets are being processed using the Chronos algorithm, rather than CERES. This would be worth clarifying.\n\nThere are typos in the example code used to load the data: “TPM <- depmap_RPPA() and RPPA <- depmap_TPM()”\n\n“Chemical dependency” should be rephrased as “chemical sensitivity”. The authors also use the term ‘molecular dependency’ which seems confusing.\n\nThe authors state that dependencies imply a given gene is needed for maintaining ‘metabolic function’, though we believe it would be clearer to state as needed for “viability” or “proliferation”.\n\nThe authors could make their example code more efficient for demonstration purposes. Namely, by filtering for genes of interest before joining tables.\n\nThe example dot plot by lineage (Fig 2) could be improved by adding boxplot or violin plots by lineage to illustrate the distribution of the data which is very difficult to see.\n\n“Genes known to be damaging mutations for a given cancer cell line are highlighted in red,...” Should be “Cell lines with damaging mutations in the selected gene…”\n\nIs the rationale for developing the new software tool clearly explained? No\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? Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-416
|
https://f1000research.com/articles/10-415/v1
|
25 May 21
|
{
"type": "Research Article",
"title": "Factors Predicting Hospital Readmission among Thais with Post Myocardial Infarction",
"authors": [
"Chuthaporn Phemphul",
"Wirat Pansila",
"Nisakorn Vibulchai",
"Chaiyasith Wongvipaporn",
"Chuthaporn Phemphul",
"Wirat Pansila",
"Chaiyasith Wongvipaporn"
],
"abstract": "Background: Readmission after an acute myocardial infarction is not only common and costly but can also impact patients’ quality of life and mortality. This retrospective observational study was conducted to determine the impact of sociodemographic variables, clinical variables, and hospital readmission among post-myocardial infarction patients in Thailand. Few, if any, previous studies have investigated the factors predicting readmission rates over variable time periods. We aimed to provide such information to prevent readmission in the future. Methods: Between October 1, 2014, to September 30, 2018 a total of 376 post-myocardial infarction patients of Roi-Et hospital were recruited for this study. The criteria of data collection concerned the rate of readmission, gender, comorbidities, anaemia, chronic kidney disease, complication, smoking, and type of myocardial infarction. A measurement period was seven-day, 30-day, six-month, and one-year of readmission. Data were analyzed using percentage, mean, standard deviation, and logistic regression analysis.\n\nResults: The highest readmission rate at six-month, 30-day, seven-day, and one-year was 52.2%, 30.4%, 10.6%, and 6.8%, respectively. None of the predictors were significant for seven-day and one-year of readmissions. Meanwhile, hypertension comorbidity and anaemia were identified as the significant predictors for early 30-day readmission whereas atrial fibrillation complication, chronic kidney disease, and smoking were the significant predictors for late six-month readmission.\n\nConclusions: Multiple factors including HT comorbidity, anaemia, atrial fibrillation, chronic kidney disease, and smoking predict readmission among Thais with post myocardial infarction. This study demonstrated that rates and predictors of readmissions in short-term and long-term periods are different. Therefore, various screening tools and interventions are required.",
"keywords": [
"Readmission",
"Risk factor",
"Myocardial infarction"
],
"content": "Introduction\n\nAcute myocardial infarction (AMI) has become a significant health problem with high morbidity and mortality rates. Despite dramatic improvement in outcomes with medical therapy, admission rates following AMI hospitalization remain high. Previous studies have found that early readmission rates within seven-day of post‐AMI discharge ranged from 4.8%1 to 11%2, while late readmissions rate of 30-day, six-month, and one-year readmissions ranged from 11% to 14%3, 20.4%1 to 33.8%2, and 21.34 to 49.9%5, respectively. The highest incidences of readmissions not only increase healthcare costs by 60%6, but also expose patients to long-term hospitalisation-associated complications. Readmissions for AMI are typically preceded by a recurrent AMI and related cardiovascular conditions1 in which are often assumed to indicate incomplete treatment in hospital, poor coordination of services or communication of discharge plans, or lack of healthcare access in early follow-up care7. As a consequence, readmission is of high interest, and considered as a quality indicator for hospital care8.\n\nIn order to reduce readmission rates in patients with AMI, the predictions on patients who are likely to be readmitted and the intervention should be taken into account. Nevertheless, due to inconsistency of risk-predictive models, and the performance of these models, the problem of readmission rate continues. Most existing models were developed in different settings and periods, thus may not be appropriate to be applied in other contexts. Previous studies1–3,9–11 have identified that clinical and laboratory parameters, including atrial fibrillation, severity of AMI, and hypertension, confer a higher risk for an early period of cardiovascular admission, whereas smoking and the burden of comorbid non-cardiac illness, including chronic kidney disease, diabetes mellitus, hypertension, anaemia, and pulmonary disease, raises the risk for AMI–related complications in late readmission. These factors may potentially modify the target for future interventions.\n\nIn Thailand, it is suggested that readmissions have negative impacts on both hospitals and patients. Also, it is a huge economic burden to the nation. A prior study in a Thai hospital12 revealed that the unplanned readmission rate at one year after hospital discharge was 13.5% and 7.8% in the group of patients with unstable angina and non-ST elevation MI (NSTEMI), respectively. Most patients had angina at presentation12,13. A recent study14 has also revealed that one-third of coronary artery disease patients had been readmitted at one year after hospital discharge once (40.2%) whereas twice and three-time readmissions were found in 35.5% and 11.2% of patients, respectively. The most significant predictive factor for readmission was social support. Nonetheless, there were few studies investigating the factors predicting rates of rehospitalization, especially in AMI patients after hospital discharge over variable time periods. According to previous studies15,16, it was indicated that different variables might have an influence on readmission period over different timescales. It is suggested that early rehospitalization is associated with clinical and laboratory parameters. On the contrary, late rehospitalization is associated with patients’ behaviours and the burden of chronic diseases. To address this gap of knowledge, this study was designed to determine predictors of hospital readmissions among Thai AMI patients in early and late periods, in which early readmission were defined as readmissions within seven-day post discharge from index hospitalisation while late readmissions were defined as readmissions within 30-day, six-month, and one-year following hospital discharge.\n\n\nMethods\n\nThis study was a retrospective study using an electronic medical database (EMD) review at Roi-Et hospital, a tertiary care hospital in a large metropolitan area of Roi-Et province, Thailand. The 820-bed hospital serves as a referral centre and an excellent centre of heart diseases in the middle north-eastern part of Thailand. Data entry into the EMD concerned post myocardial infarction patients admitted between October 1, 2014, to September 30, 2018. Patients were identified based on qualifying diagnostic-related grouping codes (ICD I210-I213, ICD I214) indicating a primary diagnosis of myocardial infarction (MI) at discharge. Hospitalizations for patients aged ≥18 years were included. In alignment with the qualifying diagnostic-related grouping codes, all MI patients at discharge were eligible (N=484). We excluded hospitalizations during which a patient died (N=27), was transferred to another hospital (N=17), or was discharged against medical advice (N=8). Incomplete clinical data of the patients were excluded (N=56). Thus, a total of 376 patients met the selection criteria. Of those discharged with a primary diagnosis of MI during the designated time period, 161 were readmitted for MI and 215 were not readmitted (Figure 1).\n\nFor this study, a readmission was defined as the first admission to Roi-Et hospital within seven-day, 30-day, six-month, and one-year of being discharge. A readmission was only counted once as a readmission, relative to the prior index admission. All subsequent admissions then re-entered the cohort as a new index admission. All elective readmissions were excluded from the data set.\n\nThis research did not involve any patients or public since its procedures included only retrospective data collection.\n\nConsidered variables were retrieved from literature reviews1–3,9–11 and selected from the existing database, as well as some that could be derived. The potential predictors of readmission among patients with AMI were gender, diabetes and hypertension comorbidities, anemia with hematocrit < 33 vol%, stage-3 chronic kidney disease with serum creatinine ≥ 2 mg/dL, atrial fibrillation, smoking, and type of myocardial infarction.\n\nModel assumptions and strategy for analysis. In order to measure the significance of the potential variables predicting the dichotomous response variable of readmission among the population in this study, the logistic regression statistic was employed. All variables studied were binary (yes/no response) and the observations were independent. We explored missing data for patterns of missingness and associations between missing and observed data; cases with missing data for variables of interest were excluded from analyses involving those variables.\n\nIn the initial stage of analysis, all study variables were tested in a univariate regression (with a p-value<0.25) aimed at looking for statistically significant factors influencing rehospitalization. After these factors were identified and concluded, a multiple logistic regression procedure was employed by using a stepwise selection method. The IBM SPSS Statistics for Windows, Version 23 (IBM Corp., Armonk, NY, USA) was used to generate indicator variables for the levels of each categorical predictor. Moreover, reference groups were selected for each predictor as well. Then, firstly, all explanatory variables of interest were tested for finding possible interactions. The highest insignificant term of each predictor was eliminated until the significance level of all variables was at 0.05 as required. Parameter estimates and odds ratio probabilities that were not above 0.05 were considered to have statistical significance and were kept in the model. For individual parameter estimates, Wald statistics were applied. Goodness-of-fit and model assumptions, as well as multicollinearity among the predictor variables, linearity of the predictor variables and log odds, Hosmer and Lemeshow goodness-of-fit test, and likelihood ratio tests were examined as well.\n\n\nEthics approval and reporting\n\nThe study was approved by the Human Research Ethics Committee of the Roi-Et Hospital and Mahasarakham University Institutional Review Board for use of deidentified data from existing hospital database. The need for consent from the participants was waived by the ethics committee due to the retrospective nature of the analysis. This study is reported following Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) guidelines (S1 Checklist)\n\n\nResults\n\nThe data of the total of 376 MI patients were extracted from a database of myocardial infarction patients. A slight majority of the patients were male (57.4%) and the mean age of all samples was 66.80 ±12.02 years. Most patients were married (81.9%) and had National Health Security support (71.3%). One-third (37.2%) were agriculturalists and a further third (35.4%) were unemployed. The majority of patients had primary school education (73.9%). For treatment types, more than half of the patients (63%) received only medication, whereas one third (30.6%) received percutaneous coronary intervention [PCI], and a small number (6.4%) received coronary artery bypass surgery [[CABG] Table 1].\n\nSTEMI= ST-elevation myocardial infarction; NSTEMI= Non ST-elevation myocardial infarction;\n\nPCI = Percutaneous coronary intervention; CABG= Coronary Artery Bypass Grafting; DM= Diabetes Mellitus ; HT= Hypertension; Hct= Hematocrit; AF= Atrial fibrillation; UGI bleeding= Upper gastrointestinal bleeding\n\nNearly half of the patients were female (42.6%). Nearly one-quarter of the patients had a STEMI diagnosis (22.9%). The highest proportion of comorbidity was hypertension comorbidity (59%), followed by diabetes (46.5%). More than half of the patients (30.1%) had anaemia with hematocrit < 33 vol%. About 17.8% of the patients had stage-3 chronic kidney disease with serum creatinine ≥ 2 mg/dL and 5.1% of the patients had atrial fibrillation complication. For risk behaviour, 12.5% of the patients were smokers [Table 1].\n\nThe highest readmission rate at six-month, 30-day, seven-day, and one-year was 52.2%, 30.4%, 10.6%, and 6.8%, respectively. The causes of readmission were classified into two categories: (a) cardiovascular causes: cardiac causes including heart failure, non ST-elevation MI, ST-elevation MI, unstable angina, and arrhythmias were vitally important reasons associated with readmission, which accounted for 92.6% of all causes after AMI; (b) non-cardiovascular causes: the non-cardiac caused including stroke, upper gastrointestinal bleeding, and depression leaded to readmission after AMI, which accounted for 7.4% of all causes after AMI. Chest pain and other cardiovascular reasons were regarded as the principal symptomatic of readmission [Table 1].\n\nFrom univariate analysis of association between potential predictors and readmissions among all study populations, the results showed that statistically significant factors for readmission among post MI patients were AF complication (ORadj=4.541, 95%CI =1.608 to 12.827] and smoking (ORadj=2.662, 95%CI =1.326 to 5.344]. Thus, they were significant predicting factors of readmission [Table 2].\n\nA logistic model for predictors of readmission according to four time periods (seven-day, 30-day, six-month, and one-year) was carried out. After adjusted analysis, this found that none of the predictors were significant for seven-day and one-year readmissions. Meanwhile, two predictors were found to be significant for 30-day readmission, these were HT comorbidity (ORadj= 2.264; 95% CI =1.098 to 4.668) and anemia with Hct < 33vol% (ORadj= 2.171; 95% CI =1.160 to 4.064). For six-month readmission, AF complication, chronic kidney disease with serum creatinine ≥2 mg/dL, and smoking were the significant predictors (ORadj=3.494; 95% CI = 1.315 to 9.284; ORadj=2.026; 95% CI = 1.103 to 3.722; ORadj=2.849; 95% CI =1.366 to 5.944, respectively) [Table 3].\n\n\nDiscussion\n\nThe results of this study highlight the predictors of readmissions in early (seven-day) and late (30-day, six-month, and one-year) periods following hospital discharge in Thai healthcare settings. As with previous studies, we found that comorbidities, health, and illness were associated with readmission. For 30-day readmission, a significant finding is that HT comorbidity was identified as the significant predictor. This finding is congruent with previous study, revealing that HT is highly prevalent in Thailand. One out of four of Thai people had HT but less than one out of three had their blood pressure under control17, even with the expanded use of antihypertensive medications. The HT is a well-known cardiovascular risk factor associated with increased cardiovascular events18. An empirical study supports that 84.4% of readmitted MI patients had additional hypertension comorbidity19. Furthermore, we also found that another significant predictor for 30-day readmission was anaemia with hematocrit < 33 vol%. Patients who were malnourished with anaemia during the index of hospitalisation had a high risk of being readmitted. Several studies revealed that malnutrition is associated with adverse health outcomes for patients and leads to increased healthcare costs20,21. A recent study2 also supported the hypothesis that malnutrition status is a strong predictor of rehospitalisation.\n\nFor six-month readmission, we also found that atrial fibrillation (AF) was a predictor that is widely known as a common complication of AMI and contributes to high rates of in-hospital adverse events22. The overall incidence of AF complicating AMI was 10.8%. Patients developing new-onset AF following AMI were at higher risk for in-hospital stroke22. In this study, there was a new-onset AF following AMI in up to 5 cases. In addition, we also found that patients who had chronic kidney disease with creatinine serum level ≥2 mg/dL admission were likely to have late readmissions at six-month after discharge. The relevant finding is that the mildly elevated admission serum creatinine markedly increased one year mortality in patients with AMI23.\n\nA significant and interesting finding of this study is that smoking predicts six-month readmission after hospital discharge. This study validates the findings of a previous study which found that smoking increases the risk of readmissions among CAD patients across all specialties. The relevant finding showed that only 33.2% of the patients underwent smoking cessation counseling during hospital admission, which highlights that a significant proportion of patients missed smoking cessation counseling. Studies indicated that smoking cessation intervention has a beneficial effect in improving clinical outcomes and preventing complications and readmission. Tan and et al.24 conducted a meta-analysis involving 1,607 patients and found that readmission rate was significantly reduced in patients who received smoking cessation counseling, and that the prolonged abstinence rate of the gradual cessation was significantly lower than that of the abrupt cessation (relative risk, RR=0.77). However, intervention effects of smoking cessation were not significant at long term follow-up25 and need to further examination, especially in primary care setting26. Therefore, this is a window of opportunity to target smoking cessation among hospitalised patients and continue the intervention in patients after discharge to help reduce readmissions.\n\nIn conclusion, multiple factors including HT comorbidity, anemia, atrial fibrillation, chronic kidney disease, and smoking predict readmission among Thais with post myocardial infarction. Moreover, this study demonstrates that rates and predictors of readmissions in short-term and long-term periods are different. Therefore, various screening tools and interventions are required.\n\nThe results of this study were interpreted in the context of the existing data using medical record reviews. Information about other important factors such as social support, functional status, and psychiatric illnesses, which is considered critically important and may lead to adverse events after discharge, was not discussed. Lastly, the data in this study was gathered from only one hospital, which could limit generalisability. For further research, the inclusion of larger sample sizes, investigation of causality for selected predictors, and different hospitals’ readmission data are suggested in order to produce more robust and clinically meaningful outcomes.\n\n\nConclusions\n\nThis study developed potential factors to identify seven-day, 30-day, six-month, and one-year readmissions in Roi-Et hospital. Among patients discharged, multiple factors predicting readmission in short-term and long-term periods are different. Therefore, various screening tools and appropriate preventive interventions are required.\n\n\nData availability\n\nFigshare: Dataset factors predicting hospital readmission. https://doi.org/10.6084/m9.figshare.14406596.v427\n\n• Dataset characteristic of subjects.xlsx. (All underlying data gathered in this study.)\n\nFigshare: Data Dictionary. https://doi.org/10.6084/m9.figshare.14406995.v328\n\nThis project contains the following data:\n\n• Data Dictionary Factors Predicting Readmission.docx\n\nFigshare: S1 STROBE Checklist. https://doi.org/10.6084/m9.figshare.14573532.v129\n\nThis project contains the following reporting checklist:\n\n• S1 STROBE Checklist.pdf\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "Acknowledgement\n\nThe authors would like to thank the targeted hospital for facilitating for data collection process.\n\n\nReferences\n\nJepma P, ter Riet G, van Rijn M, et al.: Readmission and mortality in patients ≥70 years with acute myocardial infarction or heart failure in the Netherlands: a retrospective cohort study of incidences and changes in risk factors over time. Neth Heart J. 2019; 27(3): 134–141. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSharma Y, Miller M, Kaambwa B, et al.: Factors influencing early and late readmissions in Australian hospitalised patients and investigating role of admission nutrition status as a predictor of hospital readmissions: a cohort study. BMJ Open. 2018; 8(6): e022246. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWang H, Zhao T, Wei X, et al.: The prevalence of 30‐day readmission after acute myocardial infarction: A systematic review and meta‐analysis. Clin Cardiol. 2019; 42(10): 889–898. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKhot UN, Johnson MJ, Wiggins NB, et al.: Long-term time-varying risk of readmission after acute myocardial infarction. J Am Heart Assoc. 2018; 7(21): e009650. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDharmarajan K, Hsieh AF, Kulkarni VT, et al.: Trajectories of risk after hospitalization for heart failure, acute myocardial infarction, or pneumonia: retrospective cohort study. BMJ. 2015; 350: h411. PubMed Abstract | Publisher Full Text\n\nZheng S, Hanchate A, Shwartz M: One-year costs of medical admissions with and without a 30-day readmission and enhanced risk adjustment. BMC Health Serv Res. 2019; 19(1): 155. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChang AM, Rising KL: Cardiovascular admissions, readmissions, and transitions of care. Curr Emerg Hosp Med Rep. 2014; 2(1): 45–51. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFischer C, Lingsma HF, Marang-van de Mheen PJ, et al.: Is the readmission rate a valid quality indicator? A review of the evidence. PLoS One. 2014; 9(11): e112282. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDesai MM, Stauffer BD, Feringa HHH, et al.: Statistical models and patient predictors of readmission for acute myocardial infarction: A systematic review. Circ Cardiovasc Qual Outcomes. 2009; 2(5): 500–507. PubMed Abstract | Publisher Full Text\n\nArnold SV, Smolderen KG, Kennedy KF, et al.: Risk factors for rehospitalization for acute coronary syndromes and unplanned revascularization following acute myocardial infarction. J Am Heart Assoc. 2015; 4(2): e0013524. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLenzi J, Avaldi VM, Hernandez-Boussard T, et al.: Risk-adjustment models for heart failure patients' 30-day mortality and readmission rates: the incremental value of clinical data abstracted from medical charts beyond hospital discharge record. BMC Health Serv Res. 2016; 16(1): 473. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPumprueg S, Boonyapisit W, Wongsa J, et al.: Characteristics and outcomes of treatment for non-ST-segment elevation acute coronary syndrome: results from a Single Center Registry. J Med Assoc Thai. 2016; 99(1): 1–7. PubMed Abstract\n\nKiatchoosakun S, Sutra S, Thepsuthammarat K: Coronary artery disease in the Thai population: Data from Health Situation Analysis 2010. J Med Assoc Thai. 2012; 95 Suppl 7(Supp 7): S149–S155. PubMed Abstract\n\nPolsook R, Aungsuroch Y: A cross-sectional study of factors predicting readmission in Thais with coronary artery disease. J Res Nurs. 2020. Publisher Full Text\n\nZhou H, Della PR, Roberts P, et al.: Utility of models to predict 28-day or 30-day unplanned hospital readmissions: an updated systematic review. BMJ Open. 2016; 6(6): e011060. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGraham KL, Wilker EH, Howell MD, et al.: Differences between early and late readmissions among patients: a cohort study. Ann Intern Med. 2015; 162(11): 741–749. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWorld health organization: Reducing cardiovascular disease (hypertension and sodium). [cited 2020 Oct 20]. Reference Source\n\nFuchs FD, Whelton PK: High blood pressure and cardiovascular disease. Hypertension. 2020; 75(2): 285–292. PubMed Abstract | Publisher Full Text\n\nRymer JA, Chen AY, Thomas L, et al.: Readmissions after acute myocardial infarction: How often do patients return to the discharging hospital? J Am Heart Assoc. 2019; 8(19): e012059. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLim SL, Ong KCB, Chan YH, et al.: Malnutrition and its impact on cost of hospitalization, length of stay, readmission and 3-year mortality. Clin Nutr. 2012; 31(3): 345–50. PubMed Abstract | Publisher Full Text\n\nSharma Y, Miller M, Kaambwa B, et al.: Malnutrition and its association with readmission and death within 7 days and 8-180 days postdischarge in older patients: a prospective observational study. BMJ Open. 2017; 7(11): e018443. PubMed Abstract | Free Full Text\n\nKundu A, O’Day K, Shaikh AY, et al.: Relation of atrial fibrillation in acute myocardial infarction to in-hospital complications and early hospital readmission. Am J Cardiol. 2016; 117(8): 1213–1218. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCakar MA, Gunduz H, Vatan MB, et al.: The effect of admission creatinine levels on one-year mortality in acute myocardial Infarction. ScientificWorldJournal. 2012; 2012: 186495. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTan J, Zhao L, Chen H: A meta-analysis of the effectiveness of gradual versus abrupt smoking cessation. Tob Induc Dis. 2019; 17: 09. PubMed Abstract | Publisher Full Text | Free Full Text\n\nProchaska JJ, Delucchi K, Hall SM: A meta-analysis of smoking cessation interventions with individuals in substance abuse treatment or recovery. J Consult Clin Psychol. 2004; 72(6): 1144–1156. PubMed Abstract | Publisher Full Text\n\nHersi M, Traversy G, Thombs BD, et al.: Effectiveness of stop smoking interventions among adults: protocol for an overview of systematic reviews and an updated systematic review. Syst Rev. 2019; 8(1): 28. PubMed Abstract | Publisher Full Text | Free Full Text\n\nVibulchai N, Phemphul C, Pansila W, et al.: Dataset factors predicting hospital readmission. figshare. Dataset. 2021. http://www.doi.org/10.6084/m9.figshare.14406596.v4\n\nVibulchai N, Phemphul C, Wongvipaporn C, et al.: Data Dictionary. figshare. Dataset. 2021. http://www.doi.org/10.6084/m9.figshare.14406995.v3\n\nVibulchai N, Phemphul C, Pansila W, et al.: S1 STROBE Checklist. figshare. Dataset. 2021. http://www.doi.org/10.6084/m9.figshare.14573532.v1"
}
|
[
{
"id": "88008",
"date": "30 Jun 2021",
"name": "Rapin Polsook",
"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 think this paper is good and is an important addition to the literature.\nAbstract\nThe abstract is not clear about comorbidity and kidney disease.\n\nPlease change the aim of the study to match the study design. It does not match with the aim stated in the Introduction.\n\nIntroduction\nNeed references for the two sentences at the beginning of the first paragraph.\n\nThe authors should conduct a comprehensive literature review related to readmission in this group to fulfill the gap of knowledge.\n\nFor this study, the authors collected data from just only one province in the north-eastern part of Thailand and used secondary sources. Thailand has 77 provinces. I suggest the title of the study should be: “Factors Predicting Hospital Readmission among Post Myocardial Infarction: A retrospective study.”\n\nPlease restate the gap of knowledge.\n\nFactors were selected, based on literature reviews, please clarify comorbidity and kidney disease. Why did the authors separate kidney disease from comorbidity? To the best of my knowledge, comorbidity refers to the presence of additional conditions co-occurring with acute myocardial infarction which means kidney disease is comorbidity.\n\nPlease use MI or post-AMI or AMI consistently - which one is correct.\n\nMethod\nIn Ethics approval and reporting, do you need to add an approval number? If yes, please add the approval number.\n\nIn Patient and public involvement, if the authors add the process to retrieve data after approval from the ethics committees, it will be better and clearer for data collection.\n\nResults\nPlease check the results in Characteristics of the populations. “National Health Security support” does not appear in Table 1. Symptomatic of readmission does not appear in Table 1. It will be better if the authors report each datum such as nearly one-third of the causes of readmission at six-month (27.9%) is heart failure.\n\nIn Predictors of readmission, the authors stated that “the causes of readmission were classified into two categories”, so when reporting in Table 1 it should be divided into two categories too.\n\nPlease check the results in a table and those described in the Results section are the same thing.\n\nDiscussion\nPlease revise the Discussion into four sections: seven-day, 30-day, 6-month, and one-year. Then describe the strongest predictor readmission in each period of time, seven-day, 30-day, 6-month, and one-year, with rationale, and if the result is consistent with previous studies or contrasts with previous studies.\n\nConclusion\nThis part is the same as the last paragraph of the Discussion. Please revise.\n\nThe conclusion should report the result of the strongest predictor readmission on seven-day, 30-day, 6-month, and one-year.\n\nThe authors conclude that various screening tools and appropriate preventive interventions are required. What is a screening tool? Can the authors give an example? What is the kind of intervention? The answer to this question should be based on the results.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
},
{
"id": "151376",
"date": "03 Oct 2022",
"name": "Miodrag Filipovic",
"expertise": [
"Reviewer Expertise Perioperative medicine",
"cardiac 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\nThis is a retrospective study on 376 patients with myocardial infarction, of whom 161 were readmitted to the hospital within 1 year after discharge. The authors analysed the association of several variables with early (< 7 days, n=17) and late (> 7 days, n= 144) readmission. 108 patients were excluded. In univariable analysis, atrial fibrillation and smoking were associated with readmission. In addition, the authors performed a multivariable analysis for different time intervals of readmission and found additional associations (anemia and hypertension with 30-day readmission and renal failure with 6-month readmission (Table 3)).\nI have a few comments:\nThe readmission rate (43%) is quite high and should be discussed.\n\nAt the end of the introduction, the authors define “early“ and “late“ readmission. In the results, however, they report on all readmissions (Table 2) and 30-day and 6-month readmissions. This inconsistency has to be eliminated.\n\nThe relatively small number of readmissions (49 and 84 patients) does not allow for extended multivariable regression analyses and is prone to overfitting and bias. Accordingly, I doubt if the conclusion that “…predictors of readmissions in short-term and long-term periods are different“ is correct.\n\nDid the 27 deceased patients die during the index hospitalisation or later?\n\nWhy were the 8 patients who were “discharged against medical advice“ excluded from the analysis?\n\nThe number of incomplete clinical data (n=56) is quite high. The data of these patients should also be reported as extensively as possible.\n\nThe first sentence in the paragraph “Predictors of readmission“ in the results section is confusing.\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? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
},
{
"id": "151377",
"date": "24 Oct 2022",
"name": "Mikhail S Dzeshka",
"expertise": [
"Reviewer Expertise General cardiology",
"heart failure",
"atrial fibrillation",
"hypertension",
"pharmacotherapy"
],
"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 performed an analysis of factors predicting hospital readmission among Thais after myocardial infarction. It is an important topic, however, the following issues should be addressed:\nAll clinical data and patient characteristics have to be clearly described. For example, \"AF complication\", the pathway of patient care, particularly when presenting with acute coronary syndrome and no persistent ST-segment elevation, criteria for myocardial infarction, in this case, were not well-defined. There were more readmissions among NSTEMI patients; thus, this subgroup requires in-depth analysis. No data are available on treatment during the hospital stay and after discharge, albeit inappropriate treatment or poor adherence could be the leading causes of complications during follow-up as shown in many other studies.\n\nI am wondering why not utilize Cox proportional hazards analysis if rehospitalisation as the outcome was assessed by the authors in a time-dependent manner, i.e. seven days, 30 days, six months, and one year from discharge. If the authors have chosen logistic regression, some details on statistical analysis are required. Specifically, given that the authors provide a single table (Table 2) with results of the univariate regression analysis and the number of patients included in the analysis is stated as 376, it appears that univariate analysis was performed with no relation to the time frame of rehospitalisation. What is the point first to perform univariate analysis with the whole cohort of included patients, and then multivariate one in subgroups according to time of readmission? While presenting the results of the univariate regression the authors utilize ORadj, i.e. adjusted OR. This point is not clear because univariate analysis assumes testing of a single independent variable with no adjustment used. Looks like in the multivariate analysis the authors again included all 376 patients as appears from the title of Table 3. However, if they were interested in predictors of rehospitalisation at a particular time period, those patients which were hospitalized earlier had to be excluded from the analysis of predictors for later periods, unless they required hospitalisations repeatedly. In multivariate analysis, adjustment for age and gender would be reasonable (even if age and gender were not significant predictors).\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? No\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-415
|
https://f1000research.com/articles/10-163/v1
|
01 Mar 21
|
{
"type": "Research Article",
"title": "A cross-sectional study on the pursuit of happiness among healthcare workers in the context of health systems strengthening: The case of Meru County, Kenya.",
"authors": [
"Rose Nabi Deborah Karimi Muthuri",
"Flavia Senkubuge",
"Charles Hongoro",
"Flavia Senkubuge",
"Charles Hongoro"
],
"abstract": "Background: Happiness is one of the ultimate goals of every human being. Happiness is a significant factor of health system efficiency. Healthcare workers are at the core of every health system. However, up-to-date literature on happiness among healthcare workers is limited. The purpose of this study is to investigate the factors influencing the self-assessed happiness among healthcare workers in public and mission hospitals, Meru County, Kenya. Methods: Using a cross-sectional design, a total of 553 healthcare workers in 24 hospitals completed the Orientations to Happiness questionnaire between June and July 2020.\n\nResults: Healthcare workers’ overall happiness was significantly different between hospitals of public and mission ownership (p<0.05). The orientations to happiness mean scores of both pursuits of pleasure and meaning were significantly different between public and mission hospitals (p<0.05). However, there were no statistically significant differences in the pursuit of engagement among the healthcare workers between public and mission hospitals (p<0.05).\n\nConclusion: Our results may have policy and practical implications related to healthcare workers’ happiness policies and programs in future, aimed at health workforce strengthening. Future studies should replicate this study across the remaining 46 counties in Kenya.",
"keywords": [
"Happiness",
"healthcare workers",
"human resources for health",
"physical work environment",
"health systems",
"Kenya"
],
"content": "Introduction\n\nHappiness is a prime goal of each individual1. Among these individuals are healthcare workers, who are the core of any health system2. Happiness is one of the significant factors of health system efficiency3. Happiness can result in better health outcomes, reduced health burden, better performance, increased career success, and increased possibility of a higher income at an individual, organizational and national level3. Happiness at work entails the collective experience of pleasure, positive emotions, work engagement, and a sense of meaning in life4. Experiencing happiness most of the time does not mean eliminating the negative affect aspects of life, because both are important depending on the situation5. Research on the growing epidemic of mental illness-related issues among healthcare workers, such as anxiety, burnout, depression and substance abuse, confirm the challenges they are experiencing6,7. In comparison, there is a dearth of research on healthcare workers’ positive mental health aspects such as happiness, especially in low- and middle-income countries6,7. To effectively develop and implement happiness policy among healthcare workers, empirical research is necessary8.\n\nResearchers often interchangeably use the terms healthcare workers and healthcare professionals. In this study, healthcare workers are individuals trained to practice ethical and evidence-based medicine, and to provide quality health services9. Recently, an extensive systematic review on the determinants of healthcare professionals’ happiness reported that there is currently no universal definition of happiness8. In this study, happiness is viewed as the main result of positive affect and an intrinsic feeling that one’s life is purposeful and worth living10. According to Aristotle, happiness is one of the most important motivators of individuals to make particular choices11. An extensive detailed review of published literature on healthcare workers’ motivation was also published recently12.\n\nThe theoretical framework applied in this study is the authentic happiness theory. The authentic happiness theory by Seligman13 explains the pursuit of happiness in three orientations, namely, the pursuit of pleasure, pursuit of engagement, and pursuit of meaning14. The pursuit of pleasure is a basic level of happiness, characterized by an emotional expression such as smiling or laughter and short term activities that maximize pleasure and minimize pain13. The pursuit of engagement is the experience of flow15. Flow occurs when an individual utilizes all their cognitive and emotional resources, strengths and skills when engaging in a task15,16. Csikszentmihalyi explains that, although joy is not experienced instantly while being engulfed in the activity, it is the aftermath of the flow experience that is energizing14.\n\nThe third orientation to happiness is the pursuit of meaning, which, according to the authentic happiness theory, is the ultimate level of happiness13. Seligman believes when an individual serves something that is larger than themselves, such as family, community, religion, organizations, among others, an individual stands to achieve a sense of meaning13. Peterson and colleagues14 stated the higher scores on all three orientations to happiness equate to a full life. A full life is experienced by pursuing all three orientations associated with a life driven by intrinsic goals and high self-control17. A low score on all three orientations equates to an empty life14. The sole pursuit of pleasure, also known as hedonism, is associated with an empty life and low self-control17.\n\nThe multiple acts of service that healthcare workers perform mean they can achieve the highest levels of happiness due to the essential nature of their job. However, as much as healthcare workers such as physicians are expected to attain a sense of meaning from their work and remain stoic, happiness is often a neglected component in medical training18. The World Health Assembly resolution WHA69.19 titled “The Global strategy for human resources for health: workforce 2030”, urges the member states to actively address the health workforce needs through an intersectoral approach19. Health systems are comprised of both the public and private health sectors20. Thus, this empirical study contributes to literature on healthcare workers’ happiness in both public and private not-for-profit (e.g., mission or faith-based) hospitals.\n\nThe World Happiness Report (WHR) is published annually on International Happiness Day every 20th March since the year 201221. In the WHR, the state of happiness across the globe is reviewed22. Using the science of happiness, various factors affecting happiness of the general population are reported, to inform government policy22. Some of the identified factors of happiness in the general population include age, gender, income, work, governance, education, mental and physical health, values, and family experience23. In 2020, a systematic review reported both individual and organizational factors are significant for healthcare professionals’ happiness8. The factors identified were age, gender, positive attitude, altruism, a sense of meaning, mental and physical health, time management, work-life balance, and quality of life8. Both having a job and being happy at work are important, as people with jobs spend most of their lives at work24.\n\nIn the 2020 WHR, the environment quality significantly impacted individuals’ happiness25. Thus, this study aimed to assess the relationship between the physical work environment in the hospital and healthcare workers’ happiness. Previous studies assessing healthcare workers’ happiness reported their greatest limitations being a small sample size26–28. Researchers have recommended more studies need to be done among larger and more heterogeneous samples exploring multidimensional aspects of happiness among healthcare workers in multiple health system contexts8. In Africa, only one study on happiness among physiotherapists in South Africa has been published29. To effectively facilitate growth of health systems, more studies on happiness need to be done3. The present study was conducted in Kenya, which is a lower-middle-income country in Africa30.\n\nThe objective of this study is to investigate the factors influencing the self-assessed happiness among healthcare workers in public and mission hospitals, Meru County, Kenya. To the best of our knowledge this is the first study investigating happiness among healthcare workers in Kenya. This study will contribute to bridging knowledge gaps related to the role of healthcare workers’ happiness in the Kenyan health system. Empirical evidence is paramount in informing happiness policies related to the quantity and quality aspects of employment24. By investigating the role of demographic and physical work environment factors on happiness, this study will also contribute to information-based happiness strategies and policies geared towards health workforce strengthening. The present study focuses on the following aims:\n\n1. To find the relative importance and strength of agreement of the orientations to happiness among healthcare workers.\n\n2. To assess the significant difference between healthcare workers’ overall happiness in public and mission hospitals.\n\n3. To evaluate the significant difference in the scores of orientations to happiness among healthcare workers between hospital ownership.\n\n4. To explore the relationship between healthcare workers’ overall happiness and factors related to demographics and physical work environment.\n\n\nMethods\n\nUsing a cross-sectional design, this study was performed in public and mission hospitals in Meru County, Kenya. Meru County is a rural area with a total population of 1,545,714 persons31. By 2019, the human resources for health within Meru County was 1872 with 954 medically trained healthcare workers, distributed across 183 health facilities32,33. The focus of this study was on all the 24 county referral service hospitals in Meru County, Kenya.\n\nThe present study was done between June 15, and July 31, 2020, which was during the Covid-19 global pandemic. In Meru County, by the end of June 2020, 16 cases were reported and towards the end of July 2020, 32 cases were reported in a population of 1,545,714 people31.\n\nParticipant selection within the hospitals was made among healthcare workers across different cadres using simple random sampling. To minimize selection bias, simple random sampling was selected as a sampling method because it allowed for each eligible respondent to have an equal probability of being selected. In this study, using a list of healthcare workers in each hospital was obtained from all the hospital administrations. Then respondents were selected according to a simple random number table. In person, respondents were invited and presented with an informed consent form explaining this study, subsequently the willing participants signed and voluntarily agreed to participate.\n\nThe Orientations to Happiness Questionnaire (OTH) was established and validated by Peterson et al., in 2005 to assess an individuals’ orientation to happiness (https://doi.org/10.1007/s10902-004-1278-z)14. The orientations constitute the three primary constructs that are measured in the 18-item questionnaire14. Each of the orientations to happiness has six items on a five-point Likert scale ranging from 1 representing “Not at all like me” to 5 representing “Very much like me”14. Respondents’ happiness index ranges from 18 (lowest possible), signifying an empty life, to 90 (highest possible score), signifying a full-life14. Various studies reported a Cronbach alpha for all the three orientations to range from 0.77 to 0.8814,34,35. The OTH has been used in various countries such as Australia35, South Africa34,36, Italy37, Switzerland38, USA35, and Croatia17.\n\nA section on demographic factors and physical work environment factors were added to the questionnaire. In this study, the independent variables assessed were demographic and work-related, and physical work environment namely hospital ownership, sex, age, income, marital status, qualification, years of experience, healthcare worker cadre, employment type, in-service training, number of hours worked per week, household size, and staff housing39,40. The physical work environment variables were consistent supply of water, occurrence(s) of water unavailability, safe drinking water, acceptable primary source of water, type of toilet facility, risk when using toilet facility, hospital disposal of garbage, availability of water for hand washing, constant availability of soap for hand washing, hand washing station less than five meters from the toilet, workplace safety and health committee, overall safety of hospital working environment39,40.\n\nThese were the independent variables measured, while overall happiness was the dependent variable. On a scale of 0 to 1, when the Cronbach’s alpha is greater than 0.70, this means the instrument is reliable41. In this study, the Cronbach’s alpha was 0.833, which shows that the instrument was reliable in measuring happiness among the respondents. The data analyzed in this study can be found in the Figshare repository42.\n\nStatistical analysis was done using STATA® 15.1 (StataCorp., College Station, TX, USA). We calculated measures of central tendency, the relative importance index (RII), analysis of variance (ANOVA), and used a multivariate linear regression model to determine statistical significance of slope coefficients at 90% and 95% confidence levels of each variable. To control for confounding variables, we used a multivariate model specifically multivariate linear regression analysis. A multivariate linear regression model can handle multiple confounders at the same time43. The questionnaires that were had up to 50% missing data were excluded from the data analysis.\n\nThe RIIs were calculated using the following formula:\n\n\n\nThe RII formula applied shows W represented the weighting as per each respondent on a five-point Likert scale where 1 implies lower happiness scores and 5 higher happiness score. A represented the highest weight, in this case 5 based on the five-point scale. N represented the entire sample. The RII score is between 0 and 1; thus, the high values were 0.8 ≤ RII ≤ 1, high-medium values were 0.6 ≤ RII ≤ 0.8, medium values were 0.4 ≤ RII ≤ 0.6, medium low values were 0.2 ≤ RII ≤ 0.4, and low values were 0 ≤ RII ≤ 0.244.\n\nThe mean of the median absolute deviation (MADM) was a four-step process involving: (a) calculation of the median value of each of the 18 happiness variables; (b) calculation of the absolute deviation for each dependent variable represented as (x) in the sub-formula [xi – median]; (c) calculation of the median absolute deviation; (d) calculation of the MADM39. The MADM classifications signify the following: values of < 1.08 indicates high agreement, 1.08 – 1.41 indicates moderate agreement and, > 1.41 indicates low agreement45.\n\nUsing Analysis of Variance (ANOVA), we examined if there was a statistical difference the orientations to happiness between participants working in public and mission hospitals. A linear multivariate regression analysis was performed to discover the significant factors that influence healthcare workers’ overall happiness. Where happiness (Yk) was the dependent variable and the demographic, and physical work environment factors were the 25 independent variables (Xjk). The linear multivariate regression model applied was as follows46:\n\n\n\nWhere: β0 indicates the constant or intercept term capturing the unexplained variations in the dependent variable Y. β1 indicates the slope coefficient measuring the amount by which Y will change when X changes by a single unit. k goes from 1 to n, in this case the 25 independent variables. X1k= stands for the kth observation value for the independent variable X1. ∈k is the error (disturbance) term that captures errors in model specification and other factors that influence healthcare workers’ happiness but are not explicitly considered in the model.\n\nThe protocol of this study was ethically approved by three institutions, namely:\n\n1. The Faculty of Health Sciences Research Ethical Committee, University of Pretoria, South Africa (Reference number: 718/2019).\n\n2. The Institutional Review Board (IRB), United States International University-Africa, Kenya (Reference number: USIU-A/IRB/130-2020).\n\n3. The National Commission for Science, Technology, and Innovation (NACOSTI), Kenya (Research licence number: 901924).\n\nThe Meru County Government Department of Health also provided clearance for the conduct of this study (CGM/COH/1/17(50). This was followed by hospital administrative approvals from each of the 24 hospitals. The investigator provided respondents with informed consent forms explaining: the purpose of the study; participation in the research study was voluntary; refusal to participate would not have negative effect on their job; s/he has the liberty withdraw from the study at any time; research poses no risk. Following this explanation, respondents in this study voluntarily signed the informed consent forms, agreeing to participate.\n\n\nResults\n\nIn this study, from 566 questionnaires 553 were analyzed, thus the response rate was 97.7%, as 13 questionnaires were excluded from analysis due to 50% or more missing data39,40.\n\nThe study involved a sample of n= 553 healthcare workers42. This study revealed that majority of the healthcare workers under study worked in public hospitals (78.48%), were female (61.30%), nurses (30.56%), had attained a diploma (60.58%), were employed full-time (93.49%), had attended in-service training (66.00%), were married (63.11%), and earned between 46,000–65,000 Kenyan shillings (KES) (about US$ 460–650), 10.7 years of experience, worked for 39 hours per week, lived in a median household size of three individuals, were not accommodated within the hospital compound (86.62%), and were between the ages 20 and 78 years (the mean age was 36.5 years).\n\nOut of the overall sample of respondents, 83.00% always had a water supply, but 17.00% did not; 39.78% reported experiencing occurrence of unavailability of water for one or more days at the hospital within a month, while 60.22% did not experience this challenge; 74.68% had access to safe drinking water, but 25.32% did not. In terms of sanitation facilities, 75.95% of the respondents reported that hospitals had flush or pour-flush toilets, while 24.05% reported hospitals had pit latrines.\n\nIn terms of risk when using toilet facilities, 74.50% reported no risk and 25.50% reported some risk. Of the latter, 17.90% reported health (e.g., infections) risk, 2.89% risk of injury, 2.71% harassment and 1.99% a combination of two or more types of risk. Responses regarding mechanism of disposal of hospital waste: 18.08% indicated formal collection service, 2.71% informal collection service, 32.73% disposal in a designated area, 24.95% disposal within the hospital compound, 9.40% disposal elsewhere (burning, burying or other) and 12.12% unknown.\n\nThe overall distribution of responses concerning hygiene factors was: 91.86% reported constant availability of handwash soap, but 8.14% reported unavailability; 84.63% reported receiving a consistent supply of water for hand washing, but 9.76% reported inconsistency on the same; 90.24% reported appropriate distance of either five meters or 10 steps away hand washing stations from toilet facilities; however, 9.76% disagreed with this statement. About 56.60% of respondents reported existence of an occupational (or workplace) safety and health committee, while 43.40% posited it did not exist. The overall perceived safety of the hospital working environment reported by respondents was 1.99% not safe, 17.90% slightly safe, 54.25% moderately safe, and 25.86% very safe.\n\nTable 1 shows the mean scores and standard deviations of the three orientations to happiness by the overall sample (n=553) and hospital ownership sub-samples (public hospitals n=434 and mission hospitals n=119).\n\n*Reported on 1–5 scale with higher values are suggestive of higher happiness\n\nAmong the orientations to happiness, the pursuit of meaning had the highest mean scores. In the overall sample, the pursuit of pleasure had the second highest mean scores, followed by the pursuit of engagement. The opposite order was reported for the second and third highest mean scores in mission hospitals, where the pursuit of engagement was second and pursuit of pleasure third (as shown in Table 1). The overall happiness average score was 64.59; 65.14 in public hospitals and 62.57 in mission hospitals (on an 18–90 scale).\n\nThe MADM results showed that healthcare workers moderately agreed to the pursuit of pleasure items as an orientation to happiness. Three items were moderately supported, and the healthcare workers strongly supported three other items. The healthcare workers highly agreed that the pursuit of engagement contributed to their happiness. Four items of the six were strongly supported, and the remaining two had moderate and low support in terms of their contribution to happiness. The pursuit of meaning items were all strongly supported as contributors to the healthcare workers happiness, signified by the high levels of agreement (see Table 2).\n\n1MAD: Median absolute deviation.\n\n2MADM: Mean absolute deviation from the median.\n\nThe relative importance of the orientations to happiness showed the pursuit of meaning was the most important, followed by the pursuit of pleasure. The pursuit of engagement was ranked third important orientation to their happiness (as shown in Table 3).\n\nANOVA analysis results. Hospital ownership explained 0.91% of the variance in overall happiness score among the healthcare workers. The ANOVA analysis results show there was a statistically significant difference between healthcare workers’ happiness and hospital ownership (p=0.2551) (as shown in Table 4).\n\n*p < 0.05 indicates statistical significance.\n\nThere was a statistically significant difference between the hospital ownership, in the mean score of pursuit of pleasure (p<0.001) and pursuit of meaning (p=0.024) orientations to happiness. No statistically significant difference between the ‘pursuit of engagement’ scores and hospital ownership (p=0.241) were reported (as shown in Table 5).\n\nReported on 5-point Likert scale with higher values are suggestive of higher happiness.\n\n*p < 0.05 indicates statistical significance.\n\nMultivariate regression analysis results. Table 6 presents the multivariate regression model results for overall happiness, and demographic, and physical work environment factors. Hospital ownership and qualification were the two statistically significant demographic factors of the healthcare workers’ happiness. Related to the physical work environment, the acceptable primary source of water, type of toilet and workplace safety and health committee were the three significant factors of the healthcare workers’ overall happiness. The remaining 20 demographic and physical work environmental factors were statistically non-significant (p > 0.1). The linear multivariate regression model results illustrate eight demographic factors were negatively correlated with the healthcare workers’ overall happiness. The factors included hospital ownership, income, sex, age, marital status, qualification, household size and staff housing (p > 0.1). Five physical environment factors had negative association with healthcare workers’ overall happiness (p > 0.1). The constant demonstrates the 58.32% of the variance in the overall happiness (the dependent variable) were not explained by the independent variables.\n\n*p < 0.05 indicates statistical significance at 95% confidence level.\n\n**p < 0.1 indicates statistical significance at 90% confidence level.\n\n\nDiscussion\n\nThe authentic happiness theory guided the investigation of factors influencing the self-assessed pursuit of happiness among healthcare workers in Meru County, Kenya. Our results show that five factors significantly contributed to healthcare workers’ overall happiness. The two significant demographic factors reported in this study were hospital ownership and qualification. Hospital ownership influenced the overall happiness of the healthcare workers. Healthcare workers’ overall happiness was slightly higher in public hospitals than those working in mission hospitals. Hospital ownership significantly influenced the healthcare workers’ pursuit of meaning and pleasure. However, in this study, there was insufficient evidence of hospital ownership influencing the pursuit of engagement in the larger population of healthcare workers. To date, this is the first study to investigate the association between the pursuit of happiness and hospital ownership among healthcare workers.\n\nIn the current study, the qualification or education level significantly influenced the overall happiness of healthcare workers. The more educated the respondents were, the lower their overall happiness scores. However, a study in India reported higher qualifications positively correlated with higher happiness47. The differences in our study and the Indian study could be a result of highly qualified healthcare workers in Kenya being part of the healthcare worker cadres experiencing the highest health workforce critical shortage such as doctors, clinical officers, nurses and specialists2. For skilled healthcare workers, the severe shortage results to heavier workload, thus resulting in demotivation12 and reduced happiness8. In this study, three of the five significant factors of healthcare workers overall happiness were part of the physical work environment.\n\nThis study emphasizes the importance healthcare workers place on cleanliness, water, and sanitation, and workplace health and safety in relation to their overall happiness as they provide health services. The availability of an acceptable primary source of water, functional flush toiletry facilities, and the presence of a functional workplace health and safety committee significantly contributed to the overall happiness of the healthcare workers. A Korean study similarly revealed an improved and enabling work environment significantly increased nurses happiness index48. One possibility for the significance of certain physical work environment factors in the healthcare workers happiness is that the physical work environment plays a part in the psychological attitude one has, either positive or negative. The attitude of healthcare workers in the workplace impacts the quality of healthcare, patient outcomes, and overall safety49. This study contributes to the authentic happiness theory by revealing the significant factors of happiness, and the order of relative importance of the orientation to happiness in a health setting.\n\nIn this study, the order from most to least important orientation to happiness among respondents was the pursuit of meaning, pleasure, then engagement.\n\nIn this study, living a meaningful life was the most important pursuit of happiness among healthcare workers. Similar findings have been reported regarding career meaning contributing to happiness among physicians50 and physiotherapists27. Our findings are also congruent with the African philosophy of happiness. Happiness in the African context stems from the meaningful aspect of human existence51. In African philosophy, the two ways the African people derive meaning and happiness are through the collectivist culture of communal bonds and believing in a higher supernatural being51. This signifies that attaining a sense of meaning through their work and collectivist activities, aimed at contributing to something larger than oneself, is important to healthcare workers. In the current study, the pursuit of pleasure was the second most important orientation among the respondents.\n\nThe pursuit of pleasure, also known as hedonism, is the desire to attain maximum pleasure with minimal pain and instant gratification13,17. As a result, the pursuit of pleasure is viewed as an impediment to long term happiness52. For instance, smoking among medical students53 for pleasure has been viewed as a risk-taking behavior at the price of longevity52. However, the negative or positive view of the pursuit of pleasure is dependent on the contextual meaning. In 2010, researchers reported healthcare professionals’ derived pleasure in the workplace by working as a team to save lives, minimize the pain of their patients and feeling valuable through providing quality care54. A positive pursuit of pleasure among healthcare workers involves organizational actions for instance reduced incidence of overtime and introducing leisure activity programs to promote healthcare workers’ happiness49. This implies that the pursuit of pleasure among healthcare workers can be considered as positive through maximizing pleasure and minimizing sources of pain. For example, improving the physical work environment, collectivistic activities such as team building that encourage teamwork, reducing the healthcare worker shortage, and providing psychological support aimed at promoting their happiness.\n\nAt work, the pursuit of engagement is also known as work engagement and is characterized by the experience of flow. According to Csikszentmihalyi, flow is attained through applying one’s signature strengths to perform challenging tasks, requiring high degree skill and dedication13,15. In the current study, the pursuit of engagement was the third most important pursuit of happiness. Previous studies have reported positive, significant and strong associations between healthcare workers’ work engagement and high productivity55, high job performance56, better teamwork57, improved patient safety55, and a better quality of health care55,57. Clearly, work engagement strategies need to be developed and implemented, because the score in this pursuit was the lowest of the three orientations to happiness in the current study. All orientations to happiness are essential in developing authentic happiness signified by a full life14.\n\nA full life is attained by the collective scores of all the orientations to happiness, while the opposite is true for the empty life14. Collectively, the healthcare workers in this study were about 71.7% closer to attaining the highest score of overall happiness. The present study found the overall happiness scores were slightly higher among healthcare workers employed in public hospitals than those in mission hospitals. This could be attributed to the differences in hospital ownership, which have an impact on the health facility operations and availability of resources. The current findings show that there is an opportunity for empowering healthcare workers to achieve authentic happiness. Based on the findings of this study, healthcare workers’ happiness policies are important because experiencing happiness at work enables individuals to optimally function in the workplace5. By developing happiness policies and strategies that are sensitive and solve the healthcare workers’ issues, significant progress in strengthening the health workforce and health system in Kenya will be achieved. Health systems strengthening would result in improved health workforce responsiveness, universal access to quality healthcare services, improved productivity, and better patient outcomes58.\n\nBased on these findings we believe happiness of healthcare workers should be mainstreamed into the ‘Kenya Health Policy’ and ‘Kenya Health Sector Strategic Plan’. This suggestion is based on the results of this study, and the United Nations General Assembly resolution advocating for happiness and well-being policies to be mainstreamed into public policies was passed by all Heads of State including Kenya1. The Kenyan health system stands to benefit from happier healthcare workers due to the probability of increased health system efficiency. It appears that healthcare workers’ happiness could be increased by enhancing and solving challenges related to demographic and physical work environmental factors. For example, healthcare workers’ qualification significantly contributed to their overall happiness. Thus, positive education can be mainstreamed into the healthcare workers pre-service curriculum and in-service training. Positive education would entail involving experts in the field to apply evidence-based approaches to teach healthcare workers how to be engaged, develop character strength, cultivate healthy relationships, practice physical wellbeing, and achieve a sense of meaning59. Positive education programs could empower healthcare workers to be competent enough to achieve authentic happiness.\n\nThe Government of Kenya should also consider applying a formal health care appraisal (HCA) system. According to the Global Happiness and Well-being Policy Report, a formal HCA provides an opportunity for governments to perform needs assessment, cost-benefit analysis, impact, and post-hoc analysis of regulations and interventions in health settings, to optimize the scarce healthcare resources60. Thus, the Government of Kenya can set happiness metrics, targets, and indicators to monitor and evaluate the impact of implementing happiness policies among healthcare workers. The happiness policies and implementation of happiness interventions could boost the healthcare workers’ mental health and wellbeing and the quality of care provided to patients60. At a national level, this is likely to contribute to the improvement of health indicators in Kenya.\n\nHappiness policies would promote the focus of developing mental health. To effectively develop and implement happiness policy, strategic plans, and programs, the World Health Organization (WHO) has published a report titled ‘Mental Health Policy, Plans and Programmes’61. In this report WHO explains the seven essential steps of developing mental health policies, the four steps of creating a mental health plan, plus how to develop a mental health program61. Most importantly, the seven-step process of implementing the policy, plans and programs61. Using the results from this study and guided by the WHO report61, policy makers and implementers should seriously consider developing happiness policies, plans, and programs aimed at strengthening the health workforce and health system, by promoting mental health among healthcare workers in Kenya. Lastly, the development and implementation of happiness within the health system should involve most stakeholders such as policy makers in government, health mangers and healthcare workers in the public and private health sectors.\n\nThe results from this study should be interpreted in view of the study’s shortcomings. This study utilized a cross-sectional design; hence correlational evidence not causal evidence was derived on the relationship between variables. In future, the Government of Kenya should perform experimental design studies to assess costs and benefits of alternative healthcare workers’ happiness policies, programs and interventions geared towards health systems strengthening, at the national and county levels. Secondly, this study was based on self-assessed happiness data, which presents the possibility of response and social desirability bias. To reduce the tendency of response and social desirability biases, the researchers informed the respondents that anonymity would be upheld throughout the entire research process and encouraged them to be as honest as possible.\n\nThe scope of the present study did not assess the role of job characteristics on healthcare workers’ happiness. Future studies could explore the impact of job characteristics on happiness among healthcare workers. We also acknowledge that other quantitative and qualitative studies may produce different results due to contextual factors or methodological differences. Thus, more studies using different methodologies are necessary to bridge the knowledge gaps on healthcare workers’ happiness in Kenya. Finally, this study was done in one of 47 counties in Kenya, thus restricting the generalizability of the study results. In future, research geared towards promoting healthcare workers’ happiness should be carried out across the remaining 46 counties, to provide evidence-based healthcare worker happiness policies nationwide.\n\n\nConclusion\n\nIn Kenya, this is the initial study reporting healthcare workers’ level of happiness and factors influencing their pursuit of happiness. The most important orientation to happiness among the participants was the pursuit of meaning, followed by the pursuits of pleasure and engagement. These results were contextually synchronized to the African philosophy of happiness, where the sense of meaning is believed to be a significant element of ultimate happiness. This means that happiness policies, strategies, and programs aimed at empowering healthcare workers to attain a sense of meaning are more likely to be effective in promoting happiness. The MADM results showed that healthcare workers highly agreed that both the pursuit of engagement and meaning contributed more to their happiness than the pursuit of pleasure. These findings imply that health leaders and managers aiming to improve and effectively execute healthcare workers’ happiness strategies and programs need to consider all pursuits of happiness. Based on the OTH theory, this will enable healthcare workers to achieve authentic and long-term happiness, which are attributes of a full life. The factors of happiness reported in this study were hospital ownership, qualification, acceptable primary source of water, type of toilet facility and workplace safety and existence of a health committee. The findings provide an understanding that both demographic and physical work environment factors influence healthcare workers’ overall happiness. The policy implications for the factors reported, show that an intersectoral approach in designing and implementing evidence-based happiness policies and interventions, needs to be done involving both the private and public sectors.\n\n\nData availability\n\nFigshare: Data used to investigate healthcare workers’ pursuit of happiness in Kenya. https://doi.org/10.6084/m9.figshare.13655822.v142.\n\nThis project contains the following underlying data:\n\n- Dataset used to investigate healthcare workers' pursuit of happiness in Kenya RNDKM.xlsx. (The dataset includes some demographic and work-related variables from variable 1 to 25 and, the results from the Orientations to Happiness (OTH) questionnaire (Var 26–43). The healthcare workers' overall happiness scores were calculated based on the responses from Var 26–43, which are presented in Var 44. Below the dataset on the same data spreadsheet are variable definitions. It includes the variable label e.g., Var 1, Var 2 etc.; the variable definitions and coding descriptions.)\n\nData are available under the terms of the Creative Commons Zero \"No rights reserved\" data waiver (CC BY 4.0 Public domain dedication).",
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}
|
[
{
"id": "81292",
"date": "01 Apr 2021",
"name": "Ian Couper",
"expertise": [
"Reviewer Expertise Rural health",
"human resources for health",
"health professions education",
"health service 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\nA cross-sectional study on the pursuit of happiness among healthcare workers in the context of health systems strengthening: The case of Meru County, Kenya.\nThis study, which sought to measure health workers happiness in public and mission hospitals in a county in Kenya, sets out a very interesting proposition, and, mostly, I enjoyed reading it. I found the notion that happiness can be formulated as a policy to be an interesting one, in terms of which I am still left somewhat in doubt, but that does not mean it should not be indexed.\nI think the article could be significantly improved by further work and some suggestions below:\nIn the introduction, a number of broad statements are made, without clear justification, especially in the first two paragraphs. It was unclear to me whose happiness or what happiness is being referred to every time happiness is mentioned. Does happiness at work related to the health workers rather than patients, to all staff or just healthcare workers, to healthcare professionals or all healthcare workers, etc..? The article notes that researchers often use the terms \"healthcare workers\" and \"healthcare professionals\" interchangeably, but then does not explain whether that is the case in this article or what is the definition being used. A definition of happiness is given, which is specifically linked to purpose, but then the article states that the authentic happiness theory is used, which in fact includes three orientations and not just one towards purpose. This should be clarified.\nI found the logic of the paragraph starting “the multiple acts of service that healthcare workers perform” difficult to follow.\nIn terms of the aims of the study, I was not clear on the difference between the second and third aim. Also the fourth aim (“to explore”) implies a qualitative approach which is not mentioned in the article.\nIn the methods section, it is not clear what is meant by “medically trained health care workers”. In referring to the study sample, it is stated that a list of health care workers is used, but how this is defined is not clear.\nI do not have the expertise to comment on the statistical analysis.\nIn the results section, there are two citations after to the comment about 50% or more missing data; it is not clear to me what these are referring to.\nThe subsection on the demographic factors has too much detail for the text - a table would be better with only the key issues being highlighted in the text.\nThe subsection “Factors of healthcare workers’ overall happiness” tends to repeat what is in the tables - it should only provide the highlights of those, where the information is readily accessible in the tables.\nI think the discussion section needs focus. I found it difficult to sustain my interest in reading it.\nThe discussion states that health care workers overall happiness was slightly higher in public hospitals than in mission hospitals, but I could not see that in the tables; there is no reference to which table it might be in.\nA problem that occurs almost throughout the discussion is that the last sentence in each paragraph seems to refer to the subsequent paragraph, but should in fact be part of that next paragraph. I'm happy to provide a marked-up copy of the article to demonstrate this.\nThe subsection on implications for policy and practice contains quite ambitious recommendations that are made on the basis of the study despite the acknowledged limitations of the research. These need to be clearly justified. In addition, specifically, the recommendation on research geared towards promoting happiness being carried out across the whole country is surely something that is dependent on higher quality studies being done in a limited number of locations first.\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? No",
"responses": [
{
"c_id": "6674",
"date": "24 May 2021",
"name": "Rose Nabi Deborah Karimi Muthuri",
"role": "Author Response",
"response": "Ref: Response to review report 1 Firstly, thank you very much for reviewing our article and for all the constructive suggestions and comments. Please find below our response to the comments and suggestions. The article has been revised accordingly following your review. Reviewer comments and Authors Response 1. Reviewers’ comment: “I found the notion that happiness can be formulated as a policy to be an interesting one, in terms of which I am still left somewhat in doubt, but that does not mean it should not be indexed.” Authors response: Thank you for your comment. The idea of happiness being formulated in policy stems from the decision made by all 193 heads of state (presidents) in the United Nations General Assembly, who passed the resolution on happiness and believe that it should be incorporated into public policy. Following this decision since 2012, the World Happiness Report is published annually on 20th March on the International Day of Happiness. Therefore, this study contributes to literature on happiness among healthcare workers to inform policy in the context of the health system in Kenya. The references of the resolution and first World Happiness Report are: United Nations General Assembly. Happiness: Towards a holistic approach to development. New York; 2011 19 July 2011. Contract No.: Resolution A/RES/65/309. Helliwell J, Layard R, Sachs J, (Eds). World happiness report. Columbia University: The Earth Institute; 2012. 2. Reviewers’ comment: “In the introduction, a number of broad statements are made, without clear justification, especially in the first two paragraphs. It was unclear to me whose happiness or what happiness is been referred to every time happiness is mentioned. Does happiness at work related to the health workers rather than patients, to all staff or just healthcare workers, to healthcare professionals or all healthcare workers, etc.? The article notes that researchers often use the term ”healthcare workers” and “healthcare professionals” interchangeably, but then does not explain whether that is the case in this article or what is the definition being used. A definition of happiness is given, which is specifically linked to purpose, but then the article states that the authentic happiness theory is used, which in fact includes three orientations and not just one towards purpose. This should be clarified.\" Authors response: Thank you for this constructive review and questions. In the revised version of the article, the first two paragraphs have been reorganized and slightly modified to enhance clarity. In the revised version, it has been clarified that this study focuses on healthcare workers happiness and includes operational definitions of healthcare workers and happiness. In addition, justification of the significance of studies aimed at promoting happiness and well-being was made in the introduction, by stating the problem of the rising reports of psychopathological symptoms among healthcare workers depicted in various research cited in this article. In paragraph 1, the definition of happiness was also modified to include all three orientations to happiness and to be in synchrony with the authentic happiness theory applied in this study. This study focused on healthcare workers’ happiness and not patients. However, studies have revealed that when healthcare workers are happier it has a positive impact on quality of patient care, and this is referred to in the introduction and discussion sections. Regarding the happiness of the other staff, we have included in the limitations sub-section, that further research should be done among other staff such as auxiliary and non-clinical staff and possibly workers in other sectors. This would contribute to informing the formulation of public policy in Kenya, following the resolution passed by the United Nations General Assembly. 3. Reviewers’ comment: “I found the logic of the paragraph starting “the multiple acts of service that healthcare workers perform” difficult to follow.” Authors response: In the revised version of the article, as advised to enhance logical flow, this paragraph was modified, and the information moved to other parts of the introduction. For example, the second sentence was modified and moved to paragraph one of the introduction section. And sentence 3-5 of the same paragraph were moved to second last paragraph of the introduction. 4. Reviewers’ comment: “In terms of the aims of the study, I was not clear on the difference between the second and third aim. Also the fourth aim (“to explore”) implies a qualitative a qualitative approach which is not mentioned in the article.” Authors response: Thank you for this comment. Following your advice, in the revised version of the article, the term “to explore” has been changed to “to identify” because this is a quantitative study. The second aim was about the differences in healthcare workers overall happiness between public and mission hospitals. The third aim was about the differences in the orientations to happiness among healthcare workers in public and mission hospital. In the revised version, following your suggestion, a modification has been made of merging the two objectives because they are both about differences in healthcare workers happiness in public and mission hospitals. 5. Reviewers’ comment: “In the methods section, it is not clear what is meant by “medically trained health care workers”. In referring to the study sample, it is stated that a list of health care workers is used, but how this is defined is not clear.” Authors response: Thank you for this suggestion. In the revised version, a slight modification of terminology has been made for clarification from “medically trained” to “clinically trained”. The reason being this suits’ the definition of healthcare workers in this article which is in the paragraph 1 of the introduction section. 6. Reviewers’ comment: “In the results section, there are two citations after to the comment about 50% or more missing data; it is not clear to me what these are referring to.” Authors response: The citations are examples of studies that have used a similar criterion of exclusion due to missing data. In the revised version, clarification has been made explaining that 50% missing data meant that the questionnaires were 50% incomplete thus were excluded from analysis. 7. Reviewers’ comment: “The subsection “Factors of healthcare workers’ overall happiness” tends to repeat what is in the tables- it should only provide the highlights of those, where the information is readily accessible in the tables.” Authors response: Following your recommendation, in this sub-section on “Factors of healthcare workers’ overall happiness”, in the revised version, the paragraphs highlight the key points such as the statistically significant factors shown in Table 4-7. However, details on the slope coefficients, standard error, t-value etc, are not highlighted in the text because the information is in the tables. 8. Reviewers’ comment: “The discussion states that health care workers overall happiness was slightly higher in public hospitals than in mission hospitals, but I could not see that in the tables; there is no reference to which table it might be in.” Authors response: In the discussion section in the revised version of the article, in paragraph 1 a reference to Table 5 has been presented. In paragraph 7, reference to Tables 1 and 5 have been made in the discussion. 9. Reviewers’ comment: “A problem that occurs almost throughout the discussion is that the last sentence in each paragraph seems to refer to the subsequent paragraph but should in fact be part of that next paragraph.” Authors response: Thank you for your beneficial suggestion. In the revised article, as advised, this problem has been corrected in the discussion section in paragraphs 3,4, and 5. 10. Reviewers’ comment: “The subsection on implications for policy and practice contains quite ambitious recommendations that are made on the basis of the study despite the acknowledged limitations of the research. These need to be clearly justified. In addition, specifically the recommendation on research geared towards promoting happiness being carried out across the whole country is dependent on higher quality studies being done in a limited number of locations first.” Authors response: Thank you for your comment. In the revised version of the article modification of the specified recommendation has been made by stating that the Government of Kenya use other study designs such as experimental design to assess healthcare workers happiness, can be applied in other locations. The implications and conclusion presented in this study are based on our results. To justify the implications (recommendations) in addition to the present results, references of some documented policies where possible have been included. For example, the recommendation of positive education being included in the pre-service clinical curricula and in-service training because level of qualification (education) was significant in this study. Finally, our recommendations may be ambitious, but the COVID-19 pandemic has revealed the importance of healthcare workers happiness and well-being, to provide patients with the quality health care. 11. Reviewers’ comment: “Are the conclusions drawn adequately supported by the results? No.” Authors response: In the revised version, the conclusion has been modified following the additional analysis. In the conclusion, results detailing the factors of overall happiness in public and mission hospitals separately have been presented in the conclusion of the article. We thank you for your constructive advice, comments, and review."
}
]
},
{
"id": "82106",
"date": "19 Apr 2021",
"name": "Zhuo Chen",
"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 manuscript investigated the difference in healthcare workers’ happiness between public and mission hospitals, as well as the impact of demographic and work environment factors on self-assessed happiness. The study addressed an important topic, i.e., self-assessed happiness among healthcare workers, and provided policy implications on the strategies to strengthen workforce for the healthcare system in Kenya. We have some suggestions for authors to consider in revising the manuscript.\nOne of our major comments is the lack of review of the economics and social epidemiology literature on happiness. We acknowledge the disciplinary differences but this might have a consequence on the model specifications. For instance, Blanchflower and Oswald1 presented evidence that well-being is U-shaped through life. There is also a long-lasting debate of how relative income or income inequality might affect happiness and health. The authors may want to review and discuss implications for their research.\nThe authors have conducted extensive analyses, which are mostly straightforward and clearly presented. We have some specific comments on the analysis below:\nIn the second paragraph on data collection and data source, the authors mentioned the employment type was included into demographic factors. However, the employment type in this study only contained full-time or part-time options. Job characteristics play an important role in determining both the work environment and the way to pursuit happiness.\nThe authors were concerned about the difference of correlations with happiness between public and mission hospitals. T-tests for the difference between public and mission hospitals would be useful to be included in Table 1. The results of ANOVA analysis indicated that healthcare workers in public hospitals were more likely to obtain a high level of overall happiness. We would suggest conducting a subgroup analysis for the multivariate regressions rather than using hospital ownership as the independent variable into the model. A subgroup analysis helps to detect the heterogeneity of factors affecting happiness in different hospitals.\nThe explanations of the results from Table 6 may not be sufficient. There were many variables included in the regression model but came out statistically insignificant. Some of the variables need additional explanations. For example, hospital ownership and sex categories may be labeled out. Results of those variables in the current version of Table 6 is difficult to interpret. In addition, the income variable is insignificant in this regression. However, different functional forms, logarithm, or quadratic, could be used if there is a nonlinear correlation between income and happiness, as prior literature has suggested. Some of the variables that are statistically insignificant may be dropped through stepwise regression to identify a more parsimonious specification.\n\nAn in-depth discussion on the contrast and comparison of three types of orientations of the pursuit of happiness would be very useful.\nMinor comments:\nThe study setting in methods parts could be more closely linked to the background of research and study sample. It would be useful to include, in addition to the COVID-19 pandemic, a brief description of the health system in Meru County, Kenya.\n\nA descriptive summary of the variables would help readers to understand the data and the context if presented before the multivariate regression.\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": "6675",
"date": "24 May 2021",
"name": "Rose Nabi Deborah Karimi Muthuri",
"role": "Author Response",
"response": "Ref: Response to review report 2 Firstly, thank you very much for reviewing our article and for all the constructive suggestions and comments. Please find below our response to your comments and suggestions. The article has been revised accordingly following your review. Reviewers comments and Authors Response 1. Reviewers’ comment: “One of our major comments is the lack of review of the economics and social epidemiology literature on happiness. We acknowledge the disciplinary differences, but this might have a consequence on the model specifications. For instance, Blanchflower and Oswald1 presented evidence that well-being is U-shaped through life. There is also a long-lasting debate of how relative income or income inequality might affect happiness and health. The authors may want to review and discuss implications for their research.” Authors response: Thank you for your constructive suggestions. In the revised version of this article, we have reviewed literature regarding happiness research and income. Thank you for the reference you provided, we incorporated the relevant literature as per the aim of our study (please see the introduction section, paragraph 7). In the discussion section, based on our updated results related to income and happiness, we also included literature on the same (please the discussion, paragraph 2). The social aspects of happiness are also presented in the discussion section, where collectivistic activities such as team building, and the pursuit of pleasure and meaning are associated with social aspects of life (please see paragraph 6). 2. Reviewers’ comment: “In the second paragraph on data collection and data source, the authors mentioned the employment type was included into demographic factors. However, the employment type in this study only contained full-time or part-time options. Job characteristics play an important role in determining both the work environment and the way to pursuit happiness.” Authors response: Thank you for this constructive review. In the revised version, we have included that the role of job characteristics in healthcare workers’ happiness, was beyond the scope of this study and is a possible area of study in future. Please see in the discussion section titled ‘Limitations and areas for further research’ section paragraph 2. 3. Reviewers’ comment: “T-tests for the difference between public and mission hospitals would be useful to be included in Table 1. The results of ANOVA analysis indicated that healthcare workers in public hospitals were more likely to obtain a high level of overall happiness. We would suggest conducting a subgroup analysis for the multivariate regressions rather than using hospital ownership as the independent variable into the model. A subgroup analysis helps to detect the heterogeneity of factors affecting happiness in different hospitals.” Authors response: In the revised version of the article, as advised, in addition to the ANOVA analysis, a two-sample Welch’s T-test was performed and results presented in the results section titled, “Orientations to happiness and hospital ownership”. As you suggested, a sub-group multivariate regression analysis was performed for public and mission hospitals separately and presented in Table 6 and 7. Therefore, we excluded hospital ownership as an independent variable, because a statistically significant difference was found between mission and public hospitals and overall happiness. 4. Reviewers’ comment: “In addition, the income variable is insignificant in this regression. However, different functional forms, logarithm, or quadratic, could be used if there is a nonlinear correlation between income and happiness, as prior literature has suggested. Some of the variables that are statistically insignificant may be dropped through stepwise regression to identify a more parsimonious specification.” Authors response: Thank you for this suggestion. In the revised version, in the methods section we explain that we used a double-log regression model in which the constants are elastic and allow for indifferent curves (please see the section titled “Statistical analysis” in paragraphs 9 and 10). As advised, the double-log regression results of income and happiness are presented in the section titled “Regression analyses results”. However, we chose to present all the other independent variables in the Tables 6 and 7 and not perform stepwise regression. This will allow readers to be able to see all variables that were assessed and possibly compare results in future. Therefore, following your recommendation, the previously collective Table 6 with results of all participants (n=553) was separated into Table 6 and 7 and the statistically significant variables marked with asterisks (*=p<0.05 and **p<0.1). 5. Reviewers’ comment: “An in-depth discussion on the contrast and comparison of three types of orientations of the pursuit of happiness would be very useful.” Authors response: Thank you for this suggestion. The details regarding the Orientations to happiness are presented in the introduction section (paragraphs 3-4). In the discussion section, our results regarding the orientations to happiness in relation to other relevant studies are incorporated where appropriate in paragraphs 6-9. 6. Reviewers’ comment: “The study setting in methods parts could be more closely linked to the background of research and study sample. It would be useful to include, in addition to the COVID-19 pandemic, a brief description of the health system in Meru County, Kenya.” Authors response: Thank you for your beneficial suggestions. In the revised version, specifically the methods section, information regarding the five-level health system of Meru County in Kenya has been included. Furthermore, information regarding the COVID-19 pandemic in Kenya and its impact globally has been included in the revised version. Please see the methods section titled, “Study setting”. 7. Reviewers’ comment: “A descriptive summary of the variables would help readers to understand the data and the context if presented before the multivariate regression.” Authors response: Thank you for this suggestion. In the revised version, as advised, a descriptive summary of all the variables assessed are presented in the Methods section titled, “Statistical analysis” in paragraphs 5-6, before the multivariate regression. Citations are also included in this section because the data used in this study is from a published dataset in the FigShare repository. 8. Reviewers’ comment: “Is the work clearly and accurately presented and does it cite the current literature? Partly.” Authors response: Thank you for your review. In the revised version, we have modified the introduction and discussion sections and included current literature within the scope of our study. Furthermore, to increase the clarity, we re-arranged the introduction section. We thank you both for your constructive advice, comments, and review."
}
]
}
] | 1
|
https://f1000research.com/articles/10-163
|
https://f1000research.com/articles/10-413/v1
|
24 May 21
|
{
"type": "Research Article",
"title": "Receptiveness to participating in cannabis research in pregnancy: a survey study at The Ottawa Hospital",
"authors": [
"Kira Bombay",
"Malia SQ Murphy",
"Kathryn M Denize",
"Christina Cantin",
"Amy McGee",
"Ruth Rennicks White",
"Shi Wu Wen",
"Mark C Walker",
"Daniel J Corsi",
"Kira Bombay",
"Malia SQ Murphy",
"Kathryn M Denize",
"Christina Cantin",
"Amy McGee",
"Ruth Rennicks White",
"Shi Wu Wen",
"Mark C Walker"
],
"abstract": "Background: The prevalence of cannabis use among pregnant individuals in Canada is increasing. In the design of new cohort studies to evaluate the patterns and outcomes of cannabis use in pregnancy, consideration must be given to the factors influencing participation, data sharing, and contribution of biological samples. Our objective was to assess the willingness of pregnant individuals to participate in prospective research during pregnancy. Methods: We surveyed pregnant individuals receiving obstetrical care through The Ottawa Hospital in Ottawa, Canada. The survey consisted of 23 dichotomous (yes/no), multiple-choice, Likert scale, and open-ended questions. Individuals were provided with a hypothetical research scenario and asked to report on the likelihood of their participation, use and storage of personal health information and contribution of maternal and newborn samples. Individuals provided motivating and deterring factors related to research participation. Descriptive statistics included frequencies (n) and percentages (%) for categorical variables. Continuous variables were described using means and standard deviations. Results: A total of 84 survey responses were collected. The mean age of respondents was 32.6(±5.3) years. Respondents were predominantly Caucasian (79%), college/university educated (85%) with a household income of ≥$100,000 (64%). There was a high degree of willingness to participate in prospective research by sharing data and biological samples. The most commonly cited motivating and deterring factors for participating in future research were a desire to contribute to science and health information (79%) and fear of privacy invasion (17%), respectively. Conclusions: Pregnant individuals receiving care at The Ottawa Hospital are willing to participate in prospective research studies, including those related to cannabis use. Survey respondents were predominantly of higher socioeconomic status, and few individuals reported cannabis use during pregnancy. Future studies should accommodate multiple recruitment strategies and flexible study designs to encourage enrollment from and retention across diverse sociodemographic communities.",
"keywords": [
"Pregnancy",
"cannabis",
"participation",
"willingness",
"motivators",
"birth cohort"
],
"content": "Introduction\n\nThe prevalence of cannabis use among pregnant individuals in Canada is increasing. In Ontario, self-reported cannabis use in pregnancy increased from 1.2% in 2012 to 1.8% in 2017, a relative increase of 61%.1 These increases are particularly notable among individuals 15-24 years old, among whom self-reported cannabis use in pregnancy has increased to more than 6% in recent years.2 Such findings are a significant public health concern given accumulating evidence suggesting an association between cannabis use in pregnancy and risk of stillbirth, small for gestational age, lower birth weight, and increased admission to neonatal intensive care compared with infants without cannabis exposure.1,3–5 Longer-term impacts on child neurodevelopment and mental health have also been reported.6–8\n\nAlthough information on the frequency, timing, dose and intake method of cannabis use is essential for inferring its health impacts on exposed individuals, population-based data on cannabis use in pregnancy are frequently lacking this level of information. Reports based on prospective data collection are few and frequently limited by small sample sizes, reliance on self-reported data and other methodological challenges.9,10 Cannabis use in pregnancy is associated with negative social stigma and perceived consequences of reporting drug use in pregnancy, such as fear of losing children and fear of prejudicial treatment,11 may dissuade individuals from participating in research or accurately disclosing their drug-related habits. Indeed, previous work comparing self-reported data against urine toxicology screens has demonstrated that individuals are likely to underreport substance use in pregnancy, including cannabis use.12,13 There is a pressing need to generate current, robust data on cannabis use in the Canadian obstetrical population, to improve our understanding of the trends, determinants, and outcomes of cannabis use in the post-legalization setting.\n\nThe requirements of longitudinal research are particularly burdensome for the obstetrical population, who are already faced with accommodating frequent health care appointments in addition to professional and personal obligations. In the design and enrolment of participants into large-scale birth cohorts, consideration must be given to the factors influencing participation, data sharing and contribution of biological samples. We surveyed pregnant individuals to determine their receptiveness to enrolling in a hypothetical birth cohort designed to evaluate the prevalence and safety of cannabis use in pregnancy. Our objective was to assess factors influencing pregnant individuals’ motivations and receptiveness to research participation.\n\n\nMethods\n\nThis was a cross-sectional survey study of individuals receiving obstetrical care through The Ottawa Hospital in Ottawa, Ontario. Ottawa is the second largest city in Ontario and the fourth largest in Canada. The census metropolitan area of Ottawa-Gatineau has a population of 1.3 million.14 The Ottawa Hospital is a Level 3 maternity care hospital with antenatal clinics and birthing units at two hospital campuses that provide obstetrical and neonatal care to the Ottawa-Gatineau region. During registration at The Ottawa Hospital, all patients are asked if they would like to give their permission to be contacted for future research studies through the institutional Permission to Contact program.15 For this study, individuals were eligible to participate if they gave permission to be contacted for research purposes, were 18 years of age or older, pregnant, and receiving care through The Ottawa Hospital, or if they had recently delivered and were still in hospital. Pregnant individuals receiving care at St. Mary’s Home, a satellite clinic of The Ottawa Hospital available to disadvantaged pregnant youth where clients under 18 are considered emancipated minors, were also eligible. This patient population includes youth experiencing, or at-risk for, homelessness, addictions, family and intimate partner violence, and other challenges.\n\nIn January 2020, we mailed 656 survey packages. Mailed packages included a participant information sheet, survey, pre-paid return envelopes, and a recruitment poster with a link to an online version of the survey. In this way, individuals receiving the mailed packages could complete the survey on paper or online. Recruitment posters advertising the online survey were placed in clinic waiting areas of The Ottawa Hospital and St. Mary’s Home, and postpartum wards. Using an iPad to participate in the survey was also an option for those completing the survey at St. Mary's Home. Paper-based surveys were also available alongside a secure drop-box for individuals to deposit their responses. All materials were available in both English and French. Survey responses were anonymous.\n\nThe survey consisted of 23 dichotomous (yes, no), multiple-choice, Likert scale, and open-ended questions. Respondents self-reported demographic and socioeconomic characteristics. These included age (years), race/ethnicity (Indigenous, White, Chinese, Black, Filipino, Latin American, Arab, Southeast Asian, West Asian, Korean, Japanese, Other), level of education (grade school, high school, college/university attended but not completed, college/university completed), household income (less than $25,000, $25,000-$49,999, $50,000-74,999, $75,000-$99,999, more than $100,00), marital status (married or common law; separated or divorced; single, never married; widow or widower) and obstetrical history (gravidity, parity).\n\nQuestions specific to cannabis-use covered topics including current knowledge regarding how cannabis use can affect pregnancy and postpartum health (e.g. “Do you think that using cannabis during pregnancy affects: a) your pregnancy health, b) your baby’s health, c) your breastmilk, or d) I don’t know”); and participant use of alcohol, tobacco, cannabis, or other substances (any time before pregnancy, in the current pregnancy, never). Individuals were asked if their healthcare provider had discussed the topic of cannabis use in pregnancy with them (yes, no) and to identify their primary sources for information on cannabis (friends and family; health care professionals; government websites; media, general internet searches; cannabis producers, distributors or retail providers; other).\n\nThe survey included a description of a hypothetical research study in which researchers sought to collect data and biological samples during pregnancy to explore cannabis use patterns, habits and preferences (Figure 1). After reading the description, individuals were asked how likely they would be to participate in the hypothetical research study if invited, if their partner would support their participation, and if their partner would participate themselves (answer choices: very likely, likely, unlikely and very unlikely). Questions also covered individuals’ willingness to self-report cannabis use in pregnancy and provide different types of biological samples, such as urine, blood, saliva, cord blood, newborn stool, placental tissue, and breastmilk once or multiple times throughout pregnancy. Individuals were also asked about their willingness to consent to the storage of biological samples for future use and have their data linked to their health records. Using a pre-specified, multi-select list, motivating and deterring factors for participating in cannabis-related research were captured. Individuals were asked to identify factors that would motivate them to participate the hypothetical research study described (i.e., contributing to science and health information, learning more about cannabis and pregnancy health, helping future patients, getting paid money, other), and identify any concerns they would have about sharing information related to cannabis use with researchers (i.e., being judged, feeling embarrassed, feeling guilty, being reported to child protective services, privacy concerns, changes to the healthcare they receive, no fears, other).\n\nDescriptive statistics included frequencies (n) and percentages (%) for categorical variables. Continuous variables were described using means and standard deviations, and minimum and maximum values when appropriate. Likert-scale survey responses “very likely” and “likely” were combined, as were responses of “very unlikely” and “unlikely”.\n\nEthics\n\nThis research was approved by the Ottawa Health Sciences Network (OHSN) Research Ethics Board (20190529-01H). At the start of each survey, participants were provided with information outlining the purpose and nature of the survey study. Participants were informed that the survey responses were anonymously collected, and how the data would be used (including for publication), stored, and destroyed. Participants were informed that their participation was completely voluntary and that by completing the survey, their consent to participate was implied. Thus, informed consent was obtained from all participants included in this paper. Research and ethics contacts were provided to the participants in case they had any questions or concerns about the study, or about data collection or management. The OHSN Research Ethics Board reviewed and approved all study documents, including the consent process.\n\nConsent for publication: Informed consent was obtained from all subjects.\n\n\nResults\n\nA total of 84 completed surveys were collected between January and March 2020. Of the 656 surveys sent via mail, 16 (2.4%) were returned due to invalid or change of address, meaning 640 surveys were delivered successfully. Seventy-five (89.3%) individuals reported that they had received the survey in the mail; a response rate of 11.7% (75/640). The remaining nine (10.7%) survey responses were completed by individuals who indicated that they had completed the survey after seeing recruitment posters in-hospital or because they had been recruited by research staff. Five patients were recruited from the St. Mary’s satellite clinic. The mean age of respondents was 32.6 (±5.3) years. Sixty-six (78.6%) survey participants were Caucasian, 71 (84.6%) completed college or university degrees, 78 (92.9%) were married or common-law, and 54 (64.3%) had a household income of over $100,000 (Table 1).\n\na This was a multi-select field, individuals could select multiple options. Percentages do not add to 100%. SD, standard deviation. Data are provided as N(%), unless otherwise indicated. Not all individuals provided complete information, number of individuals with non-missing values noted for each item. Percentages may not add to 100 due to rounding.\n\nSixty-three (75.0%) individuals reported previous alcohol consumption, 20 (23.8%) indicated prior tobacco use, 39 (46.4%) reported prior cannabis use and six (7.1%) reported using other non-prescription drug use at some point before their pregnancy. When asked to indicate substance use in their current pregnancies, nine (10.7%) individuals reported alcohol use, and two (2.4%) reported cannabis use. None of the surveyed participants reported tobacco or other drug use in their current pregnancies.\n\nA total of 67 (79.8%) individuals reported that their healthcare provider had not yet discussed cannabis use during pregnancy with them (Table 2). The three most common sources of information on cannabis used by individuals were family and friends, media (e.g., news, magazines, and social media), and general internet searches (44.0%, 39.3% and 32.1 %, respectively). Most individuals believed that using cannabis during pregnancy would affect pregnancy health (62, 73.8%), their baby’s health (70, 83.3%), and their breastmilk (62, 73.8%). 14 (16.7%) individuals indicated that they did not know if cannabis use in pregnancy would affect pregnancy health, infant health or breastmilk.\n\na This was a multi-select field, individuals could select multiple options. Percentages do not add to 100%.\n\n52 (61.9%) individuals reported that they would be willing to participate in the hypothetical research study (Figure 2). 72 (85.7%) individuals said they would be likely to participate if asked to complete a survey now, and 73 (86.9%) said they would be likely to participate in doing so at other times later in their pregnancy. The majority of individuals were willing to give biological samples at the time they completed the survey or at subsequent hospital visits (55 (65.5 %) and 54 (64.3%), respectively). A higher proportion of individuals indicated that they would be willing to provide urine (62 (73.8%)) or saliva samples (61 (72.6%)) than any other sample type suggested by the hypothetical study. Individuals were least willing to consider providing placental tissue, cord blood, and newborn stool samples for the hypothetical study (>30% responding unlikely/very unlikely for each sample). Over half of the individuals reported being open to consenting to the storage and use of biological specimens for other pregnancy research (55 (65.5%)). 60 (71.4%) believed that their partners would be supportive of their research participation, though fewer (44(52.4%)) believed that their partners would also agree to be in the hypothetical research study.\n\nThe most commonly cited motivating factors for participating in research was a desire to contribute to science and health information (66 (78.6%)), and the potential for helping future patients (49 (58.3%)) (Table 3). Three (3.6%) respondents answered that there were no possible motivating factors to participate in cannabis-related research. Approximately two-thirds of individuals indicated that they had no fears for participating in this type of research (53 (63.1%)). The most commonly reported deterring factors included worries about maintaining information privacy (14 (16.7%)) and being reported to Child Protective Services (if they reported using cannabis in pregnancy) (10 (11.9%)).\n\na This was a multi-select field, individuals could select multiple options. Percentages do not add to 100%.\n\n\nDiscussion\n\nIn this cross-sectional survey of 84 pregnant individuals living in Ottawa, Ontario, we demonstrate that pregnant individuals are receptive to participating in prospective research studies, including those related to cannabis use in pregnancy. A majority of individuals were willing to complete surveys, provide biological samples and consent to having their information and samples stored for future use. Nearly three-quarters of individuals believed that their partners would support their research participation, and half believed that their partners would also agree to participate. The primary motivating factors for research participation included contributing to science and health information and helping future patients.\n\nPregnancy and birth cohorts are rich sources of data on the role of early life exposures and biological mechanisms on the development of disorders and disease.17,18 In light of recent legislative changes regarding the availability and use of cannabis in Canada, prospective cohorts that collect robust clinical and biological data are needed to evaluate the impact of pre-conceptional and gestational cannabis exposures on maternal, infant, and pediatric outcomes in the Canadian population. Prospective cohorts evaluating the effects of prenatal cannabis use on pregnancy and child health are few,5,19–21 and are frequently limited by small sample size, reliance on self-reported cannabis use data, and loss to follow-up. Given increases in potency and access to varied administration routes in the post-legalization era, new data using information collected from both self-reported use histories and objective measures of cannabis use from toxicology screening may elucidate epidemiological findings.10\n\nMotivators and deterrents for research participation are important factors to consider when designing birth cohorts, so that study designs and recruitment strategies can be optimized to improve enrollment, participation and retention.18 Our findings confirm those of others that pregnant individuals are generally willing to participate in research and are motivated by altruism.22 In a qualitative assessment of pregnant individuals’ attitudes toward multiple methods of data and biological data collection, Gatny and colleagues reported that key design features likely to encourage research participation among pregnant individuals included the following: emphasizing the contribution to science and improvements in care for others, clinical/societal importance of the study, and study designs that accommodated various degrees of participation.22 The success of flexible enrollment models for birth cohorts has been demonstrated elsewhere, including the Ottawa obstetrical population.23 Altruistic motivations for research participation have also been described among non-pregnant individuals who use substances. A recent study examining willingness to participate in longitudinal research among long-time medical cannabis users found that 85% of respondents would enroll if asked.24 Motivating factors included a desire to help others and to further scientific information.\n\nOur survey assessed a large breadth of hypothetical scenarios, motivating and deterring factors for research participation. Findings that pregnant individuals are generally receptive to contributing biological samples are promising. Given the need for objective measures of cannabis use/exposure in pregnancy, standardization of data collection tools assessing cannabis use would be helpful as the frequency, dose, format, and method (smoked, ingested, etc) of cannabis consumption will provide important information on the influence of cannabis exposure and pregnancy and child health outcomes.25–27 Our findings also revealed a lack of patient-provider discussion related to cannabis use in pregnancy, and participants cited friends, family, and the media as their primary sources of information on cannabis use. Despite having at least one prenatal visit with an obstetrical care provider at a tertiary care hospital, 80% of participants had not yet discussed cannabis use with their health care providers. This is consistent with recent data demonstrating that maternity care providers feel ill-equipped to provide evidence-based counselling to patients,28,29 and highlights a need for reliable, contemporary evidence on the safety of cannabis use in pregnancy. As new data emerge on the influence of paternal and second-hand cannabis exposures, insight from our study participants on the receptivity of their partners to participating in cannabis-use research may be useful to inform the design of clinical research studies on this topic.\n\nThe strengths of this study include broad dissemination to the obstetrical population receiving care at our tertiary care center and the anonymity of the survey. Selection bias may limit the generalizability of our findings to other obstetrical populations and maternity care settings. First, surveys were distributed to individuals who had previously consented to be contacted for research; thus respondents may have been more likely to respond favourably to the hypothetical research scenario proposed in the survey than the broader population. Second, the response rate from our mailed survey strategy was low (12%). Although response rates for survey studies vary widely by subject area, study population and data collection techniques, the response rates for this study are similar to other research surveys conducted in the perinatal population, among whom response rates typically vary between 10 and 20%. Although use of incentives and electronic and telephone reminders are known to increase responses rates for survey studies, we were unable to facilitate this in order to maintain anonymity of respondents. Third, our sample consisted of individuals from higher socioeconomic status background than that of the broader Ottawa population. A large proportion of our sample had received post-secondary education, were married and white, with a total household income of over ≥$100,000. These demographics are similar to other pregnancy cohorts initiated at The Ottawa Hospital,23,30, and positive associations between education and willingness to participate in research have been previously described.31–34 Finally, although we sought responses from individuals with diverse histories of substance use, the majority of survey respondents reported not using cannabis or other substances and this may have impacted the low concern among participants being reported to Child Protective Services. Individuals who use cannabis in pregnancy have been shown to have lowered perceptions of risk related to cannabis use,35 and their perspectives on research participation, including motivating and deterring factors, should be considered when designing research studies on cannabis use in pregnancy. In contrast, alcohol was the most commonly reported substance used during pregnancy (11%). These findings are consistent with data from the Canadian Maternity Experiences Survey and the Canadian Perinatal Surveillance System’s 2013 Perinatal Health Indicators Report in which the proportions of women who reported drinking alcohol during pregnancy were 10.5% and 10.7%, respectively.36,37 Although we are unable to fully gauge differences between individuals who use cannabis in pregnancy and those who do not, our findings provide important insight into the motivating and deterring factors influencing participation in birth cohort studies.\n\n\nConclusions\n\nThis study demonstrates that pregnant individuals are willing to participate in prospective research studies, including those related to cannabis use in pregnancy. Differences in preferences for participation such as completing surveys or providing samples may warrant a flexible model whereby individuals have the freedom to opt in an out of elements of their choosing. In the design of birth cohorts, multiple recruitment strategies are needed to encourage enrolment from and retention across diverse sociodemographic communities that are representative of the broader local population. Our findings are informative for researchers seeking to develop prospective studies in this area.\n\n\nData availability\n\nOpen Science Framework: Underlying data for ‘Receptiveness to participating in cannabis research in pregnancy: a survey study at The Ottawa Hospital’, DOI 10.17605/OSF.IO/UWDHP.16\n\nThis project contains the following underlying data:\n\n• Table 1. Cannabis Survey Results\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC BY 4.0).",
"appendix": "Acknowledgements\n\nThe authors are grateful to the individuals who took the time to participate in the study survey.\n\n\nReferences\n\nCorsi DJ, Walsh L, Weiss D, et al.: Association Between Self-reported Prenatal Cannabis Use and Maternal, Perinatal, and Neonatal Outcomes. JAMA. 2019; 322(2): 145–52. Reference SourcePubMed Abstract | Publisher Full Text | Free Full Text\n\nCorsi DJ, Hsu H, Weiss D, et al.: Trends and correlates of cannabis use in pregnancy: a population-based study in Ontario, Canada from 2012 to 2017. Can J Public Heal. 2019; 110(1): 76–84. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHayatbakhsh MR, Flenady VJ, Gibbons KS, et al.: Birth outcomes associated with cannabis use before and during pregnancy. Pediatr Res. 2012; 71(2): 215–9. PubMed Abstract | Publisher Full Text\n\nVarner MW, Silver RM, Hogue CJR, et al.: Association between stillbirth and illicit drug use and smoking during pregnancy. Obstet Gynecol. 2014; 123(1): 113–25. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFergusson DM, Horwood LJ, Northstone K: Maternal use of cannabis and pregnancy outcome. BJOG An Int J Obstet Gynaecol. 2002; 109(1): 21–7. PubMed Abstract | Publisher Full Text\n\nMcLemore GL, Richardson KA: Data from three prospective longitudinal human cohorts of prenatal marijuana exposure and offspring outcomes from the fetal period through young adulthood. Data Br. 2016; PubMed Abstract | Publisher Full Text | Free Full Text\n\nFine JD, Moreau AL, Karcher NR, et al.: Association of Prenatal Cannabis Exposure With Psychosis Proneness Among Children in the Adolescent Brain Cognitive Development (ABCD) Study. JAMA Psychiatry. 2019 Jul; 76(7): 762. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCorsi DJ, Donelle J, Sucha E, et al.: Maternal cannabis use in pregnancy and child neurodevelopmental outcomes. Nat Med. 2020 Oct; 26(10): 1536–40. PubMed Abstract | Publisher Full Text\n\nBadowski S, Smith G: Cannabis use during pregnancy and postpartum. Can Fam Physician. 2020; 66(2): 98–103. PubMed Abstract | Free Full Text\n\nCorsi DJ: Epidemiological challenges to measuring prenatal cannabis use and its potential harms. BJOG An Int J Obstet Gynaecol. 2019 Oct; 1471-0528.15985. PubMed Abstract | Publisher Full Text\n\nPoole N, Isaac B: Barriers to treatment for substance-using mothers. British Columbia Centre of Excellence for Women’s Health. 2001.\n\nYonkers KA, Howell HB, Gotman N, et al.: Self-report of illicit substance use versus urine toxicology results from at-risk pregnant women. J Subst Use. 2011; 16(5): 372–80. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHardigan PC, Popovici I, Carvajal MJ: Response rate, response time, and economic costs of survey research: A randomized trial of practicing pharmacists. Res Soc Adm Pharm. 2016; 12(1): 141–8. PubMed Abstract | Publisher Full Text\n\nOttawa-Gatineau, Canada Metro Area Population 1950-2020|MacroTrends [Internet]. [cited 2020 Jul 20]. Reference Source\n\nCheah S, O’Donoghue S, Daudt H, et al.: Permission to contact (PTC) - A strategy to enhance patient engagement in translational research. Biopreserv Biobank. 2013; 11(4): 245–52. PubMed Abstract | Publisher Full Text\n\nBombay K, Murphy MS, Denize KM, et al.: Table 1: Cannabis Survey Results.2021 [cited 2021 Apr 12]; Reference Source\n\nPaneth N, Monk C: The importance of cohort research starting early in life to understanding child health.2018; PubMed Abstract | Publisher Full Text | Free Full Text\n\nLuo Z-C, Liu J-M, Fraser WD: Large prospective birth cohort studies on environmental contaminants and child health – Goals, challenges, limitations and needs. Med Hypotheses. 2010 Feb; 74(2): 318–24. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFried PA: Pergamon 0024-3205(95)00203-O Sciences,.1995; 56(95): 2159–68.\n\nGoldschmidt L, Richardson GA, Larkby C, et al.: Neurotoxicology and Teratology Early marijuana initiation: The link between prenatal marijuana exposure, early childhood behavior, and negative adult roles. Neurotoxicol Teratol. 2016; 58: 40–5. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMarroun HE, Bolhuis K, Franken IHA, et al.: Preconception and prenatal cannabis use and the risk of behavioural and emotional problems in the offspring; a multi-informant prospective longitudinal study.2019; (September 2018): 287–96. PubMed Abstract | Publisher Full Text\n\nGatny HH, Axinn WG: Willingness to Participate in Research during Pregnancy: Race, Experience, and Motivation. Field methods. 2012; 24(2): 135–54. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWalker MC, Finkelstein SA, White RR, et al.: The Ottawa and Kingston (OaK) Birth Cohort: Development and Achievements. J Obstet Gynaecol Canada. 2011; 33(11): 1124–33. PubMed Abstract | Publisher Full Text\n\nBachhuber MA, Arnsten JH, Starrels JL, et al.: Willingness to Participate in Longitudinal Research Among People with Chronic Pain Who Take Medical Cannabis: A Cross-Sectional Survey.2018; 3: 45–53. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPrenatal Exposure Effects Psychophysiology Study - Full Text View - ClinicalTrials.gov [Internet]. [cited 2020 Aug 26]. Reference Source\n\nThe Influence of in Utero Cannabis Exposure on Neonatal Brain Morphology and Structural Connectivity - Full Text View - ClinicalTrials.gov [Internet]. [cited 2020 Aug 26].. http\n\nMaternal Marijuana Use and Fetal and Infant Outcome - Full Text View - ClinicalTrials.gov [Internet]. [cited 2020 Aug 26]. Reference Source\n\nHolland CL, Rubio D, Rodriguez KL, et al.: Obstetric health care providers’ counseling responses to pregnant patient disclosures of marijuana use. Obstet Gynecol. 2016 Apr 1; 127(4): 681–7. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHolland CL, Nkumsah MA, Morrison P, et al.: “Anything above marijuana takes priority”: Obstetric providers’ attitudes and counseling strategies regarding perinatal marijuana use. Patient Educ Couns. 2016; 99(9): 1446–51. PubMed Abstract | Publisher Full Text | Free Full Text\n\nArbuckle TE, Fisher M, MacPherson S, et al.: Maternal and early life exposure to phthalates: The Plastics and Personal-care Products use in Pregnancy (P4) study. Sci Total Environ. 2016; 551–552: 344–56. PubMed Abstract | Publisher Full Text\n\nDunne MP, Martin NG, Bailey JM, et al.: Participation Bias in a Sexuality Survey: Psychological and Behavioural Characteristics of Responders and Non-Responders.1997; 26(4): 844–54. PubMed Abstract | Publisher Full Text\n\nO’Neil MJ: Estimating the Nonresponse Bias Due to Refusals in Telephone Surveys. Public Opin Q. 1979 Aug 27; 43(2): 218–32. Reference SourcePublisher Full Text\n\nKrousel-wood MA, Re RN, Abdoh A, et al.: The effect of education on patients’ willingness to participate in a telemedicine study.2001; 281–7. PubMed Abstract | Publisher Full Text\n\nTrauth JM, Siminoff L, Jewell IK, et al.: Public Attitudes Regarding Willingness to Participate in Medical Research Studies.12(2): 23–44. PubMed Abstract | Publisher Full Text\n\nWeisbeck SJ, Bright KS, Ginn CS, et al.: Perceptions about cannabis use during pregnancy: a rapid best-framework qualitative synthesis. Can J Public Heal. 2020 Aug; PubMed Abstract | Publisher Full Text | Free Full Text\n\nPublic Health Agency of Canada: Perinatal Health Indicators for Canada 2013: A Report from the Canadian Perinatal Surveillance System.2013.\n\nPublic Health Agency of Canada: What Mothers Say: The Canadian Maternity Experiences Survey.2009;"
}
|
[
{
"id": "95825",
"date": "04 Oct 2021",
"name": "Tracy Reibel",
"expertise": [
"Reviewer Expertise Maternal and infant health",
"maternity care health systems",
"Aboriginal women",
"Fetal Alcohol Spectrum Disorder",
"women's 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\nThis is an important topic, as noted by the authors, there is insufficient evidence from well-designed studies to appropriately inform women of harms that may be associated with cannabis use in pregnancy. While the impact of alcohol on the developing fetus is now well established, this is not the case with cannabis use. It is broadly acknowledged that cannabis use is rising in many developed countries, as the legislation legalising use increases in many jurisdictions.\nWhile the survey response rate was small given the mailout (although anticipated in light of similar returns in pregnancy related surveys) it does raise questions regarding generalisability. This is noted by the authors in the discussion. My view is that the limitations could be made more explicit, by stating that there are a number of limitations from the study - all of which are described, just not named as such.\nMy view also is that with just under half of the respondents disclosing cannabis use prior to pregnancy, this is a finding worthy of a stronger statement. It is highly likely that the sample was influenced by the participant's educational status, but nonetheless, an outcome that indicates that pregnant women may not only be prepared to participate in future studies on this topic but also honestly disclose cannabis use is worth stating. Especially when combined with a willingness to provide at least some biological samples.\nOverall, I found the manuscript to be well written, the methods and analysis were appropriately described, the discussion was a good reflection of the analysis. The conclusion that research is needed on this particular topic is long overdue and will eventually be an important addition to understanding the role of exposures on developing babies. This research has to be done though with sensitivity and assurance for women to be able to fully participate in 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? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
},
{
"id": "327231",
"date": "30 Dec 2024",
"name": "Omayma Alshaarawy",
"expertise": [
"Reviewer Expertise Cannabis",
"Epidemiology",
"Inflammation",
"Chronic disease",
"Maternal Health",
"Obesity",
"Diabetes mellitus",
"Cardiovascular 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\nThe authors have developed and distributed a survey to assess the willingness of pregnant individuals to participate in cannabis research and provide biological samples. Overall, the paper is well written and easy to follow. The main limitation of the study is inherent in the sample, a relatively high SES and very low prevalence of prenatal cannabis use. Hence, selection bias is a real threat to validity here. Also, the study lacks specimen collection/analysis to verify responses related to cannabis and other drug use. The authors acknowledged these limitations and compared their results to the obstetric population in Ottawa. I believe the authors should compare the characteristics of their sample to what is known about individuals who use cannabis during pregnancy as they are the cornerstone of any prenatal cannabis use study.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-413
|
https://f1000research.com/articles/9-1307/v1
|
09 Nov 20
|
{
"type": "Data Note",
"title": "Three datasets for nutrition environment measures of food outlets located in the Lower Mississippi Delta region of the United States",
"authors": [
"Jessica L. Thomson",
"Alicia S. Landry",
"Alicia S. Landry"
],
"abstract": "This data note provides details of a research database containing 266 food outlets located in five rural towns in the Lower Mississippi Delta region of Mississippi, whose nutrition environments were measured from 2016 to 2018. The food outlet types include grocery stores, convenience stores, full-service restaurants, and fast food restaurants. The purpose of this publication is to describe the three datasets for external researchers who may be interested in making use of them. The datasets are available from the USDA National Agricultural Library’s Ag Data Commons under a CC0 1.0 Universal License: https://doi.org/10.15482/USDA.ADC/1503704.",
"keywords": [
"Food environment",
"nutrition",
"grocery stores",
"convenience stores",
"restaurants",
"Nutrition Environment Measures Survey",
"Lower Mississippi Delta",
"rural"
],
"content": "Introduction\n\nThe Mississippi River Delta region is among the most socioeconomically disadvantaged areas of the United States (US) with less healthful food environments (e.g., low access to healthful foods, food insecurity) and poorer health outcomes than non-Delta counties in the same states and the nation1. Accessibility (location of healthful food outlets near neighborhoods, particularly in low-income and rural areas), availability (healthful options in local food outlets), and affordability (reasonable prices) of nutrient-dense foods are crucial to facilitate adoption of a healthful diet2–4. To inform future nutrition interventions designed for residents of the Lower Mississippi, the Delta Food Outlets Study was conducted to measure nutrition environments of towns located in this region.\n\n\nMethods\n\nDelta Food Outlets was an observational study designed to collect data on food outlets located in five rural Lower Mississippi Delta towns of interest to researchers5. Food outlet types included grocery stores, convenience stores, full-service restaurants, and fast food restaurants. The study was approved and classified as exempt by the Institutional Review Board of Delta State University. Data collection occurred from March 2016 through September 2018.\n\nGrocery stores were identified by referencing two sources – the US Department of Agriculture (USDA) Food and Nutrition Service Supplemental Nutrition Assistance Program (SNAP) retailer locator6 and the Mississippi State Department of Health Restaurant and Food Facility Inspections website7. Convenience stores were identified by referencing three sources – the SNAP retailer locator6, the B2B Yellow Pages website8, and lists of current privilege licenses obtained from city clerks. Restaurants were identified by referencing the Mississippi State Department of Health Restaurant and Food Facility Inspections website7. Food outlets were classified using operational definitions contained in the Economic Research Service’s Food Environment Atlas documentation9. While the 266 food outlets included in the datasets represent the entire population of these types of food outlets in the five towns, they may not be representative of all such outlets located in rural Lower Mississippi Delta towns.\n\nNutrition environments of the food outlets were measured using the Nutrition Environment Measures Survey (NEMS) for grocery stores (NEMS-S), convenience stores (NEMS-CS), and restaurants (NEMS-R)10. NEMS tools are validated observational measures of retail store nutrition environments that focus on the availability of healthful food choices, quality of fresh produce, and comparative pricing between healthful and less healthful options in 11 common categories11. A comprehensive description of the Delta Food Outlets Study methodology and measures has been published elsewhere5.\n\nThe NEMS tools were recreated as electronic surveys using Snap Surveys software (version 11.20, Snap Surveys Ltd). All data were collected via tablets loaded with Snap Surveys software and stored on the Snap WebHost, an online mobile and secure survey management system. For quality assurance purposes, 25% of the food outlets were randomly selected for duplicate measurement. Discrepancies between measurements were discussed and resolved.\n\nFood outlets were scored using algorithms provided for the NEMS tools. Higher scores indicate a more healthful nutrition environment. To make scores between different types of food outlets comparable, NEMS scores were transformed into ratio scores by dividing each food outlet score by the maximum score possible for that type of outlet. The use of ratio scores was necessary because each NEMS tool has a different possible score range (NEMS-S, -10 to 57; NEMS-CS, -9 to 57; NEMS-R, -7 to 27). The higher the ratio score, the more healthful the nutrition environment. Scoring was performed using SAS® (version 9.4, SAS Institute Inc).\n\n\nData availability\n\nUSDA National Agricultural Library’s Ag Data Commons: Delta Food Outlets Study, https://doi.org/10.15482/USDA.ADC/150370412.\n\nThis project contains all three datasets – NEMS-C (convenience stores), NEMS-G (grocery stores), and NEMS-R (restaurants) – along with their corresponding data dictionaries.\n\nData are available under the terms of the Creative Commons Zero \"No rights reserved\" data waiver (CC0 1.0 Public domain dedication).",
"appendix": "Acknowledgements\n\nThe authors are grateful to Melissa Goodman, Debra Johnson, and Donna Ransome for their research support and Delta Health Alliance for their in-kind support.\n\n\nReferences\n\nGennuso KP, Jovaag A, Catlin BB, et al.: Assessment of Factors Contributing to Health Outcomes in the Eight States of the Mississippi Delta Region. Prev Chronic Dis. 2016; 13(3): E33. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCohen B, Andrews M, Kantor LS: Community Food Security Assessment Toolkit. 2002. Reference Source\n\nLaraia B, Siega-Riz AM, Kaufman JS, et al.: Proximity of supermarkets is positively associated with diet quality index for pregnancy. Prev Med. 2004; 39(5): 869–875. PubMed Abstract | Publisher Full Text\n\nRose D, Richards R: Food store access and household fruit and vegetable use among participants in the US Food Stamp Program. Public Health Nutr. 2004; 7(8): 1081–1088. PubMed Abstract | Publisher Full Text\n\nThomson JL, Goodman MH, Landry AS: Measurement of Nutrition Environments in Grocery Stores, Convenience Stores, and Restaurants in the Lower Mississippi Delta. Prev Chronic Dis. 2020; 17: E24. PubMed Abstract | Publisher Full Text | Free Full Text\n\nUS Department of Agriculture Food and Nutrition Service: Where can I use SNAP EBT? Accessed March 15, 2016. Reference Source\n\nMississippi State Department of Health: Restaurant and Food Facility Inspections. Accessed March 15, 2016. Reference Source\n\nb2bBiz.com: B2BYellowpages.com. Accessed March 15, 2016. Reference Source\n\nUS Department of Agriculture Economic Research Service: Food Environment Atlas. Accessed August 8, 2019. Reference Source\n\nThe University of Pennsylvania: Nutrition Environment Measures Survey. Accessed May 23, 2018. Reference Source\n\nGlanz K, Sallis JF, Saelens BE, et al.: Nutrition Environment Measures Survey in stores (NEMS-S): development and evaluation. Am J Prev Med. 2007; 32(4): 282–289. PubMed Abstract | Publisher Full Text\n\nThomson JL: Delta Food Outlets Study. Ag Data Commons. Accessed 2020-10-19. http://www.doi.org/10.15482/USDA.ADC/1503704"
}
|
[
{
"id": "74475",
"date": "22 Dec 2020",
"name": "Donald Diego Rose",
"expertise": [
"Reviewer Expertise Public health nutrition",
"food security",
"food environment"
],
"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\nCongratulations on a great piece of primary research on the food environment in the lower Mississippi Delta! I think it is great that you are listing the datasets in a way that can be found by other researchers, and the Data Note through F1000Resaerch is a great vehicle for this. I have just a few comments to strengthen the Note for potential users. See below for some minor changes to be made:\n“located in five rural Lower Mississippi Delta towns of interest to researchers”\nI think it would be useful to explain why or how these towns were chosen. Why were they of interest to the researchers? Are they representative of a specific region? Was it just a convenience sample? Do they provide a range of geographies or socio-economic conditions? I realize this is probably in the source article (#5), but a couple of sentences here answering one or more of these questions to orient potential users of the data would be helpful.\nAlso, can you list the names of the towns? If there is a confidentiality issue, I would understand. But if not, it would be helpful for potential users of the data to know which towns.\n\n“that focus on the availability of healthful food choices, quality of fresh produce, and comparative pricing between healthful and less healthful options in 11 common categories”\nI know this is well documented in other places, but it would be useful in this Data Note to list one example of each of these and to also list all 11 food categories. You could add parenthetical comments, for example:\navailability of healthful food choices (e.g, non-fat milk or whole grain bread, etc), quality of fresh produce (as scored on a X-point scale), and…11 common categories. The categories include a, b, c, ….\n\nThen list them all. It’s easy to do and gives the reader a better sense of the data.\n\n“Discrepancies between measurements were discussed and resolved.”\nDiscussed by whom? The investigators? Graduate student assistants? Just make clear this clear.\n\n“The higher the ratio score, the more healthful the nutrition environment.”\nCan you indicate if the raw scores and the component scores are also available on the database? Either way is fine, but this would be helpful to know because some feel that the overall NEMS measures are like black box numbers that may not be helpful for a specific campaign to increase fruits and vegetables. See, for example, the references below that allow assessment for targeted campaigns to increase fruits and vegetables or decrease empty calorie snack foods. You may wish to include one or both of these references.\nFarley TA, Rice JC, Bodor JN, Cohen DA, Blumenthal RN, Rose D. \"Measuring the Food Environment: Shelf Space of Fruits, Vegetables, and Snack Foods in Stores,\" Journal of Urban Health, 2009;86:672-682.1\nMiller C, Bodor JN, Rose D. \"Measuring the food environment: A systematic technique for characterizing food stores using display counts,\" Journal of Environmental and Public Health 2012; doi:10.1155/2012/707860.2\n\nIs the rationale for creating the dataset(s) clearly described? Yes\n\nAre the protocols appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and materials provided to allow replication by others? Partly\n\nAre the datasets clearly presented in a useable and accessible format? Partly",
"responses": [
{
"c_id": "6690",
"date": "24 May 2021",
"name": "Jessica Thomson",
"role": "Author Response",
"response": "We thank Dr. Rose for their thoughtful and thorough review of our manuscript. We have incorporated Dr. Rose’s suggestions for strengthening our Data Note about the Delta Food Outlets datasets. Our responses to Dr. Rose’s comments follow. Pertaining to the towns: I think it would be useful to explain why or how these towns were chosen. Why were they of interest to the researchers? Are they representative of a specific region? Was it just a convenience sample? Do they provide a range of geographies or socio-economic conditions? I realize this is probably in the source article (#5), but a couple of sentences here answering one or more of these questions to orient potential users of the data would be helpful. Also, can you list the names of the towns? If there is a confidentiality issue, I would understand. But if not, it would be helpful for potential users of the data to know which towns. Response: We have added our reason for selecting these 5 towns – because participants of a previously conducted nutrition intervention resided in the 5 towns and assessing environmental exposures potentially influencing their dietary habits was of interest. We have chosen not to name the 5 towns due to confidentiality issues. Pertaining to the NEMS instruments: I know this is well documented in other places, but it would be useful in this Data Note to list one example of each of these and to also list all 11 food categories. You could add parenthetical comments, for example: availability of healthful food choices (e.g, non-fat milk or whole grain bread, etc), quality of fresh produce (as scored on a X-point scale), and…11 common categories. The categories include a, b, c,..Then list them all. It’s easy to do and gives the reader a better sense of the data. Response: We have added examples of the measures’ focus and listed the 11 common categories as suggested. Pertaining to measurement discrepancies: Discussed by whom? The investigators? Graduate student assistants? Just make clear this clear. Response: We have clarified that discrepancies were discussed between senior researchers and data collectors and resolved (e.g., outlet re-visited to determine correct value). Pertaining to the scores: Can you indicate if the raw scores and the component scores are also available on the database? Either way is fine, but this would be helpful to know because some feel that the overall NEMS measures are like black box numbers that may not be helpful for a specific campaign to increase fruits and vegetables. See, for example, the references below that allow assessment for targeted campaigns to increase fruits and vegetables or decrease empty calorie snack foods. You may wish to include one or both of these references. Farley TA, Rice JC, Bodor JN, Cohen DA, Blumenthal RN, Rose D. \"Measuring the Food Environment: Shelf Space of Fruits, Vegetables, and Snack Foods in Stores,\" Journal of Urban Health, 2009;86:672-682.1. Miller C, Bodor JN, Rose D. \"Measuring the food environment: A systematic technique for characterizing food stores using display counts,\" Journal of Environmental and Public Health 2012; doi:10.1155/2012/707860. Response: We apologize for this oversight in describing our datasets. Raw scores, component scores, and total scores are available in the datasets. In fact, we did not include ratio scores in the datasets because they were created specifically for the purposes of our study and may not be relevant or useful for other researchers. Hence, we have added text about the availability of raw, component, and total scores and removed the text about ratio scores. While the references provided are very interesting, we did not feel it was necessary to include them in our Data Note given the availability of raw scores in the datasets."
}
]
},
{
"id": "83927",
"date": "17 May 2021",
"name": "Caitlin Caspi",
"expertise": [
"Reviewer Expertise Food environment",
"food security",
"policies and interventions to address diet-related behaviors"
],
"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 a useful, detailed, and fairly recent data set that can be used by researchers to study the food environment in the Lower Mississippi Delta region. The data note concisely describes the data and is likely to be helpful documentation.\n\nThere were some places where more detail would have been useful.\nWhat are the characteristics of the towns of interest? Adding in the range of population size of the towns would be helpful. Were there large metropolitan areas that were excluded because this study was intentionally focused on towns? And/or can the authors make any statement in the note about how the towns may not be representative of the larger Lower Mississippi Delta area food environment? Some information like this would be helpful for readers in determining if the dataset is appropriate for use for addressing their research question.\n\nClassifying food retail outlets (i.e., grocery stores vs. convenience stores, restaurants vs. fast food outlets) can be challenging. Potential misclassification of store types is a major topic of discussion in food environment databases. Consider adding in more detail about how food stores were classified. The definitions used for the food retail outlet categories would be helpful (I see they are defined in the longer paper), but even more helpful would be a description of how decisions were made about how to classify a food outlet (e.g., based on one of the food lists, and then verified during data collection in person?).\n\nRelatedly, the authors reference the documentation for the USDA Food Environment Atlas for how stores were classified. However, the link goes to the Atlas, not the documentation, so it’s hard to find more information on how stores were classified. It would be helpful to have a direct link.\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? Partly\n\nAre the datasets clearly presented in a useable and accessible format? Yes",
"responses": [
{
"c_id": "6691",
"date": "24 May 2021",
"name": "Jessica Thomson",
"role": "Author Response",
"response": "We thank Dr. Caspi for their thoughtful and thorough review of our manuscript. We have incorporated Dr. Caspi’s suggestions for strengthening our Data Note about the Delta Food Outlets datasets. Our responses to Dr. Caspi’s comments follow. Pertaining to the towns: What are the characteristics of the towns of interest? Adding in the range of population size of the towns would be helpful. Were there large metropolitan areas that were excluded because this study was intentionally focused on towns? And/or can the authors make any statement in the note about how the towns may not be representative of the larger Lower Mississippi Delta area food environment? Some information like this would be helpful for readers in determining if the dataset is appropriate for use for addressing their research question. Response: We have added characteristics of the 5 towns including ranges for population size, percentage of African American residents, and percentage of residents living below the federal poverty level. Additionally, we added our reason for selecting these 5 towns – because participants of a previously conducted nutrition intervention resided in the 5 towns and assessing environmental exposures potentially influencing their dietary habits was of interest. We chose not to add a note about the non-representative nature of the towns because we felt it was redundant with our comment about the non-representative nature of the food outlets. Classifying food retail outlets (i.e., grocery stores vs. convenience stores, restaurants vs. fast food outlets) can be challenging. Potential misclassification of store types is a major topic of discussion in food environment databases. Consider adding in more detail about how food stores were classified. The definitions used for the food retail outlet categories would be helpful (I see they are defined in the longer paper), but even more helpful would be a description of how decisions were made about how to classify a food outlet (e.g., based on one of the food lists, and then verified during data collection in person?). Response: We have added more detail about definitions used to classify food outlets. Additionally, we added that before measurement, all outlets were physically visited to ensure that they were open, sold food, and were classified correctly. Relatedly, the authors reference the documentation for the USDA Food Environment Atlas for how stores were classified. However, the link goes to the Atlas, not the documentation, so it’s hard to find more information on how stores were classified. It would be helpful to have a direct link. Response: We have updated the Food Environment Atlas reference to include a direct link to the documentation."
}
]
}
] | 1
|
https://f1000research.com/articles/9-1307
|
https://f1000research.com/articles/10-297/v1
|
19 Apr 21
|
{
"type": "Research Article",
"title": "Medical students’ relative immunity, or lack thereof, against COVID-19 emotional distress and psychological challenges; a descriptive study from Jordan",
"authors": [
"Khalid Kheirallah",
"Sarah Bloukh",
"Wasim Khasawneh",
"Jomana Alsulaiman",
"Adi Khassawneh",
"Abdel-Hameed Al-Mistarehi",
"Mohammad Alqudah",
"Lina Elsalem",
"Samir Al Bashir",
"Hasan H. Awad",
"Tariq Al-Shatanawi",
"Tareq Saleh",
"Sarah Bloukh",
"Wasim Khasawneh",
"Jomana Alsulaiman",
"Adi Khassawneh",
"Abdel-Hameed Al-Mistarehi",
"Mohammad Alqudah",
"Lina Elsalem",
"Samir Al Bashir",
"Hasan H. Awad",
"Tariq Al-Shatanawi"
],
"abstract": "Background: Emotional distress is a major impact of COVID-19 among not only the general public but also healthcare workers including medical students. This study aimed at describing self-reported changes in emotional reactions associated with COVID-19 among medical students in Jordan and to assessing the potential effect of social media utilization on emotional distress among this group. Methods: A cross-sectional design was utilized to collect data early on during the outbreak in Jordan. All medical students in Jordan were eligible to complete an online questionnaire assessing self-reported emotional reactions to COVID-19 that covered four main domains: negative emotion (anxiety, worry, depression, panic, loneliness, and nervousness), positive emotion (happiness, joy, and excitement), sleep disorders (insomnia, shallow sleep, nightmares, and insufficient sleep), and aggression (verbal argument and physical fighting). The frequency of social media utilization as a main source of COVID-19 information was also assessed. Results: 59.9% of participants were females, 64.9% were enrolled at the two major medical schools in Jordan, and 59.6% were in the pre-clinical stage (years). A significant proportion of participants self-reported increased negative emotional levels of anxiety (49.2%), worry (72.4%), depression (23.1%), panic (22.6%), and nervousness (38.2%) and decreased positive emotional levels of happiness (44.8%), joy (47.3%), and feelings of excitement (45.1%). Self-reported sleep disorders were not as common (less than 15% for any of the four items), while arguing with others was at 26.7%. Significant differences by gender and academic year were detected. Almost half of participants reported using social media as a main source of COVID-19 information “most/all-the-times” with a significant effect of such on reducing emotional distress. Conclusion: The results suggest a potential effect of COVID-19 on the emotional distress of medical students. Addressing and mitigating such effects is crucial. The buffering effect of social media should be further investigated.",
"keywords": [
"COVID-19",
"emotional distress",
"emotional changes",
"medical students",
"Jordan",
"social media",
"medical school",
"SARS-CoV-2."
],
"content": "Introduction\n\nCOVID-19 is shadowing its effect on almost all individuals living today. The health, safety, and well-being of individuals and communities are all expected to be affected. These effects may include anxiety, fear, frustration, loneliness, anger, boredom, depression, stress, and avoidance behaviour (Talevi et al., 2020) and may simply translate into emotional disturbances not only among those with the disease but also the general population and other sub-groups (Pfefferbaum & North, 2020).\n\nCertain population subgroups may be more vulnerable than others to the psychosocial effects of COVID-19. Healthcare workers, including medical students, especially in resource-limited countries, are particularly vulnerable to emotional distress during COVID-19 given their high risk of exposure to the infection, potential shortage of personal protective equipment, longer work hours, and involvement in emotionally and ethically fraught resource-allocation decisions (Greenberg, 2020; Loch et al., 2020; Samrah, Al-Mistarehi, Aleshawi, et al., 2020; Talevi et al., 2020; Vindegaard & Eriksen Benros, 2020).\n\nStudies have reported that medical schools have one of the most demanding academic programs (Wolf, 1994) and include students at higher risk for developing anxiety disorders, compared to the general population, even under normal circumstances (Quek et al., 2019). Medical emergencies destabilize medical students’ already vulnerable psychological status leading to unfavourable effects on their learning journey (Al-Rabiaah et al., 2020), physical and mental health, and their professional identity formation (Chandratre, 2020). While medical students may experience increasing level of anxiety and stress due to the COVID-19 disruption (Lasheras et al., 2020; Ullah & Amin, 2020), they are the least likely to seek support for mental health problems (Chandratre, 2020).\n\nDuring outbreaks, medical students are expected to become part of the frontline workforce (Kinder & Harvey, 2020; O’Byrne et al., 2020), which may further expose them to psychological distress. Therefore, it is important to assess and safeguard medical students’ mental health status and to implement proper strategies to support their mental well-being. Providing a clear understanding of the extent of psychological impact of COVID-19 infection should, then, be clearly established.\n\nJordan is a developing country in the Middle East region and reported its first case of SARS-CoV-2 infection in early March, 2020 (Samrah, Al-Mistarehi, Ibnian, et al., 2020). A series of strict non-pharmaceutical intervention (NPI) measures were then implemented (Kheirallah et al., 2020; Samrah, Al-Mistarehi, Aleshawi, et al., 2020) that included a curfew and a total shutdown. By mid-March, 2020, all educational institutions, including medical schools, were ordered closed and online education was, suddenly, the only option (Sindiani et al., 2020). This may have increased the level of psychological distress among medical students (Elsalem et al., 2020). The current study described the self-reported changes in emotional reactions associated with COVID-19 among medical students in Jordan and investigated the potential effect of utilizing social media as a main source of COVID-19 information on these emotional changes.\n\n\nMethods\n\nA descriptive cross-sectional design collected data on medical students between March 17 and 20, 2020, shortly after Jordan initiated the NPI measures stated earlier. Data were collected from all medical schools (N = 6) in Jordan and included all years (year 1 to year 6). The 6-year program consists of two stages: preclinical, the first three years of the program, and clinical, the last three years. The minimum sample size required to detect a 10% difference in any of the emotional items under investigations was estimated at 600 students (alpha = 0.05, power = 0.8). Considering a response rate of around 20% for online questionnaires among the sample population (Khasawneh et al., 2020), an online data collection tool, using Google forms, was utilized and a link was emailed to a randomly selected sample (N = 3,000) that was proportionate to the year of study and the medical school.\n\nParticipants’ emotional reactions to COVID-19 pandemic were self-reported using 15 items covering four main domains: negative emotions (anxiety, worry, depression, panic, loneliness, and nervousness), positive emotions (happiness, joy, and excitement), sleep disorders (insomnia, shallow sleep, nightmares, and insufficient sleep), and aggression (verbal argument and physical fighting). Medical students compared the frequency of each item after the onset of the pandemic with before the pandemic using a three-point scale (from “1 = less compared to the days before the pandemic” to “3 = more compared to the days before the pandemic”). For selected items, responses were randomized. Participants were also asked to assess their usage of social media as a main source of information for COVID-19 using a three-point Likert scale (from “1 = never” to “3 = most/all the time”). The questionnaire was reviewed by expert panel before being piloted on 20 students.\n\nThe Institutional Review Boards of The Hashemite University (5/2/2019/2020) and Al-Balqa Applied University (26/3/1/804) approved this study. An online consent form was obtained by all participants prior to being directed to take the questionnaire.\n\nEach emotional item was reported overall and by gender, academic level and by social media utilization using numbers and percentages. A Chi-squared test was used to compare percentages for each emotional item. The Alpha level was set at 0.05.\n\n\nResults\n\nA total of 1,404 students participated in the current study. The distribution of participants by gender, university, and year is presented in Table 1. About two-thirds (59.9%) of participants were females, 64.9% were enrolled at the two well-established medical schools at the University of Jordan (39.1%) and Jordan University of Science and Technology (JUST) (25.8%), and 59.6% were in the pre-clinical stage of their medical education.\n\nOverall, almost half of the participants (49.2%) self-reported that they experienced increased levels of anxiety. This was significantly more prevalent among females (58.6%) than males (35.5%) (p<0.0001). Self-reported worry, which was the most commonly reported negative emotion experienced among all participants (72.4%), was significantly more prevalent among females than males (79.5% vs 61.9%, p<0.0001). Similarly, self-reported depression and panic, respectively, were more prevalent among females (26.8% and 28.9%) compared with males (17.8% and 13.4%) (p-value for both comparisons <0.0001) (Table 2).\n\nAbout 35% and 38% of surveyed students self-reported increased levels of loneliness and nervousness, respectively. While significantly more males (39.5%) than females reported increased level of loneliness (p=0.006), more females (45.9%) than males (26.9%) self-reported increased nervousness levels (p<0.001).\n\nOn the other hand, self-reported anxiety and worry were not significantly different between students in the pre-clinical vs clinical years while depression and panic, respectively, were significantly higher among students in pre-clinical years (25.9% and 26.8%) compared with their counterparts in the clinical years (19.0% and 16.4%) (p=0.003 and <0.001). Similarly, self-reported loneliness and nervousness, respectively, were significantly more common among students in the pre-clinical years (37.6% and 42.5%) compared to their counterparts in the clinical years (31.7% and 31.3%) (p=0.026 and <0.001).\n\nAbout 13% of students self-reported experiencing increased insomnia, shallow sleep, nightmares, or insufficient sleep. In general, females self-reported experiencing significantly more sleeping problems than males. Likewise, students in the pre-clinical years experienced sleep problems (insomnia, shallow sleep, and insufficient sleep) significantly more frequently than those in their clinical years.\n\nWhile about one-quarter of participants (26.7%) self-reported increased level of arguing with others, 5.1% self-reported increasing physical fight. However significant differences in aggression variables were not detected by gender, students in the pre-clinical years self-reported higher levels of both arguing with others (26.9%), compared with their counterparts in the clinical years (22.0%) (p=0.001), and physical fights (7.0%), compared with clinical years students (2.1%) (p<0.001).\n\nApproximately half of the participants self-reported a decrease in their level of positive emotions, namely happiness (44.8%), joy (47.8%), and excitement (45.1%). Self-reported decrease in the levels of joy and excitement, respectively, were statistically more prevalent among females (50.2% and 49.9%) compared with males (43.1% and 38.0%) (p=0.009 and <0.001). Significant differences in each of the three positive emotions by academic levels were not statistically significant.\n\nOverall, 37.9% of study participants reported never using social media as a source of information for COVID-19, while almost half (45.6%) reported using it “most/all the times” (Table 3). Statistically significant relationships were detected between social media as a source for COVID-19 information and anxiety (p=0.002), worry (0.016), panic (<0.001), loneliness (0.003), and nervousness (0.004). Among those who reported to use social media most/all the times as a source of information about COVID-19, the prevalence estimates of self-reported anxiety, worry, panic, loneliness, and nervousness, respectively, were less than that among their counterparts who never used it (47.3% vs 55.6%, 70.9% vs 77.8%, 20.3% vs 28.9%, 31.7% vs 41.5%, and 36.1% vs 44.2%). Changes in sleep disorder and aggression variables, on the other hand, were not significantly different by social media.\n\n\nDiscussion\n\nThe current descriptive study assessed the self-reported emotional changes following the COVID-19 pandemic among medical students in Jordan. Participants were found to have increased levels of almost all self-reported negative emotions and decreased levels of almost all positive emotions. These changes were more prevalently the case with females and preclinical students. Utilizing social media as a main source of COVID-19 information seems to have a “buffer effect” against emotional changes under investigation.\n\nOur results suggest that medical students may not be immune against COVID-19 emotional distress and increased psychological challenges. This could potentially usher a period of adjustment and may produce significant mental health issues. Addressing and mitigating the negative effects of public health emergencies on the mental health of medical students seem to be critical.\n\nOverall, preclinical level students seemed to have a greater increase in almost all negative emotions compared with clinical students. The reason why preclinical students might have had a greater increase in negative emotions could be attributed to their lesser experience in the clinical field and lesser understanding of the pandemic in general. However, it is interesting to note that the two negative emotions that showed no significant difference between preclinical and clinical students were worry and anxiety. When considering that medical students are already exposed to high levels of anxiety disorders (Quek et al., 2019), higher levels of anxiety are than expected. Exacerbation of a pre-existing emotional distress among medical students due to COVID-19 were previously suggested (Ullah & Amin, 2020).\n\nGender differences observed in the current study suggest vulnerability of female medical students to emotional distress more than male students. Females are generally more susceptible to emotional changes due to the hormonal fluctuations that are part of their physiology. It can be expected, thus, that several chemical mediators have a potential of elevating emotional distress in females. Beyond biological considerations, the conservative gender roles present different expectations of behaviours based on gender. Previous research have emphasized the gender roles and traits (masculinity in particular) and explained part of the gender differences in emotional distress and coping mechanisms (Mayor, 2015). On the other hand, gender differences in emotional intelligence, test stress, coping and academic stress were also suggested to contribute to similar observations (Alzahem et al., 2011; Babar et al., 2015; Elsalem et al., 2020). Our findings that female medical students self-reported higher rates of depression, anxiety, worry, nervousness, and panic, while male students reported higher rates of loneliness, are in line with the literature addressing such gender roles.\n\nIn Jordan, about 7% of medical students reported that they became obsessed with precautionary measures related to COVID-19 (Khasawneh et al., 2020), while about half self-reported distance education as a main source of worry and stress. Such negative emotions were attributed to the learning and assessment models used during the pandemic as students were not familiar with distance learning (Elsalem et al., 2020). The difference in prevalence estimates of distress in different studies may be attributed to several factors among which are the length of quarantine period, environment, contact with COVID-19 patients, and different coping styles of individuals.\n\nMedical students who self-reported utilizing social media as a source of COVID-19 information more frequently reported lower levels of emotional distress compared to those who never utilized it for such. The role that social media can play in risk perception and dissemination of reliable information during pandemics could be critical (Albarrak et al., 2019). While the information available about the pandemic may be a concern for COVID-19 infodemic among the general public, medical students seem to have utilized social media as a mitigation source to better understand the disease dynamics. This could have been reflected on the lower level of emotional distress reported among students who used social media more often. Medical students, therefore, by accessing social media, may be better equipped to avoid misinformation and to distinguish rumours from reality (Karasneh et al., 2020). Still, our results contradict reports where young people tend to obtain a large amount of information from social media which can easily be a trigger for stress and anxiety (Qiu et al., 2020). Assessment of the role of social media on medical students’ emotional distress should be further investigated using both qualitative and quantitative methods.\n\nIt is important to note that, in the current study, all estimates were self-reported and that we did not use standardized tools. This could have called out for over-estimation of the prevalence rates and over presentation of reported emotional changes. The cross-sectional nature of the study limits temporality. It will be imperative for other research groups to include longitudinal aspects in their study design and to use standardized screening tools as well as clinical assessment among this vulnerable group.\n\n\nConclusion\n\nOur results support the notion to screen for mental health problems among medical students and to invest in mental health infrastructures. Psychoeducation, and psychosocial support should be seriously considered within health education programs at medical schools and should be fine-tuned by gender. The role of social media within the context of a classical medical educational system should be further investigated and utilized as a mediating factor towards better mental health and psychosocial support.",
"appendix": "Acknowledgements\n\nThe authors would like to express their gratitude to all medical students who helped in the conduct of this study and all personnel at the medical schools for their support.\n\n\nUnderlying data\n\nIn compliance with IRB guidelines specified for this research activity, data will be shared by the corresponding author following official request for research with clear objectives that is initially approved by the corresponding author.\n\n\nReferences\n\nAl-Rabiaah A, Temsah MH, Al-Eyadhy AA, et al.: Middle East Respiratory Syndrome-Corona Virus (MERS-CoV) associated stress among medical students at a university teaching hospital in Saudi Arabia. J Infect Public Health. 2020; 13(5): 687–691. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAlbarrak AI, Mohammed R, Al Elayan A, et al.: Middle East Respiratory Syndrome (MERS): Comparing the knowledge, attitude and practices of different health care workers. J Infect Public Health. 2019. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAlzahem AM, Van Der Molen HT, Alaujan AH, et al.: Stress amongst dental students: A systematic review. Eur J Dent Educ. 2011; 15(1): 8–18. PubMed Abstract | Publisher Full Text\n\nBabar MG, Hasan SS, Ooi YJ, et al.: Perceived sources of stress among Malaysian dental students. Int J Med Educ. 2015; 6(126): 56–61. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChandratre S: Medical Students and COVID-19: Challenges and Supportive Strategies. J Med Educ Curric Dev. 2020; 7: 238212052093505. PubMed Abstract | Publisher Full Text | Free Full Text\n\nElsalem L, Al-Azzam N, Jum’ah AA, et al.: Stress and behavioral changes with remote E-exams during the Covid-19 pandemic: A cross-sectional study among undergraduates of medical sciences. Ann Med Surg. 2020; 60: 271–279. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGreenberg N: Mental health of health-care workers in the COVID-19 era. Nat Rev Nephrol. 2020; 16(8): 425–426. Nature Research. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKarasneh R, Al-Azzam S, Muflih S, et al.: Media’s effect on shaping knowledge, awareness risk perceptions and communication practices of pandemic COVID-19 among pharmacists. Res Social Adm Pharm. 2020; PubMed Abstract | Publisher Full Text | Free Full Text\n\nKhasawneh AI, Humeidan AA, Alsulaiman JW, et al.: Medical Students and COVID-19: Knowledge, Attitudes, and Precautionary Measures. A Descriptive Study From Jordan. Front Public Health. 2020; 8, 253. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKheirallah KA, Alsinglawi B, Alzoubi A, et al.: The effect of strict state measures on the epidemiologic curve of covid-19 infection in the context of a developing country: A simulation from Jordan. Int J Environ Res Public Health. 2020; 17(18): 1–11. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKinder F, Harvey A: Covid-19: The medical students responding to the pandemic. BMJ. 2020; 369: 1–2. PubMed Abstract | Publisher Full Text\n\nLasheras I, Gracia-García P, Lipnicki DM, et al.: Prevalence of anxiety in medical students during the covid-19 pandemic: A rapid systematic review with meta-analysis. Int J Environ Res Public Health. 2020; 17(18): 1–12. MDPI AG. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLoch C, Kuan IBJ, Elsalem L, et al.: COVID-19 and dental clinical practice: Students and clinical staff perceptions of health risks and educational impact. J Dent Educ. 2020. PubMed Abstract | Publisher Full Text\n\nMayor E: Gender roles and traits in stress and health. Front Psychol. 2015; 6(JUN). PubMed Abstract | Publisher Full Text | Free Full Text\n\nO’Byrne L, Gavin B, McNicholas F: Medical students and COVID-19: The need for pandemic preparedness. J Med Ethics. 2020; 46(9): 623–626. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPfefferbaum B, North CS: Mental Health and the Covid-19 Pandemic. N Engl J Med. 2020; 383(6): 510–512. PubMed Abstract | Publisher Full Text\n\nQiu J, Shen B, Zhao M, et al.: A nationwide survey of psychological distress among Chinese people in the COVID-19 epidemic: Implications and policy recommendations. Gen Psychiatr. 2020; 33(2): 100213. BMJ Publishing Group. PubMed Abstract | Publisher Full Text | Free Full Text\n\nQuek TTC, Tam WWS, Tran BX, et al.: The global prevalence of anxiety among medical students: A meta-analysis. Int J Environ Res Public Health. 2019; 16(15). MDPI AG. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSamrah SM, Al-Mistarehi AH, Aleshawi AJ, et al.: Depression and coping among covid-19-infected individuals after 10 days of mandatory in-hospital quarantine, irbid, jordan. Psychol Res Behav Manag. 2020; 13: 823–830. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSamrah SM, Al-Mistarehi AHW, Ibnian AM, et al.: COVID-19 outbreak in Jordan: Epidemiological features, clinical characteristics, and laboratory findings. Ann Med Surg. 2020; 57: 103–108. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSindiani AM, Obeidat N, Alshdaifat E, et al.: Distance education during the COVID-19 outbreak: A cross-sectional study among medical students in North of Jordan. Ann Med Surg . 2020; 59: 186–194. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTalevi D, Socci V, Carai M, et al.: Mental health outcomes of the covid-19 pandemic. Riv Psichiatr. 2020; 553). PubMed Abstract | Publisher Full Text\n\nUllah R, Amin S: The psychological impact of COVID-19 on medical students [Letter]. Psychiatry Res. 2020; 288(2): p. 113020. Elsevier Ireland Ltd. PubMed Abstract | Publisher Full Text | Free Full Text\n\nVindegaard N, Eriksen Benros M: COVID-19 pandemic and mental health consequences: Systematic review of the current evidence. Brain Behav Immun. 2020. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWolf TM: Stress, coping and health: enhancing well-being during medical school. Med Educ. 1994; 28(1): 8–17. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "83589",
"date": "22 Apr 2021",
"name": "Nedal Awad Abed Alnawaiseh",
"expertise": [
"Reviewer Expertise Epidemiologist",
"Biostatician",
"Public health and research expertise."
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis study addressed a critical point, mental health, which is considered a taboo within conservative societies. The authors addressed this issue and clearly clarified its limitation in the manuscript.\n\nI found it really interesting to cover a spectrum of indicators that assess, or screen, for potential mental health problems among medical students. The question is, then, how could this reflect on the population? Any suggestions?\nAlso, medical students are more likely to seek mental health problems if they have access to a clinic. But this is not the norm in conservative societies like Jordan. It may be considered a limitation if the authors did not assess access to mental health professional services. On the same point, how will the screening tools for the positive and negative domains investigated reflect the true problem given that self-reported mental health depression, for example, may be overestimating the actual values. Any thoughts on what the authors expect the true need for mental health advising and counseling among this population?\n\nThe mental health status of medical students is biased by multiple factors that were not addressed in the study. How will the authors direct future research considering such biases? For example, academic achievement and substance use.\n\nOn the same page of future research, will next research question encounters worry? Depression? Anxiety? Or what domain?\n\nIt seems that gender is playing a major role in defining mental health of medical students. Why didn't the authors do a regression analysis to identify the role of gender? This may be due to the fact that the tools used limit further statistical tests? Any other thoughts?\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": "6634",
"date": "24 May 2021",
"name": "khalid kheirallah",
"role": "Author Response",
"response": "The authors much appreciate your valuable feedback and thank you for the approval of this manuscript to be considered for publication at F1000Research. Below please note our response in line with your feedback. This study addressed a critical point, mental health, which is considered a taboo within conservative societies. The authors addressed this issue and clearly clarified its limitation in the manuscript. Thank you for this positive feedback and added value of the paper. I found it really interesting to cover a spectrum of indicators that assess, or screen, for potential mental health problems among medical students. The question is, then, how could this reflect on the population? Any suggestions? This study addressed such spectrum in order to fine-tune needs of this valuable population. As indicated in our submission, one can simply identify the major mental ill-health concerns as being self-identified among participants by gender and by year level. Top problems could be further explored using future research as indicated in the study. We never aimed to diagnose mental ill-health but rather point to the potential problem among this group. If 10% of self-reported issues are considered high-risk, then this could further identify where interventions could be considered and where the research focus should be. As for the population, the results reflect an image that reflects on the general population. Our focus then should also consider the general public and other subpopulations. Also, medical students are more likely to seek mental health problems if they have access to a clinic. But this is not the norm in conservative societies like Jordan. It may be considered a limitation if the authors did not assess access to mental health professional services. On the same point, how will the screening tools for the positive and negative domains investigated reflect the true problem given that self-reported mental health depression, for example, may be overestimating the actual values. Any thoughts on what the authors expect the true need for mental health advising and counseling among this population? It is a major limitation that we did not consider seeking medical help. But this is an issue that was suggested by reviewers of the questionnaire to exclude as it will not be an accurate measure for this taboo-related issue. As stated earlier, we expect that our screening self-reported results address provide 10% of self-reported issues be an actual estimate then we have an idea about the impact of mental health issues among medical students. The mental health status of medical students is biased by multiple factors that were not addressed in the study. How will the authors direct future research considering such biases? For example, academic achievement and substance use. The top 5 mental health issues identified in the manuscript could be further investigated and explored using fine-tuned questionnaires that consider other potential confounders. This is not added to the manuscript and will be part of the recommendations. On the same page of future research, will next research question encounters worry? Depression? Anxiety? Or what domain? Apparently this research pointed to the top 5 mental health issues (for each gender and year level). These could further be explored using follow-up studies. This was indicated in the study. It seems that gender is playing a major role in defining mental health of medical students. Why didn't the authors do a regression analysis to identify the role of gender? This may be due to the fact that the tools used limit further statistical tests? Any other thoughts? While a regression is a good fit for this paper, we wanted to only shed the light on the major mental health issues and point out to the policy makers of the major ones to be considered in the medical curriculum and medical services provided to students. We did not feel that adding a regression model for a self-reported mental health issue is a good fit as it may not reflect validity of self-reported depression, for example. Future research utilizing standardized screening tools may use advanced statistical analyses and have more variables relevant to mental health."
}
]
},
{
"id": "83591",
"date": "29 Apr 2021",
"name": "Tariq Kewan",
"expertise": [
"Reviewer Expertise Oncology",
"COVID-19 treatment",
"Coagulopathy",
"Acute leukemia",
"blood disorders",
"critical care"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn this article Kheirallah and colleagues studied the impact of COVID-19 pandemic on the medical student emotional distress using a self reported questionnaire. In addition Authors analyzed the impacts of social media utilization as a source of information on the the emotional factors, below are some comments to consider:\n\nThe authors used a self reported cross sectional design to analyze the outcomes, however targeted population size and response rates were not reported. It is also worth to mention the response rate by each different university.\n\nCan the authors explain why they considered response rate of 20% to be sufficient, please cite a paper.\n\nHow the authors guaranteed that each participant will respond one time only?\n\nCan you provide the time period of the study?\n\nAuthors need to provide the questionnaire used in the study to be published as a supplementary with the article.\n\nThe definition of different symptoms reported was not specified. For example what is the difference between anxiety and panic or worry and anxiety? This also will raise the question regarding participant understanding of the questions. Did the authors provide explanations for the participant to ensure understanding. Can the authors provide specific definition for each symptoms / disorder they reported, for example what is the dentition of insomnia?\n\nResults are conflicting. In table 2 , 72.2% of all participant reported worry but at the same time 44.8% reported increased happiness. This will raise the concern of appropriate understanding of the participants.\n\nAuthors concluded that social media use may have a buffering effect on emotional distress which is wrong. This conclusion cant be made based on the study design provided. Authors just described the differences in the prevalence of different symptoms / diseases between three different groups based on the use of social media as a source of information. Other variables / confounders were not taken into consideration and this conclusion is not appropriate.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? No",
"responses": [
{
"c_id": "6635",
"date": "24 May 2021",
"name": "khalid kheirallah",
"role": "Author Response",
"response": "We appreciate your opinion and feedback. Kindly note our response in line with the provided comments. In this article Kheirallah and colleagues studied the impact of COVID-19 pandemic on the medical student emotional distress using a self reported questionnaire. In addition Authors analyzed the impacts of social media utilization as a source of information on the the emotional factors, below are some comments to consider: The authors used a self reported cross sectional design to analyze the outcomes, however targeted population size and response rates were not reported. It is also worth to mention the response rate by each different university. Thank you for this comment. We have updated the manuscript to state that the total population of medical students is 10,000. Out of the sample selected for this survey, a total of 3,000 as already stated, the response rate was added to the results section (46.8%). Can the authors explain why they considered response rate of 20% to be sufficient, please cite a paper. Thank you for this comment. We have a previous experience with this population and a response rate was less than 30%. Being conservative, we have decided that a 20% is suitable. A reference is already inserted for which we had a 20% response rate. How the authors guaranteed that each participant will respond one time only? Thank you for this valuable note. We have no guarantee that each student will fill the questionnaire only once. But we have no reason to believe that medical students will fill more than one time. Can you provide the time period of the study? Thank you for this comment. The study stated, under methods, that this survey was conducted between March 17 and 20, 2020. Authors need to provide the questionnaire used in the study to be published as a supplementary with the article. Thank you for this note. We have now updated the supplementary materials to include the questionnaire. The definition of different symptoms reported was not specified. For example what is the difference between anxiety and panic or worry and anxiety? This also will raise the question regarding participant understanding of the questions. Did the authors provide explanations for the participant to ensure understanding. Can the authors provide specific definition for each symptoms / disorder they reported, for example what is the dentition of insomnia? Thank you for this note. We have defined each term as self-reported. It was meant to screen and prioritize potential mental health issues using self-reported responses. This was stated as part of the limitations. Results are conflicting. In table 2 , 72.2% of all participant reported worry but at the same time 44.8% reported increased happiness. This will raise the concern of appropriate understanding of the participants. Thank you for this note. The potential overlap is possible given the way the study was conducted. It may be true that students are worried about their educational process at the early stages of the pandemic, still feel happy being able to spend more time with their families. This issue needs further investigation using qualitative study design as positive and negative emotions are possible given the circumstances of uncertainties. Qualitative investigations of the study results was suggested and recommended as part of the study’s future directions in multiple locations. Authors concluded that social media use may have a buffering effect on emotional distress which is wrong. This conclusion cant be made based on the study design provided. Authors just described the differences in the prevalence of different symptoms / diseases between three different groups based on the use of social media as a source of information. Other variables / confounders were not taken into consideration and this conclusion is not appropriate. Thank you for this note. Social media utilization has been suggested to “moderate” the relationship between multiple variables and mental health issues. As such, our results of potential differences in mental health variables by social media utilization may suggest a buffering effect. Future studies, including follow-up designs are then needed to investigate this relationship. This is what was suggested in the conclusion of the study. As such, the effect of social media utilization may, or may not, be a factor in the buffering suggested. The conclusion, as such, has been worded to reflect this. Edits were made."
}
]
},
{
"id": "83592",
"date": "07 May 2021",
"name": "Walid Alali",
"expertise": [
"Reviewer Expertise Epidemiology",
"Infectious Diseases",
"Public Health",
"Antimicrobial Resistance."
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe manuscript present descriptive findings from a cross-sectional study conducted via a questionnaire tool to assess emotional distress during COVID-19 pandemic on medical students in Jordan. There were reports of significant increase in negative emotional mental health issues. The findings add to the scientific literature on mental health issues related to COVID-19 pandemic restrictions in a specific group of people.\nMy minor comments:\nThe probability sampling plan is not clear as authors mentioned \"students were selected randomly\". Needs explanation.\n\nThe questionnaire tool should be included as an appendix.\n\nPlease add a statistical/data analysis statement.\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": []
}
] | 1
|
https://f1000research.com/articles/10-297
|
https://f1000research.com/articles/10-181/v1
|
05 Mar 21
|
{
"type": "Research Article",
"title": "Effect of snail mucus on angiogenesis during wound healing",
"authors": [
"Yosaphat Bayu Rosanto",
"Cahya Yustisia Hasan",
"Rahardjo Rahardjo",
"Tri Wahyu Pangestiningsih",
"Yosaphat Bayu Rosanto",
"Rahardjo Rahardjo",
"Tri Wahyu Pangestiningsih"
],
"abstract": "Background: Angiogenesis is the process through which new blood vessels are formed from existing ones. This process plays an important role in supplying the oxygen and nutrients needed for cellular metabolism and eliminating cell debris during wound healing. Snail mucus can bind to several factors that stimulate angiogenesis, including vascular endothelial growth factor, platelet-derived growth factor, and fibroblast growth factor. The aim of this study is to observe changes in angiogenesis during the healing of wounds topically applied with snail mucus. Methods: Punch biopsy was performed on the back of male Wistar rats to obtain four wounds, and different concentrations of snail mucus were applied to each of these wounds. The animals were sacrificed on days 2, 4, and 7 to observe the extent of angiogenesis during wound healing by microscopy. Results: Two-way ANOVA showed differences in number of blood vessels formed (p = 0.00) and day of observation (p = 0.00) between groups. Post hoc Tukey’s HSD test showed that 24% snail mucus treatment does not significantly affect wound healing (p = 0.488); by contrast, treatment with 48% and 96% snail mucus demonstrated significant effects on angiogenesis (p = 0.01). Spearman’s test showed interactive effects between snail mucus concentration and day of observation on the extent of angiogenesis (p = 0.001, R = 0.946). Conclusion: Topical application of snail mucus gel can increase angiogenesis during wound healing in Wistar rat skin.",
"keywords": [
"new vessels",
"hematoxylin eosin",
"CMC-Na",
"glycosaminoglycans",
"heparan sulfate"
],
"content": "Introduction\n\nOral surgery is an aspect of dentistry that is often associated with skin lesions1,2. Cuts to the skin during oral and maxillofacial surgery may be achieved through incision or excision. Incision wounds are usually established during surgery, while excision wounds occur in trauma cases3–6. Excision wound models generally have a diameter of 2–20 mm. Excision wounds provide complex and detailed views of the wound healing process and allow the examination of various wound healing parameters7. This fact underlies the selection of excision wound in the present study.\n\nWhen a wound occurs in the body, physiological healing is performed by multiple biocellular and biochemical processes8. Wound healing refers to the process through which normal tissue is regenerated from damaged tissue9; it involves cells, the extracellular matrix, and a number of mediators, such as growth factors and cytokines10. The wound healing process also involves hemostasis, regeneration of peripheral cells, and restoration of muscle tissue by collagen fibers11. Wound healing is a dynamic and complex process that involves multiple phases with overlaps from one phase to another12.\n\nThe wound healing process can be divided into three phases, namely, inflammation, proliferation, and tissue remodeling. This process can be observed using several parameters, such as re-epithelialization, number of polymorphonuclear leukocytes, number of fibroblasts, density of collagen fibers, and angiogenesis13. Angiogenesis is important in healing and refers to the process through which pre-existing blood vessels generate capillary buds to produce new blood vesselss14. Angiogenesis is triggered by tissue damage, which causes local hypoxia15. When local hypoxia occurs, cells respond by increasing their production of vascular endothelial growth factor (VEGF), one of the most important mediators for wound healing and a stimulant of capillary growth. Angiogenesis is then induced to fulfil requirements for nutrients, oxygen, and inflammatory cells16.\n\nWound healing can be enhanced by chemical and natural treatments17. Traditional medicines with natural health benefits and limited side effects have been developed by many researchers18. Snail mucus is widely used by cosmetics manufacturers as a skin care material19. The resulting products usually feature high contents of hyaluronic acid, proteoglycans, glycoprotein enzymes, and antibacterial peptides to protect the skin from damage20.\n\nThe African giant snail (Achatina fulica) contains glycosaminoglycans21. Indeed, approximately 3%–5% of the dry weight of the snail is composed of glycosaminoglycans22. Glycosaminoglycans are a group of anionic polysaccharides that are typically isolated as proteoglycans connected to protein nuclei23. The biological activation of glycosaminoglycans stimulates the regulation of cell growth via the interaction of the glycosaminoglycan chains with growth factor proteins and their receptors24. The snail also contains acharan sulfate, which is stored as granules in the snail body and secreted by the animal under certain stimuli25.\n\n\nMethods\n\nThe rat cages measured at least 40 cm long, 15 cm wide, and 10 cm high, and one cage housed one rat. The cages were covered with rice husks to achieve a stress-free environment for the rats, and the animals were provided food and water ad libitum. Snails are obtained from farms in Central Java. Identification and determination of Achatina fulica species were carried out in laboratory of animal biology. The snails were adapted to a cage with moist soil and banana leaves as food for three days. Then, the snails were fasted three days before the mucus extraction. Snail mucus was extracted by stimulating the surface of the snail body with an electric shock of 6 V for 60 s, one touches namely from repetition 2 ~ 4 times. This method does not cause pain or stress on the snail. A detailed description of all protocols can be found in the google patent numbered CN102846519B (https://patents.google.com/patent/CN102846519B/en). The collected snail mucus was passed through batiste cloth to remove impurities, collected in a glass beaker, and homogenized. The snail mucus was sterilized by filtration through Whatman No. 4 filter paper. Finally, the mucus was diluted with CMC-Na to obtain gels with mucus concentrations of 24%, 48%, and 96% (w/w).\n\nThis research was approved by the Health and Medical Research Ethics Committee of the Faculty of Dentistry, Universitas Gadjah Mada (Approval No. 00272/KKEP/FKG-UGM/EC/2019). This study used nine rats based on calculations using the resource of equation method with the minimum sample calculation formula in research with ANOVA design. Sample calculation: Minimum n= 10/kr +1 =10/(4x3) +1 = 1.83. Maximum n= 20/kr +1 = 20/(4x3) +1 = 2.66 (k = number of treatments, r = number of repeated measurements). The conclusion is the use of 3 rats meets the sample size requirements.\n\nThe rats were obtained from breeding by laboratory of pharmaceutical. Healthy male Wistar rats were adapted to cages for 3 days. The rat cages measured at least 40 cm long, 15 cm wide, and 10 cm high, and one cage housed one rat. The cages were covered with rice husks to achieve a stress-free environment for the rats, and the animals were provided food and water ad libitum.\n\nThe rats were included in the study if they were 3–4 months old, weighed 250–300 mg, appeared healthy and physically active, and there were no visible anatomical defects. The rats were excluded in the study if they had postoperative infections or died before the euthanasia process. They were randomly divided into three groups of euthanasia day (three rats/group). Random numbers were generated using the standard = RAND() function in Microsoft Excel. The rats were anesthetized with 100 mg/kg BW ketamine and 4 mg/kg xylazine intramuscularly. The back of each rat was shaved, marked, and disinfected with 70% alcohol. A circular subcutaneous excision wound was made by punch biopsy of 5 mm. The skin on the back of a rat was folded and lifted by pinching the cranial and caudal skin between the thumb and forefinger. The rat was placed in the lateral position, and a biopsy punch was made through the folded skin (middle). Appearance of the resulting symmetrical and full-thickness wounds is shown in Figure 1. The minimum distance between wounds was 5 mm. Each rat was given 4 wounds which were given different experiments (24%, 48%, 96% and control gels), so the total was nine rats with 36 wounds (each experiments were nine wounds which were observed on day two, four, and seven). The total rats in each groups are described in Figure 2. The calculation of the number of samples and four wounds on the back of the rats and this fulfills the requirements of reduce, reuse, and recycle.\n\nThe rats were transferred to a warm cage until they regained complete consciousness and then returned to their original cages. The general condition and weight of the rats were recorded daily. The snail mucus (24%, 48%, 96%) and control gels (CMC-Na) were applied 1 ml once a day (in the morning) on each wound. Euthanasia was performed on postoperative days 2, 4, and 7 by overdoses of inhaled anesthetics ether. The skin of the treated wound area was removed for histological examination by hematoxylin–eosin staining. Observation and calculation of the number of new blood vessels formed were carried out using a binocular microscope equipped with an Optilab Advance V2 12,6MP camera in the five fields of view. Microscopic observations were performed at 40×, 100×, and 400× magnification. The number of new blood vessels formed was calculated by three observers. The number of new blood vessels were the only outcome measures used\n\nTwo-way analysis of variance (ANOVA) was used to determine significant differences in angiogenesis among the treatment groups. Post hoc Tukey’s test was conducted to determine which groups showed significant differences. Statistical calculations were performed using statistical package for the social sciences (IBM SPSS Statistics 23) software at a confidence level of 95% (α < 0.05).\n\n\nResults\n\nObservation at 40× magnification showed differences in the structure of wounds with healthy skin borders on days two, four, and seven at all perecentage of mucus (Figure 3). Wounds observed on day two showed tissues filled with inflammatory cells without a surface epithelium. Wounds on day four revealed reductions in inflammatory tissue and a thin layer of connective tissue. The surface epithelium covering the wound was fairly thin. On day seven of healing, the wounds showed thick connective tissue formation and a surface epithelium layer clearly covering the wounded area. Inflammatory cells could not be clearly observed on day seven.\n\nWound healing with gel 96% on day two (A), day four (B), and day seven (C), as determined using histological preparations with hematoxylin–eosin staining at 40× magnification. Blue arrows indicate the epithelium, red arrows indicate the epidermis, yellow arrows indicate the papillary stratum, green arrows indicate the reticular stratum, and orange arrows indicate adipose layers. Observation of angiogenesis was carried out on the papillary and reticular dermal layers of the stratum.\n\nObservation at 100× magnification was performed to determine relevant fields of view (Figure 4). Angiogenesis was noted in the papillary and reticular strata. Visual fields for further observation were selected from five areas in these strata.\n\nWound healing with gel 96% on day two (A), day four (B), and day seven (C), as determined using histological preparations with hematoxylin–eosin staining at 100× magnification. (a) Healthy tissue and (b) wound tissue.\n\nThe number of new blood vessels in the wounds was counted from five fields of view at 400× magnification. New blood vessels appeared in the lumen; the walls of these vessels were composed of endothelial cells and contained erythrocytes (Figure 5). Endothelial cells at the edges of cell walls were purple in color, round, and flat. Erythrocytes appeared as red irregularly rounded cells without a nucleus.\n\nThe walls of lumen vessels (yellow arrows) are formed by endothelial cells (blue arrows) and contain erythrocytes (black arrows). This picture was taken from experiments with gel 96%.\n\nThe number of new blood vessels formed are shown in Figure 6 and Table 1. The results of the calculations in Table 1 are depicted in Figure 7. The number of new blood vessels formed increased from day two to day four in all groups but was greatest in the 96% snail mucus treatment group (mean, 17.2). Whereas angiogenesis decreased from day four to day seven in the 96% and 48% snail mucus treatment groups, angiogenesis in the 24% snail mucus treatment and control groups increased over these days. The number of new blood vessels formed in the 96% snail mucus treatment group was consistently greater than those in the other treatment groups on each day assessed.\n\nThe greatest number of new blood vessels formed was observed on day four following the application of 96% snail mucus gel (p = 0.000).\n\nTwo-way ANOVA was used to determine significant differences in the extent of angiogenesis and number of observation days among the treatment groups. Differences in number of observation days, concentration, and the interaction of number of observation days and concentration were significant with 0.000, 0.000, and 0.001 (p < 0.05), respectively. These results demonstrate that each of the independent variables analyzed has a significant effect on angiogenesis.\n\nPost hoc testing of the two-way ANOVA results was conducted using Tukey’s HSD test. The difference in the number of new blood vessels formed between the control group and the 24% snail mucus treatment group was not significant. All other groups showed significant differences in mean number of new blood vessels formed. These results indicate that treatment with 48% and 96% snail mucus has significant effects on angiogenesis during skin wound healing.\n\n\nDiscussion\n\nWound healing is a biological process that involves complex interactions between cells, the extracellular matrix, and growth hormones. This process occurs in several phases, namely, hemostasis, inflammation, proliferation, and maturation26. Angiogenesis is an important process in wound healing27. The present study demonstrated that snail mucus can accelerate angiogenesis and wound healing. Prasojo et al. (2018) found that pure snail mucus without a carrier material can increase angiogenesis during wound healing compared with distilled water28. Harti et al. (2018) showed that heparan sulfate stimulates VEGF. The study found that 5% and 100% snail mucus creams could accelerate wound healing by stimulating lymphocyte proliferation29.\n\nXander and Toin (2013)30 revealed that heparan sulfate is a proteoglycan that serves as a binder and storage unit for basic fibroblast growth factor (bFGF), which is secreted into the extracellular matrix. Heparan sulfate interacts with proangiogenic factors, such as fibroblast growth factor (FGF), VEGF, and platelet-derived growth factor (PDGF), on the surface of endothelial cells and causes these factors to bind to their corresponding receptors, thereby resulting in dimerization and various signaling processes. The extracellular matrix can release bFGF to stimulate inflammatory cell recruitment, fibroblast activation, and the formation of new blood vessels during injury31,32. This hormonal mechanism may also occur in the increase of angiogenesis in this study. However, research on this subject is still our next research project. In addition, a snail mucus gel formulation is also in our next project, so that this gel will have a more effective absorption rate and can be stored for a long time. A previous study indicated that snail mucus with chitosan as a membrane can accelerate wound healing through anti-inflammatory activity. Apriyanti et al. (2017)33 also showed that 5% snail mucus gel could increase angiogenesis in alveolar bone during the healing of periodontitis in Wistar rats.\n\nAngiogenesis is a complex process involving various cells, hormones, and extracellular components34. Snail mucus contains proangiogenic glycosaminoglycans, heparan sulfate, heparin sulfate, and hyaluronic acid. These compounds can increase angiogenesis by triggering VEGF as the dominant angiogenetic growth factor against endothelial cells as blood vessel-forming cells22,35,36.\n\nEndothelial cell proliferation marks the beginning of angiogenesis. Endothelial cells grow, migrate, and then attach to the extracellular matrix, where they differentiate into new blood vessels37–39. Snail mucus can stimulate these processes remarkably. The results of this study demonstrated that the application of snail mucus could increase angiogenesis at all concentrations tested. The statistical analysis shows that the increase in angiogenesis is particularly significant at snail mucus concentrations of 48% and 96% (p = 0.000). Compared with the other groups, the 96% snail mucus treatment showed the greatest extent of angiogenesis (Figure 7).\n\nNew blood vessels were formed on day two in all treatments. Wounds applied with snail mucus showed a greater number of new blood vessels formed compared with the control treatment (p = 0.000). This finding is consistent with the research of Bauer et al. (2005)15, who found that the initial factor triggering angiogenesis is the damage that occurs in endothelial tubules following tissue damage. Tissue damage causes local hypoxia. The hypoxic state of the tissue becomes an angiogenic stimulator as growth factors and cytokines are released from inflammatory cells accumulated in the wound area during the previous inflammatory process. These factors stimulate the proliferation and invasiveness of vascular cells to promote blood vessel growth15,16,40.\n\nThe most important mediators in the early phase of angiogenesis are VEGF, FGF, and PDGF41. Heparan sulfate in snail mucus can interact with these factors on the surface of endothelial cells and enhance their ability to bind to their corresponding receptors, resulting in dimerization and various signaling processes30. An adequate supply of nutrients, oxygen, and cells with essential functions in wound healing could hasten the wound healing process. Sufficient nutrition and oxygen are required for optimal wound healing. Angiogenesis provides a new vascular system that could deliver nutrients and oxygen to the wound area and enable wound healing. Cells necessary for wound healing, such as inflammatory cells, fibroblasts, and mesenchymal cells, which secrete various growth factors, may also be delivered to the wound site through this new vascular system42,43. Mature endothelial cells can then form new blood vessel walls in the wound area44.\n\nDay four of observation revealed the greatest number of new blood vessels formed in the 96% snail mucus treatment group. The proliferation phase of angiogenesis occurs on the fourth day after the initiation phase, which could explain the extent of angiogenesis observed on this day in the present study. Kalangi (2004)45 stated that the proliferation phase begins with the degradation of old blood vessels by providing capillary shoot formation in hypoxic tissues to meet the nutritional and oxygen needs of parenchymal cells. These parenchymal cells secrete the most important proangiogenic growth factor, namely, VEGF-A. Then, there is a series of angiogenesis starting from (1) migration of endothelial cells distally from the original capillary vessels to stimulate angiogenesis; (2) proliferation of endothelial cells at the periphery of/distal to tubule formation; (3) stabilization of endothelial cells by interacting strongly with support cells, such as smooth muscle cells and pericytes; (4) maturation of endothelial cells via the formation of a lumen through intercellular and intracellular mechanisms, including the mobilization and proliferation of pericytes (from blood vessels) and smooth muscle cell (for large vessels) to support the endothelial wall and provide additional budding; (5) anastomosis with other endothelial buds and knot formation; and (6) development of circulation and adjustment of canals with arterial and venous segments45–47.\n\nGlycosaminoglycans and heparan sulfate in snail mucus significantly increased (p = 0.031) the number of new blood vessels formed in the 96% snail mucus treatment group on day four. Glycosaminoglycans stabilize cell membranes, increase the synthesis of hyaluronic acid, a known anti-inflammatory agent, and accelerate angiogenesis; as such, these compounds have positive effects on wound healing48. Angiogenesis can also be enhanced by the ability of snail mucus to bind divalent cations, such as copper(II)29. Heparan sulfate is a proteogenizer that can bind and store bFGF, which is secreted by the extracellular matrix to stimulate the recruitment of inflammatory cells, fibroblast activation, and angiogenesis49.\n\nCompared with that on the day 4, the average number of new blood vessels formed in the 48% and 96% snail mucus treatment groups decreased on day 7. By contrast, the control and 24% snail mucus treatment groups revealed continuous increases in angiogenesis (Table 1 and Figure 7) significantly (p = 0.000). This finding indicates that snail mucus not only increases the number of new blood vessels formed but also hastens the phases of angiogenesis. The decrease in number of new blood vessels formed on day seven in the 48% and 96% snail mucus treatment groups may be due to apoptosis. The number of new vessels formed is reduced until the density of blood vessels in the wound area returns to normal. This process is regulated by a selective apoptosis process that occurs simultaneously with the maturation of new blood vessels. Apoptosis refers to the automatic and programmed death of normal cells50–52.\n\nAccording to a study conducted by Ricard et al. (2014), the glycosaminoglycans and hyaluronic acid in snail mucus could increase the activity of pericyte cells. Pericyte cells are multifunctional cells capable of maintaining capillary stability and protecting capillaries from negative signals. Some selective apoptosis processes are regulated by pericyte cells51,53. Pericytes are only present in newly formed blood vessels. Researchers believe that vessels without pericytes are susceptible to the influence of antiangiogenic agents54. The apoptosis of blood vessels in a wound area decreases following the reduction of antiangiogenic factors55. Mostafa (2014)56 conducted a study on the effect of topical application of synthetic glycosaminoglycans on wound healing in mice and found an increase in wound closure speed; this study used synthetic glycosaminoglycans at a concentration of 2%. The glycosaminoglycans used in the present study are obtained naturally from snail mucus.\n\nThe most important mediators in angiogenesis are VEGF, FGF, and PDGF. This study did not examine hormonal levels of these factors to determine the effect of snail mucus on proangiogenic factors. Further research can be conducted to examine the effects of snail mucus on these factors and their corresponding receptors. In addition, a snail mucus gel formulation is also in our next project, so this gel will have a more effective absorption rate and can be stored for a long time.\n\n\nConclusion\n\nDifferent concentrations of snail mucus gel revealed different effects on angiogenesis during the healing of punch biopsy wounds on the back skin of Wistar rats. Compared with the control and 24% and 48% snail mucus treatment groups, the 96% snail mucus treatment group showed the greatest improvements in angiogenesis on day 4 (p = 0.00). Snail mucus concentration and day of observation showed interactive effects on angiogenesis during skin wound healing in Wistar rats (R = 0.946). Specifically, the higher the snail mucus concentration and the greater the number of observation days, the faster the wound healing process.\n\n\nData availability\n\nFigshare: Table 1. Results of angiogenesis observations according to day and concentration56. https://doi.org/10.6084/m9.figshare.13698871.v1\n\nThis project contains the following underlying data:\n\n- Table 1. The results of the calculations in Table 1 are depicted in Figure 7. The number of new blood vessels formed increased from day 2 to day 4 in all groups but was greatest in the 96% snail mucus treatment group (mean, 17.2). Whereas angiogenesis decreased from day 4 to day 7 in the 96% and 48% snail mucus treatment groups, angiogenesis in the 24% snail mucus treatment and control groups increased over these days. The number of new blood vessels formed in the 96% snail mucus treatment group was consistently greater than those in the other treatment groups on each day assessed.\n\nFigshare: Figure 1. Installation of excision wounds57. https://doi.org/10.6084/m9.figshare.14045033.v1\n\nThis project contains the following data:\n\n- JPG file of the installation of excision wounds on the rats. The skin on the back of a rat was folded and lifted by pinching the cranial and caudal skin between the thumb and forefinger. The rat was placed in the lateral position, and a biopsy punch was made through the folded skin (middle). Appearance of the resulting symmetrical and full-thickness wounds. No modifications have been made to this image.\n\nFigshare. Figure 3. Wound healing with gel 98% on day two (A), day four (B), and day seven (C)58. https://doi.org/10.6084/m9.figshare.14045075.v1\n\nThis project contains the following data:\n\n- JPG file showing the wound healing on day 2. Determined using histological preparations with hematoxylin–eosin staining at 100× magnification. (a) Healthy tissue and (b) wound tissue. Arrow on the image was made by Microsoft Word 2013. No others modifications have been made to this image.\n\nFigshare. Figure 4. Wound healing with gel 98% on day two (A), day four (B), and day seven (C)59. https://doi.org/10.6084/m9.figshare.14045099\n\nThis project contains the following data:\n\n- JPG file of wound healing with gel 98% on day two (A), day four (B), and day seven (C). Determined using histological preparations with hematoxylin–eosin staining at 100× magnification. (a) Healthy tissue and (b) wound tissue. Alphabet on the image was made by Microsoft Word 2013. No others modifications have been made to this image.\n\nFigshare. Figure 5. Blood vessels in the histologic preparation60. https://doi.org/10.6084/m9.figshare.14045309\n\nThis project contains the following data:\n\n- JPG file of blood vessels in the histologic preparation. The walls of lumen vessels (yellow arrows) are formed by endothelial cells (blue arrows) and contain erythrocytes (black arrows). This picture was taken from experiments with gel 96%. Arrow on the image was made by Microsoft Word 2013. No others modifications have been made to this image.\n\nFigshare. Figure 6. New blood vessels formation in the wound area on days two, four, and seven61. https://doi.org/10.6084/m9.figshare.14045342\n\nThis project contains the following data:\n\n- JPG file of angiogenesis in the wound area on days two, four, and seven. Observed from histological preparations with hematoxylin–eosin staining at 400× magnification. The greatest number of new blood vessels formed was observed on day four following the application of 96% snail mucus gel (p = 0.000). Grouping, naming, and arrow on the image were made by Microsoft Word 2013. No other modifications have been made to this image.\n\nFigshare. Figure 7. Graphic of the numbers of new blood vessels formed among treatment groups and days62. https://doi.org/10.6084/m9.figshare.14045351\n\nThis project contains the following data:\n\n- JPG graphic of the numbers of new blood vessels formed among treatment groups and days No other modifications have been made to this image.\n\nFigshare. Raw data of new blood vessels observation63. https://doi.org/10.6084/m9.figshare.14045369\n\nThis project contains the following data:\n\n- .xlxs file of the results of angiogenesis observations according to day and concentration.\n\nData are available under the terms of the Creative Commons Zero \"No rights reserved\" data waiver (CC BY 4.0 Public domain dedication).\n\nFigshare. Figure 3A. Wound healing with gel 96% on day two64. DOI: https://doi.org/10.6084/m9.figshare.14092499\n\nFigshare. Figure 3B. Wound healing with gel 96% on day four as determined using histological preparations with hematoxylin–eosin staining at 40× magnification65. DOI: https://doi.org/10.6084/m9.figshare.14092898\n\nFigshare. Figure 3C. Wound healing with gel 96% on day seven, as determined using histological preparations with hematoxylin–eosin staining at 40× magnification66. DOI: https://doi.org/10.6084/m9.figshare.14093035\n\nFigshare. Figure 4A. Wound healing with gel 96% on day two as determined using histological preparations with hematoxylin–eosin staining at 100× magnification67. DOI: https://doi.org/10.6084/m9.figshare.14093131\n\nFigshare. Figure 4B. Wound healing with gel 96% on day four as determined using histological preparations with hematoxylin–eosin staining at 100× magnification68. DOI: https://doi.org/10.6084/m9.figshare.14093227\n\nFigshare. Figure 4C. Wound healing with gel 96% on day seven as determined using histological preparations with hematoxylin–eosin staining at 100× magnification69. DOI: https://doi.org/10.6084/m9.figshare.14093289\n\nFigshare. Figure 5. Blood vessels in the histologic preparation. The walls of lumen vessels (yellow arrows) are formed by endothelial cells (blue arrows) and contain erythrocytes (black arrows). This picture was taken from experiments with gel 96%70. DOI: https://doi.org/10.6084/m9.figshare.14093357\n\nFigshare. Figure 6 Day 2 24%. Angiogenesis in the wound area on day two with control as observed from histological preparations with hematoxylin–eosin staining at 400× magnification71. DOI: https://doi.org/10.6084/m9.figshare.14093419\n\nFigshare. Figure 6 Day 2 48%. Angiogenesis in the wound area on days two with 48% of snail mucus as observed from histological preparations with hematoxylin–eosin staining at 400× magnification72. DOI: https://doi.org/10.6084/m9.figshare.14093731\n\nFigshare. Figure 6 Day 2 96%. Angiogenesis in the wound area on days two with 96& of snail mucus as observed from histological preparations with hematoxylin–eosin staining at 400× magnification73. DOI: https://doi.org/10.6084/m9.figshare.14093829\n\nFigshare. Figure 6 Day 2 Control. Angiogenesis in the wound area on days two, four, and seven, as observed from histological preparations with hematoxylin–eosin staining at 400× magnification74. DOI: https://doi.org/10.6084/m9.figshare.14093891\n\nFigshare. Figure 6 Day 4 24%. Angiogenesis in the wound area on day four with 24% of snail mucus as observed from histological preparations with hematoxylin–eosin staining at 400× magnification75. DOI: https://doi.org/10.6084/m9.figshare.14093935\n\nFigshare. Figure 6 Day 4 48%. Angiogenesis in the wound area on day four with 48% of snail mucus as observed from histological preparations with hematoxylin–eosin staining at 400× magnification76. DOI: https://doi.org/10.6084/m9.figshare.14094001\n\nFigshare. Figure 6 Day 4 96%. Angiogenesis in the wound area on day four with 96% of snail mucus as observed from histological preparations with hematoxylin–eosin staining at 400× magnification77. DOI: https://doi.org/10.6084/m9.figshare.14094623\n\nFigshare. Figure 6 Day 4 Control. Angiogenesis in the wound area on day four with control as observed from histological preparations with hematoxylin–eosin staining at 400× magnification78. DOI: https://doi.org/10.6084/m9.figshare.14094687\n\nFigshare. Figure 6 Day 7 24%. Angiogenesis in the wound area on day seven with 24% of snail mucus as observed from histological preparations with hematoxylin–eosin staining at 400× magnification79. DOI: https://doi.org/10.6084/m9.figshare.14094751\n\nFigshare. Figure 6 Day 7 48%. Angiogenesis in the wound area on day seven with 48% of snail mucus as observed from histological preparations with hematoxylin–eosin staining at 400× magnification80. DOI: https://doi.org/10.6084/m9.figshare.14094803\n\nFigshare. Figure 6 Day 7 96%. Angiogenesis in the wound area on day seven with 96% of snail mucus as observed from histological preparations with hematoxylin–eosin staining at 400× magnification81. DOI: https://doi.org/10.6084/m9.figshare.14094849\n\nFigshare. Figure 6 Day 7 Control. Angiogenesis in the wound area on day seven with control as observed from histological preparations with hematoxylin–eosin staining at 400× magnification82. DOI: https://doi.org/10.6084/m9.figshare.14094919",
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Publisher Full Text\n\nKelly-Goss MR, Sweat RS, Stapor PC, et al.: Targeting pericytes for angiogenic therapies. Microcirculation. 2014; 21(4): 345–57. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDulmovits BM, Herman IM: Microvascular remodeling and wound healing: a role for pericytes. Int J Biochem Cell Biol. 2012; 44(11): 1800–12. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWietecha MS, Król MJ, Michalczyk ER, et al.: Pigment epithelium-derived factor as a multifunctional regulator of wound healing. Am J Physiol Heart Circ Physiol. 2015; 309(5): H812–26. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRosanto YB: Table 1. Results of angiogenesis observations according to day and concentration. figshare. Dataset. 2021. http://www.doi.org/10.6084/m9.figshare.13698871.v1\n\nRosanto YB: Installation of excision wounds. figshare. Figure. 2021. http://www.doi.org/10.6084/m9.figshare.14045033.v1\n\nRosanto YB: Wound healing on day two. figshare. Figure. 2021. http://www.doi.org/10.6084/m9.figshare.14045075.v1\n\nRosanto YB: Wound healing with gel 98% on day two (A), day four (B), and day seven (C). figshare. Figure. 2021. http://www.doi.org/10.6084/m9.figshare.14045099.v1\n\nRosanto YB: Blood vessels in the histologic preparation. figshare. Figure. 2021. http://www.doi.org/10.6084/m9.figshare.14045309.v1\n\nRosanto YB: Angiogenesis in the wound area on days two, four, and seven. figshare. Figure. 2021. http://www.doi.org/10.6084/m9.figshare.14045342.v1\n\nRosanto YB: Graphic of the numbers of new blood vessels formed among treatment groups and days. figshare. Figure. 2021. http://www.doi.org/10.6084/m9.figshare.14045351.v1\n\nRosanto YB: Raw data. figshare. Dataset. 2021. http://www.doi.org/10.6084/m9.figshare.14045369.v1\n\nRosanto YB: Figure 3A. figshare. Figure. 2021. http://www.doi.org/10.6084/m9.figshare.14092499.v1\n\nRosanto YB: Figure 3B. figshare. Figure. 2021. http://www.doi.org/10.6084/m9.figshare.14092898.v1\n\nRosanto YB: Figure 3C. figshare. Figure. 2021. http://www.doi.org/10.6084/m9.figshare.14093035.v1\n\nRosanto YB: Figure 4A. figshare. Figure. 2021. http://www.doi.org/10.6084/m9.figshare.14093131.v1\n\nRosanto YB: Figure 4B. figshare. Figure. 2021. http://www.doi.org/10.6084/m9.figshare.14093227.v1\n\nRosanto YB: Figure 4C. figshare. Figure. 2021. http://www.doi.org/10.6084/m9.figshare.14093289.v1\n\nRosanto YB: Figure 4. figshare. Figure. 2021. http://www.doi.org/10.6084/m9.figshare.14093357.v1\n\nRosanto YB: Figure 6 Day 2 24%. figshare. Figure. 2021. http://www.doi.org/10.6084/m9.figshare.14093419.v1\n\nRosanto YB: Figure 6 Day 2 48%. figshare. Figure. 2021. http://www.doi.org/10.6084/m9.figshare.14093731.v1\n\nRosanto YB: Figure 6 Day 2 96%. figshare. Figure. 2021. http://www.doi.org/10.6084/m9.figshare.14093829.v1\n\nRosanto YB: Figure 6 Day 2 Control. figshare. Figure. 2021. http://www.doi.org/10.6084/m9.figshare.14093891.v1\n\nRosanto YB: Figure 6 Day 4 24%. figshare. Figure. 2021. http://www.doi.org/10.6084/m9.figshare.14093935.v1\n\nRosanto YB: Figure 6 Day 4 48%. figshare. Figure. 2021. http://www.doi.org/10.6084/m9.figshare.14094001.v1\n\nRosanto YB: Figure 6 Day 4 96%. figshare. Figure. 2021. http://www.doi.org/10.6084/m9.figshare.14094623.v1\n\nRosanto YB: Figure 6 Day 4 Control. figshare. Figure. 2021. http://www.doi.org/10.6084/m9.figshare.14094687.v1\n\nRosanto YB: Figure 6 Day 7 24%. figshare. Figure. 2021. http://www.doi.org/10.6084/m9.figshare.14094751.v1\n\nRosanto YB: Figure 6 Day 7 48%. figshare. Figure. 2021. http://www.doi.org/10.6084/m9.figshare.14094803.v1\n\nRosanto YB: Figure 6 Day 7 96%. figshare. Figure. 2021. http://www.doi.org/10.6084/m9.figshare.14094849.v1\n\nRosanto YB: Figure 6 Day 7 Control. figshare. Figure. 2021. http://www.doi.org/10.6084/m9.figshare.14094919.v1"
}
|
[
{
"id": "81121",
"date": "22 Mar 2021",
"name": "Lidia Audrey Rocha Valadas",
"expertise": [
"Reviewer Expertise pharmacology"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn general the work is interesting and well designed and with appropriate methodology and details that guarantee reproducibility.\n\nThe introduction is clear but i suggest to add the importance of the new patent on the field.\n\nI suggest to make the conclusion more concise, without statistical data, on this topic you just need to answer the objective of the study.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
},
{
"id": "82617",
"date": "04 May 2021",
"name": "Jike Lu",
"expertise": [
"Reviewer Expertise Natural product chemistry."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is an interesting study on the angiogenesis of crude snail mucus without purification.\n\nAbout the “Snail mucus gel preparation”, how to store the prepared mucus, or how to ensure the stability of snail mucus during the animal experiments in seven days?\n\nAbout the animal experiments, a positive control group is recommended. How to ensure that the mucus (1mL applied on each wound) does not flow out or affect other groups due to animal movement? Description about the animal cage and environment is repeated.\n\nFigure 2, Group 1-3 shows similar photos. It is suggested to list the wound photos at different days to observe the wound healing.\n\nThe work is descriptive and needs more mechanisms of research.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "6646",
"date": "21 May 2021",
"name": "Yosaphat Bayu Rosanto",
"role": "Author Response",
"response": "The mucus was diluted with CMC-Na to obtain gels with mucus concentrations of 24%, 48%, and 96% (w/w). This concentration produces a gel that is thick enough and does not flow out of the wound. The prepared mucus were stored in polypropylene conical tubes, covered with aluminum foil and placed in the refrigerator at 4 °C. This storage method preserved the angiogenic effect of the mucus. This was evidenced by the number of new blood vessels that were still significantly affected by the results of the study on day 7. Temperature and light could affect the stability of the mucus so that the used of opaque aluminum foil and cold temperatures could maintain product quality well. The minimum distance between wounds was 5 mm. The distance between the wounds in this study was made more than 2 cm so that it does not allow mucus to flow out or affect other groups due to animal movement. Positive control was not used in this study. The negative control showed a natural angiogenesis process for comparison with the mucus treatment group. The total rats in each groups are described in Figure 2. (Disclaimer: this image is only an illustration to explain the study grouping, not a photo of each mouse used in this study group)."
}
]
}
] | 1
|
https://f1000research.com/articles/10-181
|
https://f1000research.com/articles/10-412/v1
|
21 May 21
|
{
"type": "Review",
"title": "COVID-19 associated spontaneous barotrauma: a literature review",
"authors": [
"Razia Rehmani",
"Juan Salazar",
"Shorabh Sharma",
"Oscar Cisneros",
"Carlos E. Arias-Morales",
"Razia Rehmani",
"Juan Salazar",
"Shorabh Sharma",
"Oscar Cisneros"
],
"abstract": "Reports of spontaneous pneumothorax and pneumomediastinum as a complication of coronavirus disease (COVID-19) have been increasing. COVID-19 causes inflammatory disease mainly affecting the respiratory system. Severity varies from asymptomatic pulmonary findings on imaging to acute respiratory distress syndrome along with pleural effusions, consolidations and spontaneous pneumomediastinum and pneumothorax.\nThe aim of this paper was to review the literature to explore the association between pneumomediastinum/pneumothorax and COVID-19 respiratory disease, both in patients on ventilators and without ventilators, on a spontaneous basis. To this end, we conducted a comprehensive online literature search using PubMed for articles published with the key words of ‘spontaneous pneumothorax’, ‘pneumomediastinum’ and ‘COVID-19’. Further references were obtained through cross-referencing the bibliographies cited in each publication. We found that spontaneous barotrauma is one of the complications associated with COVID-19 infection and has been observed in patients with and without mechanical ventilation. The process of pneumomediastinum and pneumothorax development is not well understood, especially in patients without underlying lung disease or on mechanical ventilation. We identified various factors that predispose to barotrauma. First, the direct infection of the Type I and Type II pneumocytes by the virus. Second, the pressure gradient between the alveoli and the pulmonary interstitium. Finally, barotrauma can occur secondary to the severe inflammatory response from the COVID-19-related cytokine storm. These conditions are all associated with severe alveolar damage and rupture of the alveolar wall that can produce pneumomediastinum and pneumothorax, both in mechanically ventilated patients and non-ventilated patients. COVID-19 is associated complications result in prolonged mechanical ventilation and length of stay, as well as overall increase in morbidity and mortality. Spontaneous pneumothorax and pneumomediastinum are two serious complications. Education regarding the adjustment of ventilation settlings in the ventilator-dependent COVID-19 patient may perhaps offset the iatrogenic component of barotrauma seen in some such patients.",
"keywords": [
"COVID-19",
"Barotrauma",
"Pneumothorax",
"Pneumomediastinum"
],
"content": "Introduction\n\nCOVID-19 is a disease caused by a novel coronavirus (SARS-CoV-2), which was first identified in December 2019 in Wuhan China. The World Health Organization (WHO) declared the COVID-19 outbreak a Public Health Emergency of International Concern at the end of January 2020 and a pandemic on March 11, 2020.1 The presentation of COVID-19 is quite variable, which can involve multiple organ systems, ranging from asymptomatic carriers to severe disease and death. However, over the course of the disease most patients present with fever, chills, cough, and shortness of breath, new loss of taste and/or smell, nausea, vomiting and diarrhea. However, it has been reported that this entity causes mainly respiratory disease. In some severe cases, patients will require endotracheal intubation and mechanical ventilation (MV). Pneumothorax and pneumomediastinum are known complications of MV. However, there have been reports of patients infected with SARS-CoV-2 that have developed pneumothorax, pneumomediastinum or both without any barotrauma. Here, we present a literature review of the potential mechanisms that cause spontaneous pneumothorax and/or pneumomediastinum in COVID-19 patients.\n\nWe conducted a comprehensive online literature search using PubMed for articles published with the key words of ‘spontaneous pneumothorax’, ‘pneumomediastinum’ and ‘COVID-19’. Further references were obtained through cross-referencing the bibliographies cited in each publication.\n\n\nBackground to COVID-19\n\nThe COVID-19 pandemic has changed our world. Scientists identified the novel coronavirus as COVID-19, which was later named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).1 The WHO had confirmed more than 80,000 cases by the beginning of March 2020 in China and approximately 70 countries around the world were also affected. At the present time, 218 countries and territories across the globe have been infected by the COVID-19 virus.1 As of May 2021, the United States leads the world with over 32 million confirmed cases worldwide and over 570,980 deaths currently reported according to the Centers for Disease Control and Prevention (CDC).2\n\nThe presentation of COVID-19 is variable and can involve multiple organ systems, with patients ranging from asymptomatic carriers to severe disease and death. However, over the course of the disease most patients present with fever, chills, cough, and shortness of breath, new loss of taste and/or smell, nausea, vomiting and diarrhea. The median incubation period time is 4-5 days from the exposure to the onset of symptoms.3\n\n\nRadiologic characteristics of COVID-19\n\nIt has been reported that COVID-19 mainly causes respiratory disease, as observed in a large cohort study in China that included more than 44,000 patients diagnosed with the disease.1 As such, it is important to mention some important radiologic characteristics that may aid in the determination of disease severity. Chest radiography findings consist of isolated ground glass opacities, pleural effusion, pneumothorax, pneumomediastinum, and in more advanced disease findings are consistent with severe acute respiratory distress syndrome.4 In addition, computed tomography (CT) of the chest serves as an adjunct in diagnosing and assessing the severity of COVID-19, especially when chest x-rays have been reported as normal early in the course of the disease.1 CT chest imaging typically shows nonspecific bilateral peripheral ground glass opacities.5,6 This is quite non-specific and can be seen in many different pulmonary diseases for which a detailed clinical assessment is needed. Although CT imaging is of valid clinical utility, CT alone is not recommended nor for screening or diagnosis of COVID-19.5\n\n\nBarotrauma and COVID-19\n\nAs respiratory disease is the most common presentation in patients with COVID-19, in some severe cases, patients require endotracheal intubation and MV. Pneumothorax and pneumomediastinum are known complications of MV.7 Figure 1 shows extensive barotrauma with pneumomediastinum and extensive subcutaneous emphysema in a COVID-19 patient on mechanical ventilation who has ground-glass peripheral infiltrates shown both on chest radiograph (CXR) and CT scan. There have been reports of patients infected with SARS-CoV-2 that have developed pneumothorax, pneumomediastinum or both, without any barotrauma.7-9\n\nPneumothorax can be classified into spontaneous, traumatic or iatrogenic. Iatrogenic pneumothorax is most related to MV.10 Pneumothorax is rare in intubated patients with normal lungs and most patients with MV associated pneumothorax are reported to have underlying lung diseases (obstructive, interstitial and acute respiratory distress syndrome [ARDS]).11 Tension pneumothorax accounts for approximately 30-97% of all pneumothoraxes in patients with MV. It is important to mention that the presence of pneumothorax has been identified as an independent predictor of mortality in MV with a rate of 46-77%. In addition, it has been associated with increased overall length of hospital stay.10\n\nThe classic risk factors for developing spontaneous pneumothorax regardless of COVID-19 status include tobacco smoking, age, short stature, male sex, low body mass index, prolong cough, strenuous exercise and some chronic pulmonary disease such as chronic obstructive pulmonary disease.7\n\nThe etiology of pneumothorax in COVID-19 is not fully understood. It has been observed in patients with and without MV and, moreover, without significant pulmonary disease burden. The development of spontaneous pneumothorax and pneumomediastinum in COVID-19 patients who do not require MV is rare, and it has been reported in approximately 1-2 % of patients with COVID-197 vs 5.9-8% in mechanically ventilated patients, and it can also occur during disease progression.12-14 However, if present, it may indicate a worse overall prognosis.\n\n\nCauses of barotrauma in COVID-19 patients\n\nThe causes of pneumothorax in patients with MV may be related to increased peak airway pressure, high positive end expiratory pressures (PEEP), and high tidal volumes. Figure 2 demonstrates a COVID-19 patient on MV showing extensive pneumomediastinum and resolving pneumothorax post chest tube placement.\n\nSpontaneous barotrauma in the absence of MV is a rare but serious complication in COVID-19 patients, however, the etiology of such barotrauma in the absence of ventilatory support is not completely understood. Some authors report that COVID-19 pneumonia may be associated with severe alveolar damage and rupture of the alveolar wall due to pressure gradient between the alveolus and the pulmonary interstitium.13\n\nAnother proposed mechanism for the cause of pneumothorax in patients with COVID-19 could be related to direct alveolar membrane damage by the virus infecting pneumocytes I and II, leading to alveolar rupture.15 Pathological characteristics of postmortem biopsies of patients who died from SARS-CoV-2 reported pronounced desquamation of pneumocytes and hyaline membrane formation, which are consistent with a diagnosis of ARDS, acute fibrinous pneumonia, and organizing pneumonia.16,17\n\nSpontaneous pneumomediastinum has been observed in patients with mild or severe COVID-19 infection even without MV. Figure 3 demonstrates spontaneous pneumomediastinum in a non-mechanically ventilated COVID-19 positive patient, showing peripheral ground glass infiltrates. Chu et al reported cases of patients with confirmed SARS-1 and spontaneous development of pneumomediastinum with and without MV in 2004.18 It is important for clinicians to recognize the development of iatrogenic and spontaneous barotrauma in COVID-19 patients early because it may result in rapid clinical and respiratory deterioration leading to increased oxygen requirements and worsening barotrauma that can be lethal.\n\n\nCases of barotrauma in the literature\n\nSeveral reports of the development of spontaneous pneumothorax in COVID-19 patients have been published in the literature. Aiolfi et al.19 described a case of a 60-year-old male patient with no previous pulmonary disease and COVID-19 infection that developed right side pneumothorax combined with pneumomediastinum and subcutaneous emphysema after approximately 20 days of the initial infection. He was started on oxygen therapy initially, but the patient failed to improve. A repeat CT demonstrated findings of barotrauma, and subsequently patient was placed on high flow nasal cannula (HFNC) along with steroids, broad spectrum antibiotics and antivirals, without MV. The patient recovered successfully approximately 3 weeks later. In another paper, Changyu et al.20 reported a 38-year-old male patient with no past medical history or smoking history admitted for COVID-19 who developed exertional angina with palpitations along with respiratory wheezing on day 11 of admission. CT of the chest revealed multiple ground-glass opacities with bilateral parenchymal consolidations, interlobular septal thickening as well as spontaneous pneumomediastinum and subcutaneous emphysema. The patient was not on MV and continued to receive treatment with supplemental oxygen, antitussives and bronchodilators. By day 25, the patient recovered, symptoms subsided and his breathing returned to normal. Chest CT revealed resolution of previous pneumomediastinum and a reduction of parenchymal consolidation with pulmonary fibrosis and pneumatocele in the inferior left lower lobe. The patient was discharged on day 30 with follow up in the outpatient setting.\n\nSun et al.21 described a young patient with COVID-19 pneumonia that developed mediastinal emphysema, a giant bulla in the left lung and multiple bullae in the sub pleural lung zones. This patient was not ventilated and placed on HFNC. Patient had no significant relevant medical or smoking history documented. Extensive barotrauma was also reported by Wang et al.22 in a young patient in whom a CT scan of the chest showed pneumatosis extending from the mediastinal pericardium to the bilateral cervical soft tissue space. This patient clinically deteriorated despite immediate noninvasive ventilation and intensive care unit supportive care. In our institution, we also had a 37-year-old patient who was admitted for a second admission for respiratory distress related to COVID-19 infection who developed giant bullae over time in both his lung fields during his hospital stay. Figure 4 shows CXR and coronal chest CT scan of this patient demonstrating a large bullae involving the right middle lung zone, which eventually got smaller over the following days but a new bulla appeared in the left lingular region.\n\nCoronal Chest CT image (C) obtained one month after discharge showing scarring and decrease in size of the right mid-lung bullae but formation of a second large bulla in the left mid-lung zone.\n\nIn a most recent retrospective study by McGuinness et al.,23 the authors reviewed clinical and imaging data of patients seen between March 1, 2020, and April 6, 2020, who tested positive for COVID-19 and experienced barotrauma associated with invasive MV and were compared with patients without COVID-19 infection during the same period. A total of 601 patients with COVID-19 infection underwent invasive MV. They reported that 15% of patients had one or more barotrauma events with a total of 145 barotrauma events (95% confidence interval [CI]: 21%, 28%). During the same period, 196 patients without COVID-19 infection with invasive MV had one barotrauma event (0.5%; 95% CI: 0%, 3%; P < .001 vs the group with COVID-19 infection). Of 285 patients with ARDS on invasive MV during the previous four years, 10% of patients had 31 barotrauma events, with an overall barotrauma rate of 11% (95% CI: 8%, 15%; P < .001 vs the group with COVID-19 infection). The authors concluded that patients with COVID-19 infection and invasive MV had a higher rate of barotrauma than patients with ARDS and patients without COVID-19 infection. In addition, barotrauma is an independent risk factor for death in COVID-19 (odds ratio = 2.2; P = .03) and is associated with a longer hospital stay (odds ratio = 0.92; P < .001).\n\nIn contrast, Chung et al.24 in a retrospective study from China, reviewed CT chest scans of 21 symptomatic patients infected with COVID-19. Typical CT findings included bilateral ground glass opacities, consolidative pulmonary opacities with variable morphology, notably pneumothorax or pneumomediastinum lesions were not observed. This emphasizes the point that spontaneous barotrauma is not a common but a rare manifestation of COVID-19. The above study was done with only 21 COVID-19 patients and generally lacks the sample size required for a solid assessment of rare but dangerous barotrauma complication.\n\nPneumothorax is a medical emergency and a disease with a high mortality rate. It requires careful awareness, prompt recognition and immediate intervention to reduce morbidity and mortality. Most patients with pneumothorax related to mechanical ventilation have underlying pulmonary diseases, the most common of which are pneumonia, ARDS and obstructive lung disease. Pneumothorax/pneumomediastinum may have subtle or atypical features on plain radiography and may be missed early on. Most of the ventilated patients with a pneumothorax require immediate treatment with tube thoracostomy because of the high risk of progression to a tension pneumothorax. Small-bore catheters are now preferred in most ventilated patients. Management of non-ventilated barotrauma patient varies case by case but is generally conservative.\n\nIn a study by Housman et al.25 the authors hypothesized that COVID-19 patients requiring mechanical ventilation may develop significant pneumomediastinum and subcutaneous emphysema without associated pneumothorax. The study included 171 patients who tested positive for COVID-10 requiring endotracheal intubation. They identified 29 cases (17%) of mediastinal air without associated pneumothorax that were treated conservatively and 12 cases (41%) that showed improvement or resolution without intervention. In another study from Italy by Protti et al.,26 the authors aimed to describe the incidence and risk factors of barotrauma in patients with COVID-19 on invasive mechanical ventilation. The study was performed via electronic survey and involved patients with COVID-19 who developed barotrauma while on invasive mechanical ventilation from 61 hospitals the COVID-19 Lombardy Intensive Care Unit network. Thirty-eight responses were submitted and out of 2041 patients included, about 7.1% developed barotrauma.\n\nFurthermore, Udi et al.27 in their retrospective registry analysis that included 20 patients with severe COVID-19 pulmonary failure found that 40% of those patients developed severe barotrauma during mechanical ventilation that followed lung protective strategies. Their data suggested that barotrauma in COVID-19 patients may occur despite the use of recommended lung protective mechanical ventilation settings. In addition, data from a retrospective cohort study that included 343 COVID-19 positive patients suggested that these patients have a significant risk of developing barotrauma when receiving invasive mechanical ventilation with subsequent increased mortality rates. The study found that 15.4% of the patients developed barotrauma and 91% of these patients presented with pneumothorax, 3.7% with pneumomediastinum and pneumopericardium.28\n\n\nConclusion\n\nSpontaneous pneumothorax and pneumomediastinum are rare, but serious, complications of COVID-19. The most common cause of iatrogenic barotrauma is related to mechanical ventilation in the setting of underlying lung disease, with variable proposed mechanisms ranging from high peak airway pressure, high PEEP and high tidal volume, although none have been proven. Spontaneous barotrauma in COVID-19 in the absence of ventilatory support is presumed to be due to pressure gradient between the alveolus and the pulmonary interstitium due to virus associated alveolar damage. The second mechanism is due to direct alveolar membrane damage leading to its rupture, which could be secondary to direct infection of COVID-19 of the pneumocytes type I and II. This can result in rapid respiratory deterioration with life-threatening consequences if not recognized in time. Pneumothorax associated with mechanical ventilation has more than two-fold increased mortality and this risk increases further in those with tension pneumothorax. Early diagnosis particularly in ventilated patients and immediate treatment with small tube thoracostomy is crucial for a positive outcome.\n\n\nData availability\n\nNo data is associated with this article.\n\n\nConsent\n\nThe images published in this article were retrieved from patient records of patients treated at our institution. We gained IRB approval from our institution (St. Barnabas Hospital IRB; approval number, 2020.23) to use and publish the images in this article, which included a waiver of informed consent from patients. No patient identifiable data is included in the present article.",
"appendix": "References\n\nPatel A, Jernigan DB, Abdirizak F: nCoV CDC Response Team. Initial public Heal response interim Clin Guid. 2019.\n\nCDC Covid Data Tracker. Reference Source\n\nMacera M, De Angelis G, Sagnelli C, et al.: Clinical presentation of COVID-19: case series and review of the literature. Int J Environ Res Public Health. 2020; 17(14): 5062. PubMed Abstract | Publisher Full Text | Free Full Text\n\nNg M-Y, Lee EYP, Yang J, et al.: Imaging profile of the COVID-19 infection: radiologic findings and literature review. Radiol Cardiothorac Imaging. 2020; 2(1): e200034. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPlesner LL, Dyrberg E, Hansen IV, et al.: Diagnostic imaging findings in COVID-19. Ugeskr Laeger. 2020; 182(15). PubMed Abstract\n\nBrogna B, Bignardi E, Salvatore P, et al.: Unusual presentations of COVID-19 pneumonia on CT scans with spontaneous pneumomediastinum and loculated pneumothorax: a report of two cases and a review of the literature. Hear Lung. 2020. PubMed Abstract | Publisher Full Text | Free Full Text\n\nQuincho-Lopez A, Quincho-Lopez DL, Hurtado-Medina FD: Case Report: Pneumothorax and Pneumomediastinum as Uncommon Complications of COVID-19 Pneumonia—Literature Review. Am J Trop Med Hyg. 2020; 103(3): 1170–1176. PubMed Abstract | Publisher Full Text | Free Full Text\n\nYang X, Yu Y, Xu J, et al.: Clinical course and outcomes of critically ill patients with SARS-CoV-2 pneumonia in Wuhan, China: a single-centered, retrospective, observational study. Lancet Respir Med. 2020. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChen N, Zhou M, Dong X, et al.: Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study. Lancet. 2020; 395(10223): 507–513. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHsu C-W, Sun S-F, Lee DL, et al.: Clinical characteristics, hospital outcome and prognostic factors of patients with ventilator-related pneumothorax. Minerva Anestesiol. 2014; 80(1): 29–38. PubMed Abstract\n\nHsu C-W, Sun S-F: Iatrogenic pneumothorax related to mechanical ventilation. World J Crit care Med. 2014; 3(1): 8–14. PubMed Abstract | Publisher Full Text | Free Full Text\n\nYao W, Wang T, Jiang B, et al.: Emergency tracheal intubation in 202 patients with COVID-19 in Wuhan, China: lessons learnt and international expert recommendations. Br J Anaesth, Accept march. 2020; 31. PubMed Abstract | Publisher Full Text | Free Full Text\n\nYamaya T, Baba T, Hagiwara E, et al.: Pneumothorax in a COVID-19 Pneumonia Patient without Underlying Risk Factors. Intern Med. 2020; 59(22): 2921–2925. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSalehi S, Abedi A, Balakrishnan S, et al.: Coronavirus disease 2019 (COVID-19): a systematic review of imaging findings in 919 patients. Am J Roentgenol. 2020: 1–7. PubMed Abstract | Publisher Full Text\n\nMallick T, Dinesh A, Engdahl R, et al.: COVID-19 Complicated by Spontaneous Pneumothorax. Cureus. 2020; 12(7): e9104–e9104. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCopin M-C, Parmentier E, Duburcq T, et al.: Time to consider histologic pattern of lung injury to treat critically ill patients with COVID-19 infection. Intensive Care Med. 2020: 1–3. PubMed Abstract | Publisher Full Text | Free Full Text\n\nXu Z, Shi L, Wang Y, et al.: Pathological findings of COVID-19 associated with acute respiratory distress syndrome. Lancet Respir Med. 2020; 8(4): 420–422. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChu CM, Leung YY, Hui JYH, et al.: Spontaneous pneumomediastinum in patients with severe acute respiratory syndrome. Eur Respir J. 2004; 23(6): 802–804. PubMed Abstract | Publisher Full Text\n\nAiolfi A, Biraghi T, Montisci A, et al.: MANAGEMENT OF PERSISTENT PNEUMOTHORAX WITH THORACOSCOPY AND BLEBS RESECTION IN COVID-19 PATIENTS. Ann Thorac Surg. 2020. PubMed Abstract | Publisher Full Text | Free Full Text\n\nZhou C, Gao C, Xie Y, et al.: COVID-19 with spontaneous pneumomediastinum. Lancet Infect Dis. 2020; 20(4): 510. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSun R, Liu H, Wang X: Mediastinal Emphysema, Giant Bulla, and Pneumothorax Developed during the Course of COVID-19 Pneumonia. Korean J Radiol. 2020; 21(5): 541–544. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWang J, Su X, Zhang T, et al.: Spontaneous Pneumomediastinum: A Probable Unusual Complication of Coronavirus Disease 2019 (COVID-19) Pneumonia. Korean J Radiol. 2020; 21(5): 627–628. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMcGuinness G, Zhan C, Rosenberg N, et al.: Increased Incidence of Barotrauma in Patients with COVID-19 on Invasive Mechanical Ventilation. Radiology. 2020; 297(2): E252–E262. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChung M, Bernheim A, Mei X, et al.: CT imaging features of 2019 novel coronavirus (2019-nCoV). Radiology. 2020; 295(1): 202–207. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHousman B, et al.: COVID-19 ventilator barotrauma management: less is more. Annals of Translational Medicine 2020; 8(23). PubMed Abstract | Publisher Full Text | Free Full Text\n\nProtti A, et al.: Barotrauma in mechanically-ventilated patients with coronavirus disease 2019: a survey of 38 hospitals in Lombardy, Italy. Minerva Anestesiol. 2020. PubMed Abstract | Publisher Full Text\n\nUdi J, et al.: Incidence of barotrauma in patients with COVID-19 pneumonia during prolonged invasive mechanical ventilation–a case-control study. J Intensive Care Med. 2021; 36(4): 477–483. PubMed Abstract | Publisher Full Text\n\nElsaaran H, et al.: Prevalence and risk factors of barotrauma in Covid-19 patients admitted to an intensive care unit in Kuwait; a retrospective cohort study. Ann Med Surg. 2021; 63: 102141. PubMed Abstract | Publisher Full Text | Free Full Text"
}
|
[
{
"id": "94554",
"date": "05 Oct 2021",
"name": "Philippe Jouvet",
"expertise": [
"Reviewer Expertise Critical care medicine"
],
"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\nR Rehmani et al. report a literature review on COVID-19 associated spontaneous barotrauma and illustrate the manuscript with several examples including one from their experience. The topic is interesting but the methodology used and the use of spontaneous barotrauma are not adequate in this manuscript.\nMajor comments:\nA literature review can be a scoping review or a systematic review and the search methodology needs to be detailed in the methodology part of the manuscript to help the reader to understand how the literature review was done. For example, a similar review has been done in 2021 and 36 studies were included1. This manuscript does not specify the methodology, has a literature review that included fewer manuscripts than a systematic review published on the same topic, and is restricted to spontaneous barotrauma.\n\nReviewer does not understand the term 'spontaneous' in this manuscript. Usually, the term 'spontaneous' is used when the condition occurs without an obvious etiology, such as trauma or iatrogenic causes2. Mechanical ventilation is a well-known etiology of trauma and the authors included this etiology in the spontaneous. From the reviewer's point of view, any pneumothorax or pneumomediastinum associated with mechanical ventilation should be excluded from a review on spontaneous barotrauma.\n\nIs the topic of the review discussed comprehensively in the context of the current literature? The discussion is not understandable because this manuscript includes spontaneous and non-spontaneous barotrauma under the term spontaneous.\n\nAre the conclusions drawn appropriate in the context of the current research literature? Reviewer does not agree with the conclusions that include, (1) pneumothorax associated with mechanical ventilation in a manuscript on spontaneous barotrauma, and (2) specifies mechanisms that are not demonstrated but are only hypothesised.\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? No",
"responses": []
},
{
"id": "95963",
"date": "08 Nov 2021",
"name": "Kapil Dev Soni",
"expertise": [
"Reviewer Expertise Critical Care"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nRehmani and co-authors reviewed the topic of COVID-19 associated spontaneous barotrauma. They provide a summary of the literature on a relevant problem that is increasingly seen in COVID-19 patients. They discuss the common pattern of radiological manifestations seen in these patients. They also mention the common putative mechanisms underlying barotrauma in both mechanically ventilated and spontaneous breathing. The impact on patient outcomes such as increased mortality and morbidity with associated barotrauma has been reported.\nHowever, the review can be further enhanced if the authors discuss the implications of peripherally located lesions and the Macklin Effect seen in COVID-19. They can further discuss the association of the above factors and the development of pneumothorax and pneumomediastinum.\nIn the Introduction section, the authors provide a succinct introduction about the COVID-19 pandemic, the common presentations, and the varied clinical severity of the patients. They also provide the search strategy used in the selection of articles with keywords, such as “spontaneous pneumothorax and pneumomediastinum” with cross-referencing the bibliographies. However, the keyword “Barotrauma” has not been considered in the search terms. Though the likelihood of the additional article using “Barotrauma” is low, nevertheless authors may attempt a search strategy with some modification.\nThe authors present the common findings seen on imaging – chest X-ray and CT scan. They mention that CT alone is not recommended for screening or diagnosis of COVID-19, which is an important point as most scientific societies do not recommend using CT scans for the purpose of screening COVID-19. RT-PCR remains the gold standard for diagnosing the infection. It will be useful if the authors provide some details about the timing of HRCT during the course of illness and the prognostic utility of findings seen on the CT chest. Also, the subtle findings which may predict the development of pneumothorax or barotrauma on HRCT in these patients will help readers to identify high-risk patients.\nIn the following section, the authors provide a description of pneumothorax and pneumomediastinum with extensive subcutaneous emphysema in a patient of COVID-19 on mechanical ventilation. They further discuss the known risk factors of the development of pneumothorax on mechanical ventilation and spontaneous breathing. However, the author's statement: “Tension Pneumothorax accounts for approximately 30-97% of all pneumothoraxes in patients with MV” needs to be referenced.\nThe authors discuss the cases of barotrauma and multiple reports published in the literature. The cases provide some perspective about the development of pneumothorax and pneumomediastinum and the evolution of lesions in both mechanically and non-mechanically ventilated patient subgroups. An interesting observation was the development of giant bulla in some cases. The authors further cite the studies by McGuinness et al., Chung et al., Housman et al., Protti et al., Udi et al. and provide common patterns of findings of pneumothoraxes, pneumomediastinum, and subcutaneous emphysema. The absence of pneumothorax with substantial pneumomediastinum has also been mentioned. It will be useful for the readers if the authors provide details of the mechanism underlying such unique patterns in the article.\nThe authors conclude by stating the common cause of iatrogenic barotrauma related to mechanical ventilation with proposed mechanisms in both mechanically and non-mechanically ventilated patients.\nThe article attempts to provide a literature review of a common complication – barotrauma seen frequently in COVID-19 patients. It is well written with some putative mechanisms underlying the barotrauma. However, it is a narrative review and not a systematic review. The authors do not mention the number of articles retrieved with the search strategy. It’s unclear why only one database was searched and not others. Though the objective was to study the mechanisms underlying the barotrauma, no particular mechanism is yet proven and most remain speculative.\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": []
},
{
"id": "97971",
"date": "06 Dec 2021",
"name": "Giacomo Monti",
"expertise": [
"Reviewer Expertise Sepsis and septic shock",
"non-Invasive ventilation"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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, Dr. Arias-Morales and colleagues present a narrative review of COVID-19 spontaneous barotrauma. As we are now facing the fourth wave of the COVID-19 pandemic in several countries, this remains an \"up-to-date\" topic relevant to current practice.\nOverall, while the review provides a general cover of most of the relevant aspects related to barotrauma, all topics could be discussed in greater detail. Furthermore, a brief paragraph describing the management of COVID-19-related barotrauma could be useful.\nFew lines comparing the rate of barotrauma in COVID-19 vs non-COVID-19 respiratory failure and ARDS might be useful, as there is a general belief of a higher rate of barotrauma in COVID-19 ARDS. In this view, the authors may wish to discuss a recent systematic review on barotrauma in COVID-19 patients (see Belletti et al., 20211).\n\nAs a related point, the prognostic impact and risk factors for barotrauma in COVID-19 patients may be worth a discussion in a separate paragraph. Several authors now report higher mortality rates (>60%) for COVID-19 patients who developed barotrauma.\n\nThe authors may also wish to discuss tracheal damage and tracheomalacia associated with COVID-19, which is being increasingly reported and associated with the development of pneumomediastinum (see Guarnieri et al., 20212; Fiacchini et al., 20213; Rosati et al., 20214).\n\nSome authors recently described the CT finding of the Macklin-like effect as a potential predictor of barotrauma in COVID-19 patients (see Palumbo et al., 20215. I believe that these findings could be discussed in the paragraph on possible causes of barotrauma.\n\nIt might be useful to add one or more tables summarizing findings of major published studies on barotrauma rate and outcome in spontaneous breathing vs non-invasively ventilated vs invasively ventilated COVID-19 patients.\n\nIt might also be useful to add a table summarizing identified risk and predisposing factors for barotrauma development in COVID-19 ARDS patients.\n\nA separate paragraph on Methods, describing how the search strategy was performed (last update, keywords, number of reviewers screening articles, etc.) might also be useful.\n\nIs the topic of the review discussed comprehensively in the context of the current literature? Partly\n\nAre all factual statements correct and adequately supported by citations? Partly\n\nIs the review written in accessible language? Yes\n\nAre the conclusions drawn appropriate in the context of the current research literature? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-412
|
https://f1000research.com/articles/10-351/v2
|
21 May 21
|
{
"type": "Study Protocol",
"title": "Stage 1 Registered Report: Testing mediumship accuracy with a triple-blind protocol",
"authors": [
"Patrizio E. Tressoldi",
"Fernando Sinesio",
"Laura Liberale",
"Ines Testoni",
"Fernando Sinesio",
"Laura Liberale",
"Ines Testoni"
],
"abstract": "Even if mediumship is a practice that probably originated at the outset of human history and is embedded in many cultural and religious traditions, scientific investigations into mediumship are quite recent. In this study, we aim to investigate if self-defined mediums can retrieve information about specific deceased persons in an unconventional way, that is, without retrieving the information from the parents or friends of the deceased person or by other conventional means. To our knowledge, this is the first registered report related to this phenomenon. Our experimental design will be triple-blinded: the mediums and their interviewer will only know the first name of the deceased person and of the requesting person. The parents or the close friends of the deceased person will not interact in any way with the medium. Furthermore, they will be blind about which of two lists of information (readings) paired with deceased persons of the same gender is related to their parents or friend. Accuracy of information will be analysed by three criteria: (1) percentage of correct identification of the readings related to the requested person; (2) comparison of the global scores (on a scale 1 to 6) assigned to the intended readings with that of control readings; and (3) comparison of the difference between the percentage of correct minus incorrect information identified in the intended readings with that of the control readings.",
"keywords": [
"registered report",
"mediumship",
"triple-blind protocol",
"anomalous cognition"
],
"content": "Introduction\n\nThe scientific study of mediumship, notwithstanding its very old origin and its widespread diffusion in the Eastern and Western society, is relatively recent (Beischel, 2018). From a scientific point of view, the main questions are related to the level of accuracy of information given by mediums and its origin.\n\nConsultation with a medium typically involves the presence of a person, defined as a ‘sitter’, usually a close relative or friend of the deceased person, who wants to know if the deceased person is still living after his/her death. In this setting, it is quite likely that the source of the information is the sitter him/herself, who could consciously or unconsciously suggest it to the medium through what is called ‘cold reading’ (Roe & Roxburgh, 2013), that is, the transmission of verbal and non-verbal information to the medium.\n\nIn order to eliminate this source of information, research protocols must ensure a complete separation and visually and auditory isolation between the sitter and the medium.\n\nGiven that the only person who can judge the accuracy of information is the sitter, in order to prevent confirmatory bias, i.e. judging if particular information is correct even if it is wrong because of their strong need of proof that their loved one is still alive (Snyder & Swann, 1978; Rabin & Schrag, 1999), research protocols must require the sitter to be given at least two anonymous lists of information (readings) related to two deceased persons for evaluation: one related to their requested parent or friend and the second one related to another person paired with the same gender.\n\nA meta-analysis of all available studies completed between 2001 and 2019 that used research protocols with different levels of blindness, revealed an accuracy of 6-14% more than expected by chance with better performance of mediums who were preliminary screened about their abilities (Sarraf, Woodley of Menie and Tressoldi, 2020).\n\nIn this study, we aim to add a further contribution to this line of investigation by adopting the best research practices in order to prevent contamination of the results by so-called questionable research practices (John, Loewenstein & Prelec, 2012; Banks et al., 2016).\n\nThe main hypotheses are:\n\n- The percentage of correctly identified intended readings, that is those related to the requested person, will exceed the control ones at a statistical level (see section Statistical analyses);\n\n- The overall scores assigned to the intended readings will be higher with respect to the control ones at a statistical level;\n\n- The difference between the percentage of correct information minus the percentage of wrong information of the intended readings will be higher with respect to the control ones at a statistical level.\n\n\nMethods\n\nThis study has been approved by the Comitato etico della ricerca psicologica (Ethical Committee of Psychological Research) of Padova University (Protocol no. 3670). Both mediums and sitters will be requested to read and confirm orally the protocol as informed consent.\n\nEight professional self-defined mediums will be included in the study. All have been purposively selected by the authors after testing their accuracy skills in a previous study (Tressoldi et al. 2020).\n\nEight sitters will be contacted by email mailing lists by the authors, from people with a serious interest in having a reading with respect to a deceased relative or friend, regardless of cause of death or length of time since the death. The only exclusion criteria will be a not well-defined relationship with the requested deceased person that could preclude a complete knowledge of him/her and consequently a difficulty in the evaluation of information given by the mediums.\n\nEach medium will be asked to contribute a reading for each of the eight deceased persons for a total of 64 readings.\n\nEach trial, that is each consultation with the medium and each task assigned to the sitters, will comprise two readings related to deceased individuals of the same gender, male or female, as the only common characteristic.\n\nThe experimental procedure will be similar to that adopted by Tressoldi, Liberale, Sinesio et al. (2020) which was a reduced version of that presented by Beischel (2007), with some variants aimed at further excluding a mental connection with the sitter.\n\nFurthermore, in order to keep the task difficulty as similar as possible for all mediums, they were requested to obtain response to a set of ten identical questions (see Extended data) plus two or three further questions requested by the sitters to increase their confidence of the authenticity of the contact with the requested deceased.\n\nThe steps of the procedure of each session are the follow:\n\n1. To a pair of sitters interested in having a free consultation for a deceased loved parent or friend of the same gender, they will be asked to provide the deceased first name, and the time since the deceased passed.\n\n2. This information will be kept by one of the co-authors, who will be called ‘research assistant B’ (raB).\n\n3. The medium will be contacted for the consultation by another co-author, who will be called ‘research assistant A’ (raA).\n\n4. On the day of consultation, raA will contact the medium either via Skype or WhatsApp and for each of the two paired deceased persons will give the medium only the deceased and the sitter’s first name (without the family name) sent by raB.\n\n5. For each of the two paired deceased persons, the medium will be required to respond either in oral or written form to the ten fixed questions (Extended data) and to provide all information pertinent to the deceased’s identification as asked by the sitter, as well as anything the purported deceased wishes to communicate to the sitter. For oral form, the information will be recorded by raA using an audio recorder.\n\n6. At the conclusion of the reading, raA will transfer all information into a vertical list, excluding generic statements, e.g. “I love you” or “Don’t worry about me, I’m well”, and will send them to raB.\n\n7. Once raB receive the two readings from raA, the information will be listed vertically for evaluation of each piece of information and for overall evaluation (see the example in Extended data).\n\n8. Afterwards, both reading A and B will be anonymously sent to the requesting sitter, providing assistance, if needed, for the evaluation procedure, i.e. sitters will be asked to go through the two lists of information and mark as ‘perfectly correct’, ‘clearly wrong’, somewhat correct’ or ‘I do not have information for evaluation’.\n\nIn summary, the research protocol will comprise three levels of blindness for the deceased’s identity: the medium, raA; and for the sitters which of the two readings is that intended for their deceased.\n\nAll information will be classified in two categories: those comprising very detailed information, e.g. “he (the deceased person) got a car accident when very young”; “she said to you (to the sitter) do not sell her gold ring left in her bedroom”, and those comprising less detailed information e.g. “he was a very nice person”; “she was very in love with her husband”.\n\n- Each item of information from the reading list related to the “detailed” category evaluated by the sitters as “Perfectly correct” or “Clearly wrong” will be given a value of 1 or −1, respectively.\n\n- Each item of information from the reading list related to the “less detailed” category evaluated by the sitters as “Perfectly correct” or “Clearly wrong” will be given a value of .5 or −.5, respectively.\n\n- Finally, each item evaluated by the sitters as “somewhat correct” will be given a value of 0.5 regardless of being in the detailed or less detailed category.\n\nSubsequently, excluding information marked as “I don’t have information for evaluation”, the percentages of correct and incorrect information (ratio of this information with their total number) and their difference will be calculated. These differences could range from −100% if all wrong, to 100% if all correct.\n\nThe reliability of this scoring will be tested by an independent judge who will analyze all the readings following the same criteria.\n\nAs well as evaluating each item of information from the two readings, the sitter will also be asked to give an overall evaluation of each reading using a scale from 0 (totally wrong) to 6 (excellent: effectively free of errors and containing compelling evidence of authentic communication), identical to the scale used by Beischel (2007). If both readings are given identical scores, the sitter will be asked to choose the one considered to be closest to their own deceased person.\n\nStatistical Power: from the results observed by Tressoldi, Liberale, Sinesio et al. (2020), 64 readings are sufficient to detect a global score difference of 1.5 on a scale of 0-6, a 15% above chance of readings identification and 25% of correct information difference with respect to the incorrect one, that we consider to be the smallest effect size of interest, setting the statistical power to .80 and a directional hypothesis with alpha = .05.\n\nData collection will end when 64 readings are evaluated by the sitters without any missing values.\n\nIn order to test the robustness of results, we will adopt both a frequentist and a Bayesian statistical approach with the statistical package JASP v.0.14.1 (JASP Team, 2020).\n\nThe percentage of correct readings identification will be analyzed using a frequentist binomial test with chance probability equal to ½ and a Bayesian binomial test with beta prior parameter a = 1 and parameter b = 1.\n\nThe mean of the overall score assigned to correctly identified readings will be compared with that of the control readings by using a one-sided permutation t-test estimated with 5000 bootstrap samples and the confidence intervals will be bias-corrected following the procedure of Ho et al. (2019) and with a Bayesian independent sample t-test with a Cauchy prior of .707.\n\nThe same statistics will be used for:\n\n- the comparison of the difference between the percentage of correct minus incorrect information in the correctly identified readings with that of the control readings.\n\nThe syntax of the statistical analyses will be available at Figshare.\n\n\nDissemination of information\n\nRaw data and statistical analyses scripts will be made available open access in the extended data repository\n\n\nStudy status\n\nAt present we have completed the recruiting of the mediums and sitters.\n\n\nConclusion\n\nWith this study, we aim to contribute to the investigation of mediumship accuracy and the source of their information with a triple-blind protocol free of questionable research practice.\n\nEven if our results cannot be generalized beyond the participants (mediums and sitters/deceased) enrolled in the study given their large individual differences, they can be an example of how it is possible to study a controversial phenomenon, such as mediumship, with the best methodological scientific tools.\n\n\nData availability\n\nNo data is associated with this article.\n\nFigshare: Mediumship, https://doi.org/10.6084/m9.figshare.13311710.v4 (Tressoldi et al, 2020).\n\nThis project contains the following extended data:\n\n- List of common questions\n\n- Excerpt of the reading format\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 the Proof Readings Service for English revisions.\n\n\nReferences\n\nBanks GC, Rogelberg SG, Woznyj HM, et al.: Evidence on questionable research practices: The good, the bad, and the ugly. Journal of Business and Psychology. 2016; 31(3): 323–338.\n\nBeischel J: Contemporary Methods used in laboratory-based mediumship research. J Parapsychol. 2007; 71: 37–68.\n\nBeischel J: Mental Mediumship Research|Psi Encyclopedia.2018. Retrieved November 19, 2020. Reference Source\n\nHo J, Tumkaya T, Aryal S, et al.: Moving beyond P values: Everyday data analysis with estimation plots. Nat Methods. 2019: 1548–7105. PubMed Abstract | Publisher Full Text\n\nJASP Team: JASP (Version 0.14.1). [Computer software].2020. Reference Source\n\nJohn LK, Loewenstein G, Prelec D: Measuring the prevalence of questionable research practices with incentives for truth telling. Psychol Sci. 2012; 23(5): 524–532. PubMed Abstract | Publisher Full Text\n\nRabin M, Schrag J: First impressions matter: a model of confirmatory bias. Quaterly J Econ. 1999; 114(1): 37–82.\n\nRoe CA, Roxburgh E: An overview of cold reading strategies. In: Moreman C (Ed.) The Spiritualist Movement: Speaking with the Dead in America and around the World: Volume 2, Belief, Practice, and Evidence for Life after Death. 2013. (pp. 177–203). Santa Barbara.\n\nSarraf M, Woodley of Menie MA, Tressoldi P: Anomalous information reception by mediums: A meta-analysis of the scientific evidence. Explore. 2020. Publisher Full Text\n\nSnyder M, Swann WB: Behavioral confirmation in social interaction: from social perception to social reality. J Experi. Soc. Psychol. 2020; 14: 148–162.\n\nTressoldi P, Liberale L, Sinesio F, et al.: Mediumship accuracy: a quantitative and qualitative study with a triple-blind protocol. PsyArxiv. 2020. Publisher Full Text\n\nTressoldi P, Pederzoli L, Testoni I: Mediumship. figshare. Dataset. 2020. Publisher Full Text"
}
|
[
{
"id": "86295",
"date": "23 Jun 2021",
"name": "Alexander Moreira-Almeida",
"expertise": [
"Reviewer Expertise Investigation of spiritual experiences",
"specially mediumship"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis paper presents a good research protocol to investigate anomalous information reception by mediums. This protocol is based on recent studies on the topic and will help to enlarge and diversify the studies on this topic.\nBelow, some specific comments:\nIntroduction\n“scientific investigations into mediumship are quite recent”, actually, they are not recent, they started in the mid-19th century\n\nThe MS would benefit if the authors are less absolute in their statements regarding certain methodological strategies. It would be good to avoid terms such as “must” or “the only” to refer to good methodological choices made by the authors, but they are not the only ones possible and useful. For example: The “complete separation and visually and auditory isolation between the sitter and the medium” is one strategy to deal with information leakage. However, it would not proper to state that “research protocols must ensure” that complete separation. There are other ways to deal with this issue. In the same sense, it is not proper to state that “the only person who can judge the accuracy of information is the sitter”, researchers can also judge the accuracy based on documents and or interviews. Another example: “research protocols must require the sitter to be given at least two anonymous lists of information”\n\nThe study`s objective could be more clearly stated.\n\nMethods\nHow would it be assessed that the selected sitters have “a serious interest in having a reading with respect to a deceased relative or friend”?\n\nBased on the literature, perhaps restricting the length of time since the death may increase the possibility of positive results.\n\nIn addition to the “set of ten identical questions” it would be useful to have an open question regarding further features and information the medium mar have obtained about the deceased. This would be useful, since it has been often reported by mediums and researchers that we can not predict what sort of information the medium will be able to produce in a giving sitting.\n\nIt could be checked with the medium if they feel capable of contacting with the target deceased with no other information rather than the first name.\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\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": "6836",
"date": "24 Jun 2021",
"name": "Patrizio Tressoldi",
"role": "Author Response",
"response": "Thank you for your helpful comments. We had better answer after receiving a second review at least, before submitting a new version of the paper."
}
]
},
{
"id": "129346",
"date": "26 Jun 2024",
"name": "Marco Aurélio Vinhosa Bastos Jr.",
"expertise": [
"Reviewer Expertise Endocrinology",
"Psychoneuroendocrinology",
"Complementary Medicine."
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is the report of a study protocol designed to test mediumship accuracy with a triple blind technique. It appears to be a relevant research topic, as it can broaden the empirical basis for the understanding of the mind-brain relationship.\nIt aims to further investigate mediums who have already demonstrated the ability to ‘receive’ accurate mediumistic information, according to previously published work by the same research group (Tressoldi et al., 20211).\nThe following excerpt from Rocha and coworkers (2021) (https://www.bigelowinstitute.org/wp-content/uploads/2022/10/rocha-weiler-casseb-mediumship-evidence.pdf) illustrates why it may be relevant to undertake such experiments: “From this perspective, additional corroborating observations strengthen any explanation or established theory. Nonetheless, no observation can be taken as final proof of anything, a generally misunderstood idea among academics who mistakenly claim to have found proof of something through any given observation or set of observations. In our world, nothing is ever proven beyond a shadow of a doubt, and everything comes with a level of uncertainty. Instead, scientists collect evidence to favor one conceptual framework over another via experiments or simulations. The key to increasing confidence that a hypothesis or theory is correct relies on the accumulation of evidence, especially from multiple independent sources. The currently accepted theory of a phenomenon is simply the best explanation or description for it among all available alternatives.”\n\nI believe that Professor Alexander Moreira-Almeida's comments regarding the words chosen by the authors are relevant. On the other hand, the choice of such words may reflect a laudable concern by the authors with methodological rigor, which in fact is an indispensable requirement for research experiments on this highly controversial topic to be minimally taken into account by the scholarly community.\nThe following excerpt from Rocha and coworkers (2021) may illustrate this point: “If a medium can reliably and genuinely access the mind or personality of a deceased person, strong evidence accrues in favor of the mind’s survival after bodily death. To be taken seriously, however, researchers have emphasized that studies about mediumship need to be meticulous in controlling potential sensory leakage and accurately assessing the generality of the mediums’ statements and be blindly judged (Beischel, 20072). Only when all these requirements are met can researchers verify the information the mediums provide.”\nThe proposed method appears adequate and robust, and this is in line with contemporary guidelines for the study of mediumship accuracy. The same can be asserted about the statistical technique which was proposed for data analysis.\nThe work has the virtue of objectively and clearly exhibiting the main steps to be followed in a protocol for testing the accuracy of mediumship, which can be consulted by other research groups that wish to reproduce such experiments in other locations.\nMinor points:\nThe introductory section should mention the results of the recent meta-analysis of the studies on accuracy of anomalous information reception by mediums (Sarraf et al., 20213).\n\nIn the second paragraph of the Introduction section, the sentence ‘who wants to know if the deceased person is still living after his/her death’ should be changed to ‘who wants to know if the mind of the deceased person survives his/her bodily death’.\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\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": []
}
] | 2
|
https://f1000research.com/articles/10-351
|
https://f1000research.com/articles/9-775/v1
|
27 Jul 20
|
{
"type": "Research Article",
"title": "First draft genome assembly of the desert locust, Schistocerca gregaria",
"authors": [
"Heleen Verlinden",
"Lieven Sterck",
"Jia Li",
"Zhen Li",
"Anna Yssel",
"Yannick Gansemans",
"Rik Verdonck",
"Michiel Holtof",
"Hojun Song",
"Spencer T. Behmer",
"Gregory A. Sword",
"Tom Matheson",
"Swidbert R. Ott",
"Dieter Deforce",
"Filip Van Nieuwerburgh",
"Yves Van de Peer",
"Jozef Vanden Broeck",
"Heleen Verlinden",
"Lieven Sterck",
"Jia Li",
"Zhen Li",
"Anna Yssel",
"Yannick Gansemans",
"Rik Verdonck",
"Michiel Holtof",
"Hojun Song",
"Spencer T. Behmer",
"Gregory A. Sword",
"Tom Matheson",
"Swidbert R. Ott",
"Dieter Deforce",
"Filip Van Nieuwerburgh"
],
"abstract": "Background: At the time of publication, the most devastating desert locust crisis in decades is affecting East Africa, the Arabian Peninsula and South-West Asia. The situation is extremely alarming in East Africa, where Kenya, Ethiopia and Somalia face an unprecedented threat to food security and livelihoods. Most of the time, however, locusts do not occur in swarms, but live as relatively harmless solitary insects. The phenotypically distinct solitarious and gregarious locust phases differ markedly in many aspects of behaviour, physiology and morphology, making them an excellent model to study how environmental factors shape behaviour and development. A better understanding of the extreme phenotypic plasticity in desert locusts will offer new, more environmentally sustainable ways of fighting devastating swarms. Methods: High molecular weight DNA derived from two adult males was used for Mate Pair and Paired End Illumina sequencing and PacBio sequencing. A reliable reference genome of Schistocerca gregaria was assembled using the ABySS pipeline, scaffolding was improved using LINKS. Results: In total, 1,316 Gb Illumina reads and 112 Gb PacBio reads were produced and assembled. The resulting draft genome consists of 8,817,834,205 bp organised in 955,015 scaffolds with an N50 of 157,705 bp, making the desert locust genome the largest insect genome sequenced and assembled to date. In total, 18,815 protein-encoding genes are predicted in the desert locust genome, of which 13,646 (72.53%) obtained at least one functional assignment based on similarity to known proteins. Conclusions: The desert locust genome data will contribute greatly to studies of phenotypic plasticity, physiology, neurobiology, molecular ecology, evolutionary genetics and comparative genomics, and will promote the desert locust’s use as a model system. The data will also facilitate the development of novel, more sustainable strategies for preventing or combating swarms of these infamous insects.",
"keywords": [
"Eco-devo",
"large genome size",
"locust plague",
"Orthoptera",
"pest insect",
"phenotypic plasticity",
"polyphenism",
"swarm"
],
"content": "Introduction\n\nLocust plagues have been recorded since Pharaonic times in ancient Egypt. In the Bible (Exodus 10), locust swarms are described as one of the major destructive plagues and still today they form a serious threat to crops and food security of over 60 countries across more than 20% of the world’s total land surface (Figure 1a). Swarms can cover areas up to several hundred square kilometres and migrate up to 200 km per day. Per square kilometre, a swarm that contains about 40 million locusts can eat the same amount of food in one day as about 35,000 people. The damage done by a locust plague is on the same level as a major drought (FAO Locust Watch; De Vreyer et al., 2012). The long-term socio-economic impact of these swarms is significant. The loss of harvest is disastrous for local farmers and leads to towering local food prices, also affecting non-farming families. The poorest households are often hit the hardest. Malnourishment of children and expecting mothers endangers their long-term health and growth. School enrolment rate fell by a quarter during plagues in 1987–89 in Mali, with girls being particularly affected (Courcoux, 2012). Human activities in turn affect the propensity of locusts to swarm through factors such as land use (e.g. agriculture, wood extraction, urbanization), political relations between affected countries and the effects of climate change (FAO Locust Watch, http://www.fao.org/ag/locusts/en/info/info/index.html; Cullen et al., 2017; Meynard et al., 2020).\n\n(a) Geographic distribution of the desert locust. During ‘recession’ periods, desert locusts are restricted to the semi-arid and arid regions of Africa, the Arabian Peninsula and South-West Asia that receive less than 200 mm of annual rain. The recession area covers about 16 million km2 in 30 countries. Within this recession area, locusts move seasonally between winter/spring and summer breeding areas. During outbreaks, desert locusts may spill into more fertile adjacent regions, threatening an area of some 29 million km2 comprising 60 countries as outbreaks escalate into upsurges and further into plagues. The recession breeding areas and migration patterns may have predictive value to understand how the swarms will migrate. Figure based on information from FAO Locust Watch, map derived from Google Map Data ©2020 Google. (b) Phase polyphenism in desert locusts, using the example of sexually mature males. The gregarious male (right) has bright warning colours to avoid predation, while the solitarious male relies on camouflage colours. In this staged scene, the solitarious male was forced into close proximity of the gregarious male and is seen retreating from its conspecific. Photo by H. Verlinden and R. Verdonck.\n\nDesert locusts (Schistocerca gregaria Forskål) are grasshoppers (Orthoptera: Acrididae) that exhibit ‘phase polyphenism’, an extreme form of phenotypic plasticity that evolved as an adaptation to the drastic changes that can occur in their environment. Locusts can develop into two extremely divergent, population density-dependent phenotypes, which are tailored to very different ecological requirements. Under low population densities, locusts appear in the solitarious phase and live a solitary life in which they avoid each other. In periods with abundant rainfall, rapid vegetation growth creates a favourable habitat that permits large increases in local population sizes. However, when food becomes scarce again, solitarious locusts are forced to aggregate on the remaining plants. This crowding causes the transformation into the swarming gregarious phase, beginning with rapid changes in behaviour that include a switch to increased locomotion and mutual attraction. The prolonged crowding drives slower but equally profound changes in colouration, morphology (Figure 1b) and physiology. Compounded across multiple generations, locust populations can aggregate further into huge, ruinous swarms capable of crossing continents and oceans in search of food. Populations may crash in the absence of sufficient resources or following human intervention, leading once more to scattered low density solitarious phase populations. The transition between locust phases is thus reversible and occurs gradually through the expression of intermediate phenotypic states (Cullen et al., 2017; Pener & Simpson, 2009; Symmons & Cressman, 2001; Verlinden et al., 2009).\n\nOrthoptera (grasshoppers, crickets and allies) belong to the Polyneoptera, a clade that represents one of the major lineages of winged insects (Pterygota) and comprises around 40,000 known species and ten orders of hemimetabolous insects (Misof et al., 2014; Wipfler et al., 2019). Other major neopteran (Pterygota that can flex their wings over their abdomen) lineages are Acercaria (mostly sucking insects such as lice or true bugs) and Holometabola (insects with complete metamorphosis). At present, only 25 sequenced polyneopteran genomes are reported on NCBI and i5k (http://i5k.github.io/arthropod_genomes_at_ncbi), unequally distributed over five different orders (Extended data, Supplementary Table S1 (Verlinden et al., 2020)). When including S. gregaria, the genomes of five orthopteran species, representing five different subfamilies, are now available. In addition to representing a paradigmatic example of phenotypic plasticity, the desert locust is an important research model for generating advances in a wide variety of fundamental and applied scientific areas, including biomechanics, ecology, pest control, neurobiology and physiology. For instance, the relatively large body size of locusts has been instrumental in discovery of a multitude of insect neuropeptides (Schoofs et al., 1997). Moreover, the globally increasing interest in the use of insects as food or feed also applies to the desert locust, which is a highly nutrient-rich, edible insect that is gaining much attention as a potential, climate-friendly food source (van Huis et al., 2013).\n\nThe devastating socio-economic impact of locust swarms, together with the opportunity this species offers to investigate the phenotypic interface of molecular processes and environmental cues highlight the importance of sequencing the desert locust genome. However, the extremely large estimated genome size of 8.55 Gb (Camacho et al., 2015; Fox, 1970; John & Hewitt, 1966; Wilmore & Brown, 1975) predicted a formidable challenge. Moreover, previous transcriptomics and chromosome size data from the desert locust (Badisco et al., 2011; Camacho et al., 2015), as well as comparisons with the genome of the distantly related migratory locust, Locusta migratoria (6.5 Gb; Wang et al., 2014), suggested that the non-coding part of the desert locust genome might be greatly expanded as compared to other insect genomes, presenting additional challenges to sequencing and assembly. Our team has overcome these hurdles and presents here the ~8.8 Gb genome of the desert locust assembled from short Illumina Mate Pair (MP) and Paired End (PE) reads and long PacBio reads. This new genomic resource, the largest insect genome yet sequenced and assembled, will complement decades of research on this species, enhancing the desert locust’s role as an important comparative model system. The genome will permit exciting new opportunities to examine mechanisms of phenotypic plasticity, social behaviour, physiological and morphological specialization. Moreover, it will open up new avenues to find better ways of fighting the notorious swarms they can cause. The desert locust genome will also enable better understanding of genome size evolution and the early phylogeny of winged insects.\n\n\nMethods\n\nA hybrid sequencing approach was adopted consisting of both Illumina short read sequencing to get sufficient coverage for accurate contig assembly, and complementary PacBio long read sequencing to allow efficient scaffolding of the contig assembly. The Illumina and first PacBio sequencing were performed on high-molecular-weight DNA derived from the central nervous system (central brain, optic lobes, ventral nerve cord), fat body and testes of one adult male inbred for seven generations. A second round of PacBio sequencing used DNA from another male from the same lineage, with two additional generations of inbreeding (for details on the animal material and genomic DNA extraction, see Extended data, Supplementary Methods (Verlinden et al., 2020)).\n\nThe concentration of the S. gregaria high molecular weight DNA sample was measured with PicoGreen (Invitrogen) fluorimetry, after which DNA integrity was confirmed by gel electrophoresis (1% E-Gel; Invitrogen). The sample was divided for Illumina MP and PE sequencing library preparation.\n\nThe MP sequencing library was prepared from 1 µg of the sample with a “Nextera Mate Pair Library prep kit” (Illumina). The PE library was prepared with a “NEBNext Ultra II library prep kit” (NEB) from 2 µg of the sample, sheared to 500 bp fragments using an S2 focused-ultrasonicator (Covaris). Size selection (600–700 bp) was performed for both libraries in a 2% E-Gel (Invitrogen). The quality of the libraries was confirmed with a Bioanalyzer High Sensitivity DNA Kit (Agilent). The MP and PE libraries were quantified by qPCR, according to Illumina's “Sequencing Library qPCR Quantification protocol guide” (version February 2011) and pooled at a molar ratio of 25% MP – 75% PE for sequencing on Hiseq3000 (2 × 150 cycles, 16 lanes; Illumina).\n\nThe library preparation for PacBio sequencing was performed with a \"SMRTbell Template Prep Kit 1.0\" according to the PacBio protocol (version 100-286-000). For each of the two libraries, 10 µg of the S. gregaria high-molecular-weight DNA was used as input in two parallel 50-µl reactions.\n\nFor library size selection, a \"0.75% Dye-Free Agarose Gel Cassette” (ref: BLF7510) was used on a Blue Pippin (Sage Science) with the \"0.75% DF Marker S1 high-pass 15–20kb\" protocol for a lower cut-off of 12 kb. Fragment size distribution was determined with a “DNA 12000 kit” (ref: 5067-1508) for the first library and a “Fragment Analyzer (Agilent) - High Sensitivity Large Fragment 50 kb kit” (ref: DNF-464-0500) for the second library. The resulting libraries had an average length of 16.5 and 22 kb, respectively.\n\nNo extension time was used for the sequencing as recommended for size selected libraries in the “Quick Reference Card 101-461-600 version 07”. The first run was performed on a PacBio RSII System (V4.0 chemistry, polymerase P6). Fifteen additional runs were performed on a PacBio Sequel system with 2.0 Chemistry, polymerase and SMRTCells. The same conditions were used to sequence 20 more SMRTCells with the second library on the PacBio Sequel system.\n\nPE short read data were pre-processed with bbduk v38.20 from the BBTools package to remove adapters and low-quality reads. Illumina MP read data were cleaned and separated into true MP data and likely MP data in nxTrim (O’Connell et al., 2015). The long-read PacBio data were pre-processed using CANU v1.7 (Koren et al., 2017) to obtain trimmed and corrected reads. Cleaned short-read PE and MP data were then assembled using the ABySS v2.1.1 pipeline (Simpson et al., 2009) up to scaffold stage, using a k-mer value of 120. Parameters for ABySS were optimized away from default values to achieve better performance (for all parameter settings see Extended data, Supplementary Table S2 (Verlinden et al., 2020)). The assembly was further improved by using the PacBio data as input for LINKS (Warren et al., 2015).\n\nTwo strategies were used to identify and annotate repetitive elements. First, de novo annotation was carried out by RepeatModeler v2.0 and LTR_FINDER v1.0.7 (Xu & Wang, 2007) to build a custom repeat library. Second, a homology-based approach was used to search for repetitive elements in the assembled genome using the repetitive element library of RepeatMasker v4.1.0 and RepeatProteinMask v4.1.0. The results of both strategies were combined into a non-redundant set of repetitive elements. Subsequently, the library was used to mask repetitive elements by employing RepeatMasker v4.1.0 (Tarailo-Graovac & Chen, 2009).\n\nTransfer RNAs (tRNAs) were predicted by tRNAscan-SE v1.31 (Lowe & Eddy, 1997) with default parameters. To predict non-coding RNAs (ncRNAs), such as microRNAs (miRNAs), small nuclear RNAs (snRNAs), and ribosomal RNAs (rRNAs), the desert locust genome was screened against the RNA families (Rfam) v14.1 database (Griffiths-Jones et al., 2003) by the cmscan program of Infernal v1.1.2 (Nawrocki & Eddy, 2013). To supplement our predictions of miRNAs, miRNA sequences from the L. migratoria genome (Wang et al., 2015) were extracted and searched in the S. gregaria genome by BLASTN with options “-task blastn-short -ungapped -penalty -1 -reward 1” (Camacho et al., 2008). The alignment result was filtered using a mismatch cutoff of 3 bp. Specifically, the stem-loop structure of each potential miRNA was predicted by miRNAFold (Tav et al., 2016) using each alignment with 110 bp upstream and downstream sequences. Then the RNAfold program of ViennaRNA v2.4.14 (Lorenz et al., 2011) was used to calculate the minimum free energy (MFE) of each stem-loop structure. If a potential miRNA had several predicted stem-loop structures, the one with the minimum MFE was selected as representative. Putative miRNAs located within protein coding sequences or repetitive elements were discarded. Finally, the results based on Rfam and the migratory locust genome were combined into a non-redundant prediction of miRNAs.\n\nProtein-coding genes in the desert locust genome were predicted using three approaches. (1) RNA-Seq reads (see Extended data, Supplementary Methods (Verlinden et al., 2020)) were mapped to the desert locust genome using HISAT2 v2.1.0 (Kim et al., 2015) with parameter “--max-intronlen” set to 1,000,000 to increase the maximum allowed intron length during read mapping. Then, StringTie v2.1.1 (Pertea et al., 2015) was used to assemble potential transcripts based on RNA-Seq alignments to the desert locust genome. Subsequently, TransDecoder v5.0.2 was used to identify open reading frames (ORFs) within the assembled transcripts which resulted in 20,201 ORFs with start and/or stop codons. We also built de novo assembled transcripts based on the pooled RNA-Seq reads of all samples with Trinity v2.8.4 (Grabherr et al., 2011; Haas et al., 2013) and obtained 285,499 transcripts (including isoforms), of which 57,870 putative protein-coding transcripts and 305 rRNA candidates were identified by Trinotate v3.1.1 (Bryant et al., 2017). This was complemented with 34,974 ESTs of the desert locust from NCBI (Badisco et al., 2011). The assembled transcripts and ESTs were then aligned to the desert locust genome with Program to Assemble Spliced Alignments (PASA v2.4.1) (Haas et al., 2003). (2) For ab initio gene prediction, we used a hard-masked genome in which genomic repetitive elements were substituted by ‘N’. To build a training set for the ab initio gene predictors, we extracted 498 complete genes with both start and stop codons from the 500 longest ORFs predicted by TransDecoder, based on the above RNA-Seq analysis with HISAT2 and StringTie. Augustus v3.3.3 (Stanke et al., 2006) SNAP v2006-07-28 (Korf, 2004) and GlimmerHMM v3.0.4 (Majoros et al., 2004) were trained on this training set and then used to predict potential gene models. Furthermore, combined with the RNA-Seq alignments, BRAKER2 v2.1.5 (Hoff et al., 2019) was used to predict protein-coding genes based on the above-mentioned training model of Augustus. (3) The proteomes of the migratory locust, Locusta migratoria (Wang et al., 2014); the African malaria mosquito, Anopheles gambiae; the domestic silk moth, Bombyx mori; the fruit fly, Drosophila melanogaster; the kissing bug, Rhodnius prolixus; the red imported fire ant, Solenopsis invicta; the red flour beetle, Tribolium castaneum; and the Nevada dampwood termite, Zootermopsis nevadensis from Ensembl Metazoa (release-47), as well as the proteins in UniRef100 (release-2020_01) for the clade Polyneoptera (Taxonomy ID: 33341) were used to assist gene predictions with homologous proteins. Exonerate v2.4.0 (Slater & Birney, 2005) was used to perform spliced alignments of the proteins with the maximum intron length set to 1 Mb. To integrate the predictions from all three gene-prediction approaches, EvidenceModeler v1.1.1 (Haas et al., 2008) was used to produce a non-redundant gene set. Functional annotation of the predicted protein-coding genes was done by running BlastP (Altschul et al., 1990) using an e-value cut-off of 1×10-5 against the public protein databases Uniprot/SwissProt (Magrane, 2011; The UniProt Consortium 2019) and NCBI NR (RefSeq non-redundant protein record). Protein family (Pfam) domain information and Gene Ontology (GO) terms were added using InterProscan (Mitchell et al., 2019).\n\n\nResults and discussion\n\nInitial input data for the assembly comprised (i) 1,316 Gb of Illumina short read data, of which 1,009 Gb remained after cleaning and trimming, and (ii) 112 Gb of long reads from PacBio sequencing. The resulting assembly, using the ABySS pipeline, consisted of 8.5 Gb in ~1.6 M contigs with an N50 of 12,027 bp. Scaffolding with the MP data using ABySS resulted in 8.6 Gb in 1.2 M scaffolds with an N50 of 66,194 bp. The PacBio data as input for LINKS further improved the scaffolded assembly derived from ABySS, doubling the N50 and maximum length and reducing the number of sequences by half. The final assembly consists of 8,817,834,205 bp organised in 955,015 scaffolds with an N50 of 157,705 bp (Table 1).\n\nScaffolds (MP), Scaffolds reached with the Mate Pair data using the ABySS pipeline; Scaffolds (PacBio), improved scaffolds with the PacBio data as input for LINKS; N50, the sequence length of the shortest contig/scaffold at 50% of the total genome length; N90, the sequence length of the shortest contig/scaffold at 90% of the total genome length\n\nIn total, repetitive elements account for 62.55% of the desert locust genome (Table 2), which is more than the 58.86% repetitive elements in the published migratory locust genome (Wang et al., 2014). Screening the desert locust genome against the Rfam v14.1 database identified 121,581 tRNAs, 1,302 rRNAs, 121 miRNAs, and 361 snRNAs (Extended data, Supplementary Table S3 (Verlinden et al., 2020)).\n\nDNA, DNA transposons; LINE, long interspersed nuclear element retrotransposon; SINE, short interspersed nuclear element retrotransposon; LTR, long terminal repeat retrotransposon; Other, repeats classified to other than the above mentioned types; Unknown, repeats that cannot be classified; P%, percentage of the genome.\n\nIn addition to the 121 evolutionary conserved miRNAs identified from Rfam, blasting with miRNAs previously identified in the migratory locust (from small RNA sequencing-based and homology-based approaches; Wang et al., 2015) identified a further 686 miRNAs in the desert locust genome, resulting in a total of 807 identified miRNAs (Extended data, Supplementary Table S3 (Verlinden et al., 2020)). Of these 807 miRNAs, 676 are located on short scaffolds without any protein-coding gene. Among the 121 miRNAs identified based on Rfam, 81 have no homologs in the migratory locust genome.\n\nIn total, 18,815 protein-encoding genes are predicted in the desert locust genome (Extended data, Supplementary Table S4 (Verlinden et al., 2020)). The average pre-mRNA length is 54,426 bp, with an average coding sequence (CDS) length of 1,137 bp and an average intron length of 12,522 bp, values which are comparable to those of the published migratory locust genome (Wang et al., 2014). Although both locust genomes have longer pre-mRNAs with bigger introns and more exons than the Drosophila melanogaster genome (Adams et al., 2000), their average CDS and exon length are in fact shorter (Figure 2 and Table 3). The BUSCO assessment of the current gene set (protein mode) shows that it includes 79.4% complete genes in the insecta_odb10 dataset (Simão et al., 2015), which closely matches the result from the BUSCO genome completeness assessment (genome mode) of 80.9% (Extended data, Supplementary Table S5 (Verlinden et al., 2020)). The BUSCO assessment of the predicted genes in the desert locust genome shows fewer complete genes than for the published Locusta migratoria and Drosophila melanogaster genomes (Figure 2). Among the 18,815 predicted genes in the desert locust genome, 13,646 (72.53%) obtained at least one functional assignment based on similarity to known proteins in the databases. Pfam domain information could be added to 10,395 (55.25%) predicted genes, and 6,470 (34.39%) predicted genes could be assigned a GO term (Extended data, Supplementary Table S6 (Verlinden et al., 2020)).\n\n(a-e) Boxplots of (a) pre-mRNA lengths; (b) intron lengths; (c) exon numbers; (d) coding sequence (CDS) lengths; and (e) exon lengths in the three genomes. (f) BUSCO assessments of the gene sets in the three genomes. The stacked bars indicate the percentages of genes that are complete (light blue), duplicated (dark blue), fragmental (yellow) and missed (red).\n\nScaffold N50, the sequence length of the shortest scaffold at 50% of the total genome length; CDS, coding sequence.\n\n\nConclusions\n\nHere, we present the first draft genome sequence of the desert locust, Schistocerca gregaria, a swarming pest species with significant socio-economic and ecological impact. With the current locust crisis in mind, it should be clear that despite ongoing monitoring and control operations, we are still in urgent need of more locust research to foster development of effective management strategies. Sequencing and assembling the desert locust genome has been both challenging and ground-breaking due to the enormous size of the genome and its extremely large proportion of repetitive elements. The desert locust genome is the largest insect genome sequenced and assembled to date. As is the case for the second and third largest assembled insect genomes, the expanded genome size is caused by accumulation of repetitive regions and intron elongation (Locusta migratoria, 6.5 Gb; Wang et al., 2014; Clitarchus hookeri, 4.2 Gb; Wu et al., 2017). Sequencing the desert locust genome is an important step to advance our knowledge of these animals. It will enable future studies to examine the very complex relationship between environmental cues and phenotypic plasticity, and in particular the question of how this is regulated at the molecular level. A better understanding of the desert locust’s molecular biology will facilitate the development of novel, more sustainable strategies for controlling these pests.\n\n\nData availability\n\nEuropean Nucleotide Archive: First draft genome of Schistocerca gregaria, a swarm forming grasshopper species. Accession number PRJEB38779; https://identifiers.org/ena.embl:PRJEB38779.\n\nThis accession contains all genome and transcriptome data. The annotations are also available via the ORCAE platform (https://bioinformatics.psb.ugent.be/orcae/overview/Schgr).\n\nFigshare: First draft genome assembly of the desert locust, Schistocerca gregaria - extended data. https://doi.org/10.6084/m9.figshare.12654026.v1 (Verlinden et al., 2020).\n\nThis project contains the following extended data:\n\nSupplementary Methods (DOCX). Containing details of Animal material, Genomic DNA extraction, Library construction, sequencing for RNA-Seq and de novo transcriptome assembly.\n\nSupplementary Table S1 (DOCX). Available Polyneopteran genomes (incl. Schistocerca gregaria for comparison).\n\nSupplementary Table S2 (DOCX). Software parameter settings.\n\nSupplementary Table S3 (DOCX). Transfer RNA (tRNA), microRNA (miRNA), small nuclear RNA (snRNA) and ribosomal RNA (rRNA) content of the desert locust genome.\n\nSupplementary Table S4 (DOCX). Desert locust genome annotation details.\n\nSupplementary Table S5 (DOCX). BUSCO assessments for the genomes of the desert locust, Schistocerca gregaria, and the migratory locust, Locusta migratoria (Wang et al., 2014).\n\nSupplementary Table S6 (DOCX). Functional annotation of the proteome of the desert locust.\n\nExtended data are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "Acknowledgements\n\nEvelien Herinckx (KU Leuven) for technical support in desert locust rearing; Evert Bruyninckx (KU Leuven) for optimizing genomic DNA extraction. Ellen De Meester and Sarah De Keulenaer from NxtGNT Belgium for their practical expertise and assistance in the Illumina sequencing experiments. Wim Meert and Stephanie Deman (Genomics core Leuven) for optimizing the PacBio sequencing.\n\n\nReferences\n\nAdams MD, Celniker SE, Holt RA, et al.: The genome sequence of Drosophila melanogaster. Science. 2000; 287(5461): 2185–2195. PubMed Abstract | Publisher Full Text\n\nAltschul SF, Gish W, Miller W, et al.: Basic local alignment search tool. J Mol Biol. 1990; 215(3): 403–410. PubMed Abstract | Publisher Full Text\n\nBadisco L, Huybrechts J, Simonet G, et al.: Transcriptome analysis of the desert locust central nervous system: production and annotation of a Schistocerca gregaria EST database. PLoS One. 2011; 6(3): e17274. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBryant DM, Johnson K, DiTommaso T, et al.: A tissue-mapped Axolotl de novo transcriptome enables identification of limb regeneration factors. Cell Rep. 2017; 18(3): 762–776. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCamacho C, Coulouris G, Avagyan V, et al.: BLAST+: architecture and applications. BMC Bioinformatics. 2008; 10: 421. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCamacho JPM, Ruiz-Ruano FJ, Martín-Blázquez R, et al.: A step to the gigantic genome of the desert locust: chromosome sizes and repeated DNAs. Chromosoma. 2015; 124(2): 263–75. PubMed Abstract | Publisher Full Text\n\nCourcoux G: Invasions of locusts: a lasting impact. Scientific news of the Institut de Recherche pour le Développement. 2012; 411. Reference Source\n\nCullen DA, Cease AJ, Latchininsky AV, et al.: From molecules to management: Mechanisms and consequences of locust phase polyphenism. Adv Insect Physiol. 2017; 53: 167–285. Publisher Full Text\n\nDe Vreyer P, Guilbert N, Mesple-Somps S: The 1987-89 locust plague in Mali: Evidences of the heterogeneous impact of income shocks on education outcomes. No DT/2012/05, Working Papers, DIAL (Développement, Institutions et Mondialisation). 2012; 48p. Reference Source\n\nFox DP: A non-doubling DNA series in somatic tissues of the locusts Schistocerca gregaria (Forskål) and Locusta migratoria(Linn.). Chromosoma. 1970; 29(4): 446–461. PubMed Abstract\n\nGrabherr MG, Haas BJ, Yassour M, et al.: Full-length transcriptome assembly from RNA-seq data without a reference genome. Nat Biotechnol. 2011; 29(7): 644–652. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGriffiths-Jones S, Bateman A, Marshall M, et al.: Rfam: an RNA family database. Nucleic Acids Res. 2003; 31(1): 439–441. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHaas BJ, Delcher AL, Mount SM, et al.: Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res. 2003; 31(19): 5654–5666. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHaas BJ, Papanicolaou A, Yassour M, et al.: De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc. 2013; 8(8): 1494. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHaas BJ, Salzberg SL, Zhu W, et al.: Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments. Genome Biol. 2008; 9(1): R7. 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. PubMed Abstract | Publisher Full Text | Free Full Text\n\nJohn B, Hewitt, GM: Karyotype stability and DNA variability in the Acrididae. Chromosoma. 1966; 20: 155–172. Publisher Full Text\n\nKim D, Langmead B, Salzberg SL: HISAT: a fast spliced aligner with low memory requirements. Nat Methods. 2015; 12(4): 357–360. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKoren S, Walenz BP, Berlin K, et al.: Canu: scalable and accurate long-read assembly via k-mer weighting and repeat separation. Genome Res. 2017; 27(5): 722–736. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKorf I: Gene finding in novel genomes. BMC Bioinformatics. 2004; 5(1): 59. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLorenz R, Bernhart SH, Höner Zu Siederdissen C, et al.: ViennaRNA Package 2.0. Algorithms Mol Biol. 2011; 6(1): 26. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLowe TM, Eddy SR: tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997; 25(5): 955–964. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMagrane M: UniProt Knowledgebase: a hub of integrated protein data. Database (Oxford). 2011; bar009. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMajoros WH, Pertea M, Salzberg SL: TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders. Bioinformatics. 2004; 20(16): 2878–2879. PubMed Abstract | Publisher Full Text\n\nMeynard CN, Lecoq M, Chapuis MP, et al.: On the relative role of climate change and management in the current desert locust outbreak in East Africa. Glob Chang Biol. 2020; 26(7): 3753–3755. PubMed Abstract | Publisher Full Text\n\nMisof B, Liu S, Meusemann K, et al.: Phylogenomics resolves the timing and pattern of insect evolution. Science. 2014; 346(6210): 763–767. PubMed Abstract | Publisher Full Text\n\nMitchell AL, Attwood TK, Babbit PC, et al.: InterPro in 2019: improving coverage, classification and access to protein sequence annotations. Nucleic Acids Res. 2019; 47(D1): D351–D360. PubMed Abstract | Publisher Full Text | Free Full Text\n\nNawrocki EP, Eddy SR: Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics. 2013; 29(22): 2933–2935. PubMed Abstract | Publisher Full Text | Free Full Text\n\nO’Connell J, Schulz-Trieglaff O, Carlson E, et al.: NxTrim: Optimized trimming of Illumina mate pair reads. Bioinformatics. 2015; 31(12): 2035–2037. PubMed Abstract | Publisher Full Text\n\nPener MP, Simpson SJ: Locust phase polyphenism: an update. Adv Insect Physiol. 2009; 36: 1–272. Publisher Full Text\n\nPertea M, Pertea GM, Antonescu CM, et al.: StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol. 2015; 33(3): 290–5. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSchoofs L, Veelaert D, Vanden Broeck J, et al.: Peptides in the locusts, Locusta migratoria. and Schistocerca gregaria. Peptides. 1997; 18(1): 145–56. PubMed Abstract | Publisher Full Text\n\nSimão FA, Waterhouse RM, Ioannidis P, et al.: BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 2015; 31(19): 3210–3212. PubMed Abstract | Publisher Full Text\n\nSimpson JT, Wong K, Jackman SD, et al.: ABySS: a parallel assembler for short read sequence data. Genome Res. 2009; 19(6): 1117–1123. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSlater GSC, Birney E: Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics. 2005; 6(1): 31. PubMed Abstract | Publisher Full Text | Free Full Text\n\nStanke M, Keller O, Gunduz I, et al.: AUGUSTUS: ab initio prediction of alternative transcripts. Nucleic Acids Res. 2006; 34(Web Server issue): W435–W439. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSymmons PM, Cressman K: Desert Locust Guidelines. Second edition. Food and Agriculture Organization of the United Nations (Rome). 2001. Reference Source\n\nTarailo-Graovac M, Chen N: Using RepeatMasker to identify repetitive elements in genomic sequences. Curr Protoc Bioinformatics. 2009; Chapter 4: Unit 4.10. PubMed Abstract | Publisher Full Text\n\nTav C, Tempel S, Poligny L, et al.: miRNAFold: a web server for fast miRNA precursor prediction in genomes. Nucleic Acids Res. 2016; 44(W1): W181–W184. PubMed Abstract | Publisher Full Text | Free Full Text\n\nThe UniProt Consortium: UniProt: a worldwide hub of protein knowledge. Nucleic Acids Res. 2019; 47(D1): D506–D515. PubMed Abstract | Publisher Full Text | Free Full Text\n\nvan Huis A, Van Itterbeeck J, Klunder H, et al.: Edible insects: future prospects for food and feed security. FAO Forestry Paper. 2013; 171: 187. Referenece Source\n\nVerlinden H, Badisco L, Marchal E, et al.: Endocrinology of reproduction and phase transition in locusts. Gen Comp Endocrinol. 2009; 162(1): 79–92. PubMed Abstract | Publisher Full Text\n\nVerlinden H, Sterck L, Li J, et al.: First draft genome assembly of the desert locust, Schistocerca gregaria - extended data. figshare. Journal contribution. 2020. http://www.doi.org/10.6084/m9.figshare.12654026.v1\n\nWang X, Fang X, Yang P, et al.: The locust genome provides insight into swarm formation and long-distance flight. Nat Commun. 2014; 5: 2957. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWang Y, Jiang F, Wang H, et al.: Evidence for the expression of abundant microRNAs in the locust genome. Sci Rep. 2015; 5: 13608. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWarren RL, Yang C, Vandervalk BP, et al.: LINKS: Scalable, alignment-free scaffolding of draft genomes with long reads. Gigascience. 2015; 4(1): 35. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWilmore PJ, Brown AK: Molecular properties of orthopteran DNA. Chromosoma. 1975; 51(4): 337–345. PubMed Abstract | Publisher Full Text\n\nWipfler B, Letsch H, Frandsen PB, et al.: Evolutionary history of Polyneoptera and its implications for our understanding of early winged insects. Proc Natl Acad Sci USA. 2019; 116(8): 3024–3029. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWu C, Twort VG, Crowhurst RN, et al.: Assembling large genomes: analysis of the stick insect (Clitarchus hookeri.) genome reveals a high repeat content and sex-biased genes associated with reproduction. BMC Genomics. 2017; 18(1): 884. PubMed Abstract | Publisher Full Text | Free Full Text\n\nXu Z, Wang H: LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. Nucleic Acids Res. 2007; 35(Web Server issue): W265–W268. PubMed Abstract | Publisher Full Text | Free Full Text"
}
|
[
{
"id": "71637",
"date": "05 Oct 2020",
"name": "Uwe Homberg",
"expertise": [
"Reviewer Expertise neurobiology of the desert locust",
"neuropeptide research in desert locust",
"neuroanatomy of the locust brain"
],
"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 marvellous paper based on an enormous effort for genome assembly in this insect. The work is urgently needed in order to promote a large number of studies on the behavior and physiology of this insect. The data are highly likely to ultimately better understand migratory behavior in the desert locust as well as its phase polyethism. I have no comments or suggestions for further improvements of this already excellent achievement.\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": "6649",
"date": "21 May 2021",
"name": "Heleen Verlinden",
"role": "Author Response",
"response": "The authors would like to thank the reviewer for this very positive feedback on their manuscript."
}
]
},
{
"id": "72656",
"date": "27 Oct 2020",
"name": "Surya Saha",
"expertise": [
"Reviewer Expertise Arthropod genomics and transcriptomics",
"Comparative genomics and Metagenomics"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 is timely given the locust outbreaks in East Africa and recently in parts of West Asia with the devasting impact on crops of small holder farmers in these regions besides secondary impacts on nutrition and human health. The large genome size and repetitive regions make this a challenging genome to assemble. The phase polyphenism of the gregarious and solitarious adults make this a fascinating system to study for social behavior and physiology in arthropods. A high-quality chromosomal length genome assembly for S. gregaria will lay the foundation for genetics and phenotyping of this important insect pest. The methods for the genome assembly, protein coding and non-coding gene annotation are clearly described in the paper and in the extended data. Inclusion of the parameters used is helpful for the reproducibility of the genome assembly process. I commend the authors on a well written manuscript.\n\nAlthough this is a valuable contribution to Polyneoptera genomics, it is possible to do a better job of utilizing the new genome and annotation for comparison with other sequenced relatives in Polyneoptera, especially the migratory locust. In my humble opinion, the manuscript can be improved a lot if these issues are addressed.\n\n1. This manuscript can become a tour de force for locust genomics if additional analysis and discussion were to be included. Gene families related to energy consumption and detoxification already identified in the migratory locust are of particular interest. There are two other aspects that, if addressed, will be of value to the community.\n1a.The authors mention a greater presence of ncRNA elements in the S. gregaria genome. The association of these potential regulatory elements with protein coding genes based on RNA data from this paper and other public data will be useful.\n1b. The other point is about a more detailed characterization of the repeat elements that account for 62% of the genome. A GenomeScope or similar plot of the heterozygosity in the Illumina reads might be useful to understand the repetitive structure. I know this adds additional burden on the authors but I hope they see my rationale.\n2. Endosymbionts been reported for other locust genomes (https://www.mdpi.com/2075-4450/11/10/6551). These are typical by products of insect genome assembly. Were any microbial contigs found in the assembly for known endosymbionts?\n\nI had a few minor points:\n1. The introduction states that the potentially expanded non-coding portion of the genome in S. gregaria makes the assembly more challenging. Can the authors please expand on this argument?\n2. Was any kind of filtering done to remove microbial contamination? The animal material protocol in the supplementary methods does not mention starving the insects before DNA extraction. Can this have introduced microbial contamination from the feed even though the leaves were washed?\n\n3. This manuscript represents a mammoth amount of work that has gone into the genome assembly. The standard of quality for a genome assembly has increased vastly since the L. migratiria genome was published in 2014. Since sourcing high quality DNA from the insects does not seem to be a major challenge as far as I know, were long range scaffolding methods like Hi-C or BioNano explored for chromosomal scale scaffolding?\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "6650",
"date": "21 May 2021",
"name": "Heleen Verlinden",
"role": "Author Response",
"response": "We would like to thank the reviewer for this positive feedback, as well as for recognising the challenges we have faced. Since sequencing technologies are evolving very fast, we agree that future work will further improve the current genome assembly. Therefore, we designated this as the “first genome assembly”. In addition, with the release of our genome data, we are convinced that many additional analyses are becoming possible. Locusts have always been -and still are- research models for studying a wide range of research questions in different areas of interest. With this manuscript, we therefore chose not to focus on a very specific research question, but communicate the main results obtained of our genome sequencing effort. Moreover, given the current locust situation, we felt that it was important to make available this first genome draft to the international scientific community and to stimulate readers -worldwide- to address their specific research question(s). 1) We agree that these analyses will be of great value and sincerely hope to include these in future research, however they are out of scope of this first draft publication. 2)We took many precautions to reduce the risk of contamination. The locust cages were meticulously cleaned multiple times a week, all material that entered the facility was either new or sterilised or both. Food was bred separately and washed carefully. Gloves, lab coats, face masks were worn upon entering the rooms. Our animals all looked healthy, with no signs of infections. During the dissections, we were extremely careful not to damage the gut and did not include any digestive tissues. We checked for contamination by BLASTX and BLASTN with sequence databases from a number of vertebrate, plant, fungi, gregarina, amoeba, bacteria and protoctista and could not find any significant contamination. We therefore did not perform any form of filtering for endosymbiont/microbial contamination. Following sentences have now been adapted/added to the supplementary materials and methods to make this clearer for the reader: “The entire breeding facility was meticulously cleaned multiple times a week throughout the entire breeding period to avoid any form of contamination. All materials that entered the facility were either new or sterilised or even both. Food was bred separately and washed carefully. Gloves, lab coats and face masks were worn upon entering the facility. The locusts showed no external signs of disease or contamination, displayed clear phenotypic characteristics of solitarious locusts and underwent the sixth larval stage characteristic of the solitarious phase (Pener and Simpson, 2009; Cullen et al., 2017). The animals were very carefully dissected and specific attention was paid to avoid any contamination with gut material.” “We checked for contamination by BLASTX and BLASTN with sequence databases from a number of vertebrate, plant, fungi, gregarina, amoeba, bacteria and protoctista and could not find any contamination. We therefore did not perform any form of filtering for endosymbiont/microbial contamination.” Minor points: 1. In general, a bigger genome takes more reads and thus also more budget to obtain enough sequencing coverage. Although we did not concretely know how expanded the non-coding portion of the genome would be, we had expected the presence of many repetitive regions, which can indeed make assembly more complicated and challenging. We therefore anticipated to this by including a long-read technology like PacBio, to improve the assembly process of short Illumina reads. We specified that we also expected more repetitive regions and added two references here: Dominguez Del Angel, V., Hjerde, E., Sterck, L., et al.: Ten steps to get started in Genome Assembly and Annotation [version 1; peer review: 2 approved]. F1000Research 2018, 7(ELIXIR), 148. Tørresen, O.K., Star, B., Mier, P., et al.: Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases. Nucleic Acids Res 2019; 47(21), 10994–11006. 2. As clarified above, we took many precautions to avoid contaminations and indeed checked if there was contamination. Since no significant contamination was observed, we did not perform any form of filtering. 3. We performed PacBio sequencing, in addition to the Illumina sequencing, to obtain long reads. We agree that newer technologies may be very useful to further optimise the genome sequence assembly."
}
]
},
{
"id": "72658",
"date": "02 Nov 2020",
"name": "Joshua B. Benoit",
"expertise": [
"Reviewer Expertise Insect physiology",
"molecular biology",
"and genomics"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is an extremely important agricultural pest and having a genome for this species will allow for more future comparisons among locust species. This study represents a great deal of work and the techniques used are appropriate and well described. There is some room for improvement, but a valuable contribution.\n\nI would suggest to add a little more biological interpretation. Was there anything of interest and unique identified? Specifically, anything related to the transition from solitary to swarming.\n\nThe assembly is of sufficient quality for some comparisons to other insects, but there might be issues with the low BUSCO score. This was similar to the Locusta genome. Please check the BUSCO score of the Trinity assembly to determine if the missing genes are present. If the missing genes are present in the de novo assembly, I would make sure to make the de novo assembly available until a higher quality genome is available.\n\nWere any bacterial symbiont present or microbial contamination detected? How were these accounted for in the assembly?\n\nAs a future goal, I would suggest adding techniques for chromosome scaffolding (e.g. Hi-C). This genome is fine as a draft, a higher quality version will be needed for future comparisons.\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": "6651",
"date": "21 May 2021",
"name": "Heleen Verlinden",
"role": "Author Response",
"response": "We would like to thank the reviewer for this positive feedback and for recognising the challenges we have faced. Since sequencing technologies are evolving very fast, we agree that future work will further improve the current genome assembly. This is why we designated this as the “first genome assembly”. In addition, with the release of our genome data, we are convinced that many additional analyses are becoming possible. Locusts have always been -and still are- research models for studying a wide range of research questions in different areas of interest. With this manuscript, we therefore chose not to focus on a very specific research question, but communicate the main results obtained of our genome sequencing effort. Moreover, given the current locust situation, we felt that it was important to make available this first genome draft to the international scientific community and to stimulate readers -worldwide- to address their specific research question(s). The BUSCO assessment on the Trinity assembly shows that it includes 91.2% complete genes in insecta_odb10 dataset. Compared with the BUSCO values (genomic 80.9% vs geneset 79.4%) of our current genome assembly this indeed indicates that our genome assembly still misses some BUSCO genes that are present in our transcript databases. It proves that our current genome assembly can still be further improved, as we are of course aware. The Trinity assembly is included in the gene set we made available. As already clarified in our answer to a very similar comment made by reviewer 2, we took many precautions to avoid contaminations and we did not observe any. This is now specified in the supplementary materials and methods. We fully agree with the reviewer that additional techniques may further improve this draft genome assembly."
}
]
}
] | 1
|
https://f1000research.com/articles/9-775
|
https://f1000research.com/articles/10-214/v1
|
16 Mar 21
|
{
"type": "Research Article",
"title": "Influence of hybrid assistive limb gait training on spatial muscle activation patterns in spinal muscular atrophy type III",
"authors": [
"Yuichi Nishikawa",
"Kohei Watanabe",
"Naoya Orita",
"Noriaki Maeda",
"Hiroaki Kimura",
"Shinobu Tanaka",
"Allison Hyngstrom",
"Kohei Watanabe",
"Naoya Orita",
"Noriaki Maeda",
"Hiroaki Kimura",
"Shinobu Tanaka",
"Allison Hyngstrom"
],
"abstract": "Background: Despite the potential benefits, the effects of Hybrid Assistive Limb (HAL) gait training on changes in neuromuscular activation that accompany functional gains in individuals with spinal muscular atrophy (SMA) type III is not well known. In this article, we quantify the effects of HAL gait training on spatial muscle activity patterns in a patient with SMA type III using multi-channel surface electromyography (SEMG).\nMethods: A 21-years old male (168 cm, 47.8 kg) with spinal muscular atrophy type III, when diagnosed at 18-years old by genetic screening, participated in this case study. Although he presented with forearm distal muscle weakness, atrophy of the intrinsic muscles of the hand, and neuromuscular fatigue, his activities of daily living is independent. The patient underwent a separate, single 33-minute session of both HAL and treadmill gait training. To evaluate the coefficient of variation (CoV) of force and alterations in the SEMG spatial distribution patterns, modified entropy and CoV of root mean square (RMS) were calculated from the vastus lateralis (VL) muscle before and after the intervention of HAL and treadmill gait training. Each training session was separated by a period of one month to avoid cross-over effects. Results: There was a greater decrease in the ΔCoV of force and an increase in the magnitude of whole VL muscle activation from pre-intervention to post-intervention with the HAL gait training as compared to the treadmill gait training. In response to only HAL gait training, the CoV of RMS was higher, and the modified entropy was lower post-intervention than pre-intervention.\nConclusions: Our results support the notion that HAL gait training has a positive benefit on motor output not only in the magnitude of SEMG generated but also the patterns of neural activation.",
"keywords": [
"Gait training",
"Rehabilitation",
"Spinal muscular atrophy type III",
"Electromyography",
"Hybrid assistive limb"
],
"content": "Introduction\n\nSeveral clinical trials of robot-assisted gait training have been reported in neurology patients.1–4 In particular, the Hybrid Assistive Limb (HAL) gait training has resulted in improved gait and balance performance.1,3,5 The HAL exoskeleton is completely driven by the patient’s own muscle activation, which is detected by surface electrodes on key lower extremity muscle groups. Thus, this self-initiated robotic-assisted movement has the potential to induce a somatosensory feedback-loop that enhances neural plasticity and locomotor function.6 Although many previous studies have reported functional gains due to the HAL intervention (e.g., gait and balance),1,3,5,7 there are no studies that report its effects on neuromuscular activation likely to accompany functional gains. Understanding how HAL training changes neuromuscular activation patterns, will help in the evaluation and use of HAL training across various populations.\n\nMulti-channel surface electromyography (SEMG) is a recently developed techniques used to evaluate single motor unit firing behavior and whole muscle EMG patterns of activity by using multiple electrodes arranged in a two-dimensional plane.8–10 This technique provides data on the spatial distribution of SEMG within a muscle. Previous studies have demonstrated that the spatial distribution of SEMG is altered by contraction levels or fatigue during isometric contraction.11,12 This phenomenon has been explained by a spatial inhomogeneity in the location of different types of muscle fibers13 and a clustering of muscle fibers innervated by one motor unit in a limited territory.14–16 Previous studies have demonstrated that alterations in the multi-channel SEMG spatial distribution pattern can be explained by the physiological phenomenon of motor unit recruitment and suggested that the multi-channel SEMG spatial distribution pattern could be used to study changes in motor unit recruitment patterns.15,17 In addition, previous studies have used metrices such as the inhomogeneity of the spatial distribution pattern of SEMG (EMG variables; modified entropy and coefficient of variation (CoV) of root mean square (RMS)11,18 to quantify neuromuscular fatigue and the influence of force generation. The assessment of motor unit recruitment is very important for determining the effect of neurorehabilitation on neuroplasticity in patients with several types of neurological conditions. Thus, we considered that this technique (i.e., multi-channel SEMG) could be employed as a new assessment tool to evaluate changes in muscle activation as a metric of neuroplasticity in response to HAL training.\n\nIndividuals with spinal muscular atrophy (SMA) type III present with progressive proximal weakness of the legs more than arms, and the leg weakness is so profound that it can necessitate the long term need of a wheelchair for mobility.19 Rehabilitation is one treatment for SMA type III. The main objectives for rehabilitation of individuals with SMA type III who are still able to walk are to maintain, restore or promote function, mobility, and adequate joint range, and improve balance and endurance.20 HAL gait training has been an insurance supported therapy since January 2016, and SMA, amyotrophic lateral sclerosis, spinal bulbar atrophy, Charcot-Marie-Tooth disease, inclusion body myositis, distal myopathy, and congenital myopathy are targeted disease populations. Although approved by insurance, there is limited information on how the effectiveness of HAL training compares to other forms of therapy. Specifically, there is no report which compares HAL and conventional treadmill gait training on neuromuscular activation in SMA patients that likely accompany improvements in walking function. Therefore, the aim of this case report to quantify the effects of a single session of HAL gait training on SEMG spatial distribution patterns in a person with spinal muscular atrophy type III. We hypothesized that HAL gait training would induce more heterogenous muscle activation reflecting more varied motor unit recruitment than treadmill gait training.\n\n\nMethods\n\nA 21-year-old male (168 cm, 47.8 kg) with spinal muscular atrophy type III when diagnosed at 18-years old by genetic screening participated in this study. Written informed consent was obtained from the patient to perform the two types of gait training and to publish the obtained his anonymized data to be published in this article. All procedures were performed in accordance with the Declaration of Helsinki and were approved by the Hiroshima University’s Committee on Ethics in Research (approval Number No. E-53). Our institution does not require ethical approval for reporting individual cases or case series. He presented with forearm distal muscle weakness, atrophy of the intrinsic muscles of the hand, and neuromuscular fatigue. The patient’s baseline physical performance data are shown in Table 1. The age-matched normative values for knee extension strength and six minutes walking test (6MWT) are 2.82±0.38 Nm/kg and 637 m.21,22 The participants’ knee extension strength (Right: 1.59 Nm/kg, Left; 1.32 Nm/kg) and 6MWT (567 m) were lower than the above value, and we have chosen the weaker leg to measure EMS recording.\n\nThe participant performed maximal isometric voluntary contractions (MVC) of the knee extensors bilaterally at the pre- and post-intervention. Isometric knee extension was performed using a Biodex system (Biodex System 4; Biodex Medical Systems, Shirley, NY, USA). During contractions, both the hip and knee extension angles were positioned at 90 degrees. The MVC involved a gradual increase in knee extension torque from 0 Nm to his maximum torque over three seconds, with the maximum torque being held for two seconds. The participant performed at least two MVC trials with > 120 s of rest between trials and a warm-up for 10 min, including indoor walking and lower limb stretching before the MVC measurement.23 The peak MVC torque was used as the maximal effort and to calculate the target torque for the isometric sub-maximal ramp-up contractions. After MVC measurements, the participant performed an isometric submaximal ramp-up contraction of the knee extensors in the weaker leg one time from 0% to 80% of the MVC force with an increase rate of approximately 10% of the MVC per sec.24,25 The participant-generated torque and target torque were displayed on a computer monitor. Prior to motor testing, the participant practiced the MVC and sub-maximal ramp-up contraction at least 10 min before the motor testing session began. The CoV of force (standard deviation (SD)/mean x 100, CV force) was calculated from the ramp up contraction task.\n\nDuring the sub-maximal contraction, multi-channel SEMG signals were detected from the weaker side of vastus lateralis (VL) muscle using a semi-disposable grid of 64 electrodes (ELSCH064NM2; OTBioelettronica, Torino, Italy) according to the same procedures used in previous studies.23,24,26,27 The grid consisted of 13 columns and five rows of electrodes (diameter, 1mm; inter-electrode distance, 8mm in each direction), with one missing electrode in the upper left corner. The participant’s thigh hair was removed, and the skin was cleaned with alcohol. The electrode was attached to the skin with a bi-adhesive sheet (KITAD064NM2; OTBioelettronica) after a conductive paste (Elefix Z-181BE; NIHON KOHDEN, Tokyo, Japan) was applied. The center of the electrode grid was positioned at the center of the line between the superior lateral edge of the patella and the greater trochanter protuberance. The columns of the electrode grid were placed parallel to the longitudinal axis of the VL muscle. A reference electrode was attached at the anterior superior iliac spine.23,24,26,27 All procedures were performed by the same investigator.\n\nMonopolar multi-channel surface EMG signals (64 channels) were amplified by a factor of 1000, sampled at 2048 Hz, and digitized by a 12-bit analog-to-digital converter (EMG-USB2+, OTBioelettronica). The recorded monopolar signals were off-line bandpass filtered (10-500 Hz) and transferred to analysis software (MTALAB 2019a, MathWorks GK, MA, USA). Bipolar multi-channel SEMG signals (n = 59) along the columns were obtained from the 64 electrodes. The EMG signals were divided in epochs of one second centered at each 10% of MVC force increment from 10% to 80% of the MVC ramp-contraction to calculate the root mean square (RMS).24 Since the selected ramp rate was 10% of the MVC force per second, one epoch of the sampled signal was overlapped by 0.5 seconds between neighboring torque levels. We normalized the RMS estimates to the values obtained pre-intervention for each torque level.\n\nTo characterize the heterogeneity in the multi-channel SEMG spatial distribution pattern at each epoch, we determined the modified entropy and correlation coefficients. The modified entropy of the spatial distribution of the ΔSEMG amplitude was calculated over a 1-s epoch taken at 10% to 80% of the MVC during the ramp-up contraction. According to methods published by Farina et al., modified entropy was defined as the entropy of the signal power as follows:11\n\nwhere p(i) is the square of the RMS value of channel i divided by the sum of the squares of all 59 RMS values at the given contraction level. Therefore, p(i)2 represents the normalized power of each channel. Modified entropy is the normalized power of the EMG signal across the array and reflects the heterogeneity in the muscle activity. The CoV of the RMS was defined as the quotient of the SD of the Δ59 RMS measurements and the average of Δ59 RMS measurements at each given torque level.24 Both a decrease in modified entropy and an increase in CoV of RMS indicate increased heterogeneity in the multi-channel SEMG spatial distribution pattern within the electrode grid.12,18 Measures of the CoV of the RMS and modified entropy provide insight into how the nervous system regulates muscle activation across the muscle irrespective of the magnitude.28\n\nThe patient performed two types of gait training separated by a period of one month between training to avoid training effect.\n\nHAL gait training\n\nThe patient performed gait training using the HAL for 33 minutes (gait distance about 2200 m). The double leg type HAL was used for gait training, which was performed with two physical therapists for the operation of the HAL commands and support of the patient. During HAL gait training, a walking hoist (ALL IN ONE walking hoist, ROPOX, Denmark) was used to prevent falls and adjust the patient’s posture.\n\nTreadmill gait training\n\nThe patient performed gait training using the treadmill for 33 minutes (gait speed 4.0 km/h, gait distance about 2200 m). During gait training, Alter-G (Alter-G, Inc., Fremont, CA, USA) was used to prevent falls and adjust the patient’s posture without providing weight bearing and clinician’s support to leg movements.\n\n\nResults\n\nAs a neuromuscular activation assessment, multi-channel SEMG was performed on the patient before and after both gait training. Figure 1 illustrates the representative multi-channel SEMG amplitude color maps for treadmill and HAL gait training. We normalized the CoV of force and RMS estimates to the values obtained pre-intervention for each torque level. Differences were observed in the multi-channel SEMG spatial distribution pattern at each contraction torque between HAL and treadmill gait training. There was a greater decrease ΔCoV force with the HAL gait training than for treadmill gait training (Figure 2A). The increase in the magnitude of muscle activation from pre-intervention to post-intervention was greater for HAL gait training than for treadmill gait training (Figure 2B). The CoV of the RMS and modified entropy at each torque in both gait trainings are shown in Figure 3. For HAL training, both the CoV of the RMS were higher and the modified entropy was lower as compared to treadmill gait training (Figure 2C and D). No adverse events were observed with either intervention. He did not experience worsening of the symptoms during each gait training.\n\n(upper panel) treadmill gait training, (lower panel) HAL gait training. Differences in the multi-channel surface electromyography spatial distribution patterns at each torque level were observed between the treadmill and HAL gait training in these representative data.\n\nThe Δ coefficient of variation (CoV) of force (A), Δ root mean square (B), CoV of RMS (C), and modified entropy (D) of the treadmill gait training and HAL gait training.\n\n\nDiscussion\n\nWe applied multichannel SEMG as a neuromuscular activation assessment of HAL training. In addition to the overall increase in EMG activity, the HAL gait training resulted in decrease force fluctuation, and greater heterogeneity in spatial muscle distribution pattern from pre-intervention to post-intervention than for the treadmill gait training.\n\nWe used two parameters to quantify the multi-channel SEMG spatial distribution pattern: modified entropy and the CoV of the RMS. A decrease in the modified entropy and an increase in the CoV of the RMS are consistent with increased heterogeneity in the multi-channel SEMG spatial distribution pattern within the electrode grid.25 The SEMG spatial distribution pattern can be altered by contraction levels or fatigue during isometric contraction.11,12 Measures of the CoV of the RMS and modified entropy provide insight into how the nervous system regulates muscle activation across the muscle irrespective of the magnitude.28 This phenomenon has been explained by spatial heterogeneity in the location of different types of muscle fibers13 and a clustering of muscle fibers innervated by one motor unit in a limited territory,14,15 and a previous study reported that alterations in the multi-channel SEMG spatial distribution pattern can be explained by the physiological phenomenon of motor unit recruitment patterns.17 The results of the present report for the HAL training intervention showed that the CoV of the RMS was higher, and the modified entropy was lower than for treadmill gait training. These findings suggest that spatial motor unit activity patterns were enhanced by HAL training. Changes in the heterogeneity of SEMG were accompanied by a greater decreased in the Δ CoV force for the HAL gait training as compared to the treadmill gait training. This finding suggests that the participant was able to perform the submaximal ramp up task smoothly by altered spatial motor unit activity patterns.\n\nThe HAL gait training offers the possibility to monitor muscle contractions via SEMG at the extensor and flexor muscle region of the lower extremities.5,29 The voluntary drive and normalized motion assistance provided by the external device likely form the foundation for a proprioceptive feedback loop for patients with lesions involving the sensory pathway and not facilitated as well with treadmill training. The neural activity and repeated execution of specific tasks promote learning and lead to the reinstatement or restructuring of appropriate proprioceptive feedback.30,31 Here, we are the first to show that HAL gait training induced an alteration muscle activation patterns due to a single session of HAL training. Moreover, based on our findings, HAL gait training may be more effective in evoking changes in neuromuscular activation than conventional gait training. Future studies will examine the relationship between changes in gait and muscle activation using the HAL intervention across multiple sessions.\n\nThis report has several limitations. First, report included only one patient with spinal muscular atrophy type III. Future large-sample studies and studies of patients with various neurological conditions (e.g., amyotrophic lateral sclerosis, Parkinson’s disease, and stroke) are needed to clearly understand how generalizable the effects of HAL gait training on neuroplasticity. Second, this report only included data following a single session. Future studies will examine how factors such as dose, frequency, and intensity of HAL training affect changes in function and neuromuscular activation.\n\n\nConclusions\n\nThe present case report showed that HAL gait training was more effective in changing metrics of neuromuscular activation of the knee extensors than treadmill gait training despite similar training durations. These data suggest that the modes of gait training which incorporate both voluntary activation and guided movement of the legs may facilitate recovery of function.\n\n\nConsent\n\nWritten informed consent for publication of their clinical details and/or clinical images was obtained from the patient/parent/guardian/relative of the patient.\n\n\nData availability\n\nFigshare: EMG data of VL muscle, https://doi.org/10.6084/m9.figshare.14113178.v1.32\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "References\n\nMizui D, Nakai Y, Okada H, et al.: [A case of spinal and bulbar muscular atrophy with improved walking ability following gait training using the hybrid assistive limb (HAL)]. Rinsho Shinkeigaku. Mar 28 2019; 59(3): 157–159. PubMed Abstract | Publisher Full Text\n\nTanaka H, Nankaku M, Nishikawa T, et al.: A follow-up study of the effect of training using the Hybrid Assistive Limb on Gait ability in chronic stroke patients. Top Stroke Rehabil. Jul 18 2019: 1–6. PubMed Abstract | Publisher Full Text\n\nTanaka H, Nankaku M, Nishikawa T, et al.: Spatiotemporal gait characteristic changes with gait training using the hybrid assistive limb for chronic stroke patients. Gait Posture. Jun 2019; 71: 205–210. PubMed Abstract | Publisher Full Text\n\nOshima O, Kawakami M, Okuyama K, et al.: Effects of hybrid assistive neuromuscular dynamic stimulation therapy for hemiparesis after pediatric stroke: a feasibility trial. Disabil Rehabil. Jul 23 2019: 1–5. PubMed Abstract | Publisher Full Text\n\nKubota S, Nakata Y, Eguchi K, et al.: Feasibility of rehabilitation training with a newly developed wearable robot for patients with limited mobility. Arch Phys Med Rehabil. Jun 2013; 94(6): 1080–1087. PubMed Abstract | Publisher Full Text\n\nSczesny-Kaiser M, Hoffken O, Aach M, et al.: HAL(R) exoskeleton training improves walking parameters and normalizes cortical excitability in primary somatosensory cortex in spinal cord injury patients. J Neuroeng Rehabil. Aug 20 2015; 12: 68. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSczesny-Kaiser M, Trost R, Aach M, et al.: A Randomized and Controlled Crossover Study Investigating the Improvement of Walking and Posture Functions in Chronic Stroke Patients Using HAL Exoskeleton - The HALESTRO Study (HAL-Exoskeleton STROke Study). Front Neurosci. 2019; 13: 259. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFarina D, Holobar A, Merletti R, et al.: Decoding the neural drive to muscles from the surface electromyogram. Clin Neurophysiol. Oct 2010; 121(10): 1616–1623. PubMed Abstract | Publisher Full Text\n\nNegro F, Muceli S, Castronovo AM, et al.: Multi-channel intramuscular and surface EMG decomposition by convolutive blind source separation. J Neural Eng. Apr 2016; 13(2): 026027. PubMed Abstract | Publisher Full Text\n\nMurphy SA, Negro F, Farina D, et al.: Stroke Increases Ischemia-related Decreases in Motor Unit Discharge Rates. J Neurophysiol. Oct 31 2018; PubMed Abstract | Publisher Full Text | Free Full Text\n\nFarina D, Leclerc F, Arendt-Nielsen L, et al.: The change in spatial distribution of upper trapezius muscle activity is correlated to contraction duration. J Electromyogr Kinesiol. Feb 2008; 18(1): 16–25. PubMed Abstract | Publisher Full Text\n\nHoltermann A, Grönlund C, Stefan Karlsson J, et al.: Spatial distribution of active muscle fibre characteristics in the upper trapezius muscle and its dependency on contraction level and duration. J Electromyogr Kinesiol. Jun 2008; 18(3): 372–381. PubMed Abstract | Publisher Full Text\n\nChanaud CM, Macpherson JM: Functionally complex muscles of the cat hindlimb. III. Differential activation within biceps femoris during postural perturbations. Exp Brain Res. 1991; 85(2): 271–280. PubMed Abstract | Publisher Full Text\n\nLexell J, Downham DY: The occurrence of fibre-type grouping in healthy human muscle: a quantitative study of cross-sections of whole vastus lateralis from men between 15 and 83 years. Acta Neuropathol. 1991; 81(4): 377–381. PubMed Abstract | Publisher Full Text\n\nHoltermann A, Roeleveld K, Karlsson JS: Inhomogeneities in muscle activation reveal motor unit recruitment. J Electromyogr Kinesiol. Apr 2005; 15(2): 131–137. PubMed Abstract | Publisher Full Text\n\nHoltermann A, Roeleveld K, Mork PJ, et al.: Selective activation of neuromuscular compartments within the human trapezius muscle. J Electromyogr Kinesiol. Oct 2009; 19(5): 896–902. PubMed Abstract | Publisher Full Text\n\nHoltermann A, Roeleveld K: EMG amplitude distribution changes over the upper trapezius muscle are similar in sustained and ramp contractions. Acta Physiol. Feb 2006; 186(2): 159–168. PubMed Abstract | Publisher Full Text\n\nWatanabe K, Kouzaki M, Moritani T: Spatial EMG potential distribution of biceps brachii muscle during resistance training and detraining. Eur J Appl Physiol. Dec 2015; 115(12): 2661–2670. PubMed Abstract | Publisher Full Text\n\nKolb SJ, Kissel JT: Spinal Muscular Atrophy. Neurol Clin. Nov 2015; 33(4): 831–846. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMercuri E, Finkel RS, Muntoni F, et al.: Diagnosis and management of spinal muscular atrophy: Part 1: Recommendations for diagnosis, rehabilitation, orthopedic and nutritional care. Neuromuscul Disord. Feb 2018; 28(2): 103–115. PubMed Abstract | Publisher Full Text\n\nHirasawa Y, Hasegawa T, Matsushita K, et al.: Isometric knee extension torque in healthy subjects. Rigaku ryoho Janaru. 2004; 38(4): 330–333 in Japansese. Publisher Full Text\n\nHalliday SJ, Wang L, Yu C, et al.: Six-minute walk distance in healthy young adults. Respir Med. Apr-May 2020; 165: 105933. PubMed Abstract | Publisher Full Text | Free Full Text\n\nNishikawa Y, Watanabe K, Kawade S, et al.: The effect of a portable electrical muscle stimulation device at home on muscle strength and activation patterns in locomotive syndrome patients: A randomized control trial. J Electromyogr Kinesiol. Apr 2019; 45: 46–52. PubMed Abstract | Publisher Full Text\n\nNishikawa Y, Watanabe K, Takahashi T, et al.: Spatial electromyography distribution pattern of the vastus lateralis muscle during ramp up contractions in Parkinson's disease patients. J Electromyogr Kinesiol. Oct 19 2017; 37: 125–131. PubMed Abstract | Publisher Full Text\n\nWatanabe K, Kouzaki M, Merletti R, et al.: Spatial EMG potential distribution pattern of vastus lateralis muscle during isometric knee extension in young and elderly men. J Electromyogr Kinesiol. Feb 2012; 22(1): 74–79. PubMed Abstract | Publisher Full Text\n\nNishikawa Y, Watanabe K, Takahashi T, et al.: Sex differences in variances of multi-channel surface electromyography distribution of the vastus lateralis muscle during isometric knee extension in young adults. Eur J Appl Physiol. Mar 2017; 117(3): 583–589. PubMed Abstract | Publisher Full Text\n\nWatanabe K, Miyamoto T, Tanaka Y, et al.: Type 2 diabetes mellitus patients manifest characteristic spatial EMG potential distribution pattern during sustained isometric contraction. Diabetes Res Clin Pract. Sep 2012; 97(3): 468–473. PubMed Abstract | Publisher Full Text\n\nHyngstrom AS, Murphy SA, Nguyen J, et al.: Ischemic conditioning increases strength and volitional activation of paretic muscle in chronic stroke: a pilot study. J Appl Physiol (1985). May 1 2018; 124(5): 1140–1147. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAach M, Cruciger O, Sczesny-Kaiser M, et al.: Voluntary driven exoskeleton as a new tool for rehabilitation in chronic spinal cord injury: a pilot study. Spine J. Dec 1 2014; 14(12): 2847–2853. PubMed Abstract | Publisher Full Text\n\nKrakauer JW: Motor learning: its relevance to stroke recovery and neurorehabilitation. Curr Opin Neurol. Feb 2006; 19(1): 84–90. PubMed Abstract | Publisher Full Text\n\nNielsen JB: How we walk: central control of muscle activity during human walking. Neuroscientist. Jun 2003; 9(3): 195–204. PubMed Abstract | Publisher Full Text\n\nNishikawa Y: EMG data of VL muscle. figshare. Dataset. 2021. Publisher Full Text"
}
|
[
{
"id": "83012",
"date": "27 Apr 2021",
"name": "Redha Taiar",
"expertise": [
"Reviewer Expertise biomechanics",
"health disease and rehabilitation"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe objective of this study was to quantify the effects of HAL gait training on spatial muscle activity patterns in a patient with SMA type III using multi-channel surface electromyography (SEMG). The authors support in conclusion the notion that HAL gait training has a positive benefit on motor output not only in the magnitude of SEMG generated but also the patterns of neural activation.\nThe approach of the study appears very original and the contents of the manuscript are quite interesting by his methodology and through the tools of quantification used.\nThe manuscript reads smoothly and is easy to understand. The aims, scope, and results of the study are clearly stated. I have very much enjoyed reading this paper. I find it interesting and clearly written, and satisfying also all the other publication criteria of the “F1000Research”. The study provides a very valuable addition to this line of research, and adds relevantly to the subject with additional original findings. I thus find that this paper definitively delivers results that will surely be of interest to the readership of the “F1000Research”. I recommend the publication of this interesting paper after more details concerning the Ethical Committee “All procedures were performed in accordance with the Declaration of Helsinki and were approved by the Hiroshima University’s Committee on Ethics in Research (approval Number No. E-53). Our institution does not require ethical approval for reporting individual cases or case series”. The details are not clear and must be re writting. For instance \"Our institution does not require ethical approval for reporting individual cases or case series” what I recommend to the authors to delete.\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": "6627",
"date": "21 May 2021",
"name": "Yuichi Nishikawa",
"role": "Author Response",
"response": "Dear Prof. Redha Taiar, Thank you for reviewing this paper and helpful comments. We have removed the bellow sentence. \"Our institution does not require ethical approval for reporting individual cases or case series”"
}
]
}
] | 1
|
https://f1000research.com/articles/10-214
|
https://f1000research.com/articles/9-902/v1
|
04 Aug 20
|
{
"type": "Research Article",
"title": "Determinants of retention strategies and sustainable performance of academic staff of government-owned universities in Nigeria",
"authors": [
"Odunayo Salau",
"Rowland Worlu",
"Adewale Osibanjo",
"Anthonia Adeniji",
"Tolulope Atolagbe",
"Jumoke Salau",
"Rowland Worlu",
"Adewale Osibanjo",
"Anthonia Adeniji",
"Tolulope Atolagbe",
"Jumoke Salau"
],
"abstract": "Background: Retention of academic staff is gaining the attention of various educational stakeholders in many developing countries like Nigeria. However, there is little extant literature on how various determinants and risk factors affect retention strategies and sustainable performance of academic staff of government owned universities in Nigeria. Consequently, this paper showed the direct relationships between retention strategies and sustainable performance. Methods: Copies of the designed questionnaire were distributed to members of the academic staff ranging from the Professors to Graduate Assistants of the selected state-owned Universities in Southern Nigeria. Statistical analysis for the study included descriptive measures, measurement and structural models. Results: The determinants of retention strategies had significant impacts on the sustainable performance of academic staff at r = 0.660 (p < 0.05) and r = 0.558 (p < 0.05), respectively. A direct relationship was also established between academic retention and sustainable performance of staff in the selected universities (r = 0.187, p < 0.05). This implies that the 48.3% variance in sustainable performance is explained by the level of determinants/risk factors and retention of academic staff in the selected universities. Conclusions: The study concludes that adequate funding provides Nigerian universities with the opportunity to meet the needs of the growing population and to match other top universities elsewhere in the development of vital highly skilled manpower, research and innovations, which are the tools for sustainable performance.",
"keywords": [
"Determinants",
"Risk factors",
"retention",
"sustainable performance",
"Education",
"Universities"
],
"content": "Introduction\n\nGlobally, the role of teachers in the University system is recognized as crucial in realizing academic goals designed to advance learning and overall quality of university education. Teachers are pivotal to the running of an effective and efficient university academic process and central to driving teaching and learning improvements in universities. The right representation of teachers in the university system in both quantity and quality is a sine qua non for instituting quality and standards in the university system1–4.\n\nUniversities in Africa, through their traditional remits in education, research and innovation, have a major role to play in enabling the continent to achieve these noble objectives5. The Nigerian university system, being the largest and best established in the continent, should assume leadership in propelling the continent to these great heights6–8. The early decades of the Nigerian university system were characterized by impressive achievements. Graduates from the system were reputed, nationally and globally for skills that lifted them high up on the relevance scale9–11. Research output from the system was adjudged to be amongst the most impactful in solving national, regional and global challenges facing the society12. While there have been spurts of growth which sustained these achievements, a general decline in quality still pervades the system which may ultimately inhibit the delivery of Africa's Vision 2063 and addressing global Sustainable Development Goals. Several variables are implicated in explaining declining quality13,14.\n\nThese factors have also impacted the development of human capacity at multiple levels, which has developed at an uneven pace15, often determined by the level of funding and innovation available to individual institutions16. Over time, a comprehension gap has also set in between those who run tertiary institutions and the modernity of technology17. This gap in many cases has created a vacuum in the championing of innovative ICT deployment that would have undoubtedly driven advancements in science and technology18,19. This may imply that the leaderships of tertiary institutions have not been adequately motivated to champion technological innovations and create exposure for modern learning and knowledge sharing tools.\n\nFacilities such as classrooms, lecture theatres, laboratories, workshops, and employee offices are far from being optimal. Though incremental changes are being made through Tertiary Education Trust Fund (TETFund) action, facilities are still over-stretched and badly managed in many universities20,21. Hostel services are increasingly declining, the classes are overcrowded with poor infrastructure22, the low quality and quantity of lecturers23, a lack of laboratory and experimental materials24, financial constraints and weak governance25. Added to all these human failings, the environment in many of the universities in Nigeria is unfavorable25 and not conducive to good curriculum delivery, or indeed, any form of teaching and learning26. Students are overcrowded in rooms with some hanging on to windows where ventilation is poor27, or flock around shades in the open. Electricity, enabling comfort, skills acquisition or laboratory work, is often absent, public address systems inadequate and digital technology to assist with knowledge transfer and interactive sessions - internet access, smart boards - absent in many institutions26.\n\nExtant literature has also shown that the efforts and commitments of government at all levels to reverse the decline has been worrisome. It has been observed that academic staff in Nigerian state universities have not featured among the top 500 scholars in various fields across the world. Importantly, the UNESCO indicated a minimum of 26% budgetary allocation to education, while the highest in Nigeria from 1990 till date has been 14%. This may probably be the reasons for the ranking status of Nigerian state universities in the global league table26. It is in this respect that the urgency of sustainable performance among academic staff must be viewed. This paper therefore examined the determinants and risk factors on the retention strategies and sustainable performance of academic staff of government owned universities in Nigeria. Consequently, this paper developed the following three hypotheses:\n\nH1: Determinants and risk factors significantly influence academic staff retention\n\nH2: Determinants and risk factors significantly influence sustainable performance of Universities\n\nH3: Academic retention significantly influences sustainable performance of selected universities\n\n\nMethods\n\nThis study adopted the descriptive research design, which combines quantitative and qualitative stages28. The adopted descriptive survey research facilitated detailed and credible assessment of the relationship among the determinants and risk factors, retention strategies and sustainable performance of academic staff. The adopted descriptive design made use of survey method based on the impracticability of studying the entire large population of universities in Nigeria. In essence, the survey method enabled the researcher to make inferences that are applicable to the entire population, based on Khong (2005) assertion that survey research is an appropriate method to generalize from a sample to a population.\n\nThe study population for this study comprised 2759 academic staff of the six selected state Universities operating in Southern Nigeria. The government-owned universities were selected based on their performance and heightened global ranking29. The sample size for this research work was determined using Krejcie and Morgan (1970) Sample Size Determinant Table. On the Krejcie and Morgan Table, the population of 2,759 at 95% confidence level falls within 1st row/ 9th column, therefore 338 as recommended on the table was achieved. However, because of the large number of respondents from the selected universities and efforts to ensure adequate sample size representation, the initial 338 sample size was increased by 18% to arrive at 400. The sample size was calculated and distributed based on proportionate ratio or proportional affixation criterion (PAC).\n\nThis study employed the use of primary sources of data via administration of a questionnaire to the members of the academic staff (respondents) ranging from the Professors to Graduate Assistants. The questionnaire adopted a four-scale Likert format to capture the exact level of consideration and responses to the probing item. Represented thus: 1 = Strongly Disagree (SD); 2 = Disagree (D); 3= Agree (A); and 4= Strongly Agree (SA). The use of this scale in quantitative research enabled numerical representation and management of observations with the objective of clarifying and relating the mindsets signified by the observations. By standard, the Likert scale posits that the weight accorded experience by anybody is linear and is graduated from strongly agree to strongly disagree with additional postulation that attitudes are measurable26. Another key importance of Likert scale adoption in the realization of the objective of this study is that the assignment of numeric value to qualitative responses from questionnaire allows subjection of the responses to descriptive and inferential statistics.\n\nThe questionnaire was divided into sections A to D was used to gather data regarding the effect of determinants and risk factors on the retention strategies and sustainable performance of academic staff of government owned universities (see Extended data for a blank copy of the questionnaire (Salau et al., 2020)). Section A deals with demographic data of the respondents while section B captures research data for determinants and risk factors. Section C covered items on retention of academic staff; while section D focused on how to achieve sustainable performance. The items in the questionnaire were adapted from previous works in similar subject areas and modified. Items for determinants and risk factors were adopted from NUC Blueprints (2015), Okebukonla (2015) and Salau (2017). Retention strategies items were adopted and adapted from previous studies10,11,25,26. Sustainable performance items were adapted from the following works16–20.\n\nThe research instrument and data were subjected to reliability and validity test, while the data was analysed with various applicable statistical tools. To test the internal consistency and homogeneity of the items in the measures of the constructs for this study, the Cronbach’s alpha, composite reliability and average variance extracted coefficients (AVE) were used30. In the overall, the Mean Cronbach’s alpha of all constructs measuring retention strategies and sustainable performance affirmed that the constructs were reliable. This was so having scaled the set minimum value of 0.70 that was necessary to indicate that the instrument was both internally consistent and reliable\n\nTrained research assistants were employed via referral and email to support the researcher in the distribution and collection of the research instruments. The selection criteria ensured that field assistants reside in the state of the universities being sampled and the reason was basically for convenience. Participants were also made to understand the items in the research questionnaire, the procedures needed for effective administration, their administration selection, how to pick participants and the possible obstacles participants could face. Email and phone calls were made to follow up on respondents’ timely feedbacks.\n\nThe collected data were properly coded, transformed and analysed using structural variance-based model. For this reason, the datasets31 attached to this research were analysed at the university level, model level and combined, using partial least square – structural equation modelling (SEM) technique for data analysis. Smart Partial Least Square (SEM-PLS, version 3) software was used for the analysis, because this tool can be used for theory testing in early stages28,32,33.\n\nThe principal investigator submitted the survey questionnaire to the Business Management Research Ethics Committee for ethical approval. This was approved on May 16, 2019 with approval number by BMREC 19/22/217). A letter of introduction was given to the research team which was presented to selected government-owned universities stating the purpose of the research. The significance of this study was properly indicated. Our paper complied with the ethical principles as stipulated by the Covenant University Business Management ethics committee requirements in the process of data collection and their analysis. Of importance is that the authors made it a point of duty to guarantee that the data gathered were treated as anonymous and confidential. The participants in the study were all well informed of their free choice to partake or refuse, hence this gave them more confidence to express their consent. Ethical issues such as the right of respondents to privacy and free-will were envisaged while the potential risks of possible physical harm, and unanticipated measures were provided for. The self- esteems of the selected academic staff were respected, while the essence of the work was disclosed to them ahead of their responses. Above all, discreetness was applied in the presentation of data and reports of the study.\n\nIt is equally imperative to note that verbal consent was gotten from the selected respondents (academic staff) of this research. The establishment departments of the selected government-owned universities were consulted for research permission guidelines. Based on the information provided in principle, an application letter was written requesting permission to research their institutions with the objective of the study clearly stated. Also, the research ethics approval form was attached to the application letter. This type of research is categorized as exempt research that involves a survey with no or minimal risk i.e. level 1 research as presented in the Research Ethical Application Form. In the spirit of anonymity and confidentiality, exempt research work in management sciences does not require signed consent from the participants but implied consent is usually enough. By verbal consent, the researchers ensured that the respondents were well informed about the context and purpose of this research, and kept abreast of the participation process.\n\nThe reliability and validity of the construct were evaluated using composite reliability, construct reliability and validity as presented in Table 1. Variance-based structural equation modelling (CB-SEM) was used to explore the causal relationship between the exogenous variable (innovative capability) and the endogenous variable (SME’s performance). The rationale for adopting CB-SEM is because of its ability to estimate complex model as well as its powerful statistical method in testing the relationship between two or more constructs than other statistical methods.\n\nThe composite reliability (CR) was used to check for data reliability. Reliability was achieved when the alpha coefficients are above the threshold value of 0.7 which indicates an acceptable level34. All CR values were above 0.7, suggesting that all indicative objects are accurate and acceptable. Results in Table 1 revealed the reliability test for the constructs.\n\nConstruct validity was used to ensure that the selected factors have the exactness required to measure the desired constructs. The factor loadings were calculated in order to test the convergent validity35. It was recommended that the Average var1ance extracted (AVE) should be greater than 0.5 while the factor loading should also be greater than or equal to 0.5. Results in Table 2 revealed that the AVEs were all above 0.5; hence, according to Fornell and Larcker (1981), they were at an acceptable level. Also, the standardised factor loadings for the retained items ranged from 0.856 to 0.710, which were higher than 0.5 and were all significant at p < 0.05 critical level36.\n\n* p-value < 0.05.\n\n\nResults\n\nA total of 400 copies of the questionnaire were indiscriminately distributed to selected Universities' academic personnel in Southern Nigeria. There were 370 copies of the questionnaire collected, reflecting a response rate of 90%. After the data screening process, 362 respondents were retained for further analysis, while eight copies were discarded because they were not completely filled. Table 3 showed the distribution of biographical data of the respondents in terms of gender, current rank/status, work experience and highest education. Individual-level results from each participant are available as Underlying data (Salau et al., 2020).\n\nResults in Table 1 on demographic characteristics revealed that majority of the respondents were predominantly male (60.2%) and majority of the respondents fall within Lecturer II (representing 45%). Lecturer II are lecturers in higher education without professorial status. In total, 60% academic staff had masters’ degree and 62.4% had below 11 years work experience in their current universities.\n\nThe overall fit of the measurement model was assessed by examining the chi-square statistics value which was 45.987; p < 0.05; degrees of freedom = 51 as well as the absolute and relative indices which were CMIN/DF, GFI, AGFI, CFI, TLI, RMSEA, and SRMR (Usakli & Kucukergin, 2018). The results in Table 4 confirmed that the measurement model generated a satisfactory fit.\n\nGFI: goodness-of-fit index; AGFI: adjusted goodness-of-fit index; CFI: comparative fit index; TLI: Tucker-Lewis index; RMSEA: root mean square error of approximation; SRMR standardized root mean square residual.\n\nIn SEM, the structural model is the inner model. The structural model can be measured using values and significant values of the path coefficients (R2). PLS-SEM was used to analyze the path, because PLS does not need any assumptions about normal distribution. The use of bootstrapping becomes important for determining the significance level (Chin, 2010; Sanchez, 2013). Figure 1–Figure 3 showed the outcomes of the structured model with standardised parameter estimate. The independent variables (determining and risk factors) accounted for approximately (R2 = 0.436; R2 = 0.483) 43.6% and 48.3% of the variance in the academic staff retention (ASR) and sustainable performance (SP) of universities. The path coefficients and structural model results were demonstrated in Figure 1–Figure 3, respectively. The path coefficients for retention strategies and sustainable performance were presented in Table 5, while the summary of hypotheses testing was demonstrated in Table 6.\n\nΒ: beta coefficient; SE: standard error; CR, critical ratio.\n\nThe path coefficient of all constructs indicates significant relationships between retention strategies predictions and sustainable performance in the analysis at 0.05, except. The model indicated statistically significant path co-efficient, specifically, significant relationship was found between determining/risk factors and academic staff retention (β=0.66, p=0.000), determining/risk factors and sustainable performance (β=0.68, p=0.000); and academic staff retention and sustainable performance (β=0.19, p=0.010). Hence, all path coefficients were of practical importance, since they are above 0.05.\n\n\nDiscussions\n\nH1: Determinants and risk factors have significant relationship with academic staff retention\n\nThe first hypothesis tested the relationship between determinants and risk factors and retention of academic staff of selected universities. The result of the test indicated that the determinants and risk factors such as adequacies in facilities for teaching, learning and research, adequate funding, quality of graduates, efficacy of research and postgraduate training, consistent regulation and so on have strong positive impact on academic retention (β=0.66, p=0.000). This implies that a unit change of these factors will lead to increase in academic retention by 66%. This finding that showed significant and direct relationship between the variables is consistent with previous studies (Gberevbie, 2008; Oziengbe & Obhiosa, 2014; Nwagwu, 2015; Kpolovie & Obilor, 2013; Abiodun-Oyebanji, 2011)..\n\nH2: Determinants and risk factors have significant relationship with sustainable performance\n\nThe second hypothesis tested the relationship between determinants and risk factors and sustainable performance of selected universities. However, this result established that the determinants and risk factors such as consistent regulation by NUC and professional bodies, promotion of ICT-driven universities and fostering skills development and entrepreneurship programmes have strong positive impact on sustainable performance of universities. This revealed that sustainable performance of universities are influenced by some determining and risk factors. This finding that showed significant and direct relationships between the variables, consistent with previous studies (Anyim, 2012; Salau, et al, 2018; Adeniji, et al. 2018; Igbinoba, et al, 2019).\n\nH3: Academic staff retention has significant direct relationship with sustainable performance\n\nThis study posited a direct significant relationship between academic staff retention and sustainable performance. The hypothesis was found to be significant (β=0.19, p=0.000) suggesting academic staff retention impact on sustainable performance of selected universities. This implies that a unit change of academic staff retention will lead to increase in sustainable performance of universities by 19%. The current study finding was similar to previous findings (Khalid, Irshad & Mahmood, 2012; Fapohunda, 2012; Okoro, Omeluzor & Bamidele, 2014; Salau, Worlu, Osibanjo, Oludayo & Falola 2018).\n\n\nConclusion\n\nThe study concludes that urgent effort to comprehensively address the dilapidation and inadequacy of teaching and research facilities in all Nigerian universities is required in order to make them globally competitive and better positioned for excellence in teaching, learning and research. However, if adequate funding is provided, Nigerian universities will not only meet the needs of the growing population but can be at par with other top universities elsewhere in the world in the development of vital highly skilled manpower, research and innovations which are the tools for the growth of a great and dynamic economy.\n\n\nRecommendations\n\nBased on the findings and conclusion, the authors proffered the following recommendations:\n\ni. Teaching and learning in the selected universities should be driven by information technology with the support a strong internet access. As a minimum, smart boards should be available, power points, videos, links and other internet based educational approaches should be used to deliver curricula.\n\nii. There is a need for continuous and focused pedagogical training of lecturers in the Nigerian University system (NUS) to re-orient them towards the modalities of outcome-based and student-centred teaching/learning. In this paradigm, students are encouraged to take more responsibility for their own learning as they take an active part on knowledge construction.\n\niii. Since rigid departmental arrangements make it harder for teachers and learners to explore fringe ideas, interdepartmental and cross disciplinary programmes and curricula should be encouraged in which disciplines learn from one another's perspective and design courses that are suited to industry needs, lend themselves to entrepreneurship as well as the solution of common problems.\n\niv. The accreditation instrument of the NUC should be improved to ensure that the curriculum of every programme that is being assessed for accreditation at least meets some of a number of nationally defined priorities.\n\nv. Finally, there is need for improvement in the physical facilities in universities to support proper delivery of curricula. These should include adequate classrooms with seating arrangements, clean water supply, regular electricity and adequate, clean conveniences to support an environment that is conducive for teaching and learning.\n\n\nData availability\n\nFigshare: Datasets on Retention Strategies and Sustainable Performance. https://doi.org/10.6084/m9.figshare.12624410.v2 (Salau et al., 2020).\n\nThis project contains the following underlying data:\n\nSurvey datasets Retention and Sustainable Performance (SAV). (Responses to each questionnaire item from each study participant.)\n\nCSV for Manuscript 25011 (CSV). (As above, but in open CSV format.)\n\nFigshare: Datasets on Retention Strategies and Sustainable Performance. https://doi.org/10.6084/m9.figshare.12624410.v2 (Salau et al., 2020).\n\nFile ‘Questionniare for Manuscript 25011’ (DOCX) contains a blank copy of the questionnaire given to each participant.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "References\n\nAdeniji A, Osibanjo A: Human resource management: Theory and practice. Lagos, Pumark Nigeria Limited. 2012. Reference Source\n\nIgbinoba E, Salau O, Falola H, et al.: Workplace Conflict Management and Administrative Productivity of Staff of Selected ICT Driven Public Universities. International Journal of Mechanical Engineering and Technology. 2019; 10(3): 133–143. Reference Source\n\nSalau O, Worlu R, Osibanjo A, et al.: Survey data on work environments and productivity of academic staff of selected public universities in Nigeria. Data Brief. 2018; 19: 1912–1917. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSalau OP, Worlu R, Osibanjo AO, et al.: The impact of work environments on retention outcomes of academic staff of state universities in Southern Nigeria. Sage Open. 2018; 2: 1–16.\n\nStatisense.2019; Retrieved on the 10th of October, 2019.\n\nUsakli A, Kucukergin GK: Using partial least squares structural equation modeling in hospitality and tourism: Do researchers follow practical guidelines? International Journal of Contemporary Hospitality Management. 2018; 30(11): 3462–3512. Publisher Full Text\n\nIsrael GD: Determining Sample Size. Institute of Food and Agricultural Sciences (IFAS), University of Florida, PEOD-6, 2013; 1–5. Reference Source\n\nKhalid S, Irshad MZ, Mahmood B: Job satisfaction among academic staff: A comparative analysis between public and private sector universities of Punjab, Pakistan. International Journal of Business & Management. 2012; 7(1): 126–136. Publisher Full Text\n\nKpolovie PJ, Obilor IE: Adequacy-Inadequacy: Education funding in Nigeria. Universal Journal of Education and General Studies. 2013; 2(8): 239–254.\n\nAdeniji AA: Organizational Climate And Job Satisfaction Among Academic Staff in Some Selected Private Universities in Southwest Nigeria. (Unpublished PhD Thesis). Department of Business Management, Covenant University, Ogun, Nigeria. 2011.\n\nAdeniji A, Salau O, Awe K, et al.: Survey datasets on organisational climate and job satisfaction among academic staff in some selected private universities in Southwest Nigeria. Data Brief. 2018; 19: 1688–1693. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAnyim AP: Challenges and prospects in Nigeria’s university education. 2012; Retrieved on June 30, 2013. Reference Source\n\nFapohunda TM: Pay disparity and pay satisfaction in public and private universities in Nigeria. European Scientific Journal. 2012; 8(28): 100–109.\n\nFatile JO, Adejuwon KD: Conflict and conflict management in tertiary institutions: the case of Nigerian universities. European Journal of Humanities and Social Sciences. 2011; 7(1): 77–87. Reference Source\n\nFornell C, Larcker D: Evaluating Structural Equation Models with Unobservable Variables and Measurement Error. Journal of Marketing Research. 1981; 18(1): 39–50. Publisher Full Text\n\nGberevbie DE: Staff recruitment, retention strategies and performance of selected public and private organisations in Nigeria. (Unpublished Ph.D Thesis). Department of Political Sciences, Covenant University, Ogun, Nigeria. 2008. Publisher Full Text\n\nHair JF, Babin BJ, Krey N: Covariance-Based Structural Equation Modeling in the Journal of Advertising: Review and Recommendations. Journal of Advertising. 2017; 46(1): 163–177. Publisher Full Text\n\nAbdulkareem AY, Oyeniran S: Managing the performance of Nigerian universities for sustainable development using data environment analysis. Ilorin Journal of Sociology. 2011; 3(1): 37–50.\n\nAbdulsalam D, Mawoli MA: Motivation and job performance of the academic staff of state universities in Nigeria: the case of Ibrahim Badamasi Babangida University, Lapai, Niger State. International Journal of Business & Management. 2012; 7(14): 142–148. Reference Source\n\nAbiodun-Oyebanji O: Towards effective management of university education in Nigeria. Journal of Emerging Trends in Educational Research and Policy Studies (JETERAPS). 2011; 2(6): 526–530. Reference Source\n\nAdekitan AI, Salau O: The impact of engineering students' performance in the first three years on their graduation result using educational data mining. Heliyon. 2019; 5(2): e01250. PubMed Abstract | Publisher Full Text | Free Full Text\n\nIbidunni OS, Osibanjo AO, Adeniji AA, et al.: Talent Retention and Organizational Performance: A Competitive Positioning In the Nigerian Banking Sector. Periodica Polytechnica Social and Management Sciences. 2016; 24(1): 1–13. Publisher Full Text\n\nIbrahim A, Usman B, Bagudu M: Employee turnover and its effects on organisational productivity of state-owned institutions in Niger state: An impediment to achieving vision 20: 2020 in Niger state. Journal of Business and Organisational Development. 2013; 5(2): 1–8.\n\nNUC: 2015; Retrieved on the 22nd of May, 2016.\n\nNwagwu NA: One hundred years of Education in Nigeria: developmental challenges, achievements and prospects. African Journal of Studies in Education. 2015; 10(1): 41–68.\n\nOkebukola PA: Quality assurance mechanisms and academic mobility in Anglophone Countries: Case study of Nigeria. Paper presented at the capacity building workshop on the License-Master-Doctorate (LMD) reform held at Universite Gaston Berger, Saint Louis, Senegal September 19–20. 2008.\n\nFatuzzo C: Top Universities in Nigeria. 2017. Reference Source\n\nOkoro CC, Omeluzor SU, Bamidele IA: Effect of brain drain (human capital flight) of librarians on service delivery in some selected Nigerian universities. SAGE Open. 2014; 1–11. Publisher Full Text\n\nSalau O, Worlu R, Osibanjo A, et al.: The Impact of Workplace Environments on Retention Outcomes of Public Universities in Southern Nigeria. Sage Open. 2020; 10(2): 1–20. Publisher Full Text\n\nHair JF, Hult GT, Ringle C, et al.: A primer on partial least squares structural equation modeling (PLS-SEM). Sage, Thousand Oak. 2013. Reference Source\n\nSalau O, Worlu R, Osibanjo A, et al.: Datasets on Retention Strategies and Sustainable Performance. figshare. Dataset. 2020. http://www.doi.org/10.6084/m9.figshare.12624410.v2\n\nOziengbe SA, Obhiosa OB: An empirical investigation of the functionality of Nigeria’s tertiary education system. JORIND. 2014; 12(1): 16. Reference Source\n\nSalau OP, Worlu REK, Osibanjo AO, et al.: Survey data on work environments and productivity of academic staff of selected public universities in Nigeria. Data Brief. 2018; 19: 1912–1917. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSalau OP, Worlu R, Osibanjo AO, et al.: The impact of work environments on retention outcomes of academic staff of state universities in Southern Nigeria. Sage Open. 2018; 2: 1–16.\n\nHoyle RH: Structural equation modeling for social and personality psychology. Sage, London. 2011. Reference Source\n\nUsakli A, Kucukergin GK: Using partial least squares structural equation modeling in hospitality and tourism: Do researchers follow practical guidelines? International Journal of Contemporary Hospitality Management. 2018; 30(11): 3462–3512. Publisher Full Text"
}
|
[
{
"id": "68626",
"date": "03 Sep 2020",
"name": "Regis Rugira Marie Modeste",
"expertise": [
"Reviewer Expertise Nursing Research",
"Nursing Education",
"HIV"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe paper is well written, ethical clearance was obtained. the paper explores the relationship between retention strategies and sustainable performance among academic staff at universities in Nigeria. The main weakness was noted in the discussion, where an interpretation of results is given, followed by an indication that the results are consistent with previous studies. That section needs to be expanded with further discussion to provide the narrative from the authors. The referencing style in the text needs to be adhered to consistently. On page 3, reference needs to be added for the 2nd and 3rd sentences in the paragraph just before the hypothesis. Under the methodology section, it s indicated that the design combines quantitative and qualitative stages. The authors are requested to clarify that as the presented work does not include any qualitative data. Under the population section, authors are requested to review and correct the grammar. For example, in the first sentence, remove the first 'study' and add 'of' for the section to read as: \"The population for this study comprised of 2759 academic ...\" For clarity, it will be useful to specify the total number of universities in the region and indicate that six universities were selected out of so many. It is indicated that \"The government-owned universities were selected based on their performance and heightened global ranking\" the performance and ranking need to be further explained for clarity what were the performance level considered for inclusion in the study? For the second paragraph under result, correct that the demographic variables are in table 3, not table 1. For a paper that would be relevant for an international audience, clarify what lecturer 1 and lecturer 2 mean, and that will enhance the understanding. Reference No 5 and 24 seem incomplete.\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": [
{
"c_id": "6061",
"date": "21 May 2021",
"name": "Odunayo Salau",
"role": "Author Response",
"response": "Dear Editor and Reviewer, I humbly appreciate the constructive comments and insights given by the reviewer. 1. The main weakness was noted in the discussion, and this has been looked into and duly corrected. 2. The referencing style in the text has been consistently adhered to. 3. On page 3, reference needs to be added for the 2nd and 3rd sentences in the paragraph just before the hypothesis. This has been taken care of. 4. Under the methodology section, it s indicated that the design combines quantitative and qualitative stages. The authors are requested to clarify that as the presented work does not include any qualitative data. The paper is specifically quantitative. This has been corrected accordingly. 5. Under the population section, authors are requested to review and correct the grammar. For example, in the first sentence, remove the first 'study' and add 'of' for the section to read as: \"The population for this study comprised of 2759 academic ...\" This has been corrected. 6. For clarity, it will be useful to specify the total number of universities in the region and indicate that six universities were selected out of so many. There are 19 state universities in Nigeria as at February 2020. Out of the 19 state universities, only six state universities were selected based on their performance and heightened global recognition 7. It is indicated that \"The government-owned universities were selected based on their performance and heightened global ranking\" the performance and ranking need to be further explained for clarity what was the performance level considered for inclusion in the study? This has been corrected with strong justifications. Importantly, Universities are globally recognised and ranked by several indicators of academic or research performance, including alumni and staff winning Nobel Prizes and Fields Medals, highly cited researchers, papers published in Nature and Science, papers indexed in major citation indices, and the per capita academic performance of an institution 8. For the second paragraph under result, correct that the demographic variables are in table 3, not table 1. Thank you. That was an oversight. It has been changed to Table 3. 9. For a paper that would be relevant for an international audience, clarify what lecturer 1 and lecturer 2 mean, and that will enhance the understanding. This has been clarified. Lecturers 1 and II are lecturers with a Doctorate in higher education and without professorial status. 10. Reference No 5 and 24 seem incomplete. Once, again, I will like to appreciate the reviewer for these constructive comments and observations. Thank you."
}
]
},
{
"id": "76692",
"date": "08 Feb 2021",
"name": "Eniola Sokefun",
"expertise": [
"Reviewer Expertise HUMAN RESOURCE 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 sample cannot include Graduate Assistants, as the Nigerian University System no longer engages them for teaching. The minimum entry level is Assistant Lecturer.\n\nThe population of the study and sampling technique is not adequately discussed. A table of academic staff in these universities should be presented. It is also important for researchers to present how the 400 questionnaires are distributed among the six universities.\n\nResearchers need to reconfirm Figure 2759, representing academic staff in the six universities selected.\n\nResearchers should present the names of the State-Owned Universities selected and how questionnaires were allocated to each university. The global ranking of these universities as stated in the work needs to be presented.\n\nCurrent literature on Employee Retention and Sustainable Performance should be reviewed.\n\nSources of Data should be provided under each table.\n\nConclusion should be derived from the research.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? No\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": [
{
"c_id": "6453",
"date": "16 Mar 2021",
"name": "Odunayo Salau",
"role": "Author Response",
"response": "Response to ISSUES RAISED I sincerely want to appreciate the critiques given by the reviewer. I can say that all the critiques are relevant. Thank you. Basically, we have some institutions with Graduate Assistants. Graduate assistant positions usually fall under the categories of teaching assistants or research assistants, as they often help university faculty members prepare course materials, post grades, and conduct research. The population of the study and sampling technique will be adequately discussed. A table of academic staff in these universities will be presented. The researchers also presented how 400 copies of the questionnaire were distributed among the six universities. The population of academic staff (i.e. 2759), representing academic staff in the six universities selected has been re-confirmed. Presenting the names of the State-Owned Universities selected may be unethical. How the copies of the questionnaire were allocated to each university were also discussed. The link that precedes the global ranking of these universities as stated in the work was presented. Current literature on Employee Retention and Sustainable Performance has been reviewed. Sources of Data have been provided under each table. The conclusion has been worked on to reflect the major findings."
}
]
}
] | 1
|
https://f1000research.com/articles/9-902
|
https://f1000research.com/articles/10-408/v1
|
20 May 21
|
{
"type": "Clinical Practice Article",
"title": "Autologous stromal vascular fraction cells combined with platelet-rich plasma for androgenic alopecia treatment: a case series",
"authors": [
"Fonny Josh",
"Tomie Hermawan Soekamto",
"Muhammad Faruk",
"Tomie Hermawan Soekamto",
"Muhammad Faruk"
],
"abstract": "Background: Stromal vascular fraction cells (SVFs), which can be produced using a mechanical or digestive enzymatic process, are heterogeneous cells with the potential to grow hair in androgenic alopecia patients. Platelet-rich plasma (PRP) is an autologous cell source that is widely used to treat androgenic alopecia. However, the combined use of PRP and SVFs to treat alopecia is rarely reported. Case presentation: This case series describes three cases of androgenic alopecia, including a32-year-old male, a 43-year-old male, and a 65-year-old male. Androgenic alopecia in these patients was treated by injecting the bald area of the scalp with local autologous PRP combined with SVFs. Follow-up was performed 1–3 months after treatment, which showed good results. The hair grew denser, with increased thickness for each strand. The hair pull test revealed that the hair remained intact. Conclusion: The combination of PRP and SVFs affected all cycles of the hair growth process. SVFs are multipotent cells with the potential to become antioxidant, anti-inflammatory, or anti-fibrotic cells. SVFs can regenerate cells that secrete the growth factors, that are essential for angiogenesis, which can improve therapeutic outcomes. This case series will enrich the existing literature by expanding available treatment options for androgenic alopecia.",
"keywords": [
"Androgenic alopecia",
"Stem cell therapy",
"Stromal vascular fraction cells",
"Platelet-rich plasma."
],
"content": "Introduction\n\nAndrogenic alopecia, also known as androgenetic alopecia, male pattern baldness, and common baldness, represents a common form of hair loss that affects both men and women.1 Although the incidence rate of androgenic alopecia is 50% higher in men than in women, approximately 13% of premenopausal women suffer from androgenic alopecia, and the incidence increases significantly after menopause.2 In men, androgenic alopecia is typically hereditary and is strongly associated with low androgen hormone levels. A genetic process that links the 3q26 locus with the X chromosome can result in the development of androgenic alopecia in women.3 The accelerated conversion of testosterone to its derivate dihydrotestosterone (DHT) can also cause androgenic alopecia. This conversion of testosterone to DHT typically begins soon after the end of puberty, at approximately 20 years of age. DHT induces the production of a type II enzyme called 5-α reductase. Hair follicles that are exposed to DHT become weak and incapable of growing healthy hair strands, resulting in a shorter anagen phase, a more prolonged telogen phase, and hair follicle shrinkage.4 Although androgenic alopecia appears to be a mild condition, patients with an androgenic alopecia can become unhappy with their appearance, resulting in anxiety, depression, and reduced self-confidence.\n\nPlatelet-rich plasma (PRP) refers to concentrated platelets in a small plasma volume, which typically contains at least six essential growth factors, including platelet-derived growth factor (PDGF), basic fibroblast growth factor (bFGF), epidermal growth factor (EGF), vascular endothelial growth factor (VEGF), insulin-like growth factor-1 (IGF-1), and transforming growth factor-β (TGF-β). Platelet activation can stimulate the release of these growth factors. Studies have demonstrated the positive effects of PRP on undifferentiated stem cells, promoting angiogenesis and proliferation, and the stimulation of both undifferentiated and differentiated stem cells with PRP can promote cell regeneration.5‐7\n\nAdipose cells contain multipotent progenitor cells, which are capable of self-renewal and differentiation into several different cell types. Adipose-derived stem cells (ADSCs) are stem cells obtained from fat and have been widely used to accelerate the wound-healing process and promote cell regeneration.8 However, the processing necessary to obtain ADSCs can be complex. ADSCs require a good fat harvesting method, a suitable isolation procedure, and an appropriate culturing process, which all require access to excellent laboratory facilities. Stromal vascular fraction cells (SVFs) are a non-expanded version of ADSCs that contain several heterogeneous cell types, including hematopoietic stem cells, endothelial progenitor cells, and ADSCs, which allow for SVFs to differentiating into several cell types.9,10 Although the interactions between SVFs and PRP remain unclear, several experiments have explored the effects of combining these treatments. The combinations of SVFs and PRP in cultured medium has demonstrated vigorous proliferation activity compared with that in basal medium.11 The collection of SVFs utilizes simpler fat harvesting and isolation processes compared with the collection of ADSCs. For example, SVFs do not require a culturing process, and because SVFs contain ADSCs, SVFs retain a multipotent characteristic and the ability to secrete several growth factors.\n\nIn this case series, we describe the combined use of PRP with SVFs to support hair regeneration in three patients, with the aim of supplying a larger population of growth factors than can be found in either PRP or SVFs alone. SVFs were used to treat androgenic alopecia due to the following considerations: the enhanced accessibility of SVFs compared with ADSCs; the similar multipotent potential between SVFs and ADSCs; and the ease of obtaining SVFs using the laboratory facilities available at Hasanuddin University Medical Research Center (HUMRC), Hasanuddin University, Makassar, Indonesia, where the patients were treated. Because ADSCs only comprise 10% of SVFs, PRP can be used to stimulate the proliferation of both undifferentiated and differentiated stem cells to promote cell regeneration.7 This case series is reported in line with the Surgical Case Report Guidelines (SCARE Guidelines) published in 2020.12\n\n\nTreatment\n\nSVFs were prepared autologously from fat tissue that was collected from the abdominal area of each patient using liposuction. The liposuction procedure was performed by plastic surgeons and medical residents in an operating room at Wahidin Sudirohusodo Hospital, Makassar, Indonesia. A total of 200 grams of fat (Figure 1A) were obtained and cleaned with phosphate-buffered saline (PBS, Gibco-BRL, Grand Island, NY, USA). The fat was minced using scissors until a smooth consistency was obtained. The minced fat was transferred to a 50-cc tube, 0.15% collagenase (Wako, Osaka, Japan) was added and the tube was incubated in a water bath shaker with shaking at 37°C for 30 minutes. Next, we added control medium, consisting of Dulbecco’s modified Eagle medium (DMEM) (Gibco-BRL), containing 10% autologous human serum (see below) and 1% antibiotic-antimitotic (Sigma-Aldrich, St Louis, USA), to neutralize collagenase activity. The sample was centrifuged at 1,500 rpm for 5 minutes, and the pelleted cells were resuspended in sterile water (Figure 1B). Finally, the SVFs were counted using trypan blue staining (Gibco-BRL) and a Neubauer counting chamber.13\n\nSVFs, stromal vascular fraction cells; PRP, platelet-rich plasma.\n\nA total of 30cc autologous whole blood samples were obtained from the patients’ median cubital vein using an 18-gauge needle and placed into a 50-cc tube. The tube was frozen at 4°C. We centrifuged the blood samples at 2,500 rpm for 10 minutes and transferred the serum to a 15-cc tube. The serum was inactivated by heating to 56°C for 30 minutes.14\n\nA total of 20cc of blood was obtained from the patient’s vein and collected in a tube containing ethylenediaminetetraacetic acid (EDTA). First, we centrifuged the tube for 10 minutes at 2,400 rpm (450 × g), to collect the supernatant plasma with the buffy coat (Figure 1C). The plasma with buffy coat was centrifuged again at 3,600 rpm (850 × g) for 15 minutes to concentrate the platelets. The top of an 18-gauge long cannula was guided to the bottom of the plasma to gently aspirate the infranatant plasma containing the buffy coat which was used to generate the PRP end product.15 PRPs were activated through the addition of 10% CaCl2 (Merck, Germany) for a maximum of 10 minutes before use.\n\nSVFs pellets containing 2 × 107 cells were added to 5 cc PRP and mixed by pipetting (Figure 1D) before being transferred to a1-cc Eppendorf tube and activated with 0.5 cc 10% CaCl2 (Merck, Germany). A 100 μl volume containing the SVF and PRP mixture was injected into the patient’s scalp at every 1 cm2 over the bald area. An application of antibiotic ointment was applied to the area after the treatment, and no hair supplement medication was applied afterward. The treatment procedures were performed by plastic surgeons. On day three after treatment, the patient’s hair was washed with water and allowed to dry without the use of any other chemicals. After day 7, the patients were allowed to wash their hair as usual followed by air drying.\n\n\nCase series\n\nAll of the cases described here were administered only one round of injections using the SVFs and PRP combination. Due to this being a standard treatment in our institution, we did not require ethical approval; all three patients signed informed consent forms to participate in the procedures, including liposuction, blood harvesting, injection therapy, and the use of their data and pictures for scientific publications.\n\nA 32-year-old Buginese man presented with hair thinning consistent with the typical pattern of androgenic alopecia, describing onset five years ago in the vertex and temporal areas (Figure 2A). A history of the same complaint was noted for the patient’s father and brother. The patient was the only member of his family to experience baldness at a young age (30 years). The hair loss began to worsen one year prior to presentation. The patient is the third child of four sibling. The patient had no history of alcohol consumption or cigarette use and no history of cardiac disease, diabetes mellitus, or any other degenerative disease. The patient tried several hair tonic treatments (not prescribed) to resolve the problem, with no satisfactory results.\n\nA) Before treatment. B) One month after treatment.\n\nThe patient was diagnosed with androgenic alopecia Norwood Hamilton type IIIa of the vertex, based on the clinical appearance.16 The patient was treated with the local injection of combined PRP and SVFs. At one month of follow-up, the patient displayed thick and substantial hair growth. According to the patient’s self-report, additional hair loss was minimal (Figure 2B).\n\nA healthy 43-year-old Javanese man suffered from hair thinning in the vertex and temporal areas of the scalp that started eight years prior to presentation. No history of the same complaint was noted for his father or his three brothers, but the patient’s uncle suffered from alopecia. The patient had no history of alcohol consumption, but the patient was a previous smoker who had stopped smoking five years prior to presentation. The patient had visited a beauty clinic to treat the hair loss, but this treatment showed no results. The beauty clinic provided the patient with a shampoo, a hair growth tonic, and oral minoxidil therapy at daily dose of 2.5 mg for six weeks. The patient stopped treatment after six weeks because hair growth was apparent on the hands, feet, chest, and chin but not the scalp, and the patient continued to experience hair thinning and hair loss on the scalp.\n\nThe patient was diagnosed with androgenic alopecia Norwood Hamilton type IIIa of the vertex, based on clinical appearance (Figure 3A).16 The patient was treated with the local injection of combined PRP and SVFs. After one month of follow-up, the patient’s hair was beginning to grow, with a denser hair follicle (Figure 3B). Three months after the treatment, the hair grew significantly, although the hair at the injection area grew darker than hair that grew in other areas (Figure 3C).\n\nA) Before treatment. B) One month after treatment. C) Three months after treatment.\n\nA 65-year-old Buginese man suffered from thinning hair with onset 30 years ago in the vertex, temporal, and occipital areas of the scalp (Figure 4A). No similar issue was reported in his family. The patient never consumed any alcohol or smoked cigarettes. The patient maintained a healthy lifestyle and engaged in regular cycling in the mornings. The patient had no history of hypertension, diabetes mellitus, cardiac disease, or any other degenerative disease, and the patient reported never using any medications for hair loss.\n\nA) Before treatment. B) One month after treatment; C) Two months after treatment.\n\nThe patient was diagnosed with androgenic alopecia, Norwood Hamilton type IVa in the vertex, temporal, and occipital areas based on clinical appearance. The patient was treated with the local injection of combined PRP and SVFs in bald areas of the scalp. After one month of follow up, new hair started to grow densely. After three months of follow-up, the patient showed increased hair thickness on each strand, denser hair, and the hair-pull test revealed that the hair remained intact (Figure 4B and 4C).\n\n\nDiscussion\n\nTypical hair growth cycles are divided into three phases: anagen (active phase of hair follicle growth which lasts approximately 2–6 years); catagen (transition phase, lasting approximately 2–3 weeks); and telogen resting phase (lasting approximately three months). Hair growth patterns change during androgenic alopecia, associated with a shorter anagen phase and a prolonged telogen phase, which changes the anagen to telogen ratio from 12:1 to 5:1, resulting in more hair follicles in the telogen phase at any given time. Hair loss is promoted under these conditions eventually resulting in the development of baldness.17\n\nAndrogenic alopecia treatment remains challenging for many doctors. PRP has been widely used to treat androgenic alopecia, but several PRP injection sessions are required for effective treatment and more severe baldness requires more PRP injection sessions, with shorter intervals between sessions to prevent hair loss. The patient’s age can also influence the necessity for PRP injection repetitions and may affect the growth factors produced by PRP.\n\nSVFs are a mix of heterogeneous cells that consist of ADSCs, hematopoietic stem cells, progenitor cells, pericytes, and other differentiated cells (such as fibroblasts, macrophages, endothelial cells [ECs], and preadipocytes). SVFs contain essential factors for angiogenesis, including endothelial progenitor cells (EPCs) and ECs. Approximately 7% to 30% of EPCs and ECs secrete growth factors, including VEGF, PDGF subunit B (PDGF-BB), and bFGF. The secretion of the growth factors from SVFs, such as VEGF, HGF, IGF-1, and TGF-β1, can directly contribute to angiogenesis through the paracrine effect.18\n\nAccording to Trueb, androgen receptors and the microinflammation of the hair follicle can cause androgenic alopecia. The production of reactive oxygen species and reactive nitrogen species due to chemical stress can induce pro-inflammatory cytokine secretion, resulting in the development of a microinflammatory environment at the hair follicle. Inflammation can affect the hair follicle and the surrounding area, resulting in the development of perifollicular fibrosis, hair stem cell apoptosis, the shrinkage of the hair follicle, and the thinning of the scalp. The prolonged scalp thinning process makes the skin appear shiny. DHT reduces the production of IGF-1 and stem cell factor, resulting in hair stem cell apoptosis, vellus hair transformation, and permanent hair loss.4 The combination of PRP and SVFs affects all cycles of hair growth. An experiment demonstrated that SVFs had regenerative abilities, reduced the secretion of pro-inflammatory cytokines (such as Interleukin [IL-6] and tumor necrosis factor [TNF-α]), increased the production of the anti-inflammatory cytokine IL-10, and increased the proportion of the M2 macrophage phenotype.19 Treatment with SVFs has been shown to eliminate the microinflammatory process at the hair follicle. The thickening of the scalp’s hair may be caused by the differentiation of the ADSCs that can be found in SVFs. ADSCs have anti-fibrotic abilities because they can reduce the production of the fibrotic agent TGF-β1, reducing permanent hair loss by improving perifollicular fibrosis.20 The IGF-1 found in PRP plays a vital regulatory role in hair growth cycles and hair cell differentiation and inhibits the apoptosis pathway involved in hair follicle regeneration. In this case series, the treatment applied to all three patients resulted in hair that grew denser, with reduced hair loss during the hair pull test assessment. The new hair grew darker than normal hair, which may be due to the effects on melanocytes, which are involved in hair pigmentation, induced by the local injection of the PRP and SVF combination.4\n\nSVFs stimulate the angiogenesis process increasing the blood supply to the hair follicle by inducing VEGF secretion. The addition of PRP to SVFs, improves the angiogenesis process, resulting in denser hair growth and larger hair follicles.\n\nIn our patients, the therapeutic mixture was injected directly into the scalp of the bald area, allowing the components to act immediately at the alopecia site. We minimized the use of xenogeneic-based product consumption and prevented the transmission of diseases from animals or the possibility of anaphylactic reactions by replacing the fetal bovine serum in the controlled medium with autologous human serum. The injections of the PRP and SVF combination must be performed in less than 10 minutes because the combination can transform into a gel if delayed for longer than 10 minutes, which can complicate the injection process.\n\nThe patient’s age and alopecia duration could affect the therapeutic efficacy. In our patients, the younger patients had denser and thicker hair growth. In Case 1, the effects of the injection therapy were visible within 1 month, which may be due to the patient’s young age (32 years), and the duration of alopecia which only 5 years, unlike the conditions associated with Case 3. Although the hair growth in case 1 and 3 both produced satisfactory results that were almost similar to normal hair growth, Case 1 demonstrated a better effect than Case 3, which may be due to the older age (65 years) and longer disease duration (30 years) associated with Case 3. In addition, the production of growth factors and the multipotent abilities of ADSCs derived from Case 3 may have been diminished compared with those for Case 1 due to the patient’s older age.\n\nWe hope that the combined use of PRP and SVFs in alopecia can reduce the necessity for repeated injections and reduced the frequency of treatments to just one injection. This study requires more extended and continuous observations to determine the long-term therapeutic effects, which appear to promote the anagen phase of hair follicles and reduce the telogen phase duration.\n\n\nConclusion\n\nThe combination treatment with PRP and SVFs appeared to affect all cycles of hair growth. SVFs are multipotent cells that has the effects of antioxidant, anti-inflammatory, and anti-fibrotic. SVFs regenerate cells and secrete essential growth factors that are necessary for angiogenesis in the scalp. The combined effects induced by SVFs and PRP treatments provide excellent promise for the treatment of androgenic alopecia. Younger patients with shorter alopecia durations appeared to display better results. The use of all autologous materials is promising for the treatment of other types of alopecia, including alopecia areata.\n\n\nConsent\n\nWritten informed consent for publication of their clinical details and/or clinical images was obtained from the patients.\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\nMeidan VM, Touitou E: Treatments for androgenetic alopecia and alopecia areata: current options and future prospects. Drugs. 2001; 61(1): 53–69. PubMed Abstract | Publisher Full Text\n\nNyholt DR: Basis of male pattern baldness. J Invest Dermatol. 2003; 121(6): 1561–1564. PubMed Abstract | Publisher Full Text\n\nRathnayake D, Sinclair R: Male androgenetic alopecia. Expert Opin Pharmacother. 2010; 11(8): 1295–1304. PubMed Abstract | Publisher Full Text\n\nTrüeb R: Molecular mechanisms of androgenetic alopecia. Exp Gerontol. 2002; 37: 981–990. PubMed Abstract | Publisher Full Text\n\nSmith MA, Wells RS: Male-type alopecia, alopecia areata, and normal hair in women; Family Histories. Arch Dermatol. 1964; 89: 95–98. Epub 1964/01/01. PubMed Abstract | Publisher Full Text\n\nEppley BL, Pietrzak WS, Blanton M: Platelet-rich plasma: a review of biology and applications in plastic surgery. Plast Reconstr. Surg. 2006; 118: 147e–159e. PubMed Abstract | Publisher Full Text\n\nHausman GJ, Richardson RL: Adipose tissue angiogenesis1,2. J. Anim. Sci. 2004; 82: 925–934. PubMed Abstract | Publisher Full Text\n\nZuk P, Zhu M, Ashjian P, et al.: Human adipose tissue is a source of multipotent stem cells. Mol Biol Cell. 2002; 13(12): 4279–4295. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChoi J, Minn KW, Chang H: The efficacy and safety of platelet-rich plasma and adipose-derived stem cells: an update. Arch Plast Surg. 2012; 39: 585–592. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDarinskas A, Paskevicius M, Apanavicius G, et al.: Stromal vascular fraction cells for the treatment.2017.\n\nRigotti G, Marchi A, Sbarbati A: Adipose-derived mesenchymal stem cells: past, present, and future. Aesthetic Plast Surg. 2009; PubMed Abstract | Publisher Full Text\n\nAgha RA, Franchi T, Sohrabi C, et al.: The SCARE 2020 Guideline: Updating Consensus Surgical CAse REport (SCARE) Guidelines. Int J Surg. 2020. PubMed Abstract | Publisher Full Text\n\nJosh F, Kobe K, Tobita M, et al.: Accelerated and safe proliferation of human adipose-derived stem cells in medium supplemented with human serum. J Nippon Med Sch. 2012; 79(6): 444–452. PubMed Abstract | Publisher Full Text\n\nJosh F, Tobita M, Tanaka R, et al.: Concentration of PDGF_AB, BB and TGF-B1 as valuable human serum parameters in adipose-derived stem cells proliferation. J Nippon Med Sch. 2013; 80(2): 140–147. PubMed Abstract | Publisher Full Text\n\nTajima S, Tobita M, Orbay H, et al.: Direct and indirect effects of a combination of adipose-derived stem cells and platelet-rich plasma on bone regeneration. Tissue Eng Part A. 2014; 0(0): 1–11. PubMed Abstract | Publisher Full Text\n\nGupta M, Mysore V: Classifications of Patterned Hair Loss: A Review. J Cutan Aesthet Surg. 2016; 9(1): 1–10. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChin Gan D, Sinclair R: Androgenetic alopecia. Third Edition: Men’s Health;2009; 352–367. Publisher Full Text\n\nGentile P, Scioli MG, Bielli A, et al.: Concise Review: The Use of Adipose-Derived Stromal Vascular Fraction Cells and Platelet Rich Plasma in Regenerative Plastic Surgery. Stem Cells. 2017; 35: 117–134. PubMed Abstract | Publisher Full Text\n\nKotani T, Masutani R, Suzuka T, et al.: Anti-inflammatory and anti-fibrotic effects of intravenous adipose-derived stem cell transplantation in a mouse model of bleomycin-induced interstitial pneumonia. Sci Rep. 2017; 7: 1–10. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBorovikova AA, Ziegler ME, Banyard DE, et al.: Adipose-Derived tissue in the Treatment of Dermal Fibrosis: Antifibrotic Effects of Adipose-Derived Stem Cells (Review). Ann Plast Surg. 2018 Mar; 80(3): 297–307. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "86430",
"date": "04 Jun 2021",
"name": "Hiroshi Mizuno",
"expertise": [
"Reviewer Expertise Adipose-derived stem cells",
"stromal vascular fraction",
"wound healing"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 described the positive effect of the combination therapy with autologous stromal vascular fraction cells (SVFs) and platelet-rich plasma (PRP) for androgenic alopecia, which is understandable. However, the follow-up periods of all three cases are less than three months. The authors are requested to explain any speculation about the long-term results.\nIn addition, the authors are requested to explain whether such clinical results were obtained due to merely cumulative effect or synergistic effect of SVFs and PRP.\nAs the authors described, the combination use of both SVFs and PRP for androgenic alopecia may not be published elsewhere, which is of major significance.\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? Partly\n\nIs the conclusion balanced and justified on the basis of the findings? Yes",
"responses": []
},
{
"id": "86914",
"date": "13 Jul 2021",
"name": "Dewi Sukmawati",
"expertise": [
"Reviewer Expertise Histology",
"Stem Cells",
"Angiogenesis",
"Endothelial Progenitor Cells"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 case series is interesting and will potentially be a benefit for patients with alopecia. The authors clearly described the advantages of each component, the stromal vascular fraction cells (SVFs) and platelet-rich plasma (PRP), for alopecia, and claimed their novelty by combining both components, which gives the important result.\n\nAlthough it showed promise, however, the current supporting data were the pictures that the authors only descriptively explained. Thus, to provide a reliable result, it is suggested to the authors to add the details to support the countable results. This may include:\nThe objective measures, such as the hair density, hair diameter, or hair shaft thickness of the terminal follicle.\n\nThe subjective assessment of hair growth, such as patient’s self-assessment using a questionnaire or scoring.\n\nA similar observation time. The three cases were not all observed within three months (Case 1 = one month, Case 2 = three months, and Case 3 = 2 months). The authors should re-check the inconsistency between the text and the figure’s caption.\nA sufficiently long duration of follow-up should also be done to facilitate accurate assessment of clinical improvement in measures such as hair counts/density, hair thickness, patient’s subjective assessments, and overall alopecia, as well as evidence of relapse. Several studies perform further follow-up, such as within 6-12 months.\nIn addition, since there is no control for SVFs or PRP only, the authors should further explain the possible mechanism, whether the beneficial clinical effect was due to the accumulative effect, potentiates or synergistic effect of both SVFs and PRP.\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? 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 conclusion balanced and justified on the basis of the findings? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-408
|
https://f1000research.com/articles/10-407/v1
|
20 May 21
|
{
"type": "Case Report",
"title": "Case Report: Diabetic urinary auto-brewery and review of literature",
"authors": [
"Abdulrahman A. Alduraywish"
],
"abstract": "Background: Although candiduria is an expected encounter and should not be surprising in uncontrolled diabetes with glucose-enriched urine, urinary auto-brewery is rarely thought of by diabetologists. Moreover, endogenous ethanol production in humans from gut microbiome, urinary tract fungi and bacteria, and intermediary metabolism, has been reported for a long time, particularly in diabetics. Case description: To alert physicians to the overlooked implication of endogenously produced ethanol both as a biomarker for poor control of diabetes and as a complicating factor, we report this case of an elderly male smoker alcohol-abstinent insulin-dependent Type 2 diabetic patient. Because of circumstantial treatment and incompliance for one week, he developed endogenously produced alcohol intoxication. We proposed candidal urinary auto-brewery evidence sourced from the case history, urinalysis, and culture/identification tests - without excluding other sources. Fortunately, his diet and glycemic control were fairly controlled and, liver and kidney functions were almost normal. Amphotericin B I/V for five days, insulin, and a fluid therapy regimen greatly improved the case and cleared both the candiduria and ethanol from the urine and blood and the patient regained his base-line normal life.\n\nConclusion: Symptoms of alcohol intoxication should be expected in patients with uncontrolled diabetes that most often correlates with candiduria and/or constipation. These symptoms can be exaggerated in those already suffering a degree of dementia and/or comorbid psychiatric/neurologic affections. Direct wet mount examination of urine under phase contrast microscopy would show the budding yeast cells. Appropriate antifungal, insulin and fluid therapies regained the base-line norms.",
"keywords": [
"Urinary auto-brewery",
"Candiduria",
"Blood ethanol",
"Amphotericin B",
"Type 2 diabetes mellitus"
],
"content": "Introduction\n\nAuto-brewery syndrome, in the setting of little alcohol consumption or teetotalers, is rarely reported probably because of under diagnosis.1,2 High endogenous ethanol production and blood levels, due mainly to a sedentary lifestyle with a high carbohydrate diet and enhanced gut fermentation, is documented in the literature as early as the 1950s.3 Altered microbiome, caused by diet changes, immune dysfunction and other diseases and medications, is a major contributor. Such dybiogenesis is implicated in worsening and/or causation of systemic low-grade inflammation, metabolic endotoxemia, autoimmunity, changes in microbiotal metabolite/enteroendocrine hormonal profile, hyperglycemia, fatty liver, and an expanding list of cardiovascular, gastrointestinal, neurologic, oncologic, metabolic, respiratory and psychiatric disorders.4,5 Of concern, Candida albicans is able to produce 1 mg/hr of ethanol per gram of intestinal content.6 Considering the gut as the source, a minute amount of endogenous ethanol is produced as part of normal digestion. However, significant draft in the microbiome profile towards fermenting yeast (most commonly Saccharomyces and Candida species) and bacteria as pathogens, particularly in patients with co-morbidities, e.g. diabetes mellitus (DM), inherited and acquired reduced liver efficiency and the immune-compromisation with/without underlying gut problems, accumulates measurable alcohol levels in blood and breathe.1-3,7-9 After ingesting a carbohydrate-rich meal, a healthy subject had a measurable level of blood ethanol (physiological-blood ethanol; 0.3 ± 0.41 mg/dL) this becomes 16-folds higher in type 2 DM (T2DM) patients (4.85 ± 3.96 mg/dL). The latter showed levels significantly higher than liver cirrhosis patients (3.45 ± 2.65 mg/dL) that indicate that increased production and/or reduced clearance could be implicated - as proven by a more than 36-fold increase in patients with both DM and liver cirrhosis (10.88 ± 5.36 mg/dL). However, levels did not reach intoxication.8\n\nMost of these studies did not appreciate the other sources of endogenous ethanol; urinary fermentation particularly in the milieu of diabetic hyperglycemic/dyslipidemic/ketotic intermediary metabolism and glycosuria. The known susceptibility of these patients to carriage/infection with the sugar-fermenting Candida species is usually overlooked.10-13 The present case report is a red flag for diabetologists to start appreciating urinary auto-brewery among diabetic patients as a potential complicating factor.\n\n\nCase presentation\n\nAn 85-year-old diabetic male patient, who never drank alcohol, was diagnosed with T2DM 20 years ago; he was managed with diet control and oral hypoglycemics. However, he was shifted to insulin therapy over the last five years to improve glycemic control. He had a long history of renal stone formation. His family gave a history of epilepsy for the past three years, and he was given Levetiracetam 1000 mg for six months that was reduced to 500 mg for six more months. He was then maintained on Gabapentin 400 mg twice daily until now. He is a mild smoker. In the last three years, he experienced marked constipation that could last a few days. In addition, he was always on multi-vitamin, multi-mineral and Cod-liver oil food supplements.\n\nOne week before admission, due to his wife’s sickness (she took care of him) his condition worsened due to a change in diet and therapy incompliance. Initially, he started to experience dizziness and an altered mental state. Then, his condition gradually deteriorated and he had urinary and fecal incontinence, agitation, insulting and threatening others, refusing help, and refusing to shower and change his spoiled clothes. However, they did not give a history of seizure attacks during that period.\n\nAfter one week, his wife recovered and started to take care of him. She noticed that his urine was milky and his mental state significantly deteriorated. On November 2, 2019, the family transferred him to El-Rehab-2 Private Hospital (Assiut, Egypt), where he was admitted to the Department of Internal Medicine. On examination at admission, he was confused, disoriented to time, place and person, dizzy and dehydrated. His vital signs were stable, his weight was 60 kg and height was 170 cm, but no recent weight loss was revealed from his clinical history. Abdominal examination showed mild tenderness over the supra-pubic area, the chest and heart examination was unremarkable. Abdominal ultrasonography of the kidneys, urinary tract and liver was unremarkable. A complete laboratory work up was done including blood and urine ethanol, urinalysis, urine culture and sensitivity. The major finding was hyperglycemia with fair glycemic control as indicated from HbA1c ≤7.6%, high blood and urinary ethanol content (measured by enzymatic colorimetric kit, cat#TBS2090; Tribioscience, Palo Alto, CA, USA – lower detection limit of 0.1 mg/dL). Complete blood count revealed mild normocytic-normochromic anemia with relative/absolute monocytosis (Table 1). The mid-stream fresh sample of urine was cloudy, positive for ethanol (= 580 mg/dL), acidic (pH 5.5), negative for proteins, highly positive for glucose (+++), and mildly positive for ketones (+) and lactate (+) tested by urinary dip strips. The urine showed pus cells (55/HPF) and a few red blood cells (5/HPF). Numerous budding large yeast cells (nearly 1/4 of pus cell size) were easily identified upon direct examination of a wet mount of the sample sediment between slide and cover on a phase contrast microscope.\n\nData shown are contents of the investigated parameters and their normal reference range/cut-off values. CV = coefficient of variation from the mean, and, SD = standard deviation from the mean.\n\nCulture of the fresh mid-stream urine sample on Sabouraud Dextrose Agar at 37 °C for 24 hours revealed Candida sp. colonies. Subculturing, to ensure purity and optimal growth, with chloramphenicol, confirmed the presence of large white, round, curved, soft and smooth to wrinkle colonies with a characteristic yeast odor (Figure 1A). Examination of air-dried fixed smears stained with Gram's stain under a light microscope using 100× oil immersion objective showed gram positive budding yeast cells indicative of Candida albicans that was confirmed by positive germ tube formation by germ tube test (Figure 1B). Briefly, one colony was emulsified in human serum and incubated at 37 °C for two hours. Five or more germ tubes (short and aseptate germinating hyphae)/HPF were observed in a wet mount preparation. Disk diffusion antifungal susceptibility testing was conducted using C. albicans ATCC 90028 as a standard control strain. An inoculum from a 48-hour old culture with ~1 – 5 × 106 CFU/mL was plated on the dry surface of Mueller-Hinton agar supplemented with 2% glucose and 0.5 μg/mL methylene blue. After 3–5 minutes, the antifungal disks for Fluconazole (25 μg), Itraconazole (8 μg), Nystatin (100 U), and Amphotericin B (10 μg) were applied with gentle pressure (Rev.7/03.12.2012; Liofilchem® S.r.l., Italy). After 24 hours of aerobic incubation at 35 °C, the diameter of the growth inhibition zone was manually measured for comparison of the antifungal sensitivity that turned highest with Itraconazole followed by Nystatin, Amphotericin B then the least effective was Fluconazole (Figure 1C).\n\nB) Positive germ tube formation in human serum confirmed the diagnosis of Candida albicans. C) Antifungal sensitivity assay on Mueller-Hinton agar for Fluconazole (Flu; 25 μg), Itraconazole (ITC; 8 μg), Nystatin (NY; 100 U), and Amphotericin B (AMB; 10 μg) showed strongest inhibition with Itraconazole.\n\nInsulin Glargine 40 IU SC daily with Insulin Aspart SC six hourly was administered with dose adjustment according to sliding scale, along with normal saline (0.9%) I/V infused. I/V antifungal, Amphotericin B (Fungizone), 40 mg/day for five days as a five hour I/V infusion was administered.\n\nAt the end of the five day treatment period, these interventions led to rapid improvement in the short-term glycemic control marker and the patient regained his consciousness, was cooperative and oriented to time and place. Furthermore, his urine became normal, free from the yeast and no more ethanol was detectable in the urine or blood.\n\n\nDiscussion\n\nTraditional auto-brewery syndrome is linked to gut fermentation but urinary auto-brewery cases have been rarely reported.14,15 The latter author reported a postmortem case report. The drunk legal limits of 30–80 mg/dL blood ethanol level vary from country to country and from one profession to another. Endogenous sources of ethanol are gut fermentation and intermediary metabolism, and is cleared by hepatic class I alcoholic dehydrogenase, with a Km value of 5–10 mg, where the healthy liver disposes of 0.1 g/kg body weight/hour.16 Reportedly, physiological levels of blood ethanol in healthy controls have a range of 0.0–39 mg/L.8 In Saudi Arabia, a population-based study was done to measure endogenous blood ethanol level in a representative sample of 1400 abstinent residents using the sensitive headspace gas chromatography/mass spectrophotometry. Results showed a mean ± SD (and range) of 0.14 ± 0.35 (0.00–1.53) mg/dL.17\n\nThe incidence of candidiasis has increased in number over the years and is linked to significant morbidity and mortality in critically ill and immunosuppressed patients. DM is a major risk factor for candiduria. Diabetic patients have an increased propensity to Candida sp. infections due to disease-related immunosuppression, enriching glycosuria and various other physiological alterations.10-13 The rate of candiduria is 10% among T2DM patients, where Candida albicans constituted ~50% of the isolates and non-albicans Candida were more linked to symptomatic candiduria. Nearly, 80% of these T2DM patients had hemoglobin A1c >7%. There were strong positive correlations between candiduria and each of urine acidity (being acidic; 5–6 pH), glycosuria (≥3 pluses) and HbA1c % (>7%); all of them help colonization.18 Indeed, the prevalence of candiduria among T2DM patients varies greatly in the previously published studies, including Middle Eastern ones, and showed a range of 2.7–30%.11,19-22\n\nThe present case was fortunate, as 1) the patient’s liver and kidney functions seemed normal, 2) his long-term glycemic control was fair as HbA1c ≤7.6%, and 3) there is no appreciable Gaptin-ethanol drug interaction. On the contrary, Gaptin may lessen the effects of alcohol intoxication and dependency.23\n\nDespite the notion that diabetes is a risk factor for candiduria, only two case reports14,15 connected the ability of Candida to produce ethanol in vivo and in vitro from the large amount of glucose escaping into the urine in poorly controlled diabetes. However, they did not appreciate the possibility of alcohol absorption through the urinary bladder and urethral epithelium, reporting undetectable blood ethanol levels. The concentration gradient is the only driving force for the free movement of the small polar uncharged ethanol molecules through the cellular membranes and among body compartments. Such alcohol absorption has long been reported to happen during the bladder irrigation for the transurethral resection and vaporization of the prostate using ethanol-containing irrigation fluid; even to an intoxicating level.24-31 Opposite to the gut, venous drainage of the urinary bladder joins general circulation before reaching the liver.32 Therefore, absorbed ethanol circulates to the central nervous system before the subsequent hepatic clearance.\n\nLevels of endogenous ethanol reaching 300 mg/dL in blood and 600 mg/dL in urine was also reported in abstainer T2DM Pakistani patients with random blood sugar of >250 mg/dL and disease duration of more than five years. Although the investigators did not check its presence, they suggested candiduria as the source of ethanol along with the hyperglycemic ketotic intermediary metabolism. Such endogenous ethanol could be a complicating factor for the known neuropathic complication of diabetes.33 Similar results were reported by Liebich's group34-38 investigating ethanol production and excretion in both type 1 DM (T1DM) and T2DM. They reported that T1DM but not T2DM patients excreted significantly more ethanol in urine than healthy control subjects. However, the rate of urinary alcohol did not relate to diabetic peripheral neuropathy in both groups. In their earlier study, increased urinary alcohol was recorded for both T1DM and T2DM (on hypoglycemic drugs or diet control), although it was more significant for those on insulin.\n\nThe presentation and investigations of this case point to urinary ethanol as a major source. Nevertheless, a gut source of blood ethanol cannot be excluded in light of the patient’s reported frequent constipation. Moreover, incompliance with the antipsychotic Gaptin could have participated in the observed intoxication-like psychiatric and awareness deterioration in the week of chaos.\n\n\nConclusion\n\nThe reporting of this elderly case of urinary auto-brewery insulin-dependent T2DM was to alert physicians to an overlooked and a rarely encountered presentation of a poorly controlled case of diabetes. Ethanol endogenously produced by fermentation in the urinary system, and other sources, could bring more chaos to the scenario. A future large survey study could use sensitive breathe alcohol analyzers to scan a large number of diabetic patients followed by correlation with potential candiduria and prognostic factors. Ethanol absorption through the bladder and urethral walls needs further assiduous dissection.\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\nI acknowledge the kind help from Dr. Soheir M. Kasem (Associate Prof., Internal Medicine and Critical Care, Department of Internal Medicine, Faculty of Medicine, Assiut University) and El-Rehab-2 Private Hospital, Assiut, Egypt for profiling the case and reviewing the prepared draft.\n\n\nConsent\n\nThe publication of this report was approved by the local Ethical Committee of El-Rehab-2 Hospital and a written informed consent was signed by the eldest son of the patient who was the legal guardian of him.\n\n\nReferences\n\nMalik F, Wickremesinghe P, Saverimuttu J: Case report and literature review of auto-brewery syndrome: probably an underdiagnosed medical condition. BMJ Open Gastroenterol. 2019; 6(1): e000325. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTameez Ud Din A, Alam F, Tameez-Ud-Din A, et al.: Auto-Brewery Syndrome: A Clinical Dilemma. Cureus. 2020; 12(10): e10983. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCordell BJ, Kanodia A, Miller GK: Case-Control Research Study of Auto-Brewery Syndrome. Glob Adv Health Med. 2019; 8: 2164956119837566. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRosshart SP, Herz J, Vassallo BG, et al.: Laboratory mice born to wild mice have natural microbiota and model human immune responses. Science. 2019; 365(6452): eaaw4361. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMarzullo P, Di Renzo L, Pugliese G, et al.: Obesity Programs of nutrition, Education, Research and Assessment (OPERA) Group. From obesity through gut microbiota to cardiovascular diseases: a dangerous journey. Int J Obes Suppl. 2020; 10(1):35–49. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGeertinger P, Bodenhoff J, Helweg-Larsen K, et al.: Endogenous alcohol production by intestinal fermentation in sudden infant death. Z Rechtsmed. 1982; 89(3):167–72. PubMed Abstract | Publisher Full Text\n\nUshida Y, Talalay P: Sulforaphane accelerates acetaldehyde metabolism by inducing aldehyde dehydrogenases: Relevance to ethanol intolerance. Alcohol Alcohol. 2013; 48(5):526–34. PubMed Abstract | Publisher Full Text\n\nHafez EM, Hamad MA, Fouad M, et al.: Auto-brewery syndrome: Ethanol pseudo-toxicity in diabetic and hepatic patients. Hum Exp Toxicol. 2017; 36(5): 445–50. PubMed Abstract | Publisher Full Text\n\nAkhavan BJ, Ostrosky-Zeichner L, Thomas EJ: Drunk without drinking: A Case of auto-Brewery syndrome. ACG Case Rep J. 2019; 6(9): e00208. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKauffman CA: Diagnosis and management of fungal urinary tract infection. Infect Dis Clin North Am. 2014; 28(1): 61–74. PubMed Abstract | Publisher Full Text\n\nFalahati M, Farahyar S, Akhlaghi L, et al.: Characterization and identification of candiduria due to Candida species in diabetic patients. Curr Med Mycol. 2016; 2(3): 10–4. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRodrigues CF, Rodrigues ME, Henriques M: Candida sp. infections in patients with diabetes mellitus. J Clin Med. 2019; 8(1): 76. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMohd Sazlly Lim S, Sinnollareddy M, Sime FB: Challenges in antifungal therapy in diabetes mellitus. J Clin Med. 2020; 9(9): 2878. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGruszecki AC, Robinson CA, Kloza S, et al.: High urine ethanol and negative blood and vitreous ethanol in a diabetic woman: a case report, retrospective case survey, and review of the literature. Am J Forensic Med Pathos. 2005; 26(1): 96–8. PubMed Abstract | Publisher Full Text\n\nKruckenberg KM, DiMartini AF, Rymer JA, et al.: Urinary auto-brewery syndrome: A case report. Ann Intern Med. 2020; 172(10): 702–4. PubMed Abstract | Publisher Full Text\n\nJones AW: Evidence-based survey of the elimination rates of ethanol from blood with applications in forensic caseworks. Forensic Sci Int. 2010; 200(1-3): 1–20. PubMed Abstract | Publisher Full Text\n\nRagab AR, Al-Mazroua MK, Afify MM, et al.: Endogenous Ethanol Production Levels in Saudi Arabia Residents. J Alcohol Drug Depend. 2015; 3: 211. Publisher Full Text\n\nEsmailzadeh A, Zarrinfar H, Fata A, et al.: High prevalence of candiduria due to non-albicans Candida species among diabetic patients: A matter of concern? J Clin Lab Anal. 2018; 32(4): e22343. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCasqueiro J, Casqueiro J, Alves C: Infections in patients with diabetes mellitus: a review of pathogenesis. Indian J Endocrinol Metab. 2012; 16(Suppl 1): S27–36. PubMed Abstract | Publisher Full Text | Free Full Text\n\nYismaw G, Asrat D, Woldeamanuel Y, et al.: Prevalence of candiduria in diabetic patients attending Gondar University Hospital, Gondar, Ethiopia. Iran J Kidney Dis. 2013; 7(2): 102–7. PubMed Abstract\n\nGeerlings S, Fonseca V, Castro-Diaz D, et al.: Genital and urinary tract infections in diabetes: impact of pharmacologically-induced glucosuria. Diabetes Res Clin Pract. 2014; 103(3): 373–81. PubMed Abstract | Publisher Full Text\n\nNitzan O, Elias M, Chazan B, et al.: Urinary tract infections in patients with type 2 diabetes mellitus: review of prevalence, diagnosis, and management. Diabetes Metab Syndr Obes. 2015; 8: 129–36. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMason BJ, Quello S, Shadan F: Gabapentin for the treatment of alcohol use disorder. Expert Opin Investig Drugs. 2018; 27(1): 113–24. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCummings JM, Parra RO, Boullier JA, et al.: Evaluation of fluid absorption during laser prostatectomy by breath ethanol techniques. J Urol. 1995; 154(6): 2080–2. PubMed Abstract\n\nHahn RG: The use of ethanol to monitor fluid absorption during transurethral resection of the prostate. Scand J Urol Nephrol. 1999; 33(5): 277–83. PubMed Abstract | Publisher Full Text\n\nHjertberg H: The use of ethanol as a marker to detect and quantify the absorption of irrigation fluid during transurethral resection of the prostate. Scand J Urol Nephrol Suppl. 1996; 178: 1–64. PubMed Abstract\n\nShipstone DP, Inman RD, Beacock CJ, et al.: Validation of the ethanol breath test and on-table weighing to measure irrigating fluid absorption during transurethral prostatectomy. BJU Int. 2002; 90(9): 872–5. PubMed Abstract | Publisher Full Text\n\nGray RA, Moores AH, Hehir M, et al.: Transurethral vaporisation of the prostate and irrigating fluid absorption. Anaesthesia. 2003; 58(8): 787–91. PubMed Abstract | Publisher Full Text\n\nCollins JW, Macdermott S, Bradbrook RA, et al.: Is using ethanol-glycine irrigating fluid monitoring and 'good surgical practice' enough to prevent harmful absorption during transurethral resection of the prostate? BJU Int. 2006; 97(6): 1247–51. PubMed Abstract | Publisher Full Text\n\nHermanns T, Grossmann NC, Wettstein MS, et al.: Absorption of irrigation fluid occurs frequently during high power 532 nm laser vaporization of the prostate. J Urol. 2015; 193(1): 211–6. PubMed Abstract | Publisher Full Text\n\nWettstein MS, Poyet C, Grossmann NC, et al.: Absorption of irrigation fluid during XPS™ GreenLight laser vaporization of the prostate: results from a prospective breath ethanol monitoring study. World J Urol. 2016; 34(9): 1261–7. PubMed Abstract | Publisher Full Text\n\nShehata R: Venous drainage of the urinary bladder. Acta Anat (Basel). 1979; 105(1): 61–4. PubMed Abstract | Publisher Full Text\n\nShahzad MS, Bajwa JI, Wattoo JI, et al.: Association patterns of volatile metabolites in urinary excretions among Type-2 Non-Insulin dependent diabetes patients. Adv. Life Sci. 2016; 3(3): 71–4.\n\nLiebich HM, Al-Babbili O, Zlatkis A, et al.: Gas chromatographic and mass-spectrometric detection of low molecular-weight aliphatic alcohols in urine of normal individuals and patients with diabetes mellitus. Clin Chem. 1975a; 21(9): 1294–6. PubMed Abstract\n\nLiebich HM, Al-Babbili O: Gas chromatographic-mass spectrometric study of volatile organic metabolites in urines of patients with diabetes mellitus. J Chromatogr. 1975b; 112: 539–50. Publisher Full Text\n\nLiebich HM: Specific detection of volatile metabolites in urines of normal subjects and patients with diabetes mellitus using computerized mass fragmentography. J Chromatogr. 1975c; 112: 551–7. PubMed Abstract | Publisher Full Text\n\nLiebich HM, Buelow HJ, Kallmayer R: Quantification of endogenous aliphatic alcohols in serum and urine. J Chromatogr. 1982; 239: 343–9. PubMed Abstract | Publisher Full Text\n\nKrönert K, Künzel M, Reutter B, et al.: Urinary excretion patterns of endogenously produced alcohols in type 1 (IDDM) and type 2 (NIDDM) diabetes mellitus compared with healthy control subjects. Diabetes Res Clin Pract. 1990; 10(2): 161–5. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "85773",
"date": "09 Jun 2021",
"name": "Tarek Abdulraoof Salem",
"expertise": [
"Reviewer Expertise Endocrinology and immunology"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe submitted report describes the production of endogenous ethanol by fermentation in the urinary system of an 85-year-old uncontrolled diabetic patient. Auto-brewery syndrome, in the setting of little alcohol consumption or teetotalers, is rarely reported probably because of under diagnosis. High endogenous ethanol production and blood levels, due mainly to a sedentary lifestyle with a high carbohydrate diet and enhanced gut fermentation has been reported. This report is to alert physicians to an overlooked and a rarely encountered presentation of a poorly controlled case of diabetes.\nIt is well-constructed and has good originality. The author covered all clinical and laboratory aspects of the case in a good manner. Most of details related to the case were mentioned and discussed. The only concern is how the author cooperated with the Egyptian team to get the details of that case?\nI recommend accepting this case report for publishing in the journal.\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": "122175",
"date": "28 Feb 2022",
"name": "Abdel-Naser Elzouki",
"expertise": [
"Reviewer Expertise Metabolic diseases including diabetes",
"NAFLD",
"NASH and related conditions in the field of diabetes and liver diseases. Also in anticoagulation and VTE."
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe author is reporting a rare case of elderly patient known to have insulin-dependent type 2 diabetes with urinary auto-brewery syndrome treated effectively with antifungal therapy.\nThe report is well written and the figures are clear and supporting the findings and diagnosis.\n\nThis case is of important clinical impact and open the line for future studies in large cohort of diabetic patients to study in details this association.\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/10-407
|
https://f1000research.com/articles/10-406/v1
|
20 May 21
|
{
"type": "Case Report",
"title": "Case Report: Acute presentation of autoimmune hepatitis in a male patient",
"authors": [
"Aya Hammami",
"Khouloud Ben Abdessalem",
"Sarra Mestiri",
"Nour Elleuch",
"Wafa Dahmani",
"Wafa Ben Ameur",
"Mehdi Ksiaa",
"Aida Ben Slama",
"Salem Ajmi",
"Ahlem Braham",
"Hanen Jaziri",
"Ali Jmaa",
"Khouloud Ben Abdessalem",
"Sarra Mestiri",
"Nour Elleuch",
"Wafa Dahmani",
"Wafa Ben Ameur",
"Mehdi Ksiaa",
"Aida Ben Slama",
"Salem Ajmi",
"Ahlem Braham",
"Hanen Jaziri",
"Ali Jmaa"
],
"abstract": "Introduction: Autoimmune hepatitis (AIH) is one of the major immune mediated chronic liver diseases. It typically affects young and middle-aged females. Acute liver failure (ALF) is an unusual initial form of presentation of AIH and is particularly rare in male patients. Consequently, the clinical characteristics and optimal management of this entity remain poorly defined. Patients with AIH sometimes present features of the spectrum of primary biliary cholangitis (PBC), simultaneously or consecutively, suggesting the diagnosis of overlap syndrome (OS) PBC- AIH. Data concerning PBC-AIH has been scarcely published and mainly comprises small retrospective studies. Case presentation: Herein, we report the case of a 40-year-old man with no history of any chronic liver disease, who presented with ALF. After carrying out extensive etiological screening, we suspected him of having ALF due to auto-immune liver disease namely AIH. The positivity of anti-mitochondrial antibody (AMA) which is a significant serologic marker of PBC, suggested a diagnosis of OS PBC- AIH. Since urgent liver transplantation could not be performed in our country (Tunisia), the only available therapeutic option was the administration of corticosteroids. During the two years of follow up and treatment with ursodeoxycholic acid, azathioprine and a low dose of prednisolone, our patient is still asymptomatic with normal hepatic function tests. Conclusion: ALF due to AIH in a male patient is a very rare condition. The diagnosis should be considered in all patients with acute hepatitis of undetermined etiology. Corticosteroids were an effective and lifesaving therapeutic option. The association of AIH and PBC features could suggest an OS.",
"keywords": [
"Case Report",
"Biliary",
"Hepatitis",
"Autoimmune",
"Steroids"
],
"content": "Introduction\n\nAutoimmune hepatitis (AIH) is a major immune-mediated and female-dominant chronic liver disease.1,2 The association of primary biliary cholangitis (PBC) and AIH, known as overlap syndrome (OS) is a rare condition. The diagnosis of OS is generally complex and difficult to establish. It is usually defined by the presence of at least two of the three recognized biochemical, serological, and histological criteria of each disease.3 A new scoring classification has been proposed for the diagnosis of OS, with a high sensitivity and specificity, where the cut-off score is 21.4\n\nClinical manifestations of AIH are varied; however, the majority of patients present with a subclinical or chronic disease.5 The development of acute liver failure (ALF) during the initial presentation of AIH alone is uncommon.6 Few cases of ALF have been reported in relation to PBC- AIH OS,3,7 but no cases have been reported which relate to PBC alone. There are very limited published data on AIH presenting with ALF in male patients.8,9\n\nHerein, we report a case of acute presentation of AIH with features of PBC, suggesting PBC-AIH OS, in a male patient with no previously known liver disease. The patient was successfully treated with corticosteroids and ursodeoxycholic acid.\n\n\nCase report\n\nA 40-year-old male Caucasian patient, working as a salesman, was admitted to our department with the diagnosis of ALF. He had a two-week history of jaundice, dark urine, nausea, poor appetite, and pruritus that had worsened over the previous two days. His past medical history was unremarkable. There was no history of excessive alcohol or any hepatotoxic drug consumption. His family history was negative for liver diseases and autoimmune disorders.\n\nOn admission, the patient’s vital signs were stable. The body temperature was 37.4°C, pulse rate was 80 beats/minute, blood pressure was 110/70 mmHg, and jaundice was present. He was conscious, and no flapping tremor was observed. There was no abdominal distension, palpable mass, ascites, or any other clinical features of advanced cirrhosis.\n\nThe laboratory workup showed: serum alanine aminotransferase 1238 IU/L (normal value: 40 IU/ L), aspartate aminotransferase 1049 IU/L (normal value: 40 IU/L), alkaline phosphatase (ALP) 192 IU/ L (normal range: 50 to 130 IU/ L), gamma glutamyl transferase (GGT) 164 IU/ L (normal value: 30 IU/ L), total bilirubin 211 umol/L, prothrombin time (PT) 30% and international normalized ratio (INR) 2,87.\n\nSerological markers for hepatotropic viruses such as A, B, C, D and E were all negative. The patient had no clinical or serological signs of infection with other viruses, such as cytomegalovirus, Epstein-Barr virus, herpes simplex virus or human immunodeficiency virus.\n\nAll the autoantibodies (anti-nuclear antibody, smooth muscle antibody, liver-kidney-microsomal antibody, and liver soluble antibody) were negative, except for anti-mitochondrial antibody (AMA) M2, which was positive. It was detected using indirect immunofluorescence (IIF), but no quantitative analysis was carried out. Quantitative serum immunoglobulins were within normal levels: IgG: 12,4 g/L (normal range: 6,9 to 16,2 g/L) and IgM: 1, 43 g/L (0.6-2.60 g/L).\n\nAbdominal ultrasonography showed normal liver parenchyma, and normal-size spleen. Color Doppler ultrasound imaging showed normal venous flow. There were no collateral circulations or hepatic vein thrombosis. Endoscopic findings did not reveal any esophageal or gastric varices. Percutaneous liver biopsy could not initially be performed because of the significantly elevated INR. Transjugular liver biopsy would have been preferable in this case, but was unavailable at our institution. As the main potential etiologies were excluded (viral, drug-induced hepatitis, toxins, herbal medication, ischemic hepatitis, or alcohol), the underlying cause was still indeterminate. We then suspected him of having ALF due to autoimmune liver disease, namely AIH. The positivity of AMA M2 in this case implied a probable diagnosis of PBC- AIH OS.\n\nGiven the acute, severe, and life-threatening presentation, corticosteroids were promptly initiated. He was first treated with 1 mg/kg of body weight of equivalent prednisolone daily for 10 days, and then with 60 mg prednisolone, daily for approximately 60 days. Five days after the initiation of corticosteroids, his hepatic function tests started to improve. The cytolysis decreased significantly, whereas ALP and GGT levels rose slightly. PT increased to 50%. Although the diagnosis of OS was uncertain, we decided to start ursodeoxycholic acid on day seven, at the dosage of 13 mg/kg body weight daily.\n\nThat patient’s jaundice gradually subsided and we noticed an overall clinical improvement especially in fatigue. He was released from our hospital three weeks after admission. Later, during follow up, we introduced azathioprine at the dose of 100 mg daily and prednisolone was progressively tapered to a dose of 10 mg daily, without any sign of exacerbation.\n\nPercutaneous liver biopsy was performed three months after his discharge. Histopathological assessment of the liver biopsy showed a fibrous expansion of the portal triad, with severe portal inflammation consisting of lymphocytes and plasma cells and periportal piecemeal necrosis. Apoptotic bodies were found in lobules.\n\nNo evidence of lymphocytic cholangitis or ductopenia was found. These findings were compatible with AIH (Figure 1).\n\nSevere interface chronic hepatitis with apoptotic bodies associated with a dense inflammatory infiltrate (lymphocytes, plasmocytes).\n\n(d) H. E x 400: Cholangiolar proliferation, without biliary duct lesions.\n\nWe retrospectively applied the New Scoring Classification for PBC-AIH OS,4 and our patient who presented a score of 20, was identified as potentially having the diagnosis of PBC-AIH OS.\n\nThis diagnosis remained questionable as IgM level was normal, AMA M2 titer was not quantified and may have been a false positive, and the characteristic lesions of PBC were not found.\n\nThe patient was maintained on10 mg of prednisolone, 100 mg of azathioprine and 800 mg of ursodeoxycholic acid (UDCA), daily.\n\nDuring the two-year follow-up, the patient remained asymptomatic, and his hepatic function tests became utterly normal.\n\n\nDiscussion\n\nThe present case illustrated a rare presentation of autoimmune hepatitis in a male patient, with acute onset and unexpected features of PBC. The diagnosis was challenging as we have excluded the main potential etiologies of ALF, and serological markers supporting the diagnosis of AIH were absent. Little is known about the management of AIH–induced ALF as there are very limited published data.\n\nAIH is an immune-mediated chronic liver disease, with variable clinical presentations. The chronic, insidious presentation of the disease is commonly revealed by asymptomatic elevation of liver enzymes. However, acute onset hepatitis, including ALF, is rare.10 It defines a syndrome characterized by markers of liver damage (elevated serum transaminases) and impaired liver function (jaundice and INR >1.5).11 This pattern, insufficiently described in the literature, is challenging for physicians as it can mimic other types of acute hepatitis.\n\nAlthough diagnostic criteria of the acute and fulminant forms of AIH were codified by the International Autoimmune Hepatitis Group in 1992,12 and who removed the condition of six months of disease activity to establish the diagnosis, it is still difficult to diagnose and treat these forms.12 Additionally, autoantibodies can be absent or weakly positive and serum γ-globulin levels are lower than in chronic classical presentations.\n\nConsequently, AIH should be considered in all patients with acute and chronic hepatitis of undetermined cause.13\n\nWomen are four times more likely to have AIH than men.14 The rarity of AIH in men is demonstrated by epidemiological studies.2 The acute onset of AIH is a rare condition in the male gender, thus the circumstances of our case are very unique. Similarly, PBC is an autoimmune, cholestatic liver disease, characterized by chronic cholestasis, circulating AMA, and, typically, histological lesions of nonsuppurative destructive cholangitis of the small interlobular bile duct.15 PBC is a slowly progressive disease,16 and there have been no cases reported in the literature of PBC patients presenting with an ALF.11\n\nWhen PBC and AIH simultaneously coexist in the same patients, it is classified as PBC-AIH OS. Nevertheless, in the absence of clearly established diagnostic criteria, the OS of PBC- AIH is generally evoked by the association of cytolysis, hepatic cholestasis, AMA, and other autoantibodies, as well as histological lesions. Although liver biopsy is mandatory for diagnosis and to guide treatment, detailed histological criteria of AIH with clinically acute presentation have not been well-established.17\n\nTherefore, the diagnosis of AIH-PBC OS is accepted when two or three Chazouillères criteria for PBC and AIH are fulfilled.17,18 With regard to these definitions, we suspected the diagnosis of an acute presentation of AIH. Although our patient presented PBC features, OS could not be confirmed as AMA positivity is only observed in approximately 20% of AIH patients, and was not observed in this case.19 The histology of AIH with acute presentation may reveal heterogeneous patterns of hepatic injury, and typical histological findings of classic AIH can be absent or poorly demonstrated.20\n\nIn our case, the liver biopsy specimen demonstrated the absence of cirrhosis with evidence of acute damage including confluent periportal necrosis, plasma cell infiltration in portal areas, perivenular necroinflammatory activity and lymphocytic cholangitis. However, typical histological lesions of PBC, particularly nonsuppurative destructive cholangitis of the small interlobular bile duct, were not found.\n\nIt is very important that patients with ALF, such as the case presented here, are treated as soon as possible, to avoid the need for urgent liver transplantation.\n\nImmunosuppressive therapy, namely corticosteroids with or without azathioprine, can achieve sustained remission in more than 80% of patients with AIH. However, drug therapy management in severe forms of AIH remains a subject of debate, and the usefulness of corticosteroid therapy is not clear.21,22 Another crucial question that remained unanswered was whether the optimal dose of corticosteroid should be weight-based or higher doses should be given in these cases, and about the optimal route of administration, oral or intravenous hydrocortisone administration. The benefits of a high-dose regimen of corticosteroids, i.e. higher response rates and, consequently, a reduced need for liver transplantation, should be considered alongside the higher risk of septic complications.23 The decision to initiate corticosteroids in our patient who did not fulfill conventional diagnostic criteria for AIH was made because of the very severe and immediately life-threatening presentation of the illness. In addition, no underlying etiology had been determined. In such situations, the decision should be made on an individual basis, and remains the prerogative of the treating hepatologist. Although it was not evident whether the introduction of corticosteroid therapy would be beneficial, it was the only therapeutic option available, considering that urgent liver transplantation is not available in Tunisia.10 The steroid dose that we decided to prescribe to our patient was based on similar cases previously reported in the literature which had favorable outcomes.21,22 The only predictor of outcome has been the treatment response, which according to Ichai et al,21 has to be assessed over two weeks. The absence of improvement within two weeks of treatment initiation, or the deterioration of any clinical or laboratory feature during this interval, defines refractory disease and justifies the need for an alternative therapeutic option.24 For our patient, although the diagnosis of PBC- AIH OS was uncertain, we associated UDCA with prednisolone and got a favorable response. UDCA can markedly decrease serum bilirubin, ALP, and GGT levels, improve histological damage and fibrosis in patients with PBC, and long-term treatment can delay the histological progression of the disease, particularly in patients with early histological stages. Some authors might prefer to prescribe the initial therapy according to the predominant component of the OS, and to change or add other therapies during clinical follow up.\n\n\nConclusions\n\nWe described a case of ALF with overlap features of both PBC and AIH, which was successfully treated with corticosteroids.\n\nAcute onset of PBC-AIH OS during the initial presentation is uncommonly reported, and the diagnosis of this entity remains challenging.\n\nIn our case, corticosteroids were an effective and lifesaving therapeutic option that prevented urgent liver transplantation. However, identifying early predictors of corticosteroid treatment failure is very important in preventing clinical deterioration in non-responders and in selecting patients for liver transplantation.\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/or clinical images was obtained from the patient.\n\n\nAuthor contributions\n\nAya Hammami: writing – original draft preparation\n\nKhouloud Ben Abdessalem, Nour Elleuch, Hanen Jaziri: writing – review & editing\n\nWafa Dahmani, Wafa Ben Ameur, Mehdi Ksiaa, Aida Ben Slama: visualization\n\nSalem Ajmi, Ahlem Braham, Ali Jmaa: validation\n\nSarra Mestiri: resources",
"appendix": "References\n\nBoberg KM, Chapman RW, Hirschfield GM, et al.: Overlap syndromes: the International Autoimmune Hepatitis Group (IAIHG) position statement on a controversial issue. J Hepatol. 2011 Feb; 54(2): 374–85. PubMed Abstract | Publisher Full Text\n\nCzaja AJ, dos Santos RM, Porto A, et al.: Immune phenotype of chronic liver disease. Dig Dis Sci. 1998 Sep; 43(9): 2149–55. PubMed Abstract | Publisher Full Text\n\nKayacetin E, Koklu S, Temucin T: Overlap syndrome of primary biliary cirrhosis and autoimmune hepatitis with unusual initial presentation as fulminant hepatic failure. Digestive and liver disease: official journal of the Italian Society of Gastroenterology and the Italian Association for the Study of the. Liver. 2004 Jun; 36(6): 419–22. PubMed Abstract | Publisher Full Text\n\nZhang W, De D, Mohammed KA, et al.: New scoring classification for primary biliary cholangitis-autoimmune hepatitis overlap syndrome. Hepatol Commun. 2018 Mar; 2(3): 245–53. PubMed Abstract | Publisher Full Text | Free Full Text\n\nVerma S, Maheshwari A, Thuluvath P: Liver failure as initial presentation of autoimmune hepatitis: clinical characteristics, predictors of response to steroid therapy, and outcomes. Hepatology (Baltimore, Md). 2009 Apr; 49(4): 1396–7. PubMed Abstract | Publisher Full Text\n\nWakamatsu T, Kanda T, Tawada A, et al.: Acute liver failure in an antimitochondrial antibody-positive 63-year-old man. Case Rep Gastroenterol. 2012; 6(2): 394–9. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCzaja AJ: Overlap syndrome of primary biliary cirrhosis and autoimmune hepatitis: a foray across diagnostic boundaries. J Hepatol. 2006 Feb; 44(2): 251–2. PubMed Abstract | Publisher Full Text\n\nViruet EJ, Torres EA: Steroid therapy in fulminant hepatic failure secondary to autoimmune hepatitis. P R Health Sci J. 1998 Sep; 17(3): 297–300. PubMed Abstract\n\nHerzog D, Rasquin-Weber A-M, Debray D, et al.: Subfulminant hepatic failure in autoimmune hepatitis type 1: an unusual form of presentation. J Hepatol. 1997; 27(3): 578–82. PubMed Abstract | Publisher Full Text\n\nTakahashi A, Arinaga-Hino T, Ohira H, et al.: Autoimmune hepatitis in Japan: trends in a nationwide survey. J Gastroenterol. 2017 May; 52(5): 631–40. PubMed Abstract | Publisher Full Text\n\nLindor KD, Bowlus CL, Boyer J, et al.: Primary Biliary Cholangitis: 2018 Practice Guidance from the American Association for the Study of Liver Diseases. Hepatology (Baltimore, Md). 2019 Jan; 69(1): 394–419. PubMed Abstract | Publisher Full Text\n\nCzaja AJ: Corticosteroids or not in severe acute or fulminant autoimmune hepatitis: therapeutic brinksmanship and the point beyond salvation. Liver Transpl. 2007 Jul; 13(7): 953–5. PubMed Abstract | Publisher Full Text\n\nCzaja AJ, Freese DK: Diagnosis and treatment of autoimmune hepatitis. Hepatology (Baltimore, Md). 2002 Aug; 36(2): 479–97. PubMed Abstract | Publisher Full Text\n\nGuy J, Peters MG: Liver disease in women: the influence of gender on epidemiology, natural history, and patient outcomes. Gastroenterol Hepatol (N Y). 2013; 9(10): 633–9. PubMed Abstract | Free Full Text\n\nPurohit T, Cappell MS: Primary biliary cirrhosis: Pathophysiology, clinical presentation and therapy. World J Hepatol. 2015 May 8; 7(7): 926–41. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPares A, Rodes J: Natural history of primary biliary cirrhosis. Clin Liver Dis. 2003 Nov; 7(4): 779–94. PubMed Abstract | Publisher Full Text\n\nCzaja AJ: Frequency and nature of the variant syndromes of autoimmune liver disease. Hepatology (Baltimore, Md). 1998 Aug; 28(2): 360–5. PubMed Abstract | Publisher Full Text\n\nChazouilleres O, Wendum D, Serfaty L, et al.: Primary biliary cirrhosis-autoimmune hepatitis overlap syndrome: clinical features and response to therapy. Hepatology (Baltimore, Md). 1998 Aug; 28(2): 296–301. PubMed Abstract | Publisher Full Text\n\nKenny RP, Czaja AJ, Ludwig J, et al.: Frequency and significance of antimitochondrial antibodies in severe chronic active hepatitis. Dig Dis Sci. 1986 Jul; 31(7): 705–11. PubMed Abstract | Publisher Full Text\n\nNguyen Canh H, Harada K, Ouchi H, et al.: Acute presentation of autoimmune hepatitis: a multicentre study with detailed histological evaluation in a large cohort of patients. J Clin Pathol. 2017 Nov; 70(11): 961–9. PubMed Abstract | Publisher Full Text\n\nIchai P, Duclos-Vallée JC, Guettier C, et al.: Usefulness of corticosteroids for the treatment of severe and fulminant forms of autoimmune hepatitis. Liver Transpl. 2007 Jul; 13(7): 996–1003. PubMed Abstract | Publisher Full Text\n\nKarkhanis J, Verna EC, Chang MS, et al.: Steroid use in acute liver failure. Hepatology (Baltimore, Md). 2014 Feb; 59(2): 612–21. PubMed Abstract | Publisher Full Text | Free Full Text\n\nYeoman AD, Westbrook RH, Zen Y, et al.: Prognosis of acute severe autoimmune hepatitis (AS-AIH): the role of corticosteroids in modifying outcome. J Hepatol. 2014 Oct; 61(4): 876–82. PubMed Abstract | Publisher Full Text\n\nYeoman AD, Westbrook RH, Zen Y, et al.: Early predictors of corticosteroid treatment failure in icteric presentations of autoimmune hepatitis. Hepatology (Baltimore, Md). 2011 Mar; 53(3): 926–34. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "89226",
"date": "23 Jul 2021",
"name": "Atsumasa Komori",
"expertise": [
"Reviewer Expertise Hepatology",
"autoimmune liver diseases",
"cholestatic liver disease",
"hepatocellular carcinoma"
],
"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\nHammami et al. reported a case of probable autoimmune hepatitis with acute onset in a male patient. Due to the positive AMA immunofluorescence, this case really raises a question about the presence of PBC overlap during its clinical course. Nevertheless, there are concerns for its diagnostic flow, as well as clinical significance. AMA titer of immunofluorescence is missing.\n\nAMA (quantified by MIT3-ELISA) was reported to be positive in acute liver failure patients, with around 40% frequency, albeit in transient manner (Leung et al., 20071); ALF could be seropositive in AMA even in the absence of PBC. Accordingly, the authors' claim for the probable overlap syndrome (OS) should be validated with the sustained positive AMA even after biological remission.\n\nThe authors should alternatively discuss the probable diagnosis of AMA-positive genuine acute AIH because no bile duct lesions were present in the biopsy.\n\nConcerning the above, the first sentence of the Conclusions seems to be overstated.\n\nIn the Discussion: Acute onset AIH, including ALF, is not likely rare. The 2019 AASLD practice guidance and guidelines2 state that 25–75% of individuals with AIH in Western countries present with an acute onset and a disease duration <30 days. On the contrary, Reference 10 mainly focused on the frequency of acute AIH without fibrosis (F0), which is around 10%. Authors should modify the discussion, accordingly.\n\nOverall, the case is too ambiguous for its diagnosis, being not sufficient for the relevance to future understanding of diagnoses.\n\nIs the background of the case’s history and progression described in sufficient detail? Yes\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Partly\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Partly\n\nIs the case presented with sufficient detail to be useful for other practitioners? Partly",
"responses": []
},
{
"id": "100673",
"date": "13 Dec 2021",
"name": "Behzad Hatami",
"expertise": [
"Reviewer Expertise Gastroenterology and hepatology"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 sending the manuscript for peer-review. Hammami et al. have reported a case of autoimmune hepatitis(AIH) with acute presentation in a male patient. Although the article is informative, I need to point out some points here:\nAcute presentation of AIH occurs in 25-75% of patients with female preponderance according to the 2019 AASLD practice guidance1. So, it is not rare but it is usually under-reported.\n\nGiven the marked elevation of serum aminotransferase levels, the toxic or drug-induced liver injury should also be considered in differential diagnoses besides viral causes of hepatitis.\n\nANAs (antinuclear antibodies) are absent or weakly positive and the serum IgG level is normal in about one-third of patients with acute severe AIH.\n\nAntimitochondrial autoantibodies (AMAs) are present in 10% of patients with AIH in the absence of histological features of bile duct injury, as in this reported case.\n\nAccording to the 2019 AASLD practice guidance1, liver biopsy is required to exclude AIH-PBC overlap syndrome and the presence of AMA in patients with AIH is insufficient to make this diagnosis. Moreover, the diagnostic scoring systems for AIH are not developed or validated for the diagnosis of the overlap syndromes and they should not be used for this purpose according to AASLD1 and EASL guidelines2.\n\nOn the other hand, as per the revised IAIHG criteria3, given the score of 20, the diagnosis of probable overlap syndrome (not definite) can be made.\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? Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-406
|
https://f1000research.com/articles/10-403/v1
|
19 May 21
|
{
"type": "Method Article",
"title": "Supervised topic modeling for predicting molecular substructure from mass spectrometry",
"authors": [
"Gabriel K. Reder",
"Adamo Young",
"Jaan Altosaar",
"Jakub Rajniak",
"Noémie Elhadad",
"Michael Fischbach",
"Susan Holmes",
"Adamo Young",
"Jaan Altosaar",
"Jakub Rajniak",
"Noémie Elhadad",
"Michael Fischbach",
"Susan Holmes"
],
"abstract": "Small-molecule metabolites are principal actors in myriad phenomena across biochemistry and serve as an important source of biomarkers and drug candidates. Given a sample of unknown composition, identifying the metabolites present is difficult given the large number of small molecules both known and yet to be discovered. Even for biofluids such as human blood, building reliable ways of identifying biomarkers is challenging. A workhorse method for characterizing individual molecules in such untargeted metabolomics studies is tandem mass spectrometry (MS/MS). MS/MS spectra provide rich information about chemical composition. However, structural characterization from spectra corresponding to unknown molecules remains a bottleneck in metabolomics. Current methods often rely on matching to pre-existing databases in one form or another. Here we develop a preprocessing scheme and supervised topic modeling approach to identify modular groups of spectrum fragments and neutral losses corresponding to chemical substructures using labeled latent Dirichlet allocation (LLDA) to map spectrum features to known chemical structures. These structures appear in new unknown spectra and can be predicted. We find that LLDA is an interpretable and reliable method for structure prediction from MS/MS spectra. Specifically, the LLDA approach has the following advantages: (a) molecular topics are interpretable; (b) A practitioner can select any set of chemical structure labels relevant to their problem; (c ) LLDA performs well and can exceed the performance of other methods in predicting substructures in novel contexts.",
"keywords": [
"Metabolomics",
"Machine Learning",
"Mass Spectrometry",
"Structure Identification",
"LC-MS",
"Tandem Mass Spectrometry",
"MS/MS"
],
"content": "Introduction\n\nLiquid chromatography - tandem mass spectrometry (LC-MS/MS) is a powerful experimental method for identifying the small molecule metabolites in a sample of unknown composition. It provides detailed structural information from a given molecule with the only prerequisite knowledge being the parent molecule’s mass-to-charge ratio. This is especially important since a vast portion of naturally occurring small molecules are believed to remain unidentified1. Yet identifying the structure of a molecule given its MS/MS remains challenging2. Traditionally, such identification is done by hand, which is difficult, time-consuming, and poses significant reproducibility issues. The repetitive nature of this task naturally lends itself well to a computational approach3.\n\nExisting tools generally follow one of two trends. In spectral library matching, a query MS/MS spectrum is compared to reference spectra via similarity metric such as a cosine score4. For example, the National Institute of Standards and Technology (NIST) Mass Spectral Library, Human Metabolome Database (HMDB), Metlin, and the Global Natural Products Social Molecular Networking (GNPS) databases all offer spectral similarity search functionalities using spectral similarity scores5–8. However, spectral databases tend to be sparse compared to the universe of possible molecular structures3. Simulated spectra can supplement databases with new structures, though matching is usually done on entire spectra9–11. Molecular fingerprint approaches in which vector representations of molecules are predicted directly from MS/MS spectra are increasingly popular methods12–16.\n\nThis work focuses on the specific fingerprint task of substructure prediction in MS/MS spectra (Figure 1A). Chemical substructures are defined structural subunits that appear across different molecules and are useful for identifying their parent molecules13,18. Focusing on substructures benefits practitioners because substructures have directly interpretable chemical meaning. Further, predicting chemical substructures rather than relying on spectral library matching allows for novel predictions of molecules not seen in these libraries. An existing approach, MS2LDA, uses topic modeling to find regularly co-occurring sets of MS/MS spectrum fragments and neutral losses19. Here we build on this work by proposing and developing a supervised topic modeling approach, using labeled latent Dirichlet allocation (LLDA)17, to find co-occurring spectrum features associated with chemical substructures of the user’s choosing (Figure 1B–C). We find that compared to alternative methods for supervised substructure identification, LLDA performs well and provides interpretable substructure predictions. Using cosine distance k-nearest neighbors (k-NN) for spectral library matching, we find that LLDA’s relative performance improves as the test set becomes more chemically distinct from the training set and as the substructures being predicted appear with different frequencies between the two sets. This type of generalization is important for applications where the molecular identity of samples is unknown and thought to correspond to novel molecules.\n\n(a) Substructure prediction in MS/MS spectra. A tandem (MS/MS) mass spectrum of a small molecule (ergonovine). Spectrum fragments and neutral losses provide information relevant to identifying chemical structure. The goal of the supervised topic modeling approach is to assign interpretable substructure scores for a spectrum via LLDA17 (b) Supervised learning for substructure prediction. A training set is composed of MS/MS spectra with known chemical structures and a choice of substructure (topic) labels. Each spectrum is labeled with its parent molecule’s substructures. (c) The LLDA generative model. The model is defined in 17 and labeled here as it relates to MS/MS substructure prediction. The model is trained on a corpus D of MS/MS spectra and set of molecular substructures K. Given the fragment/neutral loss (feature) composition Wd,n of each spectrum and the substructure-spectrum label matrix Λ, the model will find the substructure-feature probability matrix β, the spectrum-substructure probability matrix θ, and the feature-substructure assignment matrix Z. α and η are Dirichlet parameters for the distributions from which θ and β are respectively assumed to have been drawn. Φ is a Bernoulli parameter for the distribution from which Λ is assumed to have been drawn. is a model. Figure (c) has been reproduced and modified with labels with permission from 17.\n\n\nMethods\n\nIn order to facilitate direct comparison to an existing tool, we train and test LLDA using the same data and evaluation metrics as those used in the metabolite substructure auto-recommender (MESSAR) developed in 20. We utilize the MESSAR target training corpus of 3,146 positive mode LC-MS/MS spectra (available here) originally from the Global Natural Products Social Molecular Networking database8. For validation, we use the 5,164 MASSBANK21 validation spectra and the 185 annotated test spectra as our test set both used in 20 and available here. This test dataset contains spectra for 34 drugs and 126 metabolites from MASSBANK and 25 spectra from the Critical Assessment of Small Molecule Identification 2017 contest. The 712 unique substructures provided in the rule database in 20 (available here) are used. All spectra are provided in .mgf format. Copies of the spectra and a cleaned version of the unique substructure set are included in this publication’s Underlying data22.\n\nTo model a mass spectrum using LLDA, it is necessary to represent a mass spectrum as a bag-of-words “document”23. First, any fragment having a mass-to-charge-ratio (m/z) below 30 is discarded to remove structurally uninformative fragments. Each fragment in the remaining spectrum is then assigned the molecular formula with the closest theoretical m/z and that satisfies two conditions (i) the formula’s theoretical m/z is within 0.1 of the peak’s m/z and (ii) the formula is a subformula of the parent spectrum’s parent molecular formula (Figure 2A). We assume all MS/MS spectra have a corresponding molecular formula, a reasonable assumption for a spectrum even if its parent chemical structure is unknown24. This formula matching is done using the rcdk library (version 3.5.0). Peaks with no formula match are discarded. Next, all possible neutral losses are computed as pairwise differences between kept spectrum fragments. A neutral loss consists of a m/z difference between two fragments, fa and fb. Neutral losses in which fa has both a greater intensity and m/z than fb are assigned the mean of its two respective peak intensities and matched to formulas in the same manner as fragments. Neutral losses with no matching formulas are discarded. The word count Y for a given spectrum feature (fragment or neutral loss) with intensity x is calculated using a generalized logistic function25:\n\n(a) Mapping spectrum features to molecular formula words. For representing a mass spectrum as a document, each spectrum fragment corresponding to a peak is first mapped to a molecular formula by finding the formula that matches the following criteria: (i) the theoretical mass-to-charge ratio of the formula is within 0.1 m/z of the observed fragment. (ii) the formula is a subformula of the spectrum’s parent formula. The closest such m/z formula is kept, the same process is repeated for neutral losses, and spectrum features with no formula matches are discarded. (b) Mapping feature intensity to word counts. Word counts are computed for each spectrum fragment and neutral loss using the feature’s normalized intensity as in Equation 1. A word count response for Q = 10 and B = 0.1 is illustrated here.\n\nwhere Q determines the threshold value at intensity x = 0 and B determines the growth rate of the word count growth rate as the intensity increases. Input intensities of spectrum fragments are normalized such that the maximum raw intensity is 100, with word counts rounded to the nearest integer. An example intensity response function for intensity values in the range [0, 100] is shown in Figure 2B.\n\nUsing the data and code provided, this document generation process including formula mapping and bag-of-words conversion can be run using the command:\n\n\n\nWe note that this process can be quite time consuming if run on a single core - preprocessing a single spectrum using a single core can take more than two minutes depending on the spectrum. As such, the preprocessed spectra for the specified data sets have been provided (see Underlying data22). Runtime can be decreased on a multi-core system by increasing the n_jobs input parameter.\n\nSubstructure labels for training spectra having known parent chemical structures are assigned using the RDKit library (version 2020.09.5). Training spectra are labeled with the substructures in the user-defined set that are present in the given spectrum’s parent structure. Substructure labeling can be run using the provided data and code using the command:\n\n\n\nThe LLDA model is implemented using the Python Tomotopy library (version 0.10.2)26. The model takes a set of training spectra, test spectra, and substructures as input. The spectra must be in bag-of-words format, and the training spectra must have been labeled with ground truth substructures as described above. The original LLDA model is described in full in 17. We note that every component of LLDA for modeling text documents has an analog useful for modeling a MS/MS spectrum. A document is an MS/MS spectrum, words are spectrum features (fragments and neutral losses), topics are commonly co-occurring spectrum features, and tags are chemical substructures (Figure 1). LLDA was trained for 2,000 iterations, since model perplexity tended to converge at around 2,000 iterations across various data sets generated using the preprocessing scheme. We note that the number of necessary iterations may differ across data sets. In addition to including a required input argument for the number of iterations in the LLDA model, we also include an optional flag to record and plot model perplexity.\n\nSubstructure predictions in test spectra are calculated using cosine similarity. The cosine similarity between a new spectrum i and substructure j is calculated as:\n\nHere vk is the word distribution for topic k and vd is the word count in document d that appears in the training corpus. Both vectors inherit their lengths from the number of words present across all documents. In this manner, every substructure is assigned a score for presence/absence in a test spectrum. After preprocessing, the LLDA model can be trained and tested using the commands\n\n\n\nFor comparison to the practice of spectral library matching, we also implement a k-nearest neighbors method for substructure prediction. Spectra are represented as vectors by assigning fragments to m/z bins of width 0.1. Only fragments with mass-to-charge ratio in the range [0, 1000] are kept; the vectors representing the spectra are thus of length 10,000. To make a prediction for substructures associated with a new spectrum using the k-nearest neighbors algorithm, the k nearest neighbors in the training set of spectra are computed using the cosine similarity between the vectors corresponding to spectra in the training set. The score for each substructure in the new spectrum is calculated as the mean of the substructure presence and absence labels in the k nearest neighbors’ spectra. For example, for a single substructure s and test spectrum d, if 4 of the 5 nearest neighbor spectra contain s, the predicted score for s in d will be 4/5 = 0.8. After data preprocessing, k-NN can be run using the command:\n\n\n\nFurther code documentation including required libraries and optional arguments can be found in the README file included in this publication’s Underlying data22. A Docker image containing all necessary software and library requirements is also available at Docker Hub (see Extended data).\n\n\nResults and discussion\n\nAs described in the preprocessing pipeline, the generalized logistic function (GLF) is used to convert normalized feature intensity values into word counts to represent spectra as documents. To evaluate the hyperparameter choices in the GLF, LLDA was evaluated using a range of Q and B values corresponding to a wide range of intensity response functions. This performance was measured using the same metric as in 20. Specifically, the metric, denoted as t3≥2, measures the number of spectra in which at least two of the top-3 scoring substructures are true positives. This is similar to the standard metric of recall used in recommender systems27. In this experiment, LLDA predicted substructures most sensitively for Q and B values corresponding to binarized word counts. In other words, for a given document, words that appear in the given spectrum receive a word count of 1 and all other words receive a word count of 0; this corresponds to Q = 10.0 and B = 0.001 (Figure 3A). This finding deserves further research and means that in this formulation, intensity information may harm model performance. This could be for a number of reasons. One possibility is that the GLF formulated in Equation 1 is not an optimal choice of function to map intensities to word counts. There are many options of function for this conversion, the GLF was chosen because of its flexibility to produce a diverse set of intensity-word count relationships. Another possibility is that neutral loss intensity encoding must be revisited. There may be better methods of representing a neutral loss’s intensity other than taking the mean of its two constituent fragments. Additionally, valuable information might potentially be destroyed when raw ion counts are converted to normalized intensities as is standard practice14,18.\n\n(a) Empirical study of normalized intensity response function. The performance of the LLDA model using the intensity response shown in Figure 2b with various values of Q and B on the validation set of 5,164 MASSBANK spectra used in 20. Performance is measured by counting the number of spectra in which at least 2 of the top-3 predicted substructures are correct (t3≥2). The binarized response function performs best (Q = 10, B = 0.001), meaning that a generative process that does not include normalized intensity information outperforms other choices in this formulation. (b) LLDA outperforms k-nearest neighbors (k-NN) in generalizing to evaluation sets with less overlap in substructure or chemical similarity. The difference between LLDA performance (measured by the area under the receiver operating characteristic or AUC) and k-NN performance is computed. The average chemical similarity is computed between the train and test sets using the RDKit fingerprint. Colors represent the substructure appearance difference between the training and test sets. Increasing the difficulty of generalization along either axis of molecular similarity or substructure overlap increases LLDA performance relative to the k-NN model. (c) LLDA can recognize substructures outside train context. A test spectrum is shown in which substructure 528 appears. The parent structure (Pubchem ID 57509371) is displayed with the portions of the structure containing substructure 528 highlighted. Fragments in red are in the 95th percentile of words in the topic for substructure 528 in the LLDA. The k-NN model performs poorly on such substructures that appear out of context in the test set, while LLDA maintains predictive performance in this case.\n\nLLDA, with the best-performing values of Q and B (Q = 10.0, B = 0.001, corresponding to binary word counts) was then run on the benchmark test dataset from 19, consisting of 185 spectra. On this data, the authors of 20 report the following results for MESSAR on the top 3 recommended substructures for each spectrum: 79 spectra in which at least 1 recommendation is correct (t3≥1) and 40 spectra in which at least 2 recommendations are correct (t3≥2). The LLDA model yields 125 cases for t3≥1 and 82 cases for t3≥2.\n\nThe k-nearest neighbors method was studied using k = [1, 5, 10] on the same set of evaluation data. For these experiments, we find that the t3≥1 metric is [111, 128, 130] respectively and that t3≥2 is [74, 117, 121]. These results indicate that the k-nearest neighbors method with k=10 outperforms all other methods on this set of train/test data according to these metrics. These results are shown in Table 1. However, it is unclear whether it is possible to extract an analogue to ‘topics’ from the k-nearest neighbors algorithm, as is common in LLDA and topic models. Further research is needed to develop methods that perform as well as k-nearest neighbors while retaining the interpretability and modularity of topic modeling approaches to substructure identification, such as LLDA. As the output of machine learning methods for mass spectrometry data is typically inspected by a human in an experimental procedure, developing interpretable methods remains important. We note that the same train spectra, test spectra, and evaluation metrics as used in 20 were used in this work. This was done to maximize the comparability between methods. Future development of community-wide standards for benchmark datasets and evaluation metrics will greatly facilitate development of new methods.\n\nTo study how well k-nearest neighbors performs compared to LLDA on novel test molecules poorly represented in the training set, increasingly difficult subsets of the test data were constructed using two notions of how data might be limited in a real-world experimental setting (i) chemical similarity between training and test molecules and (ii) differential train-test appearance for substructures.\n\nFor chemical similarity, the RDKit fingerprint similarity was calculated between each test set of spectrum parent structure and all structures in the training set. These similarity scores were then used to set similarity thresholds for selecting increasingly difficult subsets of the test data. For example, a maximum similarity threshold of 0.4 produced a subset of the test spectra in which the maximum pairwise structure fingerprint similarity to the train structures is at most 0.4. For substructure appearance, the number of times a substructure appears in the training set is counted and normalized according to the number of spectra. The same is done for the test set. Next, substructures are ordered by these differences and percentile cutoffs are used to produce subsets of test spectra of increasing difficulty in terms of test - train appearance. For example, a 60th percentile cutoff means testing only substructures whose normalized test minus train appearance values are above the 60th percentile of all such values across all substructures. The performance of the LLDA model compared to the k-NN model was calculated as the LLDA area under the receiver operating characteristic curve (AUC) averaged across the given test set minus the average AUC for the k-NN model.\n\nThe results of this study are shown in Figure 3B. Increasing difficulty along either axis of chemical similarity or substructure overlap improved the performance of the LLDA model relative to the k-NN model. This effect was especially pronounced as test-train molecular similarity became more distant. These results indicate use cases in which an approach such as LLDA may be especially useful compared to spectral library searching. LLDA may be able to better recognize novel chemical configurations of substructures in new spectra. As such it may be a better-suited model for characterizing spectra measuring molecules coming from new and understudied areas of chemical space not well represented in spectral libraries.\n\n\nConclusions\n\nMetabolites are central in biology, yet the vast majority are likely unidentified28. Untargeted metabolomics via LC-MS/MS is a promising option for identifying new metabolites in a high throughput pipeline. Improved computational methods for identifying chemical structure from MS/MS spectra are needed for this promise to become a reality. With this in mind, we developed, described, and open-sourced a supervised topic modeling method for identifying chemical substructures in tandem mass spectrometry data via LLDA17. In a series of empirical studies, this supervised topic model was trained and tested on publicly available benchmark data and substructures, and LLDA was compared to an alternative method, MESSAR20. A k-nearest neighbors (k-NN) was also implemented as a means of testing spectral library matching to predict substructure labels based on neighbor averages.\n\nWe report several benefits of the LLDA method. First, when trained and tested using the same spectra, LLDA provides interpretable, probabilistic substructure topics and performs well using the same metrics as in 20. These topics can incorporate a large number of spectrum fragments and neutral losses, so the patterns of spectrum fragments and neutral losses associated with substructures can be as complex as necessary for good predictive performance. LLDA is a probabilistic model that can compensate for ambiguity, redundancy, and other noise that arises from computing substructure labels. The advantage of such a probabilistic method is that substructure labels often have significant overlap12. Finally, the LLDA model offers a flexible supervised framework. A practitioner may choose any set of substructure labels on which to train the LLDA model, allowing the user to tailor the output of the model to a specific application requiring accurate and interpretable substructure identification. LLDA offers a supervised topic modeling approach that complements both the benefits of MS2LDA19, circumventing the need to pick an arbitrary number of unsupervised topics or to map output topics to substructures - this relationship is predetermined by the user.\n\nBy systematically exploring the preprocessing pipeline used to map spectrum features to a representation of spectra as documents, we find that this LLDA model performs best when intensity information is hidden from the model and binary word counts are used to represent MS/MS spectra (Figure 3A). This aligns with existing work in probabilistic topic models used in recommender systems, such as collaborative topic Poisson factorization, where binarized ratings lead to improved predictive performance29. However, we also note that this effect may arise from the choice of train, test, and validation sets that were taken from publicly available spectra with potential heterogeneity in collision energies. We further note the possibility that a different function for translating intensities to word counts, especially for neutral losses, may result in better performance. Neutral losses may be more robust against systemic uniform measurement error in a spectrum and as such could represent more stable sources of information. However, the manner in which intensities are assigned to neutral losses and which neutral losses are kept will heavily affect model performance.\n\nThe k-nearest neighbors (k-NN) model with k=10 performs very well using the same data and evaluation metrics, raising important considerations about trade-offs between predictive performance of substructure identification and interpretability of results. We find that the k-NN model may perform well for the task of substructure identification in situations in which substructures appear in similar patterns between train and test sets. Similarly, k-NN may perform well when a test spectrum corresponds to a molecule that is similar to those in the train set. But as explored in Figure 3B, the k-NN model suffers when these similarities are reduced, and the test spectra correspond to increasingly different molecules from those in the train set or when the substructure appearance varies between train and test sets. This observation is important to consider in the development and evaluation of machine learning methods for substructure identification; assessing generalization performance in real-world settings should reflect cases in which a new spectrum is coming from an underexplored area of chemical space that is not well represented by existing spectral libraries. We leave to future work the problem of including such quantities into evaluation metrics to more accurately assess generalization. Ablation studies such as the one presented here can provide the foundation for better metrics and ways of construct evaluation sets relevant to a substructure identification task in a specific problem setting.\n\nAn example case study: the substructure with identifier 528 in the unfiltered train/test set corresponds to SMARTS string C1Cc2ccccc2CN1 and appears in one test spectrum. In this test spectrum, substructure 528 appears without many of its co-substructures from the training set, and these co-substructures from the training set appear in the test set without substructure 528. As such, the k-NN (k = 10) model produces false positive predictions for substructure 528 in the test set, resulting in an AUC of 0.43. But the LLDA model picks up on this substructure’s presence in the test set without suffering from false positives, achieving an AUC of 0.99. The spectrum (corresponding to spectrum 128 in the test set) containing substructure 528, its structure, and spectrum fragments in the top 0.95 percentile of substructure 528’s LLDA topic are shown in Figure 3C.\n\nFurther work is required to better optimize LLDA. Additional preprocessing steps can be explored, such as keeping spectrum fragments that do not map to a child molecular formula but appear consistently across spectra (rather than discarding them as described in the Method). The inclusion of such orphaned fragments could improve downstream ranking of substructures. A similar preprocessing step is effective in processing amplicon sequencing data30. A number of limitations remain in LC-MS/MS metabolite identification including a paucity of training data31, difficulties in selecting a vocabulary of substructures12, and the heterogeneity involved in instrument choice, acquisition method, and sample conditions. Performance drops resulting from these issues are often difficult to disentangle from features of the data that result solely from chemical structure. Future work includes optimization of substructure label sets, incorporation of prior knowledge such as ionization mode or instrument type, and testing these models on a larger dataset. The work presented here highlights the increasing interest and relevance of representing MS/MS spectra in manners that can capture more information than a mass-to-charge ratio binning scheme and applying a metric for predictions such as cosine similarity. Another recent example of such an effort can be found in 32.\n\nBy releasing all code and preprocessed training data for the methods developed here, we encourage reproducibility efforts alongside the development of machine learning methods to solve de novo identification of unknown metabolites in LC-MS/MS data as computational metabolomics stands to benefit from community engagement, consistent public evaluation methods, and open-source models.\n\n\nList of abbreviations\n\nMS/MS: Tandem mass spectrometry\n\nLC-MS/MS: Liquid chromatography - tandem mass spectrometry\n\nm/z: mass-to-charge ratio\n\nLLDA: Labeled latent Dirichlet allocation17\n\nMESSAR: Metabolite substructure auto-recommender20\n\nk-NN: K-nearest neighbors\n\nAUC: Area under the receiver operating characteristic curve\n\nGLF: Generalized logistic function\n\n\nData availability\n\nZenodo: MS2 LLDA Topic Model.\n\nhttps://doi.org/10.5281/zenodo.458965322.\n\nThis project contains the following underlying data:\n\n– readme.md (file containing descriptions, specifications, and instructions for included data and using code).\n\n– requirements.txt (exported conda environment containing the necessary Python dependencies – R decencies must be installed separately. See readme.md).\n\n– data.zip (data used in paper’s empirical study, see readme.md).\n\n– code.zip (code for preparing data, running LLDA, and running kNN. See readme.md).\n\nData are available under the terms of the Apache License 2.0.\n\nDocker image: https://hub.docker.com/r/gkreder/ms2-topic-model\n\nAnalysis code available from Github: https://github.com/gkreder/ms2-topic-model\n\nArchived code at time of publication: https://doi.org/10.5281/zenodo.458965322.\n\nLicense: Apache License 2.0.",
"appendix": "References\n\nViant MR, Kurland IJ, Jones MR, et al.: How close are we to complete annotation of metabolomes? Curr Opin Chem Biol. 2017; 36: 64–9. PubMed Abstract | Publisher Full Text | Free Full Text\n\nde Vijlder T, Valkenborg D, Lemière F, et al.: A tutorial in small molecule identification via electrospray ionization-mass spectrometry: The practical art of structural elucidation. Mass Spectrom Rev. 2018; 37(5): 607–29. PubMed Abstract | Publisher Full Text | Free Full Text\n\nNguyen DH, Nguyen CH, Mamitsuka H: Recent advances and prospects of computational methods for metabolite identification: a review with emphasis on machine learning approaches. Brief Bioinform. 2019; 20(6): 2028–43. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBlaženović I, Kind T, Ji J, et al.: Software Tools and Approaches for Compound Identification of LC-MS/MS Data in Metabolomics. Metabolites. 2018; 8(2): 31. PubMed Abstract | Publisher Full Text | Free Full Text\n\nStein S: Mass Spectral Reference Libraries: An Ever-Expanding Resource for Chemical Identification. Anal Chem. 2012; 84(17): 7274–82. PubMed Abstract | Publisher Full Text\n\nWishart DS, Feunang YD, Marcu A, et al.: HMDB 4.0: the human metabolome database for 2018. Nucleic Acids Res. 2018; 46(D1): D608–17. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGuijas C, Montenegro-Burke JR, Domingo-Almenara X, et al.: METLIN: A Technology Platform for Identifying Knowns and Unknowns. Anal Chem. 2018; 90(5): 3156–64. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWang M, Carver JJ, Phelan VV, et al.: Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. Nat Biotechnol. 2016; 34(8): 828–37. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAllen F, Greiner R, Wishart D: Competitive fragmentation modeling of ESI-MS/MS spectra for putative metabolite identification. Metabolomics. 2015; 11(1): 98–110. Publisher Full Text\n\nWei JN, Belanger D, Adams RP, et al.: Rapid Prediction of Electron-Ionization Mass Spectrometry Using Neural Networks. ACS Cent Sci. 2019; 5(4): 700–8. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDjoumbou-Feunang Y, Pon A, Karu N, et al.: CFM-ID 3.0: Significantly Improved ESI-MS/MS Prediction and Compound Identification. Metabolites. 2019; 9(4): 72. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSkinnider MA, Dejong CA, Franczak BC, et al.: Comparative analysis of chemical similarity methods for modular natural products with a hypothetical structure enumeration algorithm. J Cheminformatics. 2017; 9(1): 46. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKlekota J, Roth FP: Chemical substructures that enrich for biological activity. Bioinformatics. 2008; 24(21): 2518–25. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDührkop K, Shen H, Meusel M, et al.: Searching molecular structure databases with tandem mass spectra using CSI:FingerID. Proc Natl Acad Sci U S A. 2015; 112(41): 12580–5. PubMed Abstract | Publisher Full Text | Free Full Text\n\nNguyen DH, Nguyen CH, Mamitsuka H: SIMPLE: Sparse Interaction Model over Peaks of moLEcules for fast, interpretable metabolite identification from tandem mass spectra. Bioinformatics. 2018; 34(13): i323–32. PubMed Abstract | Publisher Full Text | Free Full Text\n\nJi H, Deng H, Lu H, et al.: Predicting a Molecular Fingerprint from an Electron Ionization Mass Spectrum with Deep Neural Networks. Anal Chem. 2020; 92(13): 8649–53. PubMed Abstract | Publisher Full Text\n\nRamage D, Hall D, Nallapati R, et al.: Labeled LDA: a supervised topic model for credit attribution in multi-labeled corpora. In: Proceedings of the 2009 Conference on Empirical Methods in Natural Language Processing - EMNLP ’ 09. Singapore: Association for Computational Linguistics; 2009; 1: 248. Reference Source\n\nMa Y, Kind T, Yang D, et al.: MS2Analyzer: A Software for Small Molecule Substructure Annotations from Accurate Tandem Mass Spectra. Anal Chem. 2014; 86(21): 10724–31. PubMed Abstract | Publisher Full Text | Free Full Text\n\nvan der Hooft JJJ, Wandy J, Barrett MP, et al.: Topic modeling for untargeted substructure exploration in metabolomics. Proc Natl Acad Sci U S A. 2016; 113(48): 13738–43. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLiu Y, Mrzic A, Meysman P, et al.: MESSAR: Automated recommendation of metabolite substructures from tandem mass spectra. PLoS One. 2020; 15(1): e0226770. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHorai H, Arita M, Kanaya S, et al.: MassBank: a public repository for sharing mass spectral data for life sciences. J Mass Spectrom. 2010; 45(7): 703–14. PubMed Abstract | Publisher Full Text\n\nReder G: MS2 LLDA Topic Model. Zenodo . 2021. http://www.doi.org/10.5281/zenodo.4655149\n\nHaCohen-Kerner Y, Miller D, Yigal Y: The influence of preprocessing on text classification using a bag-of-words representation. PLoS One. 2020; 15(5): e0232525. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKind T, Fiehn O: Advances in structure elucidation of small molecules using mass spectrometry. Bioanal Rev. 2010; 2(1–4): 23–60. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRichards FJ: A Flexible Growth Function for Empirical Use. J Exp Bot. 1959; 10(2): 290–301. Publisher Full Text\n\nbab2min, Fenstermacher D: bab2min/tomotopy: 0.10.0. Zenodo. 2020; [cited 2021 Feb 1]. Reference Source\n\nDacrema MF, Cremonesi P, Jannach D: Are We Really Making Much Progress? A Worrying Analysis of Recent Neural Recommendation Approaches. Proc 13th ACM Conf Recomm Syst. 2019; 101–9. Publisher Full Text\n\nda Silva RR, Dorrestein PC, Quinn RA: Illuminating the dark matter in metabolomics. Proc Natl Acad Sci U S A. 2015; 112(41): 12549–50. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGopalan P, Charlin L, Blei DM: Content-based recommendations with Poisson factorization. In: Proceedings of the 27th International Conference on Neural Information Processing Systems. Cambridge, MA, USA: MIT Press; 2014; 2: 3176–84. (NIPS’ 14). Reference Source\n\nCallahan BJ, McMurdie PJ, Rosen MJ, et al.: DADA2: High-resolution sample inference from Illumina amplicon data. Nat Methods. 2016; 13(7): 581–3. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKind T, Tsugawa H, Cajka T, et al.: Identification of small molecules using accurate mass MS/MS search. Mass Spectrom Rev. 2018; 37(4): 513–32. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHuber F, Ridder L, Verhoeven S, et al.: Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships. PLoS Comput Biol. 2021; 17(2): e1008724. PubMed Abstract | Publisher Full Text | Free Full Text"
}
|
[
{
"id": "88758",
"date": "11 Aug 2021",
"name": "Joe Wandy",
"expertise": [
"Reviewer Expertise Metabolomics",
"machine learning",
"topic modelling."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nPredicting substructural information from LC-MS/MS fragmentation data is an important problem in untargeted metabolomics. In this work, the authors introduced a novel workflow to preprocess fragmentation data and perform supervised topic modelling approach using labeled latent Dirichlet allocation (LLDA). The LDDA model finds co-occurring fragment and loss features that are associated with chemical substructures provided by users.\nThe main benefit of incorporating label information through LLDA is that it allows for a list of substructures of interest to be inferred. Topics in LLDA are associated with meaningful substructure labels, aiding in model interpretation and improving from standard LDA where users are required to specify the number of topics in advance and manually annotate topics to provide chemical meaning - a time consuming and laborious process.\nIn this study, LLDA was evaluated on a benchmark dataset of 185 chemicals having known substructural annotations against a rule-based alternative (MESSAR) and a baseline k-nearest neighbour method, and it was found to perform competitively in retrieving substructural hits particularly when applied to new and unseen test data.\nOverall I think the work done in this manuscript is interesting and advances the field of substructural discovery in metabolomics. I am happy to recommend this for indexing as long as my comments below are addressed. The comments are separated into major and minor categories, and further divided by the corresponding sections of the manuscript.\nMajor comments\nSection: Data sets\nPlease make it clear that the ‘712 unique substructures provided in the rule database in [20]’ are obtained by selecting unique substructures entries from the final MESSAR database of 8378 association rules after filtering on FDR and recall. It’s also worth emphasising in the manuscript that these 712 unique substructures are mined from the GNPS dataset in [20]. Additionally please indicate in the manuscript how users could also generate their own list of substructures if they have unique/special datasets where the pre-generated GNPS list of substructures from [20] don’t apply.\nSection: Data Processing\nThe authors remarked that the process of extracting a document from a spectra is a computationally expensive process.- We note that this process can be quite time consuming if run on a single core - preprocessing a single spectrum using a single core can take more than two minutes depending on the spectrum. - Please provide more details what’s the breakdown of computational cost in the feature extraction script. Which part is the slowest? As I understand it, there are two steps to document creation: formula mapping and bag-of-words conversion. It seems that the largest computational cost would come from elemental formula enumeration via cdk. A typical fragmentation data set easily consists of a few thousand fragmentation spectra, and at two minutes each, the total feature extraction process could easily run up to days (for a single core) or many hours (for multicores). If true, please state this clearly in the manuscript so the reader is aware of it.\n\nIs performing elemental formula mapping actually necessary? The author comments that ‘keeping spectrum fragments that do not map to a child molecular formula but appear consistently across spectra (rather than discarding them as described in the Method)’ could be beneficial. This raises the question, is it necessary to perform such expensive procedure to map formulae to fragment and loss features, while the LDA (and LLDA model) could also work on the binned fragment and loss features that appear consistently across spectra, e.g. using ‘fragment_132.0152’ and 'loss_100.9203' as words of the document, following MS2LDA [19]. Filtering features by formula could also potentially remove frequently occurring fragment or loss features that are important to substructural identification. It would make the manuscript stronger if the authors could investigate how an alternative and simpler feature extraction scheme performs in comparison to what’s been done in the manuscript.\n\nSection: Training LLDA and predicting substructures in a new spectrum\nPlease expand the description of LLDA below. - The original LLDA model is described in full in 17. We note that every component of LLDA for modeling text documents has an analog useful for modeling a MS/MS spectrum. A document is an MS/MS spectrum, words are spectrum features (fragments and neutral losses), topics are commonly co-occurring spectrum features, and tags are chemical substructures (Figure 1). - I would like to see some textual elaboration of the plate diagram in Figure 1C, in particular the generative process of LLDA (using mass spec vocabularies) and how it differs from standard LDA. What are the advantages of LLDA vs LDA in this application? I had to refer to the original LLDA paper [17] and deduced all these things myself, but really it should be made explicit in the manuscript.\n\nWhat's the perplexity/log likelihood of LLDA compared to standard LDA on the training and test data sets? Also please report the wall clock of running 2000 iterations of LLDA. And what are the hyperparameters used for alpha and eta in the experiments? Were they using the defaults in tomotopy or were they optimised? How sensitive are the results in Table 1 to the choice of alpha and eta?\n\nIs there any particular reason why substructure predictions in test spectra are performed using the cosine similarity in equation 2, instead of directly inferring topic distributions for the new document using the trained model -- as what’s commonly done with LDA? It seems that in tomotopy this can be easily done using the make_doc and infer commands, so I don't understand why cosine similarity is used instead.\n\nSection: Preprocessing hyperparameter search\nPlease elaborate on how ‘t3>2’ is computed, specifically what are the meaning of the entries in the confusion matrix (TP, FP, TN, FN), and how precision and recall are defined in this context. I can see this is already defined in the MESSAR paper [20], but it would be useful to have it self-contained in this manuscript too (even if it’s in the supplementary) -- particularly since the terminology used here (‘t3>2’) is slightly different from [20].\n\nPlease include the results of t5≥3 and t10≥5 for completeness in the comparison to MESSAR? Also how's a ‘hit’ calculated in this manuscript? In MESSAR: - Small substructures with fewer than 5 non-hydrogen atoms were discarded. Based on the output of both tools, we retrieved the number of hits (when the predicted substructure is an exact match of ground-truth) among top 3, 5 and 10 recommended substructures.- Is it also done the same when computing the results in Table 1? If yes, please mention it here..\n\nSection: Conclusions\nIs there any downsides of using LLDA vs standard LDA?\n\nMinor comments\nSection: Data Processing\nIt should be made clearer that the ‘words’ used as input to the model are the elemental formulae, rather than the binned fragment and loss features - unless my understanding is incorrect?\n\nIn the code block of make_documents.py, the purpose of passing an R script (evaluate_peak.R) to --eval_peak_script is to be able to perform elemental formula annotation via rcdk, right? If yes, the manuscript should make it clearer. Also this is only my preference, but I prefer not to mix languages (Python and R) in a script, so would it be better to run the R script separately and generate an output file that can be read by the Python script later on?\n\nThe author notes that - “Substructure labels for training spectra having known parent chemical structures are assigned using the RDKit library (version 2020.09.5). Training spectra are labeled with the substructures in the user-defined set that are present in the given spectrum’s parent structure.\" - I think this paragraph can be made clearer as to what RDKit is used for. My understanding is: using RDKit, the SMILES of the parent structure of the training spectra are used to check for the presence of substructures from the list of 712 unique substructures. Present substructures are then used as labels of the training spectrum. Is this correct? If yes, please make it clearer in the manuscript.\n\nSection: Training LLDA and predicting substructures in a new spectrum\nThe text above equation 2 says that ‘the cosine similarity between a new spectrum i and substructure j’ but in the equation 2 below it, it shows the similarity between k and d instead. Please clarify.\n\nSection: K-nearest neighbors\nI found the description in this paragraph (below) to be somewhat confusing with regard to which spectrum is in the test, training and validation sets, although I could try to guess. 'To make a prediction for substructures associated with a new spectrum using the k-nearest neighbors algorithm, the k nearest neighbors in the training set of spectra are computed using the cosine similarity between the vectors corresponding to spectra in the training set. The score for each substructure in the new spectrum is calculated as the mean of the substructure presence and absence labels in the k nearest neighbors’ spectra.'\n\nSection: Preprocessing hyperparameter search\nThe figure caption mentions that the grid search on Q and B are done using the validation data set (MassBank), but the manuscript doesn’t seem to mention this. Please mention it too in the main text.\n\nSection: Conclusions\nThe paragraph that begins with ‘An example case study: …’ it seems to me it should be in the results rather than in the conclusion.\n\nCode availability\nPlease include the requirements file (or the conda equivalent) in the project github.\n\nCould also include a link to the data at https://doi.org/10.5281/zenodo.4589653 in the github, since the readme file mentioned ‘data’ but it isn’t found anywhere.\n\nThe script `run_baseline.py` is also mentioned in the readme but can’t be found in the github.\n\nThe manuscript should mention where the codes are that were used to calculate the performance in Table 1 (Substructure identification benchmark) and also for the Ablation study so it can be used for benchmarking and reproduction by the community. If they were not included in the code repository, perhaps they should be there.\n\nIs the rationale for developing the new method (or application) clearly explained? Yes\n\nIs the description of the method technically sound? Partly\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? Yes\n\nAre the conclusions about the method and its performance adequately supported by the findings presented in the article? Partly",
"responses": []
},
{
"id": "92355",
"date": "06 Sep 2021",
"name": "Hunter Moseley",
"expertise": [
"Reviewer Expertise metabolomics data analysis",
"metabolic network analysis",
"bioinformatics",
"systems biology"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is a paper that describes the use of labeled latent Dirichlet allocation (LLDA) in combination with k-nearest neighbor selection of library spectra to develop a set of molecular substructure classifiers for MS/MS spectra. While the paper is reasonably written and the results are interesting and useful for further methods development, there are the following major issues that should be addressed.\nMajor Issues:\nWhile Figure 1 is a very helpful introduction to how LLDA is being used, the combination of this figure and the main text is still difficult to discern the full mathematical form being used. As this reviewer (who has degrees in mathematics and computer science, but also teaches statistics) can discern, there is a deconvolution of per-substructure spectral feature probabilities from a training set of substructure-labeled spectra. This is done in terms of pairs of co-occurring spectral features per substructure. This reviewer suspects that a set of 2-dimensional Dirichlet’s are being deconvoluted (i.e., derived) during the supervised training. The authors should improve their description of the supervised learning so that these details are clear. Providing mathematical definitions of alpha, theta, beta, Z, W, Bernouli, and lambda would greatly aid this fundamental understanding of the methodology.\n\nThe authors point about k-NN for spectral library matching improving LLDA relative performance as the test set becomes more chemically distinct from the training set is important. However, it may highlight a more fundamental problem with utilizing k-NN to help identify all substructures for a given MS/MS spectrum. The fundamental issue may be missing the combination of spectral library spectra that provides complete coverage of spectral features in the test spectrum. If this is the case, then k-NN should not be blindly applied. This reviewer wants the authors to consider this possibility in their discussion.\n\nThe authors should indicate how heterogeneous in terms of analytical platforms and spectral resolution the LC-MS/MS spectra in the GNPS and MassBank spectra used in training and testing. Were any filtering criteria utilized in selecting these sets of spectra? There appears to be a de facto filtering of spectra which do not contain any peaks with associated molecular formulas.\n\nCoding style of the codebase is at the typical research programming level, which needs improvement. Here is a non-exhaustive list of needed improvements. There is no use of python docstrings. Many variable names are not descriptive. There is no main function defined and utilized in the accepted pythonic manner. There is global namespace pollution with some of the import statements. Codebase is also not designed as a full python package that allows both command line execution or use as a library. These comments come from an expectation for industrial standards of coding, even in scientific programming projects.\n\nIs the rationale for developing the new method (or application) clearly explained? Yes\n\nIs the description of the method technically sound? Partly\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? Yes\n\nAre the conclusions about the method and its performance adequately supported by the findings presented in the article? Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-403
|
https://f1000research.com/articles/7-1468/v1
|
14 Sep 18
|
{
"type": "Research Article",
"title": "A thermodynamic description for physiological transmembrane transport",
"authors": [
"Marco Arieli Herrera-Valdez"
],
"abstract": "A generic formulation for both passive and active transmembrane transport is derived from basic thermodynamical principles. The derivation takes into account the energy required for the motion of molecules across membranes, and includes the possibility of modeling asymmetric flow. Transmembrane currents can then be described by the generic model in the case of electrogenic flow. As it is desirable in new models, it is possible to derive other well known expressions for transmembrane currents as particular cases of the generic formulation. For instance, the conductance-based formulation for current turns out to be a linear approximation of the generic current. Also, under suitable assumptions, other formulas for current based on electrodiffusion, like the constant field approximation by Goldman, can also be recovered from the generic formulation. The applicability of the generic formulations is illustrated first with fits to existing data, and after, with models of transmembrane potential dynamics for pacemaking cardiocytes and neurons. The generic formulations presented here provide a common ground for the biophysical study of physiological phenomena that depend on transmembrane transport.",
"keywords": [
"Transmembrane transport",
"ion channels",
"passive transport",
"active transport",
"rectification",
"bidirectional assymetric flow",
"AMPA-Kainate receptor",
"excitable cell"
],
"content": "Introduction\n\nOne of the most important physiological mechanisms underlying communication within and between cells is the transport of molecules across membranes. Molecules can cross membranes either passively (Stein & Litman, 2014), or via active transport (Bennett, 1956). Molecules are passively transported across a membrane when they move along their (electro)chemical gradient and occurs through channels that may be spontaneously formed within the lipid bilayer (Blicher & Heimburg, 2013), or lined by transmembrane proteins (Hille, 1992; Stein & Litman, 2014) that may be selective for molecules of specific types (Almers & McCleskey, 1984; Doyle et al., 1998; Favre et al., 1996). Therefore, passive transport is (electro)diffusive in nature. In contrast, active transport takes molecules against their electrochemical gradients, and is mediated by transmembrane proteins commonly called pumps (e.g. symporters, exchangers) that mechanically translocate the molecules they transport (Bennett, 1956; Ussing, 1949a, Ussing, 1949b). The energy for active transport of molecules may be obtained from biochemical reactions (e.g. ATPases, light-driven pumps) or from the electrochemical gradients of molecules transported in parallel to the molecule that is actively transported (SKou, 1965). One important functional distinction between channels and pumps is that the rate of transport for channels is generally several orders of magnitude faster than the rate for pump-mediated transport (Gadsby, 2009; Ussing, 1949c). Such differences are reflected in the sizes of different transmembrane currents typically observed in excitable cells (Herrera-Valdez & Lega, 2011).\n\nTheoretical models of transmembrane transport play a critical role in developing our understanding of the function and mechanisms underlying electrical signaling and cellular excitability (Barr, 1965; Cole, 1965; DiFrancesco & Noble, 1985; Endresen et al., 2000; Gadsby, 2009; Goldman, 1943; Kell, 1979; Läuger, 1973; Stevens & Tsien, 1979; Wiggins, 1985a; Wiggins, 1985b; Wiggins, 1985c), and some of its associated pathologies (Ashcroft, 2005; Marbán, 2002). The best known transmembrane transport models include the widely used conductance-based formulation from the seminal work of Hodgkin & Huxley (1952), the Goldman-Hodgkin-Katz equation (Goldman, 1943; Hodgkin & Katz, 1949; Pickard, 1976), and several other expressions for carrier and channel mediated transport with many different functional forms (DiFrancesco & Noble, 1985; Rasmusson et al., 1990a; Rasmusson et al., 1990b; Rosenberg & Wilbrandt, 1955). Other formulations for ionic transport across membranes derived from biophysical principles available in the literature include those in the seminal work by Jacquez & Schultz (1974); Pickard, 1969; Pickard, 1976; see also Jacquez (1981) and similar work by Endresen et al. (2000), and those in the excellent book by Johnston et al. (1995). Such formulations describe the relationship between the activity and permeability of ions across membranes, and the transmembrane potential. However general models that describe physiological transport that include passive and active transport of charged or non-charged molecules, possibly including bidirectional but asymmetric flows, are still missing. The work presented here builds upon the results previously mentioned by describing transport macroscopically in terms of the energy required to move molecules across a membrane. The result is a generic formulation with a common functional form for both passive and active transport (Herrera-Valdez, 2014) that also includes a term that regulates the asymmetry in the flow (rectification).\n\nThe details of the derivation can be found are explained in the next section. Examples of fits to experimental data and features like asymmetric bidirectional flow. An application of the generic formulation is illustrated with models for the transmembrane potential dynamics in cardiac pacemaker cells and striatal fast spiking interneurons (Supplementary File 1) using the same functional forms for the currents. Derivations of formulas and specific examples of noncentral issues addressed in this article can be found in the Supplementary File 1.\n\nAn earlier version of this article is available on PeerJ as a preprint https://doi.org/10.7287/peerj.preprints.1312v8.\n\n\nGeneric formulation for transmembrane flux and current\n\nConsider a system consisting of a biological membrane surrounded by two aqueous compartments (e.g. extracellular and intracellular). Assume, to start with, that the compartments contain molecules of a single type s (e.g. Na+, K+, glucose), possibly in different concentrations. Let ΔGs be the energy required for the transport of the molecules across the membrane in a specific direction (e.g. inside to outside). To write an expression for ΔGs it is necessary to take the direction of motion of the s-molecules into account. To do so, label the extracellular and intracellular compartments as 0 and 1, respectively, and let cs and ds represent the source and the destination compartments for the transport of the s-molecules. The pair (cs, ds)=(0,1) represents inward transport and the pair (cs, ds)=(1,0) represents outward transport. The work required to transport ns molecules of type s from compartment cs to compartment ds can then be written as\n\n\n\n(Aidley, 1998; Blaustein et al., 2004; De Weer et al., 1988) where q, zs, [s]0, and [s]1 represent the elementary charge, the valence, the extracellular, and the intracellular concentrations for the molecules of type s, respectively. Two particular cases are worth noticing. First, if s is an ion, then zs ≠ 0 and Equation (1) becomes\n\n\n\nwhere vs is the Nernst potential for the s-molecules1 (Nernst, 1888). Second, if the s-molecules are not charged, then zs = 0 and the work required to move the s-type molecules from cs to ds simplifies to\n\n\n\nIf ΔGs < 0, then the molecules can be transported passively (e.g. electrodiffusion), decreasing the electrochemical gradient for s across the membrane. In contrast, if ΔGs > 0, the transmembrane transport of s from cs to ds is not thermodynamically favorable, which means the transport from cs to ds requires energy that is not available in the electrochemical gradient for s (active transport). As a consequence, active transport of s would increase the driving force for the motion of s across the membrane.\n\nTo find an expression for ΔG that describes a more general transport mechanism, assume that transport takes place as single events in which molecules of m different types move in parallel, or possibly sequentially (e.g. first Na+, then K+), across the membrane. Let S be a set that represents the types of molecules that are jointly transported in a single event. For instance, for Na+-H+ exchangers, S = {N a, H}, with m = 2. The energy required to transport these molecules is the sum of the energies required to transport each of the molecules in S. In other words,\n\n\n\nAs before, transport is thermodynamically favorable when ΔGs ≤ 0. If not, extra energy is required. To distinguish between these two cases, define the total energy of the transport mechanism as\n\n\n\nwhere δExt = 1 if ΔGs > 0, and 0 otherwise. In particular, for ATP-driven transport, the extra energy supplied by hydrolysis of ATP (De Weer et al., 1988; Tanford, 1981) is\n\n\n\nwhere vATP ≈ −450 mV (Endresen et al., 2000), but could vary depending on the amounts of ATP, ADP, and Pi (De Weer et al., 1988). Similar expressions could be derived for active transport driven by light, or other sources of energy.\n\nThe formulation in Equation (10) can be combined with Equation (1) to derive a generalized expression for flux and model different known mechanisms of physiological transmembrane transport, possibly combining the transport of different molecules simultaneously (e.g. Na-H exchange). In this case, the forward direction of the transport would be described by the combined forward transport of each of the different molecules under consideration. For instance, the source and target compartments for Na+ and Ca2+ are different in Na-Ca exchangers. The stoichiometry for the transport mediated by Na-Ca exchangers in the forward direction involves three Na+ molecules moving inward (along their electrochemical gradient) in exchange for one Ca2+ molecule moving outward (against their electrochemical gradient) (Mullins, 1979; Venetucci et al., 2007).\n\nLet α and β be the flux rates in the forward and backward directions, in units of molecules per ms per µm−2. These rates depend, a priori, on the energy required for the transport of the molecules in S. The net flux rate associated to the net transmembrane transport, can then be written as\n\n\n\nHow do α and β depend on ΔG? The steady state relationship between the energy ΔG and the the forward and backward flow rates, hereby represented by α and β, can be written as\n\n\n\nwhere k is Boltzmann’s constant, and T the absolute temperature.\n\nAssuming that α and β are continuous functions, the rates α and β can be rewritten as\n\n\n\nwhere r (molecules per ms per µm−2) may depend on temperature (Sen & Widdas, 1962), the transmembrane potential (Starace et al., 1997), the concentrations inside and outside of the membrane (Yue et al., 1990), and other factors (Novák & Tyson, 2008). Note that the functional form of the rates in Equations (9) are similar to those by Butler (1924); Erdey-Grúz & Volmer (1930). Also, notice that the steady state relationship between α and β in Equation (8) can be obtained from Equations (9), for any r and any b. However, it should be the case that r and b vary in specific ranges depending on the physico-chemical characteristics of the pore through which molecules cross the membrane, and in general, on the transport mechanism. As mentioned earlier, the rate r should be larger for electrodiffusive transport in comparison to the slower transport rates for pumps and other carrier proteins. If the parameter b ∈ [0, 1], then bΔG and (b−1)ΔG have opposite signs and can be thought of as the energies required to the transport of the molecules in S in the forward and backward directions, respectively, with b biasing the transport in the forward direction when close to 1, and in the backward direction when close to 0 (Figure 1).\n\nSee Table 1 for examples.\n\nThe flux can then be written explicitly combining Equation (7) and Equations (9) to obtain,\n\n\n\nTaking the above observations into account, it is possible to combine Equation (4) and Equation (5), to write an expression similar to Equation (8) for the steady state balance between the forward and backward transport of all the molecules in S.\n\nSubstitution of the formulas for ΔG from Equation (4) Equation (5) into Equation (10), the flux rate resulting from simultaneously transporting molecules in S across the membrane can be written explicitly\n\n\n\nwhere vT = kT/q and\n\n\n\nrepresents the net number of charges moved across the membrane.\n\nIf the transport is electrogenic, then the product qη (in Coulombs) represents the net charge moved across the membrane, relative to the extracellular compartment. Non electrogenic transport yields η = 0, which means the flow does not depend on the transmembrane potential, and\n\n\n\nIf only ions are involved in the transport, the flux simplifies to\n\n\n\nwhere\n\n\n\nThe quantity vo/η can be thought of as a reversal potential. If η < 0, then positive charge is transported inward, or negative charge is transported outward. In contrast, η > 0 means that positive charge is transported outward or negative charge transported inward. For instance, inward electrodiffusion of single Na+ ions gives an η = −1, which can be thought of as loosing one positive charge from the extracellular compartment in each transport event (see Table 1). In particular, for electrodiffusive (passive) transport of ions of type l, vo reduces to nlzl (cl − dl) vl. A list with examples of energies and total charge movements for different transport mechanisms can be found in Table 1.\n\nThe first, more complex, form of the flux in Equation (13) could be useful when working with models for which changes in the concentrations of different molecules are relevant.\n\nTransmembrane current. The flux that results in electrogenic transport (Equation (13) and Equation (14)) can be converted to current density after multiplication by qη. In short form,\n\n\n\nwith qr in amperes/m2 or equivalent units.\n\nSubstitution of Equation (13) or Equation (14) into Equation (16) yields a general formula for the current generated by transmembrane ionic flux (Figure 2), that uses the same functional form for channels (protein or lipid) and pumps. Recall that Equation (16) can also be written explicitly in terms of the transmembrane concentrations of one or more of the ions involved using Equation (13). It is possible to derive expressions for r that take into account biophysical variables like temperature and the shape and length of the pore through which the molecules cross (Endresen et al., 2000; Pickard, 1969).\n\nInward rectification occurs for bK < 1/2 and outward rectification for bK > 1/2 and qrK NK = 1.\n\nA number of nontrivial and important properties of transmembrane ionic currents, including rectification, are also described by Equation (16). Also, different models for current already in the literature can be obtained by making approximations or setting particular cases from Equation (16). Examples include electrodiffusive currents that result from integration of the Nernst-Planck equation along the length of membrane pore (Jacquez & Schultz, 1974; Johnston et al., 1995; Pickard, 1969). Of particular interest, conductance-based currents are linear approximations of the formulation (16), around the reversal potential for the current.\n\nLower order approximations to the generic formulation and conductance based models. Conductance-based currents (Hodgkin & Huxley, 1952) are linear approximations of the generic current from Equation (16), around the reversal potential vo/η. To see this, use Taylor’s theorem (Courant & John, 2012; Spivak, 2018) to rewrite the generic current from Equation (16) as a series around vo\n\n\n\nTruncation of the series to first order gives\n\n\n\nwhere g = η2qr/vT is in units of nS/µm2, which has the functional form of the conductance-based current used in the Hodgkin & Huxley (1952) model. For instance, the linear approximation for the current through an open sodium channels around vNa in Equation (18) gives gNa = qrNa/vT, and vo = ηNavNa, with ηNa = −1, so that iNa ≈ gNa(v − vNa).\n\nNotice that third order approximations to Equation (14) can also capture rectification. In contrast, first order approximations (conductance-based models) cannot capture rectification.\n\nRectification results from asymmetric bidirectional flow. The flux of molecules across the membrane can be biased in either the outward or the inward direction when mediated by proteins. This was first called ”anomalous rectification” by Katz (1949), who noticed that K+ flows through muscle membranes more easily in the inward, than in the outward direction (Adrian, 1969; Armstrong & Binstock, 1965). It was later found that some K+ channels display the bias in the opposite direction (Woodbury, 1971). The former type of K+ current rectification is called inward, and the latter outward.\n\nRectification is a bias in either of the two directions of transport, which may result from changes in the structure of the proteins or pores through which the molecules cross the membrane (Hollmann et al., 1991; Riedelsberger et al., 2015). The type of rectification (inward or outward) depends on what molecules are being transported and on the structure of the proteins mediating the transport. Rectification is therefore not only a property of ions, as shown by molecules like glucose, which may cross membranes via GLUT transporters bidirectionally, but asymmetrically, even when the glucose concentration is balanced across the membrane (Lowe & Walmsley, 1986).\n\nRectification can be described by Equation (13) by setting b to values different from 1/2, and becomes more pronounced as b is closer to either 0 or 1. These values represent biases in the transport toward the source, or the target compartment, respectively. As a consequence, rectification yields an asymmetry in the graph of α − β as a function of ΔG (Figure 2). For electrogenic transport, rectification can be thought of as an asymmetric relationship between current flow and voltage, with respect to the reversal potential vo. The particular case b = 1/2 (non-rectifying) yields a functional form for current similar to that proposed by Pickard (1969), and later reproduced by (Endresen et al., 2000), namely\n\n\n\nFrom here on, subscripts will be used to represent different transport mechanisms. For instance, the current for a Na-Ca pump will be written as iNaCa.\n\nElectrodiffusion of K+ through channels (η = 1 and v0 = vK), is outward for v > vK, and inward for v < vK. The K+ current through the open pore is therefore\n\n\n\nCurrent flow through inward rectifier channels (Riedelsberger et al., 2015) can be fit to values of bK < 1/2. For instance,\n\n\n\ndescribes a current with limited flow of K+ in the outward direction, similar to the currents described originally by Katz (1949). Analogously, bK > 1=2 limits the inward flow. For example, the current\n\n\n\ndescribes outward rectification (Riedelsberger et al., 2015).\n\nBased on the work of Riedelsberger et al. (2015) on K+ channels, inward (outward) rectification arises when the S4 segment in K+ channels is located in the inner (outer) portion of the membrane. These two generic configurations can be thought of in terms of ranges for the parameter bK, namely, bK < 1/2 for inward, and bK > 1/2 for outward rectification.\n\nIn general, ion channels are typically formed by different subunits, that may combine in different ways, resulting in structural changes that may restrict the flow of ions through them, causing rectification. For instance, non-NMDA glutamatergic receptors that can be activated by kainic acid and α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid (AMPA) conduct Na+, K+, and Ca2+, with different permeabilities depending on the subunits that form the receptor (Hollmann et al., 1991). The reason is that the specific combination of GluR subunits forming the receptor restrict ionic flow in different ways. In particular, the currents recorded in oocytes injected with combinations of GluR1 and GluR3 cRNA have different steady state amplitudes and show different levels of rectification (Figure 3).\n\nThe curves were fit with (vo, b, rq)=(-30,0.45,21), for GluR3 and (vo, b, rq)=(-35,0.35,20), for GluR1+GluR3. The data was digitized from Figure 3B in the article by Hollmann et al. (1991), using the ginput function from the python module matplotlib (Hunter, 2007) - see Supplementary File 2.\n\nPrimary active transport. The Na-K ATPase is a primary active transporter that uses the energy from the hydrolysis of one molecule of ATP for the uphill transport of Na+ and K+ (De Weer et al., 1988). The kinetics of the Na-K ATPase can be assumed to translocate 3 Na+ ions outward and 2 K+ ions inward (ηNaK = 1) with a reversal potential νNaK = vATP + 3νNa − 2vK (see Table 1) in a single transport event (Chapman, 1973; Garrahan & Glynn, 1967; Gadsby et al., 1985; Post & Jolly, 1957). Importantly, the transport kinetics of the Na-K ATPase and by extension, the current, reverse for potentials smaller than vNaK (De Weer et al., 1988).\n\nThe current-voltage relationships recorded from Na-K ATPases in guinea pig ventricular cells are shaped as hyperbolic sines (Gadsby et al., 1985). Those currents would be fit with bNaK ≈1/2, yielding currents of the form\n\n\n\nThe voltage-dependence of the Na-K ATPase currents is reported to show a plateau as v increases past the reversal potential for the current, in response to steroids like strophandin (Nakao & Gadsby, 1989). In such cases, the Na-K ATPase current can be assumed to be inwardly rectifying and fit with values of bNaK ≈ 0, so that,\n\n\n\nor alternatively,\n\n\n\nThe rectification for the Na-K pump ATPase has also been reported to occur in small neurons of the dorsal root ganglion in rats (Hamada et al., 2003). The alternative expression (25) also explains qualitatively different behaviors of the Na-K current as a function of the transmembrane concentrations of Na+ and K+. For instance, if either [Na]1 or [K]0 increase and v > vNaK, then the amplitude of iNaK would increase at a smaller rate of change in comparison to when v < vNaK, which grows exponentially in size. This is also in line with reports of non significant changes in the transport by Na-K ATPases in response to elevated intracellular Na+ during heart failure (Despa et al., 2002), in which the transmembrane potential is likely to be depolarized.\n\nSecondary active transport. An example of a pump that mediates secondary active transport is the Na-Ca exchanger, which takes 3 Na+ ions from the extracellular compartment in exchange for one intracellular Ca2+ ion in forward mode (Pitts, 1979; Reeves & Hale, 1984). The reversal potential for the current is vNaCa = 2vCa − 3vNa, with ηNaCa = 1. Assuming bNaCa = 1/2, the Na-Ca current is\n\n\n\nThe driving force v − vNaCa could reverse in sign with large enough increases in the intracellular concentration of Ca2+, or in the membrane potential. As a result, the current could have a dual contribution to the change in transmembrane potential, as predicted by some theoretical models of cardiac pacemaker activity (Rasmusson et al., 1990a; Rasmusson et al., 1990b).\n\nElectrodiffusive transport. Consider transmembrane electrodiffusive transport of a single ionic type x, with zx and vx representing the valence and the Nernst potential for x-ions, respectively. In this case, the reversal potential satisfies\n\n\n\nand the generic expression (16) can be rewritten as\n\n\n\nIn the absence of rectification (bx = 0.5),\n\n\n\nFor calcium channels,\n\n\n\nSee Jacquez & Schultz (1974); Pickard (1969) Table 1 for other examples.\n\nThe applicability of the general formulations described above is illustrated next with models of cardiac and neuronal membrane potential.\n\n\nTransmembrane potential dynamics\n\nTo show the application of the formulations discussed earlier, let us build a generic model of transmembrane potential dynamics with currents generated by N different electrogenic transport mechanisms. For simplification purposes, consider only one such mechanism, labeled as l, with plNl active sites, where Nl is the number of membrane sites where the lth transport mechanism is found, and pl is the proportion of active sites (might be voltage or ligand dependent). Then the total current mediated by the lth mechanism in a patch of membrane can be written as ālplφl(v) with āl = qNl rl (in pA/µm2), and\n\n\n\nwhere vl/ηl is the reversal potential for the lth current, l ∈ {1, …,N}. There is experimental evidence for some ion channels that supports the replacement of āl as a constant (Nonner & Eisenberg, 1998). The time-dependent change in transmembrane potential can written as\n\n\n\nwith v is in mV and āl = āl/CM in mV/mS (pA/pF) represents the current amplitude for the lth transport mechanism, normalized by the membrane capacitance, for l ∈ (1, …, N). Only electrogenic transport mechanisms are included.\n\nThe pacemaking dynamics of cells in the rabbit sinoanatrial node (Figure 4) can be modeled using low dimensional dynamical systems based on the assumption that v changes as a function of K+, Ca2+, and some Na+ transmembrane transport, (Herrera-Valdez & Lega, 2011; Herrera-Valdez, 2014). Transmembrane currents are assumed to be mediated by a combination of channel-mediated electrodiffusion and pumping mechanisms. Explicitly, Ca2+ transport is mediated by L-type Cav13 channels (Mangoni et al., 2003) and Na+-Ca2+ exchangers (Sanders et al., 2006). K+ transport is mediated by delayed-rectifier voltage-activated channels (Shibasaki, 1987), and Na+-K+ ATPases (Herrera-Valdez & Lega, 2011; Herrera-Valdez, 2014). In this model, the activation for the L-type Ca2+ channels is fast, and assumed to be at steady state (Herrera-Valdez & Lega, 2011). The proportion of activated K+ channels and the proportion of inactivated Ca2+ channels are both represented by a variable w (Av-Ron et al., 1991; Herrera-Valdez & Lega, 2011). The activation phase of currents recorded in voltage-clamp experiments often displays sigmoidal time courses (Covarrubias et al., 1991; Hodgkin & Huxley, 1952; Tsunoda & Salkoff, 1995). Therefore, the activation dynamics represented by w are described by solutions to equations of the form\n\n\n\nA. Transmembrane potential and the reversal potential vNaCa as a function of time. B,C. Dynamics of large currents and small currents, respectively.\n\nwhere Fw and Rw represent the voltage-dependent steady state and rate (1/ms) for the opening of Kd channels (Willms et al., 1999). The steady state for the activation of voltage-dependent channels is described by the function\n\n\n\nwhich has a graph with increasing sigmoidal shape as a function of v. The parameters gu and vu control the steepness and the half-activation potential, for u ∈ {m, w}. The activation rate for K+ channels is a voltage-dependent function of the form\n\n\n\nwhere bw represents a bias in the conformational change for activation. The function Rw has the shape of a hyperbolic cosine when bw is 1/2. The transmembrane (normalized) currents are given by\n\n\n\n\n\n\n\n\n\nwhere c represents the intracellular Ca2+ concentration, and φx is a difference of exponential functions as defined above, with x ∈ {NaK, NaCa, KD, CaL}. The temporal evolution for v is then described by\n\n\n\nDuring pacemaking the concentrations of Na+ and K+ across the membrane are assumed to change negligibly, but the Ca2+ concentration does change at least 10-fold (Herrera-Valdez & Lega, 2011; Rasmusson et al., 1990a; Rasmusson et al., 1990b). Therefore, the system includes an equation for the dynamics for c in which c converges to a steady state c∞ in the absence of Ca2+ fluxes, and increases proportionally to the total transport of Ca2+ ions via L-type channels and Na+-Ca2+ exchangers (Figure 4). Explicitly,\n\n\n\nwhere kc (µM/mV) represents the impact of the transmembrane Ca2+ fluxes on the free intracellular Ca2+ concentration. The minus sign in front of kc accounts for the fact that the sign of the JCaL is negative. The sign in front of JNaCa is because the forward flux of Ca2+ mediated by the Na-Ca exchanger is opposite to that of electrodiffusive Ca2+.\n\nA. Behavior of the inactivating L-type Ca2+ current with respect to the transmembrane potential (blue line) and a non-inactivating current (gray line), and (B) with respect to the time-dependent change in v.\n\nThe solutions of Equation (32)–Equation (40) with parameters as in Table 2 reproduce important features of the membrane dynamics observed in the rabbit’s central sinoatrial node, including the period (ca. 400 ms), amplitude (ca. 70 mV), and maximum ∂t v (<10 V/s) of the action potentials (Zhang et al., 2000).\n\nThe amplitudes al can be thought of as āl/CM where CM is a constant that represents the rate of change in charge around the membrane as a function of v, and l ∈ {CaL, K, NaK, NaCa}.\n\nThe solutions of the system show a number of interesting features related to ionic fluxes. First, the Na-Ca current reverses when v = vNaCa (Figure 4A, blue line). During the initial depolarization and until the maximum downstroke rate, approximately, vNaCa < v, which means JNaCa > 0, so that Ca2+ extrusion by the Na-Ca exchanger occurs only for a brief period of time during the downstroke and also after each action potential (Figure 4C, blue line). Second, as previously reported in different studies involving spiking dynamics, the time course of the Ca2+ current shows a partial inactivation with a double peak (Figure 4B, blue line) around a local minimum (Carter & Bean, 2009; Rasmusson et al., 1990a; Rasmusson et al., 1990b), and in agreement with data from voltage-clamp experiments (Mangoni et al., 2006). A number of models have made attempts to reproduce the double activation by making extra assumptions about gating (Rasmusson et al., 1990a; Rasmusson et al., 1990b). For instance, some models include a second activation variable, or the multiple terms in the steady state gating, or in the time constant for activation or inactivation. However, the explanation for the double peak can be much simpler. The calcium current JCaL is a negative-valued, non monotonic function for v < vCa, which can be thought of as a product of a amplitude term that includes gating and the function φCaL. The normalized current JCaL has a local minimum (maximum current amplitude) around -10 mV (Figure 4B, blue line and Figure 5A, blue line), after which the current decreases, reaching a local maximum as the total current passes through zero, at the peak of the action potential around 10 mV, (Figure 4B, where ∂t v = 0). The first peak for the Ca2+ current occurs when v reaches the maximum depolarization rate (Figure 5B). As v increases (e.g. upstroke of the action potential). The second peak for the current occurs as the membrane potential decreases, and passes again through the region where the maximal current occurs (local minimum for JCa). The two local minima for JCaL represent peaks in the Ca2+ current that have different amplitudes due the difference in the time course of v during the upstroke and the downstroke of the action potential (Figure 5A, blue line, and Figure 5B, where ∂t v = 0). It is important to remark that the dual role played by w is not the cause of the double activation. This is illustrated by analyzing the behavior of a non-inactivating JCaL without the inactivation component, (Figure 5A, gray line). The double activation can also be observed in models in which the activation of K+ channels and the inactivation of Ca2+ or Na+ channels are represented by different variables (Rasmusson et al., 1990a) and in dynamic voltage clamp experiments on neurons in which there are transient and persistent sodium channels (Carter & Bean, 2009).\n\nThe double peak in the Ca2+ current is reflected in the intracellular Ca2+ concentration (Figure 6, gray line), and by extension, on the Nernst potential for Ca2+ (Figure 6, blue line), which display two increasing phases and two decreasing phases, respectively. The first and faster phase in both cases occur during the initial activation of the L-type channels. The second phase occurs during the downstroke, as second peak of the Ca2+ current occurs. As a consequence, the reversal potential for the Na-Ca exchanger, vNaCa = 3vNa − 2vCa (Figure 6, orange line) also has two phases, this time increasing. Increasing the intracellular Ca2+ (Figure 6, gray line) concentration decreases the Nernst potential for Ca2+, and viceversa. By extension, the reversal potential for the Na-Ca exchanger, vNaCa = 3vNa − 2vCa becomes larger when c increases. Ca2+ enters the cell in exchange for Na+ that moves out when v > vNaCa, during most of the increasing phase and the initial depolarization phase of the action potential (blue lines in Figure 4A and C, and Figure 6).\n\nTime courses of the intracellular calcium concentration (gray, left axis), the Nernst potential for Ca2+ (orange, right axis), and the reversal potential for the Na-Ca exchanger (blue, right axis).\n\n\nDiscussion\n\nA generic, macroscopic model for transmembrane fluxes has been derived by directly calculating the work required to transport molecules across the membrane. The derivation is based on a general thermodynamic scheme that takes into account the rate, stoichiometry, and the direction in which the molecules are transported across the membrane. These biophysical parameters are then combined to write expressions for directional fluxes based on van’t Hoff (1884) and Arrhenius (1889) formulations, weighted as in the Butler/Erdey-Gruz/Volmer equation (Butler, 1924; Erdey-Grúz & Volmer, 1930). The result is a general description (Equation 16) of the transmembrane molecular flux as a difference of exponential functions, that describes the transport dynamics in the \"forward\" and \"backward\" directions, relative to a source compartment. The two exponential functions depend on a common expression involving the transmembrane concentrations of the molecules being transported, and possibly the transmembrane potential when transport is electrogenic.\n\nRectification, an asymmetry in the flow, is typically modeled modifying the dynamics of the gating variables of the current. The general formulas for transmembrane transport include a bias term b that controls the relative contribution of inward and outward components the transport. Hence, different types of rectification can be described by favoring one of the directions for transport, conceptually in line with the ”anomalous rectification\" originally reported by Katz (1949) for K+ in muscle cells. The bias term is not part of any gating mechanism. Instead, it represents the asymmetry in bidirectional flux Based on the work of Riedelsberger et al. (2015), the inward (outward, respectively) rectification in K+ channels occurs when the fourth transmembrane segment of the channel (S4) is located closer to the intracellular (extracellular) portion of the membrane in its open configuration. There are other reports that show that asymmetries in bidirectional transport occur as a consequence of changes in the three dimensional structure of the protein mediating the transport (Halliday & Resnick, 1981; Quistgaard et al., 2013). Therefore, the rectification term can be thought of as representing a structural component of the transmembrane protein through which molecules move (Figure 2). Outward rectification in K+ channels can be explained, for instance, by biasing the flux of K+ the forward (outward) direction (bK > 1/2). Instead, inward rectification can be obtained by biasing the transport in the backward (inward) direction (bK < 1/2). It is important to remark that non-rectifying currents with b = 1/2 are nonlinear functions of ΔG, which shows that the nonlinearity of the current-voltage relationships is not the defining characteristic of rectification; as argued in some textbooks (see Kew & Davies, 2010).\n\nThe formulation for transmembrane flux may be rewritten in different alternative forms that can be found throughout the literature (see Equation (13) and Equation (14), Goldman, 1943; Johnston et al., 1995). Of particular interest, the widely used conductance-based models for current from the seminal work of Hodgkin & Huxley (1952) turn out to be linear approximations of the generic current described here (Herrera-Valdez, 2012; Herrera-Valdez, 2014). This explains why the Hodgkin & Huxley (1952) model captures many of the defining features of action potential generation, in spite of modeling ionic currents as resistive. Another interesting case is that electrodiffusive transmembrane currents derived from the Nernst-Planck equation (Nernst, 1888; Planck, 1890), turn out particular cases of the generic formulation presented here (see also Herrera-Valdez, 2014, for details). Examples include the constant field approximation (Clay et al., 2008; Hille, 1992; Johnston et al., 1995), the non-rectifying currents proposed by Endresen et al. (2000), and more general electrodiffusive currents that includes a bias term accounting for rectification (Herrera-Valdez, 2014; Johnston et al., 1995).\n\nPossibly of interest to mathematicians working on bifurcation theory, a third order approximation (Equation (17)) resembling the Fitz-Hugh equations (FitzHugh, 1955; FitzHugh, 1961; Fitz-Hugh, 1966), can be used to construct models that give very close approximations to the full model, while keeping biophysical characteristics like rectification and the multiplicative interaction between the slow variable w and the fast variable v. Further, the third order approximation opens the possibility of expanding on the analysis of dynamical systems based on these generic formulas to study normal forms and bifurcations. Another possible use of the third order approximations is in the construction of network models.\n\nOne question of interest because of its possible impact on the interpretation of results from existing modeling studies is how does the excitability and the resulting dynamics in a model of membrane dynamics change when using the thermodynamic transmembrane currents or their approximations? The question has been addressed in a study in which two simple neuronal models with currents mediated by Na+ and K+, each equipped with the same biophysical gating properties and the same relative contributions for the currents, but one with currents as in Equation (19), the other with conductance-based currents. The two models display a number of qualitative and quantitative differences worth considering while making the choice of a model in theoretical studies (Herrera-Valdez, 2012). For a start, the two models are not topologically equivalent across many ratios of the relative contributions of K+ and Na+ channels (Herrera-Valdez, 2012); as would be expected by the fact that conductance-based formulations are only linear approximations of the generic currents. One of the most notable differences is the contribution of the nonlinear, high order terms from Equation (16), which results in more realistic upstrokes for action potentials and an overall increased excitability; in this case characterized in terms of the minimum sustained current necessary to produce at least one action potential. The increased excitability of the membrane is due, in part, to the large, exponential contribution of the open Na+ and Ca2+ channels, but not the K+ channels, to the change in the transmembrane potential near rest. The time course of the Na+ current during the beginning of the action potential with the generic model is much sharper than that of the conductance-based formulation, resulting in a faster upstroke of the action potential; and in better agreement with observations in cortex and other tissues (Naundorf et al., 2006). It is important to remark that the sharper increase in the change of the membrane potential is a consequence of the nonlinear driving force terms of the current (the flux term in the generic formulation) and not in the activation dynamics for the transient Na+ current.\n\nThe generic formulation for both passive and active transmembrane transport can be thought of as a tool that facilitates the construction and analysis of models of membrane potential dynamics. The generality and versatility of the thermodynamic transmembrane transport formulations is illustrated with a model of the dynamics of cardiac pacemaking (Equations (39)-(34)). Another example with a model for a fast spiking interneuron can be found in Supplementary File 1. The ion fluxes in the model are assumed to be mediated by two different types of voltage-gated channels and two different types of pumps, all represented with the same functional form (see DiFrancesco & Noble (1985); Herrera-Valdez & Lega (2011); Rasmusson et al. (1990b) for examples in which that is not the case).\n\nOne important advantage of the generic formulation is that it includes the possibility of explicitly estimating the number of channels or pumps mediating each of the transport mechanisms of interest. This has proven to be useful to study the relative contributions of different currents to the excitability of neurons (see Herrera-Valdez et al., 2013) and cardiocytes (Herrera-Valdez, 2014).\n\nAnother extension of possible interest is that of modelling the transmembrane transport between organelles and the cytosolic compartment, which can be done by directly replacing the difference cs − ds in Equation (1) with 1 or -1, accounting for the direction of transmembrane motion of molecules relative to the outer compartment. This and other generalizations enable the possibility of studying the interdependence between electrical excitability across tissues and animal species (Herrera-Valdez et al., 2013), and its cross-interactions with metabolism and other processes of physiological importance, all from a general theoretical framework with common formulations.\n\nImplications for experimentalists. One of the main advantages of the generic expressions is that fits to ionic currents can be made straight from the voltage-clamp data without much effort, and without having to calculate conductances, which amounts to imposing the assumption that the current to voltage relationship is linear. Fits to experimental currents can then be directly put into equations describing the change in the membrane potential, and model membrane dynamics of interest without having to make many extra adjustments, as it is the case for most conductance-based models restricted to data.\n\nThe model for current in Equation (19) has been used to construct simplified models for the membrane dynamics of different cell types using experimental data. Examples include motor neurons in Drosophila melanogaster (Herrera-Valdez et al., 2013), pyramidal cells in the young and ageing hippocampus of rats (McKiernan et al., 2015), medium spiny neurons in the mouse striatum (Suárez et al., 2015), rabbit sinoatrial node cells (Herrera-Valdez, 2014), and other types of excitable cells (McKiernan & Herrera-Valdez, 2012).\n\n\nConclusions\n\nA generic model that describes physiological transmembrane transport of molecules has been derived by considering basic thermodynamical principles. The model unifies descriptions of transport mediated by channels and pumps, it can model biases in either one of the directions of flow, and it can be easily converted into a model for current in the case of electrogenic transport. As it is desirable in all models, the generic expressions can be thought of as extensions of some previous models. In particular, it is shown that the conductance-based model for current turns out to be a first order approximation of the generic formulation.\n\nThe expressions for current and molecular fluxes across the membrane based on the generic formulation can be used to build general models of transmembrane potential using a unified framework (Shou et al., 2015).\n\n\nData availability\n\nAll data underlying the results are available; two source data files are included with this article (Supplementary File 2).\n\n\nNotes\n\n1The transmembrane potential for which there is a zero net flux of s-ions across the membrane, as given by the Nernst-Planck equation, is\n\n",
"appendix": "Grant information\n\nThis work was supported by UNAM-PAPIIT IA208618.\n\nThe funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.\n\n\nAcknowledgements\n\nThe author wishes to thank Joceline Lega, Timothy Secomb, and Raphael Gruener at the University of Arizona; Jose Bargas-Diaz and Antonio Laville from the Cellular Physiology Institute at UNAM; and Erin C. McKiernan from the Physics Department at UNAM for all the time spent in discussions that helped to solidify and deepen the ideas presented in this paper.\n\n\nSupplementary material\n\nSupplementary File 1: The Goldman constant field approximation from the general formulation.\n\nClick here to access the data.\n\nSupplementary File 2: CaPermeabilityKA-AMPA-GatedGluR_Hollman et al. (1991). Figure 3B GluR3 and GluR1+3.\n\nClick here to access the data.\n\n\nReferences\n\nAdrian RH: Rectification in muscle membrane. 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{
"id": "38363",
"date": "01 Oct 2018",
"name": "Kyle C.A. Wedgwood",
"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\nThank you for inviting me to review the article entitled \"A thermodynamic description for physiological transmembrane transport\". This article presents a unifying mathematical formulation for passive and active transport across plasma membranes. This is achieved by considering the energy required to achieve transport of the molecules. For active transport, in which molecules are transported against their concentration gradient, the required energy is positive. In contrast, passive movement down a concentration gradient does not require energy transfer. In previous modelling frameworks, active and passive transport have been described via distinct models for pumps and channels respectively. The major contribution of this paper is to combine these models into one formulation.\nAfter presenting the initial mathematical formulation, the article proceeds to make comparisons with existing literature and demonstrates that earlier mathematical models of channels are special cases of the more general framework. The article ends with an example in which the full model can explain a double activation event of Ca2+ channels, which cannot be done so satisfactorily by existing models.\nIn general, the article is well-written, with arguments made concisely and coherently. Aside from a few points which require further clarification, I believe that this article is sufficiently rigorous and of interest to the community to warrant publication. In particular, channel and pump models have long been used in the mathematical study of excitability in cell membranes. These models have been used to support and guide experimental studies as well as advancing the applied mathematics field in its own right. As such, improvements to these models should be welcomed by the field.\nI will now address specific issues with the article:\nIn general, I believe that the figure captions could do with expanding to guide the reader's eyes to the features of the plot that they should be focusing on.\n\np2, first paragraph: At present, the discussion of passive and active transport in the Introduction is a little confusing. In particular, there are transmembrane proteins that undergo conformational changes to transport molecules down their concentration gradient and channels that achieve this by effectively forming pores through the membrane (so that further conformational change is not needed to effect transport). Furthermore, the reference Blicher & Heimberg, 2013 reports on spontaneous (protein-free) formation of channels in synthetic membranes. Whilst this is an interesting topic, it should be made clearer how this relates to physiological membranes. Finally, it might also be useful to the reader to give an example of how some of the different pump configurations work (e.g. uniporter, symporter) to facilitate understanding of where energy transfer is required.\n\np2, 3rd paragraph: \"Examples of fits to...\" This is not a sentence. Please revise.\n\np2, 3rd paragraph: The author should highlight what \"noncentral issues\" they are referring to.\n\np2, 5th paragraph, minor: It would be useful to highlight that cs, ds \\in {0,1}.\n\np2, Eq. (1): v is not defined.\n\np2, footnote, minor: Change \"log\" to \"ln\" here for consistency with Eq. (1) and (3).\n\np3, 2nd paragraph: It would be good to clarify in this first sentence the distinction between \\Delta G and \\Delta G_s (or avoid using the former entirely).\n\np3, 2nd paragraph: S = {Na,H} typo here.\n\np3, Eq. (5): Similarly to point (7), it is not clear what \\Delta G represents here.\n\np3, Eq. (6): Terms in this equation need defining properly in several regards. Firstly, \\Delta GATP0 should be defined. Secondly, it should be made clear that concentrations are intracellular (as opposed to in Eq. (1) (3), which correspond to both extra- and intracellular compartments). This is particularly confusing for Pi in which the subscript could easily be misread as being an intracellular label. Finally, it is not clear how the equality \\Delta GATP = qvATP holds. Perhaps, as in footnote (1), it could be made clear that this relies on the definition of the reversal potential for ATP.\n\np3, Eq. (6): I would also here like to take the opportunity to raise a point about the general framework. The models here account for the energy required to move molecules with and against their concentration gradients. In cases of active transport, as indicated by Eq. (10), ATP is then hydrolysed to meet the energy deficit required to power the pump. This then means that the concentration of ATP, relative to ADP is then changing. Indeed, at maximal rates of exercise, the ATP concentration in skeletal muscle can fall by up to 20% of its initial value. Moreover, in certain cell types, local ratios between ATP and ADP affect the opening and closing of ion channels (e.g. KATP). Eq. (10) implies that ATP and ADP in the cell are constant, in spite of the necessity that it must change. One must, therefore, conclude that an assumption is being made that ATP changes are small relative to the total amount of ATP. This assumption should be stated, or a discussion around how changes to ATP concentrations effect Eq. (10) should be made.\n\np3, final paragraph of first column: Wrong equation being referred to.\n\np3, Eq. (9): A physical interpretation for parameters r and b should be given. Additionally, and referring back to my previous comment (1), the text here discusses the relative magnitudes of r for electrodiffusive and active transport. Thus, this point should make clear that ion channels should be faster than both facilitated diffusion through carrier proteins and active transport via pumps.\n\np4, Eq. (11): For consistency with Eq. (5), 'Extra' in the subscripts should read 'Ext'. Also, it should be noted that vExtra should be the vATP from Eq. (6).\n\np4, \"In particular, for electrodiffusive (passive) transport of ions of type l\": It is not clear what the author is referring to here (or how it is different from what is written in Eq. (15)).\n\np4, \"The first, more complex form...\": Does the author mean to reference Eq. (11) here?\n\np4, After Eq. (16), minor: \"Ampere\" needs capitalising.\n\np5, Table 1: Is v0 here the same as in Eq. (15)? If so, the dependency on vExt seems to have disappeared.\n\np6, Fig. 2: What is plotted on the ordinate axis in this graph? It appears to have units of pA, but the text says that this is a plot of alpha/beta, which should be dimensionless.\n\np8, \"Electrodiffusive transport\": I'm not really sure what the point of this section is since the results presented here have mostly been mentioned previously in this manuscript.\n\np8, after Eq. (31): Is the N written here supposed to be N_l? Also, there is a typo after Eq. (31) (with -> where).\n\np9, Eq. (33): m is not defined.\n\np9, Eq. (35-39): Change symbol for current to ix for consistency with previous equations.\n\np9, after Eq. (39): Presumably, the author here means that the intracellular Ca2+ concentration changes (rather than the extracellular). This should be clarified. Also, the text below Eq. (40) appears to imply a distinction between free and bound Ca2+, but there is no buffering process described in the model, which may cause confusion.\n\np9, Fig. 2: Please state what im and iCaL13 are in these plots.\n\np10, Table 2: The units of \\bar{a} are inconsistent with the main text.\n\np12, \"Another possible use of the third order approximations is in the construction of network models.\": Please could the author state what they mean here?\n\np13, discussion on action potential shape: I was wondering if the author could here compare their argument surrounding the shape of the action potential near initiation with those put forward here (Brette, 20131), which puts forward a case for multi-compartment models to describe the sharpness of the spike.\n\nSI1, after (A3): There appears to be a reference missing here.\n\nSI2: Headers are required in these data files so that the values herein can be related to the physical quantities they represent.\n\nIt would be useful for the author to upload any code used to generate the plots in the article.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\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? Yes",
"responses": [
{
"c_id": "4107",
"date": "08 Nov 2018",
"name": "Marco Arieli Herrera-Valdez",
"role": "Author Response",
"response": "The answers to comments made by reviewers are written in italics after each comment. Answers to comments from Reviewer 1Thank you for inviting me to review the article entitled \"A thermodynamic description for physiological transmembrane transport\". This article presents a unifying mathematical formulation for passive and active transport across plasma membranes. This is achieved by considering the energy required to achieve transport of the molecules. For active transport, in which molecules are transported against their concentration gradient, the required energy is positive. In contrast, passive movement down a concentration gradient does not require energy transfer. In previous modelling frameworks, active and passive transport have been described via distinct models for pumps and channels respectively. The major contribution of this paper is to combine these models into one formulation.After presenting the initial mathematical formulation, the article proceeds to make comparisons with existing literature and demonstrates that earlier mathematical models of channels are special cases of the more general framework. The article ends with an example in which the full model can explain a double activation event of Ca2+ channels, which cannot be done so satisfactorily by existing models.In general, the article is well-written, with arguments made concisely and coherently. Aside from a few points which require further clarification, I believe that this article is sufficiently rigorous and of interest to the community to warrant publication. In particular, channel and pump models have long been used in the mathematical study of excitability in cell membranes. These models have been used to support and guide experimental studies as well as advancing the applied mathematics field in its own right. As such, improvements to these models should be welcomed by the field.Thank you for your comments. They make the article clearer and better.. Please find answers to each of them below.I will now address specific issues with the article:1. In general, I believe that the figure captions could do with expanding to guide the reader's eyes to the features of the plot that they should be focusing on.I have added phrases pointing to specific parts of the graphs or mentioning specific things to notice in each of the figures.2. p2, first paragraph: At present, the discussion of passive and active transport in the Introduction is a little confusing. In particular, there are transmembrane proteins that undergo conformational changes to transport molecules down their concentration gradient and channels that achieve this by effectively forming pores through the membrane (so that further conformational change is not needed to effect transport). Furthermore, the reference Blicher & Heimberg, 2013 reports on spontaneous (protein-free) formation of channels in synthetic membranes. Whilst this is an interesting topic, it should be made clearer how this relates to physiological membranes. Finally, it might also be useful to the reader to give an example of how some of the different pump configurations work (e.g. uniporter, symporter) to facilitate understanding of where energy transfer is required.The first paragraph in p2 has been rewritten taking into account the above observations.3. p2, 3rd paragraph: \"Examples of fits to...\" This is not a sentence. Please revise.Thank you, corrected.4. p2, 3rd paragraph: The author should highlight what \"noncentral issues\" they are referring to.Rewrote the paragraph for clarity and punctuality.5. p2, 5th paragraph, minor: It would be useful to highlight that cs, ds \\in {0,1}.Highlighted6. p2, Eq. (1): v is not defined.Added definition7. p2, footnote, minor: Change \"log\" to \"ln\" here for consistency with Eq. (1) and (3).Changed log to ln8. p3, 2nd paragraph: It would be good to clarify in this first sentence the distinction between \\Delta G and \\Delta G_s (or avoid using the former entirely).Corrected.9. p3, 2nd paragraph: S = {Na,H} typo here.Corrected.10. p3, Eq. (5): Similarly to point (7), it is not clear what \\Delta G represents here.Added a phrase to explain it.11. p3, Eq. (6): Terms in this equation need defining properly in several regards. Firstly, \\Delta GATP0 should be defined. Secondly, it should be made clear that concentrations are intracellular (as opposed to in Eq. (1) (3), which correspond to both extra- and intracellular compartments). This is particularly confusing for Pi in which the subscript could easily be misread as being an intracellular label. Finally, it is not clear how the equality \\Delta GATP= qvATP holds. Perhaps, as in footnote (1), it could be made clear that this relies on the definition of the reversal potential for ATP.Added square brackets and subindices to indicate that the intracellular concentrations of ADP, ATP, and Pi are intracellular. Also corrected a typo, there was an extra q in the term for $\\Delta G_0$12. p3, Eq. (6): I would also here like to take the opportunity to raise a point about the general framework. The models here account for the energy required to move molecules with and against their concentration gradients. In cases of active transport, as indicated by Eq. (10), ATP is then hydrolysed to meet the energy deficit required to power the pump. This then means that the concentration of ATP, relative to ADP is then changing. Indeed, at maximal rates of exercise, the ATP concentration in skeletal muscle can fall by up to 20% of its initial value. Moreover, in certain cell types, local ratios between ATP and ADP affect the opening and closing of ion channels (e.g. KATP). Eq. (10) implies that ATP and ADP in the cell are constant, in spite of the necessity that it must change. One must, therefore, conclude that an assumption is being made that ATP changes are small relative to the total amount of ATP. This assumption should be stated, or a discussion around how changes to ATP concentrations effect Eq. (10) should be made.Added a comment about the assumptions and a comment about the possibility of changes in concentration for ATP, ADP, and Pi13. p3, final paragraph of first column: Wrong equation being referred to.Corrected cross reference14. p3, Eq. (9): A physical interpretation for parameters r and b should be given. Additionally, and referring back to my previous comment (1), the text here discusses the relative magnitudes of r for electrodiffusive and active transport. Thus, this point should make clear that ion channels should be faster than both facilitated diffusion through carrier proteins and active transport via pumps.Added clarification and phrases providing interpretation for the two parameters.15. p4, Eq. (11): For consistency with Eq. (5), 'Extra' in the subscripts should read 'Ext'. Also, it should be noted that vExtra should be the vATP from Eq. (6).Added clarification and deleted the “ra” in the extra suffix.16. p4, \"In particular, for electrodiffusive (passive) transport of ions of type l\": It is not clear what the author is referring to here (or how it is different from what is written in Eq. (15)).Rephrased the sentence for correction.17. p4, \"The first, more complex form...\": Does the author mean to reference Eq. (11) here?Moved the sentence up to the paragraph with Eq. (11) and added the cross reference18. p4, After Eq. (16), minor: \"Ampere\" needs capitalising.Corrected19. p5, Table 1: Is v0 here the same as in Eq. (15)? If so, the dependency on vExt seems to have disappeared.vExt is not written in those cases where it is zero.20. p6, Fig. 2: What is plotted on the ordinate axis in this graph? It appears to have units of pA, but the text says that this is a plot of alpha/beta, which should be dimensionless.Corrected text.21. p8, \"Electrodiffusive transport\": I'm not really sure what the point of this section is since the results presented here have mostly been mentioned previously in this manuscript.Added sentences making the point more explicit and took away the sentence in previous paragraphs where the single ion energy was discussed to avoid repetition.22. p8, after Eq. (31): Is the N written here supposed to be N_l? Also, there is a typo after Eq. (31) (with -> where).Changed N for M to avoid confusion.23. p9, Eq. (33): m is not defined.Changed the order in which equations are presented and rephrased so that variables and parameters are better explained24. p9, Eq. (35-39): Change symbol for current to ix for consistency with previous equations.The currents in equations 35-39 are normalized by the membrane capacitance. Therefore, to avoid abuse of notation, added a note remarking the change in the letter for the functions, explaining it is due to normalization.25. p9, after Eq. (39): Presumably, the author here means that the intracellular Ca2+ concentration changes (rather than the extracellular). This should be clarified. Also, the text below Eq. (40) appears to imply a distinction between free and bound Ca2+, but there is no buffering process described in the model, which may cause confusion.Added sentences to clarify these points.26. p9, Fig. 2: Please state what im and iCaL13 are in these plots.im represents the total current.Added a sentence to the figure caption.27. p10, Table 2: The units of \\bar{a} are inconsistent with the main text.Corrected by deleting the bars in the table for normalized amplitude entries. \\bar{a} is in pA, a = \\bar{a}/Cm in pA/pF28. p12, \"Another possible use of the third order approximations is in the construction of network models.\": Please could the author state what they mean here?Expanded the sentence to clarify the point. The idea is to use cubic approximations to build network models taking advantage of the possible reduction in computational cost. However, as is explained in the paragraph, cubic approximations need to be tested first to address possible issues that may arise from using approximations.29. p13, discussion on action potential shape: I was wondering if the author could here compare their argument surrounding the shape of the action potential near initiation with those put forward here (Brette, 20131), which puts forward a case for multi-compartment models to describe the sharpness of the spike.Added a comment about the results in the paper by Brette, 2013.Thank you for pointing it out. Added a reference to his work too.30. SI1, after (A3): There appears to be a reference missing here.Edited the reference, it is for Equation 31.31. SI2: Headers are required in these data files so that the values herein can be related to the physical quantities they represent.Edited data files to include headers.32. It would be useful for the author to upload any code used to generate the plots in the article.Uploaded the code in an jupyter notebook."
}
]
},
{
"id": "38997",
"date": "30 Oct 2018",
"name": "Moisés Santillán",
"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\nI found this paper quite interesting. It introduces a mathematical formulation for ion transport across cell membranes, based in thermodynamic principles. The author further shows that other, more common formulations, are special cases of the more general one introduced here. Finally, the author employs the introduced formulation to study the dynamics of SA pacemaker cells, and is able to explain the experimentally-observed double activation of calcium channels.\nOverall, I have a good opinion of this paper and recommend its indexing. There are only a few minor points that should be addressed:\n1. Page 3, first column, beginning of last paragraph: Eq. (10) is referred to before being introduced.\n2. In my opinion, Eq. (8) is not self-evident, and its origin should be explained.\n3. Same thing for Eq. (33).\n4. The procedure to estimate the parameter values in Table 2 must be explained. Moreover, a parameter sensitivity analysis should be performed to assess the robustness of the obtained 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?\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": [
{
"c_id": "4136",
"date": "08 Nov 2018",
"name": "Marco Arieli Herrera-Valdez",
"role": "Author Response",
"response": "The answers to comments made by reviewers are written in italics after each comment. Answers to comments from reviewer 2Overall, I have a good opinion of this paper and recommend its indexing. There are only a few minor points that should be addressed:1. Page 3, first column, beginning of last paragraph: Eq. (10) is referred to before being introduced.Corrected the error in the cross reference.2. In my opinion, Eq. (8) is not self-evident, and its origin should be explained.Added a reference pointing to a Boltzmann distribution.3. Same thing for Eq. (33).Added a reference for the work of Willms et al., 1999.4. The procedure to estimate the parameter values in Table 2 must be explained. Moreover, a parameter sensitivity analysis should be performed to assess the robustness of the obtained results.The reviewer points to a very important issue. There are different publications and books addressing the robustness of conductance-based models (which are similar to the current one), from a dynamical systems perspective, using bifurcation theory. That being said, I agree that the parameter sensitivity analysis should be done for completeness, as this is a different model, but that analysis is beyond the scope of this paper. Nevertheless, parameter sensitivity analysis is addressed in a publication currently in preparation. In that publication, I address a few issues, including whether the gating formulas yield correct predictions in consideration of the work of Hodgkin and Huxley and the powers used for the fits on voltage clamps, and whether the relationships between parameters are correct, as a consequence of the modeling using those powers. It is worth mentioning that the parameters are in line with the experimentally measured magnitudes for cardiocytes and neurons, as those being modeled."
}
]
}
] | 1
|
https://f1000research.com/articles/7-1468
|
https://f1000research.com/articles/10-397/v1
|
18 May 21
|
{
"type": "Opinion Article",
"title": "Rationality over fashion and hype in drug design",
"authors": [
"José L. Medina-Franco",
"Karina Martinez-Mayorga",
"Eli Fernández-de Gortari",
"Johannes Kirchmair",
"Jürgen Bajorath",
"Karina Martinez-Mayorga",
"Eli Fernández-de Gortari",
"Johannes Kirchmair",
"Jürgen Bajorath"
],
"abstract": "The current hype associated with machine learning and artificial intelligence often confuses scientists and students and may lead to uncritical or inappropriate applications of computational approaches. Even the field of computer-aided drug design (CADD) is not an exception. The situation is ambivalent. On one hand, more scientists are becoming aware of the benefits of learning from available data and are beginning to derive predictive models before designing experiments. However, on the other hand, easy accessibility of in silico tools comes at the risk of using them as “black boxes” without sufficient expert knowledge, leading to widespread misconceptions and problems. For example, results of computations may be taken at face value as “nothing but the truth” and data visualization may be used only to generate “pretty and colorful pictures”. Computational experts might come to the rescue and help to re-direct such efforts, for example, by guiding interested novices to conduct meaningful data analysis, make scientifically sound predictions, and communicate the findings in a rigorous manner. However, this is not always ensured. This contribution aims to encourage investigators entering the CADD arena to obtain adequate computational training, communicate or collaborate with experts, and become aware of the fundamentals of computational methods and their given limitations, beyond the hype. By its very nature, this Opinion is partly subjective and we do not attempt to provide a comprehensive guide to the best practices of CADD; instead, we wish to stimulate an open discussion within the scientific community and advocate rational rather than fashion-driven use of computational methods. We take advantage of the open peer-review culture of F1000Research such that reviewers and interested readers may engage in this discussion and obtain credits for their candid personal views and comments. We hope that this open discussion forum will contribute to shaping the future practice of CADD.",
"keywords": [
"artificial intelligence",
"computer-aided drug design",
"drug discovery",
"chemoinformatics",
"education",
"open science"
],
"content": "Computer-aided drug discovery\n\nComputer-aided drug discovery (CADD) has become a key technology in drug discovery, providing guidance to experimentalists on which compounds and experiments to focus on next. The capacity of CADD has further increased by the development of powerful machine learning approaches, deep learning in particular.1 In recent years, software for CADD has become more widely accessible. Today, a range of software packages are available that are open-source or free to use for academic research.2–5 Together with significant alterations of the scientific landscape induced by the COVID-19 pandemic and the ensuing re-orientation of some early-career but also established research groups towards the use of computational tools, this has boosted the use of CADD methods in particular in academic research environments. However, low-barrier access to computational tools and computing power increasingly leads to the use of CADD techniques also by scientists who have not received formal training on these methods. Many newcomers to CADD employ easy-to-use software without realizing the complexities involved and without being aware of the many potential pitfalls. Improper use of CADD techniques can have a contrary effect on research than intended. The risk of generating meaningless or false predictions is high. Flawed predictions can lead to dedicating significant resources to futile experiments. In particular, publishing invalid predictions can lead to error propagation, eventually resulting in a loss of confidence in CADD. Moreover, uncritical or naive use of artificial intelligence (AI) methods that are being heavily promoted in many research fields has similar negative effects, working against the credibility and acceptance of CADD as a scientific discipline.\n\nGood practices to conduct and report studies in computational medicinal chemistry and chemoinformatics have been outlined in several articles.3,6,7 Similarly, best practices in different stages involved in CADD have been discussed, for instance, in quantitative structure-activity relationship (QSAR) analysis,8 data curation,9 molecular docking10,11 and virtual screening.12\n\nIn this contribution, we discuss common misconceptions and false expectations associated with CADD, especially in the AI era, and make recommendations on how to avoid common pitfalls when using CADD software. We aim to stimulate an open discussion within the community to help improve our perception and practice of CADD and contribute to shaping its future.\n\n\nCADD and related fields\n\nExperts from various disciplines involved in drug discovery, such as chemical synthesis and biochemistry, are increasingly making use of computational tools to guide their experimental research and rationalize their observations. This is a positive trend, as developers of CADD tools have been aiming for a long time to make their software more widely accessible and intuitive to use. Prominent examples include web servers, and commercial, free and open-source software. But to develop further, it is of paramount importance to avoid confusion about the concepts and differences between the different areas in drug discovery such as molecular modeling, chemoinformatics, and theoretical chemistry. Conceptual and practical differences between these disciplines are clearly described in the literature.13,14 Importantly, theoretical disciplines are an integral part of CADD, establishing its scientific foundations. The ability to apply such approaches using software does by no means guarantee that reasonable research is carried out. Therefore, any conclusions or claims should be carefully considered.\n\n\nCommon misconceptions and false perceptions when CADD is superficially viewed\n\nThe advent of more advanced computational tools, many of which are open source, freely accessible, and promoted as “easy-to-use,” also increases the widespread use of “buzz words,” and misconceptions among newcomers to CADD.\n\nTable 1 gives examples of incorrect expressions and misconceptions frequently affecting students and researchers with little or no expertise in CADD. Readers and peer reviewers are welcome to comment openly on these points and modify or enrich the list according to their own experience.\n\n\nWhen is a study “complete”?\n\nTraditionally, there is a widespread belief in experimental sciences that experimental results represent reality, disregarding the different way in which natural phenomena can be represented and perceived and the relativity associated with varying representations. This ideological attitude works against “out of the box”, hinders intellectual progress, and indirectly de-values scientific disciplines such as CADD. With the rise of AI as one of the most heavily promoted approaches in contemporary society, the academic community has been encouraged to redirect its attention to computational tools to enhance its research impact and appeal. Nevertheless, unconditional trust in “experimental reality” reduces CADD to a “tool provider” and does not regard it as an independent scientific discipline in its own right. Consequently, computational models are often used without the necessary theoretical understanding and the rigor needed to apply them systematically.\n\nIn the authors’ opinion, one of the first requirements a new computational practitioner needs to address is realizing that both experimental and computational results are constrained by the model or experimental framework applied to determine them and, in no case, an absolute account of reality. Among medicinal chemists, there is the frequent misconception that purely theoretical or computational studies are in principle “incomplete” because there are no “real” experiments. However, such views require reconsideration and correction, as pointed out above. Rigorous computational studies answer questions that are difficult to address without “in silico experiments”. As such, they are comprehensive and self-contained, regardless of whether the computational approach has led to experiments. “Complete” computational investigations are often consistent with prior experimental observations, but may also chart new scientific territory. Of course, new computational insights leading to experimental work trigger interdisciplinary research. This is a noted strength of CADD, if conducted properly. However, there are misconceptions at interfaces between computation and experiment. For instance, a common malpractice is trying to replace enzymatic inhibition assays with predictions based on molecular docking or dynamics simulations. Another misunderstanding is that black box predictions from machine learning would represent a form of “alchemy”. What we cannot understand is not necessarily incorrect and may have value. The catch is that we are left with making decisions in such cases, for example, about new experiments that go beyond our reasoning and hence require trust in computational work and prior experience. It is also false to believe that AI in its current state would provide solutions to questions that replace our judgment capacity. Data volumes quickly go beyond our comprehension but results of statistical analysis of pattern recognition do not replace human reasoning (algorithms and machines do not “think” -- at least so far). Furthermore, there is a severe misconception that computational predictions might demonstrate or “validate” the bioactivity of compounds. Notably, these and other misunderstandings may not be evident to researchers and students who are just beginning to use computational methods. We encourage the community to avoid judging a computational research project to be “incomplete” because it does not include experiments or to be “complete” just because it incorporates many different computational methods. The question of completeness is not separable from scientific rigor and adequate conduct of methodologies, be they computational or experimental in nature. Furthermore, let us not consider a computational analysis as a “luxury item” to decorate a project report, grant application, or scientific paper with “pretty pictures”.\n\n\nUsing methods for the right reasons\n\nMainstream media usually disseminate inaccurate or exaggerated reports about the capabilities of computational methods without also mentioning their limitations and flaws. Simultaneously, mass job search engines commonly offer job opportunities with extensive lists of different computational tools as requirements. These factors, among others, continuously put pressure on researchers to increase their productivity and academic credentials to further their careers at the expense of scientific rigor and the quality of research. CADD is not the exception of the increasing trend that disrupts the traditional academic structure in favor of a more market-oriented approach. One of the consequences of this phenomenon is that many young professionals and new CADD practitioners direct their efforts to increase the volume of their curriculum vitae rather than using CADD methods to answer relevant scientific questions.\n\nThe popularity of computational methods or tools often jeopardizes rational selection. Newcomers often turn to frequently used methods that are well-validated. However, the justification is questionable if the technique is merely used because it is “popular” (e.g., “follow the crowd” because “it should be right.”). Without properly addressing the question at hand, computational analysis applying irrelevant approaches is misleading or propagates errors. Arguably, one of the most misused guidelines in drug discovery is the Lipinski Rule of Five,15 which is often confused with assessing “drug-likeness”. Another common pitfall among newcomers to CADD is using docking to predict “real” protein-ligand complexes, given its popularity and easy-of-use. Practitioners should use methods for the right reasons and not just because everybody else is using them. This requires knowledge of underlying theories and sound scientific judgment.\n\n\nGeneral recommendations for the proper use of CADD resources\n\nIn the authors’ opinion, the following recommendations should be helpful to CADD novices and multidisciplinary research teams attempting or planning to use computational approaches to guide drug discovery projects. Similar to Table 1, the list is not exhaustive, but is also intended to stimulate an open discussion within the scientific community.\n\n• Intense study of the literature is essential to acquire knowledge. Like experimental techniques, also CADD methods require proper training to become familiar with their applicability domains, approximations and limitations.\n\n• Computational research projects should primarily be problem-oriented rather than technique-oriented, unless the development of new techniques themselves is the focus of the problem to be addressed. Projects (including dissertations) should be well-structured according to scientific criteria or milestones, but by no means represent a compilation or aggregated use of techniques applied to the same data. Before deciding which computational approaches and tools to use, a comprehensive research of the literature should be conducted and exemplary applications should be reviewed. Then, based on the experimental information available, appropriate computational methods and strategies should be applied. Rushing into calculations with software packages, even with excitement, is typically detrimental if the applied methods are not scientifically justified. In addition to researching methodological aspects, it is also mandatory to carefully review the available experimental findings. For example, prior to applying virtual screening techniques to search for new compounds with activity against high-profile and extensively explored targets, care should be taken not to overlook prior art in the field and avoid engaging in scientifically naive computational efforts. One should avoid setting the goals of a drug discovery project relative to a technique by pursuing a “tool-oriented approach”. Instead, planning computational components of an interdisciplinary research project should focus on the ultimate scientific goals. Students should realize and keep in mind that learning and applying different techniques across disciplines is desirable, but they should be used in harmony to answer research questions.\n\n• Seek supervision or advice from experts and do not hesitate to ask. Consultation prior to engaging in a new scientific adventure will not only save time and resources but also help to plan a scientifically sound approach.\n\n• Avoid excessive use of buzzwords such as “artificial intelligence” or “machine learning” when they are not applicable, which contributes to inappropriate hype associated with computational methods. For example, there is no need to use the AI or “machine intelligence” label for compound classification methods that are already applied for decades.\n\n• Keep in mind that many theoretical disciplines contribute to CADD, which have a long history on their own such as machine learning.\n\n• As in any wet lab experiment, input data quality is of critical importance for the outcome of computational studies. Awareness of data curation requirements is essential for the integrity of computational work.\n\n• The uncritical or uneducated use of web-accessible computational tools or servers to generate new compounds, calculate molecular properties, or predict target structures and protein-ligand complexes is a major source of errors propagating through interdisciplinary projects.\n\n\nConcluding remarks\n\nThe current pandemic and related funding constraints in some countries and institutions have motivated many researchers at different levels to redirect their efforts from difficult to sustain experimental studies to easy-to-use computational tools that can be employed remotely. Also, reviewer panels of many current grant applications from academia, non-for profit, or the industry currently tend to give priority to research proposals that involve AI. Although this contributes to the popularity of CADD, it also comes at a cost. If uneducated CADD studies enter the realm of science fiction harm is done to this field, its credibility and acceptance, and further scientific development. This must be avoided at all costs. The methods used in CADD should not be applied as black boxes, which can be enabled by just a few hours of hands-on experience such as provided in workshops. Without sufficient understanding of the scope, complexity, and theoretical foundations of these computational methodologies such efforts will inevitably fail and discredit investigators and their work as well as the field as a whole. Newcomers to the area, including students, early-career scientists, and seasoned investigators attempting to re-focus their efforts should be fully aware that, similar to experiments, profound knowledge of CADD concepts and informed use of CADD tools is a must. A simple yet fundamentally important rule applies: “Don’t compute what you don’t understand”. In addition to the general recommendations outlined in this Opinion, we wish to encourage students, newcomers, and practitioners of CADD to use the computational tools and resources for the right reasons, not just because they are easily accessible. Similarly, we highly encourage the scientific community to avoid applying computational methods just because they are popular. Instead, it is strongly recommended to identify scientific questions that can be addressed appropriately using CADD approaches - and avoid others where computational efforts become questionable. In general, computational studies that cannot be reported in established peer-reviewed journals whose scope includes CADD are to be considered with appropriate caution, both by experts and novices to the field. This also applies to the use of modeling web servers. While the integrity of publicly accessible computational tools can be guaranteed by the developers, addressing ill-defined questions or tasks using these tools is beyond their control. Recognizing the benefits of the open post-publication review culture of F1000Research, we would be delighted if this contribution would catalyze open discussions among readers to raise further awareness of latent problematic issues in the CADD area and support its further scientific development.\n\n\nData availability\n\nNo data is associated with this article.",
"appendix": "Acknowledgments\n\nWe thank Zoe Sessions for critically proofreading the manuscript.\n\n\nReferences\n\nGasteiger J: Chemistry in Times of Artificial Intelligence. ChemPhysChem. 2020; 21(20): 2233–2242. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSingh N, Chaput L, Villoutreix BO: Virtual Screening Web Servers: Designing Chemical Probes and Drug Candidates in the Cyberspace. Brief. Bioinform. 2021; 22(2): 1790–1818. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWillems H, De Cesco S, Svensson F: Computational Chemistry on a Budget: Supporting Drug Discovery with Limited Resources. J. Med. Chem. 2020; 63(18): 10158–10169. PubMed Abstract | Publisher Full Text\n\nClick2Drug: Accessed Apr 7, 2021.Reference Source\n\nMacs in Chemistry: Accessed Apr 7, 2021.Reference Source\n\nBajorath J: Progress in Computational Medicinal Chemistry. J. Med. Chem. 2012; 55(8): 3593–3594. PubMed Abstract | Publisher Full Text\n\nMerz KM Jr, Amaro R, Cournia Z, et al.: Editorial: Method and Data Sharing and Reproducibility of Scientific Results. J. Chem. Inf. Model. 2020: 60(12): 5868–5869. PubMed Abstract | Publisher Full Text\n\nMuratov EN, Bajorath J, Sheridan RP, et al.: QSAR without Borders. Chem. Soc. Rev. 2020; 49(11): 3525–3564. PubMed Abstract | Publisher Full Text | Free Full Text\n\nFourches D, Muratov E, Tropsha A: Trust, but Verify II: A Practical Guide to Chemogenomics Data Curation. J. Chem. Inf. Model. 2016; 56(7): 1243–1252. PubMed Abstract | Publisher Full Text | Free Full Text\n\nTemml V, Schuster D: Molecular Docking for Natural Product Investigations: Pitfalls and Ways to Overcome Them. In: Molecular Docking for Computer-Aided Drug Design. Elsevier; 2021; pp 391–405.\n\nScior T: Do It Yourself—Dock It Yourself: General Concepts and Practical Considerations for Beginners to Start Molecular Ligand–Target Docking Simulations. In: Molecular Docking for Computer-Aided Drug Design. Elsevier; 2021; pp 205–227.\n\nScior T, Bender A, Tresadern G, et al.: Recognizing Pitfalls in Virtual Screening: A Critical Review. J. Chem. Inf. Model. 2012; 52(4): 867–881. PubMed Abstract | Publisher Full Text\n\nVarnek A, Baskin II: Chemoinformatics as a Theoretical Chemistry Discipline. Mol. Inform. 2011; 30(1): 20–32. PubMed Abstract | Publisher Full Text\n\nLópez-López E, Bajorath J, Medina-Franco JL: Informatics for Chemistry, Biology, and Biomedical Sciences. J. Chem. Inf. Model. 2021; 61(1): 26–35. PubMed Abstract | Publisher Full Text\n\nLipinski CA: Lead- and Drug-like Compounds: The Rule-of-Five Revolution. Drug Discov. Today Technol. 2004; 1(4): 337–341. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "85580",
"date": "19 May 2021",
"name": "Bruno O. Viloutreix",
"expertise": [
"Reviewer Expertise drug discovery",
"structural bioinformatics",
"chemoinformatics",
"molecular medicine"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis review about fashion and hype in the field of drug design, written by experts, is indeed very timely and of high interest. The observation applies to many fields related to medicine and biology, to most technologies and even research topics.\nThis opinion paper should be read by politicians, decision makers, journalists, students, the citizens not involved in research and many scientists. Even more so, it should be read by people defining guidelines for grant applications and by investors that are ready to put millions on a new “in silico” technology that is going to save the world but that has never been published and is only documented on some nice brochures full of buzz words (the so-called proprietary tools that nobody can try or evaluate).\nIndeed, nowadays, if a grant or a research paper does not use every two sentences words like game-changer, disruptive, AI, big data, multi-scale, large scale, ultra-large something or quantum something, it has little chance to succeed (in my opinion “quantum whatever” is going to be the next hype after AI, and if you have both, AI + quantum computing or quantum scoring or quantum ADMET or quantum digital twin, then you win the lottery, meaning grants, investors’ money, promotion, medals, prize, fame, and the person will definitively go on TV, get numerous \"like\" in social networks and become a scientific star invited by politicians to guide the remaining ignorant scientists that do not buy buzz words…).\nThe complexity is that, in some cases, these methods are going to help, in some others, this is the wind blowing in the forest. Experts in the field know but they are not invited to comment or, if they are, they do not say anything because they are afraid to be considered old school. The reality is of course very different, no problem being enthusiastic about some approaches, about developing \"user-friendly\" methods, about testing new concepts, but global brainwashing, overselling and propaganda about AI and related are damaging research and in the field of health, these promises will hurt patients, and confuse even more people.\nHow to stop this given the millions of dollars behind, given global mass brainwashing and the fact that most humans prefer fairy tales than truth? I do not know.\nDefinitively the present opinion paper can help, the one difficulty I see is that people who should read it will not do so and worse, do not want to hear about such discussion as it may kill their business plan or chance of getting famous. Maybe, if the scientific community that refuses “fashion research” starts to make noise, some changes will occur.\n\nIs the topic of the opinion article discussed accurately in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nAre arguments sufficiently supported by evidence from the published literature? Yes\n\nAre the conclusions drawn balanced and justified on the basis of the presented arguments? Yes",
"responses": []
},
{
"id": "86331",
"date": "10 Jun 2021",
"name": "Maria Sorokina",
"expertise": [],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors discuss the dangers of the growing trend of using computer assisted drug discovery tools without a proper training nor understanding of the fundamental concepts laying behind such approaches. The topic is indeed very important to discuss, and the past year of working away from the bench and the tremendous amount of publications produced using, often not totally correctly, CADD and other bioinformatic tools and the examples illustrated in Table 1, emphasize this need of reminding that computational tools, although easy to use, still require understanding of the concepts they are built on.\nRegarding the sentence ‘Avoid excessive use of buzzwords such as “artificial intelligence” or “machine learning” when they are not applicable, which contributes to inappropriate hype associated with computational methods', I would also add to avoid the usage of “deep learning” another very trendy buzzword, too often misused.\nI thank the authors for this article, as such topics are extremely important to be voiced out.\n\nIs the topic of the opinion article discussed accurately in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nAre arguments sufficiently supported by evidence from the published literature? Yes\n\nAre the conclusions drawn balanced and justified on the basis of the presented arguments? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-397
|
https://f1000research.com/articles/10-127/v1
|
18 Feb 21
|
{
"type": "Research Article",
"title": "Identifying potential drug targets and candidate drugs for COVID-19: biological networks and structural modeling approaches",
"authors": [
"Gurudeeban Selvaraj",
"Satyavani Kaliamurthi",
"Gilles H. Peslherbe",
"Dong-Qing Wei",
"Satyavani Kaliamurthi"
],
"abstract": "Background: Coronavirus (CoV) is an emerging human pathogen causing severe acute respiratory syndrome (SARS) around the world. Earlier identification of biomarkers for SARS can facilitate detection and reduce the mortality rate of the disease. Thus, by integrated network analysis and structural modeling approach, we aimed to explore the potential drug targets and the candidate drugs for coronavirus medicated SARS. Methods: Differentially expression (DE) analysis of CoV infected host genes (HGs) expression profiles was conducted by using the Limma. Highly integrated DE-CoV-HGs were selected to construct the protein-protein interaction (PPI) network. Results: Using the Walktrap algorithm highly interconnected modules include module 1 (202 nodes); module 2 (126 nodes) and module 3 (121 nodes) modules were retrieved from the PPI network. MYC, HDAC9, NCOA3, CEBPB, VEGFA, BCL3, SMAD3, SMURF1, KLHL12, CBL, ERBB4, and CRKL were identified as potential drug targets (PDTs), which are highly expressed in the human respiratory system after CoV infection. Functional terms growth factor receptor binding, c-type lectin receptor signaling, interleukin-1 mediated signaling, TAP dependent antigen processing and presentation of peptide antigen via MHC class I, stimulatory T cell receptor signaling, and innate immune response signaling pathways, signal transduction and cytokine immune signaling pathways were enriched in the modules. Protein-protein docking results demonstrated the strong binding affinity (-314.57 kcal/mol) of the ERBB4-3cLpro complex which was selected as a drug target. In addition, molecular dynamics simulations indicated the structural stability and flexibility of the ERBB4-3cLpro complex. Further, Wortmannin was proposed as a candidate drug to ERBB4 to control SARS-CoV-2 pathogenesis through inhibit receptor tyrosine kinase-dependent macropinocytosis, MAPK signaling, and NF-kb singling pathways that regulate host cell entry, replication, and modulation of the host immune system. Conclusion: We conclude that CoV drug target “ERBB4” and candidate drug “Wortmannin” provide insights on the possible personalized therapeutics for emerging COVID-19.",
"keywords": [
"Biological network analysis",
"COVID-19",
"drug targets",
"ERBB4",
"growth factor receptor binding",
"Limma",
"protein-protein docking",
"SARS-CoV-2",
"signal transduction pathways",
"Walktrap algorithm",
"wortmannin"
],
"content": "Introduction\n\nCoronavirus (CoV) are the largest group of enveloped and single-stranded-ribonucleic acid (ssRNA) pathogens1. The genome of CoV is typically larger (27-33Kb) than all other RNA viruses. Briefly, the genome contains an envelope protein, membrane protein, nucleoprotein, and spike protein which are responsible for capsid formation, assembly of virus particles and entry of the virus particle into the host2. The CoVs are zoonotic in nature, i.e. transmitted between animals and humans. There were three unforgettable zoonotic infectious diseases outbreak caused by CoVs recorded in the past two decades. In the 20th century (2002–2003), the foremost epidemic outbreak was originated in China by the severe acute respiratory syndrome (SARS)3. Later, in the 21st century (2012), the next epidemic outbreak happened in Saudi Arabia and the gulf countries with the Middle East respiratory syndrome (MERS)4. In December 2019, the third epidemic outbreak was recorded in China, especially from Wuhan city through a novel severe acute respiratory syndrome CoV-2 (SARS-CoV-2) (COVID-19)5. Paraskevis et al. (2020)2 reported that the SARS-CoV-2 full-genome belongs to betacoronavirus, but it differs from the epidemic causing SARS and MERS6. Moreover, the SARS-CoV-2 genome exhibits 96.3% similarity with the Bat-SARS viruses like CoVs. Among the various human CoVs (229E, NL63, HKU1, OC43, SARS, and MERS), SARS and MERS caused severe respiratory-related mortality rates of 10% and 37% respectively7.\n\nRecently, Huang et al.8 reported that the most widespread symptoms of COVID-19 patients at the beginning of the disease's condition were respectively fever (98%), cough (76%), fatigue (44%) followed by sputum production (28%), headache (8%), blood-stained mucus (5%) and diarrhea (3%). Moreover, nearly one-fifth (19.2%) of individuals with COVID-19 were asymptomatic9. COVID-19 positive cases showing the most common symptoms were cough hyposmia, sputum, and fever respectively9. In this current pandemic situation, identification of novel biomarkers, which plays an effective role in prognosis and monitoring the status of the SARS-COV-2 disease condition, is necessary. A high-throughput oligonucleotide microarray profiling has been widely employed in measuring the expression of genes (>1000) level significantly. In addition, microarray facilitates the identification of biomarkers (diagnosis/therapeutic), classification of the disease condition, treatment options, and mechanism of action of the gene involved in pathogenesis10. Biomarkers are identified through the determination of DEGs between the control and diseased/infected subjects, conversely finding the proteins that each biomarker is in connection with them, assisting to discover the key pathways related to the mechanism of the disease11–13. Many genes were involved in the pathogenesis, which make-up very complicated network systems. Coronavirus and influenza are pathogens causing severe respiratory illness to humans14. Recent reports demonstrated that SP110, HERC5, SAMD9L, RTP4, ESPT11 genes were identified to control and improve the immune system and defense mechanism against influenza by network analysis15. It has the supremacy to act as biomarkers and targets for pediatric influenza mediated therapy. A recent systematic review by 16 and his colleagues showed the increased level of biomarkers such as C-reactive protein, serum amyloid A, interleukin-6, lactate dehydrogenase, D-dimer, cardiac troponin and renal biomarkers (urea and creatinine) were higher, and low level of lymphocytes and platelet count were recorded in severe complicated COVID-19 patients than non-severe COVID-19 patients’ plasma and infected lung tissues.\n\nThus, the present study aimed to identify modules consists of the highly interconnected genes, which are involved in the pathogenesis of coronavirus medicated respiratory syndrome in humans. Microarray analysis of gene expression profiles is a standard and well-known method to identify potential targets and pathways17,18. Initially, we collected the gene expression profiles from the Gene Expression Omnibus (GEO) database. Then, we performed differential expression of CoV infected host genes (DE-CoV-HGs) using the Limma algorithm. The protein-protein interaction (PPI) network was constructed with DE-CoV-HGs and extracted different modules from the network using the Walktrap algorithm. Besides, the potential targets were predicted from the selected modules based on the degree and betweenness centrality measures, and determined their functional and pathway enrichment terms. The possible validation of potential targets interaction with proteins of SARS-CoV-2 was performed using protein-protein docking (PPD) and molecular dynamics (MD) simulations. Further, possible candidate drug for defined potential drug target (PDT) “ERBB4” using Drug Gene Budger. An insight into the study provides possible personalized therapeutic target and candidate drug for coronavirus medicated respiratory syndrome. Figure 1 illustrates the work flow of the study.\n\nWGM-whole genome microarray; SARS-CoV- ; MERS-; HGs-host genes; PPI-protein-protein interaction; SRBD-spike receptor binding domain; 3cLpro-3C-like protease; N pro-nucleocapsid protein;\n\n\nMethods\n\nThe coronavirus infected host gene expression profiles were extracted from the GEO database19. Agilent-014850 whole human genome microarray 4x44K G4112F platform was employed to GSE100509, GSE86529, GSE47962, GSE47961, GSE47960, GSE45042, GSE37827 and GSE33267 studies and one study GSE56677 which was performed based on Agilent-039494 SurePrint G3 human GE v2 8x60K microarray 039381 platform was included20–24. All the selected studies contain control and CoV infected human lung epithelial cells samples. The samples infected with other viruses were excluded. The sample details of different datasets are indicated in Table 1.\n\nNote: C- Control; I- Infected; GPL13497 -Agilent-026652 Whole Human Genome Microarray 4x44K v2; GPL17077-Agilent-039494 SurePrint G3 Human GE v2 8x60K Microarray 039381; GPL6480 -Agilent-014850 Whole Human Genome Microarray 4x44K G4112F\n\nUsing NetworkAnalyst (NA) web interface, the tab-delimited text (.txt) files of selected datasets were given as an input for preprocessing, normalization, and probe identification25. Variance stabilizing normalization (VSN) and quantile normalization was applied to reduce false-positive errors and equal distributions of datasets for statistical analysis26,27. R package “LIMMA” (Linear models for microarray analysis) of from the Bioconductor project were used to perform differential expression of CoV infected host genes28. Log2 transformation, Benjamini and Hochberg and t-test were used to perform normalization and calculate false discovery rate (FDR; p<0.05) of samples29.\n\nWe constructed the PPI network from identified DE-CoV-HGs using Search tool for retrieval of interacting genes/proteins (STRING) interactome30. The highest confidence interaction score was set to 0.9, which reduces false positive interactions31. The random walks (R package “igraph”) was used to extract modules based on the Walktrap algorithm from the DE-CoV-HGs interaction network32. It runs several short random walks within a group of nodes that are highly connected to detect small modules. From the modules, the hub genes (nodes) were identified using two different centrality measures “degree” and “betweenness”32. The degree of the gene is the many connections it has to other genes. Genes with a high degree act as hubs within the network. The betweenness of a gene is the number of paths that pass through it when considering the pair-wise shortest paths between all genes in the network. A node that occurs between two dense clusters will have a high betweenness. In the present study, the PDTs of DE-CoV-HGs were identified based on the degree centrality and betweenness centrality measures.\n\nWe have used ClueGO v2.5.3, which is a Cytoscape plugin for function and pathway enrichment analysis of DE-CoV-HGs33. A list of PDTs were provided as input into ClueGO with select specific parameters like species such as-Homo sapiens; ID type-Entrez gene ID; enrichment functions -KEGG pathways for the analysis. Each enrichment was calculated based on the Bonferroni method (kappa score 0.96; p > 0.005). ImageGP was employed to visualize the results of functional enrichment analysis.\n\nPreparation of host and SARS-CoV-2 viral receptor. The FASTA sequence of selected proteins namely 3C-like protease (3cLpro), angiotensin I converting enzyme 2 (ACE2), B-cell lymphoma 3 (BCL3), casitas b-lineage lymphoma (CBL), CCAAT enhancer binding protein beta (CEBPB), CRK like proto-oncogene (CRKL), histone deacetylase 9 (HDAC9), Kelch-like protein 12 (KLHL12), v-myc myelocytomatosis viral oncogene (MYC), mothers against decapentaplegic homolog 3 (SMAD3), nucleocapsid protein (Npro), nuclear receptor coactivator 3 (NCOA3), receptor tyrosine-protein kinase erbB-4 (ERBB4), spike protein-receptor binding domain (SRBD), SMAD-specific E3 ubiquitin protein ligase 1 (SMURF1), ubiquitin C (UBC), and vascular endothelial growth factor A (VEGFA) were obtained from Uniprot for protein-protein docking studies (Table 3)34.\n\nProtein-protein docking. PPD was performed in the HDOCK web-interface using ab initio docking with a fast Fourier transform (FFT) based hierarchical algorithm35,36. The FASTA sequence of the selected protein (protein 1 and protein 2) was given as input. The server obtained and chosen one of the highest sequence coverage and similarity and with the highest resolution template automatically from PDB and then, the homology modeling was performed using MODELLER. Then, the corresponding structures constructed by superimposing the modeled protein structure on to the template, where 5,000steps of AMBER MD minimization was also performed to remove severe atomic clashes at the interfaces. The putative binding modes between the protein-1 and protein-2 are systematically samples based on the FFT algorithm. In total 4,392 binding modes are ranked depending on their cluster and binding energy scores. The final complex was selected with RMSD of two binding modes was below a cut off 5Å. RMSD was calculated based on the backbone atoms of the protein 236.\n\n\n\nWhereas, “a” indicates as iterative step. “x” and “y” indicates the types of a pair of atoms in the protein 1 and protein 2. hxyobs (z) is the pair distribution function for atom pair xy calculated from the ensemble of experimentally measured protein 1- protein 2 complex structures. hxya (z) is the pair distribution function calculated from the ensemble of the binding modes of the protein 1 – protein 2 complexes predicted with the trial potentials {hxya (z)} at the a-th step. uxya+1 (z) are the improved potentials from uxya (z).aBT. is the generality value set as 137.\n\nMolecular dynamics simulations. The results of the PPD complex with the highest binding affinity were used to prepare input files for MD simulations. Solution builder in the CHARMM-GUI web interface was employed to solvate the complex with TIP3P and neutralized by potassium chloride (KCl) ions at the 0.15 mol-1 concentration under CHARMM36 force field38,39. The initial configuration of KCl ions is then estimated using short Monte Carlo simulations (2000 steps) through Coulombic and the van der Waals (vdW) interactions. The solvated complex was simulated by using Nanoscale molecular dynamics (NAMD)40. Full system long-range Coulombic interactions were determined by the particle mesh Ewald (PME) method41. The integrator parameters time was set to 2 fs/step. The simulations were executed in the constant pressure and temperature (NpT ensemble) with pressure bar (1) and temperature (303 K) through the Langevin dynamics with a damping coefficient of 1/ps. After 9×107 steps of minimization, water molecules and ions were equilibrated for 2 ns around proteins, which were restrained using harmonic forces. MD simulation of selected drug target (ERBB4-3cLpro) was started from the last frame of restrained equilibration. The production was carried out for 150 ns.\n\nDrug Gene Budger a web-interface was employed to identify possible candidate drugs or small molecules in LINCS L1000 data that significantly regulated selected drug target (ERBB4) expression based on LIMMA algorithm42. While entering the gene symbol of drug target, we could retrieve the following information such as log-transformed fold change, p-value and q-value for each potential small molecule. Small molecules/drugs that are liable for considerable overexpression and under expression of downregulated and upregulated drug target can increase the therapeutic action against COVID-19. The threshold q value was derived from the following equation\n\n\n\nWhere X is the number of false discoveries and Z is the number of true discoveries. Y=X+Z is the number of rejected null hypotheses. The false discovery rate (FDR) is as follows\n\n\n\nWhere E [Q] is the expected value of Q. The drugs/small molecule have the highest log2FC value was selected for further protein-docking studies. The drug target ERBB4 sequence was retrieved from the Uniprot database (ID: Q15303) for three structure modeling. The protein structure modeling was performed in a Swiss modeling server. The structure of the candidate drug “wortmannin” was retrieved from the ZINC database (ID: ZINC1619592). Then, protein-ligand docking was performed to calculate the binding energy of the docked complex in the Swiss dock web-interface, which was developed based on the EADock dihedral space sampling (DSS) algorithm. The energy functions were calculated using the CHARMM force field. Each docking cluster was the output of 250 different sequential runs. The binding models (BM) having the most favorable energies were calculated by fast analytical continuum treatment of solvation (FACTS) and clustered. Binding modes were estimated through Full fitness and clustered. Then, the Full fitness of the clusters was estimated by averaging 30% of the most favorable effective energy of their elements.\n\nThe effective energy calculated by the following formula\n\n\n\nWhereas, EintraLigand, Eintrareceptor are the internal energies of ligand and receptor; Einter is interaction energy between the receptor and ligand; σ value (0.0072 kcal/mol); SASA is the solvent accessible surface area. The results were visualized in Maestro Visualizer. All the supporting data associated with this study freely available (http://doi.org/10.5281/zenodo.4458252).\n\n\nResults\n\nIn total, 1,968 DE-CoV-HGs in human lung epithelial cells were obtained from the initial analysis. To obtain better results of biomarker identification, we have selected 315 overexpressed and 112 under expressed DE-CoV-HGs based on the log-fold changes -1>log2FC>1. Table 2 illustrates the top 10 DE-CoV-HGs, their description, and their fold change and p value.\n\nNote: * denotes ERBB4 selected as drug target; 3cLpro -3C-like protease; ACE2-angiotensin I converting enzyme 2; Bcl3-B-cell lymphoma 3; CBL- casitas b-lineage lymphoma; CEBPB- CCAAT enhancer binding protein beta; CRKL- CRK like proto-oncogene; C-cytosol; CP-cytoplasm; ERBB4- receptor tyrosine-protein kinase erbB-4; EN-Endosome; EX-exosome; FC -fold change; HDAC9- histone deacetylase 9; KLHL12- Kelch-like protein 12; M-mitochondria; MYC- v-myc myelocytomatosis viral oncogene; GM-golgi membrane; N protein- nucleocapsid protein; N-Nucleus; NP-nucleoplasm; PM-plasma membrane; PPD- protein-protein docking; SMAD3-mothers against decapentaplegic homolog 3; NCOA3- nuclear receptor coactivator 3; SMURF1-SMAD-specific E3 ubiquitin protein ligase 1; SRBD- spike protein-receptor binding domain; UBC-ubiquitin C; VEGFA-vascular endothelial growth factor A; FC-Fold change\n\nPPI network was constructed using 427 DE-CoV-HGs (Figure 1a). The major subnetwork contains 531 edges with an average local clustering coefficient 0.353 and the PPI enrichment p-value was 2.36 ×10-3. Then, using the Walktrap algorithm, 47 modules were retrieved from the subnetwork. Among them, highly interconnected modules includes module 1 (No. of nodes=202; p=5.20×10-32); module 2 (No. of nodes=126; p=1.90×10-28) and module 3 (No. of nodes=121; p=3.13×10-26) was employed to identify the PDTs (Figure 2b–d). Table 3 demonstrated that list of PDTs identified from different modules based on the degree and betweenness centrality measures. BCL3, CBL, CEBPB, CRKL, HDAC9, KLHL12, MYC, SMAD3, NCOA3, ERBB4, SMURF1, UBC, VEGFA were identified as PDTs which are highly expressed in human cells after CoV infection.\n\n(A) PPI network with highly interconnected nodes; (B) Module-1; (C) Module-2; (D) Module-3. Overexpressed genes are represented in green color, under-expressed genes in red color, interconnected nodes in gray color.\n\nMany important gene ontology terms and pathways were identified from the PPI network namely, cellular response to growth factor stimulus, wound healing as a biological process term; growth factor receptor binding as a molecular function term; and TNF signaling pathway and transcriptional mis-regulation in cancer as a pathway enrichment terms (Figure 3). Moreover, the biological process term that is directly or indirectly related to the viral life cycle and human immune system includes RNA polymerase II promoter in response to hypoxia, peptidyl-tyrosine auto-phosphorylation, ERBB2 signaling pathway, anaphase-promoting complex dependent catabolic process, interleukin-1 mediated signaling pathway, TAP dependent antigen processing and presentation of peptide antigen via MHC class I, regulation of cellular amino acid and metabolic process, negative regulation of protein acetylation, negative regulation of gene silencing by miRNA, white fat cell differentiation and histone H4 deacetylation enriched in three different modules. Besides, stimulatory c-type lectin receptor signaling pathway (module 1), regulation of hematopoietic stem cell differentiation, T cell receptor signaling, innate immune response signaling and Fc-epsilon receptor signaling pathway (module 2), lymphocyte co-stimulation (module 3) were highly enriched immunological terms of three different modules (Figure 4). Further, pathways enrichment of modules demonstrated that numerous signal transduction pathways and cytokine immune signaling pathways were illustrated in Figure 5.\n\n(A) Biological process term; (B) Molecular function term; (C) Pathway enrichment terms of PPI network\n\n(A) Biological process terms of three different modules; Immunological terms of (B) Module-1; (C) Module-2; (D) Module-3.\n\n(A) Signal transduction pathways; (B). Cytokine immune signaling pathways. The figures are retrieved from Reactome pathway analyzer using PTGs.\n\nProtein-protein docking interaction. The potential target genes encoding proteins are defined as drug targets to control the pathogenesis of SARS-CoV-2. The drug targets regulated (overexpressed or under-expressed) by SARS-CoV-2 during pathogenesis in the host cytoplasm and different cellular components. Accordingly, PPD of SRBD, 3cLpro, and N-protein of SARS-CoV-2 with proposed drug targets happened by different biological signaling pathways. Thus, we hypothesized, proposed drug targets may control the pathogenesis of SARS-CoV-2 through the respective signaling pathways. The possible molecular interaction of host drug targets with SRBD, 3cLpro, and N-protein of SARS-CoV-2 was determined by PPD method. In the present study, we performed protein-protein rigid-body docking, which treats both proteins as rigid and discovers only six degrees of translational and rotational freedom. It excludes any kind of flexibility. Drug targets include HDAC9, SRBD, SMURF1, SRBD, CBL, ERBB4, BCL3, CEBPB, CRKL, KLHL12, MYC, NCOA3, SMAD3, UBC, and VEGFA were in the human respiratory system, which was possibly able to interact with the S-RBD, 3cLpro, and N - protein of SARS-CoV-2 and regulate the viral pathogenesis through replication and development. PPD binding affinities were illustrated in Table 3. Among the drug targets, ERBB4 demonstrated showed high binding affinity -260.46, -314.57 and -291.72 kcal/mol with SRBD, 3cLpro and N-protein of SARS-CoV-2 respectively. Thus “ERBB4” was selected as potential drug target and used for candidate drug selection study. Hydrogen bond forming residues between the ERBB4 and SRBD, 3cLpro, and N-protein of SARS-CoV-2 complexes represented in Figure 6.\n\n(A) Possible pathological action of SRBD, 3cLpro, and N-protein of SARS-CoV-2 with “ERBB4”. Results of PPD of (B) ERBB4-SRBD; (C) ERBB4-3cLpro; and (D) ERBB4-N-protein complex by using LigPlot. The interacting residues of ERBB4 (magenta) are labelled in green color and SARS-CoV-2 protein structures (brown) are labelled in blue color. The interacting hydrogen bonds indicated in green color.\n\nMD simulation of ERBB4-3cLpro complex. MD simulations demonstrated the stability of the ERBB4-3cLpro complex. The structure and dynamic properties of the complex were followed by monitoring the backbone Cα root mean square deviation (RMSD) from the initial structure during the simulation period (150ns). The RMSD of the ERBB4-3cLpro complex gradually increased for the first 95 ns before steadily oscillating around a value of ~0.85 nm, indicative of the ERBB4-3cLpro complex stability over the simulation timescale (Figure 7a). The root mean square fluctuation (RMSF) reflects the fluctuations in the positions of the ERBB4-3cLpro complex residues. Briefly, notable fluctuations have been observed in the multiple furin-like cysteine-rich domains, a tyrosine kinase domain, and a phosphatidylinositol-3 kinase binding site of ERBB4. However, the other amino acid residues in the PDZ binding domain (amino acid range 400–600) were not deviating more (Figure 7b). This indicates the reason for the stable RMSD plot of the ERBB4-3cLpro complex. The strong hydrogen bonding interaction (average ~1.89) between ERBB4 and 3cLpro observed throughout the 150ns of MD simulation (Figure 7c).\n\n(A) NAMD trajectories of RMSD; (B) RMSF; (C) Total number of intermolecular hydrogen bond formation trajectories of ERBB4-3cLpro complex.\n\nThe results of Drug Gene Budger demonstrated that Wortmannin (q- value = 3.31×10-21; log2 Fold change = 2.997; Specificity = 1.09×10-04) was identified as the candidate drug for the proposed target ERBB4. The ERBB4 was downregulated after the coronavirus infection that was then upregulated by the possible use of the Wortmannin as candidate drugs, which may inhibit the pathological cycle and development of SARS-CoV-2 in the human hosts. 30 different protein-ligand cluster of binding modes were obtained after molecular docking. Among them, the binding mode of cluster 1 indicated that the ERBB4-Wortmannin complex has the energy in term of full fitness -2563.6987 kcal/mol and Gibbs free energy ∆G was -7.93 kcal/mol (Figure 8).\n\n(A) Two dimensional (hydrogen bond formation between Cys523 residue of ERBB4 and OH atom of Wortmannin showed in magenta line) and (B) three-dimensional interaction (hydrogen bond formation between Cys523 residue of protein-ligand complex showed in yellow color dotted line).\n\n\nDiscussion\n\nThe discovery of biomarkers from gene-expression profiles as well as key functions in a pathogenic-related pandemic disease like COVID-19 is of consequence for diagnosis, drug development, and monitoring of disease progression. Network analysis provides new insights into the biological and cellular organization. The single gene can be involved in many biological functions and regulated different genes at different times43. Thus, biomarkers from gene-expression profiles of coronavirus infected subjects have the potential to be employed as drug-targets for COVID-19. Therefore, the present study aimed to identify drug targets from modules containing highly interconnected potential target genes which involve in the pandemic coronavirus pathogenesis. DEGs analysis demonstrated that 315 overexpressed and 112 under expressed genes between normal and CoV-infected subjects. Besides, the potential target genes namely MYC, HDAC9, NCOA3, CEBPB, VEGFA, BCL3, SMAD3, SMURF1, KLHL12, CBL, ERBB4, and CRKL were identified from Walktrap modules, which are significantly associated with the coronavirus infection. Then, the potential target genes encoding proteins employed as PDTs (receptor) for further analysis. Thus, we discussed the possible association of PDTs with pathogenesis of SARS-CoV-2.\n\nMYC regulates numerous cellular functions including cell activation, differentiation, cell cycle progress, transformation, and apoptosis in virus (HIV, hepatitis C, influenza, and Epstein-Barr virus (EBV)) infected host cells44–46. In addition, mutation of MYC can disturb human B cells to proliferate indefinitely47,48. Further, influenza A virus infection dysregulates the expression of miRNA-22 and induces CD147 in asthmatics through the MYC transcription factor49. Moreover, overexpression of the MYC gene associated with PHACTR3 and E2F4 mutation in NSCLC is considered as a potential biomarker of NSCLC and its specific subtypes50. This information suggesting that targeting MYC for COVID-19 or CoV mediated respiratory disease has a potential role in the SARS-CoV-2 pathogenesis. SMAD3 is a transcriptional regulator and plays as a mediator of the cellular signals initiated by the transforming growth factor-beta (TGF-β) superfamily of cytokines, which control proliferation, differentiation, and apoptosis. It is a complex regulator in adipose physiology and the pathogenesis of chronic obstructive pulmonary disease, diabetes, inflammatory disease, and obesity51,52. In addition, TGF-β/SMAD3-induced repression of target genes, it required repression of the MYC gene. Moreover, SMAD3 deficiency induces inflammatory abnormal bulge on aortic in angiotensin II-infused animal models through the activation of nitric oxide synthases53. This information suggesting that under-expressed SMAD3 in CoV mediated respiratory disease has a prospective role in the pathogenesis of SARS-CoV-2. CBL is a proto-oncogene, encoding one of the ubiquitin ligase protein CBL involving in cell signaling, and causes a mutation in the lung, colon, endometrial adenocarcinoma, cutaneous, and breast cancer54. In addition, CBL is a potential gatekeeper of immune activation through its function as a non-redundant negative regulator of immune activation. Further55, reported that targeting CBL and lipid rafts have the potential to block Kaposi's sarcoma-associated herpesvirus infection of endothelial cells. Moreover, CBL was identified as modulators of immature dendritic cell (DC) activation. The deficiency of CBL in DC upregulates toll-like receptors and inducing pro-inflammatory cytokines and chemokines56. Then, reduced expression of CBL in CD4+T cells is reported in several autoimmune diseases namely asthma, lupus erythematodes, multiple sclerosis, and type 1 diabetes57. This information is proposing that overexpressed CBL in CoV infected subjects have a prospective role in the host immunological system.\n\nHDAC9 belongs to class II histone deacetylases, and plays a crucial role in regulating adipocyte and myocyte differentiation, and cardiac muscle development. It generally applies its function in the nucleus, and thus its activity is inhibited due to cytoplasmic retention58. In addition, HDAC9 transcription is observed significantly high in CD4+ T-cells from lupus subjects compared with healthy subjects59. NCOA3 is a transcriptional coactivator that directly binds different nuclear receptors and stimulates hormone-dependent transcriptional activities. In addition, it plays a central role in the remodeling of chromatin, histone acetyltransferase activity, and NF-kB pathway60,61. It is effectively used as a biomarker in breast and hepatocellular cancer62,63. VEGFA is a signaling protein produced by different types of cells includes macrophages, tumor cells, platelets, keratinocytes, and renal mesangial cells, which play an active role in endothelial cell functions including the formation of bones, and the angiogenesis and hematopoiesis processes. Moreover, the VEGF-A isoform enhanced the entry of the virus into the host cells through the activation of this Akt pathway64. Furthermore, SARS coronavirus can diffuse alveolar damage with changeable degrees of acute edema and hyaline membranes, organization, fibrosis, macrophagic infiltration, multinuclear giant cells, atypical reactive pneumocytes, and vascular injury65,66. This literature information suggested that accepting the relationship between coronavirus mediated respiratory disease and VEGF signaling biomarkers will cover the way to design targeted and effective therapeutic approaches for emerging COVID-19. BCL3 is a proto-oncogene that resides in the nucleus and plays a key role in the regulation of inflammatory response through the transcription of genes dependent on the NF-κB. In the context of respiratory syncytial virus (RSV) infection, the BCL-3 changes the status of histone acetylation and transcription factors on activated inflammatory (chemokines) promoters67. In another study, the BCL-2 gene was significantly up-regulated in PBMC samples of SARS patients (5 fold) than compared to healthy individuals68. BCL-3 prevents the inflammation in injured lungs through pinning-down the emergency granulopoiesis process69. The SARS-CoV open reading frame 7a (SARS-CoV-7a) protein participated in various pathogenesis processes including interaction with host protein and inhibiting their synthesis, promoting apoptosis, and activation of p38MAPK in the host system70. Further, the overexpression of BcL-xL protein in transected Jurkat T-cells significantly block the induction of apoptosis by SARS-CoV-7a protein71.\n\nFor the biological process, we determined that cellular response to growth factor stimulus wound healing was the key function of the PPI network. The top five functional terms were RNA polymerase II promoter in response to hypoxia, peptidyl-tyrosine auto-phosphorylation, ERBB2 signaling pathway, anaphase-promoting complex dependent catabolic process, interleukin-1 mediated signaling pathway of the modules. For molecular function, growth factor receptor binding is the major term. Growth factor receptor (GFR) mostly belongs to tyrosine kinase receptors or serine-threonine kinases. The cytoplasmic domain of GFR acts as an enzyme or binds to another protein and forms a complex that acts as an enzyme. In addition, binding of GFR leads to phosphorylation of tyrosine residue and transmitting cell signals within the cell72. After, viral infection, the ligand (viral proteins) binds to the GFR through cell signaling, phosphorylation, and rearrangement and activates different downstream signaling that enhances cell survival, proliferation, angiogenesis, and endocytosis73. Moreover, a recent report demonstrated that GFR as a potential target for drug repurposing against emerging viral diseases such as COVID‐1974,75.\n\nMoreover, we also expected to determine which immunological terms linked with coronavirus pathogenesis; namely stimulatory c-type lectin receptor (CLR) signaling pathway, regulation of hematopoietic stem cell differentiation, T cell receptor signaling, innate immune response signaling, and Fc-epsilon receptor signaling pathway, lymphocyte co-stimulation were highly enriched immunological terms of three different modules. The carbohydrate-recognition domains of CLRs are important pattern recognition receptors to identify viral pathogens and induce antiviral innate immune responses and T helper differentiation76. Further, reports suggested that the activation of CLRs and RIG-I-like receptors enhances pro-inflammatory response in MERS coronavirus-infected macrophages77.\n\nFor KEGG pathways, we identified 12 important pathways that might have an essential role in the pathogenesis and human immune system. Eight different signal transduction pathways include nuclear receptor, MAPK, and WNT signaling pathway, receptor tyrosine kinase, intracellular signaling by second messenger, TGF-β, Notch and Hedgehog signaling pathway; four key cytokine immune signaling pathways namely signaling of interleukins, TNFR2-NF-kB pathway, FLT3, and interferon signaling pathways were identified using the hub-genes. Many studies reported that MAPK, WNT, receptor tyrosine kinase, intracellular signaling by the second messenger, TGF-β, Notch, and Hedgehog signaling pathway regulated in viral pathogenesis78,79. As we stated above, overexpression of HDAC9, NCOA3, KLHL12, CBL, and CRKL and under expression of MYC, CEBPB, VEGFA, BCL3, SMAD3, SMURF1, and ERBB4 may be involved in the regulation of pathways in signal transduction and cytokine immune signaling pathways. It might act as a novel drug target of coronavirus infected patients and plays a key role to improve host immune system.\n\nMany biological functions, like cell signaling, cellular metabolism, enzyme inhibition and antibody-antigen recognition, have essential molecular interaction whether receptor-receptor or receptor-drug interaction. These molecular interactions frequently lead to form protein-protein or protein-drug complexes to carry out molecular functions80. Unfortunately, there are insufficient gene expression profiles of SARS-CoV-2 infected patients in the GEO database. Thus, in the present study, we have validated that drug targets identified from SARS-CoV-1 infected patients can have the possible interaction with SRBD, 3cLpro and N-protein of SARS-CoV-2 to define possible drug targets. Understanding the binding mode and affinity between PTs encoded host proteins and target proteins of SARS-CoV-2 requires tertiary structure of these proteins. However, it is generally difficult and expensive to obtain complex structures by nuclear magnetic resonance spectroscopy and X-ray crystallography. Thus, protein-protein docking is an important method for understanding interactions of drug targets with SRBD, 3cLpro and N-protein of SARS-CoV-2. In the present study, the protein-protein docking results demonstrated that drug-targets with three different protein of SARS-CoV-2 showed the highest interaction energies Hydrogen bond forming residues between the protein complexes. Among them, the highly under-expressed gene ERBB4 (Table 3) encoding drug target “ERBB4” demonstrated high docking interaction energies -260.46, -314.57 and -291.72 kcal/mol with SRBD, 3cLpro and N-protein of SARS-CoV-2 respectively, which was selected for further candidate drug selection studies.\n\nIn the present study, the highly downregulated gene ERBB4 was selected as a drug target to control SARS-CoV-2 infection. Figure 9 illustrates the hypothesized mechanism action of downregulated ERBB4 in SARS-CoV-2 infected cells. A key receptor tyrosine kinase ERBB4 contains four domains includes multiple furin-like cysteine-rich domains, a tyrosine kinase domain, a phosphatidylinositol-3 kinase binding site, and a PDZ binding domain. Ligands are binding to the ERBB4 which induces different cellular response including alveolarization, alveolar epithelial type 2 cells (AEC2) differentiation, anchoring of cell surface receptor, and morphogenesis via extracellular-signal-regulated kinase pathway81,82. Downregulation of ERBB4 inhibits regular action namely alveolarization, morphogenesis, and AEC2 differentiation. Many proteolytic events allow for the release of ERBB4 cytoplasmic fragments. The downregulation of ERBB4 by the SARS-CoV-2 in ACE2 cells may induce receptor tyrosine kinase-mediated macropinocytosis for the host cell entry. Besides, activation of macropinocytosis can increase non-specific fluid uptake, the pH in the vesicle is not decreased and, in that scenario, SARS-CoV-2 may be recycled to the cell surface. Interestingly, fluid-phase uptake (macropinocytosis and cell-to-cell spread) was reported in murine coronavirus and SARS-CoV infection83–85. Both macropinocytosis and PI3K signaling are directly associated with the progression of the number of tumor cells including pancreatic and lung cancer86,87. Further, growing evidence suggested that PI3K signaling involves the generation of the second messenger lipids and activates Rac-Pak signaling which plays a critical function namely macropinocytosis, mTOR signaling clathrin-mediated endocytosis, and cytoskeletal rearrangements88,89. A recent systematic review by 16 and his colleagues showed the increased level of biomarkers such as C-reactive protein, serum amyloid A, interleukin-6, lactate dehydrogenase, D-dimer, cardiac troponin and renal biomarkers were higher in severe complicated COVID-19 patients’ plasma and infected lung tissues. Another study reported that low levels of type I and III interferons reduced innate antiviral defenses, which act as driving features of COVID-1990. In addition, proteome analysis of SARS-CoV-2 infected hosts demonstrated that proteins involved in translation, splicing, carbon metabolism, proteostasis and nucleic acid metabolism could act as a drug target for SARS-CoV-291. Moreover, Gordon et al. reported 67 druggable targets and repurposed 69 FDA-approved drugs for COVID-1992. This information supports the technical concept of the present study which enhances drug repurposing strategy and advances on precision-based therapeutics to COVID-19.\n\nThere are three possible mechanisms (1) SARS-CoV-2 an enveloped single-strand RNA virus, virions are internalized probably by receptor tyrosine kinase (EGFR) family receptor ERBB4 dependent macropinocytosis like SARS-CoV-1 (the process of macropinocytosis indicated in magenta circle). The cellular entry of SARS-CoV-2 involves binding to ERBB4 expressing AEC2 in the plasma membrane, macropinocytosis, and cathepsin based cleavage of the spike glycoproteins. The host transmembrane serine protease 2 (TMPRSS2) for spike priming and cathepsin cleaves spike glycoprotein S1 domain, permits fusion with endosomal membranes and release virions genome into the host cytoplasm; (2) Single-strand RNA translated polypeptides cleaved by the 3cLpro of SARS-CoV-2 possibly attached with mitochondrial ERBB4 and involve viral replication through MAPK signaling pathway. Then, the cell to cell spread action, the replicated SARS-CoV-2 attached to the uninfected AEC2 receptor and then restart macropinocytosis; (3) The part of S2 domain presents peptides into antigen-presenting cells (APC) to modulate host immune system through NFkB- signaling.\n\nIn the present study, we repurposed Wortmannin as a candidate drug that can inhibit PI3K signaling and receptor tyrosine kinase (ERBB4) mediated macropinocytosis, to control virus-cell proliferation and may enhance ERBB4 functions namely alveolarization, morphogenesis, and AEC2 differentiation. Wortmannin is a covalent inhibitor of phosphatidylinositol-3-kinase (PI3K) and related enzymes include the mammalian target of rapamycin (mTOR), DNA-dependent protein kinase catalytic subunit (DNA-PKcs), and mitogen-activated protein kinase (MAPK)93,94. In humans, PI3K activates cell signaling pathways in the head and neck, urinary tract, cervical, ovarian, and lung cancer. Studies reported that the inhibition of PI3K signaling enhances tumor suppression and anti-tumor activity95. Besides, Wortmannin is an extensively used cell biology research includes to inhibit cell proliferation, DNA repair, and receptor-mediated endocytosis96,97. This report supported that the repurposed Wortmannin may have the potential to control SARS-CoV-2 infection in COVID-19 patients with downregulated expression of receptor tyrosine kinase ERBB4.\n\n\nConclusion\n\nBiomarkers can be used as part of a personalized medicine paradigm to customize treatment to the specific disease characteristics of an individual patient. It can also be used to better understand disease mechanisms and to identify novel disease targets. In the present study, the highly downregulated gene ERBB4 was selected as a drug target and Wortmannin was repurposed as candidate drug to control SARS-CoV-2 infection. Further, this study provides insights on the possible personalized therapeutics for emerging COVID-19.\n\n\nData availability\n\nZenodo: Datasets for SARS-CoV-2 drug target and candidate drug identification, http://doi.org/10.5281/zenodo.445825298\n\nThis project contains the following underlying data:\n\nList of selected differentially expressed coronavirus infected host genes for protein-protein interaction network construction\n\nList of protein-protein interaction subnetworks\n\nList of Walktrap modules and potential drug targets\n\nPotential Drug Targets and SARS-CoV-2 drug targets docking results\n\nList of predicted candidate drugs for proposed drug target\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
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}
|
[
{
"id": "79888",
"date": "22 Mar 2021",
"name": "Sugunadevi Sakkiah",
"expertise": [
"Reviewer Expertise Cheminformatics",
"Endocrine disrupting chemicals"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 put a great effect to identify the potent target and candidate drugs for COVID-19 applying biological networks and structural modeling approaches. The authors should address the below comments before the indexing of this paper:\nMinor revision:\nIn the introduction, Ref. 16, the authors should mention the authors' name.\n\nIn methods, data collection, the authors should be clear whether they selected all CoV infected samples or only CoV2 infected samples?\n\nIn Figure 1, SARS-CoV means 1 and 2 or only 2?\n\nAny particular reason for the authors setting the 303K in molecular dynamics simulations?\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": "6488",
"date": "06 Apr 2021",
"name": "Gurudeeban Selvaraj",
"role": "Author Response",
"response": "Comment 1: In the introduction, Ref. 16, the authors should mention the authors' name. Author Response 1: Thanks for your suggestion. The author name is included in the text as follows----A recent systematic review by 16 Kermali and his colleagues showed the increased level of biomarkers such as C-reactive protein, serum amyloid A, interleukin-6, lactate dehydrogenase, D-dimer, cardiac troponin, and renal biomarkers (urea and creatinine) were higher, and low level of lymphocytes and platelet count were recorded in severe complicated COVID-19 patients than non-severe COVID-19 patients’ plasma and infected lung tissues. Comment 2: In methods, data collection, the authors should be clear whether they selected all CoV infected samples or only CoV2 infected samples? Author Response 2: Thanks for the question. All the selected studies contain control and CoV-infected human lung epithelial cells samples. In earlier days the inadequate information of the CoV-2 genomic datasets in Public databases (i.e. NCBI), the authors have selected CoV samples (i.e. CoV-1 genomic information is more than 96% similar to CoV-2). Comment 3: In Figure 1, SARS-CoV means 1 and 2 or only 2? Author Response 3: Thanks for the key question. The initial drug targets were identified from the SARS-CoV-1 whole-genome datasets. Then, the targets verified and validated with RBD-spike receptor binding domain; 3cLpro-3C-like protease; N pro-nucleocapsid protein of SARS-CoV-2 using protein-protein docking. The protein-protein docking results confirm molecular interaction of the identified drug targets with proteins of SARS-CoV-2. Thus, the first box of Figure 1, represents the SARS-CoV or SARS-CoV-1. Comment 4: Any particular reason for the authors setting the 303K in molecular dynamics simulations? Author Response 4: Thanks for the key question. Yes, most computational and experimental studies have focused on room temperature (298K to 303K). The MD simulation input file preparation using the Charmm-gui web-interface was set at 303K as a room temperature (Jo et al., 2008 and Lee et al., 2016). Thus, the authors followed the same."
}
]
}
] | 1
|
https://f1000research.com/articles/10-127
|
https://f1000research.com/articles/10-169/v1
|
02 Mar 21
|
{
"type": "Research Article",
"title": "Effectiveness of turmeric-enriched pellets to improve the immunity of Clarias batrachus toward motile Aeromonas septicemia disease",
"authors": [
"Morina Riauwaty",
"Yusni I. Siregar",
"Isma Mulyani",
"Yusni I. Siregar",
"Isma Mulyani"
],
"abstract": "Background: Turmeric is known as a natural remedy to improve the immunity of organisms. This study aims to understand the effectiveness of turmeric-enriched pellets to improve the immunity of Clarias batrachus to Aeromonas hydrophila. Methods: The study was conducted from May to August 2020. C. batrachus fingerlings, 7-8 cm total length (TL) and 4-5 g (BW) at baseline, were kept in 30 L aquaria (10 fishes/aquarium; three replicated/treatment). Commercial pellets were mixed with turmeric powder. There were five treatment groups: P0 (control, no turmeric); P1 (0.5 g turmeric per Kg of pellets); P2 (0.7 g/Kg); P3 (0.9 g/Kg); Pp (positive control). Thirty days after being feed with turmeric-enriched pellets, all groups of fish were infected with 0.1 ml (108) of A. hydrophila suspension, intramuscularly. The P0 group did not receive injection, while Pp group were not fed with turmeric-enriched pellets but were infected with the bacteria. Fourteen days after infection, clinical signs and hematology of the fish were studied. Results: Pp fish showed heavy clinical signs of A. hydrophila, such as loss of balance, pigmentation, hemorrhages and ulcers. P0 fish did not show any symptoms, while the treated fish reveled some clinical signs of A. hydrophila to a lesser extent than Pp, indicating that the fish is able to face the A. hydrophila attack. Hematology for Pp fish revealed high white blood cells, indicating that the fish were infected. The blood condition of the P0 fish, as well as those of the turmeric-treated fish were normal. In general, the P3 fish showed the least clinical signs of A. hydrophila and normal blood condition, indicating that P3 treatment is best. Conclusion: The best turmeric dosage to improve the immunity of C. batrachus toward A. hydrophila infection is 0.9 g/Kg pellets.",
"keywords": [
"Aeromoniasis",
"catfish",
"clinical sign",
"MAS diseases",
"self-defense"
],
"content": "Introduction\n\nClarias batrachus or the catfish is a favored fish in Riau Province, Indonesia, due to its high economic value and high protein content. The demand of this fish is high, leading to the community culturing the fish, at large and household scale.\n\nC. batrachus is relatively easy to be cultured. It is able to live in fair quality water and consumes a wide range of feed, including commercial pellets, food remains, and fish or chicken remains. This fish grows quickly and achieves marketable size, around 125 grams, within two months. However, this fish is vulnerable toward Aeromonas hydrophila attack, which causes motile Aeromonas septicemia (MAS) disease. This disease may cause mass death in fish or cause ulcers and hemorrhage in fish skin. Fish that suffer from the disease may die or be unmarketable, and this problem causes great loss in fish culture1.\n\nSo far, MAS disease is commonly prevented or cured using antibiotics. The use of antibiotics, however, has negative impacts as its residues may stay in fish flesh and endanger the health of consumers2. Another alternative in preventing MAS disease in fish is by improving the immunity of the fish using natural remedies, such as turmeric. The root of turmeric contains natural materials, namely curcumin that is antibacterial and has immune-modulatory agents1. The chemical components of turmeric are curcumin (diferuloylmethane), desmethoxycurcumin, and bisdemethoxycurcumin3.\n\nTurmeric is well known as a traditional remedy for humans and it has been widely used for its antimicrobial, anti-inflammatory, antioxidant properties, as a detoxification of toxins and is able to increase the immune system against disease2. Therefore, turmeric has been used to improve fish health through immersing method4. Unfortunately, that method is not very effective as the treated fish became stressed and it is not practical for large scale fish culture. Turmeric is not poisonous, and it can be consumed, but feeding fish with turmeric-enriched pellets has never been studied. To understand the effectiveness of turmeric-enriched pellets to improve the immunity of fish to A. hydrophila, this study aimed to assess the effectiveness of turmeric-enriched pellets in improving the immunity of C. batrachus towards A. hydrophila.\n\n\nMethods\n\nThis research was conducted from May to August 2020 at the Parasite and Fish Diseases Laboratory, Aquaculture, Fisheries and Marine Science Faculty, Riau University. The experiments were carried out within the ethical guidelines provided by the research institution and national or international regulations.\n\nC. batrachus fingerlings were obtained from the hatchery of the Riau Province’s Marine Fisheries and Department in Tibun, Pekanbaru. Fish chosen were actively swimming with no wounds or parasites. They were approximately 7–8 cm total length (TL) and 4–5 g body weight (BW) . The fish were reared in aquaria (30×40×40cm3; 10 fish/aquarium) with aerators and filters. Prior to the treatment, the fish were acclimated to the laboratory environment for four days. A total of 150 fish (30 fish per treatment for five treatments). Blood samples were taken from 3 fish/treatment (total 15 fish).\n\nA completely randomized design with five treatment groups (three replications per treatment) was used in this research. The aquaria were grouped based on the turmeric treatments and in each group the aquaria were placed randomly based on lottery method. The treatments applied are as follows:\n\nP0 = negative control, no turmeric feed, no infection\n\nPp = positive control, no turmeric feed, infected with A. hydrophila\n\nP1 = 0.5g turmeric in 1 Kg feed, infected with A. hydrophila\n\nP2 = 0.7g turmeric in 1 Kg feed, infected with A. hydrophila\n\nP3 = 0.9g turmeric in 1 Kg feed, infected with A. hydrophila\n\nTurmeric powder was made by slicing the turmeric, drying and grinding it using a blender. During the research, the fish were feed with commercial fish feed pellet (F999 with 35% protein content from the PT Central Proteina Prima Tbk). The powder was then mixed with fish feed pellets before the feed was given. The turmeric used in this study was obtained from the local market in Delima Street Pekanbaru and the turmeric was planted by local farmer. During the study the fish were fed ad libitum. The turmeric was mixed with a spoon of water and then mixed well with 1 Kg of pellets. The enriched pellet was then directly given to the fish, three times per day (morning, noon and afternoon).\n\nOn the 30th day, the fish were infected with A. hydrophila bacteria (intramuscularly 0.1 ml with a bacterial density of 1.0x108 CFU/mL). Prior to injection, the fish was sedated using clove oil, approximately 0.25 ml or 5 drops/L fresh water. The fish was put in the clove mixture for around 3 minutes until it shown inactive movement. After the injection the fish was returned to the rearing tank.\n\nAfter being infected, clinical sign of MAS disease (namely rotting of the tail, increased respiration rate and swollen abdomen, exophthalmia and lethargy) was monitored every day. By the 45th day of the experiment (14th days after infection) the blood condition of fish was studied.\n\nBlood parameters were conducted two times, at baseline and in the 8th week (end of the research period). Three fish from each aquaria were taken and their blood were obtained; fish were anesthetized using clove oil (5 drops/L) and blood was taken from the caudal vein, by inserting an EDTA (Merck) 10% wet syringe. Blood samples was kept in EDTA moistened vials, in a cool box filled with crushed ice. Total erythrocytes and leukocytes were counted using a Neubauer hemocytometer and then were calculated3 and analyzed4. Hematocrite and leucocrite levels were determined using heparinized micro-hematocrit capillaries that was centrifuged at 12,000 rpm for 3 minutes. Hemoglobin content in blood was measured using Sahli method5.\n\nThe parameters studied are as follows:\n\n1. Survival rate: survival of the fish was monitored every day and data obtained were analyzed using ANOVA.\n\n2. Growth: growth of fish was monitored one per week and data obtained were analyzed using ANOVA.\n\n3. Clinical signs: after being treated with turmeric enriched pellet for 30 days, the fish was injected with A hydrophyla and the clinical sign of the MAS diseases in fish was monitored everyday (started at the injection day) for 7 days. Data obtained were described.\n\n4. Hematological condition: Blood samples were taken 2 times. The first samples were taken prior to turmeric enriched pellet treatment. The second blood sampling was conducted in the 45th day (14 days after the fish being infected with A hydrophyla). Hematological parameters measured were total erythrocyte, hematocrit levels, hemoglobin, total leucocyte and leucocyte differentiation. Data obtained were then described.\n\nData were analyzed using Microsoft Excel program for creating graphics and SPSS program to calculate the ANOVA of growth data.\n\n\nResults\n\nThe survival of the fish various among treatment groups. After being fed with turmeric-enriched pellets for 30 days, the survival of the fish was 100% in all treatments. After infection, however it is clear that the survival rate of the infected fish decreased. In P0 group (no turmeric feed nor A. hydrophila infection), the survival rate was 100%. In contrast, in the Pp group (no turmeric with A. hydrophila infection), the survival of the fish by the end of the experiment was low (43.33%). The survival rate of C. batrachus for all groups is presented in Table 1.\n\nP0, control (no turmeric/not infected); Pp, positive control (no turmeric/infected); P1, 0.5g turmeric in 1 Kg feed and infected; P2, 0.7g/Kg and infected; P3, 0.9g/Kg and infected.\n\nMean with standard error followed by different letters are significantly different (P<0.05)\n\nAll infected fish showed various clinical signs of MAS disease, namely ulcers, hemorrhage, pigmentation, swollen abdomen and eroded fins. MAS signs worsened as the turmeric dose was reduced: P1, rotting of the tail, increased respiration rate and swollen abdomen; P2, exophthalmia and lethargy; P3, clinical symptoms were unclear.\n\nThe growth pattern of C. batrachus is presented in Table 2. In general, the growth of fish in all treatment groups showed a similar pattern: they gained length throughout the experiment. However, by the end of the experiment, TL varied between groups. Fish that were treated with turmeric shown better growth than that of fish that do not receive any turmeric. The growth of fish reduced as the turmeric dosages decreased (Table 2; Figure 1).\n\nPo, control (no turmeric/not infected); Pp, positive control (no turmeric/infected); P1, 0.5g turmeric in 1 Kg feed and infected; P2, 0.7g/Kg and infected; P3, 0.9g/Kg and infected.\n\nPo, control (no turmeric/not infected); Pp, positive control (no turmeric/infected); P1, 0.5g turmeric in 1 Kg feed and infected; P2, 0.7g/Kg and infected; P3, 0.9g/Kg and infected.\n\nAs well as body length, BW of the treated fish increased throughout the experiment. The daily growth rate of fish in each treatment, varied. Fish that were fed with turmeric-enriched pellets showed a higher daily growth rate and as a consequence had a heavier BW than those with non-turmeric enriched pellets (Table 3; Figure 2).\n\nPo, control (no turmeric/not infected); Pp, positive control (no turmeric/infected); P1, 0.5g turmeric in 1 Kg feed and infected; P2, 0.7g/Kg and infected; P3, 0.9g/Kg and infected.\n\nP0, control (no turmeric/not infected); Pp, positive control (no turmeric/infected); P1, 0.5g turmeric in 1 Kg feed and infected; P2, 0.7g/Kg and infected; P3, 0.9g/Kg and infected.\n\nAs shown in Figure 2, the highest BW is in fish that are fed with feed pellets with 0.9 turmeric/Kg pellets. The lowest BW is in the fish that were not fed with turmeric-enriched pellets and infected with A. hydrophila. From the beginning (D0) to the end (D45) of the research, fish in all treatments grew well. Even after A. hydrophila infection, the growth of fish increased steadily. The growth of fish that are belonged to the Pp group had the lowest growth compared to growth of fish in other treatment groups.\n\nIn fish, the function of leucocytes is mainly related to the immune system. Feeding the fish with turmeric enriched pellets in this study aimed to improve the immunity of the fish. The immunity status of the fish was expected based on the leucocyte condition in general. The leucocyte condition of the fish before and after being fed with turmeric-enriched pellets is presented in Table 4.\n\nPo, control (no turmeric/not infected); Pp, positive control (no turmeric/infected); P1, 0.5g turmeric in 1 Kg feed and infected; P2, 0.7g/Kg and infected; P3, 0.9g/Kg and infected. Day14inf = 14 days after infection with A. hydrophila. Mean with standard error followed by different letters are significantly different (P<0.05)\n\nData obtained indicate that the number of leucocytes in the turmeric-fed fish and in the fish with no turmeric differs. The turmeric-fed fish showed a higher number of leucocytes (2–15×104cells/mm3). Before being feed with turmeric (day 0), the average number of leucocyte was 8.18–8.43×104 cells/mm3 and after being fed with turmeric enriched pellets for 30 days, the leucocytes slightly increased. P3 group fish has the highest number of leucocytes at day 30 (9.60×104 cells/mm3).\n\nAfter being infected, the number of leucocytes in the fish of each treatment increased due to infectious agents. The leucocyte of the P0 group is steady as the fish were not infected. The highest number of leucocytes was again seen in group P3 (11.29×104cells/mm3), while the lowest was in group Pp (9.71×104cells/mm3) (Figure 3). These data suggest that the provision of turmeric increased the leucocyte number, before as well as after being infected with A. hydrophila.\n\nPo, control (no turmeric/not infected); Pp, positive control (no turmeric/infected); P1, 0.5g turmeric in 1 Kg feed and infected; P2, 0.7g/Kg and infected; P3, 0.9g/Kg and infected. Day14inf = 14 days after infection with A. hydrophila.\n\nThe population of each leucocyte cell type in the treated fish are presented in Figure 4. The composition of leucocyte types in all treated fish showed a similar pattern. Lymphocytes were around 70% of the total population. From day 0 to the 30th day, the fish were fed on turmeric and it is clear that in turmeric fed fish the lymphocyte proportion (>70%) is higher than fish not fed with turmeric. After being infected with A. hydrophila, the lymphocyte of the turmeric fed fish decreased slightly (lowest was 70%). On the other hand, the fish in group Pp, lymphocytes decrease moderately to approx. 65%. As the normal lymphocyte population in catfish is 71.66–73%, the leucocytes of the Pp group is relatively low and it means that the immunity of these fish is less able to combat the A. hydrophila infection.\n\nP0, control (no turmeric/not infected); Pp, positive control (no turmeric/infected); P1, 0.5g turmeric in 1 Kg feed and infected; P2, 0.7g/Kg and infected; P3, 0.9g/Kg and infected. Day14inf = 14 days after infection with A. hydrophila.\n\n\nDiscussion\n\nIn general, the survival of the fish treated with turmeric-enriched pellets in this study varied. Survival of the control positive fish (infected with A. hydrophila and no turmeric fed) was low (43.33%). The infected fish showed various clinical symptoms of MAS disease, namely ulcers, hemorrhage, pigmentation, swollen abdomen and eroded fins. Similar clinical signs have been found in common carp that suffer from MAS disease6–8. In addition, fish infected with 1.8×108 CPU/ml of A. hydrophila die between 8 and 24 h and show alterations in behavior, which are not observed in control fish9,10.\n\nIn this study, the growth of fish that were fed with turmeric-enriched pellets was higher than the growth of the control positive fish. This suggests that turmeric improves the growth of fish, as shown by the increase in TL as well as BW. As the fish in the control positive group did not receive turmeric, their feeding appetite may be lower than the turmeric-fed fishes and this is reflected in their growth rate. The infection of A. hydrophila may worsen the health of the fish in general as their immunity is not being boosted by the turmeric and as a consequence, by the end of experiment, the BW of fish in Pp group is the lowest.\n\nThe fish that were treated with turmeric revealed better growth than that of the fish that do not receive any turmeric. This fact suggests that turmeric improves the growth of the fish. Curcumin supplementation has been shown to improve growth and feed appetite in Nile tilapia11. Fish fed with feed enriched with curcumin exhibited enhanced antioxidant status and immune responses, and tilapia fed with curcumin supplemented diets had highest post-challenge survival rate12. The higher curcumin content in fish feed resulted in a higher growth rate, as turmeric acts as a antibacterial, anti-inflammatory and antiviral agent13. Curcumin has been shown to improve the immunity of fish and acts as a defense agent to combat the A. hydrophila infection14. Curcumin is a strong antioxidant and acts as anti-free radical that negatively affects the physiological process of the fish2. Turmeric contains curcumin, an active compound that is able to improve immunity as well as increases the appetite of the fish toward feed provided1. As the turmeric-fed fish had a strong immunity and good appetite, they grew better than the fish with non-enriched pellets. In our study, after being infected on the 30th day, the turmeric-fed fish was able to cope with the A. hydrophila attack and continue to grow.\n\nIn our study, after being infected, the number of leucocytes in the fish of each treatment group increased due to presence of an infectious agent. Among the infected fish, the increment of leucocyte number in the control positive group was the lowest, as most leucocytes are transferred to the infected area and leucocytes in blood vessels are reduced15. On the other hand, the fish provided with turmeric had higher leucocyte numbers, which means that they are better at facing the infection, as leucocytes act as non-specific defense agents that are able to localize and eliminate pathogens. The immunogenic agents in natural remedies may trigger the increment of leucocytes in general15. Increasing leucocyte numbers indicate that cellular immunity (non-specific immunity) of the fish is good16.\n\nImprovement of the immune system can be studied based on leucocyte cell type composition. In this study, the leucocytes of the control positive group was relatively low. A decrease of lymphocytes on the 14th day after infection indicated that antibodies were formed to fight A. hydrophila. The fight may reduce lymphocyte cell numbers, as the lymphocyte in the peripheries are allocated to the infected area17. Even though the lymphocytes in P1, P2 and P3 groups decreased after infection, their amount remained in the normal range. The ability of the fish to maintain the amount of lymphocytes may be caused by the presence of curcumin, which has been shown to trigger the formation of those cells18.\n\nThe presence of pathogens in the fish may trigger monocyte cells to regenerate. If the immunity of the fish is good, phagocytosis succeeds and the pathogen is defeated. The fish becomes healthy and the monocyte number increases to a normal range. The production of antibodies is crucial for the immune response12. The monocyte percentage of N. tilapia fish ranges between 17 and 25% when present in freshwater12. In less healthy fish, immunity is low, and monocyte action may not succeed. As result many monocyte cells die, the monocyte number decreases and the pathogen thrives. Monocytes or macrophages are able to phagocyte any pathogens, and if there is infection monocytes will move to the infected area19. A decrease in monocytes may be caused by an increase in lymphocyte amount that produce antibodies; therefore leading to an obstruction of monocyte production. The pathogen present may disrupt the fish physiology and clinical signs of diseases occur. In this research, the clinical sign of MAS disease were present in the control positive group. This fact indicated that the fish with no turmeric fed had low immunity. In fish that were fed with turmeric (P1, P2 and P3) the number of monocytes was in the normal range. The condition of the fish in general showed few clinical symptoms of MAS disease. This fact indicates that the provision of turmeric is able to improve the immune system in fish, and fish in all treatment are able to defeat A. hydrophila infection.\n\nAmong the turmeric-fed fish, the P3 group showed the fewest clinical symptoms of MAS disease. This may be due to the best immune performance in P3 fish, as they had the highest number of lymphocytes (up to 80%). Based on data obtained, it can be concluded that the fish feed with 0.9g/Kg pellets provide the best result to improve fish immunity to fight A. hydrophila infection.\n\nThe lymphocyte level in this study ranged between 60–70%. The lymphocyte level of the freshwater fish ranged between 42 and 51%. The amount of lymphocytes could increase during stress. Stress in fish may interfere with non-specific immune responses, such as lymphocyte proliferation (increase in cell amount and alterations in T and B cells). Leukocyte increase is related to the decrease in cortisol levels in the body. When cortisol level decreased, DNA synthesis of the lymphocyte cells occurred and led to the high amount of lymphocytes20.\n\n\nConclusions\n\nFeeding C. batrachus with turmeric-enriched pellets is effective in improving the immune system of the fish. The number of lymphocytes maintained a normal range even though the fish were infected with A. hydrophila. The clinical signs of MAS disease were fewer lighter in fish that were fed with turmeric, and the most effective dose of turmeric for improving the immune system of the fish was shown to be 0.9g/Kg of pellets.\n\n\nData availability\n\nFigshare: Survival Rate, TL and Growth, https://doi.org/10.6084/m9.figshare.13606265.v121.\n\nThis project contains the following underlying data:\n\n- Survival rates for all aquaria (n=15),\n\n- Clinical signs of MAS for all aquaria (n=15),\n\n- Body weight of all fish (n=15),\n\n- Total length of all fish (n=15),\n\n- Number of leucocytes in all fish (n=15),\n\n- Number of lymphocytes, monocytes, neutrophils, thrombocytes in all fish (n=15).\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "Acknowledgements\n\nThe authors thank the students who supported the research.\n\n\nReferences\n\nSahu S, Das BK, Mishra BK, et al.: Effect of dietary Curcuma longa on enzymatic and immunological profiles of rohu, Labeo rohita (Ham.), infected with Aeromonas hydrophila. Aquac Res. 2008; 39(16): 1720–1730. Publisher Full Text\n\nNagpal M, Sood S: Role of curcumin in systemic and oral health: An overview. J Nat Sci Biol Med. 2013; 4(1): 3–7. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBlaxhall PC, Daisley KW: Routine haematological methods for use with fish blood. J Fish Biol. 1973; 5(6): 771–781. Publisher Full Text\n\nAnderson DP, Siwicki AK: Simplified assays for measuring nonspecific defense mechanisms in fish. Seattle, WA: Fish Health Section/American Fisheries Society Meeting. 1994; 26–35.\n\nPatil PJ, Thakare GV, Patil SP: Variability and accuracy of Sahli’s method in estimation of haemoglobin concentration. Natl J Integr Res Med. 2013; 4(1): 38–44. Reference Source\n\nSaharia P, Pokhrel H, Kalita B, et al.: Histopathological changes in Indian Major Carp, Labeo rohita (Hamilton), experimentally infected with Aeromonas hydrophila associated with hemorrhagic septicemia of Central Brahmaputra valley of Assam, India. J Entomol Zool Stud. 2018; 6(5): 6–11. Reference Source\n\nSong X, Zhao J, Bo Y, et al.: Aeromonas hydrophila induces intestinal inflammation in grass carp (Ctenopharyngodon idella): an experimental model. Aquaculture. Elsevier, 2014; 434: 171–178. Publisher Full Text\n\nSarker J, Faruk MAR: Experimental infection of Aeromonas hydrophila in pangasius. Progress Agric. 2016; 27(3): 392–399. Publisher Full Text\n\nDias MKR, Sampaio LS, Proietti-Junior AA, et al.: Lethal dose and clinical signs of Aeromonas hydrophila in Arapaima gigas (Arapaimidae), the giant fish from Amazon. Vet Microbiol. 2016; 188: 12–15. PubMed Abstract | Publisher Full Text\n\nVan Doan H, Doolgindachabaporn S, Pensee AS, et al.: The LD50 of Asian Catfish (Pangasius bocourti, Sauvage 1870) challenge to pathogen Aeromonas hydrophila FW52 strain. Accessed: Nov. 26, 2020.\n\nHassan S, Abdel-Rahman M, Mansour ES, et al.: Prevalence and Antibiotic Susceptibility of Bacterial Pathogens Implicating the Mortality of Cultured Nile Tilapia, Oreochromis niloticus. Egypt J Aquac. 2020; 10(1): 23–43. Publisher Full Text\n\nRahman AA, El-Bouhy Z, Wahbah M, et al.: Effects of dietary turmeric and clove powder on growth and immune response of the Nile tilapia. Egypt J Aquat Biol Fish. 2020; 24(5): 589–608. Publisher Full Text\n\nKhalil F, Emeash H: Behavior and Stereotypies of Nile Tilapia (Oreochromis niloticus) in Response to Experimental Infection with Aeromonas hydrophila. Aquat Sci Eng. 2018; 33(4): 124–130. Publisher Full Text\n\nRiauwaty M, Sari T, Adelina A: Potency of Turmeric in Reducing Motile Aeromonas Septicaemia (Mas) in Pangasius hypopthalmus. IOP Conf Ser Earth Environ Sci. 2020; 430(1): 012025. Publisher Full Text\n\nParrino V, Cappello T, Costa G, et al.: Comparative study of haematology of two teleost fish (Mugil cephalus and Carassius auratus) from different environments and feeding habits. Eur Zool J. 2018; 85(1): 193–199. Publisher Full Text\n\nHoseinifar SH, Zoheiri F, Dadar M, et al.: Dietary galactooligosaccharide elicits positive effects on non-specific immune parameters and growth performance in Caspian white fish (Rutilus frisii kutum) fry. Fish Shellfish Immunol. 2016; 56: 467–472. PubMed Abstract | Publisher Full Text\n\nDawood MAO, AbdEl-Kader MF, Moustafa EM, et al.: Growth performance and hemato-immunological responses of Nile tilapia (Oreochromis niloticus) exposed to deltamethrin and fed immunobiotics. Environ Sci Pollut Res Int. 2020; 27(11): 11608–11617. PubMed Abstract | Publisher Full Text\n\nRiauwaty M, Windarti W, Sari TEY, et al.: Blood condition of Pangasius hypophthalmus fed with turmeric enriched pellets and infected with Aeromonas hydrophila. IOP Conf Ser Earth Environ Sci. 2019; 348(1): 012036. Publisher Full Text\n\nRiauwaty M, Windarti W, Sari TEY, et al.: Blood condition of Pangasius hypophthalmus fed with turmeric enriched pellets and infected with Aeromonas hydrophila. IOP Conf Ser Earth Environ Sci. 2019; 348(1): 012036. Publisher Full Text\n\nFazio F: Fish hematology analysis as an important tool of aquaculture: a review. Aquaculture. 2019; 500: 237–242. Publisher Full Text\n\nRiauwaty M, Siregar YI, Mulyani I: Survival Rate, TL and Growth. figshare. Dataset. 2021. http://www.doi.org/10.6084/m9.figshare.13606265.v1"
}
|
[
{
"id": "80812",
"date": "19 Mar 2021",
"name": "Christopher Marlowe Caipang",
"expertise": [
"Reviewer Expertise fish health management",
"aquatic biotechnology"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe present study describes the use of turmeric in improving immunity of Clarias batrachus against infection with MAS. Results showed incorporation of 9g turmeric powder per kilogram of feeds improved immunity of the fish.\nThe results presented are straightforward. However, the manuscript needs improvement on the following aspects, which I hope the authors would consider:\nThe authors mentioned that turmeric causes stress when fish are immersed in a solution containing that rhizome. Please cite studies that turmeric is beneficial to fish when incorporated in the diets.\n\nThe authors claimed that feeding fish with turmeric-enriched diets has not been studied. I suggest that the authors make a thorough literature search to indeed claim that no studies have done so.\n\nIn the preparation of the enriched diets, there was no mention how turmeric powder was incorporated in the feed pellets. Based from the manuscript, the turmeric powder was just mixed with the feed pellets. If this the case, upon feeding the turmeric powder would immediately leach out from the feeds and thus may not be consumed by the fish.\n\nFor the blood sampling, only 3 fish per treatment was used and there were 3 replicate tanks per treatment with 10 fish in each replicate. So this means that only 1 fish was taken per replicate tank to make up for 3 fish/treatment? Please explain.\n\nWere the same fish used for blood sampling at initial, day 30 of feeding and at 14th day of infection?\n\nPlease indicate the statistical tool that was used.\n\nAs all fish survived the challenge, then there is no need for Table 1. The authors can mention in the manuscript that all fish survived the experimental infection.\n\nI suggest to combine Table 2 and Fig 1, as well as Table 3 and Fig 2 as these provide same information.\n\nIf the authors can show photos of the WBC for catfish that would add more strength to the manuscript, as the morphology of leukocytes in fish varies. This would be helpful to other researchers who would be working similar studies in the future as they can refer to the photos of the different leukocytes from this manuscript.\n\nI suggest to revise Fig 4 to make the data presentation clear. The trend of each leukocyte type in the different treatments must be compared statistically rather than presenting the leukocyte populations of every treatment as what the authors presented in the present manuscript.\n\nI hope that the authors will incorporate these comments/suggestions when they revise their manuscript.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": [
{
"c_id": "6620",
"date": "28 Apr 2021",
"name": "Morina Riauwaty",
"role": "Author Response",
"response": "The present study describes the use of turmeric in improving immunity of Clarias batrachus against infection with MAS. Results showed incorporation of 9 g turmeric powder per kilogram of feeds improved immunity of the fish. The results presented are straightforward. However, the manuscript needs improvement on the following aspects, which I hope the authors would consider: 1. The authors mentioned that turmeric causes stress when fish are immersed in a solution containing that rhizome. Please cite studies that turmeric is beneficial to fish when incorporated in the diets. I have added the literature on the turmeric beneficial in culturing the fish. 2. The authors claimed that feeding fish with turmeric-enriched diets has not been studied. I suggest that the authors make a thorough literature search to indeed claim that no studies have done so. I have added the literature on the use of turmeric for feeding fish. 3. In the preparation of the enriched diets, there was no mention how turmeric powder was incorporated in the feed pellets. Based from the manuscript, the turmeric powder was just mixed with the feed pellets. If this the case, upon feeding the turmeric powder would immediately leach out from the feeds and thus may not be consumed by the fish. I have explained that the turmeric powder was mixed with water and the powder was stuck in the pellet granule. The powder was swallowed when the fish was eating the pellets. 4. For the blood sampling, only 3 fish per treatment was used and there were 3 replicate tanks per treatment with 10 fish in each replicate. So this means that only 1 fish was taken per replicate tank to make up for 3 fish/treatment? Please explain. I have added information on the blood sampling. In this research there were 5 treatments and in each treatment there were 3 replications (in 3 aquaria). For blood sampling, 3 fishes were taken from each aquarium, it means that there were 9 fishes/ treatment or total 45 fishes were used for blood study. 5. Were the same fish used for blood sampling at initial, day 30 of feeding and at 14th day of infection? The fish for blood sampling were returned to each aquarium and for the next sampling the fish was taken randomly. It means that the sampled fish might be accidentally captured for the next samplings. 6. Please indicate the statistical tool that was used. I have added the statistical tool that was used. 7. As all fish survived the challenge, then there is no need for Table 1. The authors can mention in the manuscript that all fish survived the experimental infection. I have removed Table 1 and explained the survival information in manuscript. 8.Suggest to combine Table 2 and Fig 1, as well as Table 3 and Fig 2 as these provide same information. OK, I have combined Table 2 and Fig 1, as well as Table 3 and Fig 2. 9.If the authors can show photos of the WBC for catfish that would add more strength to the manuscript, as the morphology of leukocytes in fish varies. This would be helpful to other researchers who would be working similar studies in the future as they can refer to the photos of the different leukocytes from this manuscript. I have added the photo of the WBC of catfish. 10. I suggest to revise Fig 4 to make the data presentation clear. The trend of each leukocyte type in the different treatments must be compared statistically rather than presenting the leukocyte populations of every treatment as what the authors presented in the present manuscript. OK, I have revised Fig 4."
}
]
},
{
"id": "80815",
"date": "22 Mar 2021",
"name": "Indra Junaidi Zakaria",
"expertise": [
"Reviewer Expertise Aquaculture (marine and freshwater)",
"Ichthyology",
"Fish Biology",
"Marine 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\nWhat about the influence of the water qualities in which the fish were kept during the experiment? Such as temperature, pH, DO, BOD, ammonia and phosphate and otherwise; is there no data? The health of the fish during cultivation also depends on the water quality. Or you should make the statement that the aquatic environment has no effect.\n\nOn the tree treatment of adding turmeric to the pellets, it was seen that up to the day of observation, the movement of the graph was almost the same, which was the same as upward. Will this be valid for how many days after that?\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? No\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": [
{
"c_id": "6621",
"date": "28 Apr 2021",
"name": "Morina Riauwaty",
"role": "Author Response",
"response": "What about the influence of the water qualities in which the fish were kept during the experiment? Such as temperature, pH, DO, BOD, ammonia and phosphate and otherwise; is there no data? The health of the fish during cultivation also depends on the water quality. Or you should make the statement that the aquatic environment has no effect. OK, the water quality data has been provided and the relation between water quality and the fish health has been explained. On the tree treatment of adding turmeric to the pellets, it was seen that up to the day of observation, the movement of the graph was almost the same, which was the same as upward. Will this be valid for how many days after that? I have explained that the growth rate of the turmeric feeding fish is higher and the graph is valid as long as the fish is fed with turmeric enriched pellets."
}
]
}
] | 1
|
https://f1000research.com/articles/10-169
|
https://f1000research.com/articles/10-394/v1
|
17 May 21
|
{
"type": "Research Article",
"title": "Virtual screening of curcumin analogues as DYRK2 inhibitor: Pharmacophore analysis, molecular docking and dynamics, and ADME prediction",
"authors": [
"La Ode Aman",
"Rahmana Emran Kartasasmita",
"Daryono Hadi Tjahjono",
"La Ode Aman",
"Rahmana Emran Kartasasmita"
],
"abstract": "Background: Curcumin reduces the proliferation of cancer cells through inhibition of the DYRK2 enzyme, which is a positive regulator of the 26S proteasome. Methods: In the present work, curcumin analogues have been screened from the MolPort database using a pharmacophore model that comprised a ligand-based approach. The result of the screening was then evaluated by molecular docking and molecular dynamics based on binding the free energy of the interaction between each compound with the binding pocket of DYRK2. The hit compounds were then confirmed by absorption, distribution, metabolism, and excretion (ADME) prediction. Results: Screening of 7.4 million molecules from the MolPort database afforded six selected hit compounds. By considering the ADME prediction, three prospective curcumin analogues have been selected. These are: 2‐[2‐(1‐methylpyrazol‐4‐yl)ethyl]‐1H,5H,6H,7H,8H‐imidazo[4,5‐c]azepin‐4‐one (Molport-035-369-361), methyl 4‐(3‐hydroxy‐1,2‐oxazol‐5‐yl)piperidine‐1‐carboxylate (Molport-000-004-273) and (1S)‐1‐[5‐(furan‐3‐carbonyl)‐4H,6H,7H‐pyrazolo[1,5‐a]pyrazin‐2‐yl]ethanol (MolPort-035-585-822). Conclusion: Pharmacophore modelling, combined with molecular docking and molecular dynamics simulation, as well as ADME prediction were successfully applied to screen curcumin analogues from the MolPort database as DYRK2 inhibitors. All selected compounds that have better predicted pharmacokinetic properties than that of curcumin are considered for further study.",
"keywords": [
"Curcumin analogues",
"DYRK2",
"pharmacophore",
"docking",
"molecular dynamics simulation",
"ADME"
],
"content": "Introduction\n\nCurcumin is a compound derived from turmeric (Curcuma longa), which is responsible for the yellow rhizome extract coloration. Traditionally, a large number of people in India, China, Indonesia and other Asian countries have applied turmeric powder in therapeutic herbs and as a food additive.1–5 The curcumin (diferuloylmethane) constituent is a tautomeric compound known to exist as an enolic form in organic solvents, and in keto form in water.6 The wide range of biological activities are currently being tested in vivo and in vitro to develop the numerous potentials in treating various diseases. These include the application of curcumin as an antioxidant, antibacterial, antifungal, antiviral, anti-inflammatory, and anti-angiogenic agent. Furthermore, there are reports on the promising anti-Alzheimer, as well as anticancer properties of curcumin, and its antagonistic effects against other degenerative diseases.7 The curcumin component is also a non-toxic compound, as no toxicity has been reported following the administration of high doses to animals.8 Previous reports have shown biological activities related to cancer, including lymphomas, breast, prostate, cervical, lung and colorectal cancers, alongside leukemia.1,4 There are numerous pathways involved in regulation, including p53, BAX, cyclin D1, various BCL, p21, p27, AKT, COX-2, protein kinase, and others.9\n\nThe facts and opinions on the biological effects of curcumin as a drug candidate indicate that it is a PAIN (pan-assay interference) compound or IMP (invalid metabolic panacea). Moreover, this unstable compound is known to easily degrade into others,10 and a total of eight have been reported to date. These include vanillin, ferulic acid,11,12 feruloyl methane, 2-hydroxy-6-(4-hydroxy-3-methoxyphenyl)-4-oxohexa-2,5-dienal,11 bicyclopentadione,13 ferulic aldehyde, vanillic acid,12 and 4-[(1e)-3-(propan-2-yloxy)prop-1-en-1-yl)guaiacol.14 In addition, numerous pharmacokinetic evaluations have indicated the poor absorption, low solubility, rapid metabolism and elimination as well as poor bioavailability properties of curcumin.15\n\nThere have been several suggestions of methods to solve these challenges, including co-administration with adjuvants. In addition, studies have shown the possible development into a nanoparticle form, complexations with metallic and radioactive elements, using the derivatives or analogue products, and application in the bioconjugation form.4,16 One of the current research strategies involves the screening of compounds from a large database to obtain analogues with the pharmacophore features of curcumin.\n\nOne of the purposes of studying curcumin and its analogues is to find analogues that are targeted to reduce cell proliferation by interacting with dual-specificity tyrosine-regulated kinase 2 (DYRK2). This is achieved through the positive regulation of the 26S proteasome, particularly in cancer cells. The inhibition property is observed in terms of cell proliferation with IC50 5 nM.17 DYRK2 is a family of protein kinases with members involved in cellular growth and development.18 In addition, there have also been reports on its function as a tumor suppressant by regulating cell survival, differentiation, proliferation and apoptosis.19 The mechanism adopted to control further involves the regulation of CDK14 expression.19 Furthermore, DYRK2 as an enzyme is capable of phosphorylating serine substrates and threonine residues. This action regulates apoptotic cell death in response to DNA damage by impacting the phosphorylation effect of Ser46 on p53.19,20 Furthermore, reports have shown the negative regulatory impact on breast cancer formation through the transcriptional downregulation of Kruppel-like factor 4 (KLF4).20\n\nTherefore, the aim of this study is to explore the curcumin analogues for their potential application as a DYRK2 inhibitor through virtual screening by using pharmacophore molecular modelling as well as docking and molecular dynamics. The compounds of screening results are expected to be applied as lead compounds in discovering and developing a prospective anticancer molecule through DYRK2 inhibition.\n\n\nMethods\n\nFigure 1 shows the chemical structure of curcumin and the analogues21 used to model the dataset for ligand-based pharmacophore. The 2D chemical configuration was constructed with MarvinSketch 19.2, prior to an analysis with LigandScout 4.3 win64 evaluation version22 (the analysis can be replicated using PharmaGist Webserver). Subsequently, each structure’s geometry was optimized using the energy minimize module with MMFF9423 force field set at a default setting.\n\n5ZTN was the Protein Data Bank accession number of the DYRK2 protein used in this study,17 and curcumin acted as the native ligand. In addition, the target for molecular docking and dynamics was prepared using Molecular Operating Environment (MOE) 2014.0901 software (this can be replicated using MGLTools 1.5.6 and USCF Chimera 1.13.1) in order to correct the break residues, charging, and protonation of the protein structure. The protein molecule was opened in AutoDockTool (ADT) 1.5.6, and the water molecule(s) were then removed. In grid menu, macromolecule was chosen, and the protein structure was then saved as a.pdbqt extension.\n\nThe ligand-based pharmacophore observed in this work was analyzed through multiple flexible alignment. Therefore, the model was generated from 24 dataset compounds using LigandScout 4.3 software (or PharmaGist Webserver). This was achieved through the 3D superposition of chemical features constructed by the flexible conformation alignments of all dataset compounds. In addition, the enrichment factor (EF) and receiver operating characteristics (ROC) analysis were used to validate the pharmacophore model using ROC Analysis: Web-based Calculator for ROC Curves. Active compounds were all of the 24 dataset compounds, and decoy compounds were obtained from zinc decoy database generated via DecoyFinder 2.0.\n\nMolPort provided a large database with over 7.4 million catalogue compounds. The process of curcumin analogue filtration from the compounds database was performed on the Pharmit webserver. Filtering the compounds from database was then conducted using the pharmacophore query file as obtained from the above pharmacophore modeling.\n\nThe goal of molecular docking was to assess the binding affinity of compound(s) upon interaction with the receptor. Therefore, all results obtained from the database filtering process were docked to the DYRK2 protein. In addition, the docking module of MOE was used for docking protocol detection and also for the docking score calculation of all hits (this can be replicated using AutoDock 4.2.6). Moreover, the molecular docking protocol was evaluated through virtual screening with the alpha triangle methods, London dG scoring and GridMin refinement.\n\nThe aim of molecular dynamics was to evaluate the physical movement of molecules and atoms. This activity was intended to stimulate the interaction stability between the ligand and DYRK2, and was further investigated in combination with protein-ligand complexes obtained from the docking score calculation and characterized by the highest binding affinity. In addition, the interaction dynamics between ligands and receptors was measured using Gromacs 2018.3.24–29 The stability of ligands in the binding pocket of DYRK2 protein were simulated by the molecular dynamic for 50 ns. In addition, Gormos96 54a7 force field was used to prepare the protein topology, while the PRODRG webserver was applied for ligand topology, using Gromos forcefield. The complex protein-ligand was solvated in a dodecahedron with 1 nm dimensions. Moreover, an aqueous environment was created in the system with the simple point charge (SPC) water model, and this was neutralized by adding Na+ and Cl–. The electrostatic interaction and periodic boundaries were calculated in all conditions using Particle-mesh Edward (PME) methods. Meanwhile, the cut-off radius for short-range van der Waals and Coulomb interactions was set to 0.9 nm. Furthermore, the linear constraint solver for molecular simulations (LINCS) method was used to constraint all bond lengths, while minimization, NPT and NVT equilibration as well as system production were performed at constant temperature (300K) and pressure (1 atm). The minimization process was conducted for 50 ps, NPT and NVT were collectively simulated for 100 ps, while the production process for 50 ns were saved at every 2 ps with coordinates of each simulation.\n\nThe interaction of ligand-receptor was visualized with LigandScout 4.3 (and can be replicated in USCF Chimera 1.13.130 and Discovery Studio Visualiser v20. The energy from ligand-receptor interactions were further estimated using the g-mmpbsa31 platform.\n\nThe absorption, distribution, metabolism and excretion (ADME) prediction values for hit compounds were calculated using ADMET Prediction by ADMETLab Webserver. Furthermore, ADME properties applied in the current research include caco-2 permeability, bioavailability 30% (F30), plasma protein binding (PPB), blood-brain barrier (BBB), Cyp450 1A2 inhibitor, Cyp450 1A2 substrate, half-life (T1/2) and clearance (CL).\n\n\nResults\n\nThe hypothetic pharmacophore was grouped based on the number of features, comprising 3 to 7, and each has 10 models, totaling to 50. Figure 1 shows the structure of the dataset molecules used to construct the pharmacophore model, where the validation process including ROC and EF analysis were implemented. These were performed on 24 active compounds and 717 decoy compounds obtained from zinc decoy database generated by DecoyFinder 2.0. Table 1 summarizes the values of area under the curve (AUC), ROC curve and EF for all models.\n\nTable 1 shows the adequacy of AUC values for all models, where the highest EF value of EF100% was observed in model4-10 and was consequently selected as the best model. Figure 2 shows the ROC curve indicating the composition of 45 hit compounds, including 17 active and 28 decoy. Meanwhile, AUC values shown on 1%, 5%, 10% and 100% were 1.00, 1.00, 1.00 and 0.85, respectively, while the corresponding EF values were 30.8, 14.2, 11.7, and 11.7.\n\nThe output file of the selected pharmacophore model generated from LigandScout 4.3 (or PharmaGist Webserver) was used to filter the compound database. Furthermore, the Pharmit interface was used for 3D visualization of the features, including details on the coordinate position and radius. The presence of hydrophobic, H-bond acceptor and donor features with radius 1.5 Å, and 0.9 Å for the aromatic variant were observed in the default setting. Moreover, filtering on Pharmit allowed the users to modify the feature’s radius, and consequently increase or decrease the amount of hit(s) as a result. However, manually changing this value is also possible by modifying the hit reduction and screening criteria. The Pharmit developers enter some criteria to set up the maximum hits per conformation, and molecule number, as well as the total limit for reduction, molar weight, rotated bond, logP, polar surface area (PSA), aromatic ring, H-bond donor and acceptor for screening.\n\nThis novel work involves database filtering with default settings for pharmacophore features and hit screening, with the exception of reduction. The model ultimately produced 1,130 hits, and a lot more compounds exist for continued screening. Therefore, the feature radius and screening procedure were modified. In particular, the hydrophobic, H-bond acceptor and donor radius were reduced to 1.4 Å for each, while the Rule of Three (RO3)32 was applied during hit screening. These rules include molar weight (300 Dalton), rotated bond (3), logP (3), aromatic ring (3), H-bond donor (3) and H-bond acceptor (3). Meanwhile, PSA was set to the maximum value according to another reference, at 90 Å,33 and these filtering protocols collectively produced 566 hits.\n\nGroups of model3, model4, model5, model6, and model7 have 3, 4, 5, 6 and 7 chemical features, respectively. Every group has 10 model candidates. AUC, area under the curve; EF, enrichment factor.\n\nBinding affinity is an indicator of the connection strength between ligand and receptor. This was determined by a docking score calculated using the MOE software (and can be replicated using AutoDock 4.2.6). This procedure was then validated by redocking the native ligand of DYRK2 protein (5ZTN) present in curcumin. The lowest RMSD value for successful docking was 0.7788, indicating the propensity to apply this protocol to other ligands.\n\nThis protocol docking validation process involved calculating the binding affinity (docking score) for each curcumin analogue complex and DYRK2 protein. Moreover, the value obtained for curcumin during redocking was –12.46 kcal/mol. This was used to filter the hits, as the specimens with greater and relatively close values between the native ligand and the binding pocket of target were selected. Figure 3 shows the chemical structure of ligand (hit compounds) and ligand-DYRK2 interaction with docking score lower than –10 kcal/mol, and Figure 4 indicates the overlay of each, with pose characterized by the highest value.\n\nThe complexes (ligand-protein) motion during simulation were expressed in Root Mean Square Deviation (RMSD) (Figure 4(a)), while the movements of protein backbone during simulation was estimated in a Root Mean Square Fluctuation (RMSF) curve (Figure 4(b)). Figure 4(a) showed that the interactions are stable after 30 ns of simulation.\n\nThe ADME (absorption, distribution, metabolism, and excretion) provide a description for drug disposition within an organism. These pharmacokinetic parameters influence the overall level and kinetics in the tissues, and consequently influence the pharmacological effect of the active compounds. In addition, it is possible to represent the ADME of active compounds as a prediction value.\n\nThe results obtained with the selected compounds in this current investigation were caco-2 permeability and F30 for absorption; PPB and BBB for distribution, Cyp450 1A2 inhibitor and Cyp450 1A2 substrate for metabolism; while T1/2 and CL represented excretion. Table 2 shows the summary of ADME prediction for selected compounds in contrast with curcumin.\n\nF30, 30% bioavailability; PPB, plasma protein binding; BBB, blood-brain barrier, T1/2, half-life CL, clearance.\n\n\nDiscussion\n\nThe pharmacophore is the physicochemical feature of a molecule known to interact with a specific target receptor. This is modelled in a 3D pattern and the basic characteristics are also shared by a set of molecules. The ligand-based pharmacophore model was constructed without needing a protein target structure, through a 3D superposition of the ligand conformed physicochemical features.\n\nThe chemical characteristics of a selected pharmacophore model include three H-bond acceptors provided by the oxygen in keto, methoxy and hydroxyl groups, a H-bond donor from the hydroxyl, an aromatic feature and hydrophobicity contributed by aromatic group. Figure 5(a) shows the 2D visualization of pharmacophore model, while Figure 5(b) and 5(c) demonstrates it in 3D.\n\n3D visualization of pharmacophore model (red balls are H-bond acceptors, the green are H-bond donors and the yellow are aromatic and hydrophobic features) (b). Alignment of 17 hits of active compounds in the pharmacophore features (c).\n\nThere is rule of three (RO3) beside Lipinski’s rule of five (RO5), which applies in searches pertaining to drug-likeness. Particularly, RO5 stipulates the criteria to be satisfied, including the presence of no more than five hydrogen bond donors, 10 hydrogen bond acceptors, a molecular weight (MW) of less than 500 Daltons, and an octanol-water partition coefficient (logP) below 5.34,35 Furthermore, all numbers are in the multiple of five, hence the RO3 criteria requires a multiple of three. These criteria include logP not greater than 3, MW less than 300 Daltons, the presence of no more than three hydrogen bond donors and acceptors, respectively, and no more than three rotatable bonds.36\n\nThe Pharmit platform allows users to customize the pharmacophore feature criteria based on RO5 or RO3. In addition, the value modification potentially increases or decreases the amount of hits. The application of RO3 in this research instigated a decline in the number of hit compounds from 1,130 (default criteria) to 566 (modified criteria). The latter was determined to be more rational during molecule screening.\n\nMolecular docking is one of the in silico approaches of interaction studies between ligand(s) and receptor. The 566 hits are further filtered through this means, and 11 compounds were selected after using the specified protocol. In addition, the binding affinity (docking score) of samples in each hit were better than or close to curcumin (native ligand). Figure 6 shows the respective overlay with the binding pocket of DYRK2 protein. It was observed that all selected hit compounds occupy the DYRK2’s binding site.\n\nFigure 4(a, b) shows the stability performance of RMSD for each ligand, as well as the RMSF for the respective protein backbone on each complex, after the initial 25 ns simulation. Therefore, an average of the system binding energy was calculated at the end. The van der Waals, electrostatic, polar solvation, non-polar (Solvent-Accessible Surface Area) and binding energy were calculated every 200 ps, in order to obtain an average value for each complex. Table 3 shows the summarized system energy report obtained from 200 snapshots.\n\nThe native ligand (curcumin) has a binding energy of –53.058 kJ/mol with the DYRK2 protein. Table 3 showed six selected hit compounds have more negative values compared to that of Curcumin, i.e. Molport-035-369-361 (–71.35±24.85), Molport-000-004-273 (–83.56±18.24), MolPort-029-697-986 (–61.69±14.89), MolPort-035-585-822 (–74.24±15.55), MolPort-000-156-336 (–54.49± 15.09), and MolPort-002-747-457 (–69.36±12.58).\n\nThis shows that van der Waals and polar solvation energy are the main impact on binding factors for curcumin and all selected compounds. The respective values were negative and positive. This indicates the tendency to generate more positive effect on binding energy at more negative van der Waals. The binding energy of all six selected compounds were larger (more negative) than that of curcumin. This discrepancy was attributed to the lesser polar solvation characteristics. Moreover, significantly higher values of positive polar solvation energy tend to decrease binding energy.\n\nFigure 7 showed the position of curcumin and other selected hit compounds in the binding pocket of DYRK2 during the molecular dynamic simulation. These results confirm those of our docking study. The interaction of 5ZTN-curcumin (Figure 8(a)) and 5ZTN-Molport 000-004-273 (Figure 8(b)) show the binding mode which involves H-bonds and hydrophobic interactions.\n\nTable 4 summarizes the percentage of H-bond occupancy between the selected hit compounds and residues of DYRK2. It was observed that LYS178, GLU193, ASP295 have important roles in the ligand interaction in the DYRK2 binding pocket.\n\nThe absorption prediction results recognized all 11 selected compounds to be better than curcumin in terms of Caco-2 permeability, where the optimal output for active compound is suggested to be more than –5.15 log cm/s.37 The calculated values were above –5.0, whereas a value of –5.13 was recorded for curcumin. In addition, the bioavailability (F30) was also better, as the curcumin was categorized 0 (<30), while the selected compounds were attributed as 1 (>30%) except MolPort-029-697-986 or tert-butyl-3-hydroxy-2H,4H,5H,7H,8H-pyrazolo[3,4-d] azepine-6-carboxylate.38\n\nThe PPB was higher in curcumin, at 88.84% compared to the others. Hence, the native ligand is considered to have a more significant bond with plasma protein, although less than the suggested 90%, and consequently has a lower therapeutic index.39 Conversely, the selected compounds have a greater propensity to attach to the target receptors and provide the desired therapeutic effect.\n\nThe BBB is a highly selective semipermeable border separating the circulating blood from the brain and other extracellular fluids in the central nervous system (CNS).40 This parameter is calculated as a ratio of compounds, and is improved by H-bond numbers as well as molecular weight.41 The ADMETLab webserver categorizes the BBB value of a drug as 0 (BBB negative) indicating the inability to penetrate, whereas 1 (BBB positive) demonstrates a barrier permeation potential. In addition, all compounds, including the curcumin were categorized with a BBB value of 1, and a positive BBB is derived in instances where the ratio probability was above 0.1.\n\nThe cytochrome P450 (CYP) gene family are responsible for drug metabolism. Here, the ADMETLab webserver was used to predict the interaction potentials of curcumin and all selected compounds as an inhibitor and substrate of the cytochrome P450 enzyme. However, the drugs were unable to act as inhibitors but could act as a substrate of cytochrome P450. The prediction results showed the tendency for 2-[2-(1-methylpyrazol-4-yl)ethyl]-1H,5H,6H,7H,8H-imidazo[4,5-c]azepin-4-one (Molport-035-369-361), (1S)-1-[5-(furan-3-carbonyl)-4H,6H,7H-pyrazolo[1,5-a]pyrazin-2-yl] ethanol (MolPort-035-585-822), and methoxytyramine (MolPort-000-156-336) to act as a substrate and not as CYP1A2 inhibitor. Furthermore, 4-hydroxy-1-[2-(imidazol-1-yl)ethyl]-6-methylpyridin-2-one (Molport-046-067-592), and 3-(1,3-oxazol-5-yl) phenylboronic acid (MolPort-028-957-184) potentially act as substrate and inhibitor. Curcumin or (1E,4Z,6Z)-5-hydroxy-1,7-bis(4-hydroxy-3-methoxyphenyl)hepta-1,4,6-trien-3-one, Methyl 4-(3-hydroxy-1,2-oxazol-5-yl)piperidine-1-carboxylate (Molport-000-004-273), and tert-butyl 3-hydroxy-2H,4H,5H,7H,8H-pyrazolo[3,4-d]azepine-6-carboxylate (MolPort-029-697-986) were predicted as being unable to act as inhibitor and a substrate of cytochrome. The three other compounds can only act as a cytochrome inhibitor but cannot act as a substrate.\n\nCL refers to the volume of plasma of the drug freed per unit time, where (T1/2) is half-life in plasma. The results indicate lower values with hits and curcumin at < 5 mL/min/kg and < 3 hours, respectively.39 Curcumin possessed the comparable CL and the highest T1/2. Thus, selected hit compounds are considered to have relatively better excretion properties.\n\nFinally, the selected compounds demonstrated similar or better overall pharmacokinetic parameters than that of curcumin, as observed with the ADME discussed above.\n\n\nConclusions\n\nA combined pharmacophore model and molecular docking for virtual screening has been conducted to find a potential DYRK2 inhibitor.\n\nBased on a gradual virtual screening process using a ligand-based pharmacophore model and molecular docking, 11 hit compounds have been selected. Further detailed study using molecular dynamics simulation afforded six hit compounds with better binding interaction with DYRK2 compared to that of curcumin, i.e. Molport-035-369-361 (-71.35±24.85) kJ/mol, Molport-000-004-273 (-83.56±18.24) kJ/mol, MolPort-029-697-986 (-61.69 ±14.89) kJ/mol, MolPort-035-585-822 (-74.24±15.55) kJ/mol, MolPort-000-156-336 (-54.49±15.09) kJ/mol, and MolPort-002-747-457 (-69.36±12.58) kJ/mol.\n\nThe six compounds obtained after a gradual virtual screening process have similar pharmacophore characteristics. Considering the pharmacokinetic properties, Molport-035-369-361, MolPort-035-585-822 as well as Molport-000-004-273 are now under in vitro study for further investigation as lead compounds, and the results will be reported elsewhere.\n\n\nData availability\n\nProtein Data Bank: DYRK2 data from Protein Data Bank. Accession number PBD5ZTN; https://identifiers.org/structure/5ztn.\n\nDataset of compounds with biological activity for ligand-based pharmacophore modeling were obtained from21 and are shown in Figure 1.",
"appendix": "Acknowledgements\n\nLOA wishes to thank the Ministry of Research, Technology, and Higher Education of the Republic of Indonesia for their financial support through a BPPDN Scholarship.\n\n\nReferences\n\nAggarwal B, Sundaram C, Malani N: Curcumin: the Indian solid gold. The Molecular Targets and Therapeutic Uses of Curcumin in Health and Disease. 2007; 1–75. PubMed Abstract | Publisher Full Text\n\nAkram M, Shahab-Uddin A, Usmanghani K: Curcuma longa and curcumin: A review article. Rom J Biol Plant. 2010; 55(2): 65–70.\n\nAlamdari N, O’Neal P, Hasselgren PO: Curcumin and muscle wasting-A new role for an old drug? Nutrition. 2009; 25(2): 125–129. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAnand P, Thomas SG, Kunnumakkara AB, et al.: Biological activities of curcumin and its analogues (Congeners) made by man and Mother Nature. Biochem Pharmacol. 2008; 76(11): 1590–1611. 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}
|
[
{
"id": "90128",
"date": "25 Aug 2021",
"name": "Mohd Athar",
"expertise": [
"Reviewer Expertise Computational chemistry"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe manuscript uses standard procedure for computational modelling and can be considered for indexing underlying below mentioned concerns:\nAs per reference paper (JMC, 1998, 41, 21), the 24 ligands are HIV-1 IN inhibitors. Hence these ligands can be active ligands against HIV-1 IN and may not be against DYRK2. Please check.\n\nIs pharmacophore a 'physicochemical feature' or '3D structural feature'?\n\nWhat kind of alignment/superposition was used for the pharmacophore mapping?\n\nFigure should be numbered in order of their description in text. Pharmacophore model should come first before pharmacophore screening results.\n\nBetter to number the ligand mentioned in the text for making the discussion simpler.\n\nDiscussion section can be combined without any subheading.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
},
{
"id": "95613",
"date": "04 Oct 2021",
"name": "Hrvoje Rimac",
"expertise": [
"Reviewer Expertise Computational chemistry",
"CYP enzymes"
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn the article entitled “Virtual screening of curcumin analogues as DYRK2 inhibitor: Pharmacophore analysis, molecular docking and dynamics, and ADME prediction” the authors performed in silico analysis of the curcumin analogues as DYRK2 inhibitors and have decided on 3 compounds which will undergo further in vitro study as possible lead compounds. While the research seems to be performed correctly, there are several issues that require attention and need to be corrected and more thoroughly explained before the article is approved:\nEnglish should be corrected in the entire manuscript, especially in the title “Virtual screening of curcumin analogues as DYRK2 inhibitors…”\n\nSentences where the authors explain in which programs can the analyses be replicated are irrelevant. The authors should just write how they did what they did, not all the ways it is possible to do it.\n\nIn Methods section a lot of details concerning the filtering and docking parameters are missing.\n\nThe authors said they performed MD simulation in total length of 50 ns and that the complexes are stabilize after 30 ns. 50 ns is not enough time to draw any conclusion about the stability of the complexes, the simulations should be at least 100 ns long, if not more.\n\nWhy did the authors check if the ligands are CYP1A2 substrates or inhibitors? Why just 1A2? If the influence on CYP metabolism is evaluated, CYP3A4 should definitely be included.\n\nCorrect writing of ZINC Directory of Useful Decoys (DUD), Caco-2 etc. should be used.\n\nOn page 8 the authors write about the possibilities of Pharmit. This should be removed as this manuscript is not the point of this article.\n\nMD results are not explained. What are the conclusions from RMSF? Which are the most important interactions and the most important amino acids? Is this in agreement with the literature and the known inhibitors? There is no real discussion and comparison with other research.\n\nThe authors should analyze and discuss more thoroughly the 3 best compounds.\n\nWhat is the point of Figure 7? It takes a lot of space and the same is shown in Figure 6.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-394
|
https://f1000research.com/articles/9-1292/v1
|
02 Nov 20
|
{
"type": "Research Article",
"title": "The varying openness of digital open science tools",
"authors": [
"Louise Bezuidenhout",
"Johanna Havemann",
"Johanna Havemann"
],
"abstract": "Background: Digital tools that support open science practices play a key role in the seamless accumulation, archiving and dissemination of scholarly data, outcomes and conclusions. Despite their integration into open science practices, the providence and design of these digital tools are rarely explicitly scrutinized. This means that influential factors, such as the funding models of the parent organizations, their geographic location, and the dependency on digital infrastructures are rarely considered. Suggestions from literature and anecdotal evidence already draw attention to the impact of these factors, and raise the question of whether the open science ecosystem can realise the aspiration to become a truly “unlimited digital commons” in its current structure. Methods: In an online research approach, we compiled and analysed the geolocation, terms and conditions as well as funding models of 242 digital tools increasingly being used by researchers in various disciplines. Results: Our findings indicate that design decisions and restrictions are biased towards researchers in North American and European scholarly communities. In order to make the future open science ecosystem inclusive and operable for researchers in all world regions including Africa, Latin America, Asia and Oceania, those should be actively included in design decision processes. Conclusions: Digital open science tools carry the promise of enabling collaboration across disciplines, world regions and language groups through responsive design. We therefore encourage long term funding mechanisms and ethnically as well as culturally inclusive approaches serving local prerequisites and conditions to tool design and construction allowing a globally connected digital research infrastructure to evolve in a regionally balanced manner.",
"keywords": [
"Open Science",
"digital",
"reproducible",
"low/middle-income countries"
],
"content": "Introduction\n\nOpen science encompasses a collection of activities, principles and tools oriented at making scientific research accessible to all levels of society proposed to increase transparency and efficiency in research workflows and scholarly publishing (Rahal & Havemann, 2019). Open science activities are clustered around a number of areas of action, including open data, open access (OA), open educational resources (OER), free and open source software (FOSS), open hardware, open methodologies and open peer review, including the growing citizen science movement and broader societal engagement.\n\nThe open science movement has garnered support from both individual researchers as well as high-level policy and funding around the world and given rise to a range of influential regional high-level and grassroots initiatives alike in Africa1, IberoAmerica2, Europe3, North America4, Asia5 and Oceania6 as well as several independent and cross-regional networks and community initiatives7. The global scientific community is increasingly recognizing the benefits of learning from each other and aligning technically feasible approaches adopted to regional infrastructure prerequisites. At the same time, research communities are contributing to the development of resources, practice change and activism to establish Open Science and incorporate it into mainstream research workflows; The Open Science MOOC, FOSTER Open Science and the Open Scholarship Knowledge Base (OSKB) are just a few of many examples8. The oldest and most visible of these communities are within free and open source software (FOSS) development (Powell, 2012). In recent years, community activities are extending to a wide range of areas, including community-driven and often volunteer-run preprint repository platforms9, open peer review services10, and capacity building programs and training resources11. These wide-ranging activities are united under core values, such as openness, equitable sharing, access to resources and optimized re-use (Tennant et al., 2019).\n\nThe ongoing coronavirus 2019 (COVID-19) pandemic has drawn attention to the key role of openness in research (OECD, 2020). Widespread commitment to openness in COVID-19 research by funders, governments, research institutions and individual researchers has showcased the impact of rapid OA publishing, open data sharing and the open and collective design of hardware (Maia Chagas et al., 2020; Zastrow, 2020)12. All of these areas have underscored the importance of open research practices as a means to increase efficiency and speed of information sharing. This has been vital not only for medical research, but also for policy makers and practitioners in responding to the impact of COVID-19 on society.\n\nThe increasing support for open research activities provides an opportune moment for critical reflection on the open science movement so far. In particular, it prompts a critical assessment of the evolution of the digital infrastructures, tools and online working practices that underpin open research activities. Of these different areas, the design, deployment and use of the digital tools that support open science activities are the least scrutinized. Indeed, critical evaluations of the evolving landscape of interlinked digital tools supporting open science are scarce (Kramer & Bosman, 2016).\n\nDigital tools are a ubiquitous part of open science. Most steps of the research workflow are nowadays complemented or replaced by online applications. These tools assist researchers to share and collaborate, and thus increase openness and transparency at all stages of the research lifecycle. Many of these tools have changed the way that research is done and how research resources – including datasets, publications, educational resources and software – are circulated globally (Kramer & Bosman, 2016).\n\nIn this paper, we collectively term these tools “digital open science tools” (DOSTs). This category encompasses the wide range of digital tools that are involved in facilitating openness during the research lifecycle. In this paper, the term ‘DOST’ includes any digital tool (for-profit, non-profit and community-led entities) used in open research, irrespective of whether they were designed explicitly for open science or have been co-opted into open science practices.\n\nGrowing efforts to promote interoperability and open workflows have made interconnection key to the success of any DOST (Wilkinson et al., 2016). The interconnection of tools and the interoperability of their outputs enable users to move between tools at different stages of the research lifecycle to facilitate research, data dissemination and publication. The interconnectedness of the tools, as well as the overlaps in their function within the DOST landscape (“multiplicity”), means that multiple “pathways” exist for data to progress through a research lifecycle (see Figure 1). How these “pathways” are selected depend on a variety of issues such as user preference, access to specific DOSTs, demands of the research project and preferences of the research community.\n\nA) Diagram from Kramer & Bosman (2016)13 demonstrating diversity of DOSTs, linkages between tools at different stages of workflow. Green line demonstrates a potential research workflow involving DOSTs. Image shared under CC-BY license. B) Pictogram of a random digital tool representing the tools displayed in 1A with influencing aspects addressed in this paper: underlying values, financial models, language choices, geographical location, user communities.\n\nNew tools are continually being added to the DOST landscape, and new connections between tools are regularly emerging to populate this ecosystem. We use the term “ecosystem” in contrast to the more common “landscape” to designate the dynamism of the online environment as an interconnected system through which resources move. We ground this understanding in biological understandings of ecosystems as biological communities of interacting organisms and non-living components that interact as a system. This DOST ecosystem is dynamic, multiplicitous and subject to internal and external pressures. It includes interconnected/interdependent DOSTs, as well as the information and communication infrastructures, communities of users and socio-political stakeholders. Internal and external pressures from these actors determine the persistence of the DOSTs and the structure of the ecosystem.\n\nThe underlying dynamics and influences within the evolving DOST ecosystem have been extremely influential in driving forward the Open Science movement as a whole. Tools within the ecosystem, such as GitHub, are changing the way collaborations are managed. Publishers like PLoS and F1000Research are redefining transparent publishing models, and repositories such as Zenodo, Open Science Framework (OSF) and DSpace are offering open platforms for sharing and re-using data.\n\nThe constantly growing uptake in usage of DOSTs, and their increasing interconnectivity and interoperability may give the impression that the digital landscape of open science is positively unfolding and developing to support the growing needs of the open science community. Widespread endorsement of many DOSTs, support from socio-political actors and the rapid organization of “user communities” associated with specific tools has left little time for critical reflection on how the ecosystem is evolving and what power dynamics are shaping its evolution. How, it is increasingly being asked, do the tools developed by multiple scholarly for-profit service providers, non-profit organizations and open source communities contribute to the open science vision and mission to make research workflows and results accessible to all sectors of society across the globe?\n\nIn this paper we critically interrogate the DOST ecosystem. We ask how its current structure enables knowledge availability and question whether social, political or economic barriers linked to DOST design and deployment undermine this objective. To do so, we ask three main questions of the ecosystem and its actors:\n\n1. What is the impact of a small number of countries dominating DOST design and deployment?\n\n2. Do heterogeneities in values, funding, and stakeholders that influence tool design and interconnection affect the openness of the DOST ecosystem?\n\n3. How (if at all) are external power dynamics and influences recognized and addressed in the DOST ecosystem?\n\nThe subsections below provide a short background to these three questions, and frame the empirical data presented in the following sections.\n\nThe Open Science movement supports the democratization of research resources. Increasing openness in research will make resources available to all individuals in all nations and at all levels of society14. In this way, Open Science promotes equitable access to resources through the (self-described) model of the “knowledge commons” (Hess & Ostrom, 2007) which promotes a form of direct democracy, where every individual has the right---and ability--to access information, data, and content that is collectively owned and managed by a community of users. While this direct democracy model works well as a model of resource distribution, it complicates the evolution of the DOST ecosystem. The distribution of researchers and resources around the world is unevenly weighted towards a small number of high-income countries (HICs). A 2013 report by UNESCO highlighted that China, the European Union, Japan, the Russian Federation and the USA together accounted for 72% of researchers worldwide. Unsurprisingly, the evolution of DOSTs reflects this distribution, with the majority of tools being developed in countries with a high density of researchers and considerable investment in research and national digital infrastructures. As a result, the design of the tools and the evolution of user communities – as dictated by the majority of users – is weighted in favour of a small number of countries.\n\nThe specific geographic location of many DOSTs, as reflected by the location of their development, registration and hosting, contrasts to the approach championed by the FOSS movement. FOSS has long been calling for and implementing a more representative form of democracy for software development and distribution by promoting models that avoid specific geographically-clustered nodes (Tennant et al., 2020; Vermeir et al., 2018). This model of “software mirrors”15 is commonly used in systems such as GNU as well as Linux distributions like Debian and Fedora. Nonetheless, and likely due in part to economies of scale, this approach of mirroring services to increase access has not been replicated within the DOST ecosystem.\n\nThe open science movement promotes widely agreed values that also define good scientific practice. These include openness, credibility, reproducibility, and verifiability of any research output (Bartling & Friesike, 2014). Nonetheless, the endorsement of these core values can cause the widespread value/practice-heterogeneity within the open science movement to be overlooked. Indeed, Open science can be thought of both as a practice and as a philosophy (Levin et al., 2016), implying that the motivations for individuals to get involved can vary considerably (Fecher & Friesike, 2014).\n\nFecher & Fiesike (2014: 17) mention five different open science schools of thought: The infrastructure school (which is concerned with the technological architecture), the public school (which is concerned with the accessibility of knowledge creation), the measurement school (which is concerned with alternative impact measurement), the democratic school (which is concerned with access to knowledge) and the pragmatic school (which is concerned with collaborative research). It can thus not be assumed that everyone is motivated to a similar degree by the core values. A number of pragmatic reasons also play important roles in the uptake of Open Science practices and tools, including efficiency, career advancement, journal and institutional requirements and community expectations (Ferguson, 2014).\n\nThis heterogeneity is further complicated by the number of actors within the DOST ecosystem. The unrestricted development of DOSTs has caused this space to be populated by stakeholders ranging from community projects to commercial companies. These different actors may have highly variable reasons for developing the DOSTs, and rely on highly disparate funding sources to ensure their longevity. While some DOSTs are explicitly designed to further open research practices, some may be a commercial venture responding to a gap in the market. Indeed, the highly variable development of DOSTs has led to the uncoordinated evolution of the DOST ecosystem, meaning that the financial, governmental and infrastructural influences are poorly understood.\n\nThe ways and reasons through which user-communities are recruited around DOSTs – as with any form of technology – are similarly diverse. These may range from bottom-up community endorsement, advertising, integration with other DOSTs or commercial endorsement. The persistence of a DOST within the ecosystem can thus depend on a range of different reasons, including accessibility, ease of use, visibility through advertising and promotion, or simply that the size of the user community allows it to dominate similar DOSTs (Mody, 2011).\n\nRecognizing the heterogeneity inherent in the motivations for creating DOSTs and recruiting user communities is critical. It negates the assumption that endorsement from members of the open science community means that the tool is designed or deployed to optimally promote the values of the open science movement. To the contrary, the persistence of certain DOSTs over others depends as much on market forces and user preferences as on alignment with open science values.\n\nResearch occurs within highly complex networks of power and influence of financial, governmental and societal actors (Vermeir et al., 2018). As discussed above, the DOST ecosystem, while digital, relies on funders, hosts and infrastructures that are very much located in the physical world. DOSTs are thus subject to national legislation and regulation. Moreover, the ecosystem relies on information and communication infrastructures that are neither open nor designed with openness in mind. Service providers, content delivery networks, and cloud storage facilities, for example, are largely user-agnostic and operated by large international companies, yet are becoming extremely influential in the construction of the DOST ecosystem.\n\nThe rapid and diverse evolution of DOSTs has caused an exponential expansion of the ecosystem. In this dynamic space, researchers are continually provided with more options for integrating openness into their daily research workflow. Nonetheless, the rapid expansion of DOSTs and their insertion into the Open Science ecosystem requires careful scrutiny. At present, there is little critical examination of what tools are integrated into–and persist in–this ecosystem, what forces/values/preferences dictate how they are connected, why they are used, and what underlying infrastructures are being endorsed/supported by their presence within the DOST ecosystem.\n\nRecognizing such concerns makes it apparent that the DOST ecosystem cannot be taken as de facto open, equitable and transparent. The range of actors and the interconnectivity of the tools makes it likely that there are a range of barriers that hamper certain users from engaging both in the tools and the workflows that they are embedded within. Key considerations include:\n\n- Tools may be uncritically integrated into the ecosystem causing existing power dynamics to be perpetuated, leading to the marginalization of certain user groups\n\n- Governments and commercial companies have undue influence on the landscape due to their hosting, financing, and otherwise influential roles\n\n- The existing DOST ecosystem may become prescriptive of a specific way of “doing”, as one tool becomes hyper-dominant\n\nTable 1 adapts the concept of “data assemblages” developed in Critical Data Studies for use in outlining the DOST ecosystem. Data assemblage refers to the technological, political, social and economic apparatuses and elements that constitute and frame the generation, circulation and deployment of data (Kitchin & Lauriault, 2014). Just as data assemblages map the complex set of stakeholders and pressures that influence the production, dissemination and reuse of data, Table 1 highlights some of the key pressures on the DOST ecosystem and their potential impact on the evolution of these spaces.\n\nTo our knowledge, there have not yet been attempts to provide an overview of how the DOST ecosystem shifts and adapts to these pressures. Indeed, the heterogeneity not only of the ecosystem, but also the actors and pressures that influence it, make this a challenging task. This paper presents a methodological attempt to map a selection of the DOST ecosystem including links between the tools. Our intention is to generate an interactive map of the DOST ecosystem so as to be able to test pressure and tipping points that shape ecosystem make-up and functioning.\n\n\nMethods\n\nDOSTs were identified from a range of different sources. The primary database was developed from two key studies, conducted on open science tools16. The database was extended by web searches and tools foregrounded in key open science communities such as the Research Data Alliance and the Open Science MOOC. As mentioned in the introduction, we used a very broad definition of DOSTs and included commercial, non-profit and community-driven digital tools that are currently used in open research. We did not make the availability of source code a prerequisite for inclusion. Neither did we limit the tools to those provided free to users. Inclusion criteria for the database were:\n\n- The tool must be currently active and available for use online\n\n- The tool must have a website detailing its function and activity\n\n- There must be evidence of the use of the tool in an open or collaborative research project\n\nEach tool was assessed according to the criteria outlined in section below. We developed the categories based on our analysis of ecosystem pressures presented in Table 1. The information used to populate these categories was freely available on the respective websites, each of which was examined by both of authors. Database entries were cross-checked by the authors in duplicate. Discrepancies were discussed until consensus was reached. Using the network mapping criteria above, a database was developed for analysis.\n\nThe paper is based on the 3 September 2020 version of this database (Bezuidenhout & Havemann, 2020). It is anticipated that the database will continue to evolve with community input. Contributions to the evolving database are encouraged through communication with authors.\n\nIn this paper we examine the current dataset which includes 242 DOSTs focusing on the information about language, T&Cs, Host institution, and sponsor or funding institutions. The columns in the dataset display the sorting criteria that were applied as follows:\n\nWorkflow step: At what point(s) during the research workflow is the tool primarily used? – Discovery, Analysis, Writing, Publishing, Outreach, Assessment17\n\nOpen science category: Which subsection of the open science movement is the tool most closely related? – Open hardware, Open educational resources, Open methodology, Open access, Open data, Open peer review, FOSS (free and open source software), Open lab notebook, Open Science [general category for multi-purpose tools].\n\nHost (where applicable): Is the tool hosted by an organization other than itself? – Named organization, otherwise ‘Self’, i.e. self-hosted\n\nLocation / host location: In which world region is the tool or host located or registered? – US (United States of America), UK (United Kingdom), EU (European Union), other|specific country, unspecified\n\nLanguage: What interface and description language is offered by the tool? – Named language\n\nFunding source: How is the tool funded? – Commercial, Various commercial, Grant, Various grant, Various mixed [commercial and grant], Institution\n\nType of entity: How are the tool activities governed? – NPO (nonprofit organization), Host affiliated, Commercial, Independent\n\nUser fee: Does the tool require a fee to use all or part of its services? – Free, Freemium, Membership fee, Services fee, APC (article processing charge)\n\nTerms and Conditions: Are users in specific countries prohibited to use the tool? – Explicit prohibition, Flags possible problems, No terms of use given, None mentioned\n\nWhile the database produced provides an extensive list of OS tools, it is by no means exhaustive. By making the database an open resource we anticipate that it will be continually discussed and updated, both by ourselves and other practitioners in the field. In this way, the DOST dataset may become a reference resource for the Open Science community for digital tools development and optimization.\n\nMost of the tools included in the database have been developed in Anglophone countries with English interfaces. The authors recognize this linguistic bias and are committed to working with Open Science community members from various linguistic communities to make the future iterations of the database more representative of the global scholarly community and tools available.\n\nFinally, it was not possible to map all the existing institutional repositories due to their high numbers and transitional states and unclear or lacking institutional affiliations. The repositories represented in the database are hosted and maintained by NGOs or small companies. It is anticipated that institutional repositories can be added over time by community crowdsourcing.\n\n\nResults\n\nAn interactive visual map of the 242 DOSTs was generated in Kumu. The interactive plot can be viewed here: https://kumu.io/a2p/dost. The Kumu software allows users to sort the data according to any of the sorting criteria discussed above. Figure 2 below illustrates the distribution of DOSTs according to research workflow steps. As can be seen from this figure, DOSTs actively contribute to all stages of research, but are particularly concentrated around analysis of data and publication.\n\nA) Clustering overview of all tools sorted by workflow step (url: https://kumu.io/a2p/dost#dataset/workflow-step); B) Clustering overview by geographical location of the tool or the respective host institution (url: https://kumu.io/a2p/dost#dataset/workflow-step); C) Clustering overview by host institution for the tool (url: https://kumu.io/a2p/dost#dataset/host); D) Focus view on hist self-hosted tools – closeup from square in C).\n\nThe majority of DOSTs included in the database were explicitly connected to specific countries and regions. The geographic location of the DOST was available on the web pages through contact details, named host institutions or details of registration in the terms and conditions (T&Cs). Of these, 18 listed tools did not give a specific geographic location on their websites.\n\nAs can be seen from Figure 3 below, a high proportion of DOSTs available to the international research community are registered in (or linked to) the United States. It is therefore likely that the design and deployment of many of these tools was influenced by the needs and preferences of high income countries (HICs) researchers. Of the tools linked to a specific country, the vast majority were connected to the United States, either as a registered non-profit organization (NPO 501(c)3), a registered commercial company or hosted by a US American institution such as a university or government body. Others were also hosted by parent organizations, such as the Centre for Open Science, Wikimedia Foundation or GitHub. The numerical distribution of the countries hosting DOSTs is demonstrated in Figure 3.\n\nRegions displayed are the United States of America (US), the European Union (EU), the United Kingdom (UK) and other parts of the world with concentration on US territory. ‘Other’ includes Argentina (n=1), Australia (n=2), Brazil (n=1), Canada (n=7), Colombia (n=1), Mexico (n=1), South Africa (n=1), Switzerland (n=5), with a total of n=242.\n\nThe funding sources for the respective tools were classified as a) Commercial (n=56, 23.1%); b) Grant (n=19, 7.9%); c) mixed (commercial and grant, n=122, 50.4%), and d) Institutional (n=44, 18.2%). 0.4% of the tools (n=1) had no funding source specified. n=242.\n\nThere was considerable heterogeneity in the financial models of the DOSTs within the database. In an attempt to simplify this heterogeneity, the tools were classified into the categories Commercial, Grant, mixed (commercial and grant), and Institutional. The distribution of these funding models is visualized in Figure 4. Half of the DOSTs used a mixed model of funding, combining grants, commercial support, membership fees, freemium models, consulting or crowdsourcing.\n\nThe geographic location of the DOSTs (Figure 3) and the variations in funding (Figure 4) together highlight how the DOST ecosystem is governed by a complex network of financial legislation. NPOs and commercial entities are subject to the respective national legislation governing financial transactions. Similarly, if tools are hosted by an NPO, academic institution or governmental organization they are subject to the legislation governing the host organization.\n\nThe complexity of the underlying funding mechanisms has significant implications for the DOST ecosystem. In particular, it complicates efforts to make the DOST ecosystem transparent with regards to funding sources and legislative influence. It also impacts on the financial viability and longevity of the DOSTs within the ecosystem. Indeed, the reliance of many DOSTs on crowdsourcing and time-limited grants means that many will struggle to achieve financial independence and sustainability.\n\nWe have documented selected interlinkages between the DOSTs in the database (Bezuidenhout & Havemann, 2020). From the analysis of the database it became apparent that certain entities are highly interlinked within the DOST ecosystem, such as GitHub, Center for Open Science and Digital Science. Figure 5 below details 8 highly influential organizations within the DOST landscape, demonstrating how these organizations/institutions are linked to DOSTs operating throughout the research workflow.\n\nAs shown in Figure 5, 80.9% of the DOSTs in the database are linked to one or more of these 8 entities. These interlinkages were diverse and included direct sponsorship, hosting of the DOST, or the hosting of DOST resources. These interlinkages can also be visualized in the Kumu plot.\n\nExamination of the Terms and Conditions (T&Cs) of the DOSTs revealed a range of different factors that limited usage/accessibility or imposed liability on users. Strikingly, these T&C limitations were mainly found in DOSTs registered directly in the US, or sponsored by companies/organizations registered in the US, linked to US trade control laws, and thus restrict the services that can be made available to users in countries and territories under US sanctions. Two examples of companies that have explicitly clarified these limitations in their T&Cs are presented in Table 2. It is important to note that the lack of explicit prohibition within the T&Cs of other companies does not necessarily indicate that they are available for access by researchers in US sanctioned countries. More research on the extent of geoblocking is urgently required to clarify these issues.\n\nAs many other DOSTs rely on GitHub for infrastructure and hosting of resources, the T&Cs of one commercial company can have far-reaching consequences for the Open Science ecosystem. In contrast, there has been no systematic study to date examining whether access to the numerous preprint services hosted by the Center for Open Science are blocked in US-sanctioned countries. These T&Cs remain problematic as they place the responsibility on the user of the site to comply with the legislation alluded to. This raises challenges for users as they have to identify and read the relevant legislation – often in English – and access the T&Cs when they are hosted on GitHub.\n\nUS-sanctioned were explicitly mentioned in 79 of the DOSTs in the database. While many of these did not explicitly state that their services were blocked to users in countries under US sanctions, this could still be the case. Indeed, there is considerable anecdotal and documented evidence of research tools and databases being geoblocked to users in countries under sanction from the US. These could include countries such as Sudan (Bezuidenhout et al., 2019), Iran20, Myanmar, North Korea, Venezuela, Cuba, Crimea and Zimbabwe.\n\n\nDiscussion\n\nFor the open science movement to progress and the DOST ecosystem to flourish, the evolving digital ecosystem must ensure that “the primary outputs of publicly funded research results – publications and the research data – [are] publicly accessible in digital format with no or minimal restriction” (OECD, 2015, p. 7). It also requires “extending the principles of openness to the whole research cycle, fostering sharing and collaboration as early as possible thus entailing a systemic change to the way science and research is done”.\n\nAn effective DOST ecosystem thus has two key roles: 1) to facilitate practices that enhance open and transparent research as well as 2) to ensure that these practices – and the resultant resources - are available to researchers across the world. The analysis of the current DOST ecosystem presented above suggests that it may struggle to deliver on these roles. The unequal geographic distribution of the tools, the dominance of certain languages, cultures and entities, and the diversity of the funding models supporting the development of new tools all add complexities to the DOST ecosystem. Recognizing these power dynamics, value clashes, and infrastructural bottlenecks is essential for the future of the open science movement. In the section below, we discuss the results and their implications for open science in more detail.\n\nThe current structure of the DOST ecosystem means that the persistence of individual tools depends on attracting a community of users and securing stable funding. This might suggest that these features support a meritocracy, whereby the “best” DOSTs persist by common consent and investment. Such a position, however, overlooks key issues such as diversity within user communities and accessibility of funding. Overlooking such issues can undermine the open science values described above - particularly the aspiration that the open science ecosystem be globally accessible and useful.\n\nAs illustrated in Figure 2, many of the presented DOSTs are hosted in the United States. It is therefore likely that these tools have been piloted and beta-tested within the immediate research communities and therefore many of the design decisions integrated into the DOSTs dominantly reflect the US research environment and the preferences of the researchers in this region. Similarly, DOSTs created by commercial companies, or designed with commercialization in mind, will likely reflect the most immediate user community, namely North-American and European researchers.\n\nWhile these biases could be eliminated by subsequent user-community feedback, this is not always feasible. Limited funds for long-term responsive design, and slow roll-out beyond the US and other High-Income Countries (HICs) along with the unequal distribution of researchers around the world can mean user communities develop around DOSTs before they have had any meaningful engagement from researchers working outside of these “geographical epicentres”. For example, in 2013 the Europe Union (11.4% of the global population) hosted 31% of the world’s researchers21.\n\nThis can mean that voices from other research communities can easily be overlooked - including non-English speaking countries or low- and middle-income countries (LMICs) with small research communities. These different research communities have to date played a marginal role in the evolution of the DOST ecosystem due to the low level of involvement in elucidation and design of tools and infrastructure. If DOSTs are designed with a specific research community in mind and tested in the same community, it can mean that the design of the DOSTs “closes” before these marginal research communities are able to engage with them (Bijker et al., 2012). This “technological closure” means that the DOSTs available for use by marginal research communities will already have a fixed design and dedicated user community. Fundamental design decisions are unlikely to alter once the DOST has become operational in the original user community. Consequently, certain tools may be integrated into the DOST ecosystem that do not suit use in non-HIC research contexts. As a result, it is possible that certain communities get “locked-in” to the use of these DOSTs without having the opportunity to feed back into design decisions (Arthur, 1989; Leonelli, 2016).\n\nSituations of “locking” research communities into certain DOSTs and digital workflows can cause the ecosystem to unintentionally perpetuate marginalizations. The design and persistence of the DOSTs not only influence the “pathways” that the research follows through the ecosystem, but also the research methods, data collection and curation methods and analysis tools used. The selection of certain tools over others can thus have far-reaching implications. The decisions incorporated into its design reflect a specific geographic context and value system can influence research practices across the globe.\n\nSuch concerns relate to the “Juan Valdez problem” discussed by Busch and Juska, (Busch & Juska, 1997) in relation to agricultural systems and technologies. Juan Valdez, a South American coffee farmer, is born into a world in which his choices are limited. Many of these limitations relate to the environment he lives in, and which he accepts as default. On the other hand, certain choices may be deliberately denied to him. “The coffee company may have a local monopoly over purchasing the beans. The state may not have invested in adequate physical infrastructure for the area, thereby making transportation costs high” (Busch & Juska, 1997, p. 696). Thus, what is possible for Juan is dictated by human and non-human relationships alike. Similarly for open science tools, what is possible for marginal research communities may be determined less by their preferences than by decisions made between human partners in geographically remote locations.\n\nIt becomes apparent that more research is urgently needed. Qualitative research on the development of DOSTs would shed light on how potential design biases are addressed during the design of these tools. More information on the (lack of) diversity within user communities would highlight issues of “lock in”, while engagement with LIMC researchers about the use of existing DOSTs would provide further information on the usability of these tools in non-HIC research settings.\n\nFrom Figure 4 above it is evident that the DOST ecosystem is dominated not only by certain countries, but also by certain companies, organizations and institutions. Such clustering - in light of funding, access to target audiences, permissive legislation and business cultures - is not particularly surprising. Indeed, it may be said to follow other models of technical expansion throughout history. Accepting this expansion as entirely normal from the user perspective, however, does not make it unproblematic.\n\nThe DOST ecosystem and the DOSTs themselves are intended to be distributed and multiplicitous to allow the maximal flexibility of research practices. Allowing a small number of entities to dominate the ecosystem and its evolution thus presents challenges to these aims. In particular, two key concerns arise: first, the dominance of certain entities causes centralization and interdependence on individual actors. Second, the dominance of certain entities allows specific approaches to open science, and related values, practices and preferences to be prioritized. This can affect the heterogeneity of the open science movement and foster a perception that there is consensus on how open science “should be done” (Fecher & Friesike, 2014).\n\nIn recognizing the former, the DOST ecosystem must confront a paradox. While interconnectedness is vital for fostering open, global research and removing national, disciplinary, and linguistic siloes, the same tools that facilitate this connectedness can lead to a centralism that drives out regional and local expertise and diversity. In particular, having tools such as GitHub dominate various stages of the research lifecycle in a number of tools not only enhances interoperability, but also centralization and dependence, thereby diminishing accessibility to some.\n\nThe latter concern relates to an often-overlooked aspect of technology: The intentions, experiences, priorities and cultures of the IT-professionals influence the design and deployment of the technology (Winner, 1986). All DOSTs are created against a backdrop of social values, and designed with specific interpretations of open science in mind. This can lead to considerable heterogeneity in what is foregrounded, prioritized and included in the design of the DOSTs. As a result, DOSTs, like other technologies, are at once both the sites and objects of politics (Jasanoff & Kim, 2009, p. 126), and foreground certain views of openness through their positioning in the DOST ecosystem.\n\nGitHub, for example, is a commercial company based in the US. The design of GitHub, and its operating practices thus align to a specific set of values. As a result of its dominance within the DOST ecosystem, its position on key issues such as inclusion, sharing and transparency are increasingly becoming the “norm” for many users despite its political constraints and accessibility restrictions for many researchers. Recognizing such issues highlights the need for closer scrutiny of the value structures of the tools within the DOST ecosystem. Asking questions such as why tools were created, how users were recruited and why they favour one tool over another will shed light on these issues. In particular, it will highlight the limitations of allowing certain countries, tools and organizations to dominate the DOST ecosystem.\n\nThe decisions influencing the design of DOSTs do not only reflect user community preferences and perspectives of open science, but also assumptions about the availability of infrastructures and resources. These include a wide range of different issues, including access to funding and the ability to make online payments, linguistic competence, access to software and hardware, as well as infrastructure availability relating to internet connectivity and bandwidth.\n\nFor many DOSTs developed in Europe or the US there is an emphasis on the tools being cloud-based. On the one hand, such an emphasis makes sense in many ways such as the ease of having nothing to install, being able to deliver the latest version of software via the browser and having access to the content from any device anywhere in the world, as long as it is connected to the internet. On the other hand, some institutions especially in the European Union prefer the tools to operate on their own servers to keep them confidential from potential competitors for patenting and to ensure data and content ownership through territorial storage. For research communities in LMICs these same design decisions form a usage barrier because of low bandwidth and intermittent internet connection that make an over-reliance on “online only” tools problematic (Bezuidenhout et al., 2016).\n\nWhile multiplicity in the DOST landscape can allow marginal researchers to plot alternative pathways through the OS ecosystem, this can mean that they must resort to using less popular tools. As a result, there is a chance that these researchers continue to be excluded from the user communities that are driving research forward. This has obvious implications for collaborations, visibility/engagement with researcher communities and perceptions of worth.\n\nDesigning DOSTs for infrastructure present in the dominant geographical regions (such as the US) legitimizes a specific expectation of service access and provision. In this way, the DOST ecosystem fails to address the recognized imbalance between central and marginalized countries and research communities. Indeed, the cost for internet access and [institutional as well as private] connectivity varies drastically across world regions and tends to be extraordinarily high in LMICs22. By perpetuating aset of embedded assumptions like web interfaces or connectivity, open science continues to perpetuate a limited perspective for \"inclusion\" that often falls short of being inclusive. Ensuring more inclusive design structures and processes will require ethnically and regionally diverse teams of DOST designers to ensure that infrastructural challenges are considered and responses incorporated into design decisions.\n\nAs demonstrated in the results section, the DOST ecosystem has to contend with a range of power dynamics external to research infrastructure. Perhaps the most pernicious of these is the role that financial legislation plays in dictating access to open resources (Bezuidenhout et al., 2019). This is perhaps best demonstrated by the impact that US financial sanctions have on access to DOSTs. As demonstrated by Table 2 a number of DOSTs explicitly prohibit use from individuals located in countries currently under financial sanctions from the US.\n\nThe reasons for these prohibitions are complex and often relate to the financial requirements of the funding bodies. DOSTS developed by commercial companies registered in the US, or those funded by commercial companies registered in the US, are subject to US tax law that explicitly prohibits transacting with countries under sanction. As a result, the values and political positions of the US government are integrated into the open science landscape via a range of different tools. From the data available, it was not possible to determine whether US organizations registered as NPO 501(c)3 or receiving fiscal sponsorship would be similarly subject to restrictions. Nonetheless, the limitations elucidated in the T&Cs represented in Table 2 suggest that this issue requires considerable further examination.\n\nIn addition to the explicit restrictions noted on T&Cs, users in countries under sanction from the US may be restricted access via three additional pathways. Many of the DOSTs in the database required some form of account or login (see Figure 4). This implied that the location of the users is being monitored via the tool and could provide a means to deny certain users access to the services. Additionally, the DOSTs requiring some kind of payment for services - either freemium or membership fees - could restrict access from countries under sanction, as online financial transactions are largely prohibited from these countries. Third, governance of certain elements of the Open Science landscape by high-level but poorly elucidated legislation - such as cryptography software by the Wassenaer agreement23 - can mean that providers restrict access as a means of precaution. Expanding analytical services such as AlternativeTo and Terms of Service Didn’t Read24 to DOSTs will help researchers make informed decisions as they navigate through the open science ecosystem.\n\nThis creates situations of marginalization and lack of access for certain communities of end-users. Even more concerning, however, is that one country’s political preferences are able to dictate the evolution of aspects of the DOST ecosystem. While it is important to note that the introduction of these political values is likely done unintentionally or via funding-related necessity, the impact is nonetheless severe. Acknowledging that certain aspects of the DOST ecosystem are unavailable to certain communities of users is vital for further critical reflection on the evolution of open science. In particular, what does this mean for the core values of the open science movement and the notion of a “digital commons” (Bezuidenhout, 2020; Hess & Ostrom, 2007)?\n\nThe results and discussion presented in this paper draw attention to problems within the current DOST ecosystem. Without detracting from the importance of the emergence of more and more discipline- and region-specific DOSTs, and the work of dedicated individuals who create them, words of caution are appropriate. The results of this paper demonstrate the heterogeneity of the actors, power dynamics and stakeholders that are currently driving and dominating the evolution of the DOST ecosystem. Even if all DOSTs were created by well-meaning individuals who wish to promote open science, one cannot simply assume that the resultant ecosystem will automatically reflect and perpetuate the core values of open science. Instead, a range of different factors inherent within DOST design create a landscape that continues to perpetuate marginalization and exclusion.\n\nThis marginalization is multifaceted. Not only are marginal research communities excluded from design decisions of DOSTs, they are likely also sidelined in the user communities that develop around them. Moreover, DOST (un)availability/accessibility does more than exclude researchers from sharing communities, it also dictates research practices and digital workflows. In this way, the design of the DOST ecosystem can affect both present and future research. While the DOST ecosystem is dynamic and multiplicitous, the dominance of a few entities is rapidly driving forward a “status quo” of how research should be done. Once such practices reach a “carrying capacity” within the global research community, they are unlikely to be easily adapted. This can mean that the current design of the DOST ecosystem marginalizes future, as well as present, researchers.\n\nThe results and discussion in this paper point towards the need for a new model to critically evaluate the evolving DOST ecosystem. In particular, it highlights the need for more active inclusion of diverse user communities in all stages of DOST development and deployment25. This will make the embedded politics of the DOSTs ecosystem more transparent. Conversely, there is an imperative to identify examples of DOSTs developed in, for and by researchers in Africa, Asia and Latin America which can serve as examples of alternative design practices. This will provide a better understanding of how diversity can be better supported in the DOST ecosystem. This will allow critical reflection on the politics that are not visible in centrally-located tools that are being made explicit in the non-central ones.\n\nMany of the issues mentioned and concerns raised in this paper will not come as a surprise to open science practitioners. Nor will it be surprising to add that the current model of persistent barriers continues to place certain members of the open science community in uncomfortable and sometimes unethical positions. These include having the choice of open science tool dictated to them through lack of engagement in community consensus or due to feasibility in a local context with digital infrastructure deficiencies. It also includes having to operate in an ecosystem that regularly requires the decision making between non-participation or breaking law by consulting scholarly pirate software.\n\nAllowing such situations to persist undermines the aims of the open science movement. Recognizing this places a responsibility on the global open science community members to make discerning decisions about the tools that they use. This requires that the T&Cs of DOSTs, their funding structures and their infrastructural constituencies are all closely scrutinized before new tools become embedded in the DOST ecosystem. Similarly, funders, research institutions and other stakeholders need to critically assess the impact of introducing DOSTs to the ecosystem, and advocating their use amongst their researchers (ie. through the San Francisco Declaration on Research Assessment).\n\nThe section above highlighted how inequalities, marginalization and injustices were perpetrated by the current structure of the DOST ecosystem. The design of DOSTs, the ways in which they are interlinked, and the dependencies/dominances of certain entities raises the question of whether the DOST ecosystem can realise the aspiration of becoming a truly “unlimited digital commons” in its current structure. From the data presented above, it would seem that things need to change.\n\nNonetheless, the DOST ecosystem is a complicated landscape, and imposing a specific value set or “way of doing things” will harm the richness and diversity of this rapidly evolving field. Rather than imposing restrictions on what should constitute a DOST, we suggest that those designers and users be supported to critically reflect on the values that they are introducing into the ecosystem. There are many models currently in use on how to balance well-intentioned innovation with pragmatic requirements, and these need to be more strongly developed for DOSTs.\n\nOne such model, responsible research and innovation (RRI), has made considerable contributions to discourse around socially responsible innovation. Opening up access to data and support of open science are fundamental components of the RRI model (Stilgoe et al., 2013). To date, little has been done to turn the RRI lens back on the open science movement that it evolved from to ask what an RRI model for Open Science tools could look like. Such a model needs to address questions such as how to foster a free and open “ecosystem” when the OS tools are generated by a diversity of actors - NPO, NGO, governmental, commercial, volunteer) that can hold highly divergent values while supporting open science. Similarly, how a free and open landscape can be created when financial and governmental regulations and requirements influence tool design needs to be looked at as well; a promising assessment is currently underway by the Invest in Open Infrastructure initiative.\n\nIt is important to note that community-determined standards for what constitutes “Open Science” already exist in a number of different areas. Within open access publishing, for example, both ROMEO Sherpa and the Directory of https://doaj.org/ (DOAJ) clearly define what is required of a publication to be open access. Similarly, re3data has developed a list of criteria that any open repository needs to demonstrate. Such community standards have been highly influential and are being widely adopted by research communities and provide for cross-regional and cross-disciplinary agreement and functionality. While conversations about open science tool standards have existed for more than a decade, the broader community needs to be engaged for such standards to become a reality.\n\nThe design of the DOST ecosystem not only determines how research is conducted today, but also determines the directions and practices of future research. Allowing certain actors, pathways or regions to become too entrenched will allow inequality and marginalizations to persist and become a future norm. Research practices are changing rapidly (ie. AI, big data), international politics are in flux (ie. Brexit, COVID-19 pandemic) and historically marginalized research communities (ie. citizen scientists and LMIC researchers) are increasingly vocal and influential (Aspesi & Brand, 2020). It is now the right time to critically assess what has already been built, and what the united global research community wants to take forward into the future.\n\n\nConcluding comments\n\nMuch of the OS ecosystem has been developed by volunteers, who donate time and expertise to developing DOSTs, infrastructures and interoperable practices. This community has the history, expertise and perspectives to take up the challenges raised in this paper. How, they need to ask, can they guide and adapt the ecosystem that is rapidly changing research? This requires a reframing of open science responsibilities, from contributing labour and data to discussing the complex power dynamics underpinning the evolving ecosystem. Only then will the UNESCO theme 2019 of “Open Science: leaving no one behind” become a reality.\n\nThe OS landscape is ever increasing globally, also in historically underrepresented regions such as Latin America, Africa and Asia. We therefore suggest to tie the digital development and regional adaptation of DOSTs on the Open Science Manifesto, Towards an Inclusive Open Science for Social and Environmental Well-being26. In particular for the more dominant digital tools for open research and communities in Europe and North America, there is a dire need for more active consultation and inclusion of research stakeholders from various parts of the world in order to successfully design a truly global open science community, culture and infrastructure (Albornoz et al., 2018)27. Moreover, key expertise from development networks, such as ICT4Dev and Tech4Dev (Hostettler et al., 2018) can play an important part in developing a more equitable open science ecosystem.\n\nFor the moment, however, building a body of evidence detailing DOSTs, their uses and the communities they use them is vital. Only through gathering this evidence can strategic and informed decisions about future ecosystem investments be made inclusively.\n\n\nData availability\n\nZenodo: The Varying Openness of Digital Open Science Tools. http://doi.org/10.5281/zenodo.4013812 (Bezuidenhout & Havemann, 2020)\n\nThis project contains the following underlying data:\n\n- DOST dataset 3 September 2020.xlsx (Full table of DOST information organized according to the categories described in the methods, together with hyperlinks to homepages)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "Footnotes\n\n1 Africa: http://africanopenscience.org.za/; https://info.africarxiv.org/; https://savoirs.cames.online/jspui/, http://africaosh.com/\n\n2 Ibero America: http://amelica.org/index.php/en/home/; https://www.redalyc.org/; https://scielo.org/ ; http://mutabit.com/grafoscopio/index.en.html\n\n3 Europe / EU: https://ec.europa.eu/research/openscience/index.cfm; Germany: https://www.osc.uni-muenchen.de/toolbox/index.html\n\n4 North America / USA: https://www.cos.io/; https://our-research.org/; Canada: https://pkp.sfu.ca/ops/\n\n5 Asia / Indonesia: https://rinarxiv.lipi.go.id/lipi; India: https://indiarxiv.in/; Japan: https://openscience.jp/\n\n6 Oceanio / Australia: https://www.freeourknowledge.org/\n\n7 Cross-regional: https://opensciencetools.org/; http://openhardware.science/;\n\n8 For example, https://opensciencemooc.eu/, https://www.fosteropenscience.eu/, https://www.oercommons.org/hubs/OSKB\n\n9 For example, https://osf.io/preprints/; https://www.preprints.org/ - and for an overview of biological-focused pre-print archives see https://asapbio.org/preprint-servers\n\n10 For example, https://prereview.org/, https://peercommunityin.org/\n\n11 For example, www.fosteropenscience.eu https://asapbio.org/preprint-servers\n\n12 https://www.eurekalert.org/pub_releases/2020-08/hl-crr081220.php and http://www.oecd.org/coronavirus/policy-responses/why-open-science-is-critical-to-combatting-covid-19-cd6ab2f9/, https://asapbio.org/preprints-and-covid-19\n\n13 https://101innovations.wordpress.com/workflows/ (accessed 10 August 2020)\n\n14 https://en.unesco.org/science-sustainable-future/open-science\n\n15 A software mirror is a server that provides an exact copy of data from another server. These mirrors can be held in different geographic locations and are intended to provide fault tolerance, or a means of redundancy in case something goes wrong with the primary or \"principal\" server.\n\n16 https://101innovations.wordpress.com/ and https://jrost.org/ (accessed 17 June 2020)\n\n17 Workflow steps as defined by Bianca Kramer and Jeroen Bosman from the University of Utrecht. http://innoscholcomm.silk.co/page/Workflows. Accessed 20 March 2020.\n\n18 https://help.github.com/en/github/site-policy/github-and-trade-controls (accessed 16/03/2020)\n\n19 https://github.com/CenterForOpenScience/cos.io/pull/1025/files (accessed 16 March 2020)\n\n20 https://github.com/pi0/github-is-blocked-in-iran (accessed 16 March 2020)\n\n21 The Big Five (China, European Union, Japan, Russian Federation and USA) still account for 72% of researchers worldwide but the share of China has progressed considerably since 2009, to the detriment of Japan, the Russian Federation and the USA. The share of the European Union (7.1% of the global population) has remained stable, at 22.2% in 2013, compared to 22.5% in 2009. Europe as a whole (11.4% of the global population) hosts 31% of the world’s researchers. https://en.unesco.org/node/252277 (accessed 17 March 2020)\n\n22 https://www.visualcapitalist.com/cost-of-mobile-data-worldwide/\n\n23 https://www.wassenaar.org/ (accessed 17 June 2020)\n\n24 https://alternativeto.net/, https://tosdr.org/\n\n25 Key resources such as the Open Science Grassroots Community Networks listing by CoS will provide valuable further evidence for inclusion https://twitter.com/Gen_R_/status/1146069028546523136?s=20\n\n26 https://ocsdnet.org/manifesto/open-science-manifesto/\n\n27 https://en.unesco.org/science-sustainable-future/open-science\n\n\nReferences\n\nAlbornoz D, Huan M, Marti I, et al.: Framing Power: Tracing Key Discourses in Open Science Policies. Open Science Policies. ELPUB. 2018. Publisher Full Text\n\nArthur WB: Competing technologies, increasing returns, and lock-in by historical events. The Economic Journal. 1989; 99(394): 116–131. Publisher Full Text\n\nAspesi C, Brand A: In pursuit of open science, open access is not enough. Science. 2020; 368(6491): 574–577. PubMed Abstract | Publisher Full Text\n\nBartling S, Friesike S: Opening Science. Heidelberg. 2014. Publisher Full Text\n\nBezuidenhout L, Rappert B, Leonelli S, et al.: Beyond the Digital Divide: Sharing Research Data across Developing and Developed Countries. 2016. Publisher Full Text\n\nBezuidenhout L, Karrar O, Lezaun J, et al.: Economic sanctions and academia: Overlooked impact and long-term consequences. PLoS One. Public Library of Science (PLoS). 2019; 14(10): e0222669. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBezuidenhout L: Being Fair about the Design of FAIR Data Standards. 2020. 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SocArXiv Papers. 2020. (Accessed: 17 June 2020). Reference Source\n\nVermeir K, Leonelli S, Tariq ASB, et al.: Global Access to Research Software: The Forgotten Pillar of Open Science Implementation. 2018. (Accessed: 28 September 2018). Reference Source\n\nWilkinson MD, Dumontier M, Aalbersberg IJJ, et al.: The FAIR Guiding Principles for scientific data management and stewardship. Sci Data. Nature Publishing Group. 2016; 3: 160018. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWinner L: Do Artifacts Have Politics? Daedalus. 1986; 109(1): 121–136. Reference Source\n\nZastrow M: Open science takes on the coronavirus pandemic. Nature. Springer Science and Business Media LLC. 2020; 581(7806): 109–110. PubMed Abstract | Publisher Full Text"
}
|
[
{
"id": "74157",
"date": "27 Nov 2020",
"name": "Björn Brembs",
"expertise": [
"Reviewer Expertise Biology",
"Neuroscience",
"infrastructure modernization",
"open science",
"open access",
"open data",
"FOSS."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 amazing piece of work, one of its kind (hopefully the first of its kind) in breadth and scope. It is highly timely and dearly needed. I also fully support the social agenda the authors are promoting in this work and my suggestions below are aimed towards strengthening their important arguments. To achieve change, arguments for change need to be convincing. The goals and direction of the authors' arguments are clear and I support them. However, the way they are articulated here, weakens their power and makes them too easy to dismiss. Below my suggestions of making the arguments more powerful.\nOne of the main conclusions from the work here is that DOSTs are heavily biased towards scholars in rich countries. While this is an expected outcome, a more critical reader could counter that this may be purely a result of the bias of the authors: selection bias confirming the perspective the authors had when they started to work. To counter this argument, the authors need to explain in great detail, how the database they analyzed was derived. For instance, the Kramer and Bosman database consists of currently 696 DOSTs, but the one presented here only contains 242 DOSTs. The authors need to explicitly state, in sufficient detail, how the 242 were selected from the 696 in order to ensure that \"selection bias\" cannot be used against them. For instance, a critical reader may claim that the remaining, un-analyzed 454 DOSTs may all have been from LMICs and have been left our in order to score political points. More perniciously, a more critical reader may claim that LMIC are not represented with many DOSTs because they either lack the ability to design DOSTs or that the designed DOSTs from LMICs are so bad, nobody would ever want to use them, so they never make it into any database. Such alternative (and analogous) explanations for the findings must be invalidated (e.g. in the methods section), or the authors' valid arguments will be ignored. It must be absolutely clear and reproducible how the 243 DOSTs were selected from the 696 (and the limitations even of the 696 be made explicit). Ideally, there should be a graph showing which fraction of the 454 DOSTs were rejected for which reason, if the selection was not done at random. Reference to 101innovations and JROST is not nearly sufficient. At the very least, inasmuch as they cannot be addressed methodologically, these alternative explanations (see also below) must be mentioned and discussed. Some more examples:\nStatements like: \"The results of this paper demonstrate the heterogeneity of the actors, power dynamics and stakeholders that are currently driving and dominating the evolution of the DOST ecosystem.\", are not valid in this form as long as it is not clear that these results cannot be explained by selection bias. Without ruling out selection bias, it would be admissible to write “indicate” or “suggest”, but not “demonstrate”.\nAlso drawing from the skewed distribution of countries and organizations in their sample (about 35% of the total 696 DOSTs in the Kramer & Bosman database), the authors make the very valid case of “lock-in”, “centralization” and “dominance” that should be avoided or at least mitigated. One of several good arguments the authors are using to make their case is that the decision about “how open science is done” should not be put in the hand of the dominant players. However, the authors argue as if politics, power, history and other such unrelated factors were the only explanation for the observed dominance in their sample. They fail to consider and provide arguments against alternative explanations for the dominance, such as selection bias in their sample; superior quality of the DOSTs; larger proportion of researchers/developers being able to produce more DOSTs; more opportunities for alternative careers in DOST production for ex-scholars in developed countries; etc. If the reader is supposed to understand why the dominance ought to be mitigated or balanced, the reader needs to understand why the dominance is a bug and not an inevitable outcome of the status quo beyond science or even a feature. Otherwise, readers will just stop reading.\nThe authors also only briefly mention in their penultimate paragraph of their discussion (instead of prominently featuring) one of the most powerful mitigation strategies both against a dominant “way to do open science” and lock-in: open, community-derived standards. It may be counter-productive to admonish readers to behave better and then only mention in passing what such better behavior would actually be, towards the end when most readers have already 'tl;dr-ed'. To keep people reading, in my humble opinion, this aspect should even be mentioned in the abstract as a potential recommendation or outcome prompted by the data.\nIt would also strengthen the authors’ arguments if they emphasized the area between arbitrarily setting a standard of \"how open science should be done\" and the demarcation towards pseudo-science and non-science. Ultimately, there is a distinction between science and other forms of knowledge (or pseudo-science) and there is a distinction between open science and other forms of science. There is a difference between aiming for broad participation and “anything goes”. This distinction is missing from this discussion and this omission, again, makes it too easy to attack the authors’ valid and important argument simply by making an “anything goes” strawman out of it, to be dismissed and ignored. Especially in an age of fake news and alternative facts, this distinction cannot be left out of this discussion.\nAlong the same lines, the authors write: \"Nonetheless, the DOST ecosystem is a complicated landscape, and imposing a specific value set or “way of doing things” will harm the richness and diversity of this rapidly evolving field.\" In science, diversity cannot be a value in itself, it must be a means to an end; to improve science. After all, not all results are equally valid, we often design experiments with the explicit goal to find out which result is the valid one. The diversity of valid results is important, not diversity in and of itself (An aside: analogous arguments can be made for openness. Openness in science is also a means to an end, and not a value in and of itself). The kind of diversity that does not improve science, science can do without. This is why there is education and training - to reduce the diversity that does not improve science and increase the diversity that moves science forward. The authors need to make clear what should happen to ensure the right kind of diversity and prevent the wrong kind of diversity, instead of emphasizing diversity as if it would be an unmitigated good under all circumstances.\nA similarly easy to dismiss argument is when the authors point out that internet connectivity is still a problem in many countries. At least for this reader, this passage read as if DOST designers ought to keep this in mind when designing their DOSTs. However, the internet is what allowed open science to be invented. No internet, no open science. I would consider such critique misdirected.\nI hope I have provided a few examples of how some of the authors’ arguments may be all too easily dismissed by a more critical reader than me. I also hope these examples were sufficient to allow the authors to go over all of their arguments in the discussion and think of ways to dismiss them, such that the authors are empowered to revise their discussion section to make it more forceful, convincing and less easy to dismiss. I see no issues with the introduction and results section.\nMinor comments: The authors briefly mention “institutional repositories” as missing from their database. This statement is somewhat too narrow. In my field, biology, alone, there are about 1500 databases for raw data that serve not only to archive and make the data accessible (often sequences of biological molecules, but also structures, measurements etc.), but also to provide the respective communities with means to navigate and evaluate the gigantic amounts of data being collected in such ‘big science’ fields. Physics and climatology spring to mind as other fields with likely similarly large and diverse databases. All of these ought to be classified as DOSTs and together with institutional repositories may even number in the low tens of thousands in total. In the light of such numbers, it becomes even more important to emphasize the way the 242 DOSTs were selected.\n\"IT-professionals influence the design and deployment of the technology\" sounds a bit like it were better if amateurs would have that influence, or at least that they ought to have the same influence. Experts and professionals may be biased, but they are nonetheless the best we have to offer. Using amateurs only because of their different biases will not improve piloting a plane, nor medical surgery, nor science.\n\"The section above highlighted how inequalities, marginalization and injustices were perpetrated by the current structure of the DOST ecosystem.\" - 'perpetrated' or 'perpetuated'?\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?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": [
{
"c_id": "6424",
"date": "17 May 2021",
"name": "Louise Bezuidenhout",
"role": "Author Response",
"response": "This is an amazing piece of work, one of its kind (hopefully the first of its kind) in breadth and scope. It is highly timely and dearly needed. I also fully support the social agenda the authors are promoting in this work and my suggestions below are aimed towards strengthening their important arguments. To achieve change, arguments for change need to be convincing. The goals and direction of the authors' arguments are clear and I support them. However, the way they are articulated here, weakens their power and makes them too easy to dismiss. Below my suggestions of making the arguments more powerful. One of the main conclusions from the work here is that DOSTs are heavily biased towards scholars in rich countries. While this is an expected outcome, a more critical reader could counter that this may be purely a result of the bias of the authors: selection bias confirming the perspective the authors had when they started to work. To counter this argument, the authors need to explain in great detail, how the database they analyzed was derived. For instance, the Kramer and Bosman database consists of currently 696 DOSTs, but the one presented here only contains 242 DOSTs. The authors need to explicitly state, in sufficient detail, how the 242 were selected from the 696 in order to ensure that \"selection bias\" cannot be used against them. In the text it is noted that the list of DOSTs we were working from was by no means exhaustive. Rather, by basing our list primarily on the JROST and 101innovation lists we were starting our analysis with a selection of - to our knowledge - the most prominent and widely-used DOSTs in current circulation. It is true that the 101innovations list has since it’s publication 2016 has expanded widely, and offers many more DOSTs to potentially include in our future analyses. In order to address the concerns raised by reviewer 1, the following additions have been made: Footnote 16 has been expanded to include the above paragraph. This footnote highlights the expansion of the 101innovations list that identifies a range of additional DOSTs that require analysis. It also emphasises the intention of this project, and our dataset, as a dynamic and ongoing venture that will require continual and collective updating and revision. A more comprehensive description of inclusion and exclusion criteria has been added to the methods section. This includes the text on page 12 that states: The inclusion criteria inevitably was subject to selection criteria, as DOSTs with smaller user groups might not have been included. Similarly, DOSTs designed to operate in languages outside of English, French, Spanish and Portuguese were less likely to be included. While these selection biases are important to note, it is important to recognize that the current method of DOST selection ensured the final list represented tools that were in common use by international researcher communities (as verified by 101Innovations and JROST) and covered a broad range of disciplines. For instance, a critical reader may claim that the remaining, un-analyzed 454 DOSTs may all have been from LMICs and have been left our in order to score political points. More perniciously, a more critical reader may claim that LMIC are not represented with many DOSTs because they either lack the ability to design DOSTs or that the designed DOSTs from LMICs are so bad, nobody would ever want to use them, so they never make it into any database. Such alternative (and analogous) explanations for the findings must be invalidated (e.g. in the methods section), or the authors' valid arguments will be ignored. While the reviewer’s concerns are both extremely pertinent and appreciated, in our view they do not necessarily detract from the strength of our argument or analysis. In our methods we recognise limitations relating to our sampling, namely that we were focused predominantly on prominent DOSTs within the research ecosystem. Because DOST development often requires considerable time and financial investment, it is not particularly surprising that many of these DOSTs have originated in countries with well-developed and well-funded research ecosystems. This, however, in no way casts any negative light on DOSTs developed in LMICs. Indeed, the evolution of this dataset - and the work of 101innovations and JROST - might represent a very different geographical distribution of DOSTs in the coming years. This observation has been included in the text on page 12: The final list of DOSTs did not contain a high proportion developed in low/middle-income countries. This was not due to any selective bias during the list construction, but rather is likely a reflection of the current DOST ecosystem. Because DOST development often requires considerable time and financial investment, it is not particularly surprising that many of these DOSTs have originated in countries with well-developed and well-funded research ecosystems. This, however, in no way casts any negative light on DOSTs developed in LMICs. Indeed, the evolution of this dataset - and the work of 101innovations and JROST - might represent a very different geographical distribution of DOSTs in the coming years. It must be absolutely clear and reproducible how the 243 DOSTs were selected from the 696 (and the limitations even of the 696 be made explicit). Ideally, there should be a graph showing which fraction of the 454 DOSTs were rejected for which reason, if the selection was not done at random. Reference to 101innovations and JROST is not nearly sufficient. At the very least, inasmuch as they cannot be addressed methodologically, these alternative explanations (see also below) must be mentioned and discussed. As discussed above, the inclusion and exclusion criteria in the methods section has been expanded to justify the DOSTs included in our analysis. The DOST ecosystem is rapidly evolving, so any accuracy here and years after both initiatives have been actively curated would be redundant/misleading/irrelevant in our view. We have included the following text on page 11: As the DOST ecosystem is rapidly expanding, the use of these two independently verified lists provided an important starting basis for our analysis. Statements like: \"The results of this paper demonstrate the heterogeneity of the actors, power dynamics and stakeholders that are currently driving and dominating the evolution of the DOST ecosystem.\", are not valid in this form as long as it is not clear that these results cannot be explained by selection bias. Without ruling out selection bias, it would be admissible to write “indicate” or “suggest”, but not “demonstrate”. The text has been amended by replacing “demonstrate” with “indicate” Also drawing from the skewed distribution of countries and organizations in their sample (about 35% of the total 696 DOSTs in the Kramer & Bosman database), the authors make the very valid case of “lock-in”, “centralization” and “dominance” that should be avoided or at least mitigated. One of several good arguments the authors are using to make their case is that the decision about “how open science is done” should not be put in the hand of the dominant players. However, the authors argue as if politics, power, history and other such unrelated factors were the only explanation for the observed dominance in their sample. They fail to consider and provide arguments against alternative explanations for the dominance, such as selection bias in their sample; superior quality of the DOSTs; larger proportion of researchers/developers being able to produce more DOSTs; more opportunities for alternative careers in DOST production for ex-scholars in developed countries; etc. If the reader is supposed to understand why the dominance ought to be mitigated or balanced, the reader needs to understand why the dominance is a bug and not an inevitable outcome of the status quo beyond science or even a feature. Otherwise, readers will just stop reading. While the reviewer makes a valuable counter-argument, we believe that our analysis stands. We do not speculate as to the cause of this unequal distribution of DOSTs - and indeed some of the suggestions offered by the reviewer are highly likely. Rather, we suggest that regardless of the multiple causes underpinning this distribution, that unequal distribution nonetheless occurs. This is both highly influential on the future of the DOST ecosystem, but unlikely to be rectified by any one cause. More text has been added to the paper on page 28 to clarify this issue: It is important to recognise that the power dynamics shaping the DOST ecosystem are likely influenced by multifarious pressures. These include community decisions regarding the quality of the DOSTs, the unequal distribution of DOST users and researchers/developers around the globe, economic issues including the opportunities for alternative careers in DOST development in developed countries. The limits of this study make it impossible to engage with the influence of these different pressures in detail. Rather, the study seeks to highlight not only the complexities of the DOST ecosystem, but also the critical need for more scholarship on its evolution. This paper highlights how these pressures cause the dominance of certain DOSTs to be a “bug” in the current structuring of the ecosystem, rather than as an inevitable outcome of the status quo of scientific research. The authors also only briefly mention in their penultimate paragraph of their discussion (instead of prominently featuring) one of the most powerful mitigation strategies both against a dominant “way to do open science” and lock-in: open, community-derived standards. It may be counter-productive to admonish readers to behave better and then only mention in passing what such better behavior would actually be, towards the end when most readers have already 'tl;dr-ed'. To keep people reading, in my humble opinion, this aspect should even be mentioned in the abstract as a potential recommendation or outcome prompted by the data. We thank the reviewer for this suggestion, and have incorporated it into the abstract. It would also strengthen the authors’ arguments if they emphasized the area between arbitrarily setting a standard of \"how open science should be done\" and the demarcation towards pseudo-science and non-science. Ultimately, there is a distinction between science and other forms of knowledge (or pseudo-science) and there is a distinction between open science and other forms of science. There is a difference between aiming for broad participation and “anything goes”. This distinction is missing from this discussion and this omission, again, makes it too easy to attack the authors’ valid and important argument simply by making an “anything goes” strawman out of it, to be dismissed and ignored. Especially in an age of fake news and alternative facts, this distinction cannot be left out of this discussion. Footnote 15 has been added: While there are many interpretations of how openness can be enacted in research, there is a growing community of researchers who recognize open science practices such as open publishing, data sharing and reproducible research. There is also a growing consensus on the values underpinning the open research movement and its commitment to equity and access. Our argument attempts to problematize the extent of this value and practice consensus within research communities, rather than to engage in the boundaries between science and pseudo-science. To address these boundaries we regard as beyond the scope of this paper. Along the same lines, the authors write: \"Nonetheless, the DOST ecosystem is a complicated landscape, and imposing a specific value set or “way of doing things” will harm the richness and diversity of this rapidly evolving field.\" In science, diversity cannot be a value in itself, it must be a means to an end; to improve science. After all, not all results are equally valid, we often design experiments with the explicit goal to find out which result is the valid one. The diversity of valid results is important, not diversity in and of itself (An aside: analogous arguments can be made for openness. Openness in science is also a means to an end, and not a value in and of itself). The kind of diversity that does not improve science, science can do without. This is why there is education and training - to reduce the diversity that does not improve science and increase the diversity that moves science forward. The authors need to make clear what should happen to ensure the right kind of diversity and prevent the wrong kind of diversity, instead of emphasizing diversity as if it would be an unmitigated good under all circumstances. This point is well-taken, and we have qualified our support for diversity with clarification that we support diversity of data, methods and perspectives. The following text has been added to page 30: While methodological diversity is not inherently a value of research, it remains a core element of scientific research. Finding a balance between centralized efficiency and freedom to innovate is a central element of flourishing research systems. Similarly, finding that balance within the DOST ecosystem will be extremely influential in its future successes. Rather than imposing restrictions on what should constitute a DOST, we suggest that those designers and users be supported to critically reflect on the values that they are introducing into the ecosystem. There are many models currently in use on how to balance well-intentioned innovation with pragmatic requirements, and these need to be more strongly developed for DOSTs. A similarly easy to dismiss argument is when the authors point out that internet connectivity is still a problem in many countries. At least for this reader, this passage read as if DOST designers ought to keep this in mind when designing their DOSTs. However, the internet is what allowed open science to be invented. No internet, no open science. I would consider such critique misdirected. We have added footnote 20: While some scholars argue that access to the internet allowed open science to be invented, we take a more nuanced view. Both openness and internet access are not “binary” positions in which users are either open/closed or online/offline. Having poor internet connections can allow some participation in open science, but severely restrict the amount of activity - or the types of DOSTs - available to the individual working in these settings. Openness, like internet access, is a continuum. I hope I have provided a few examples of how some of the authors’ arguments may be all too easily dismissed by a more critical reader than me. I also hope these examples were sufficient to allow the authors to go over all of their arguments in the discussion and think of ways to dismiss them, such that the authors are empowered to revise their discussion section to make it more forceful, convincing and less easy to dismiss. I see no issues with the introduction and results section. Minor comments: The authors briefly mention “institutional repositories” as missing from their database. This statement is somewhat too narrow. In my field, biology, alone, there are about 1500 databases for raw data that serve not only to archive and make the data accessible (often sequences of biological molecules, but also structures, measurements etc.), but also to provide the respective communities with means to navigate and evaluate the gigantic amounts of data being collected in such ‘big science’ fields. Physics and climatology spring to mind as other fields with likely similarly large and diverse databases. All of these ought to be classified as DOSTs and together with institutional repositories may even number in the low tens of thousands in total. In the light of such numbers, it becomes even more important to emphasize the way the 242 DOSTs were selected. Institutional repositories were not included because of the capacity of the research team. We hope to include their analysis in future iterations of this project, of which we hope that this paper is the first proof of concept. \"IT-professionals influence the design and deployment of the technology\" sounds a bit like it were better if amateurs would have that influence, or at least that they ought to have the same influence. Experts and professionals may be biased, but they are nonetheless the best we have to offer. Using amateurs only because of their different biases will not improve piloting a plane, nor medical surgery, nor science. We feel that the reviewer misinterpreted the sentence. What this sentence does is highlight how the intentions, experiences, priorities and cultures of the IT-professionals are introduced into the design of DOSTs. We believe that their inclusion in design decisions can influence the overall design of DOSTs, in keeping with scholarship in the field of Science and Technology Studies. The statement has nothing to do with amateurs - or the reviewer’s rather trite suggestion of amateurs piloting planes or contributing to surgery. \"The section above highlighted how inequalities, marginalization and injustices were perpetrated by the current structure of the DOST ecosystem.\" - 'perpetrated' or 'perpetuated'? Correction made."
}
]
},
{
"id": "74156",
"date": "07 Dec 2020",
"name": "Chris H. J. Hartgerink",
"expertise": [
"Reviewer Expertise meta-research",
"statistics",
"methodology",
"library and information sciences",
"psychology"
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors present “a methodological attempt to map a selection of the DOST [digital open science tools] ecosystem including links between the tools” (p. 6) to answer three research questions revolving the (1) geographic impact of DOSTs, (2) whether funding/values/stakeholders impact the openness of DOSTs, and (3) whether external power dynamics are recognized and addressed in DOSTs (p. 5).\nI think the authors present a valuable open dataset and research questions, although the manuscript does not answer the questions set out by the authors themselves.\nAs a research paper, I noticed the research paper is heavily weighted towards a perspective piece. As the core function of the manuscript is described to answer the three aforementioned research questions, 60 paragraphs for the introduction and discussion, in contrast to 26 paragraphs for the methods and results sections, seems unbalanced. It seems like the authors are trying to make a lot of points in this piece above and beyond the research questions, and I wonder whether those parts of the analysis make sense in this research paper in its current form. To me personally, it also distracted from understanding the manuscript's core points.\nStarting out with the self-described goal of the paper on p.6 and mentioned at the start of this review, I do not see the description of how links between the various DOSTs are determined, or what the results of these links were. Would the authors be able to shed more light on this? As I inspected the open data I was able to find some links (column \"Reliant on other DOSTs\") but these are not presented in the paper.\nRegarding RQ1 (impact of geographical origin of DOSTs), I think the authors make a valuable point and that such an investigation is worthwhile. The results show there is inequity in where the DOSTs originate from. The authors do not clarify how they operationalize and assess impact, which makes it difficult to assess the results in that light. Implicitly, it assumes usage numbers or other indicators are irrelevant to assess the impact. Impact is a non-trivial thing to measure, and without a definition, I would argue it is increasingly difficult to even answer RQ1. Similarly, the impact on what is left undefined in RQ1.\nFor RQ2, the impact of funding/values/stakeholders on openness is left undefined. In the results, descriptive statistics are given for the funding and providers, without dependent measures where differences could be measured. What is the openness that the funding/values/stakeholders would have an impact on? Again, an operationalization is not included. Additionally, the mentioned values are not included in the methods or results, hence, it might've been omitted in the reporting or it is superfluous in RQ2.\nFor RQ3, whether external power dynamics are recognized and addressed in DOSTs, external power dynamics seem to be operationalized as geoblocking due to trade sanctions. This was not clear from the introduction. If the authors want to focus on trade sanctions, which is a valuable perspective, I would suggest limiting the RQ to this instance and clarify that external power dynamics are operationalized as such. Speculative remarks such “While many of these did not explicitly state that their services were blocked to users in countries under US sanctions, this could still be the case.”\n\nWhether the DOSTs address these external power dynamics (second part of RQ3) is left unanswered and comes across as a difficult question to begin with. How can DOSTs address (eg) trade sanctions? Maybe if the DOST is run by a multibillion dollar corporation, they could lobby for this, but I fail to understand how any smaller organization could address such external power dynamics? Maybe I am missing the point, and it refers more to other ideas the authors have but are not included at the moment. I would be interested to read those ideas.\nAll in all, I think the authors investigate an incredibly valuable set of research questions and that their methods limit their findings. I would recommend the authors to focus on the research questions and add operationalizations to provide a clearer indication of what their results indicate. The answers I currently get from the manuscript for their original three research questions are:\nMany DOSTs originate from a few countries/regions. May lead to neglecting needs of researchers outside those countries/regions (no evidence provided).\n\nNot answered.\n\nProvides insight regarding superstructures of how the origin country of a DOST is affected by trade sanctions, and data on how many DOSTs recognize this in their Terms of Use (72/242).\n\nI hope that the authors can address these remarks, because in its current for the manuscript does not seem to achieve the goals it sets out for itself. I think there is a lot of value in their work.\nTangential remarks:\nFunding models are categorized in this study, and for mixed funding it is all seen as one and the same, despite potential variation in the degree of how mixed the funding is (e.g., 9:1 grant funding to own revenue is denoted as mixed, just like 1:9). This is now an implicit assumption and an implicit limitation that might be worth mentioning.\n\nWould it be possible to include some information on how much disagreement there was in the coding? That would be informative to understand how easy it was to code all of these data\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? No\n\nAre sufficient details of methods and analysis provided to allow replication by others? 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": "6425",
"date": "17 May 2021",
"name": "Louise Bezuidenhout",
"role": "Author Response",
"response": "Reviewer 2 The authors present “a methodological attempt to map a selection of the DOST [digital open science tools] ecosystem including links between the tools” (p. 6) to answer three research questions revolving the (1) geographic impact of DOSTs, (2) whether funding/values/stakeholders impact the openness of DOSTs, and (3) whether external power dynamics are recognized and addressed in DOSTs (p. 5). With respect to the reviewer, these research aims are slightly mis-stated. The object of the paper - and the study - was not to investigate the openness of specific DOSTs, but rather to speculate as to whether issues such as geographic location, funding source or legal restrictions might have an impact on the overall openness of the DOST ecosystem, and thus on the Open Science landscape. We do not try to assess or evaluate the openness of individual DOSTs. In order to make this more apparent we have included additional text in the introduction and methods sections. I think the authors present a valuable open dataset and research questions, although the manuscript does not answer the questions set out by the authors themselves. As a research paper, I noticed the research paper is heavily weighted towards a perspective piece. As the core function of the manuscript is described to answer the three aforementioned research questions, 60 paragraphs for the introduction and discussion, in contrast to 26 paragraphs for the methods and results sections, seems unbalanced. It seems like the authors are trying to make a lot of points in this piece above and beyond the research questions, and I wonder whether those parts of the analysis make sense in this research paper in its current form. To me personally, it also distracted from understanding the manuscript's core points. As stated above, the objective of this paper is to highlight characteristics of the DOST ecosystem that require further discussion and investigation. In no way does this paper attempt to provide an exhaustive analysis of the limitations of each individual DOST. Rather, this paper attempts - unlike many other papers that look at individual digital tools applied in the research workflow and across disciplines - to look at DOSTs as an interlinked ecosystem. The categories in the dataset were populated from the publicly available information on the DOST websites. Thus, due to the variation in websites and documentation, some of the categories are not complete. All information about funding, geographic location and links to other DOSTs were obtained in this manner. As discussed above, the methods section has been extended. Starting out with the self-described goal of the paper on p.6 and mentioned at the start of this review, I do not see the description of how links between the various DOSTs are determined, or what the results of these links were. Would the authors be able to shed more light on this? As I inspected the open data I was able to find some links (column \"Reliant on other DOSTs\") but these are not presented in the paper. As above, and similarly relating to the comments below, assessing individual impact of DOSTs is beyond the scope of this paper. Regarding RQ1 (impact of geographical origin of DOSTs), I think the authors make a valuable point and that such an investigation is worthwhile. The results show there is inequity in where the DOSTs originate from. The authors do not clarify how they operationalize and assess impact, which makes it difficult to assess the results in that light. Implicitly, it assumes usage numbers or other indicators are irrelevant to assess the impact. Impact is a non-trivial thing to measure, and without a definition, I would argue it is increasingly difficult to even answer RQ1. Similarly, the impact on what is left undefined in RQ1. Please see text on p28: It is important to recognise that the power dynamics shaping the DOST ecosystem are likely influenced by multifarious pressures. These include community decisions regarding the quality of the DOSTs, the unequal distribution of DOST users and researchers/developers around the globe, economic issues including the opportunities for alternative careers in DOST development in developed countries. The limits of this study make it impossible to engage with the influence of these different pressures in detail. Rather, the study seeks to highlight not only the complexities of the DOST ecosystem, but also the critical need for more scholarship on its evolution. This paper highlights how these pressures cause the dominance of certain DOSTs to be a “bug” in the current structuring of the ecosystem, rather than as an inevitable outcome of the status quo of scientific research. For RQ2, the impact of funding/values/stakeholders on openness is left undefined. In the results, descriptive statistics are given for the funding and providers, without dependent measures where differences could be measured. What is the openness that the funding/values/stakeholders would have an impact on? Again, an operationalization is not included. Additionally, the mentioned values are not included in the methods or results, hence, it might've been omitted in the reporting or it is superfluous in RQ2. While assessing the openness and limitations of funders would be a useful activity, it was out of the scope of this paper. What this category aimed to highlight was the diversity of the funding within the DOST landscape, rather than attempting to quantify it in any way. The following text has been added to P16: Because this study was a desktop review, it was not possible to gather specific financial details about each DOST. The information included was publicly-available funding reporting on the DOST websites. We do mention that financial backing of a tool has a direct effect on its sustainability/longevity in our analysis. For RQ3, whether external power dynamics are recognized and addressed in DOSTs, external power dynamics seem to be operationalized as geoblocking due to trade sanctions. This was not clear from the introduction. If the authors want to focus on trade sanctions, which is a valuable perspective, I would suggest limiting the RQ to this instance and clarify that external power dynamics are operationalized as such. Speculative remarks such “While many of these did not explicitly state that their services were blocked to users in countries under US sanctions, this could still be the case.” Whether the DOSTs address these external power dynamics (second part of RQ3) is left unanswered and comes across as a difficult question to begin with. How can DOSTs address (eg) trade sanctions? Maybe if the DOST is run by a multibillion dollar corporation, they could lobby for this, but I fail to understand how any smaller organization could address such external power dynamics? Maybe I am missing the point, and it refers more to other ideas the authors have but are not included at the moment. I would be interested to read those ideas. All in all, I think the authors investigate an incredibly valuable set of research questions and that their methods limit their findings. I would recommend the authors to focus on the research questions and add operationalizations to provide a clearer indication of what their results indicate. The answers I currently get from the manuscript for their original three research questions are: Many DOSTs originate from a few countries/regions. May lead to neglecting needs of researchers outside those countries/regions (no evidence provided). Not answered. Provides insight regarding superstructures of how the origin country of a DOST is affected by trade sanctions, and data on how many DOSTs recognize this in their Terms of Use (72/242). As highlighted above, we feel that the reviewer has perhaps mistaken the objectives of the paper and the source of the data used for this analysis. We present this paper as a novel perspective on DOSTs that takes into consideration their geographic, online and financial interlinkages. We present this analysis and speculative discussion based on our personal experience from working in global south contexts and being in close collaboration with researchers living and working in those regions as well as assessment of publicly-available information on DOSTs, not on in-depth interviews or data mining. We aim for this paper to highlight areas within the Open Science landscape that require further scrutiny and research, rather than per se offering a definitive analysis of the pitfalls of the highly complex and diverse DOST ecosystem. I hope that the authors can address these remarks, because in its current for the manuscript does not seem to achieve the goals it sets out for itself. I think there is a lot of value in their work. Tangential remarks: Funding models are categorized in this study, and for mixed funding it is all seen as one and the same, despite potential variation in the degree of how mixed the funding is (e.g., 9:1 grant funding to own revenue is denoted as mixed, just like 1:9). This is now an implicit assumption and an implicit limitation that might be worth mentioning. Further studies on the funding models of DOSTs are undoubtedly needed. However, as this paper was based on publicly available knowledge from DOST websites, being able to ratio the contributions of various donors was not possible and in such detail also not the focus of our work. We deem any mixed funding approach as preferable to reliance on a single funding /revenue source. Would it be possible to include some information on how much disagreement there was in the coding? That would be informative to understand how easy it was to code all of these data The methods section has been expanded and includes the explanation on p13: Discrepancies were discussed until consensus was reached."
}
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}
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https://f1000research.com/articles/9-1292
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https://f1000research.com/articles/10-392/v1
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17 May 21
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{
"type": "Research Article",
"title": "A TRIZ-driven conceptualisation of finger grip enhancer designs for the elderly",
"authors": [
"Dominic Wen How Tan",
"Poh Kiat Ng",
"Ervina Efzan Mhd Noor",
"Dominic Wen How Tan",
"Ervina Efzan Mhd Noor"
],
"abstract": "Background: Elderly people with severe finger weakness may need assistive health technology interventions. Finger weakness impedes the elderly in executing activities of daily living such as unbuttoning shirts and opening clothes pegs. While studies have related finger weakness with ageing effects, there appears to be no research that uses an algorithmic problem-solving approach such as the theory of inventive problem-solving (TRIZ) to recommend finger grip assistive technologies that resolve the issue of finger weakness among the elderly. Using TRIZ, this study aims to conceptualise finger grip enhancer designs for elderly people. Methods: Several TRIZ tools such as the cause-and-effect chain (CEC) analysis, engineering contradiction, physical contradiction, and substance-field analysis are used to conceptualise solutions that assist elderly people in their day-to-day pinching activities. Results: Based on the segmentation principle, a finger assistant concept powered by a miniature linear actuator is recommended. Specific product development processes are used to further conceptualise the actuation system. The study concluded that the chosen concept should use a DC motor to actuate fingers through tendon cables triggered by a push start button. Conclusions: Finger pinch degradation worsens the quality of life of the elderly. A finger grip enhancer that assists in day-to-day activities may be an effective option for elderly people, not only for their physical but also their mental well-being in society.",
"keywords": [
"TRIZ",
"elderly",
"finger grip",
"conceptualisation",
"design"
],
"content": "1. Introduction\n\nThe term ‘elderly’ is defined by the United Nations as a person who has reached or exceeded 65 years of age.1 As age progresses, the firing rate of motor units and twitch tension reduces, thus slowing down movements. This occurrence harmfully impacts a person’s muscle health on the whole.2\n\nThe increase in the global elderly population leads to challenges in ensuring that elderly people can stay consistently healthy and active.3,4 Muscle, nerve, and brain degeneration among older people causes finger functions and fine motor skills to deteriorate.5,6\n\nResearchers have found that elderly people often struggle when loosening or removing the caps of bottles used for storing medicine.7,8 In connection with this issue, pinching is a task of daily living that many elderly people have trouble with.\n\nA pinch refers to the act of gripping an object with the fingers and thumb with no palmar contact. The usual pinching techniques are the three-jaw-chuck pinch, tip pinch, and lateral pinch.9,10 While individuals generally use pinching techniques that they are accustomed to using, their exertions of pinch force might be inconsistent across the various techniques.11 Studies have been conducted on various pinch exertion aspects, including a study on the association between grasp stiffness and grasp force.12 The strength of a finger is an underlying component frequently evaluated among elderly stroke survivors.13–15\n\nIt is not uncommon for people to have suffered an injury to the hands or fingers, causing inflammation or pain. Some of these symptoms might have been triggered by wear and tear or overuse injuries from activities of daily living. Aside from injuries, issues in the hands or fingers may also be aggravated by ageing effects.16 This age-related weakness in hand and finger grip strength has been found to significantly reduce elderly people’s quality of life.17–19\n\nSeveral studies have explored finger pinch health from different perspectives, including normative data collection of certain populations,20–22 pinch strength dependent factors,23–25 and the effect of pinch strength on day-to-day activities.26 Many of these studies are statistically oriented and look into providing basic conjectures on pinching or gripping, along with their effects on people and society. However, there has yet to be a study that uses an algorithmic problem-solving approach, like the theory of inventive problem-solving (TRIZ), to systematically examine pinch function degradation among the elderly and propose innovative solutions for this issue. Hence, using the TRIZ approach, this study aims to conceptualise finger grip enhancer designs that potentially facilitate the day-to-day pinching activities of elderly people.\n\n\n2. Literature review\n\nThe increasing pace of population ageing around the world is concerning as elderly people are prone to having poorer health than young people, and so are more susceptible to mental and physical disorders.27,28 Elderly people might also experience major health problems with their fingers and hands. For instance, they might experience poor grip and pinch capabilities, which can be a risk factor for carpal tunnel syndrome.\n\nIt is likely that one of the contributing factors to hand weakness among the elderly is age-related changes in muscle mass29 and the nervous system.30,31 Studies have found that by the age of 50, adults experience a reduction in cortical neurons of up to 35 %32,33 which causes a deterioration of the sensory, motor and even muscle functions. The ageing-induced reduction in strength and skeletal muscle mass is known as sarcopenia. According to Doherty,34 about 30 % of people above the age of 60 experience symptoms of sarcopenia to some extent. This age-related degradation could be caused by a slower pace of life, which could lead to immobilisation and reduced overall muscle health. The number of muscle fibres and the total muscle area decrease with age.35 When this happens, the maximum firing rate of motor units and twitch tension also reduce.2,36\n\nAgeing affects force variation, especially in the application of submaximal force.37 In one particular study,38 elderly people of 65-79 years were found to possess a gripping force 30 % smaller and a peak pinch grip force 26 % smaller than young people of 20-35 years. It was also found that elderly people were less able to sustain a stable submaximal pinch grip force and an accurate pinch position. The study concluded that there is an overall worsening of finger and hand capabilities as people age.38 A positive and significant correlation was found to exist between age and the time required to complete various hand movement subsets.39 Similarly, the decline in hand strength and dexterity was also seen at a smaller scale in the fingers.39–43\n\nIn addition, elderly people with poor eyesight can also experience a weakened finger grip. As an old person’s grip strength slowly reduces, he/she may become dependent on visual feedback. Such a reliance serves to counterbalance the reduced muscular strength whilst engaging with day-to-day tasks. According to Shumway-Cook and Woollacott,44 once people’s eyes are open, their ocular motor system and attention span are triggered to reinforce neuromuscular control and render more sensory input. Vuillerme, Nougier45 found that with vision, people could acclimatise to the destabilisation stemming from muscle fatigue. Vision reduction impacts a person’s proprioception. As proprioception degrades, an individual can slowly fail to perceive precise movements, leading to an increased risk of falling, deteriorating joint disorders, and uncommon joint biomechanics during functional activities. Ageing is connected with impaired proprioception.46\n\nMore often than not, elderly people possess reduced hand dexterity and decreased tactile sensitivity. This phenomenon leads to over-gripping in day-to-day tasks. In one study, young and elderly subjects were asked to pinch small objects with varying slipperiness. It was found that the elderly participants exerted double the amount of average force of the young participants. This excessive grip force was a feedback to diminished tactile perception.47\n\nPoor tactile sensitivity reduces the ability of the thumb and fingers to direct force, which is an important factor for securing objects in the hand.48–51 Young adults were found to have the ability to produce a fingertip force that was nearly perpendicular to the object surface while elderly people produced a force that diverged in the ulnar direction of the vertical plane and proximal direction of the horizontal plane. This outcome adversely affected elderly people’s ability in using hand-held objects as it required the accurate specification of the direction and magnitude of three-dimensional fingertip force vectors.\n\nA common solution for poor finger function is for elderly people to stay regularly active, helping to strengthen muscles and preserve proprioception. Ribeiro and Oliveira46 suggested that keeping oneself physically active on a regular basis could slow down the deterioration of proprioception. Basic long-term finger exercises could lessen fluctuations in the motor output of hand muscles, increase finger dexterity and lower the motor unit discharge rate irregularity.52 Maintaining proper nutrition and performing resistance exercises could also play an important role.34\n\nAn artificial hand is usually required to mimic how the real human hand works. The prosthesis mechanism is analogous to the biological bones of the hand. The synthesis of the finger mechanism is the first step in designing a gripper for the prosthetic arm. The anatomy of the human finger has bones connected by joints (DIP: Distal interphalangeal joint, PIP: proximal interphalangeal joint, MCP: Metacarpophalangeal joint) that are actuated by tendons.53 This anatomy is used as a structure for underactuated systems when coupled with mechanical joints and artificial tendons. There have been studies on human-like prosthetic mechanisms that emphasise the use of underactuated mechanisms.54–56 An underactuated mechanical system is a system that has a fewer number of control inputs compared to their degrees of freedom (DOFs). These systems have been used in surface vessels, robots, and road vehicles, where the actuators were replaced with passive elastic elements (springs) or limit switches to improve machine adaptability.57\n\nA natural way of grasping an object similar to a human’s grasp can be achieved using an underactuated mechanism.57 This outcome is possible because underactuation allows for adaptive grasping. The geometric configuration of fingers is automatically determined by external constraints related to the shape of the objects. The two main underactuated finger designs utilise linkages and tendon-actuated mechanisms.58 Tendon systems are generally limited to accommodate a small grasping force while linkage mechanisms are suited for a large grasping force.\n\nAlthough underactuated mechanical systems have been designed for finger prostheses, the concept could be extended to a finger assistive device. The advantage is that it is anthropomorphic, which ensures that the fingers are able to adapt to objects of different shapes.58\n\nIn basic underactuated cable mechanisms for prosthetic devices, the fingers function with a thread running through the inner part of the whole finger, which is connected to a servo motor that controls the movement.58 When the finger is flexed, the bottom wire is pulled while the top wire relaxes, and vice versa.\n\nPons, Rocon60 designed a four-underactuated, multi-fingered dexterous hand which was able to accomplish cylindrical, precision, hook, and lateral grasps. A crossed tendon mechanism was designed to control the fingers. The Federica hand used tendons and pulleys to move its fingers.61 The fingers were connected to tendons actuated by a control pulley mechanism for flexion. Finger extension was achieved with an elastic spring element.\n\nElectronically powered finger prostheses generally use a DC motor-gearhead that requires battery power to drive the motors.62 This external actuated system is usually placed on the forearm, which becomes a challenge in terms of housing all the required components such as the power unit, control unit and actuator.63\n\n\n3. Methods\n\nThe research methodology flow chart is shown in Figure 1. The main problem is defined by reviewing past literature to establish a cohesive understanding of the current research landscape (see Underlying data125 for descriptions of the literature and data sources used). The second step is to identify the root causes of the main problem. In this step, a problem-solving tool known as TRIZ is used. A cause-and-effect chain (CEC) analysis diagram is constructed from key findings of past research to help identify potential causes of the problem and to narrow them down to specific root causes. The method of formulating contradictions is pivotal in TRIZ64 and is applied in the next step. Three methods are used in this research, namely the engineering contradiction, physical contradiction and substance-field analysis. These methods are used in resolving the root causes. After generating the conceptual solutions, the next stage is product development. Selection methods are also applied in various parts of the methodology.\n\nTRIZ is a Russian acronym which stands for the theory of inventive problem-solving. It is an algorithmic problem-solving approach that utilises logic instead of intuition to arouse problem-solving skills inventively.65 The approach involves a methodical process that is predictable, repeatable and reliable.66 It is a systematic problem-solving methodology which originated from patent studies and is suitable for new product innovation.\n\nTRIZ is chosen for this research as it is capable of resolving challenging issues that require problem-solvers to think unconventionally.65,67 The structure of employing the TRIZ approach for this study is shown in Figure 2. In general, the main problem or initial disadvantage is typically caused by only a few underlying root causes or key disadvantages. The CEC analysis diagram is used to break down the main problem into root causes. In this study, the main problem is identified as “elderly people have degrading finger pinch function”.\n\n3.1.1. Cause-and-effect chain (CEC) analysis\n\nThe CEC analysis is a systematic method of deriving the cause of a problem. This method helps the researcher focus on the process where an issue has occurred and allows for the practical use of facts to refine the real causes. Starting from the main problem, the question “why” and “why else” is asked until the researcher arrives at a cause that includes a basic theory or law of science, or a cause that has reached a technological limit. The use of literature support is key in the validation of every probable cause. The chain’s end includes a possible root cause to the main problem. Figure 3 shows the CEC diagram constructed for this study.\n\nAs shown in the CEC diagram, many different factors contribute to the degrading finger pinching functions of the elderly. Nonetheless, since there are many studies pertaining to the second branch (excessive grasp strength), third branch (variable grip force) and fifth branch (reduced pinch/grip strength) (see Table 1), the exploration for the probable root cause to the problem is refined here for a more focused study.\n\nThe coloured boxes in the CEC diagram are the chosen root causes of the sub-problems. The root causes are basic key disadvantages, recurring across dissimilar branches and convincingly supported by scholarly research. Towards the end of the second branch, the causes point towards fundamental biological factors which would be beyond the scope of this study as far as resolving the main problem is concerned. Therefore, by falling back one level, i.e. to the cause before that branch, diminished tactile sensitivity is selected as one of the root causes. Thus, at the end of the CEC analysis, the following root causes are obtained:\n\nRoot cause 1: Poor-visual feedback (yellow box in Figure 3)\n\nRoot cause 2: Worsening coordination of individual digit force (red box in Figure 3)\n\nRoot cause 3: Diminished tactile sensitivity (green box in Figure 3)\n\n3.1.2. Engineering contradiction\n\nAfter identifying the root causes, various tools in the TRIZ database can be utilised in the next problem-solving step. Inventive principles were defined by Genrich Altshuller75 who analysed 40,000 patents and discovered that all engineering problems can be resolved using a limited set of generalised solutions. An engineering contradiction statement describes an improvement in one characteristic of a system which results in the degradation of another characteristic.\n\nUpon creating the engineering contradictions, proposed recommendations can be filtered by identifying the suitable inventive principles of TRIZ. The inventive principles of TRIZ include a set of 40 generalised recommendations which can potentially resolve an engineering contradiction that is linked with a set of system parameters.65\n\nWith reference to the three root causes, three engineering contradictions are constructed and presented in Table 2 together with their respective system parameters and inventive principles. Some of the 39 system parameters of TRIZ76 are linked with the positive and negative aspects in the engineering contradiction. Using the TRIZ matrix of contradictions, these parameters are intersected to obtain the inventive principles.\n\nAn automated version of this step is available online. The inventive principles can be auto-generated by entering the system parameters based on the worsening and improving characteristics from the engineering contradiction (refer to www.triz40.com/TRIZ_GB.php). Each combination or pair of system parameters yields a different set of inventive principles.\n\nIn an earlier study by77 the above-stated methodology of formulating engineering contradictions were similarly used to explore finger grip degradation in the elderly. While the contradiction for the second root cause presented here (worsening coordination of individual digit force) is similar to the one proposed in the earlier study, the contradiction formulations for the first and third root causes are different.\n\nFor the first contradiction, the earlier study’s worsening variable contends that digital displays were not able to effectively transfer information to the elderly. However, the present study’s worsening variable argues that elderly people may not be accustomed to visual feedback substitutions without sufficient practice.\n\nThe third contradiction in the present study is entirely different from the one discussed in the earlier study because the identified root cause is also entirely different. The earlier study identified the third root cause as the variability in grip force and motor unit discharge rate. However, further literature reviews suggested that this variability in force was predominantly caused by diminished tactile sensitivity.\n\nIn view of the foregoing reasons, it was still necessary to reformulate the contradictions from the earlier study in order to uncover different possibilities in the TRIZ solution models.\n\n3.1.2.1. Engineering contradiction 1 (mechanics substitution/another sense)\n\nElderly people face problems with their hearing and vision capabilities. With degrading eyesight, developing an instrument that can replace visual feedback is essential.78,79 Presently, dynamometers are the most common tools used to evaluate finger strength, due to the simple operations involved and accuracy level. Nevertheless, these tools either use a digital display or a traditional dial that can turn out to be ineffective if the elderly person suffers from low vision.71,74 This limitation results in decreased stability control and gripping force. Substitutions to visual feedback are essential for constantly rendering information to users especially when their eyesight starts to deteriorate.\n\nThe inventive principle known as mechanics substitution/another sense is an appropriate principle to address this contradiction. This principle revolves around the substitution of mechanical factors with sensory (acoustic, smell, taste or optical), electric or magnetic factors. Poor eyesight greatly impacts finger function. Hence, it is reasonable to consider other modes for elderly people to effortlessly process information regarding finger grips. An arm motor network incorporates audio feedback and responds by altering the force applied as well as it does with visual feedback.80 Through practice, auditory feedback can support daily living tasks and can help in avoiding domestic accidents. Researches have suggested the likelihood of auditory feedback as an alternative to visual sensors.81,82\n\nAn alarm- or buzzer-based auditory feedback may be appropriate in monitoring, assisting, and rendering feedback to elderly people. With pressure sensors attached to fingertips, the buzzer can be designed to activate when the required pinch force is reached. It can also be designed to trigger when the user surpasses the demanded force. This system ensures that the elderly person can pinch with the acceptable amount of force, avoiding finger injuries.\n\n3.1.2.2. Engineering contradiction 2 (dynamisation)\n\nWhile extended “fingers” with latching abilities could assist in improved force applications, the interface between the fingers and the device relies on friction to provide the intended force output. With degrading tactile perception, elderly people may face challenges in operating some devices. One study found that indistinct tactile sensory inputs reduced vertical shear force flexibility and increased interdigit shear force coupling in precision grips in order to assure a stable grip control of an object.83 Li, Wei84 found that tactile deficits increased in the inter-digit centre of pressure distribution, causing the force data to stray from the normal distribution, thus impairing finger torque and force control.85\n\nDynamisation is defined as the act of optimising the characteristic of an object, process, or external environment. Due to the deteriorating coordination of individual digits, elderly people have issues applying the suitable amount of force needed to carry out daily tasks. For instance, they may overexert or apply an inadequate pinch force which could lead to injury. As an analogy, a special tool known as the NuMuv Grip-Aid was developed so that it could be attached to objects like pens or toothbrushes to help people with grasping issues.86 An appropriate tool could be similarly developed to support elderly people in pinching objects more effectively. With the dynamisation principle, the pinched object could be made to interconnect better with the fingers. By developing a kind of latching mechanism, the object could hook, hold, or grasp onto the fingers, thus allowing users to pinch without relying entirely on finger strength.\n\n3.1.2.3. Engineering contradiction 3 (partial action)\n\nElderly people have been reported to possess reduced tactile sensitivity and hand dexterity.87,88 This limitation could lead to over-gripping issues during activities of daily living.89 Shim, Lay69 suggested that grip force may be energetically suboptimal but could still benefit the elderly. A larger grip force would stop objects from slipping off the hand even when the grip force fluctuates. Such an application may be useful for less steady and frail elderly people.90,91 However, this high grip force could be a strategic response to tactile sensitivity impairment which also contributes to impaired dexterity.\n\nA high force produces a stronger pinch grip yet causes more stress on the finger muscles and could lead to long term injuries. The partial action principle refers to the use of more or less of the originally desired action, effort, or field when the exact output is difficult to achieve.65 This strategy is appropriate for helping elderly people avoid overexerting their fingers in a pinch application. The strategy can be accomplished by pinching with less of the initially required force instead of overexerting the force in one shot when the exact intended force level is difficult to achieve. Moreover, researchers discovered that elderly people use a probing pinch strategy, which causes a large force fluctuation.91 Improving friction would indeed allow people to grip more securely, thus allowing for improved pinch force control. An unconventional method of improving pinch force control would include exploring the use of dampers which absorb the added force without compromising the firmness and strength of the pinch.\n\n3.1.3. Physical contradiction\n\nA physical contradiction comprises two opposing conditions in a single object.92 These conditions cause a conflicting requirement in the object’s functionality. Compared to an engineering contradiction, a physical contradiction is resolved through separation principles of the contradictory requirements in time, space, or physical state.93 For this study, three physical contradictions are formulated.\n\nPhysical contradiction 1:\n\nElderly people need visual feedback substitutions to be informed about pinch force performance, AND elderly people do not need visual feedback substitutions as injuries may occur from unaccustomed use.\n\nPhysical contradiction 2:\n\nElderly people need to pinch with higher pinch force using a pinching device for better pinching results, AND elderly people need to pinch with reduced pinch force without a pinching device to not injure the fingers with external mechanisms.\n\nPhysical contradiction 3:\n\nElderly people need to pinch with reduced tactile sensitivity in order to hold their pinch tightly for a longer duration, AND elderly people need to pinch with increased tactile sensitivity in order to not overexert their pinch grip.\n\nThe approach used to solve all three physical contradictions is the separation-in-space strategy. The strategy is suitable for the first contradiction because there is an operating space to have visual feedback substitutions and an operating space to reduce the risk of the unaccustomed use of these substitutions. In the second contradiction, there is an operating space to have higher pinch force using pinching devices and an operating space to avoid injuring fingers from external mechanisms. In the third contradiction, an operating space exists in pinching firmly and an operating space exists in avoiding overexertion. According to the separation-in-space approach, the inventive principles prescribed to resolve the physical contradictions include:\n\nThe taking out principle is selected to resolve physical contradiction 1, while the segmentation principle is selected to resolve physical contradiction 2. The other way around principle is selected to resolve physical contradiction 3. Further deliberation is carried out on these principles for possible recommended solutions.\n\n3.1.3.1. Physical contradiction 1 (taking out)\n\nAccording to Oscari, Secoli,80 it was found that arm motor networks incorporate auditory feedback in achieving desired trajectories. This finding implied that auditory feedback is a suitable sensory substitution in motor training. The taking-out principle is used to separate a particular portion from the main object or isolate a critical part/property from the rest of the object.\n\nWith our bodies often relying on visual feedback while performing day-to-day activities, practice would be required for any form of visual substitution. From an experiment by Portnoy, Halaby,81 blindfolded participants who received auditory feedback showed that the water-spilling error (the output variable measured) between the first and last trial was significantly reduced. Based on the taking-out principle, a solution could be proposed to remove the time required for a person to be familiar with any form of visual feedback substitution. Exploring different combinations of sensors could help realise this idea by combining various levels of feedback such as a buzzer (auditory), LED lamp (visual) or vibrating device (kinaesthetic).\n\n3.1.3.2. Physical contradiction 2 (segmentation)\n\nApart from finger strength, finger individuation is a significant component of hand function. Finger individuation is the ability to subtly operate the fingers, something which is often a struggle among stroke patients and elderly people.94 Independent finger movements were found to be restricted as the motor cortex or corticospinal tract deteriorates with age.95,96 This restriction is predominantly noticeable for the little, middle and ring finger as these fingers were found to be considerably impaired.95\n\nWhen gripping small objects, one must have the individuation ability to position fingers in the correct orientation and exert enough force to grip the object.97 Understanding the differences in how each finger changes with age could influence the process of developing a finger grip enhancing device. Segmentation is used to divide an object into independent parts. Rather than researching pinch as a general finger action, it would be more suitable (as suggested by past researches98,99) to refine the action into minor elements of individual fingers. Using this principle in the development of a pinch assistant, more focus should be allotted to weaker fingers like the little, middle and ring fingers to make up for the seriously impaired individuation.\n\n3.1.3.3. Physical contradiction 3 (the other way around)\n\nIn finger prehension tasks, elderly people were found to produce a higher opposing moment which acts against the direction of total moment.69 Similar to the produced excess force, this action can be viewed as an inefficient gripping method, though it increases stability. Opposing moments increase the apparent stiffness of the hand and can be a passive resistance to variations in torque. In other studies, researchers found that the central nervous system was unable to organise finger synergies such that finger forces cancelled each other out.100,101 During prehensile tasks, fingers produce a nonzero force prior to the task which acts against the external torque.69 These phenomena occur instinctively in elderly people to increase the safety margins as they use their fingers.\n\nThe other way around principle is used to invert actions or reverse processes for problem-solving. Using this principle, it is beneficial to view opposing moments from another perspective. Instead of trying to eliminate these natural, age-related responses of the fingers, factoring these responses into future studies or medical devices helps people age gracefully as their bodies intend.\n\nA device utilising the other way around principle should pay attention to the preloading force of the elderly person’s fingers. Instead of designing something that restricts initial force application entirely, the device should allow fingers to apply a preloading force first before assisting it with mechanisms. This application would allow elderly people to remain active as a countermeasure for expected loss of strength and endurance. A study among elderly people over the age of 90 found that with resistance training, functional mobility improved, while strength increased by up to 175 %,102 suggesting the possibility of reversal of age-related effects on skeletal muscles.\n\n3.1.4. Substance-field modelling\n\nThe substance-field (Su-Field) analysis is another TRIZ problem-solving tool. It is used to analyse and improve the efficacy of technical systems. The Su-Field mainly consists of a few main fields including the mechanical, acoustic, thermal, chemical, electric, and magnetic fields. A field makes up the most basic model of an interaction. Any interaction can be formulated as the interaction between two substances.66 The interaction between the fingers and a pinched object can be modelled using the Su-Field analysis, with the main problem being that elderly people have degrading finger pinch function. The type of model identified determines the class of standard inventive solutions (from the 76 TRIZ standard inventive solutions) to be used for the modelled problem.65\n\nFigure 4 presents the Su-Field model of this study. S1 refers to the first substance, which in this case represents fingers. S2 represents the pinched object. F1 is the mechanical field, which includes the interaction between fingers and objects. This model is known as an ineffective Su-Field model, which is normally represented by a dotted arrow from S1 to S2. The model implies that the fingers are ineffectively pinching the object. From the list of 76 Standard Inventive Solutions, class 2 and 3 are used as a reference to resolve the problem. These classes include various methods of increasing Su-Field effectiveness. Sub-classes 2.1.1 and 2.1.2 are finally chosen as the solution models because the researchers were able to visually conceptualise practical solutions from these two sub-classes.\n\n3.1.4.1. Chain Su-Field model (2.1.1) - converting single model to chained model\n\nFigure 5 shows a chain Su-Field model, which is a modified version of the previous ineffective Su-Field model (Figure 4). Another field (F2) and substance (S3) have been added. S3 is added to separate substances S1 and S2. The additional substance should potentially increase the effectiveness of the fingers while pinching. In this scenario, S3 could include the addition of friction between the fingers and pinched object. This proposition, which can take the form of rubber pads or gloves, improves tactile sensibility, leading to a plausible increase in force accuracy and reduced overexertion. F2 represents a mechanical field.\n\nAs people age, the tactile sensibility of hands becomes impaired,38,42,47 worsening their ability to pinch accurately, moderately and securely. Adding a new substance between the finger and the object can potentially eliminate this effect.\n\nWhen the finger pinches an object, it slips against the object surface when the direction of the finger force is such that the ratio of shear to normal force becomes larger than the coefficient of friction between the finger and the object.103 Fingers generate forces within a range that is dependent on the coefficient of friction. A low-friction surface would require finger forces to be applied in a direction close to perpendicular to the object surface which would be harder to maintain, resulting in slippage.104\n\nRubber gloves are popular tools used for increasing friction between the fingers for any hand-holding application. This idea can be incorporated into devices for activities of daily living. A study in 2015 discovered a progressive increase in grip-to-load force during the precision pinch of low-mass objects (less than 30 g).105 The same study discussed the possibility of how a decreased level of tactile feedback played a role in inefficient low-mass grip force control. By considering these findings on tactile sensitivity effects on pinching, a tool can be introduced for the elderly to increase finger friction and reduce the ineffectiveness caused by pinching slippery objects.\n\n3.1.4.2. Double Su-Field model (2.1.2) - a second field applied to S2\n\nFigure 6 is a double Su-Field model, which is a modified version of the original ineffective Su-Field model (Figure 4). Another field (F2) has been added to allow better control of the system. The mechanical field F1 produced by the fingers pinching the object is ineffective. These effects can be improved by adding F2. Some of the possible fields include the optic or acoustic fields. This solution model does not separate S1 and S2 and ensures that the fingers remain in contact with the pinched object. As people age, their eyesight begins to deteriorate. Poor eyesight has a strong correlation with poor finger pinching.44,46,71 The incorporation of LED sensors on a device that aids pinching should provide a clear signal to indicate to the user that sufficient force is detected for the pinching action.\n\nIt is also important to consider other mediums in which information regarding finger gripping can be easily conveyed to elderly people. Auditory feedback is one of the possible substitutes to visual sensors.81,82\n\n\n4. Results and discussion\n\nThe solution models generated from all three approaches (engineering contradiction, physical contradiction and substance-field analysis) were compiled and used to initiate the concept design process. The following list summarises the generated principles and sub-classes used as solution models.\n\n1. Engineering contradiction:\n\na. Mechanics substitution/another sense\n\nb. Dynamisation\n\nc. Partial action\n\n2. Physical contradiction:\n\na. Taking out\n\nb. Segmentation\n\nc. The other way around\n\n3. Substance-field analysis:\n\na. Chained Su-Field for independent control of substance\n\nb. Improving ineffectiveness with F2 without changing elements of system\n\nThe concept design for the mechanics substitution, another sense, and taking-out principles were combined as shown in Figure 7. The combination included different feedback sensors that notify the user when a sufficient force has been applied while pinching objects.\n\nFigure 8 shows a concept based on the dynamisation principle. In this concept, palmar grip, which is normally inactive in the pinch action, would provide grip strength to the fingers during pinching. Figure 9 shows a device specifically used to open bottle caps. For the elderly people found to be using a probing pinch approach, the large contact area of this device would allow them to use the palm for more force exertion and an easier twisting action due to the increase in the moment of the force.\n\nFigure 10 shows a finger assistant powered by a miniature linear actuator. Based on the segmentation principle, weaker fingers could benefit from a device like this. The other way around principle suggested a concept that allows the elderly person to initiate the pinching action instead of relying totally on devices. Figure 11 shows a clamp device that has the ability to lock the pinched object in place after the pinch force is applied by the user. All contact points between the fingers and the device would have sufficient friction, as suggested by the sub-class 2.1.1. For sub-class 2.1.2, visual feedback substitution was also suggested and shown in Figure 7.\n\nThe TRIZ methodology was used up to this stage of the research. Five different concept designs have been generated using this problem-solving tool. The concept screening was based on a numerically weighted concept scoring method by Stuart Pugh.106,107 A set of general criterions108 is directly adopted to avoid bias selection.\n\na. Criterion A - compatible with the overall task and with one another\n\nb. Criterion B - fulfils demands of the requirements list\n\nc. Criterion C - realisable in respect of performance, layout, etc.\n\nd. Criterion D - expected to be within permissible costs\n\ne. Criterion E - incorporates direct safety measures or introduces favourable ergonomic conditions\n\nf. Criterion F - preferred by the designer’s company supervisor\n\nSome modifications were made to the criteria to accommodate this project. Criterion A was defined in this study as the ability of a concept to be compatible with other concepts, or in other words, to be flexible. Criterion B was modified to represent the ability of a concept to solve the root of the problem. Criterion C was amended to reflect general feasibility, while criterion D was amended to reflect costing. Criterion E was modified to reflect safety measures. Criterion F was changed to reflect the preference of author PKN as an advisor, since a company does not exist in this study’s context. Table 3 presents the concept-screening matrix of the finger pinch enhancer for elderly people.\n\nThe design concept for segmentation was selected to be the reference for concept selection since there have been studies on finger rehabilitation devices that have used similar working principles, such as linkages and actuators.109–112 From the concept-screening matrix, it was found that the segmentation concept ranked the highest. This concept was brought forward to the product development stage as the main concept.\n\nThe segmentation concept suggested that in order to improve pinching abilities, weak fingers should be identified and strengthened. However, this concept still requires a product design method to advance from a conceptual idea into a feasible product.\n\nDesign methods are often seen as procedures or a set of tools used to assist design engineers.113 These methods can be complex and vary for each design expert. Pugh106 suggested a four-stage design process beginning with 1) exploration, 2) generation, 3) evaluation and 4) communication. Pahl, Beitz108 also used a four-stage process but with a different classification; 1) conceptualising, 2) embodying, 3) detailing and 4) computing. Karl and Steven114 introduced a similar but more customer-centric design process that allows each step to move flexibly rather than in a single direction as decisions often need to be revisited due to the complexity of the process.\n\nThe design mission statement, which was created to provide the general direction for the pinch enhancer, is shown in Table 4. The concept generation process in this research used a four-step method inspired by Karl and Steven:114\n\n1. Functional decomposition\n\n2. Patent search\n\n3. Systematic exploration\n\n4. Concept selection\n\n\n\n• A portable device that assists elderly people during pinching actions\n\n\n\n• Able to pinch more effectively with device\n\n\n\n• Power-assisted\n\n• Lightweight\n\n• Device attached to the hands\n\n\n\n• Senior citizens\n\n• People with weak finger pinching abilities\n\n4.3.1. Functional decomposition\n\nFunctional decomposition is a generic term used to describe the process of resolving a relationship into constituent parts such that the original function can be recreated from those parts.115 It was used in this study to divide the problem into subproblems. The functional decomposition of the proposed finger pinch enhancer concept is shown in Figure 12. This functional diagram represents the initial problem described as a function of its energy, material, and signal flows.\n\nThe functional decomposition was then divided into its subfunctions based on operations such as storing energy, isolating fingers and sensing a trip (Figure 13). The smaller subfunctions represent elements that are needed for the product to function holistically. The signal, or trip of tool, describes components used to trigger the device to carry out programmed instructions.\n\n4.3.2. Patent search\n\nWith the problem broken down into smaller sections, an external search was required to find existing solutions or possible concepts that address the overall problem or any of the subfunctions. This information-collecting process was executed through a patent search conducted on 29th December 2020. The inclusion criteria for the patent search comprised finger support, finger grip, finger pinch assistant, and pinch stabiliser, while the exclusion criteria comprised of finger exercise devices, arm exoskeleton, and stationary finger support. Google Patents was the search engine used for keyword searches. The keywords used were finger support, finger grip, and pinch stabiliser. Table 5 shows the function and strengths of the patents reviewed.\n\n4.3.3. Systematic exploration\n\nUpon gathering many different conceptual solutions to the subproblems, three of the subproblems were chosen to be explored further, namely storing energy, sensing trip, and applying translational energy. These subproblems were chosen as they are the pillars of the product and greatly define the remaining subfunctions. As an illustration, if an external mechanical switch was chosen as the sense trip, then the trip tool could be a push start button while the method of storing energy could involve using dry cells or a suitably rated power supply. Table 6 shows a list of solutions for the three selected subproblems.\n\nWith the three listed subproblems and their respective solutions, there were a total of 147 possible combinations (7 × 3 × 7). It was almost impossible to explore all these options due to the amount of time and energy required. Therefore, a concept classification tree (see section 4.3.3.1) and concept combination table (see section 4.3.3.2) were used to streamline the process into a more focused and manageable direction.\n\n4.3.3.1. Concept classification tree\n\nThe classification tree is often used in data mining to group cases or objects into classes of dependent variables.121 The classification tree was used in this product development process to group solutions into classes for improved decision making. The selection criteria depended on the likelihood of the classification in constraining the remaining subproblems. Figure 14 shows the classification tree for storing energy.\n\nThe pneumatic, chemical, and natural branches were disregarded from the tree, for being less portable, more expensive, and inefficient, respectively. In terms or refining the functional decomposition, the electrical method of storing energy was deemed the most suitable method. This decision was largely due to the fact that in order to store enough mechanical energy to move the fingers, a complex and bulky mechanism would be required. This limitation would violate the design needs of being lightweight and non-movement-restricting. Therefore, the functional decomposition diagram was refined as per Figure 15.\n\n4.3.3.2. Concept combination table\n\nBased on the refined functional decomposition diagram and the pruning steps from the concept classification tree, the concept combination table was used to match different solutions together to generate different concepts. Table 7 presents the three possible concept combinations of the three key subproblems.\n\nThe first combination uses voice command and linkages powered by a linear actuator (see Figure 16). The second combination uses a DC motor to actuate the fingers through tendon cables triggered by a push start button (see Figure 17). This type of exoskeleton design has the advantage of flexibility and safety. The third concept recommends a DC motor to actuate linkages to move the fingers for better finger control (see Figure 18). The activation of this device would be achieved through the sensing of finger movements (pressure sensors).\n\n4.3.4. Concept selection\n\nConcept selection is a process that refines and selects from the pool of generated concepts. A concept selection process was applied to the three generated concepts described in Table 7.\n\n4.3.4.1. Digital logic method\n\nA modified digital logic approach introduced by Dehghan-Manshadi, Mahmudi122 was used to justify a reasonable selection. The digital logic approach has been used to rank material properties on a binary scale, where a score of one (1) is given to the more important property while zero (0) is given to the less important property.123 The level of importance for each property is determined by the researcher or designer based on his/her self-assessment of the criterion. The modified approach ranks the more important property with a score of three (3) and the less important property with a score of one (1). However, when two properties have equal importance, they will both be given an equal numerical score of two (2). This method presents the advantage of keeping the least important property on the list.\n\nIn this study, the modified digital logic method was utilised with some adjustments. When two properties were compared in this study, it was challenging to consider them as equally important. Therefore, the numerical score of two (2) was not used the selection process. This condition, however, caused a large numerical gap to exist between the most important and least important properties due to the distance between scores one (1) and three (3). In the end, the score of two (2) was assigned to the more important property while the score of one (1) was given to the less important one. Table 8 shows the digital logic method in a pairwise table used to determine the weightage of each selection criterion.\n\n4.3.4.2. Concept scoring\n\nWith regard to concept scoring, the VDI Guideline 2225 published in 1964,124 is the first catalogue of relative costs of materials. Although the guideline was meant to measure the costs of products in different size ranges, materials, and manufacturing process relative to a basic cost, it could also be used to rank value. Pahl, Beitz108 used the VDI Guideline 2225 with a range of zero to four to evaluate different parameters along the design process. Table 9 shows the selection points and description used in the current study, which was also based on the VDI Guideline 2225.\n\nTable 10 presents the concept scoring matrix of the finger pinch enhancer for elderly people. The ratings were solely proposed by the main author based on his specific experience and knowledge on various hand and finger assistive devices. In reference to the main author’s superior design sense in the specific area of hand and finger assistive devices, the co-authors of this study concurred to the ratings and rankings provided by the main author. In this case, instead of selecting one reference concept, the reference for each criterion was selected individually as not one single concept was suited to be the reference. Finally, concept 2, which recommended the use of wires for flexible finger control, was selected based on its strengths in user comfort and ease-of-use.\n\n\n5. Conclusion\n\nUsing the TRIZ approach, this study aimed to conceptualise finger grip enhancer designs that potentially facilitate elderly people’s day-to-day pinching activities. Using the segmentation principle, a finger assistant concept powered by a miniature linear actuator was selected. The concept recommended the use of a DC motor to actuate the fingers through tendon cables triggered by a push start button.\n\nUsing the TRIZ tool to identify root causes of degrading finger pinch function and generate solutions helped to unearth a more mechanical and product-oriented perspective of the biological challenge of finger weakness among elderly people. Although changes in the body would require physiological investigations, the systematic nature of TRIZ could lead researchers to solutions from other branches such as biomechanical, design and human factors engineering that may have been overlooked by experts of the field.\n\nPoor finger pinch is an effect of ageing which negatively impacts elderly people’s quality of life. An assistive pinching device to aid in activities of daily living may be an effective option for them. Such a solution may give rise to implications related not only to the physical but also to the emotional and mental well-being of the elderly people in society.\n\nA potential limitation of this study was found in the product development stage. With the end goal of developing an assistive device for the fingers, it would have been advantageous to consider the inclusion of kinesiology studies on finger movements. The embodiment of kinesiology literature during the conceptualisation stage may have altered the dynamics of the ideation process for finger grip enhancers. However, this consideration was beyond the scope of this research project as the budget and resources available for this research did not account for finger movement test kits such as the Purdue pegboard, finger dexterity test kit or tweezer dexterity test kit.\n\nUsing the TRIZ recommended solutions and shortlisted concepts, this study could be extended to the product design and proof-of-concept stages. It would be viable and of interest for researchers to prototype and test this concept, which uses DC motors to actuate wires for the flexible control of fingers.\n\n\nData availability\n\nFigshare: A TRIZ-driven conceptualisation of finger grip enhancer designs for the elderly. http://doi.org/10.6084/m9.figshare.14498649.125\n\nThis project contains the following underlying data:\n\n- Data Availability Sheet.pdf (descriptions of the literature and data sources used in CEC analysis).\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "Acknowledgements\n\nThis research article is in partial fulfilment of the requirements for the Master of Engineering Science degree at the Faculty of Engineering and Technology, Multimedia University (MMU), Malaysia. The researchers sincerely thank the faculty and university for their support in allowing this research to be carried out. The researchers also thank the Technology Transfer Office of MMU for granting the public disclosure approval for this paper. Special thanks go to Ms. Chiew Fen Ng for her constructive criticism of the manuscript.\n\n\nReferences\n\nWorld Health Organisation: Health statistics and information systems: Proposed working definition of an older person in africa for the mds project.2016 [1 May 2018]. Reference Source\n\nDuchateau J, Hainaut K: Effects of immobilization on contractile properties, recruitment and firing rates of human motor units. J Physiol. 1990 1990/03/01;422(1): 55–65. 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PubMed Abstract | Publisher Full Text\n\nWeinstock-Zlotnick G, Bear-Lehman J, Yu T-Y: A test case: Does the availability of visual feedback impact grip strength scores when using a digital dynamometer? J Hand Ther. 2011 2011/07/01/; 24(3): 266–276. PubMed Abstract | Publisher Full Text\n\nLin SY, Wu CT: Application of TRIZ inventive principles to innovate recycling machine. Adv Mech Engg. 2016 2016/05/01; 8(5): 1–8. Publisher Full Text\n\nDomb E: The 39 features of altshuller's contradiction matrix. TRIZ J. 1998; Reference Source\n\nTan DWH, Ng PK, Noor EEM: A TRIZ-based approach in investigating finger grip function degradation among elderlies. ARPN J Engg Appl Sci. 2019; 14(16): 2864–2873.\n\nZulkifli AN, Mazida A, Juliana A, et al.: Examining the influence of interactive persuasive learning among elderly. ARPN J Engg Appl Sciences. 2015; 10(3): 1145–1153.\n\nAzir RN, Zulisman M, Naim CP: Tackling design issues on elderly smartphone interface design using activity centered design approach. ARPN J Engg Appl Sci. 2014 08/08/2014; 9(8): 1190–1196.\n\nOscari F, Secoli R, Avanzini F, et al.: Substituting auditory for visual feedback to adapt to altered dynamic and kinematic environments during reaching. Exp Brain Res. 2012 2012/08/01; 221(1): 33–41. PubMed Abstract | Publisher Full Text\n\nPortnoy S, Halaby O, Dekel-Chen D, et al.: Effect of an auditory feedback substitution, tactilo-kinesthetic, or visual feedback on kinematics of pouring water from kettle into cup. Appl Ergon. 2015; 51(1): 44–49. PubMed Abstract | Publisher Full Text\n\nLevy-Tzedek S, Hanassy S, Abboud S, et al.: Fast, accurate reaching movements with a visual-to-auditory sensory substitution device. Restor Neurol Neurosci. 2012; 30(4): 313–323. PubMed Abstract | Publisher Full Text\n\nLi K, Wei N, Yue S: Effects of tactile sensitivity on structural variability of digit forces during stable precision grip. Biomed Res Int. 2016. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLi K, Wei N, Yue S: Effects of tactile sensitivity on fingertip center-of-pressure distribution during stable precision grip. 2016 9th International Congress on Image and Signal Processing. BioMed Engg Informatics (CISP-BMEI). 2016; 2016: 1696–1700. Publisher Full Text\n\nZhang W, Johnston JA, Ross MA, et al.: Effects of carpal tunnel syndrome on adaptation of multi-digit forces to object mass distribution for whole-hand manipulation. J Neuroeng Rehabil. 2012 Nov 21; 9(1): 83. PubMed Abstract | Publisher Full Text | Free Full Text\n\nIndiegogo OR: Indiegogo, Inc.2015 [cited 2019 31 March 2019]. Reference Source\n\nAbe T, Soma Y, Kitano N, et al.: Change in hand dexterity and habitual gait speed reflects cognitive decline over time in healthy older adults: A longitudinal study. J Phys Ther Sci. 2017; 29(10): 1737–1741. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKeenan KG, Massey WV: Control of fingertip forces in young and older adults pressing against fixed low- and high-friction surfaces. PLOS ONE. 2012; 7(10): e48193. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCole KJ, Rotella DL, Harper JG: Mechanisms for age-related changes of fingertip forces during precision gripping and lifting in adults. J Neurosci. 1999; 19(8): 3238–3247. Publisher Full Text\n\nBurnett RA, Laidlaw DH, Enoka RM: Coactivation of the antagonist muscle does not covary with steadiness in old adults. J Appl Physiol. 2000 2000/07/01; 89(1): 61–71. PubMed Abstract | Publisher Full Text\n\nEnoka RM, Christou EA, Hunter SK, et al.: Mechanisms that contribute to differences in motor performance between young and old adults. J Electromyogr Kinesiol. 2003 2003/02/01/; 13(1): 1–12. PubMed Abstract | Publisher Full Text\n\nKo Y-T, Lu C-C, Lee L-H: A contradiction-based approach for innovative product design. MATEC Web Conf. 2016; 68. Publisher Full Text\n\nAltshuller G: 40 principles: TRIZ keys to technical innovation. 3rd ed Worcester, MA: Technical Innovation Centre; 2002.\n\nKim Y, Kim W-S, Yoon B: The effect of stroke on motor selectivity for force control in single- and multi-finger force production tasks. NeuroRehabilitation. 2014; 34(3): 429–435. PubMed Abstract | Publisher Full Text\n\nLang CE, Schieber MH: Differential impairment of individuated finger movements in humans after damage to the motor cortex or the corticospinal tract. J Neurophysiol. 2003 2003/08/01; 90(2): 1160–1170. PubMed Abstract | Publisher Full Text\n\nSchieber MH, Lang CE, Reilly KT, et al.: Selective activation of human finger muscles after stroke or amputation. In: Sternad D, editor. Progress in motor control: A multidisciplinary perspective. Boston, MA: Springer US; 2009. p. 559–575.\n\nWolbrecht ET, Rowe JB, Chan V, et al.: Finger strength, individuation, and their interaction: Relationship to hand function and corticospinal tract injury after stroke. Clin Neurophysiol. 2018 2018/04/01/; 129(4): 797–808. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKilbreath SL, Gandevia SC: Limited independent flexion of the thumb and fingers in human subjects. J Physiol. 1994; 479(3): 487–497. PubMed Abstract | Publisher Full Text | Free Full Text\n\nLang CE, Schieber MH: Human finger independence: Limitations due to passive mechanical coupling versus active neuromuscular control. J Neurophysiol. 2004 Nov; 92(5): 2802–2810. PubMed Abstract | Publisher Full Text\n\nLatash ML, Scholz JF, Danion F, et al.: Structure of motor variability in marginally redundant multifinger force production tasks. Exp Brain Res. 2001 2001/11/01; 141(2): 153–165. PubMed Abstract | Publisher Full Text\n\nLatash ML, Scholz JF, Danion F, et al.: Finger coordination during discrete and oscillatory force production tasks. Exp Brain Res. 2002 2002/10/01; 146(4): 419–432. PubMed Abstract | Publisher Full Text\n\nFiatarone MA, Marks EC, Ryan ND, et al.: High-intensity strength training in nonagenarians: Effects on skeletal muscle. JAMA. 1990; 263(22): 3029–3034. PubMed Abstract\n\nMacKenzie CL, Iberall T: The grasping hand. Amsterdam, Netherlands: North-Holland/Elsevier Science Publishers; (The grasping hand.) 1994.\n\nEngel AKJ, Enders LR, Keenan KG, et al.: Grip surface friction affects maximum tip pinch force. The 34th Annual Meeting of the American Society of Biomechanics 2010. August 2010; 18-21: 9.\n\nHiramatsu Y, Kimura D, Kadota K, et al.: Control of precision grip force in lifting and holding of low-mass objects. PLOS ONE. 2015; 10(9): e0138506. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPugh S: Total design: Integrated methods for successful product engineering. Boston, MA: Addison-Wesley Publishing Company; (Engineering technology and design) 1991.\n\nKremer G, Tauhid S: Concept selection methods - a literature review from 1980 to 2008. Int J Design Engg. 2008 01/01; 1(3): 243–277. Publisher Full Text\n\nPahl G, Beitz W, Feldhusen J, et al.: Engineering design: A systematic approach. London, UK: Springer London; 2007. (Solid mechanics and its applications).\n\nRahim AA, Patar MNAA, Amin AM, et al.: The development of finger rehabilitation device for stroke patients. Appl Mech Materials. 2013 09/03; 393(1): 604–610. Publisher Full Text\n\nMohamaddan S, Osman MS: Development of grip mechanism assistant device for finger rehabilitation. London, England: Springer London. (Shirase K, Aoyagi S, editors. Service robotics and mechatronics) 2010.\n\nRahman MA, Al-Jumaily A: Design and development of a hand exoskeleton for rehabilitation following stroke. Procedia Engg. 2012 2012/01/01/; 41(1): 1028–1034. Publisher Full Text\n\nZaid A, Tee CC, Sukor JA, et al.: Development of hand exoskeleton for rehabilitation of post-stroke patient. AIP Conf Proceed. 2017; 1891(1): 020103. Publisher Full Text\n\nAndrews D, Nieuwenhuis P, Ewing PD: Living systems, ‘total design’ and the evolution of the automobile: The significance and application of holistic design methods in automotive design, manufacture and operation. WIT Transactions on State-of-the-art in Science and Engineering. 2006; 27(1): 381–446. Publisher Full Text\n\nKarl TU, Steven DE: Product design and development 5ed. New York: McGraw-Hill Irwin. (Product design and development) 2012.\n\nMo JPT, Bil C, Sinha A: Systems design. Engineering systems acquisition and support.Cambridge, England: Woodhead Publishing; 2015. p. 51–73. Publisher Full Text\n\nBlair CL: US Patent No 6,732,374.2004Washington DC: U.S. Patent and Trademark Office.\n\nStarr G: US Patent No 8,146,968.2012Washington, DC: U.S. Patent and Trademark Office.\n\nLiu Y, Nelson RJ: US Patent No 9,326,909.2016Washington, DC: U.S. Patent and Trademark Office\n\nKamper D, Triandafilou K, Ochoa J: US Patent No 10,478,370.2019Washington, DC: U.S. Patent and Trademark Office.\n\nGu X: US Patent No 10,423,227.2019Washington, DC: U.S. Patent and Trademark Office.\n\nLahoti S, Mathew K, Miner G: Predictive process control: Qc-data mining using statistica data miner and qc-miner. In: Nisbet R, Elder J, Miner G, editors. Handbook of statistical analysis and data mining applications. Boston, MA: Academic Press; 2009. p. 513–530.\n\nDehghan-Manshadi B, Mahmudi H, Abedian A, et al.: A novel method for materials selection in mechanical design: Combination of non-linear normalization and a modified digital logic method. Materials Design. 2007 2007/01/01/; 28(1): 8–15. Publisher Full Text\n\nFarag MM: Quantitative methods of materials selection. In: Kutz M, editor. Handbook of materials selection. . p. 1–24. Publisher Full Text\n\nEhrlenspiel K, Kiewert A, Lindemann U: Cost-efficient design. Heidelberg, Germany: Springer Berlin Heidelberg; 2007.\n\nTan DWHow, Ng PK, Noor EEM: A TRIZ-driven conceptualisation of finger grip enhancer designs for the elderly. figshare. Dataset. 2021. Publisher Full Text"
}
|
[
{
"id": "86104",
"date": "02 Jun 2021",
"name": "Adi Saptari",
"expertise": [
"Reviewer Expertise Optimization of linear and Non Linear Operations Research and human factors engineering"
],
"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 has fulfilled certain criteria that make it a good research article, such as purpose, rigor, objectivity and replicability. The authors have shown comprehensive steps when applying the TRIZ method to come out with a reliable, conceptual design of a grip enhancer. One particular comment about what needs to be improved is on the screening of 5 different concepts. A set of general criteria were used, and modified. However, it was not explained in detail how the selection process was done, such as who are the evaluators and on what capacity. Furthermore, criteria F mentioned in the text was not clear, who is PKN? This step is key and significant for the next process of selection of the right concept chosen.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "6748",
"date": "02 Jun 2021",
"name": "Poh Kiat Ng",
"role": "Author Response",
"response": "Many thanks to the reviewer for his constructive comments. Comment 1: “It was not explained in detail how the selection process was done, such as who are the evaluators and on what capacity”. Response to Comment 1: The ratings were solely proposed by the main author based on his specific experience and knowledge of various hand and finger assistive devices. This reasoning has been clarified in the last paragraph just before the conclusion. Comment 2: “Who is PKN?”. Response to Comment 2: PKN is actually the second author of the article and the main supervisor of the main author. He is mentioned in section 4.2 as “the author PKN as an advisor”, which is reflective of the original criterion F “designer’s company supervisor”. As such, no changes were made to the current article. But the authors appreciate the reviewer comments very much. Thank you."
}
]
},
{
"id": "85521",
"date": "04 Jun 2021",
"name": "Leonid Chechurin",
"expertise": [
"Reviewer Expertise Control and Oscillation theory",
"System modelling",
"optimization",
"Heuristic methods in design."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe topic of the paper is important. Society is ageing and the more we help the elderly to be active members of the community and, more importantly, self-supportive, the more resources we have. I would also notice that the problem of finger grip enhancement is very important for children/people with special needs suffering from multiple sclerosis or CRH paralysis.\nThe paper presents a story of enhancer design from the analysis of situation to the selection of the best to the criteria design. TRIZ, Root cause analysis, literature analysis and landscaping, functional analysis and decomposition and concept scoring matrix are used as design tools.\n\nThe paper has clear value from engineering point of view as it brings a story, develops a design case study and presents several concepts of finger grip enhancer. They can be used (and I have to say I already recommended the paper to several designers) by practicing engineers, physiotherapists and Do-It-Yourself enthusiasts who want to improve the life of people around them.\n\nThe paper has questionable scientific value, as it does not provide proofs that:\n\nThese designs are actually helping, solving the problem or they are better in any way that any existing enhancers.\n\nThe results are reproducible, the method of design is reliable.\nIn other words, it is very good that that paper presents an invention, a way of doing things, but the paper does not prove that this way of doing things is better than others. Would other design technics result in better designs? Would other engineers (not the authors) come to the same design if they use the same tools? These questions sound academic but that is why research papers are different to other texts.\nMaybe it would be good idea to change the title of the paper telling that it reports a Design Case Study, it reduces the scientific expectations of the reader.\nOther comments:\n\nAbstract and page 3. Authors state that there is no study yet that applies TRIZ methodology to pinch function degradation. However, there are two publications by the same group of authors on this topic dated 2019 and 2021. Please, indicate what is different in the presented paper.\n\nPage 5. When a theory or a method is first introduced in a paper it is better to cite the founder of the theory. So, I believe it is fair to cite the first paper of Altshuller and Shapiro here, not a modern textbook (it can be recommended to the readers if the authors believe it is worth to).\n\nPage 7. When authors first time introduce Genrich Altshuller it is better to cite the original work, not a modern study with TRIZ application in mechanics.\n\n“suitable for new product innovation”. I would argue that TRIZ is the tool for invention, not for innovation. Innovation is different process of different scale.\n\nThe authors used RCA for the analysis of initial situation, that is legitimate tool of cause. In modern TRIZ it is recommend providing the analysis of the situation with RCA (or better CECA) and with Function modelling. Function model makes a model of what is happening, a snapshot. While CECA often reveals cause + effect chains, that means we dive into the history.\n\nFigure 1 will be more informative if it is presented in input-output way. With current design and content, it doesn't give a visual explanation of the workflow.\n\nPage 5-6. I would anxiously say that what the authors use in their analysis is NOT cause-effect-chain-analysis of TRIZ, it is Root Cause Analysis, that was introduced by General Electric and by Lean/Taguchi (fishbone diagram). But, they all do the same job. The difference is that CECA uses operators OR and AND in the chains, that is really insightful sometimes. And CECA uses the term “Key disadvantage”, not “Root disadvantage” and have a reason for calling them so. I would recommend to the authors to go through original papers on CECA of Val Souchkov (Example Souchkov et al. (20051)) or recent papers by Min Gyu Lee (S.Korea) (Example Lee et al. (20182)).\n\nFigure 2. It is not exactly how contradictions are treated in classical TRIZ. Altshuller recommends resolving engineering contradiction with Contradiction matrix and those 40 inventing principles. But - he says - if we analyze the engineering contradictions deeper, we end up with physical contradictions, that are sharper (as they require THE SAME component of parameter to have opposite properties). Having formulated physical contradictions, we apply SEPARATION PRINCIPLES (one of 11 in classical TRIZ), not again 40 inventive principles. It is recommended to either reformulate the applied principles as separation (in time, in space, …) or at least give a comment on it.\n\nPage 16. It is interesting that the authors use Function Decomposition as product development tool. I would anxiously suggest that this approach, when a system is considered as a transformation unit for various flows (of energy, information, materials…) has the roots in NIST standards for functional basis in engineering design. Plz see and if you agree cite this document https://www.nist.gov/publications/functional-basis-engineering-design-reconciling-and-evolving-previous-efforts.\n\nIt has already mentioned above (as well as by another reviewer) that the choice of the best concept seems to be subjective, it is based on author’s experience and preferences. It would have been much more reliable to collect as many as possible evaluations of the design(s) by other engineers, for example in a form of a survey.\n\nAuthors reference medical literature that tend to update fast. However, over 50% of references are more than 5 years old.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
},
{
"id": "87151",
"date": "19 Jul 2021",
"name": "Shamsul Bahri Md Tamrin",
"expertise": [
"Reviewer Expertise Physical ergonomics",
"Industrial Hygiene and occupational 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\nAbstract:\n\nThe conclusion should be focusing on the finding and suggestions of the case study\n\nIntroduction:\nCan you include pictures of several different types of pinching that can be performed?\n\nIn the problem statement, you did mention several studies on problem-solving related to pinching issues among the elderly, therefore can you mentioned the outcome and issues on some of the studies conducted and their solution previously?\n\nLiterature review:\nPlease double-check regarding carpal tunnel since carpal tunnel has a different etiology. Your study focused more on age-related than work-related.\n\nSubchapter on Factors contributing is not focused on what are the factors that lead to reduced pinch ability but more on the effect of age and reduction of systemic motor reduction. I advise revising with literature on factors or change the subtitle for this chapter.\n\nSubchapter 2.4 – do you have any pictures of some basic exoskeleton.\n\nMethodology:\n3.1.1 CEC Analysis – can you suggest the reference in developing CEC as suggested in Figure 3.\n\nFigure 3 – does the color-coding have a different interpretation. Although described on the next page, in the figure legend, the figure should stand and be clearly understood.\n\nIn Figure 3, how do you verify the CEC? Each variable is cited through references or based on the opinion of the subject matter expert?\n\nTable 1 – you had listed the source of examples in numbers. I suggest listing the name and numbers in easing the reading for readers.\n\nIn 3.1.2 – the 40 generalized recommendation is a default recommendation, or you had pre-selected or based on the 40,000 patents?\n\nIn an earlier study by (77)..I suggest changing, in the earlier study by Tan (77), so that the sentence is having much clarity.\n\nThe root cause of contradiction 2 as you had mentioned is similar to the previous study, please mentioned which one that the root cause is similar to? And does it have the same inventive principles and system parameters?\n\nTable 2 – I really don’t understand the mechanism and the method from the principle of engineering contradiction leading to how to do you select system parameters and inventive principle.\n\nTable 2 – why the certain principle is bold? Is it automatically selected by TRIZ or manually selected by the author?\n\n3.1.2.1 – physical contradiction, the table below should be Table 4 under physical contradiction for each root cause?\n\n3.1.2.1 – physical contradiction, how do you categorize for list of segmentation, the other way around, and asymmetry?\n\nFigure 10 – suggested sub-class 2.1.1 and 2.1.2 – what part of this sub-class? I did not find which one.\n\nProduct development:\nThere are several methods in design development, - which one from the study that you had emulate?\n\nFor Table 3 – maybe you should explain the calculation of the total rank score. How the score was made and what is the significant calculation of the score. Patent search – how do you come out with the right keywords for the patent search?\n\nConcept scoring – in Table 8, the number of decisions – I need to understand where you have 10 observations. Please explain whether the decision was done by a single evaluator repeatedly or 10 different evaluators?\n\nTable 10 – can you show an illustration of each concept? If not maybe only focus on concept 2 which had been selected.\n\nConclusion:\nFrom the conclusion, do you mean concept 2?\n\nHow effective is the use of TRIZ method? And overall this study is a combination with TRIZ and the overall process of engineering in product development and not solely on TRIZ.\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? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-392
|
https://f1000research.com/articles/10-391/v1
|
17 May 21
|
{
"type": "Research Article",
"title": "Evidence of misuse of nonparametric tests in the presence of heteroscedasticity within obesity research",
"authors": [
"Cynthia M Kroeger",
"Bridget A Hannon",
"Tanya M Halliday",
"Keisuke Ejima",
"Margarita Teran-Garcia",
"Andrew W Brown",
"Bridget A Hannon",
"Tanya M Halliday",
"Keisuke Ejima",
"Margarita Teran-Garcia"
],
"abstract": "Background: Classic nonparametric tests (cNPTs), like Kruskal–Wallis or Mann–Whitney U, are sometimes used to detect differences in central tendency (i.e., means or medians). However, when the tests’ assumptions are violated, such as in the presence of unequal variance and other forms of heteroscedasticity, they are no longer valid for testing differences in central tendency. Yet, sometimes researchers erroneously use cNPTs to account for heteroscedasticity. Objective: To document the appropriateness of cNPT use in obesity literature, characterize studies that use cNPTs, and evaluate the citation and public sharing patterns of these articles. Methods: We reviewed obesity studies published in 2017 to determine whether the authors used cNPTs: (1) to correct for heteroscedasticity (invalid); (2) when heteroscedasticity was clearly not present (correct); or (3) when it was unclear whether heteroscedasticity was present (unclear). Open science R packages were used to transparently search literature and extract data on how often papers with errors have been cited in academic literature, read in Mendeley, and disseminated in the media. Results: We identified nine studies that used a cNPT in the presence of heteroscedasticity (some because of the mistaken rationale that the test corrected for heteroscedasticity), 25 articles that did not explicitly state whether heteroscedasticity was present when a cNPT was used, and only four articles that appropriately reported that heteroscedasticity was not present when a cNPT was used. Errors were found in observational and interventional studies, in human and rodent studies, and only when studies were unregistered. Studies with errors have been cited 113 times, read in Mendeley 123 times, and disseminated in the media 41 times, by the public, scientists, science communicators, and doctors. Conclusions: Examples of inappropriate use of cNPTs exist in the obesity literature, and those articles perpetuate the errors via various audiences and dissemination platforms.",
"keywords": [
"Nonparametric tests",
"heteroscedasticity",
"research rigor",
"statistical methods",
"open science",
"nutrition",
"obesity"
],
"content": "Introduction\n\nConcerns have been raised as to whether scientific research generally1–3 and nutrition and obesity research specifically4–6 meet modern standards of research rigor and quality. Various suggestions for improvement in conceptualization, design, or analysis, have been published by the National Institutes of Health, National Academies of Sciences, Engineering, and Medicine, and within nutrition and obesity disciplines.7–10 One domain that requires attention is using statistical procedures in ways that foster valid inferences. Indeed, it is not uncommon in nutrition and obesity research for inappropriate statistical models and procedures to be chosen and implemented,4,11,12 which can erode the quality of the science and trust in the field.13\n\nWe previously reported on the consequences of one area of statistical error: erroneously using classic nonparametric tests (cNPTs) to test for differences in central tendency (i.e., means or medians) when heteroscedasticity is present.14 Heteroscedasticity is a difference in statistical dispersion (e.g., variance, as used here) among groups. Therein, we defined cNPTs as “tests that do not rely on any assumptions about the data having a particular distribution, other than having a finite mean and a finite variance.” Such methods include Kruskal–Wallis, Wilcoxon signed-rank, and Mann–Whitney U-tests, and exclude methods that do not involve explicit resampling (e.g., bootstrap). We refer readers to our previous paper to learn more about further intricacies on cNPTs, the misconceptions of using nonparametric tests in the presence of heteroscedasticity, why this error can be of particular concern to nutrition and obesity research, and some guidance on how to avoid some errors.14\n\nThe objective of the present study was to determine whether misuse of cNPTs in the presence of heteroscedasticity exists in the obesity literature. Specifically, we sought to identify publications where heteroscedasticity was used as a justification for choosing a cNPT. We also aimed to describe the characteristics of included studies, such as design and model type, open science practices adopted by included studies, and the extent to which the studies have been disseminated since publication, in order to understand the context in which this error occurred and its dissemination impact.\n\n\nMethods\n\nA pilot search was conducted in Google Scholar (Google LLC) using combinations and permutations of the terms “nonparametric,” “bootstrapping,” “obesity,” “overweight,” and “adiposity”. Herein, we use the word ‘term’ to mean words and phrases (that is, in contrast to a statistical ‘term’ in a model). This search provided evidence of the use of cNPTs in the presence of heteroscedasticity and helped to inform our search terms for this study. We searched the literature for studies 1) reporting obesity outcomes, 2) mentioning use of nonparametric tests, 3) acknowledging the presence or potential for unequal variances, and 4) published in 2017. Our use of the year 2017 coincided with preparing these materials for our tutorial article14 and allows for the follow up period of three years for the assessment of dissemination impact. The citation and dissemination impacts of those articles are current as of December 9, 2020 (see Screening and Data Extraction). Search terms were expanded based on input from J.J. Pionke, a librarian at the University of Illinois at Urbana-Champaign. The PubMed Central platform was used because it allows for full-text searches. Nutrition and obesity outcome search terms were limited to abstracts, whereas the article body was also searched for heteroscedasticity and nonparametric terms. Because heteroscedasticity and nonparametric terms are key inclusion criteria and are often not included in abstracts, this methodological choice was key to improve the feasibility of this study, considering the large number of nutrition and obesity papers published each year. To make our search reproducible, we used the Open Science R package rEntrez (SCR_021062)15 to conduct our search within PubMed Central. The full search strategy can be found in the study repository.16\n\nFull texts were obtained and assessed for eligibility and data extraction. Articles were considered eligible if they contained an obesity outcome, a heteroscedasticity term (e.g., heterogeneous variances, unequal variances, or homogeneity of variance), and a nonparametric term (e.g., Kruskal–Wallis, rank-sum test, or Wilcox test), and were published in 2017. An obesity outcome was defined as a body composition outcome within a study that aimed to address the problem of overweight or obesity. Heteroscedasticity and nonparametric terms were defined by those used for the literature search, which can be found in the study repository.16 Articles were independently screened, and the data independently extracted by two investigators (CMK and either BAH or TMH). Discrepancies were resolved by consensus among CMK, BAH, and TMH.\n\nThe following data were manually extracted from each eligible article: study design (intervention or observational), subject type (human, rodent, or other), type of cNPT used, reason for use of heteroscedasticity terms, and whether findings obtained from the cNPT were statistically significant. The reason the authors referenced a heteroscedasticity term was categorized according to Table 1.\n\nTo determine whether improper use of a cNPT was potentially avoided and to gain insight on the prevalence of responsible research practices that help to improve the transparency of data analysis, we also extracted the following information from each included article: whether a study was registered in a study registry (e.g., clinicaltrials.gov), whether a study was preregistered (i.e., before the start of data collection), whether statistical analysis plans and outcomes were prespecified, and whether the study data or analysis code were described as “publicly available”, “available upon request,” or not.\n\nOpen Science R packages were used to automatically extract data on the relative impact of articles containing errors and ambiguity since their publication in 2017 to December 9, 2020. For instance, rAltmetric17 was used to extract the articles’ overall Altmetric Attention Score (Altmetric LLP), their total number of mentions (e.g., in news outlets, social media, blogs), and the cohorts giving the articles attention (e.g., members of the public, doctors, scientists, and science communicators). The Altmetric Attention Score is made up of weighted approximations for volume (total number of original mentions), sources (e.g., mentions in newspaper articles weigh more than blog posts, which weigh more than tweets), and authors (e.g., articles shared by doctors to other doctors weigh more than automatic posts from an academic journal account). The package rCrossref17 was used to extract the number of times articles were cited in academic literature. The package rEntrez was used to automatically extract publication date to determine the number of days since publication. The full code for the implemented search strategy, automatic data extraction, included studies, manually obtained data, and associated figure generation can be found at our study repository.16\n\nGiven the descriptive nature of this study and having not conducted any formal a priori power calculations nor establishing any a priori hypotheses, results are presented as counts, frequencies, and other summaries, sometimes stratified by cNPT appropriateness or study characteristics. No formal between-group comparisons or statistical inferences are calculated herein.\n\n\nResults\n\nFigure 1 depicts the flow diagram of included studies, with 38 ultimately being included. Inclusion of heteroscedasticity and nonparametric terms were not considered if the study did not contain a nutrition obesity outcome or heteroscedasticity term, respectively. Figure 2 shows the proportion of included studies that used cNPTs in clear error,9 ambiguously (25), or correctly.4\n\nError, used a nonparametric test and explicitly stated that the test was used in the presence of heteroscedasticity or to correct for heteroscedasticity; No Link, used at least one nonparametric test but made no explicit statement of whether heteroscedasticity was tested for or present; Ambiguous, used a nonparametric test and stated that variance assumptions were tested for, but did not explicitly state whether heteroscedasticity was present; Correct, used a nonparametric test and explicitly stated that heteroscedasticity was not present.\n\nA breakdown of study characteristics by appropriateness of cNPT use is depicted in Figure 3. Study designs consisted of interventional (n = 14) or observational (n = 24), and model types of rodents (n = 10) and human participants (n = 28). P-values obtained from the cNPT were statistically significant in n=18 studies, statistically insignificant in n = 2 studies, or a mix of statistical significance depending on the outcome (n = 18). The prevalence of responsible research practices among studies by appropriateness of cNPT use can be viewed in Figure 4. Clear errors were only found in studies that were not registered. Only two studies were preregistered, and no studies preregistered a statistical analysis plan. Raw data were indicated as available for seven studies, including one study with a clear error. Analysis code was only listed as available for two studies but for none of the studies with clear errors.\n\n*Nonparametric Tests: Description of the test used was only “non-parametric tests.” Observed statistical significance: Number of articles that report results obtained from a nonparametric test as statistically significant (significant), mixed (mixed significance), or not significant. Correct, used a nonparametric test and explicitly stated that heteroscedasticity was not present; Ambiguous, used a nonparametric test and stated that variance assumptions were tested for but did not explicitly state whether heteroscedasticity was present; No Link, used at least one nonparametric test, but made no explicit statement of whether heteroscedasticity was tested for or present; Error, used a nonparametric test and explicitly stated that the test was used in the presence of heteroscedasticity or to correct for heteroscedasticity.\n\nCorrect, used a nonparametric test and explicitly stated that heteroscedasticity was not present; Ambiguous, used a nonparametric test and stated that variance assumptions were tested for but did not explicitly state whether heteroscedasticity was present; No Link, used at least one nonparametric test, but made no explicit statement of whether heteroscedasticity was tested for or present; Error, used a nonparametric test and explicitly stated that the test was used in the presence of heteroscedasticity or to correct for heteroscedasticity. For Raw Data Available, “No” means the authors stated the data are not available, the paper had no data availability statement, or the data availability statement was left blank.\n\nAs of December 9, 2020, the included studies had been cited a total of 531 times across all studies after an average of 1268 days since publication. A total of 323 of these citations were of articles containing ambiguities as to whether heteroscedasticity was present when a cNPT was used, 113 citations were of articles that erroneously used a cNPT to correct for heteroscedasticity or in the known presence of heteroscedasticity, and 95 citations were from articles that transparently reported correct use of nonparametric tests. Altmetrics were available for 28 studies, which had been read and mentioned 1578 and 564 times, respectively, and have received a net Altmetric Attention Score of 634. The cohorts that have been documented engaged in dissemination are the public (n = 225), scientists (n = 62), science communicators (n = 16), and medical doctors (n = 79). Dissemination data are depicted in Figure 5, where they are grouped by appropriateness of cNPT use. Papers with clear errors have been cited in peer-reviewed journals 113 times, read in Mendeley 123 times, obtained an Altmetric Attention Score of 131.8, and shared on the internet by the public (n = 11), science communicators (n = 4), doctors (n = 2), and research scientists (n = 6).\n\nTotal number of journal citations, reads on Mendeley reference library (Mendeley Ltd), internet posts, and total Altmetric Attention Score (Altmetric LLP) by appropriateness of nonparametric test use. Sample size of included articles with dissemination data: Error: n = 4; No Link: n = 11; Ambiguous: n = 9; Correct: n = 4. Citation counts were available for all included studies. B. Total number of internet posts (e.g., news, blogs, Twitter, Wikipedia, LinkedIn, Facebook) by cohort and appropriateness of nonparametric test use. Sample size of included articles with dissemination data: Error: n = 4; No Link: n = 11; Ambiguous: n = 8; Correct: n = 4. Correct, used a nonparametric test and explicitly stated that heteroscedasticity was not present; Ambiguous, used a nonparametric test and stated that variance assumptions were tested for but did not explicitly state whether heteroscedasticity was present; No Link, used at least one nonparametric test, but made no explicit statement of whether heteroscedasticity was tested for or present; Error, used a nonparametric test and explicitly stated that the test was used in the presence of heteroscedasticity or to correct for heteroscedasticity.\n\n\nDiscussion\n\nExamples of improper use of cNPTs in nutrition and obesity research were easy to find among articles indexed in PubMed Central in 2017. A common reason for use of cNPTs in statistical analysis was the presence of heteroscedasticity, because assumptions of equal variances were not met. Over half of the included studies also did not clearly state the rationale for use of cNPTs with respect to heteroscedasticity or that heteroscedasticity was not present when a cNPT was used. These studies 1) did not link the rationale for using a cNPT with the use of the heteroscedasticity term, 2) reported that variance assumptions were tested for or met but did not specify for which outcomes or for all cases a cNPT was used, or 3) reported that variance assumptions were tested for or met but did not explicitly state that heteroscedasticity was not present. This lack of transparency in reporting creates ambiguity when interpreting such results, as the reader cannot determine whether a cNPT was used appropriately. The use of inappropriate tests may also lead researchers to draw the wrong conclusion, further muddying the scientific record and increasing mistrust. Without clear explanation of statistical methodology and results, these findings cannot be readily reproduced. Further, because some authors clearly and erroneously used a cNPT with heteroscedasticity, concern is raised as to whether similar misunderstandings are present in cases where reporting is vague, which in our sample occurred in two-thirds of cases. Responsible research practices, such as preregistering statistical analysis plans or clarifying whether data and analysis code are publicly available or available upon request, were not prevalent. Such practices are tools that can help improve replication of statistical findings and make details of the statistical methods more transparent.\n\nDespite containing misused and unclearly used statistical methods, many of the included articles are being cited within both scientific and lay communities. Dissemination of research with improper statistical methods may reinforce the misuse of cNPTs in the presence of heteroscedasticity within the scientific community. If misused or unclearly used cNPTs led to invalid conclusions, both the lay and scientific communities and those they share with can become misinformed of the magnitude or statistical significance of such results.\n\nIn some cases, authors explicitly used cNPTs to erroneously attempt to address deviations from homoscedasticity. The use of cNPTs in the presence of unequal variances among experimental groups, especially if sample sizes are imbalanced, will result in an increased type I (false-positive) error rate, as shown using simulations in our previous work.14 These improper statistical methods can lead to incorrect conclusions and dissemination of misleading findings.\n\nStrengths of our approach include the transparent and reproducible research process. Conducting the literature search programmatically and sharing the code in a study repository allows the possibility of exact replication, as well as clarity around how the search was done. Further, extracting citation counts, date published, and Altmetric data programmatically may help improve the speed of data acquisition while minimizing extraction error that comes with independently manually extracting data.18 Our study repository16 transparently describes the research process for this project. Dissemination data were extracted for a conference presentation in 2018,19 simulations on why this error is a problem statistically were published in 2020,20 and dissemination data were updated for submission of this manuscript and data for peer review publication. The repository explains the differences and reasons for each publication, shows how the dissemination data have changed over time, and foster transparency and reproducibility of each step of the project process. In addition, the use of papers in 2017 is relatively recent to investigate the field’s use of such tests, while also allowing enough lag-time to observe accumulation of dissemination trends.\n\nLimitations of our approach include that we do not know whether our findings are representative of all nutrition and obesity papers, even those published in 2017, but only to those that met our inclusion criteria in PubMed Central. Limiting our review to PubMed Central allowed us to use the R packages “rentrez” and “fulltext” to programmatically search full texts of articles for key inclusion criteria, but excludes studies not indexed in PubMed Central and thus may not be representative. Future work might expand these methods to other databases by using packages to download full texts and text mine them. Furthermore, our approach used terms for heteroscedasticity, nonparametric tests, nutrition, and obesity from a preliminary search of the literature, but may not capture all search terms, and thus may have resulted in some relevant literature being excluded from our review. Consistent with these limitations, we do not present our numbers as evidence of the prevalence of the problem within the literature, but rather as a systematically obtained case series to illustrate issues with cNPT reporting and use within the literature.\n\n\nConclusion\n\nThe use of cNPTs in the presence of heteroscedasticity was present among nutrition and obesity articles indexed in PubMed Central and published in 2017. In some cases, the cNPT was erroneously used to correct for heteroscedasticity, while many of the statistical methods and results sections of the included articles were ambiguous. Better reporting and appropriate use of cNPTs is needed in nutrition and obesity literature.",
"appendix": "Acknowledgments\n\nWe would like to thank J.J. Pionke (University of Illinois) for his insight on development of the search strategy. We also would like to thank David B. Allison, John A. Dawson, David B. King, and Bryan McComb for their helpful feedback on earlier drafts of materials presented herein as part of our tutorial paper on cNPT. 14\n\n\nData availability\n\nZenodo: Underlying data for ‘Evidence of misuse of nonparametric tests in the presence of heteroscedasticity within obesity research’. https://doi.org/10.5281/zenodo.4733330. 16\n\nThis project contains the following underlying data:\n\nRaw data\n\nCode book\n\nAnalytical code\n\nData are available under the terms of the Creative Commons Attribution-ShareAlike 4.0 International license (CC BY-SA 4.0).\n\n\nReferences\n\nMunafò MR, Nosek BA, Bishop DVM, et al.: A manifesto for reproducible science. Nat Hum Behav. 2017; 1: 0021. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHsieh T, Vaickus MH, Remick DG: Enhancing Scientific Foundations to Ensure Reproducibility. A New Paradigm. Am J Pathol. 2018; 188(1): 6–10. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAllison DB, Brown AW, George BJ, et al.: Reproducibility: A tragedy of errors. Nature. 2016; 530(7588): 27. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGeorge BJ, Beasley TM, Brown AW, et al.: Common scientific and statistical errors in obesity research. Obesity (Silver Spring). 2016; 24(4): 781–90. PubMed Abstract | Publisher Full Text | Free Full Text\n\nByrne JL, Yee T, O'Connor K, et al.: Registration status and methodological reporting of randomized controlled trials in obesity research: A review. Obesity (Silver Spring). 2017; 25(4): 665–70. PubMed Abstract | Publisher Full Text\n\nBrown AW, Ioannidis JP, Cope MB, et al.: Unscientific Beliefs about Scientific Topics in Nutrition. Oxford University Press; 2014.\n\nBrown AW, Kaiser KA, Allison DB: Issues with data and analyses: Errors, underlying themes, and potential solutions. Proc Natl Acad Sci U S A. 2018; 115(11): 2563–70. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWood AC, Wren JD, Allison DB: The Need for Greater Rigor in Childhood Nutrition and Obesity Research. JAMA Pediatr. 2019; PubMed Abstract | Publisher Full Text\n\nNational Institutes of Health: Implementing Rigor and Transparency in NIH & AHRQ Research Grant Applications.2015.\n\nNational Academies of Sciences, Engineering, and Medicine: Reproducibility and Replicability in Science. Washington, DC: The National Academies Press; 2019.\n\nGeorge BJ, Brown AW, Allison DB: Errors in statistical analysis and questionable randomization lead to unreliable conclusions. J Paramed Sci. 2015; 6(3): 153–4. PubMed Abstract | Free Full Text\n\nMehta T, Allison DB: From Measurement to Analysis Reporting: Grand Challenges in Nutritional Methodology. Front Nutr. 2014; 1(6). PubMed Abstract | Publisher Full Text | Free Full Text\n\nKroeger CM, Garza C, Lynch CJ, et al.: Scientific rigor and credibility in the nutrition research landscape. Am J Clin Nutr. 2018; 107(3): 484–94. PubMed Abstract | Publisher Full Text | Free Full Text\n\nKroeger CM, Ejima K, Hannon BA, et al.: Persistent confusion in nutrition and obesity research about the validity of classic nonparametric tests in the presence of heteroscedasticity: evidence of the problem and valid alternatives. Am J Clin Nutr. 2021. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWinter D: rentrez: Entrez in R. R package version 1.1.0 ed, 2017:RRID: SCR_021062.\n\nKroeger CM: Data and analysis code for manuscript: Evidence of misuse of nonparametric tests in the presence of heteroscedasticity within obesity research. Zenodo. 2021. Publisher Full Text\n\nChamberlain S, Boettiger C, Hart T, et al.: Client for various ‘CrossRef’ ‘APIs’. R package version 0.7.0 ed. 2017.\n\nBuscemi N, Hartling L, Vandermeer B, et al.: Single data extraction generated more errors than double data extraction in systematic reviews. J Clin Epidemiol. 2006; 59(7): 697–703. PubMed Abstract | Publisher Full Text\n\nKroeger CM: Data and analysis code for published abstract: Misuse of nonparametric tests with heteroscedasticity: A semi-automated review of obesity research. Zenodo. 2018. Publisher Full Text\n\nKroeger CM, Ejima K: Data and analysis code for manuscript: Persistent confusion in nutrition and obesity research about the validity of classic nonparametric tests in the presence of heteroscedasticity: Evidence of the problem and valid alternatives. Zenodo. 2019. Publisher Full Text"
}
|
[
{
"id": "99209",
"date": "10 Nov 2021",
"name": "Joscha Krause",
"expertise": [
"Reviewer Expertise Statistics",
"data science",
"Monte Carlo simulations"
],
"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\nShort summary: The presented paper provides a literature review on the use of nonparametric tests for the detection of central tendency differences in grouped obesity research data. In particular, the authors investigate how often corresponding tests have been applied in the presence of heteroscedasticity. Since many common tests (e.g., Kruskal-Wallis, Mann-Whitney-U) assume variance homogeneity between groups, their application in such circumstances can lead to false conclusions. To evaluate how common such misuse is in the literature, the authors review articles published in 2017. They evaluate whether the nonparametric tests were applied correctly, incorrectly, or whether it cannot be determined.\nComments:\nBeing a statistician, I can only comment on the statistical aspects of the presented paper.\n\nThe paper is compact and well-written. It is well-known that a significant number of empirical studies in this field suffer from inaccuracies due to a lack in statistical rigor. Accordingly, a quantitative evaluation providing evidence on this problem is a welcome contribution.\n\nThe authors give a transparent description on how they searched for relevant papers, and how they categorized the studies. They further provided the necessary programming code for reproduction. The presentation of the results is clear and expedient. The authors point out that their study is purely descriptive and does not provide any statistical inference. Against this background, there is not much room for methodological points of critique. Within this scope, the study is well done.\n\nMaybe the authors would like to consider the subsequent minor points as a proposal for some additions to the manuscript.\n\nFor readers from statistics, it would have been interesting to see how exactly a violation of the homogeneity assumption affects the test outcomes. An increase in type-1-errors is mentioned. However, is this due to the asymptotic distributions of the test statistics being invalid, are the tests biased, do they lose testing power? I understand that this paper is a ‘follow-up’ to a previous technical study on this matter by the authors. Nevertheless, maybe they can add a few more words on that aspect.\n\nAnother interesting point would have been to see how often the false application of the tests in the literature has actually led to seriously wrong conclusions. However, even without that aspect, the presented paper makes a convincing case for addressing this important issue.\n\nRecommendation:\nI have no serious concerns from a statistical perspective and, thus, approve the indexing of the paper.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": []
},
{
"id": "120824",
"date": "26 Jan 2022",
"name": "Rand R Wilcox",
"expertise": [
"Reviewer Expertise Robust statistical 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\nYes, these classic methods are indeed inappropriate for dealing with measures of central tendency under general conditions. This has been known in the statistics. literature for many years. This paper underscores the fact that these insights remain unknown by many researchers. Generally, there is a serious gap between advances relevant to basic techniques and how the typical researcher is trained. Hopefully this paper will help motivate others to deal with this problem.\nThere is a vast literature dealing with robust methods for making inferences about measures of central tendency (Wilcox (20221)). They deal with heteroscedasticity as well as concerns about non-normality. It might help readers if this is pointed out.\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": []
}
] | 1
|
https://f1000research.com/articles/10-391
|
https://f1000research.com/articles/10-389/v1
|
17 May 21
|
{
"type": "Research Article",
"title": "Prevalence of comorbidities associated with type 2 diabetes in patients attending a disease management program, Medellín, Colombia 2014 - 2019: a descriptive study.",
"authors": [
"Uriel Palacios-Barahona",
"Jaime Ordoñez Molina",
"Nelson Alvis Guzmán",
"José Fernando Botero Arango",
"Jaime Ordoñez Molina",
"Nelson Alvis Guzmán",
"José Fernando Botero Arango"
],
"abstract": "Background: Type 2 diabetes is a significant cause of morbidity and mortality worldwide. The prevalence has increased due to population aging, obesity, and longer life expectancy. Likewise, the development of complications related to the disease has contributed to a more significant disease burden and is the leading cause of death in people with diabetes. Methods: A descriptive study of patients in a disease management program in Medellín, Colombia, from June 10, 2014 to March 30, 2019 was carried out. Sociodemographic and clinical data were collected from clinical records. Descriptive analysis was performed using absolute and relative frequencies and the prevalences presented by sex. The Chi-square test was used to calculate the prevalence ratio with a 95 % confidence interval, with a p-value < 0.05 being considered statistically significant. Results: There were 1,018 patients with type 2 diabetes analyzed. The mean age was 66.0 years (SD: 12.93), the mean duration with diabetes was 12.9 years (SD:9.3), 55 % of patients were women, and 60.6 % of patients had no metabolic control. The main comorbidities were dyslipidemia in 67.9 %, obesity in 61.4 %, and hypertension in 59 % of patients. Differences were observed in the prevalence ratio (PR) of women versus men for dyslipidemia (PR 0.68 [CI: 0.52 - 0.89]), coronary artery disease (PR 0.41 [CI: 0.28 - 0,61]) and obesity (PR 0.23 [CI: 0.17 - 0.30]). Conclusions: Patients with type 2 diabetes have a high prevalence of comorbidities: dyslipidemia, obesity and arterial hypertension. A lower prevalence of comorbidities was observed in women than men for dyslipidemia, coronary heart disease, and obesity.",
"keywords": [
"Diabetes Mellitus Type 2",
"Prevalence",
"Comorbidity",
"Epidemiology",
"Colombia."
],
"content": "Introduction\n\nType 2 diabetes is a critical cause of morbidity in the adult population. 1 Among the most significant risk factors for the increase of diabetes are obesity, an aging population, and a longer life expectancy. 2 However, the trend and magnitude of diabetes-related disease burden varies substantially across regions and countries. The global incidence, prevalence, death, and disability-adjusted life-years (DALYs) associated with diabetes has increased. 3\n\nAt the time of type 2 diabetes diagnosis, patients already have some micro or macrovascular complication and an increased probability of dying from any complications developed. 4 Although there are complications clearly associated with diabetes, information regarding their prevalence is scarce in low and middle-income countries. Therefore, the need for data that accounts for the magnitude of the disease is essential. In Colombia, information has been scarce in the last five years. Health systems need data on comorbidities to prevent or delay the development of disease complications. 5\n\nGiven that the highest probability of dying from diabetes is given by the prevalence of comorbidities, 6 we consider it essential to describe the patients most frequently attending an outpatient program for type 2 diabetes. There is an urgent need to delay complications of diabetes and to identify and quantify those most affected as part of the fundamental requirements for the formulation and strengthening of health policies. 7 Valid and consistent estimates of the prevalence of diabetes and its comorbidities over time are needed to assess the effect of interventions and measure progress towards agreed health policy goals. This study aims to determine the prevalence of the main comorbidities related to type 2 diabetes in patients who attend a disease management program.\n\n\nMethods\n\nClinical Integral de Diabetes (CLID) is a diabetes management healthcare team (endocrinologist, general practitioner, nutritionist, pharmaceutical chemist, professional nurse and psychologist) based in Medellín, Colombia. Patients with diabetes are referred to CLID by primary care providers. Once the patient is referred, an endocrinologist or a doctor of internal medicine conducts an initial assessment, following the clinical practice guidelines of Colombia and American Diabetes Association (ADA) standards of appropriate physical and laboratory exams and specialist referrals. Hemoglobin A1C (A1C) is monitored, lipids, urine microalbumin, thyroid stimulating hormone (TSH), and retinal exams are completed yearly or as often as required. At each visit, the patient receives medication instruction, recommendations on lifestyle changes, nutritional assessment, and general recommendations in the disease management.\n\nThe dietician and pharmaceutical chemist are the case managers responsible for following up on missed patient appointments and identifying the individual service and access needs of their panel of patients. The dietician and pharmacologist also communicate with the primary care physician regarding clinical care issues. The program operates as ambulatory care. CLID have a diabetes electronic management system software. The database contains demographic, health status, treatment, laboratory, and behavioral factors for each patient and collects this information over time. This study included data from June 10, 2014 to March 30, 2019 and was approved by the CES university ethics committee.\n\nFor the purpose of this analysis, we selected patients with type 2 diabetes, reducing the population size to 1,018. To avoid selection bias the entire population was used, atypical or missing data were reviewed and recovered from the clinical records. The information was reviewed by Uriel Palacios-Barahona. Patients were only excluded if they did not have HbA1c, clinical and sociodemographic variable records.\n\nDemographic variables included sex, age, educational level (primary, secondary, university), marital status, and type and regime of social security system affiliation. Clinical variables were measured dichotomously (yes or no): hypertension, obesity (Body Mass Index, kg/m2 ≥ 30), dyslipidemia, retinopathy, nephropathy, neuropathy, amputation, peripheral arterial disease (PAD), coronary heart disease, and cerebrovascular disease (CVD), HbA1c is a laboratory value that indicates glycemic control over a two-to-three-month period. Values less than 7 % are considered optimal. The variables were measured when the patient entered the program. 8\n\nContinuous variables were presented as mean ± standard deviation (SD). Categorical variables are shown as numbers (valid percentage). An exploratory analysis of the prevalence according to sex was carried out, since for diabetes there are differences by sex in comorbidities and complications. An overall crude prevalence ratio (PR) was measured using the Chi-square test with a 95 % confidence interval (CI95 %). A Statistical significance threshold was considered using a p-value < 0.05. The analysis was performed with Stata 12 software, 9 licensed by CES University. Informed consent was obtained from all patients following clinical research standards in Colombia. The study protocol was reviewed and approved by the Institutional Review Board of CES University (Project number 734/2017).\n\n\nResults\n\nThere were 1,018 patients with type 2 diabetes; the mean age was 66 ± 12.93 (median: 66.4 [min: 21.2 - max: 99.4]), mean HbA1c on admission was 7.8 ± 1.86 (median: 7.3 [min: 4.3 - max: 17.1]), mean years with diabetes: 12.7 ± 9.3. (median: 10.3 [min: 0.4 - max: 56.7]); 25.6 % of the patients had basic primary education, 53.4 % were married. At the time of entry into the program, 60.6 % of the patients did not have metabolic control (HbA1c ≥ 7%) ( Table 1).\n\nThe main comorbidities associated with diabetes were dyslipidemia (67.9 %), obesity 61.4 %, and arterial hypertension (59 %). When comparing women versus men, a prevalence ratio (PR) of 0.68 (CI: 0.52-0.89) was observed for dyslipidemia, 0.41 (CI: 0.28-0.61) for coronary disease and 0.23 (CI: 0.17-0.30) for obesity of ( Table 2).\n\n\nDiscussion\n\nThis study describes the prevalence of the main comorbidities and complications associated with type 2 diabetes in a population of patients attending a disease management program. This description contributes to updating the implications of the disease upon the healthcare system. Furthermore, this information contributes to health risk management activities and prioritizing health policies in Colombia.\n\nThe main comorbidities were dyslipidemia, obesity and hypertension. These findings are consistent with previous studies in Colombia; 10,11 however, obesity prevalence has increased (previous studies were 35 %) in people with diabetes. 12 This finding can be a warning of how the prevalence of risk factors is changing. National studies have shown an increase in the prevalence of obesity (body mass index of 13.9 % in 2005 and 16.4 % in 2010 [difference in prevalence = 2.7 %; CI95 %: 1.9-3.4 %]). 13\n\nLikewise, a high prevalence of coronary disease and microvascular disease stands out, consistent with previous studies that have observed a high disease burden in these patients. 10 These are factors that contribute to mortality from diabetes. Tancredi et al. 14 analyzed the excess mortality of people with type 2 diabetes in a cohort with 4.5-year follow-up, observing that the rate of mortality from cardiovascular disease was 7.9 % among the patients compared to 6.1 % between controls (adjusted hazard ratio, 1.14, CI 1.13-1.15). Excess all-cause and cardiovascular disease mortality risk increased the younger the diabetic patient was, the lower the glycemic control and the greater the severity of kidney complications. A systematic review also shows that cardiovascular complications contribute directly to mortality from diabetes. Therefore, the health system must strive to control risk factors for diabetes and avoid or delay the development of micro and macrovascular complications. 15\n\nThe prevalence ratio was lower in women than men for dyslipidemia, coronary heart disease, and obesity. A cardioprotective effect has been reported in women with coronary heart disease, the same in dyslipidemia. However, in obesity, the findings are contrary to the national reports of obesity, which have found a prevalence of obesity of 22.4 % in women and 18.7 % in men. 16 This finding requires a review of the obesity trend in diabetes by sex.\n\nAt the time of admission to the clinical management program, only 41.5 % of the patients had HbA1c levels < 7 %, which indicates a high prevalence of no metabolic control (60.6 %). The number of patients in a clinical management program in Colombia who achieve metabolic control have been reported between 27 to 53.4 %. 10,17,18 Although treatment must be individualized, 19 it is clear that it has been difficult for healthcare teams and patients to achieve more significant metabolic control figures. It has been observed that 80 % of patients with diabetes have some associated comorbidity, 18,20 however a high prevalence of comorbidities suggests a failure in care or disease prevention. Mortality is associated with complications, 21 deterioration in the quality of life of patients 22 and increased costs in healthcare. 13,23\n\nIn this study, administrative data were used. There could be underreporting to the extent that patients may not have reported all the conditions of interest or the health professional did not record important information for identifying a clinical condition. Furthermore, the patients could have consulted in other institutions, and the related interventions or diagnoses are unknown. This study is grounded in the reported data, and there is a systematic process of collecting the information. Up-to-date information is reported with a large patient sample, which can help health professionals to gain insight into the behavior of diabetes comorbidities.\n\n\nConclusion\n\nPatients with type 2 diabetes have a high prevalence of comorbidities: dyslipidemia, obesity and arterial hypertension. A lower prevalence of comorbidities was observed in women than men for dyslipidemia, coronary heart disease, and obesity.\n\n\nData availability\n\nThis project contains the anonymized raw data for each patient assessed in the study and are available at;\n\nZenodo: Prevalence of comorbidities associated with type 2 diabetes in patients attending a disease management program, Medellín, Colombia 2014-2019: a descriptive study. http://doi.org/10.5281/zenodo.4644290. 8\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\nThe study protocol was reviewed and approved by the Institutional Review Board of CES University (Project number 734/2017).\n\n\nConsent statement\n\nWritten consent was obtained from all patients following clinical research standards in Colombia.",
"appendix": "Acknowledgements\n\nDr. Palacios-Barahona is the recipient of a doctoral scholarship from the Government of the Department of Chocó-Technological University of Chocó.\n\n\nReferences\n\nCardiovascular disease, chronic kidney disease, and diabetes mortality burden of cardiometabolic risk factors from 1980 to 2010: a comparative risk assessment. Lancet Diabetes Endocrinol. 2014; 2(8): 634–47. PubMed Abstract | Publisher Full Text | Free Full Text\n\nZhou B, Lu Y, Hajifathalian K, et al.: Worldwide trends in diabetes since 1980: a pooled analysis of 751 population-based studies with 4·4 million participants. Lancet. 2016; 387(10027): 1513–30.PubMed Abstract | Publisher Full Text | Free Full Text\n\nLin X, Xu Y, Pan X, et al.: Global, regional, and national burden and trend of diabetes in 195 countries and territories: an analysis from 1990 to 2025. Sci Rep. 2020; 10(1): 14790. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDeshpande AD, Harris-Hayes M, Schootman M: Epidemiology of Diabetes and Diabetes-Related Complications. Phys Ther. 2008; 88(11): 1254–64. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAfroz A, Alramadan MJ, Hossain MN, et al.: Cost-of-illness of type 2 diabetes mellitus in low and lower-middle income countries: a systematic review. BMC Health Serv Res. 2018; 18(1): 972. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAfkarian M, Sachs MC, Kestenbaum B, et al.: Kidney Disease and Increased Mortality Risk in Type 2 Diabetes. J Am Soc Nephrol. 2013; 24(2): 302–8. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWorld Health Organization:Global action plan for the prevention and control of noncommunicable diseases: 2013-2020. [Internet]. 2013 [citado 22 de julio de 2019].Reference Source\n\nPalacios-Barahona U, Ordoñez Molina J, Alvis Guzmán N, et al.: Prevalence of comorbidities associated with type 2 diabetes in patients attending a disease management program, Medellín, Colombia 2014-2019: a descriptive study.2021.Reference Source\n\nStataCorp: Stata Statistical Software: Release 12. College Station, TX:StataCorp LP;2011.\n\nVillegas Perrasse A, Abad SB, Faciolince S, et al.: El control de la diabetes mellitus y sus complicaciones en Medellín, Colombia, 2001-2003. Rev Panam Salud Pública. 2006; 20(6): 393–402.\n\nMachado Alba JE, Escobar Moncada JC, Mesa EG: Patrones de prescripción de antidiabéticos en un grupo de pacientes colombianos. Rev Panam Salud Pública. 2007; 22(2): 124–31.\n\nLlinás-Castro R, Alvis-Estrada L, Durán-Lengua M: Clinical inertia in insulin prescription for patients with type 2 diabetes mellitus at a primary health care institution of Cartagena. Colombia. Rev Fac Med. 2018; 66(4): 551–5. Publisher Full Text\n\nKasper NM, Herrán OF, Villamor E: Obesity prevalence in Colombian adults is increasing fastest in lower socio-economic status groups and urban residents: results from two nationally representative surveys. Public Health Nutr. 2014; 17(11): 2398–406. PubMed Abstract | Publisher Full Text\n\nTancredi M, Rosengren A, Svensson A-M, et al.: Excess Mortality among Persons with Type 2 Diabetes. N Engl J Med. 2015; 373(18): 1720–32. PubMed Abstract | Publisher Full Text\n\nDal Canto E, Ceriello A, Rydén L, et al.: Diabetes as a cardiovascular risk factor: An overview of global trends of macro and micro vascular complications. Eur J Prev Cardiol. 2019; 26(2_suppl): 25–32. PubMed Abstract | Publisher Full Text\n\nEncuesta Nacional de Situación Nutricional de Colombia (ENSIN):2015 [citado 24 de febrero de 2021].Reference Source\n\nAlba LH, Bastidas C, Vivas JM: Prevalencia de control glucémico y factores relacionados en pacientes con diabetes mellitus tipo 2 del Hospital Universitario de San Ignacio, Bogotá. Colombia. 2009; 145(6): 6.\n\nPantalone KM, Hobbs TM, Wells BJ, et al.: Clinical characteristics, complications, comorbidities and treatment patterns among patients with type 2 diabetes mellitus in a large integrated health system. BMJ Open Diabetes Res Care. 2015; 3(1): e000093. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAmerican Diabetes Association:6. Glycemic Targets: Standards of Medical Care in Diabetes—2019. Diabetes Care. 2019; 42(Supplement 1): S61–70. PubMed Abstract | Publisher Full Text\n\nPapa G, Degano C, Iurato MP, et al.: Macrovascular complication phenotypes in type 2 diabetic patients. Cardiovasc Diabetol. 2013; 12(1): 20. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMorrish NJ, Wang SL, Stevens LK, et al.: Mortality and causes of death in the WHO Multinational Study of Vascular Disease in Diabetes. Diabetologia. 2001; 44(Suppl 2): S14–S21. PubMed Abstract | Publisher Full Text\n\nTrikkalinou A, Papazafiropoulou AK, Melidonis A: Type 2 diabetes and quality of life. World J Diabetes. 2017; 8(4): 120. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAmerican Diabetes Association:Economic Costs of Diabetes in the U.S. in 2017. Diabetes Care. 2018; 41(5): 917–28. PubMed Abstract | Publisher Full Text | Free Full Text"
}
|
[
{
"id": "85589",
"date": "26 May 2021",
"name": "Juana Patricia Sanchez Villamil",
"expertise": [
"Reviewer Expertise Epidemiology and biomedical 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\nIt is a very small study, but as the authors describe it is important for monitoring of morbidity and risk factors trends in our country and establishment of public health policies.\nIntroduction is short but is concise with current references.\n\nMethods: I found the methodology well described. However, it is necessary to say if CLID is a unique diabetes management healthcare center in Medellín, with the intention to assess external validity and of course relevance of the results.\n\nI am left wondering if reference 8 is this same article.\n\nTables: In table 1, it is desirable that the decimals be uniform in the numerical figures. Some numerical data have two and others a single decimal.\n\nDiscussion: In the last paragraph, it is reported that patients could have under-reported information. So, it is necessary to list the variables that are exclusively reported by the patients or variables subject to error or not determined by clinical parameters or medical diagnosis.\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/10-389
|
https://f1000research.com/articles/10-388/v1
|
14 May 21
|
{
"type": "Correspondence",
"title": "Heterogeneity and other problems in a pooled analysis of snus use and mortality",
"authors": [
"Brad Rodu",
"Nantaporn Plurphanswat",
"Nantaporn Plurphanswat"
],
"abstract": "A recent analysis of Swedish snus use and mortality combined eight Swedish datasets and found that exclusive Swedish male snus users have statistically significant increased mortality from all causes, cardiovascular diseases and other causes. These findings, from the Swedish Collaboration on Health Effects of Snus Use, are in sharp contrast with previous pooled results from the same group. The discrepant results may be indicative of unresolved statistical problems that haven’t been addressed by the collaboration authors in any of their studies. The most important problem is unresolved heterogeneity among the eight cohorts, which we describe in detail, and we show how the use of the random effects method by the authors was not sufficient. We explain why the tables in the article are uninformative, and we demonstrate why the exclusion of smokers in the analysis was not validated and eliminated important information. Finally, we strongly recommend some straightforward and easily implemented corrective measures.",
"keywords": [
"snus use",
"smokeless tobacco",
"mortality follow-up study",
"Swedish Collaboration on Health Effects of Snus Use",
"heterogeneity"
],
"content": "Introduction\n\nA recent analysis by Byhamre et al. of Swedish snus use and mortality combined eight Swedish datasets and found that exclusive Swedish male snus users have statistically significant increased mortality from all causes (adjusted hazard ratio, aHR = 1.28, 95% confidence interval, CI = 1.20 – 1.35), cardiovascular diseases (aHR = 1.27, CI = 1.15 – 1.41) and other causes (aHR = 1.37, CI = 1.24 – 1.52), as well as a 12% elevation in cancer mortality (aHR = 1.12, CI = 1.00 – 1.26).1 These findings, from the Swedish Collaboration on Health Effects of Snus Use, are in sharp contrast with previous pooled results from the same group that found no significant increases in incidence and/or mortality from acute myocardial infarction,2 stroke,3 atrial fibrillation,4 pancreatic cancer,5 oral cancer6 and colorectal cancer.7 The latter study did report a significant association of exclusive current snus use and rectal cancer (aHR = 1.38, CI = 1.07 – 1.77).7\n\nWe are concerned that the discrepant results between the latest analysis and previous published studies may be indicative of unresolved statistical problems that haven’t been addressed by the collaboration authors in any of their studies. These problems include unresolved heterogeneity among the eight cohorts, for which the random effects method the authors used was not a sufficient remedy. In addition, the tables in the article are uninformative, and the exclusion of smokers in the analysis was not validated and eliminated important information. There are straightforward and easily implemented corrective measures that the authors could undertake.\n\n\nThe pooled cohorts are highly heterogeneous\n\nFirst, the cohorts in the study are heterogeneous, as our Table 1 demonstrates. The eight cohorts were all described as “population-based,” but only four fit that description, and two of those were duplicative. The population-based cohorts were from: (a) the most populous Swedish County – the Stockholm Public Health Cohort (StPHC); (b) a Diet and Cancer Study in the third most populous city, Malmö; (MDCS) (c) the Scania Public Health Cohort (ScPHC), which contains Malmö; and (d) the Multinational Monitoring of Trends and Determinants in Cardiovascular Disease (MONICA) cohort, from rural Västerbotten and Norbotten Counties, which make up 34% of Sweden’s land area but only 5% of its population. The other four cohorts were convenience samples (the first three are from throughout Sweden). They consisted of: (a) the construction worker cohort (CWC); (b) participants in a charity walk, the National March Cohort (NMC); (c) twins born from 1926 to 1958 (Screening Across the Lifespan Twin, or SALT, Study); and (d) employees in three counties (Work, Lipids and Fibrinogen, WOLF study), which included Stockholm.\n\nThe heterogeneity of the samples is further illustrated by other characteristics described in Table 1, including the mean age at death. It was 61 years among employees, which was much lower compared not only with the other cohorts, but with men in Sweden during the same recruitment and follow-up periods.8 Other diverse variables were the prevalence of smoking and snus use. As we discuss in detail later, Byhamre et al.1 excluded smokers from their analysis, but didn’t justify their choice, which is not innocuous and contributes to the estimates that the authors conclusions are based upon. They also, misleadingly, included these omitted observations in their table describing their cohorts. So, we point out that smoking and snus use prevalence varied from very low (7% and 9%, respectively) among charity walkers to very high (46% and 27%) among construction workers.\n\nThe construction workers account for 72-73% of both the sample and the number of deaths. Their mean enrollment age was 34 years, which was vastly different than four other cohorts that recruited men aged 50+ years. The first mortality follow-up study of snus use involving this cohort, published in 1994,9 had an unusual and unresolved distribution of excess deaths.10\n\nPooled analyses are intended to yield results that are generalizable to the pool. However, the vast differences in the characteristics of the cohorts that have been disclosed raise a concern whether the findings are interpretable as population estimates. As discussed, only four cohorts were from population-based samples, and three enrolled very small numbers. The participant selection process in the vastly larger convenience sample cohorts is the dominant influence of this study’s results and, given that the employee cohort is by far the largest and makes up a large majority of the pooled sample, the very different snus use and mortality in this cohort is reason alone to question the external validity of the results even if they are correct, which we do not think is the case.\n\n\nThe methodology was flawed\n\nByhamre et al.1 used a random-effects method to account for the variation in mortality across cohorts, in which they assumed that there is no correlation between individual cohorts and snus use. However, that method also assumes that unmeasured factors specific to a cohort are unrelated to either snus use or mortality, which is almost surely unlikely to hold in practice. For example, as we show in Table 1, the mean age at enrollment in the four population-based cohorts was 48 to 59 years, compared with 34 years in the construction workers, the latter accounting for over 70% of the combined sample. Furthermore, the mean age at death was highly variable, ranging from 61 years in the employee sample and 66 years in construction workers to 70+ years in the other cohorts.\n\nAt a minimum, the authors could have addressed these problems by other methods11,12 providing the following information:\n\n• Estimate adjusted hazard ratios for each cohort separately. This provides information about which cohorts are driving the pooled results, and it is especially important when over 70% of the sample was in the construction worker cohort.\n\nThis also addresses the selection problem tied to cohort populations with considerably different age distributions and demographic characteristics. Consider the four cohorts (two population-based and two convenience samples) that enrolled participants at or above a mean age of 50 years. By definition, everyone in these cohorts had already lived at least 50 years and was alive at enrollment. Now compare them with the construction worker cohort, which was enrolled at a mean age of 34 years. Sixteen years later, at age 50, less than 100% of this cohort was still living and contributing person-years, which makes the survivors fundamentally different people compared with those who were enrolled after age 50. The pooled analysis methodology from Byhamre et al. ignored this serious problem, and their outcomes may have been significantly biased.\n\n• Estimate a “fixed effects” model by assigning indicator (dummy) variables for cohorts and interacting the cohort variables with age and education. This will allow correlation between the cohorts and snus use and between the cohorts and mortality. Furthermore, the interaction between cohorts and age would allow the effect of age on mortality to differ by cohorts.\n\n\nThe tables are uninformative\n\nByhamre et al. provided the “Characteristics of included cohorts...” in Table 1 of their publication, and we have used some of this information to illustrate heterogeneity and other problems.1 However, this table does not reflect Byhamre et al.’s actual analytic sample (n = 169,103), because it includes the characteristics of all male participants from the eight cohorts (n = 383,025), including ever regular smokers and others that the authors excluded. Simply put, including information on 214,000 participants that aren’t in the analysis is not only uninformative, it is misleading and must be revised.\n\nAlthough Byhamre et al.’s Table 2 provides information on some baseline characteristics in the analytic sample, it presents the pooled characteristics, which is uninformative because it further conceals large differences between the cohorts. For example, variations in enrollment ages across the cohorts have substantial impact on BMI, physical activity, and alcohol use that may overwhelm and obfuscate any differences due to snus use. The authors should have reported the baseline characteristics according to cohorts, and cohorts by snus use.\n\nFurthermore, the authors did not provide adequate definitions for snus use, the sole exposure of interest in the study. Thus, questionnaires containing actual questions about snus use from each cohort is a prerequisite. According to the authors, baseline snus use was not consistent throughout the cohorts. Some studies did not have information on former snus use, while others did not have information on amount and/or duration.\n\n\nThe exclusion of smokers was not validated and eliminates important information\n\nThe authors excluded participants “reporting ever regular use of cigarettes” (emphasis added), which was intended “to eliminate potential residual effects”, a vague reference to an unspecified statistical problem. The authors provided no foundation for this choice and no evidence that their objective was met. Furthermore, snus users who were less-than-regular cigarette smokers – those with a smoking history and some dual users – were still in the pooled analytic cohort.13 Less-than-regular smoking is likely because of the lower social acceptability of smoking vis-à-vis snus in Sweden.14,15\n\nThe authors could validate whether their analytic tactic excluded smoking by reporting the results for two disease categories: cancer of the trachea, bronchus, and lung (ICD-10 codes C33–C34) and chronic lower respiratory diseases (J40-J47). If they truly eliminated smokers from their analyses, they should not have found any significantly increased hazard ratios for these diseases among snus users.\n\nExcluding “ever regular” smokers is a routine practice in Swedish follow-up studies of snus use, but it also eliminates a lot of valuable information and may bias the results. First, partial exclusion of an exposure closely associated with snus use precludes assessment of interactions. Second, the findings on snus use in this and similar studies completely lack context with respect to the effects of smoking on mortality.16\n\n\nSummary\n\nIn conclusion, Byhamre et al.1 published an analysis with several flaws that render their results uninformative and possibly misleading. The authors should publish revised tables and re-estimate their analyses as described above to address these problems. These measures are readily achievable, and the validity of the results will be considerably enhanced.\n\n\nData availability\n\nNo data is associated with this article.",
"appendix": "References\n\nByhamre ML, Araghi M, Alfredsson L, et al.: Swedish snus use is associated with mortality: a pooled analysis of eight prospective studies. Int J Epidemiol. 2021; 49: 2041–2050. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHansson J, Galanti MR, Hergens M-P, et al.: Use of snus and acute myocardial infarction: pooled analysis of eight prospective studies. Eur J Epidemiol. 2012; 27: 771–779. PubMed Abstract | Publisher Full Text\n\nHansson J, Galanti MR, Hergens M-P, et al.: Snus (Swedish smokeless tobacco) use and risk of stroke: pooled analyses of incidence and survival. J Int Med. 2014; 276: 87–95. PubMed Abstract | Publisher Full Text\n\nHergens M-P, Galanti R, Hansson J, et al.: Use of Scandinavian moist smokeless tobacco (snus) and the risk of atrial fibrillation. Epidemiol. 2014; 25: 872–876. PubMed Abstract | Publisher Full Text\n\nAraghi M, Galanti MR, Lundberg M: Use of moist snuff (snus) and pancreatic cancer: pooled analysis of nine prospective observational studies. Int J Cancer. 2017; 141: 687–693. PubMed Abstract | Publisher Full Text\n\nAraghi M, Galanti MR, Lundberg M: No association between moist oral snuff (snus) use and oral cancer: pooled analysis of nine prospective observational studies. Scand J Public Health. 2020, May 28: 1403494820919572. Online ahead of print. PubMed Abstract | Publisher Full Text\n\nAraghi M, Galanti MR, Lundberg M: Smokeless tobacco (snus) use and colorectal cancer incidence and survival: results from nine pooled cohorts. Scand J Public Health. 2017; 45: 741–748. PubMed Abstract | Publisher Full Text\n\nStatistics Sweden: Life expectancy. 1751-2019. Reference Source\n\nBolinder G, Alfredsson L, Englund A, et al.: Smokeless tobacco use and increased cardiovascular mortality among Swedish construction workers. Am J Public Health. 1994; 84: 399–404. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRodu B, Cole P: Excess Mortality in Smokeless Tobacco Users Not Meaningful (Letter). Am J Public Health. 1995; 85: 118. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBlettner M, Sauerbrei W, Schlehofer B, et al.: Traditional reviews, meta-analyses and pooled analyses in epidemiology. Int J Epidemiol. 1999; 28: 1–9. PubMed Abstract | Publisher Full Text\n\nFriedenreich CM: Methods for Pooled Analyses of Epidemiologic Studies. Epidemiol. 1993; 4: 295–302. PubMed Abstract | Publisher Full Text\n\nRodu B, Stegmayr B, Nasic S, et al.: Impact of smokeless tobacco use on smoking in northern Sweden. J Int Med. 2002; 252: 398–404. PubMed Abstract | Publisher Full Text\n\nNorberg M, Malmberg G, Ng N, et al.: Who is using snus? - Time trends, socioeconomic and geographic characteristics of snus users in the ageing Swedish population. BMC Public Health. 2011; 11: 929. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRamström L, Borland R, Wikmans T: Patterns of Smoking and Snus Use in Sweden: Implications for Public Health. Int J Environ Res Public Health. 2016; 13(11): 1110. Published 2016 Nov 9. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRodu B, Plurphanswat N: Mortality among male smokers and smokeless tobacco users in the U.S. Harm Red J. 2019; 16. Reference Source Accessed 8 February 2021."
}
|
[
{
"id": "85432",
"date": "03 Jun 2021",
"name": "Marewa Glover",
"expertise": [
"Reviewer Expertise Behavioural science",
"tobacco dependency and cessation",
"tobacco control",
"harm reduction",
"mixed methods from trial design to in-depth qualitative",
"narrative and systematic reviews."
],
"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 letter 'Heterogeneity and other problems in a pooled analysis of snus use and mortality' raises concerns about the method used in a paper by Byhamre et al., 2021 that was published in the International Journal of Epidemiology (Vol.49). The Byhamre et al. paper entitled 'Swedish snus use is associated with mortality: a pooled analysis of eight prospective studies' claimed to have found a positive association between snus use and mortality, where previous studies by the same group had not found this association. Rodu and Plurphanswat outline a range of methodological flaws in the Byhamre et al. analysis.\nThe critique is straightforward and clearly written. The authors have narrowly focused on the poor use of statistical analysis methods. They could have gone further.\nA more in-depth critical and systematic review of the literature being produced by the Swedish Collaboration on Health Effects of Snus is warranted. Particularly, future reviews should include an analysis of Risk of Bias. It is a minor example, but it is indicative that the authors on the Byhamre et al. paper do not consider the potential bias inherent in their focus on mostly their own previous work. Nine of the Byhamre et al. authors were investigators and authors on one or more of the eight studies the ‘pooled’ data were extracted from. This is a form of authorship bias.\nThere is a much larger pool of research that has sought to determine and quantify the risks of snus than indicated by Byhamre et al.’s selection. Future critical reviews would need to identify if selection bias is a further limitation of the Byhamre et al. analysis.\n\nCritiques of published science make an important contribution to science. To ensure knowledge is sound, these types of critiques could even be said to be essential. Seriously flawed studies can mislead policy makers and politicians and lead to decisions about healthcare that could cause harm.\n\nIs the rationale for commenting on the previous publication clearly described? Yes\n\nAre any opinions stated well-argued, clear and cogent? Yes\n\nAre arguments sufficiently supported by evidence from the published literature or by new data and results? Yes\n\nIs the conclusion balanced and justified on the basis of the presented arguments? Yes",
"responses": []
},
{
"id": "124659",
"date": "11 Mar 2022",
"name": "Tord Finne Vedoy",
"expertise": [
"Reviewer Expertise Social explanations of tobacco use and social inequality in tobacco use."
],
"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 debate on the degree to which snus is associated with increased morbidity or mortality, and how, has been going on for some time. Although the discussion may seem most relevant for those relative few who use snus or live in a society where snus use is common, the debate should interest tobacco researchers generally for (at least) two reasons: First, snus is one of the products that has been both a popular and long-lasting harm reducing alternative to cigarette smoking. Correct estimates of the harms associated with snus use are necessary to assess the harm-reducing potential of snus use. Second, estimating the harmfulness of snus use requires that researchers take into account the use of two distinct but related tobacco products. Both these dimensions can inform similar discussions on the harm-reducing potentials of other and more recent nicotine products, for example, e-cigarettes. Because few countries have a long history of snus use, there is limited data on individual snus and other tobacco use patterns and health outcomes from national registers. Consequently, many of the studies concerning the association between snus use and registered mortality has been based on the same set of (Swedish) cohorts and examined by the same researchers. I find that the issues raised by Rodu and Plurphanswatare are warranted and should be relatively easy to address. A revised study by Byhamre et al. would be of great interest to both debates on snus use and public health and snus use and harm reduction.\n\nIs the rationale for commenting on the previous publication clearly described? Yes\n\nAre any opinions stated well-argued, clear and cogent? Yes\n\nAre arguments sufficiently supported by evidence from the published literature or by new data and results? Yes\n\nIs the conclusion balanced and justified on the basis of the presented arguments? Yes",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-388
|
https://f1000research.com/articles/10-386/v1
|
14 May 21
|
{
"type": "Research Article",
"title": "Implementation of discovery learning in a digital class and its effect on student learning outcomes and learning independence level",
"authors": [
"Wasis Wuyung Wisnu Brata",
"Firmanul Catur Wibowo",
"Nadia Rahmadina",
"Firmanul Catur Wibowo",
"Nadia Rahmadina"
],
"abstract": "Background: The need to use online learning is inevitable during the Covid-19 pandemic. There has been a call for action in education policy to provide a more flexible, digitally based learning strategy. It is presumed that this change in learning methods will reduce meaningful learning experiences. Methods: This study examines the application of discovery learning in the digital classroom and its effect on learning outcomes and independent learning. The research employed a quasi-experiment method, and the sample was taken using a randomized sampling technique. Two classes with the same initial knowledge value were used as experimental and control groups. The instrument used was a cognitive test and a Self-Directed Learning (SDL) questionnaire. Results: The results of this research show that there is a significant difference in learning outcomes and SDL in the experiment and control group. Students that apply discovery learning with a combination of face-to-face and digital classes get better results on both variables than in conventional discovery class. Conclusions: It can be concluded that the application of discovery learning through the digital classroom has a positive effect on learning outcomes and students' level of independence. This study was only conducted in one secondary school and more samples are recommended for further study. The limitations of the application of face-to-face discovery learning can be overcome by the application of online learning, which facilitates meaningful learning experiences for students.",
"keywords": [
"Digital class",
"discovery learning",
"self-directed learning"
],
"content": "Introduction\n\nThe fast development of Information and Communication Technologies (ICT) has had an impact on the development of learning strategies, especially the use of the internet in learning. The use of the internet, and information and communication technologies have become an everyday occurrence for learners. The presence of e-learning makes it easier for teachers to monitor, supervise, and deliver assignments without the need for them to be face-to-face.1 The rapid advances in technology have enabled educational institutions to reach and educate students beyond the constraints of space and time.2 In addition, the need to use online learning is inevitable during the Covid-19 pandemic.\n\nIn response to this, the Ministry of Education and Culture, an educational institution in Indonesia, has designed a portal that supports e-learning. The education policy has called for a national call to provide a more flexible learning strategy based on digital resources. It is assumed that this change in learning methods will reduce meaningful learning experiences due to the ease with which students learn the subject matter instantly. It is therefore necessary that the implementation of online learning ensures a constructive and meaningful learning experience.\n\nDigital classrooms can allow teachers to create their own classes by designing student worksheets, adding contextual problems to solve and answer questions about specific material.3 The learning process through digital classrooms can be done anytime and anywhere without having to engage in face-to-face learning activities.4 In this case, the teacher can provide material enrichment to complement additional face-to-face learning in class.5\n\nThe features of the digital classroom are expected to enhance students' learning independence in a constructive way so that it can support students' learning outcomes. Learning independence is one of the factors that determine student success in learning, having an impact on the growth of optimal learning independence that supports good learning outcomes.6,7\n\nToday, online learning has become the new norm in learning, yet specific studies on the effects of implementing discovery-based learning in online environments are not clearly understood. This study considers the use of discovery-based online learning, in particular aiming to understand how it can provide learning experiences that support independence and learning outcomes.\n\n\nMethods\n\nThis research was approved by the Research and Community Service Institute, Medan State University (approval number: IC220121/IC2RSE/LPPM/2020). Written informed consent was obtained from participants and approved by the parents/guardians and the school principal.\n\nThis research is quasi-experimental with a non-equivalent control group and post-test design. The study was conducted in state secondary school 11 Medan, Indonesia, in the period January to March 2020. The population of the study was the grade 12 science class of the middle school 11 Medan, which consists of three classes. As the sample inclusion criteria, the classes must have an average initial knowledge in biotechnology that does not differ significantly. Based on these criteria, only two classes passed.26 These two classes were randomly selected: one class as an experimental group and the other as a control group. The experimental group received a discovery learning treatment in blended mode, using digital classroom in addition to face-to-face learning. The treatment is, they can access learning materials flexibly, and can have online discussions with the teacher using the online discussion feature in the LMS. In the control group, face-to-face learning based on discovery learning takes place as usual. Both classes learn the same material and do the same thing in different ways.\n\nThe follow-up period was carried out for three weeks with five meetings. The learning took place twice a week. At the first meeting, a pre-test was given to measure students' initial knowledge. Learning of biotechnology was carried out in the second to fourth meetings, according to the scenario in the experimental and control class. The post-test was conducted at the fifth meeting to measure student learning outcomes and learning independence. The total number of students in this study was 68, with 35 students in the experimental group (10 males, 25 females) and 33 students in the control group (13 males, 20 females). The sample size in each group follows the number and list of students in each class. This consideration is made to avoid bias that can arise if the composition of students in the class changes. The number of samples in each group is also under the Frankel & Wallen method for causal-comparative, with at least 30 people per group.27\n\nThis study focuses on the variable cognitive learning outcomes and student learning independence. The instrument for measuring learning outcomes used a test instrument of 25 items of cognitive questions on biotechnology.26 Learning independence was measured using Fisher's Self-Directed Learning questionnaire8 with 42 items related to self-management indicators, desire to learn, and self-control.26\n\nThe rules for scoring on the learning outcome data were that for each correct answer, the value is 1 and for the wrong answer, the value is 0. The questionnaire scoring rules use a Likert scale with four choices: strongly agree (score 4), agree (score 3), disagree (score 2), and strongly disagree (score 1). All items in the questionnaire are positive statements. The data were analysed using SPSS 21 software. Data on cognitive learning outcomes and student learning independence were tested for normality and homogeneity as prerequisites for testing research hypotheses. Hypothesis testing uses the Independent T-Test to compare the average scores of the two groups that are not related to each other.25 Sig. < ½ α (0.025) was considered to indicate a significant difference.\n\nSteps to overcome the potential bias were made by preventing the possibility of student access to the control group into the Learning Management System (LMS). The LMS is provided for online learning support for the experimental class through their respective accounts and can only be done with the teacher's permission. Also, all instruments and learning tools were validated by experts from Universitas Negeri Medan. As for the test instrument, it was checked for validity, reliability, level of difficulty of questions, and distinguishing features.25 The instrument was tested on other students who had studied biotechnology. During the study, no data was lost as all participants completed the necessary data.\n\n\nResults\n\nThe data was taken after students in both classes had carried out the learning from January to March 2020. In both classes, students studied biotechnology with discovery learning models. The difference was that students in the experimental class did mixed learning that combines face-to-face and online learning by utilizing the digital class feature in the Learning Management System developed by the researcher. During using digital classroom, students in experimental class had accessed to Biotechnology material that include content and videos. They also could download worksheet from tasks, uploaded them back after finishing the tasks and discussed biotechnology outside learning hours. The data obtained in the study were the cognitive learning outcomes and learning independence of the students (Table 1). An independent t-test (Table 3) was performed to determine whether there is a significant difference between the two groups.24\n\na Learning outcomes.\n\nb Self-directed Learning.\n\nAnalysis of student learning outcomes and SDL based on gender was carried out to see if there were differences influenced by gender (Table 2). In the experimental class, the mean score of male students was 83.33. The mean score of female students was 82.09. In the control class, the average score of male students is 79.50, and the average score of female students is 76.95. Student learning independence data shows that the mean score of male and female students in the experimental class is 86.90 and 82.12, respectively. Whereas in the control class, the SDL average for male and female students was 79.56 and 80.44, respectively.\n\nThe t-test results for student learning outcomes and student learning independence with Sig. (2-tailed) was less than ½ α. Moreover, the scores obtained for students' learning outcomes and students' learning independence are higher than the t-table. Consequently, it can be stated that there are significant differences in the experimental and control groups.24\n\nThe data on the acquisition of students' learning independence is based on the fact that the average value of students' learning independence in the experimental group was 83.86, while in the control group was 78.85. The difference in values for each indicator of students' learning independence is shown in Table 5. On all indicators, the experimental class that applies discovery learning in a combination of face-to-face and digital classes has a higher score than the control class.\n\nThe students' learning independence level (Figure 1) is very varied. The students' learning independence criteria in the experimental group were 23 students with very high criteria, 11 students with high criteria, and one student with low criteria. In contrast, the learning independence level of the students in the control group are 14 students with very high criteria, 16 students with high criteria and three students with low criteria. These categories were decided to see the distribution of students' independence levels in both classes. Knowing the difference in the distribution of the level of learning independence in the two sample groups can provide an argument for the assumption that differences in the level of independence in the experimental and control groups may affect learning outcomes.\n\nFour criteria determine the level of independence with a range of scores that are arranged by considering the number of answer choices, the minimum, and maximum scores. The four criteria for the level are very high (81.25 <SDL≤ 100), high (62.5 <SDL≤ 81.25), low (43.75 <SDL≤ 62.5), and very low (25 <SDL≤ 43.75). The three indicators with the level of students' learning independence are shown in Figure 2. There was no additional analysis took place in this study.\n\n\nDiscussion\n\nThe digital classroom (Figure 3) in the study was used as a treatment in the experimental group. Students are free to access the digital classroom at any time without being limited in time according to their wishes. Teachers can support students by providing them with learning content, offering feedback during discussions, and providing help to engage students in the learning activities.9 The teacher's role in face-to-face classroom learning can be optimized by using digital classrooms so that students who do not understand can learn anytime, anywhere.\n\nURL: https://belajar.kemdikbud.go.id. This content is available under the terms of the Attribution-NonCommercial-ShareAlike 4.0 International license (CC BY-NC SA 4.0). Modifications are made by adding biotechnology content for purposes tailored to the learning objectives. The images were deidentified and consent was received from participants for screenshots of their discussion to be taken.\n\nThe content of the learning materials provided in the digital classrooms varies, including reading materials, worksheets, images, and videos related to biotechnology. Findings from previous studies indicate that e-learning influences improved learning outcomes10 and learning independence.6 The use of e-learning and the features available in e-learning can improve learning outcomes.11\n\nAccording to the research design, the experimental group was treated using a digital classroom which allowed students to discuss through the LMS about the material taught outside of learning hours. The discussion can take place using the existing discussion forum functions (Figure 4).\n\nCopyright 2021 © Rumah Belajar. URL: https://belajar.kemdikbud.go.id. This content is available under the terms of the Attribution-NonCommercial-ShareAlike 4.0 International license (CC BY-NC SA 4.0). Modifications are made by adding biotechnology content for purposes tailored to the learning objectives. The images were deidentified and consent was received from participants for screenshots of their discussion to be taken.\n\nDiscussion forums are a tool that students can use to question teachers about learning.4 In these spaces, students can discuss various issues, such as constraints and developments in the assigned discovery project. Similarly, the teacher can also provide group-directed questions.\n\nIn the control group, students did not have access to the use of digital classrooms. If students in the control group do not have the initiative to learn independently at home by repeating what they learn in class or learning material using books, the internet, or other learning resources, then this may affect students' learning outcomes.\n\nThe success of learning through e-learning depends on whether the learning has achieved the desired outcomes,12 i.e., the cognitive learning outcomes of the learner. From the analysis of the research data, it is clear that the learning outcomes of students in the experimental group are higher than in the control group. Learning outcomes are influenced by students' experiences with the learning environment.13 Students' access to a learning environment that is systematically designed to provide meaningful learning experiences is thought to be a factor that contributes to a positive impact.\n\nThe acquisition of higher learning outcomes in the experimental groups can be assumed due to the existence of a learning environment with the application of e-learning in the form of digital classrooms in the activities. These results are in line with previous studies in relation to e-learning based learning by indicating that six out of 10 teachers who apply e-learning based learning in class claim that the use of e-learning has a positive impact on students' learning outcomes.14 The application of e-learning by using certain platforms can develop students' cognitive abilities and skills.15 In addition, the application of e-learning can influence students' learning outcomes, and 73% of students agree that the use of e-learning is applied in the learning process.1\n\nOn the use of e-learning, students can learn the material they need at any time and from anywhere.9 With the use of digital classrooms, students in the experimental group get more time to learn independently. The ease of access to learning anywhere makes it easier for students to understand the subject matter.16 All students (males and females) have been confirmed to have smartphones that can be used to access digital classes. Even though, in its implementation, network constraints have been experienced by some students in accessing digital classes.\n\nLearning activities using e-learning should involve learners in an experimental way.17 In the study, the experimental group had the opportunity to discuss in the digital classroom, which is one of the advantages that the face-to-face learning control group does not have. In addition, students in the experimental group tend to be more active during face-to-face learning activities in the classroom or online outside the classroom. Students in the control group do not show the same behavior, and the material obtained by them is only limited to that given during face-to-face classroom learning. The advantages that exist in e-learning are the reasons why the cognitive learning outcomes in the experimental group were recorded as superior to those of the control group. The use of digital classrooms in learning has also been reported to have received positive responses from students as users.18\n\nThe analysis of self-management indicators in the experimental group was 6.23 higher than the control group (Table 4). This means that students' ability to manage learning time is higher than that of the control group. Students' learning independence can be seen from students' ability to take responsibility for their own learning activities.19 In this case, students in the experimental group are more disciplined and skilled in time management. When the researchers determine the time for discussion in a digital classroom, the students in the experimental group are prepared before the discussion takes place. The same is true for face-to-face classroom learning. Students in the experimental group always learn on time. In contrast, the control group tends to lack discipline, e.g., by delaying study time with late entry during class hours.\n\nThe analysis of the learning desire indicator in the experimental group was 7.49 higher than in the control group (Table 3). This shows that the students in the experimental group are more interested in learning. As the research progresses, students in the experimental group have a strong desire to learn, especially if the researcher provides them with the latest information on biotechnology materials. In contrast, in the control group, the researchers must encourage the students' willingness to learn.\n\nThe analysis of the indicators of self-control in the experimental group was 9.72 higher than in the control group (Table 3). This can be observed during learning, where students in the experimental group use more time in the learning process. With the availability of learning materials in digital classrooms, the time spent by students is certainly more effective. In addition, students in the experimental group are more responsible in completing the given task. When given a task in the form of practice, they performed better than those in the control group.\n\nFrom the analysis of the research data, benefits are assumed due to the use of digital classrooms in the learning activities in the experimental group. The results show that learning through digital classes has a positive effect on students' learning independence.20 In this sense, in the experimental group, students are expected to study independently at home using digital lessons. So, a learning environment with the help of technology can provide opportunities and positive influence on students to achieve learning independence.21,22\n\nDuring learning, students who have a high level of learning independence exhibit characteristics such as they are used to learning with technology and are active in learning activities. Furthermore, students who are independent learners can determine their own study time.23 Students who have independence in their learning tend to be more actively engaged in independent learning, such as reading online learning materials, completing class assignments, and planning and assessing their own learning.6 In addition, the involvement of technology in learning has a positive impact on students' learning independence.24\n\nIt is important to be aware of some limitations of this research despite all possible efforts. During the conduct of the research, both male and female students have adequate tools to access the internet such as smartphones or laptops, still some students reported that they had experienced network connection problems when accessing the digital classroom, and this condition may have affected the results.\n\n\nConclusion\n\nIn this study, we examined the differences between conventional and blended discovery learning implementations. Our findings show that the combination of face-to-face and digital classrooms positively impacts student learning independence and achievement of learning outcomes. This research was conducted with participants who have a relatively good chance of access to technology and the internet, and it might not generally be representative of all general high school students.\n\n\nData availability\n\nFigshare: Instrument validity, sampling and result of implementation discovery learning in online setting https://doi.org/10.6084/m9.figshare.14419262.v1.25\n\nThis project contains the following extended data:\n\n- the validity, reliability, discrepancy and difficulty level of the questions.\n\n- sample selection.\n\n- data on learning outcomes and student independence, including the calculation of the t-test.\n\nFigshare. Biotechnology test and Fisher's self-directed learning (SDL questionnaire) https://doi.org/10.6084/m9.figshare.14398943.v1.26\n\nThis project contains the following extended data:\n\n• This data contains the 25 item biotechnology cognitive test instrument and Fisher's SDL questionnaire\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\nFayanto S, Yosephien M, Tinon R, et al.: Indonesian Journal of Science and Education. Indonesian J Sci Edu. 2019; 3(2): 93–102. Publisher Full Text\n\nLiaw S, Huang H: Developing a Collaborative E-Learning System Based on Users' Perceptions. Lecture Notes in Computer Science. 2007: 751–759. Publisher Full Text\n\nKusnohadi: Pendidik Online: Perluasan Tugas dari Kelas Konvensional menuju Kelas Maya. Jurnal Teknodik. 2014; 18(3): 284–294.\n\nSetiawan Y: Pemanfaatan Kelas Maya Untuk Pembelajaran Daring.Jakarta: Pustekkom Kemdikbud; 2018.\n\nPutri VR: Memaksimalkan Kompetensi Guru Melalui Fitur Kelas Maya Dalam Pembelajaran Bahasa Arab Sebagai Inovasi Pembelajaran Jaman Now. 3rd International Conference on Education. 2018: 323–332.\n\nGeng S, Law KM, Niu B: Investigating self-directed learning and technology readiness in blending learning environment. Int J Edu Technol Higher Edu. 2019; 16(1): 1–22. Publisher Full Text\n\nBrata WWW, Suriani C, Simatupang H, et al.: Prospective Science Teachers’ Learning Independency Level on Blended Learning. In: Journal of Physics: Conference Series. 2020, February; Vol. 1462, No. 1, p. 012070. IOP Publishing.\n\nFisher M, King J, Tague G: Development of a self-directed learning readiness scale for nursing education. Nurse Educ Today. 2001; 21: 516–525. PubMed Abstract | Publisher Full Text\n\nPaechter M, Maier B: Online of Face-To-Face? Students' Experience and Preference in E-Learning. Internet and Higher Education. 2010; 13: 292–297. Publisher Full Text\n\nReynolds R: Information Uses and Learning Outcomes During Guided Discovery in a Blended E-Learning Game Design Program for Secondary Computer Science Education. Hawaii Int Conf Sys Sci. 2017: 2076–2085. Publisher Full Text\n\nKintu MJ, et al.: Blended Learning Effectiveness: The Relationship Between Student Characteristics, Design Features and Outcomes. Int J Edu Technol Higher Edu. 2017; 14(7), 1–20. Publisher Full Text\n\nPanigrahi R, Srivastava PR, Sharma D: Online learning: Adoption, continuance, and learning outcome — A review of literature. Int J Information Management. 2018; 43: 1–14. Publisher Full Text\n\nYazdi M: E-learning Sebagai Media Pembelajaran Interaktif Berbasis Teknologi Informasi. Jurnal Ilmiah Foristek. 2012; 2(1): 143–152.\n\nDe Smet C, Valcke M, Schellens T, et al.: A qualitative study on learning and teaching with learning paths in a learning management system. JSSE-Journal of Social Science Education. 2016: 27–37.\n\nHidayat WN, et al.: Cognitive Ability Improvement in Learning Resource Development Course Through Implementation of Life-Based Learning Models Using LMS. Int Conf Computer and Informatics Engineering (IC2IE). 2019; 1–6. Publisher Full Text\n\nWicaksana GA, Nurhayati S, Cahyono E: Efektivitas Media Pembelajaran E-Learning Berbasis Chemo-Edutainment terhadap Hasil Belajar Materi Hidrokarbon dan Minyak Bumi Siswa Kelas X. Chemistry in Education. 2013; 2(1): 1–10.\n\nLadyshewsky RK: E-Learning Compared With Face To Face: Differences In The Academic Achievement of Postgraduate Business Students. Aust J Edu Technol. 2004; 20(3): 316–336. Publisher Full Text\n\nBrata WWW, Arsila P: The Effectiveness of Online Supported Learning in High School Students on Invertebrate Topics. J Phy: Conf Series. 2021, March; Vol. 1819, No. 1, p. 012048. IOP Publishing.\n\nHsu C-L, Zhao Y, Wang W-C: Self-directed Learning Oriented Assessments in the Asia-Pacific, Education in the Asia-Pacific Region.Tai Po: Springer. Publisher Full Text\n\nMuthmainnah S, Johan RC, Riyana C: Hubungan Antara Pembelajaran Menggunakan Kelas Maya Dengan Kemandirian Belajar Mahasiswa. Jurnal Edutechnologia. 2019; 3(1): 30–40.\n\nFahnoe C, Mishra P: Do 21st century learning environments support self-directed learning? Middle school students' response to an intentionally designed learning environment. In Society for information technology & teacher education international conference (pp. 3131-3139). Association for the Advancement of Computing in Education (AACE); 2013, March.\n\nBartholomoew SR, et al.: Relationships Between Access to Mobile Devices, Student Self-Directed Learning, and Achievement. J Technol Edu. 2017; 29(1): 2–24. Publisher Full Text\n\nRachmawati DO: Penerapan Model Self-Directed Learning Untuk Meningkatkan Hasil Belajar dan Kemandirian Belajar Mahasiswa. Jurnal Pendidikan dan Pengajaran. 2010; 3: 177–184.\n\nRashid T, Asghar HM: Technology Use, Self-Directed Learning, Student Engagement and Academic Performance: Examining The Interrelations. Comp Human Behav. 2016; 63: 604–612. Publisher Full Text\n\nBrata WWW, Rahmadina N: Instrument validity, sampling and result of implementation discovery learning in online setting. figshare. Dataset. 2021. Publisher Full Text\n\nBrata WWW, Rahmadina N: Biotechnology test and Fisher's self-directed learning (SDL questionnaire). figshare. Dataset. 2021. Publisher Full Text\n\nFraenkel J, Wallen N: How to Design and evaluate research in education. 2nd ed New York: McGraw-Hill Inc.; 1993."
}
|
[
{
"id": "88023",
"date": "01 Jul 2021",
"name": "Rasmitadila Rasmitadila",
"expertise": [
"Reviewer Expertise Inclusive education",
"elementary education"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe title of this manuscript describes the use of the discovery learning method in the two selected classes, but these two classes are not comparable in terms of the learning system. The experimental class uses blended learning, while the control class uses face-to-face. In this case, both classes use the discovery learning method. In fact, both classes should use the same learning system so that they can be compared. Regarding learning methods, this must be distinguished. One class uses discovery learning, and the other class uses other learning methods. This resulted in a bias in the results of the study, as conditioned that the experimental class was \"better\" than the control class.\nI recommend that the research method should be replaced with the correlation method so that it can measure the increase in learning outcomes and learning independence. This manuscript also highlights more problems for the experimental class only compared to the control class, especially in the Discussion section. So, the research method is more likely to use correlation research methods with data analysis, such as path analysis, etc.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
},
{
"id": "164378",
"date": "09 Mar 2023",
"name": "Kyeorda Kemp",
"expertise": [
"Reviewer Expertise Self-directed learning in education and increasing access to pipeline programming in medicine and science."
],
"suggestion": "Not Approved",
"report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis study compares a hybrid online/in-person model (experimental) and traditional face-to-face learning (control). Both utilize \"discovery learning.\" The authors find individuals in the experimental group have higher scores on SDL and learning outcomes. This is an exciting result that should be published; however, the paper has numerous issues.\nOverall concerns\nThe language used in the paper is informal at times. There is also a lot of awkward and repetitive language. The report would benefit from a substantial review and restructuring.\n\nIt is not clear what discovery learning is. Initially, I believed it to be unique to the experimental group and linked to using the online platform. Please clarify.\nIntroduction\nA substantial review of SDL should be included, discovery learning should be defined, and the connection between discovery learning and SDL should be explored.\n\nAlso, the thesis statement in paragraph 2 is confusing. Is this based on conjecture or evidence? If evidence, please provide the citations. \"It is assumed that this change in learning methods will reduce meaningful learning experiences due to the ease with which students learn the subject matter instantly.\"\n\nPlease define what \"good learning outcomes\" means in paragraph 3.\nMethods\nPlease organize by headings: Ethical Approval, Setting, Population demographics, Procedure, Instruments utilized, and statistical analysis. Please reorganize the methods, so the appropriate information is arranged within these sections.\n\nPlease make a procedure figure for ease of review.\n\nI am very excited that you tested for validity, but you did not indicate this in the methods until the last paragraph as an afterthought. Please state this in the section with instruments and report the Cronbach alpha for Fisher's Self-Directed Learning questionnaire. Please indicate that this information can be accessed at figshare with a web link.\n\nPlease remove information regarding scoring and cite the original publication that explains this.\n\nThe last paragraph seems unnecessary. Please state that the control group couldn't access the learning management system and put this information with the information explaining the groups.\nResults\nPlease place tables so that they are referenced in the correct order.\n\nPlease provide statistical analysis for data in table 2. Are there gender-based differences?\n\nI assumed cognitive and student learning outcomes are the same, but please clarify and define.\n\nParagraph 3 belongs in the discussion.\n\nPlease explain how students' learning independence criteria were defined in the methods.\n\nPre-scores are mentioned, but how does this compare to post? Please also report if there were differences in the group pre-intervention start. This is important.\nTables and Figures\nFigures 3 and 4 add little to the paper and should be removed. Figure 2 duplicates data in table 4. Please delete. If you choose to keep it, provide statistics and error bars.\n\nProvide captions for all tables and figures.\n\nFigure 1's title does not seem accurate.\n\nTable 3 has commas instead of periods.\n\nIn table 4, the max is 55, the min is 67, and the average is 70.88. Is there an error here?\nDiscussion\nPlease do a thorough reading and remove redundant information. Also, please structure the discussion.\n\nPlease start with a very brief summary of your key findings that you will then expand upon in the discussion.\n\nPlease compare and contrast your work with the available literature and discuss how your work expands the field.\n\n\"The digital classroom (Figure 3) in the study was used as a treatment in the experimental group\" can be removed.\n\nParagraph 2 is repeated in paragraph 8; however, the information makes more sense in paragraph 8.\n\nYou may want to remind the reader of the statistical significance of your data by including the value after statements such as, \"From the analysis of the research data, it is clear that the learning outcomes of students in the experimental group are higher than in the control group.\"\n\nThere are numerous times when the author seems to make a logical jump or assumptions. See below:\n- \"... especially if the researcher provides them with the latest information on biotechnology materials. In contrast, in the control group, the researchers must encourage the students' willingness to learn.\"- How do we know this? Could other factors account for the difference?\n- \"This can be observed during learning, where students in the experimental group use more time in the learning process.\"- Is this evident somewhere and not reported? Did you survey them about time?\n- \"When given a task in the form of practice, they performed better than those in the control group.\"- Is this information reported?\nLimitations\nDid you survey face-to-face students about their behavior regarding using outside tools? Is it possible that both groups explored content, but those with access to the LMS had appropriate materials readily available?\nAdditional questions/suggestions\nDid the authors ever explain to students the importance of validity in assessing sources for study? If not, it may be that the face-to-face individuals utilized inferior resources.\n\nWas the importance of discovery learning explained to both groups?\n\nWould it be appropriate also to run correlation and regression analysis of SDL and CLO? It seems as if there is an assumption that SDL is influencing CLO. So, analysis should 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? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-386
|
https://f1000research.com/articles/10-154/v1
|
26 Feb 21
|
{
"type": "Research Article",
"title": "Growth and health status of Pangasionodon hypophthalmus reared under manipulated photoperiod conditions",
"authors": [
"Windarti Windarti",
"Bintal Amin",
"Asmika H. Simarmata",
"Bintal Amin",
"Asmika H. Simarmata"
],
"abstract": "Background: In general, the length of photoperiod affects the physiology of Pangasionodon hypophthalmus. This study aimed to understand the growth and health status of this fish reared under manipulated photoperiods. Methods: The study was conducted between May and August 2020. Three treatments were applied: control (natural photoperiod); 18 hours of darkness (18D6L; tanks were placed under a dark tarp tent for 18 hours); and 24 hours of darkness (24D0L; tanks were placed under a dark tarp tent continuously). Three replications were performed per treatment. At baseline, fish were approx. 3 inch total length (TL) and 4 g body weight (BW), and were reared in circular plastic tanks (100 L; 30 fish/tank) with aerators and filters, and fed with commercial fish feed pellet (2 times/day to satiation). Fish growth and survival were studied once/week, and blood and tissue samples were taken at the end of the experiment (8th week). Tissue was formalin fixed and HE stained. Results: The survival of fish in all treatment was 100%. The fish reared in 24D0L and 18D6L grew better than control, achieving a mean TL of 23 cm and BW of 98 g (control = 19 cm TL and 72 g BW). There was no difference in hematology condition or tissue structure between the three groups. Tissue structure of gill, kidney and liver were normal, but light abnormality due to parasites was present in the gill of fish reared in 24D0L. Blood samples for all three groups showed mean red blood cell count of 1,800,000 cells/ml and white blood cell (WBC) count of 55,200 cells/ml. WBC consisted of lymphocyte 65%, monocyte 24%, thrombocyte 6%, neutrophil 3%, eosinophil 1% and basophile 1%. Conclusion: Data obtained indicate that a short photoperiod improves the growth of P. hypophthalmus fish and does not negatively affects their health.",
"keywords": [
"light",
"hematology",
"tissue structure",
"effective fish culture"
],
"content": "Introduction\n\nIn Riau, Indonesia, Pangasionodon hypophthalmus or “patin” fish is one of the most favored fish. This fish is commonly smoked or freshly sold and is a main ingredient for many types of Riau’s traditional cuisine. Due to high demand and high economic value, the fish is commonly cultured1.\n\nTo increase the effectiveness of fish culture, various techniques are commonly applied. For example, fish farmers in Riau feed the fish abundantly or to satiation. Using this technique, the fish may grow well, but the cost of fish feed becomes high. As the fish are provided with a high quantity of food, the amount of uneaten feed and metabolism discharge, such as urine and fish feces, that enter the water may also increase, contaminating water in the surrounding area. Another technique to improve fish culture is the use of chemicals to maintain fish health and boost growth. However, the remains of the chemicals may be present in fish meat and may also pollute the environment.\n\nAn environmentally friendly method that can be applied to fish culture is the manipulation of the photoperiod. This technique may be categorized as a “natural method”. The application of this method is cheap, no veterinary medicines used, and it is environmentally friendly. Several studies have proved that this method is effective to improve the growth of several fish species, such as the nocturnal fish Clarias batrachus2, Ompok hypophthalmus3 and P. hypophthalmus reared in tarp pond4. A short photoperiod positively affects the growth of these fish. Fish that are reared under dark condition are shown to be less active in swimming, but react positively toward feed provided5,6.\n\nEven though dark condition improves the growth of fish, water quality in the rearing tank may poor. As there is no light, phytoplankton are not able to thrive and as a consequence there is no organism consuming organic materials present in the water. High content of organic materials in the rearing media may decrease the water quality and provide suitable conditions for growth of parasites and pathogens of fish. The fish may become more vulnerable towards parasite and pathogen, affecting the health of the fish. Pathogens and parasites will negatively affect the physiology of fish and this may be reflected in the hematology and tissue structure of the fish. According to Fazio7, blood cell count represents a important and powerful tool to diagnose the health status of fish. Hematological condition may be used to evaluate fish health and welfare in cultured fish and in free-living fish8.\n\nHealth status, especially blood condition and tissue structure of fish’s main organ such as gill, liver and kidney, has never been reported in the context of photoperiods. In order to understand the effects of shortened photoperiod on P. hypopthalmus growth and health status, this study was conducted. Information obtained in this study might be used as a basis to design healthy, effective, and environmentally friendly P. hypopthalmus culture conditions.\n\n\nMethods\n\nThis study was conducted at the Aquatic Biology Laboratory, Fisheries and Marine Science Faculty, Riau University, from June to August 2020. The experiments were carried out within the ethical guidelines provided by the research institution and national or international regulations.\n\nFingerlings of P. hypopthalmus were obtained from the hatchery of the Riau Province’s Marine and Fisheries Department in Tibun, Pekanbaru. The fish samples were selected based on their performance. The fish that showed active swimming, no wounds or external parasites and were approximately 3 inches total length (TL) and 4 g (BW) were chosen for the research. The density of fish was 30 fish/tank (total of 270 fish in 9 tanks = 3 per treatment).\n\nFish were reared in 110 L circular grey plastic tanks that were filled with 100 L freshwater obtained from a bored well. The tanks were fitted with an aerator, recirculating pump and filter. During the research, the fish were feed with commercial fish feed pellet (F999 with 35% protein content for weeks 1–5; and F718-1 for weeks 6–8; PT Central Proteina Prima Tbk Indonesia). The feed was given two times/day, in the morning and in the afternoon, ad libitum until satiation. To maintain the water quality, any feed remains were removed every day. The filter was washed or replaced once/week, and around 25% the water volume was removed and replaced with clean freshwater once/week.\n\nThree treatments (each with three replications) were applied: 24D0L, fish were cultured under continuous dark condition (24 hours of darkness); 18D6L, fish were cultured with 18 hours of darkness and 6 hours of light; control (Co), the fish was reared under natural photoperiod. The rearing tanks were grouped based on the photoperiod treatments and in each group the tanks were placed randomly based on lottery method.\n\nThe light used in this study was natural sunlight, while the dark condition was created by placing the tanks under dark blue colored tarp tent. In 24D0L treatment, the tanks were placed under the tent continuously, which was only opened during feeding times (around 5 minutes/feeding time), two times/day in the morning and in the evening. In 18D6L treatment, the tanks were exposed to natural light for 6 hours (7 am to 1 pm). For the natural photoperiod treatment, the tanks were exposed to sunlight and were placed under transparent plastic tent to prevent evaporation and to avoid rainwater input.\n\nFish growth (TL and BW) was at baseline and then monitored weekly. Each week, 3 fish from each tank were randomly sampled. The total length was measured using a ruler and the body weight was measured using a digital scale (0.01 gr).\n\nBlood and tissue sampling were conducted two times, at baseline and in the 8th week (end of the research period). Three fish from each tank were taken and their blood were obtained; fish were anesthetized using clove oil (5 drops/L). As the fish were sedated (inactive and no response to touching), blood was then taken from the caudal vein, by inserting an EDTA (Merck) 10% moistened syringe. Blood samples was kept in EDTA moistened vials, in a cool box filled with crushed ice. Total erythrocytes and leukocytes were counted using a Neubauer hemocytometer and then were calculated9 and analyzed10. Hematocrit and leucocrit levels were determined using heparinized micro-hematocrit capillaries that was centrifuged at 12,000 rpm for 3 minutes. To calculate the hematocrit or leucocrit levels, the length of the column of packed red cells or the packed white blood cells was measured and divided by the length of the whole column of blood (cells and plasma) and then multiply this number by 100%. Hemoglobin content in blood was measured using Sahli method11.\n\nTissue samples (gill, kidney and liver) were taken from three different fish/tank at the end of the research period. The samples were processed for histological study12. After tissue removal, they were fixed in 10% formalin for 48 hours and in 4% formalin for three days. Then the samples were processed using alcohol series and paraffin, 5µm sliced and hematoxylin-eosin stained. The histological study of the tissue was conducted using a binocular microscope Olympus CX-21. Any abnormality in the tissue was noted.\n\nData collected were analyzed with Microsoft Excel (to create graphics) and SPSS (to calculate ANOVA of growth data).\n\n\nResults\n\nDuring the research, survival of the fish was monitored every day. There is no difference in the survival of fish in all treatments applied. Survival was 100%, and no fish showed any behavioral abnormality, i.e. actively swimming and responding well to the food provided.\n\nUnlike survival, the growth of fish varied according to treatment (Figure 1). Fish reared in shortened photoperiod (24D0L and 18D6L) exhibited better growth than fish reared under natural photoperiod (control). By the end of the experiment, the fish that were reared under continuous dark (24D0L) were longer and heavier than control fish, but were not that different compared with fish reared in 18D6L. Fish reared in 24D0L and 18D6L treatments were >20 cm TL and 84.74–98.78 g BW, while control fish were on average 18.93 cm TL and 17.2 g BW. Data obtained indicate that the 24D0L treatment resulted in the best treatment condition as the fish has the greatest TL and BW (Table 1).\n\n24D0L, 24 hours of darkness; 18D6L, 18 hours of darkness; Co, control – normal conditions.\n\n24D0L, 24 hours of darkness; 18D6L, 18 hours of darkness; Control, normal conditions.\n\nMean with standard error followed by different letters are significantly different (P<0.05)\n\nHematological conditions of the fish in all treatments were similar. There is no difference in the blood condition of all fish treated (Table 2). The number of red blood cells (RBC) as well as the number of white blood cells (WBC), and hematocrit and leucocrit levels were normal. In all treatments, the number of RBC was around 1,800,000 cells/mL with 25.62–36.63% hematocrit level.\n\n24D0L, 24 hours of darkness; 18D6L, 18 hours of darkness; Control, normal conditions.\n\nData presented in Table 2 show that the number of WBC and leucocrit level in fish of all treatment are almost the same, ranging from 54,213 to 55,563 cells/ mL and 1.27–1.54%, respectively. WBC cell examination showed that the WBC component of P. hypopthalmus consisted of lymphocytes, monocytes, thrombocytes, neutrophils, basophils and eosinophil (Table 2; Figure 2).\n\n24D0L, 24 hours of darkness; 18D6L, 18 hours of darkness; Co, control – normal conditions.\n\nData presented in Table 3 shows that the most common WBC type present in all treated fish is lymphocytes: lymphocytes, 69.55–74.29%, followed by monocytes (14.31–22.80%), thrombocytes (1.00–17%), and few amount granulated cells (neutrophil, eosinophil and basophil).\n\nLooking at the gill structure of the fish revealed that the fish are healthy (Figure 3). There is no abnormality such as hyperplasia, hypertrophy, lifting epithelium or hemorrhage. The abnormality in fish gill tissue is mainly caused by environmental factors, including poor water quality, pollutants, and also pathogens and parasites13. Among the 27 fish studied, the only gill abnormality was found in the gills of three fish that that were reared in under 24D0L treatment, in the third replication tank. The gills of these fish are pale with dark red spots due to hemorrhage. Detailed study using a binocular microscope showed that many secondary lamellae exhibited hyperplasia and the half base of the lamellae are fused. Further investigation releveled that there are several parasitic worms, Dactylogyrus sp (Monogenea) present in the gills, between the secondary lamellae. Dactylogyrus is a parasite that commonly attacks freshwater fish and may cause serious problems in the fish. This worm inserts its sucker to the blood vessel in the gill, causing a wound. The area around the wound becomes damaged as the epithelium proliferates (hyperplasia) and becomes abnormally enlarged (hypertrophy) causing hemorrhage and the cells may be die creating necrosis12. Dactylogyrus sp. was presence in one tank only. As each tank has its own circulatory system, the parasite was not distributed to the other research tanks.\n\nPL: primary lamellae; SL: secondary lamellae; HPL: hyperplasia; G: glomerulus; H: hepatocyte cells.\n\nThe kidney and liver structures of all fish did not show any abnormality. The cells of these organs were normal and there are no deformities such as hemorrhage, necrosis and hypertrophy. These facts indicate that the fish are normal and healthy.\n\nWater quality in each of the tanks was maintained individually. Each tank is completed with a circulatory pump, filter and aerator. The water is maintained by replacing the filter and replacing 25% of the water with clean fresh water. The accumulated materials in the bottom of the tank was cleaned regularly. Through maintenance, the water was of good quality and suitable for the life of P. hypophthalmus. As the water was maintained regularly, the manipulated photoperiod treatments applied did not affect the water quality, as well as fish health in general.\n\n\nDiscussion\n\nIn all treatments applied, the survival of the fish was 100%, indicating that the media used in this study and the treatments applied do not provide any negative affect toward the fish. P. hypophthalmus is a nocturnal fish that is active at night. In nature, it hides during the day and active in hunting prey at night. Nocturnal fish such as Ompok hypophthalmus5 and P. hypophthalmus6,13 are less active in swimming but very responsive to feed provided during darkness. As the fish in this study were used to being active during the dark, the application of shorten photoperiod does not disturb their biological time keeping and as a consequence, they adapt well to the research tank.\n\nThe fish that were reared in continuous dark grew better than that of fish in other treatments. P. hypophthalmus as a nocturnal fish prefers to inhabit dark colored water such as peat water, and therefore continuous dark might be a suitable environment for this fish. Studies on P. hypophthalmus behavior indicate that during darkness, fish are less active in swimming but they are very responsive to feed provided2,4. As the movement of the fish is lower in darkness, the fish may allocate their energy more for growing and as a result they grow faster4.\n\nIn our hematological study, blood parameters of fish in all treatments were categorized as normal, normal number of RBC in fish ranges from 1,000,000 to 3,000,000 cells/ml14. A normal hematocrit level in Teleostei fish is around 30%15. The number of erythrocyte of healthy P. hypophthalmus is 1.91–2.83×106 cells/mm316. As the number of RBCs of an organism determines the dissolved oxygen carrying capacity17, the number of RBCs, hematocrit level and hemoglobin amount of fish in this study indicates that the fish are healthy. Data obtained in this research shows that the application of manipulated photoperiod do not cause any negative effects on fish health in general. The physiological condition, such as RBC values, may be associated with quick movement and high activity of the fish, or is affected by environmental factors such as water salinity18. Hematology parameters of fish may also be used to monitor the fish’s health status in response toward changes in nutrition, disease, water quality and therapy response7. In our recent, the fish were reared in tanks with comparable conditions and the same feed. The only difference in the rearing method was the manipulated photoperiod applied. As there is no difference in the number of RBCs and hematocrit levels between groups, the data obtained in this study demonstrate that the manipulated photoperiod does not affect the blood condition of the fish.\n\nThe amount of the WBCs, as well as the leucocrit level can be categorized as normal in this study. In healthy fish, the number of WBCs is <150,000 cells/mL11. The number of WBCs as well as leucocrit level in all treated fish were relatively low, indicating that the fish are healthy and there is no pathogen infection. Even though the WBC number of the fish in this study is slightly higher than that of the cultured P. hypopthalmus from Sidoarjo, East Jave, Indonesia (34,600 cells/mL), it is lower than Edwardsiella tarda infected fish (77,950) cells/mL19.\n\nIn this study, WBCs contained lymphocytes, monocytes, thrombocytes, eosinophils, basophils and neutrophils. The composition of this type of WBC indicate that the fish are healthy. Lymphocytes are the most common leukocytes found in healthy teleosts, and they represent an important function in the cell immunity of fish20. The lymphocyte proportion in healthy cultured fish in Riau is around 70% of total WBC, while the lymphocytes of Aeromonas hydrophyla infected fish was around 30% of total WBC11. As the number of phagocytic cell types (monocyte, basophil, eosinophil and neutrophil) in the fish in this present study is relatively low, it means that the fish is not being infected by any pathogen.\n\nHematological parameters have been used as indicators of fish health18. In our study, hematology data of all fish indicated that the fish were normal and healthy. It suggests that the media and rearing methods applied during the study are suitable for the fish and the photoperiod treatments did not affect the hematology of the fish.\n\nThe health status of the fish in this study was also assessed by examining the tissue structure of the main organs, namely gill, kidney and liver. The condition of these tissue were similar between all treatments. The structure of the organs were normal and did not shown any abnormalities. However, light abnormality, namely hyperplasia was found to occur in the gill of fish reared in continuous dark treatment. The gill’s secondary lamella had suffered from hyperplasia and had become thicker and even fused. This condition may hamper water flow as well as reducing the gill area that is used for oxygen diffusion. As a consequence, the fish may have problem conducting respiration21 and even causing mass death in cultured fish22.\n\nIn the gill of fish three fish reared in continuous dark, Dactylogyrus (Monogenean) parasites were found (Figure 3). The abnormalities in the gill of the fish in this study seemed related to the presence of parasites and not related to manipulation of the photoperiod. The presence of the parasite might be related to the general condition of the water in the tank. In the 24D0L treatment, there is almost no light penetrating the water. The lack of light may hamper the growth of phytoplankton that are able to use organic materials in the water to support their life, and which reduce the organic material content in the tank. Due to the absence of phytoplankton, the organic materials in the tank may accumulate and the water condition worsens. The rich organic material water is a suitable habitat for parasites, but this water condition causes stress in fish22. As the fish becomes weak due to stress, the parasite is able to attack the fish and lead the fish to worsen further or even die. The parasitized fish became pale with excess mucus throughout their body, increasing respiration, causing imbalanced swimming, and causing ulcers at the fin edge21. In this study, the parasitized fish became less responsive to feed provided, but none of them died, suggested that the treated fish are able to cope with the parasite. These data indicate that the application of manipulated photoperiod in general improved the growth of the fish, but fish health in general is not negatively affected.\n\n\nConclusion\n\nData obtained in this study showed that the application of 24 hours of darkness is effective in improving the growth of P. hypopthalmus. The fish reared in the dark grew better than the fish reared under 18 hours dark or a natural photoperiod. The manipulated photoperiod treatment did not have any negative impact on the hematology, tissue structure or general health of the fish. It is recommended to apply the 24 hours dark treatment to culture P. hypopthalmus.\n\n\nData availability\n\nFigshare: Hematology data, https://doi.org/10.6084/m9.figshare.13601417.v123.\n\nThis project contains the following underlying data:\n\n- Length data at baseline and weekly (n=27);\n\n- Body weight data at baseline and weekly (n=27);\n\n- Hematological analysis and WBC composition at baseline and week 8 (n=27).\n\nFigshare: Tissue structure, https://doi.org/10.6084/m9.figshare.13602104.v124.\n\nThis project contains the following underlying data:\n\n- Uncropped and unedited tissue structure slide images for gills (n=27), kidney (n=27) and liver (n=27).\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "Acknowledgements\n\nThe authors thanks to the University of Riau that provided grant through “Perceparan Guru Besar Research Scheme” for conducting this research. The authors also thanks the Aquatic Laboratory technician and the students that support this research.\n\n\nReferences\n\nMabroke RS, El-Husseiny OM, Zidan AEFA: Floc meal as potential substitute for soybean meal in tilapia diets under biofloc system conditions. J Oceanol Limnol. 2019; 37(1): 313–320. Publisher Full Text\n\nWindarti W, Riauwaty H, Syawal H, et al.: Penyuluhan manipulasi fotoperiod pada budidaya ikan patin (Pangasius hypopthalmus) di RW VIII Kelurahan Delima Kecamatan Tampan Pekanbaru. Unri Conference Series: Community Engagement. 2019b; 1: 678–683. Publisher Full Text\n\nWindarti BH: Manipulasi fotoperiod untuk memicu pematangan gonad pada ikan selais (Ompok hypopthalmus). Laporan Penelitian. Lembaga Penelitian Universitas Riau. Tidak diterbitkan. 2017.\n\nMagwa RJ: Aspek biologi ikan patin (Pangasius.sp) yang diperlakukan dengan fotoperiod dan diberi makanan yang diperkaya dengan kunyit. Thesis. Program Studi Magister Kelautan. Universitas Riau. Tidak diterbitkan. 2019.\n\nSyafri R: Tingkah laku ikan selais (Ompok hypopthalmus) yang dipelihara pada fotoperiod yang berbeda. Skripsi. Fakultas Perikanan dan Kelautan Universitas Riau. Tidak diterbitkan. 2016.\n\nWindarti, Riauwaty M, Putra RM: Biological aspects of Pangasius hypopthalmus reared under controlled photoperiod. ICFAES 2019 IOP Conf Ser Earth Environ Sci. IOP Publishing, 2019; 348: 012050. Publisher Full Text\n\nFazio F: Fish hematology analysis as an important tool of aquaculture: A review. Aquaculture. 2019; 500: 237–242. Publisher Full Text\n\nIvanc A, Haskovi E, Jeremi S, et al.: Hematological Evaluation of Welfare and Health of Fish. Praxis veterinaria. 2005; 53(3): 191–202 . Reference Source\n\nBlaxhall PC, Daisley KW: Routine haematological methods for use with fish blood. J Fish Biol. 1973; 5(6): 771– 781. Publisher Full Text\n\nAnderson DP, Siwicki AK: Simplified Assays for Measuring Non-specific Defense Mechanism in Fish. Fish Health Section/ American Fisheries Sociaty Meetings. Washington. 1994; 26. Reference Source\n\nPatil PJ, Thakare GV, Patil SP: Variability and Accuracy of Sahli’s Method in Estimation of Haemoglobin Concentration. Natl J Integr Res Med. 2013; 4(1).\n\nWindarti, dan Eddiwan AHS: Buku Ajar Histologi. UNRI Press. 100 hal. 2017.\n\nWindarti, Riauwaty M, Putra RM: Efektivitas Manipulasi Fotoperiod dan Pemberian Pakan yang Diperkaya Dengan Sari Kunyit pada Budidaya Ikan Patin (Pangasius Hypopthalmus) di Kolam Terpal. Laporan Penelitian. Tidak diterbitkan. 2019.\n\nBond CE: Biology of Fishes. W. B. Saunders Company. 1979; 514. Reference Source\n\nMorgan JD, Iwama GK: Measurement of stressed states in the fied in Iwama. G.K., Pickering, A.D.; Sumpter, J.P. and Schreck, C.B. (eds). Fish stress and Health in Aquaculture. Cambridge University Press. Cambridge. 1997; 247–278.\n\nGrant KR: Fish hematology and associated disorders. Veterinary Clinics: Exotic Animal Practice. 2015; 18(1): 83–103. Publisher Full Text\n\nAl V: Organic phosphates in the red blood cells of fish. Comp Biochem Physiol A Mol Integr Physiol. 2000; 125(4): 417–435. PubMed Abstract | Publisher Full Text\n\nParrino V, Cappello T, Costa G, et al.: Comparative study of haematology of two teleost fish (Mugil cephalus and Carassius auratus) from different environments and feeding habits. Eur Zool J. 2018; 85(1): 193–199. Publisher Full Text\n\nA’yunin Q, Budianto B, Andayani s, et al.: Health Condition Analysis of Catfish Pangasius sp. Infected by Edwardsiella tarda. Bacteria. Journal of Aquaculture and Fish Health. 2020; 9(2): 164–172. Publisher Full Text\n\nDal’Bó GA, Sampaio FG, Losekann ME, et al.: Hematological and morphometric blood value of four cultured species of economically important tropical foodfish. Sociedade Brasileira de Ictiologia. Neotrop Ichthyol. 2015; 13(2). Publisher Full Text\n\nMas’ud F: Prevalensi dan Derajat Infeksi Dactylogyrus sp. pada Insang Benih Bandeng (Chanos chanos) di Tambak Tradisional, Kecamatan Glagah, Kabupaten Lamongan. Jurnal Ilmiah Perikanan dan Kelautan. 2011; 3(1): 27–39. Publisher Full Text\n\nŠimková A, Benovics M, Rahmouni I, et al.: Host-specific Dactylogyrus parasites revealing new insights on the historical biogeography of Northwest African and Iberian cyprinid fish. Parasit Vectors. 2017; 10(1): 589. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAmin WW, Bintal A: Hematology data. figshare. Dataset. 2021. http://www.doi.org/10.6084/m9.figshare.13601417.v1\n\nAmin WW, Bintal A: Tissue structure. figshare. Figure. 2021. http://www.doi.org/10.6084/m9.figshare.13602104.v1"
}
|
[
{
"id": "80362",
"date": "08 Mar 2021",
"name": "Hafrijal Syandri",
"expertise": [
"Reviewer Expertise Aquaculture"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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: Initial fish length (inches), please convert to units (cm).\nKeyword: I suggest adding 'Aquaculture'.\nIntroduction: Please add the quantity data about its high demand and economy value of Pangasionadon hypophthalmus in Riau Province.\nMethods: Study design and fish:\nIn the methodology, the research was conducted in June and August 2020, while in abstract was carried out in May and August 2020, please write it correctly.\n\nThe initial length data of fish measured in inches should be converted into cm, because fish growth is measured in units of cm (see. Table 1).\n\nIt is advisable to write down the time for feeding fish in the morning and evening (for example: 09.00 AM and 17.00 PM) and the term adlibitum, please replace it with the feeding rate (% / day).\nData collection and analysis:\nPlease write accuracy of ruler i.e. 1 mm to measure the length of the fish and state the type of electronic scale and the model (for example: OHAUS, CT 1200-S USA model).\n\nWrite down the formulas used to analyze growth in total length and body weight, and it is suggested to analyze the specific growth rate (% / day) and feed conversion ratio of fish each treatment.\nResults:\nAdd the results of the analysis of specific growth rate (% / day), and feed conversion ratio (FCR) for each treatment and present them in Table 1.\nDiscussion:\nThe growth of Pangasionadon hypopthalmus from each experiment has not been discussed, and therefore I recommend discussing it.\n\nReferences written in Indonesian are exchanged with English, except for journal names (references numbers 2, 3, 4, 5, 12, 13, 21).\nFor example: Windarti BH: Photoperiod manipulation to trigger gonadal maturation of Selais (Ompok hypophthalmus). Research Report, Research Service Universitas Riau, Unpublished, 2017 (In Indonesian), or (In Indonesian with English abstract).\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Yes",
"responses": [
{
"c_id": "6619",
"date": "14 May 2021",
"name": "Windarti Windarti",
"role": "Author Response",
"response": "Abstract: Initial fish length (inches), please convert to units (cm). I have converted the unit of fish length from inches to cm Keyword: I suggest adding 'Aquaculture'. I add “aquaculture” into the keywords. Introduction: Please add the quantity data about its high demand and economy value of Pangasionadon hypophthalmus in Riau Province. I have added information on the quantity data of high demand and economy value of P. pangasionodon Methods: Study design and fish: In the methodology, the research was conducted in June and August 2020, while in abstract was carried out in May and August 2020, please write it correctly. I have revised the research time, from June to August The initial length data of fish measured in inches should be converted into cm, because fish growth is measured in units of cm (see. Table 1). I have converted the fish length unit, from inch to cm It is advisable to write down the time for feeding fish in the morning and evening (for example: 09.00 AM and 17.00 PM) and the term adlibitum, please replace it with the feeding rate (% / day). I have revised the feeding time, at 06.00 in the morning and 06.00 evening. The fish was fed at satiation and I stopped feeding the fish when most of them were not positively response to feed. Data collection and analysis: Please write accuracy of ruler i.e. 1 mm to measure the length of the fish and state the type of electronic scale and the model (for example: OHAUS, CT 1200-S USA model). I used a ruler with 1 mm accuracy, a plastic USA model ruler Write down the formulas used to analyze growth in total length and body weight, and it is suggested to analyze the specific growth rate (% / day) and feed conversion ratio of fish each treatment. I have added the formulas used to analyze growth in total length and body weight and also add the information on specific growth rate (% / day) and feed conversion ratio of fish each treatment. Results: Add the results of the analysis of specific growth rate (% / day), and feed conversion ratio (FCR) for each treatment and present them in Table 1. I have added the specific growth rate (% / day), and feed conversion ratio (FCR) for each treatment Discussion: The growth of Pangasionadon hypopthalmus from each experiment has not been discussed, and therefore I recommend discussing it. I have added the information of fish growth in each treatment References written in Indonesian are exchanged with English, except for journal names (references numbers 2, 3, 4, 5, 12, 13, 21). I have changed the references written in Indonesian to English"
}
]
}
] | 1
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https://f1000research.com/articles/10-154
|
https://f1000research.com/articles/9-346/v1
|
11 May 20
|
{
"type": "Study Protocol",
"title": "Evaluating adults’ health-related values and preferences about unprocessed red meat and processed meat consumption: protocol for a cross-sectional mixed-methods study",
"authors": [
"Claudia Valli",
"Victoria Howatt",
"Anna Prokop-Dorner",
"Montserrat Rabassa",
"Bradley C. Johnston",
"Joanna Zajac",
"Mi Ah Han",
"Fernando Kenji Nampo",
"Gordon H. Guyatt",
"Malgorzata M. Bala",
"Pablo Alonso-Coello",
"Claudia Valli",
"Victoria Howatt",
"Anna Prokop-Dorner",
"Montserrat Rabassa",
"Bradley C. Johnston",
"Joanna Zajac",
"Mi Ah Han",
"Fernando Kenji Nampo",
"Gordon H. Guyatt",
"Pablo Alonso-Coello"
],
"abstract": "Background: People need to choose from a wide range of foods, and in addition to availability and accessibility, people’s values and preferences largely determine their daily food choices. Given the potential adverse health consequences of red and processed meat and the limited knowledge on individuals’ health-related values and preferences on the topic, such data would be useful in the development of recommendations regarding meat consumption. Methods and analysis: We will perform an international cross-sectional mixed methods study in four countries across two continents. The study population will consist of adult omnivores currently consuming a minimum of three weekly servings of either unprocessed red meat or processed meat. We will explore participants’ willingness to stop or reduce their unprocessed red meat, or their processed meat consumption through a direct-choice exercise. This exercise will consist of presenting a scenario tailored to each individual’s average weekly consumption. That is, based on a systematic review and meta-analysis of the best estimate of the risk reduction in overall cancer mortality and cancer incidence, we will ask participants if they would stop their consumption, and/or reduce their average consumption. We will also present the corresponding certainty of the evidence for the potential risk reductions. Finally, for all included participants, we will measure their meat consumption three months after the interview and determine if they have made any changes to their average consumption. Ethics and dissemination: The research protocol was approved by the ethics committees in Canada (Research Ethics Board, Dalhousie University), Spain (Comitè Ètic d'Investigació Clínica de l'IDIAP Jordi Gol), Poland (The Bioethics Committee of the Jagiellonian University), and Brazil (National Research Ethics Commission). The study is based on voluntary participation and informed written consent. Results from this project will be disseminated through publications and presentations.",
"keywords": [
"health",
"values and preferences",
"red meat",
"processed meat",
"cross-sectional study",
"mixed methods"
],
"content": "Introduction\n\nFood choices are important for the overall health of each individual1. On a daily basis, people need to choose from a wide range of food in order to meet their nutritional requirements2. People’s dietary values and preferences influence the types of foods they consume, as well as the quantity of consumption3,4. However, nutritional guidelines have consistently ignored the systematic identification and incorporation of people’s values and preferences in the development of their recommendations5.\n\nIn light of recent studies showing an association between unprocessed red meat and processed meat consumption and adverse health outcomes, such as all-cause mortality, cardiovascular mortality, cancer risk, and stroke6–11, dietary guidelines have generally endorsed limiting meat intake (e.g. limiting processed meat)12–14. However, limited information exists regarding how much people value meat in their diet and their willingness to reduce meat consumption in the face of undesirable health effects15. Recently, an international panel of 14 members noted the low quality evidence supporting the causal relation of meat and adverse effects, and the small protective effect of reducing meat consumption if indeed such an effect exists. The panel formulated a weak recommendation in favor of continuing usual consumption16. The recommendation was also based on a systematic review of studies addressing peoples’ values and preferences regarding meat consumption; however, the evidence was also judged to be of low quality given identified issues with risk of bias and indirectness15.\n\nWe have therefore designed a study to evaluate adults’ values and preferences regarding meat intake and their willingness to change their consumption in the face of possible undesirable health consequences. Given the general importance of reducing cancer, the recent claims on cancer risk associated with meat consumption from the International Agency for Research in Cancer and the World Cancer Research Fund7,17, and in an attempt to avoid overwhelming participants with too much information, based on a systematic review of the literature10, we chose the risk estimates for two cancer outcomes to share with participants, specifically cancer incidence and cancer mortality.\n\nThis study is part of NutriRECS (Nutritional Recommendations; www.nutrirecs.com)18, an initiative that aims to: 1) apply rigorous systematic review and guideline methods using the GRADE approach to investigate the association between diets, foods and nutrients and health outcomes; 2) incorporate patient and community values and preferences to inform guideline recommendations; 3) apply strict and transparent management of conflicts of interest, and; 4) disseminate nutritional recommendations via open-access peer-reviewed publication.\n\n\nMethods and analysis\n\nWe are conducting an international cross-sectional mixed-methods study including a quantitative assessment followed by a qualitative evaluation in four different sites in four countries (Spain, Brazil, Canada and Poland). Study settings will include primary health care centers, universities, and the general community. The study began in 2019 with recruitment and data cleaning ongoing, with expected completion in early 2021.\n\nWe will enroll adults 18 to 80 years of age who currently consume a minimum of three serving per week of either unprocessed red meat or processed meat. Unprocessed red meat is defined as mammalian meat (e.g. beef, pork, lamb), and processed meat is defined as white or red meat preserved by smoking, curing, salting, or by the addition of preservatives (e.g., hot dogs, charcuterie, sausage, ham, and cold cut deli meats)19. We will exclude adults who have active cancer; those who have severe cardiovascular disease (history of stroke, acute coronary syndrome, heart failure, and symptomatic peripheral arterial disease); those who are pregnant; and participants unwilling or unable to provide informed consent.\n\nWe will conduct in-person and online surveys. For the in-person surveys, we will recruit a convenience sample of participants visiting primary health care centres or other public facilities. We will provide to the health centres with posters and flyers, including information describing the objectives of the study, and the amount of time and effort required to participate in the study. The research team member on site will ask eligible people visiting the centre if they are willing to participate.\n\nFor the online surveys, we will recruit a convenience sample of participants studying and/or working at the university. For instance, we will send an email to registered students and/or employees including study’s details, eligibility criteria, contact information of the researcher carrying out the study, and the related link to access the online survey.\n\nFor the quantitative assessment, to ensure feasibility, in 2019, we conducted a pilot study in a sample of 32 participants recruited in the general community in Nova Scotia and Prince Edward Island, Canada. In the pilot study, the proportion of people willing to reduce unprocessed red meat was 0.53 and the proportion of people willing to reduce processed meat was 0.4420. Based on these results we have made a best estimate of the proportion willing to reduce their meat intake of approximately 0.5, which is also the proportion yielding the widest confidence intervals and thus the most conservative sample size projection. We decided that a confidence interval around this estimate of as much as ± 10 is acceptable. We can achieve this precision with a 0.5 estimate in our primary outcome, the proportion of individuals ready to reduce or stop eating meat. Our sample size estimate is 96 participants at each site (95% confidence interval with ± 10 percent margin of error)21,22.\n\nFor the qualitative evaluation, through a maximum variation sampling strategy, in each site, we will include a subsample of participants until data saturation. Data saturation is achieved when no additional concepts emerge23. During data collection and analysis, if the research team determines that we have not reached data saturation, recruitment will be extended to include more participants until saturation is achieved. The maximum variation technique consists of the inclusion of a highly heterogeneous sample, and a description of the variability or dispersion for the relevant variables3,24. We will attempt to include an approximately equal number of participants with the following characteristics of these variables: gender (men and women); age (those between 18 to 66 years old, and those between 67 and 80 years older); education level (those with some high school or less, those with a high school degree, and those with a college degree) and willingness to stop or reduce meat consumption (willing ≥5 from the Likert-Scale and unwilling <4 from the Likert-Scale).\n\nFor the sites conducting in-person surveys, the research team member on site will explain the study’s purpose and carry out the informed consent process. If participants decline to participate, we will document the reasons for refusal; their age and gender and, if possible, their current meat consumption. If participants cannot participate due to time constraints, we will offer them to complete the survey online. If participants agree to be part of the study, the research team member will ask them to complete a questionnaire including demographic characteristics, medical history information and meat consumption beliefs and behavior. The research team member will enter the data in the study database. We will then determine participants’ willingness to change their meat consumption through a direct choice exercise, by presenting scenarios tailored to each individual’s consumption and, based on our systematic review and dose-response meta-analysis10, reflecting the best estimate of absolute risk reduction in cancer mortality and overall cancer incidence over their lifetime. Based on the calculated risk reductions, we will ask if participants would a) stop or b) reduce consuming either unprocessed red meat or processed meat (whichever they are eating more of). For the qualitative evaluation, we will conduct semi-structured interviews in which we will ask participants additional questions regarding their motives to reduce or continue with their current unprocessed red meat or processed meat consumption.\n\nFor sites conducting online surveys, participants interested in participating will access to the online survey and will be able to complete the questionnaire and the direct choice exercise, similar to the in-person survey described above. If participants agree to participate in the semi-structured interviews, we will arrange a meeting (in person or through a secured Skype or Zoom call) in which we will ask additional questions addressing their motives to reduce or continue with their current unprocessed red meat or processed meat consumption.\n\nFinally, for all sites, we will conduct a follow-up interview, either by phone or by email, at three months to ask participants, who agreed to be contacted, if they have made any changes in their meat consumption.\n\nQuestionnaire. Based on our phase one pilot study in Canada, we will further develop and pilot a questionnaire in each centre to collect the following data: age, sex, socioeconomic status, educational level, employment status, household size, religious beliefs, the presence of chronic and other health conditions, and family history of cancer, and meat consumption beliefs and behavior information. For the piloting process, we will ask both men and women with different educational backgrounds and of different ages (those between 18 to 66 years old, and those between 67 to 80 years older) to complete the questionnaire in order to identify ways of improving the content and/or structure of the questionnaire.\n\nWe will assess participants’ current consumption of unprocessed red meat and processed meat and determine their relative consumption. We will facilitate these questions related to their meat consumption habits by providing pictures illustrating types of meats and serving size. In addition, we will determine which factors participants take into account when choosing their diet, whether their food choices influence or are influenced by other people (e.g. preparing food for children) and to what extent they are satisfied with their current diet.\n\nServing size estimate and participant’s current meat consumption assessment. We estimated that each serving of unprocessed red meat is equal to 120g, and 50g for processed meat10. In Spain, the mean ± standard deviation of meat intake, according to 2016 Spanish National dietary survey in adults, conducted by the Spanish Agency for Consumption, Food Safety and Nutrition, is 37 ± 63g/day (2 servings/week) of unprocessed red meat and 32 ± 65g/day (4 servings/week) of processed meat25. In Brazil, according to the Health Survey conducted in São Paulo in 2008, the mean ± standard error of meat intake is 71 ± 2 g/day (4 servings/week) of unprocessed red meat and 28 ± 1 g/day (4 servings/week) of processed meat26. In Poland, according to the domestic deliveries and consumption report of 2017, the average intake of both unprocessed meat and processed meat is 115 g/day (9 servings/week)27. In Canada, according to the Statistics Canada’s Canadian Community Health Survey, the mean intake among Canadians is 52 g/day (3 servings/week) of unprocessed red meat and 22 g/day (3 servings/week) of processed red meat28. Based on these data, we defined the lower boundary of the average intake of both unprocessed red meat and processed meat as 3 servings per week. Starting from the average meat intake at the population level, we determined all meat consumption frequency categories (servings/week) as follows: 3 to 4, 5 to 6, 7 to 8, 9 to 10, 11 to 12, 13 to 14, and more than 15 servings per week. We will report in servings per week their current meat consumption for both unprocessed red meat and processed meat.\n\nDirect choice exercise. Following standard methodologies used in previous work in the field of obstetrics from members of our team29,30, we will use a direct choice experimental design to assess the proportion of people willing to change their consumption when faced with a risk reduction of cancer mortality and overall cancer incidence. To ensure that participants have a similar understanding of these two outcomes, we will describe the development of each outcome through the use of health states examples (Table 1 and Table 2). We will present our data from our systematic review that addressed the possible impact of reducing meat intake on overall cancer mortality and overall cancer incidence10. We will first present the baseline risk and the risk reduction participants might achieve by stop eating meat and its certainty. We will develop an interactive electronic decision aid using MagicApp software (http://magicproject.org/research-projects/share-it/) to show the probabilities of reducing the risk of overall cancer mortality and overall cancer incidence if participants’ would stop eating unprocessed red or processed meat (three servings/week scenarios in Figure 1 for processed meat and Figure 2 for unprocessed red meat intake – see Extended data31 for all servings/week scenarios ). In addition to the risk reductions, the overall certainty of evidence based on the GRADE approach for cancer mortality and incidence will be shared with the participant32. If participants are unwilling to stop eating meat to achieve the possible associated health benefits, we will ask them if they would be willing to reduce their meat intake but remind them that the cancer risk reduction, they might anticipate will be less by reducing their meat intake then stopping completely. We will develop and pilot a script at each centre in the language native to the country to guide the direct choice exercise and assess people’s willingness to change meat consumption on a seven-point Likert-scale.\n\nSemi-structured interview. We will also develop and pilot a script in each centre for a semi-structured interview. We will conduct these interviews among those participants included in the subsample in order to explore peoples’ motives regarding their willingness to change. Interviews will take approximately 30 additional minutes.\n\nFollow-up interview. We will contact participants by phone or by email three months after the interview and ask them if they have made any changes in their meat consumption. In case of the phone follow-up, we will follow a semi-structured telephone script previously piloted; in case participants preferred to be contacted by email, we will send them an online survey with similar content of the phone script.\n\nThe primary outcome measure for all included participants will be willingness to change meat consumption in the face of the undesirable cancer health risks. We will show participants the cancer risk reduction they may achieve if they would stop eating unprocessed red meat or processed meat tailored to their consumption and ask them if they are willing to stop, on a scale from 1 (meaning definitely not) to 7 (meaning definitely yes). If participants are not willing to stop eating meat (<7 from the Likert-scale), we will ask them if they will be willing to reduce any amount of their weekly meat intake, on a scale from 1 (meaning definitely not) to 7 (meaning definitely yes). As a secondary outcome, only among the subsample participants, we will explore participants’ motives around their willingness or not to make such changes. We will ask participants in the qualitative evaluation, which factors determine their unprocessed red meat or processed meat intake, and to what extent these factors influence their willingness/unwillingness to stop/reduce their meat consumption. Finally, for all included participants we will estimate their meat consumption at three months after the interview and determine if they have made any changes.\n\nQuantitative analysis. We will describe participants’ demographic and medical history information as well as meat consumption behaviors using means and standard deviations or frequencies and proportions, as appropriate.\n\nWe will describe the distribution of the continuous variable “willingness to reduce meat consumption in the face of the undesirable cancer health risks” by presenting histograms and using means and standard deviations or median and IQR, as appropriate. We will call this variable b1. Then, we will conduct an exploratory linear regression analysis using b1 as the dependent variable and the participants’ characteristics (sex, age, level of education, occupational status, religious belief, and family history of cancer) as the independent variables. We will conduct the same analysis for the variable “willingness to avoid meat consumption in the face of the undesirable cancer health risks”. We will call this variable b2. We will calculate the beta coefficients and the associated 95% confidence interval of participants who are willing to avoid and reduce meat consumption in the face of undesirable cancer risks.\n\nAdditionally, we will conduct an exploratory logistic regression analysis using b1 and b2 as categorical variables: those willing (≥5 from the Likert-Scale) and unwilling (<4 from the Likert-Scale). We will calculate the odds ratio and the associated 95% confidence interval of participants who are willing to avoid and reduce meat consumption in the face of undesirable cancer risks.\n\nWe will calculate the frequency and proportion of participants who made any changes in their meat consumption at three months of follow-up.\n\nQualitative analysis. We will audio-record and transcribe verbatim all semi-structured interviews and use thematic analysis for the qualitative analysis33,34. For our iterative analysis, we will use constant comparison within and across cases to identify any patterns. We will code all transcripts and then the codes will be sorted into themes. We will subsequently compare the identified themes with demographic and participant characteristic information collected to demonstrate any patterns among groups such as sex, age, and education level.\n\nIntegrating qualitative and quantitative analyses. We will conduct a sequential analysis of the quantitative and qualitative components of the data. We will analyze each dataset separately and then, at the end of the study, draw meta-inferences informed by the findings from both data sets. We expect the qualitative results to provide a better understanding of the decision-making process than if the quantitative results were considered alone.\n\nResearch approval was obtained by the Research Ethics Board, Dalhousie University (Canada; 2019-4715), the Clinical Research Ethics Committee of the Jordi Gol University Institute for Primary Care Research (IDIAP; Spain; 19/121-P), the Bioethics Committee of the Jagiellonian University (Poland; 1072.6120.141.2019), and the National Research Ethics Commission (Brazil; CAAE 21826419.4.0000.8527), and if needed will be obtained from all other participating sites. We will explain the entire process of the study to the participants and we will present the potential benefits and risks of participation. The potential benefits of this study to participants include gaining an understanding of the current research regarding overall cancer mortality and incidence based on an up to date high quality dose-response systematic review and meta-analysis10, which participants could use in future dietary decisions. There are no potential physical or psychological risks to participating in this study.\n\nParticipation in the study is voluntary and participants may withdraw from the study at any time without penalty. Should they choose to withdraw; participants will decide whether they want us to discard all or some of the data they have provided. Participants willing to participate will have to sign a written consent form, and they will be assigned a number to anonymize all data collected. Consent forms will be kept separately in a secure cabinet. All interviews will be audio-recorded and transcribed onto a computer file. The recording device will be stored in a secure cabinet and the recordings will be deleted upon completion of the study. Participants will not be identified by name nor otherwise identified when research results are shared. It is possible that a participant could be quoted to highlight results, however, they will be anonymized and neither their name, nor their assigned alphanumeric code, will be shared. Participants will be made aware of this possibility during the consent process and may, if they wish, choose not to allow the use of direct quotations. No compensation will be provided to participants. We will share with participants a copy of our published final results by email or by postal service.\n\nWe will adhere to the checklist of good practice in the conduct and reporting of survey research35 when reporting our results. Results will be disseminated through publications and presentations.\n\n\nDiscussion\n\nOur international mixed-methods study will be the first to explicitly explore peoples’ health-related values and preferences, and their willingness to stop and/or reduce meat consumption when informed of the potential adverse cancer risk, and the uncertainty around this evidence. The information patients will receive will be based on a recent systematic review and dose-response meta-analysis10.\n\nBecause there is limited information in the literature on how people value their health in relation to their diet, developing nutritional recommendations based on health-related values and preferences of community members is a major challenge. Previous studies addressing people’s meat preferences did not adequately present the undesirable health effects of meat consumption in ways that captured the current evidence and its uncertainty36,37.\n\nIn the context of the NutriRECS initiative, our team conducted a systematic review that summarized evidence that omnivores are attached to meat and are reluctant to reduce their meat consumption. However, we rated the certainty of evidence as low due to issues with risk of bias, indirectness, and because of the small number of participants and limited information regarding data analysis15.\n\nA NutriRECS international panel using an individual patient perspective formulated a weak recommendation in favor of continuing current unprocessed red meat and processed meat consumption, acknowledging the low certainty regarding the values and preferences evidence16. This experience triggered the design of the present study, aiming to overcome the limitations of the studies to date15.\n\nOur study has some potential limitations. Our sample includes participants living in high-income countries or from high income strata in low to middle income countries. Therefore, we cannot generalize these findings to low-income populations. We will, however, collect information on participants’ socioeconomic status and education level in order to explore the effect of these characteristics on participants’ dietary values and preferences.\n\nA second limitation of our study is the exclusive focus on cancer outcomes, despite evidence suggesting that reducing meat consumption may reduce the risk of diabetes and cardiovascular outcomes11,38. However, due to the recent claims of meat consumption and cancer risks7,39, the inconsistency in data on cardiometabolic risk associated with both unprocessed and processed meat9,38, and to not overburden participants with too much information, we prioritized two cancer outcomes.\n\nRegarding strengths of our study design, we will address some of the limitations in the previous studies by following a systematic and transparent approach with the use of questionnaires, direct choice exercises and open-ended questions to assess peoples’ health values in relation to their unprocessed red meat and processed meat consumption. We will inform people of the most recent evidence of meat consumption and its related cancer risks10, including the certainty of evidence for these risks, according to their current weekly average consumption. In addition, we will explore their willingness to make any changes to their diet based on the potential risk reduction in cancer.\n\nOur international multicentre study will help ensure generalizability of the results. In addition, the collection of both quantitative and qualitative data will enable an accurate identification of the current health values and preferences regarding meat consumption. In addition to our initial pilot study20, we have further piloted the questionnaires and scripts in each center among both men and women, both with different educational backgrounds, and of different ages to ensure readability and understandability in the general population. We have trained research staff and we will monitor study procedures to ensure quality implementation throughout the interview process. Ultimately, we will follow-up participants to determine if they have made any changes in their meat consumption according to what they have reported during the initial interview; this will allow us to assess the consistency and reliability of our study findings.\n\nOur international study has direct implications for decision makers, guideline developers and policy makers in the development of nutritional recommendations. Up to now, this aspect has been neglected when formulating recommendations. Panels will now have access to international research evidence on values and preferences specific to actual estimated risk reductions in cancer, and the relevant certainty, associated with decreased meat intake. Based on international GRADE standards40, this information will prove crucial for guideline panels moving from the evidence to recommendations on red and processed meat.\n\nOne potential area of further research will be the evaluation of how panels are using this new evidence when formulating recommendations. This work will also inform clinicians regarding community values and preferences when considering the implementation of diet related changes with their patients. Our proposal will use innovative approaches to assess people’s health values and preferences in relation to their diet. The study will provide a rigorous and transparent methodology that can be further utilized in the context of other nutritional scenarios.\n\n\nData availability\n\nNo data are associated with the article.\n\nOpen Science Framework: All servings/week scenarios for processed meat and for unprocessed red meat intake, https://doi.org/10.17605/OSF.IO/T95VN31.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "Acknowledgments\n\nThis study will be conducted using MagicApp software (http://magicproject.org/research-projects/share-it/). MAGIC (Making GRADE the Irresistible Choice) is a non-profit Foundation, aiming to increase value and reduce waste in healthcare through a digital and trustworthy evidence ecosystem. MAGICapp is the core platform in the evidence ecosystem bringing digitally structured guidelines, evidence summaries and decision aids to clinicians and patients.\n\nClaudia Valli is a doctoral candidate for the PhD in Methodology of Biomedical Research and Public Health (Department of Paediatrics, Obstetrics, Gynaecology and Preventive Medicine), Universidad Autònoma de Barcelona, Barcelona, Spain.\n\n\nReferences\n\nAstrup A, Dyerberg J, Selleck M, et al.: Nutrition transition and its relationship to the development of obesity and related chronic diseases. Obes Rev. 2008; 9 Suppl 1: 48–52. 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}
|
[
{
"id": "72360",
"date": "21 Oct 2020",
"name": "Mary Dicklin",
"expertise": [
"Reviewer Expertise Design and conduct of clinical studies in human nutrition",
"metabolism",
"and chronic disease risk factor management."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis paper describes a protocol for a study designed to investigate the potential impact on participants’ thoughts and actions with regard to reducing or avoiding red and processed meat intake when educated about the potential effects on cancer incidence and cancer mortality. The study began in 2019 with expected completion early next year (2021).\nThe NutriRECS investigation has grouped unprocessed red meat and processed meat into a single category. It is not clear in the description of the questionnaires for this study whether these will be distinguished. Entry for the study is based on consumption of a minimum of 3 servings/week of either unprocessed red meat or processed meat. It appears that the investigators will only be asking the participants 1 question about their willingness to stop or reduce “consuming either unprocessed red meat or processed meat (whichever they are eating more of).” The “whichever they are eating more of” part of the question is confusing. I think a better approach would be to investigate their willingness to stop or reduce consumption of each of these types of meats in separate questions.\n\nDoes “four different sites in four countries” mean a total of 16 sites, which would be a total of 1536 participants, or 4 sites total, which would be 484 participants?\n\nThe participants’ educational backgrounds are being analyzed, but do your questionnaires also ask the participants about their baseline knowledge of the potential relation between diet and cancer (including specific types of cancer)?\n\nIn the sample size section, you refer to the proportions as 0.44 (44%) and 0.5 (50%), but then indicate that a confidence interval of ±10 is acceptable. I think this should be 0.1 for consistency.\n\nCan you make the current meat consumption questionnaire available as supplemental material? Also, can you please provide more details about the question(s) that will be asked of the participants at the 3-month follow-up interview?\n\nCan you provide data showing the average intake of unprocessed red meat vs. processed meat in Poland, instead of total unprocessed and processed meat that you have reported?\n\nTable 1: In the 2nd bullet point, I think “other” should be “others are”; something appears to be missing in “a combination of subsequent is needed.”\n\nTable 2: Some of the statements about mortality seem obvious, and I am not sure how they will be interpreted by the participants, i.e., “You are dead and you do not feel any pain or breathlessness” and “You will leave everything that was important in short time span”.\n\nFigures 1 and 2: Although these figures will likely be understandable if described to the participants by the investigator, as stand-alone figures, the “2 fewer” and “9 fewer” may not be clear to them. I think the statement “Among a 1000 patients like you…” could be expanded to include a description of the 2 fewer (or 9 fewer) to make this clearer.\n\nIn a few places you refer to a “subsample” but it is not clear in the Study procedures section where you discuss asking additional questions about motives that this is the subsample.\n\nWill you analyze the data separately according to countries/sites?\n\nIn the Quantitative analysis section you say that you will describe “willingness to reduce meat consumption in the face of undesirable cancer health risks” and “willingness to avoid meat consumption in the face of the undesirable cancer health risks.” I think these should specify that the meat is red and processed meats.\n\nI appreciate your desire to “not overburden participants with too much information, we prioritized two cancer outcomes” – cancer incidence and cancer mortality. However, I wonder in your interviews with the participants if you will be providing them with more information about the relation between meat intake and specific types of cancers, e.g., colorectal, breast, etc.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Partly\n\nAre sufficient details of the methods provided to allow replication by others? Partly\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable",
"responses": [
{
"c_id": "6647",
"date": "13 May 2021",
"name": "Claudia Valli",
"role": "Author Response",
"response": "Comment: This paper describes a protocol for a study designed to investigate the potential impact on participants’ thoughts and actions with regard to reducing or avoiding red and processed meat intake when educated about the potential effects on cancer incidence and cancer mortality. The study began in 2019 with expected completion early next year (2021). The NutriRECS investigation has grouped unprocessed red meat and processed meat into a single category. It is not clear in the description of the questionnaires for this study whether these will be distinguished. Entry for the study is based on consumption of a minimum of 3 servings/week of either unprocessed red meat or processed meat. It appears that the investigators will only be asking the participants 1 question about their willingness to stop or reduce “consuming either unprocessed red meat or processed meat (whichever they are eating more of).” The “whichever they are eating more of” part of the question is confusing. I think a better approach would be to investigate their willingness to stop or reduce consumption of each of these types of meats in separate questions. Reply: We would like to clarify that red meat and processed meat have not been considered as one category, instead they will be presented to participants as two different types of meat. Unprocessed red meat is defined as mammalian meat (e.g., beef, pork, lamb) and processed meat is defined as white or red meat preserved by smoking, curing, salting, or by the addition of preservatives (e.g., hot dogs, charcuterie, sausage, ham, and cold cut deli meats) (World Cancer Research Fund, 2007). We will include participants consuming a minimum of 3 servings per week of either unprocessed red meat or processed meat. Each participant will be presented with one question to assess their unprocessed red meat intake and one question to assess their processed meat intake per week. That means we will determine unprocessed red meat intake and processed meat intake separately for all included participants. Based on the reported intake of unprocessed red meat and processed meat, participants will be presented with scenarios tailored to their consumption. After presenting them with the scenario, participants will be asked series of questions regarding their willingness to change their meat intake. First, participants will be presented with one question about their willingness to stop eating unprocessed red meat. If participants are unwilling to stop (≤4 of the Likert-scale), they will be presented with an additional question about their willingness to reduce. In case participants are willing to stop their unprocessed red meat intake (≥5 of the Likert-scale), the questions on reduction will be no longer relevant. Subsequently, for those that consume processed meat, they will be presented with the scenario on processed red meat and they will be asked to answer a question about their willingness to stop eating processed meat. If participants are willing to stop processed meat, we will use the same logic for questions explained above. That means that we will determine participants’ willingness to stop eating unprocessed red meat and participants’ willingness to stop eating processed meat separately. Additionally, for those participants who report being unwilling to stop, we will determine their willingness to reduce unprocessed meat and their willingness to reduce processed meat intake. Comment: Does “four different sites in four countries” mean a total of 16 sites, which would be a total of 1536 participants, or 4 sites total, which would be 484 participants? Reply: To clarify, the study is conducted in 3 different sites in total (one site in each country: Spain, Poland and Brazil). In 2019, we conducted a pilot study in Canada allowing us to obtain preliminary data to inform our sample size calculation. Based on the pilot data, we calculated a sample size of at least 96 participants per site. Comment: The participants’ educational backgrounds are being analysed, but do your questionnaires also ask the participants about their baseline knowledge of the potential relation between diet and cancer (including specific types of cancer)? Reply: Although we inquired their consumption of meat related to health, we did not specifically ask participants questions about their knowledge regarding potential cancer risks associated with dietary behaviours. Instead, we asked participants if they had reduced their unprocessed red meat and processed meat intake in the past because of health reasons. Comment: In the sample size section, you refer to the proportions as 0.44 (44%) and 0.5 (50%), but then indicate that a confidence interval of ±10 is acceptable. I think this should be 0.1 for consistency. Reply: Thank you, we have edited the text to correct this oversight. Comment: Can you make the current meat consumption questionnaire available as supplemental material? Also, can you please provide more details about the question(s) that will be asked of the participants at the 3-month follow-up interview? Reply: Due to the COVID-19 pandemic, we administered the questionnaire online and thus, we do not have the final version on paper in English. We have provided access through a link in the protocol to the Spanish version of the online survey. The only survey in English available is the one used in the pilot study in Canada and therefore, does not represent the final version used. For the 3- months follow up assessment we have provided the questionnaire as a supplementary material of the protocol. Comment: Can you provide data showing the average intake of unprocessed red meat vs. processed meat in Poland, instead of total unprocessed and processed meat that you have reported? Reply: The information on meat consumption in Poland was based on the data available at Statistics Poland https://stat.gov.pl/en/topics/prices-trade/trade/domestic-deliveries-and-consumption-of-selected-consumer-goods-per-capita-in-2018,9,8.html, which is the main Polish agency offering a national-wide data. Unfortunately, the available data did not report unprocessed red meat and processed meat separately. Comment: Table 1: In the 2nd bullet point, I think “other” should be “others are”; something appears to be missing in “a combination of subsequent is needed.” Reply: Thank you, we have corrected Table 1 following the reviewers’ suggestions. Comment: Table 2: Some of the statements about mortality seem obvious, and I am not sure how they will be interpreted by the participants, i.e., “You are dead and you do not feel any pain or breathlessness” and “You will leave everything that was important in short time span”. Reply: The application of health states is commonly used in studies that elicit participants’ health values and preference to help ensure a similar understanding of the presented health outcomes (Thomson 2002; Thomson 2009). Although, the cancer mortality health state seems to be obvious, the symptoms, treatments and consequences of dying of cancer are not the same as the ones for dying of other diseases, for example heart failure. Thus, we believe it is helpful to provide the descriptions of both outcomes separately. Comment: Figures 1 and 2: Although these figures will likely be understandable if described to the participants by the investigator, as stand-alone figures, the “2 fewer” and “9 fewer” may not be clear to them. I think the statement “Among 1000 patients like you…” could be expanded to include a description of the 2 fewer (or 9 fewer) to make this clearer. Reply: In the online survey, we are providing an explanatory video that will describe to participants how to read/interpret the data presented in the scenarios to facilitate their understanding. In addition, we will provide an explicit text tailored to each scenario. Below, we have provided examples: According to a recent high quality systematic review of the available scientific literature, for people like you who consume 3 servings a week of processed meat, the probability of developing cancer is 18.5%. This means that 185 people out of 1,000 may develop cancer and 815 may not. For people who consume 3 fewer servings per week of processed meat, the probability of developing cancer is 18.3%. This means that 183 people out of 1,000 may develop cancer and 817 may not. Overall, in a population of 1,000 people, 2 fewer people may develop cancer by consuming 3 fewer servings per week of processed meat compared to a population of 1,000 people who do not reduce their consumption. In other words, a reduction of 3 servings per week of processed meat may reduce the probability of developing cancer and the certainty of this effect is very low. This means that the results we present come from studies with important limitations. Therefore, there is a possibility that a reduction in the consumption of processed meat may not result in a reduction in the risk of developing cancer. Comment: In a few places you refer to a “subsample” but it is not clear in the Study procedures section where you discuss asking additional questions about motives that this is the subsample. Reply: We have addressed the reviewers’ comments in the protocol and removed the term subsample to avoid confusion. Comment: Will you analyze the data separately according to countries/sites? Reply: Each country will run their own analysis separately that will result in three different publications. Additionally, the pilot study methods and results will also be published in a separate publication. Comment: In the Quantitative analysis section, you say that you will describe “willingness to reduce meat consumption in the face of undesirable cancer health risks” and “willingness to avoid meat consumption in the face of the undesirable cancer health risks.” I think these should specify that the meat is red and processed meats. Reply: We have addressed and have now added “red and processed” meat in the protocol. Comment: I appreciate your desire to “not overburden participants with too much information, we prioritized two cancer outcomes” – cancer incidence and cancer mortality. However, I wonder in your interviews with the participants if you will be providing them with more information about the relation between meat intake and specific types of cancers, e.g., colorectal, breast, etc. Reply: We have decided to prioritize cancer incidence and cancer mortality because we believed these two general outcomes would be more familiar to the general population. Also, cancer mortality and cancer incidence were the two outcomes showing the largest absolute risk reduction. Being a cross-sectional study requiring participant’s involvement, we had to consider the length of the survey and time people would be willing to dedicate to the study. References World Cancer Research Fund, American Institute for Cancer Research. Food, nutrition, physical activity, and the prevention of cancer: a global perspective. Amer Inst for Cancer Research; 2007. Han MA, Zeraatkar D, Guyatt GH, Vernooij RWM, El Dib R, Zhang Y, Algarni A, Leung G, Storman D, Valli C, Rabassa M, Rehman N, Parvizian MK, Zworth M, Bartoszko JJ, Lopes LC, Sit D, Bala MM, Alonso-Coello P, Johnston BC. Reduction of Red and Processed Meat Intake and Cancer Mortality and Incidence: A Systematic Review and Meta-analysis of Cohort Studies. Ann Intern Med. 2019. Blake P, Durão S, Naude CE, Bero L. An analysis of methods used to synthesize evidence and grade recommendations in food-based dietary guidelines. Nutr Rev. 2018; 76(4):290-300. Rabassa M, Garcia-Ribera Ruiz S, Solà I, Pardo-Hernandez H, Alonso-Coello P, García LM. Nutrition Guidelines vary widely in methodological quality: An overview of reviews. J Clin Epidemiol. 2018; pii: S0895-4356(18)30374-3 Thomson R. Decision analysis - utility for everyday use? Shared decision-making in health care: achieving evidence-based patient choice (paperback). Edited by: Edwards A, Elwyn G. 2009, Oxford University Press, Oxford Thomson R, Robinson A, Greenaway J, Lowe P: Development and description of a decision analysis-based decision support tool for stroke prevention in atrial fibrillation. Qual Saf Health Care. 2002, 11: 25-10. Erickson J, Sadeghirad B, Lytvyn L, Slavin J, Johnston BC; The Scientific Basis of Guideline Recommendations on Sugar Intake: A Systematic Review. Ann Intern Med. 2017;166(4):257-267. Dedios MC , Esperato A , De-Regil LM , et al. Improving the adaptability of WHO evidence-informed guidelines for nutrition actions: results of a mixed methods evaluation. Implement Sci. 2017;12:39."
}
]
},
{
"id": "79343",
"date": "23 Feb 2021",
"name": "Tomás Meroño",
"expertise": [
"Reviewer Expertise Nutrition",
"nutritional epidemiology."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe study protocol presented by Valli et al. aims to evaluate the willingness to change their consumption of unprocessed and processed red meat in light of risk reductions in cancer incidence and mortality. The \"mixed-methods\" refers to the combination of quantitative and qualitative research methodologies. The qualitative research aims to study the factors behind the willingness or not to modify red meat consumption.\nIn addition, they propose to evaluate the preferences of consumption of the participants; however the relevance for this data is not clear in the actual version of the protocol.\nGeneral comments\nFrom a participant point of view, the tables with information of cancer incidence and mortality are more shocking than the low certainty estimates produced by the MAGICApp. Also, the figure is not of easy understanding. It does not translate in a clear message of what will happen to me if I do not reduce my red meat consumption.\n\nThe meta-analysis from which estimates of risk reduction are taken has low to very low certainty in every case. Maybe the rather low level of certainty undermines the risk estimate impact on changing the consumption of red meat. What is the rationale behind choosing cancer despite of the low certainty evidence supporting the meta-analysis?\n\nI don't see clearly what is the rationale behind the assessments of the preferences on red meat consumption if the red meat target is the same for all the populations. How is this information going to be used in the analysis? Why is it important?\n\nThe sample size of the subsample for the qualitative study is not stated. Moreover, which are the domains or the main issues in which the participants will be interviewed? If it is semi-structured, then the manuscript will require a brief description of the main questions or topics.\n\nI am wondering which would constitute a better outcome: i) the willingness to reduce red meat consumption or ii) the reduction of red meat consumption in the follow-up survey. In my opinion, the intervention is the initial survey and the result is the reduction of red meat consumption. Actually, we do not expect changes or at least there is not a pre and post examination after the direct-choice exercise.\n\nDoes risk reductions from the meta-analysis consider differences in age, sex and smoking?\n\nLast, how the research team will address the differences between country, site and type of interview when doing the statistical analysis. My guess is that participants in face-to-face interviews will feel pushed towards a \"positive\" answer, while the ones taking the online survey might be free of this effect. Perhaps, a subsample of the participants could take both surveys to see if such an effect is present and the evaluations are consistent one with the other.\nMinor comments\n\nReference number 5 is not adequate for supporting the claim in the text. Please use a more relevant one.\n\nPage 3, Study population. When describing the exclusion criteria please delete the word \"severe\" cardiovascular disease.\n\nSample size, instead of +/- 10, 0.1.\n\nWhat is the rationale for recruiting 96 in each site? From sample size calculation I would say that 96 participants in total are enough. Will the results be analysed by site or all-together? Anyway, I think the researchers choice is valid enough but some explanation would be appreciated. The definition of the main outcome and its rather high probability to occur with a quite large confidence interval might be behind this somehow small sample size for a multicenter study. On the other hand, please manifest at least some approximation to the total number of interviews for the qualitative analysis.\n\nPage 6, some typos, please revise.\n\nRevise definition of outcomes.\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": [
{
"c_id": "6648",
"date": "13 May 2021",
"name": "Claudia Valli",
"role": "Author Response",
"response": "Comment: The study protocol presented by Valli et al. aims to evaluate the willingness to change their consumption of unprocessed and processed red meat in light of risk reductions in cancer incidence and mortality. The \"mixed-methods\" refers to the combination of quantitative and qualitative research methodologies. The qualitative research aims to study the factors behind the willingness or not to modify red meat consumption. In addition, they propose to evaluate the preferences of consumption of the participants; however, the relevance for this data is not clear in the actual version of the protocol. Reply: Participants’ values and preferences regarding meat intake will inform us on their related motives around their willingness or unwillingness to make any changes. We have improved the section of Outcomes in the protocol to better explain the relevance of such data. Comment: From a participant point of view, the tables with information of cancer incidence and mortality are more shocking than the low certainty estimates produced by the MAGICApp. Also, the figure is not of easy understanding. It does not translate in a clear message of what will happen to me if I do not reduce my red meat consumption. Reply: In the online survey, we will provide an explanatory video that will describe to participants how to read/interpret the data presented in the scenarios to facilitate their understanding. In addition, the online survey will provide an explicit text tailored to each scenario right below the image of the scenario. Below, we have provided the examples used with participants: According to a recent high quality systematic review of the available scientific literature, for people like you who consume 3 servings a week of processed meat, the probability of developing cancer is 18.5%. This means that 185 people out of 1,000 may develop cancer and 815 may not. For people who consume 3 fewer servings per week of processed meat, the probability of developing cancer is 18.3%. This means that 183 people out of 1,000 may develop cancer and 817 may not. Overall, in a population of 1,000 people, 2 fewer people may develop cancer by consuming 3 fewer servings per week of processed meat compared to a population of 1,000 people who do not reduce their consumption. In other words, a reduction of 3 servings per week of processed meat may reduce the probability of developing cancer and the certainty of this effect is very low. This means that the results we present come from studies with important limitations. Therefore, there is a possibility that a reduction in the consumption of processed meat may not result in a reduction in the risk of developing cancer. Comment: The meta-analysis from which estimates of risk reduction are taken has low to very low certainty in every case. Maybe the rather low level of certainty undermines the risk estimate impact on changing the consumption of red meat. What is the rationale behind choosing cancer despite of the low certainty evidence supporting the meta-analysis? Reply: We have decided to prioritize cancer incidence and cancer mortality because we believed these two general outcomes would be very familiar and of general interest to the public. Regarding the certainty of the evidence, for all outcomes the certainty was low- to very low because of observational design as well as issues with imprecision and/or risk of bias (Han 2019). Among the cancer outcomes, we have selected those that demonstrated the largest risk reduction effect. The certainty would be no higher had we selected cardiovascular outcomes, the other reasonable choice in terms of outcomes of most important to patients. Comment: I don't see clearly what is the rationale behind the assessments of the preferences on red meat consumption if the red meat target is the same for all the populations. How is this information going to be used in the analysis? Why is it important? Reply: Assessing the values and preferences from representative members of the population will inform us on the variability between the participants and between the countries, the objective of the study. We tailored our questions to each participant in each country depending on that average weekly intake. For instance, if participants consumed 6 servings of unprocessed red meat per week, we showed them the absolute risk reduction if they were to consume 6 fewer servings per week (stop completely), as well as 3 fewer servings in case they were unwilling to stop completely. Values and preferences from those who will actually use guideline recommendations, in this case -- members of the public -- are an important component of guideline development (Dedios 2017; Erickson 2017). Comment: The sample size of the subsample for the qualitative study is not stated. Moreover, which are the domains or the main issues in which the participants will be interviewed? If it is semi-structured, then the manuscript will require a brief description of the main questions or topics. Reply: For qualitative evaluations, it is unusual to predetermine the sample size. As stated, and referenced in the manuscript, the number of needed participants will be determined by data saturation method, that is, we will continue interviewing new participants until no additional concepts or themes emerge. For the semi-structured interview, we have provided the draft of questionnaire as a supplementary material of the protocol. Please note, that being a semi-structured interview, questions might change and be adapted according to the conversation with the participant and to his/her responses given in the online survey. Comment: I am wondering which would constitute a better outcome: i) the willingness to reduce red meat consumption or ii) the reduction of red meat consumption in the follow-up survey. In my opinion, the intervention is the initial survey and the result is the reduction of red meat consumption. Actually, we do not expect changes or at least there is not a pre- and post-examination after the direct-choice exercise. Reply: Not totally clear to us what the reviewer means by “better”. From some peoples’ perspective a good outcome might be that respondents who say they are willing to reduce their meat consumption as a result of the information presented would actually do so. Our aim is to assess both outcomes, report the results and reflect on their implications. To clarify, the outcome “willingness” will inform us about participants willingness to change only after being informed on the potential undesirable health outcomes, the first study of its kind to our knowledge. On the other hand, assessing participants’ meat consumption in the follow-up will show us if participants have made any changes in their meat intake compared to what they reported to consume in the online survey and also compared to what they affirmed to be willing to do in the direct-choice exercise (3 months earlier). This will allow us to detect if participants have been made any changes. Comment: Do risk reductions from the meta-analysis consider differences in age, sex and smoking? Reply: Some of the studies included in the meta-analysis had limitations due to limited adjustment for potential confounders (Han 2019). That means that some studies took into account potential confounders such as age and sex and smoking but others did not. Lack of adequate adjustment for potential confounders (e.g., age, sex, smoking, socioeconomic status, exercise etc.) was one of the main sources of potential bias. Limitations in adjustment was an important reason for rating down the certainty of the evidence. Comment: Last, how the research team will address the differences between country, site and type of interview when doing the statistical analysis. My guess is that participants in face-to-face interviews will feel pushed towards a \"positive\" answer, while the ones taking the online survey might be free of this effect. Perhaps, a subsample of the participants could take both surveys to see if such an effect is present and the evaluations are consistent one with the other. Reply: Thanks for the suggestion to compare responses online versus face-to-face surveys. Due to the COVID-19 pandemic, all sites will conduct the study remotely through an online survey. The pilot study was conducted in-person since it was implemented before the start of the pandemic. Each country will run their own analysis separately resulting in four different publications. Comment: Reference number 5 is not adequate for supporting the claim in the text. Please use a more relevant one. Reply: We believe the said reference Rabassa 2018 is appropriate since it refers to a recent study assessing the quality of nutrition guidelines with the use of the AGREE tool, an internationally recognized instrument used to evaluate the process of practice guideline development and the quality of reporting. We have added an additional reference Blake 2018, which is an analysis the appropriateness of methods used to synthesize evidence and grade recommendations in food-based dietary guidelines. Comment: Page 3, Study population. When describing the exclusion criteria please delete the word \"severe\" cardiovascular disease. Reply: Thank you, we have edited the text according to the reviewer’s suggestion. Comment: Sample size, instead of +/- 10, 0.1. Reply: Thank you, we have edited the text by following the reviewers’ suggestions. Comment: What is the rationale for recruiting 96 in each site? From sample size calculation I would say that 96 participants in total are enough. Will the results be analysed by site or all-together? Anyway, I think the researcher’s choice is valid enough but some explanation would be appreciated. The definition of the main outcome and its rather high probability to occur with a quite large confidence interval might be behind this somehow small sample size for a multicenter study. On the other hand, please manifest at least some approximation to the total number of interviews for the qualitative analysis. Reply: The more variable the response, the larger the sample size necessary to assess whether observed results are representative of the target population or simply reflects random variation. The sample size calculation does not take into account the multi-centred nature of the study. Since we are conducting the study in different sites/countries and considering the cultural differences, the responses of approximately 20 participants in each site/country (96 participants in total) will not give us representative results within each country. Therefore, we have used a more conservative approach by attempting to recruit at least 96 participants per site. As stated above, for qualitative evaluations, it is unusual to predetermine the sample size, rather we will sample participants until we reach data saturation, meaning that we will continue interviewing new participants until no additional concepts or themes emerge. Comment: Page 6, some typos, please revise. Revise definition of outcomes. Reply: Thank you, we have made the corrections in the text. References World Cancer Research Fund, American Institute for Cancer Research. Food, nutrition, physical activity, and the prevention of cancer: a global perspective. Amer Inst for Cancer Research; 2007. Han MA, Zeraatkar D, Guyatt GH, Vernooij RWM, El Dib R, Zhang Y, Algarni A, Leung G, Storman D, Valli C, Rabassa M, Rehman N, Parvizian MK, Zworth M, Bartoszko JJ, Lopes LC, Sit D, Bala MM, Alonso-Coello P, Johnston BC. Reduction of Red and Processed Meat Intake and Cancer Mortality and Incidence: A Systematic Review and Meta-analysis of Cohort Studies. Ann Intern Med. 2019. Blake P, Durão S, Naude CE, Bero L. An analysis of methods used to synthesize evidence and grade recommendations in food-based dietary guidelines. Nutr Rev. 2018; 76(4):290-300. Rabassa M, Garcia-Ribera Ruiz S, Solà I, Pardo-Hernandez H, Alonso-Coello P, García LM. Nutrition Guidelines vary widely in methodological quality: An overview of reviews. J Clin Epidemiol. 2018; pii: S0895-4356(18)30374-3 Thomson R. Decision analysis - utility for everyday use? Shared decision-making in health care: achieving evidence-based patient choice (paperback). Edited by: Edwards A, Elwyn G. 2009, Oxford University Press, Oxford Thomson R, Robinson A, Greenaway J, Lowe P: Development and description of a decision analysis-based decision support tool for stroke prevention in atrial fibrillation. Qual Saf Health Care. 2002, 11: 25-10. Erickson J, Sadeghirad B, Lytvyn L, Slavin J, Johnston BC; The Scientific Basis of Guideline Recommendations on Sugar Intake: A Systematic Review. Ann Intern Med. 2017;166(4):257-267. Dedios MC , Esperato A , De-Regil LM , et al. Improving the adaptability of WHO evidence-informed guidelines for nutrition actions: results of a mixed methods evaluation. Implement Sci. 2017;12:39."
}
]
}
] | 1
|
https://f1000research.com/articles/9-346
|
https://f1000research.com/articles/9-224/v1
|
01 Apr 20
|
{
"type": "Study Protocol",
"title": "Effectiveness of pre-operative anaemia screening and increased Tranexamic acid dose on outcomes following unilateral primary, elective total hip or knee replacement: a statistical analysis plan for an interrupted time series and regression discontinuity study",
"authors": [
"Ashley B. Scrimshire",
"Caroline Fairhurst",
"Catriona McDaid",
"David J. Torgerson",
"Caroline Fairhurst",
"Catriona McDaid",
"David J. Torgerson"
],
"abstract": "Perioperative blood transfusion is associated with poorer postoperative outcomes following hip and knee replacement surgery. Evidence for the effectiveness of some measures aimed at reducing blood transfusions in this setting are limited and often rely on weak pre-post study designs. Quasi-experimental study designs such as interrupted time series (ITS) and regression discontinuity design (RDD) address many of the weaknesses of the pre-post study design. In addition, a priori publication of statistical analysis plans for such studies increases their transparency and likely validity, as readers are able to distinguish between pre-planned and exploratory analyses. As such, this article, written prospective of any analysis, provides the statistical analysis plan for an ITS and RDD study based on a data set of 20,772 primary elective hip and knee replacement patients in a single English NHS Trust. The primary aim is to evaluate the impact of a preoperative anaemia optimisation service on perioperative blood transfusion (within 7 days of surgery) using both ITS and RDD methods. A secondary aim is to evaluate the impact of a policy of increased tranexamic acid dose given at the time of surgery, using ITS methods.",
"keywords": [
"Regression discontinuity",
"interrupted time series",
"quasi-experimental",
"anaemia",
"orthopaedics"
],
"content": "Introduction\n\nPeri-operative red blood cell (RBC) transfusion is associated with poorer post-operative outcomes across surgical disciplines, including elective total hip (THR) and knee replacement (TKR) surgery1–3. Multi-modal patient blood management (PBM) programmes aim to reduce blood transfusions and the associated complications. Two core elements of PBM are peri-operative tranexamic acid (TXA) and pre-operative anaemia optimisation. However, debate exists around optimal TXA dose and there is a lack of high quality randomised controlled trials (RCT) into preoperative anaemia optimisation, with much of the evidence coming from pre-post design observational studies. The pre-post study design is common in the medical literature and causal associations are often inferred from them. However, they are subject to several flaws, including being unable to separate temporal changes from intervention effect and not accounting for regression to the mean4. This frequently leads to over-estimation of a treatment effect and has been described as the weakest observational study method4,5.\n\nAlthough RCTs are considered the gold standard for evaluating changes in healthcare, they are not always feasible and the results may not always be generalisable to real world populations4,6,7. A recent study comparing characteristics of patients recruited to peri-operative medicine RCTs and national registry data, shows significant differences in age, sex and ethnicity exist, potentially limiting the generalisability of RCT results8. In addition, an RCT into preoperative anaemia optimisation may prove challenging as this practice is already recommended in multiple guidelines, as part of wider PBM programmes9–11. Where an RCT is not feasible quasi-experimental study designs such as interrupted time series (ITS) and regression discontinuity (RDD), can provide more robust evidence as they eliminate some of the threats to internal validity seen in pre-post studies.\n\nThe prospective publication of statistical analysis plans (SAP) for observational studies increases their transparency and likely their validity, as readers are able to distinguish between pre-planned and exploratory analyses12. This paper, written prospective of any analysis being performed, provides the SAP for a quasi-experimental study using ITS and RDD methods on a large dataset of elective THR and TKR patients from an English NHS Trust.\n\nThe primary aim of this study is to evaluate the clinical effectiveness of introducing a preoperative anaemia optimisation programme, using iron, for patients undergoing primary elective THR or TKR surgery. A secondary aim is to evaluate the clinical effectiveness of introducing a policy of increased intravenous TXA dose on induction of anaesthesia (15mg/kg maximum 1.2g increased to 30mg/kg max. 2.5g). Both interventions take place in the presence of a well-established, multi-modal enhanced recovery programme, detailed elsewhere13.\n\nAlthough similar in design, ITS and RDD examine data from a different perspective. ITS is concerned with population level changes over time, whilst RDD uses patient level data to focus on effects on outcomes around intervention thresholds. These two analyses will provide complimentary results on the effectiveness of introducing a preoperative anaemia optimisation programme and an increased TXA dose of 30mg/kg in an NHS Trust14.\n\n\nStatistical Analysis Plan\n\nOver time the orthopaedic department at Northumbria Healthcare NHS Foundation Trust (NHCT) has introduced a range of interventions aimed at improving post-operative outcomes for patients undergoing elective lower limb arthroplasty. These have been well documented in a series of pre-post cohort studies13,15,16. Details of the interventions and a timeline are given in Table 1 and Figure 1.\n\n* Includes introduction of IV Tranexamic acid, 15mg/kg max 1.2g, at induction of anaesthesia\n\n** Policy introduced in August 2011. This study allowed a 6-month implementation period to ensure the change in practice had been adopted\n\nLoS = length of hospital stay\n\nERP = Enhanced Recovery Programme IV = Intravenous, TXA = Tranexamic acid, ITS = interrupted time series, RDD = regression discontinuity design.\n\nAs part of on-going service evaluation, a large dataset of 20,772 patients who have undergone primary elective THR or TKR at NHCT has been compiled. This includes data from hospital electronic record systems, such as the Patient Administration System and Blood Transfusion database, and a prospectively maintained database for the pre-operative anaemia screening service. Data includes patient demographics, comorbidities, pre-operative anaemia screening results (i.e. haemoglobin concentration, Hb), anaemia treatment given, operative details, post-operative complications, blood transfusions and length of hospital stay (LoS). The full dataset covers a time period from January 2008 to March 2019.\n\nEthical approval was not required as this is a retrospective study of routinely collected data. Local Caldicott guardian approval was given for use of this data. Data flow will be presented in a STROBE diagram in the resulting publication17. Population characteristics (age, gender, comorbidities, type of surgery) and descriptive statistics will be presented in tables for the cohorts being studied. Analyses will be performed using R and RStudio (version R-3.6.2 for mac, R Core Team 2013, http://www.R-project.org/) on an intention to treat basis. Results will be presented in terms of absolute and relative values with 95% confidence intervals where appropriate. Results will be considered statistically significant if the p-value ≤0.05.\n\nThe primary outcome is the proportion of patients receiving perioperative allogenic RBC transfusion (within 7 days of surgery). Secondary outcomes are the quantity of blood transfused (RBC units), LoS (in days), critical care admission rate (within 30 days) and emergency readmission rate (within 30 days)1,2,16.\n\nITS using segmented regression has several strengths over the pre-post study design. In particular, it controls for secular trends over time, provides powerful, easy to understand visual outputs and may improve generalisability to the wider population6,7,18. For this study, data are available to evaluate both policies described above in an ITS analysis.\n\nThe two interventions in this study were introduced at specific, well defined time points, allowing for clear separation of pre- and post-intervention periods (Figure 1). An early step in ITS analysis is to generate summary statistics for each time period and undertake simple pre-post comparisons19. This will be performed in this study and later compared to the results from ITS and RDD analyses.\n\nData description. ITS is said to work best with short-term outcomes that change quickly after implementation of an intervention or after a clearly defined lag period7. This study is examining short-term outcomes, however, some delays to observed changes in outcomes are expected. The orthopaedic department has previously reported that a 6-month lag period was required to fully adopt the increased TXA dose policy15. This same lag will therefore be incorporated into the ITS analysis. Regarding the introduction of the preoperative anaemia optimisation programme, staff running the anaemia service report that this started promptly on 01/02/2013, after detailed planning, and uptake was rapid. However, a lag to observed changes in outcomes will be inevitable due to surgical waiting list times. Comparing screening and surgery dates for the first 10 anaemic and 10 non-anaemic patients from the cohort shows all but one had their surgery within 6 months of screening. Therefore, a 6-month implementation period is also considered appropriate following introduction of the anaemia optimisation service (Figure 1). Lag periods will be accounted for by excluding this data from analysis20. ITS requires sequential measures of the outcome, at regular intervals, before and after the intervention time points19,20. In keeping with many ITS studies, individual level outcome data will be converted to, and presented as, proportions or means at monthly intervals and a segmented-regression analysis performed20. ITS plots will be generated and visually inspected to determine if linear or non-linear regression modelling is appropriate. A minimum of 8 data points pre- and post-intervention are desirable19,20. It is expected the shortest time frame being analysed in this study will include 12 months/data points, thus surpassing this requirement.\n\nAddressing threats to validity. Time varying confounders are the main threat to validity of ITS studies20. These are specific to each ITS study and are carefully considered later in this SAP. However, the most robust way to account for time varying confounders, even those that are unknown, is to model against a control group. This could either be a different population not exposed to the intervention, or if individual level data are available, by splitting the data into two groups, one group targeted by an intervention and another who are not. In this study, data for a different group of patients is not available for either intervention. The TXA policy is targeted at all THR or TKR patients so this data cannot be split. However, the anaemia optimisation policy targets a specific group of anaemic patients so the population can be split into two groups to increase the robustness of this analysis. As such the two interventions will be modelled separately, the TXA intervention without a control group, the anaemia screening intervention with a control group.\n\nTime varying confounders specific to the primary outcome of this study may include other PBM interventions, those relevant will be discussed in turn. A restrictive blood transfusion policy was introduced Trust-wide in 2007 and has been unchanged since15,16. A multimodal enhanced recovery programme (ERP), including IV TXA on induction of anaesthesia, was introduced in May 2008. In keeping with other similar policy changes in this unit a 6-month implementation period for the ERP is considered appropriate. To account for this, data from 1st January 2008 to 31st October 2008 will be excluded from this analysis. In addition, patient warming has been introduced locally21 but a Cochrane review shows this does not affect surgical transfusion rates, so will not be considered any further22. Intra-operative cell salvage has never been routinely used locally for the procedures being studied. To the best of our knowledge, no other relevant cointerventions have been introduced during the study period. Any unaccounted for, gradual changes in practice, would be detected in the pre-intervention slope of the TXA analysis and in the control group for the anaemia analysis.\n\nOther considerations include changes in data coding, validity and reliability over time. The data for this study is considered reliable as it comes from a number of NHS Trust electronic databases detailed earlier in this paper. There have been no material changes to data collection methods or outcome reporting over the study period.\n\nChanges in the population over time can also affect ITS reliability, however there have been no known substantial changes in the population served by NHCT over the study period. This study includes a continually enrolled population, so is not subject to population attrition over time. Although no changes to diagnostic criteria for ischaemic heart disease (IHD) are known to have occurred during the study period, this comorbidity is specifically mentioned in the NHCT transfusion policy and lowers the threshold for considering transfusion. For completeness, rates of IHD will be plotted against time and visually inspected for any patterns, particularly around the time of the interventions. If required IHD will be included in the ITS modelling.\n\nDeveloping the model. Autocorrelation, including seasonality, will be tested using the Durbin-Watson test including a lag of up to 12 time points (to account for seasonality), visual inspection of residual plots for patterns over time, and interpretation of autocorrelation and partial autocorrelation function plots. If identified, autoregressive and/or moving average relationships will be included in the final ITS model19,23. Data will be inspected for wild data points and where identified, explanations will be sought, and exclusion considered.\n\nSensitivity analysis. An optimal model will be developed and described for these ITS analyses. The impact of decisions taken during this process such as inclusion/exclusion of wild data points and autocorrelation adjustments will be tested in sensitivity analyses. Further analyses of data stratified by surgery type (THR or TKR) and/or by patient gender, will be conducted if data permits, as these may impact on outcomes.\n\nRDD estimates the local average treatment effect when treatment decisions are based around a cut-off value for a continuous variable24. For example, giving iron (the treatment) with the intention of reducing RBC transfusion and LoS (the outcomes) to patients whose Hb (the assignment variable) falls below a pre-defined cut-off of 120g/L for females or 130 g/L for males (the threshold). RDD makes use of this threshold and assumes that individuals who lie just above it belong to the same populationas those who lie just below it, and assignment to treatment or not is considered random25.\n\nThe main strength of RDD lies in its ability to achieve a balance of unobserved factors in patients that fall, by chance, either side of the threshold value, much like an RCT26. The local nature of the effect examined in RDD can also be used in optimising threshold levels. In this case we may be able to examine if a threshold Hb of 120 or 130g/L may be more appropriate for females, as is being suggested in some studies11,26–28. As the TXA policy affects all patients it is only possible to conduct an RDD analysis for the anaemia screening programme, using data since the inception of this programme (1st February 2013, Figure 1).\n\nData description. In this study the continuous assignment variable will be preoperative Hb concentration. The outcome assessment, for primary and secondary outcomes (listed above), are observed universally for patients who receive treatment with iron or not. Details of how treatment is assigned has been previously reported, and is shown in Figure 216. Notably the treatment thresholds are different for males (Hb 130g/L) and females (120g/L), so data will be split by gender for analysis. Also, some patients are referred back to their GP for further investigations and surgery is deferred (Hb <105g/L (female) or <115g/L (male), ferritin <12 or >100ng/mL). As such patients referred back to their GP will be excluded from this analysis as allocation to iron treatment or not is unclear16.\n\nAddressing threats to validity. Manipulation of treatment status by patients through the assignment variable (Hb) is highly unlikely. However, it is possible the reporting of the assignment variable could be manipulated by clinicians, though there is a protocol which healthcare professionals are required to strictly adhered to. To assess the statistical integrity of the data assignment variable (Hb) data will be plotted on a histogram and visually inspected for bunching around the threshold values.\n\nTo test if groups either side of the threshold are comparable, plots of Hb against average number of comorbidities per patient and age will be generated. If no differences are seen just either side of the threshold, this will support the assumption that assignment around the threshold is random and establish there has been no manipulation of treatment status, similar to an RCT26. If differences are seen, and it is possible the more anaemic patients (lower Hb) have more comorbidities and/or are older, then this will be factored into optimal bandwidth size selection, detailed below. Similar to ITS, RDD is sensitive to co-interventions introduced around the threshold Hb value. There are no known co-interventions introduced locally for this patient cohort around the threshold Hb values.\n\nDeveloping the model. Hb data will be presented in bins, the size of which will depend on the data available, but will be either 1, 2 or 5 g/L each. Outcome data for this study is in the form of discrete variables (transfused/readmitted/critical care admission; yes/no, number of inpatient days). As such outcome data will be converted to a probability (i.e. risk of transfusion) or average (i.e. mean number of days) for each bin. 95% confidence intervals will be plotted alongside the probabilities or averages where applicable.\n\nA plot of assignment variable (Hb) against treatment status will be created to confirm if a sharp or fuzzy discontinuity design is most appropriate26. Separate scatter plots of primary and secondary outcomes against Hb will be created. These will be inspected visually for a jump at the threshold value, indicative of a treatment effect, and to determine if linear or non-linear modelling is most appropriate. Data driven methods will be used to determine optimal bandwidth sizes either side of the threshold value.\n\nSensitivity analysis. The robustness of the resulting effect size estimate will be tested by constructing multiple models of varying bandwidth size. Data will be inspected for wild data points and consideration given to exclusion. Sensitivity analysis with and without wild data points will be performed. Further analyses with data stratified by surgery type (THR or TKR) will be conducted where data permits.\n\nBoth ITS and RDD have significant advantages over the typical pre-post analysis often seen in medical literature. When an intervention is introduced rapidly and short-term outcomes are frequently assessed, ITS can be considered a sub-type of RDD in which the assignment variable is time and the cut-off occurs when the policy is introduced26.\n\nIt is unusual to have a dataset amenable to both types of analysis, however they provide different perspectives. Whilst both deigns share the strength of not being bound by the selective inclusion criteria of an RCT, thus potentially improving generalisability, they also have their limitations.\n\nIn the case of RDD, in order to ensure groups either side of the threshold are similar the focus is on an effect close to the threshold value. (i.e. patients with Hb 119 or 121g/L are likely very similar, but patients with Hb 90 or 140 are likely different in other, unmeasured parameters). This limits the generalisability of findings to values that lie far from the threshold. In the case of ITS the results can be impacted by several factors such as autocorrelation and unmeasured confounders, which we have attempted to address in the analysis design. Also, the findings from ITS can only indicate an associative not a causal relationship between intervention and outcomes. Whereas RDD has the potential to demonstrate causation.\n\nPublication of study results will be sought in a high impact journal.\n\n\nStudy status\n\nStudy data has been collected and analysis pending awaiting publication of this statistical analysis plan.\n\n\nData availability\n\nNo data is associated with this article.",
"appendix": "References\n\nFowler AJ, Ahmad T, Phull MK, et al.: Meta-analysis of the association between preoperative anaemia and mortality after surgery. Br J Surg. 2015; 102(11): 1314–24. PubMed Abstract | Publisher Full Text\n\nViola J, Gomez MM, Restrepo C, et al.: Preoperative anemia increases postoperative complications and mortality following total joint arthroplasty. J Arthroplasty. 2015; 30(5): 846–8. PubMed Abstract | Publisher Full Text\n\nMusallam KM, Tamim HM, Richards T, et al.: Preoperative anaemia and postoperative outcomes in non-cardiac surgery: a retrospective cohort study. Lancet. 2011; 378(9800): 1396–407. PubMed Abstract | Publisher Full Text\n\nTorgerson DJ, Torgerson CJ: Designing Randomised Trials in Health, Education and the Social Sciences.. Palgrave Macmillan. 2008. Publisher Full Text\n\nCook TD, Campbell DT: Quasi-Experimentation: Design and Analysis Issues for Field Settings. Boston: Houghton Mifflin. 1979. Reference Source\n\nKontopantelis E, Doran T, Springate DA, et al.: Regression based quasi-experimental approach when randomisation is not an option: Interrupted time series analysis. BMJ. 2015; 350: h2750. PubMed Abstract | Publisher Full Text | Free Full Text\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. PubMed Abstract | Publisher Full Text\n\nLindsay WA, Murphy MM, Almghairbi DS, et al.: Age, sex, race and ethnicity representativeness of randomised controlled trials in peri-operative medicine. Anaesthesia. 2020; 1–7. PubMed Abstract | Publisher Full Text\n\nNICE Guideline NG24 Methods, evidence and recommendations. Natl Inst Heal Care Excell. 2015. Reference Source\n\nMueller M, Van Remoortel H, Meybohm P, et al.: Patient Blood Management: Recommendations from the 2018 Frankfurt Consensus Conference. JAMA. 2019; 321(10): 983–97. PubMed Abstract | Publisher Full Text\n\nMuñoz M, Acheson AG, Auerbach M, et al.: International consensus statement on the peri-operative management of anaemia and iron deficiency. Anaesthesia. 2017; 72(2): 233–47. PubMed Abstract | Publisher Full Text\n\nHiemstra B, Keus F, Wetterslev J, et al.: DEBATE-statistical analysis plans for observational studies. BMC Med Res Methodol. 2019; 19(1): 233. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMalviya A, Martin K, Harper I, et al.: Enhanced recovery program for hip and knee replacement reduces death rate. Acta Orthop. 2011; 82(5): 577–81. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPortela MC, Pronovost PJ, Woodcock T, et al.: How to study improvement interventions: a brief overview of possible study types. BMJ Qual Saf. 2015; 24(5): 325–36. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMorrison RJ, Tsang B, Fishley W, et al.: Dose optimisation of intravenous tranexamic acid for elective hip and knee arthroplasty: The effectiveness of a single pre-operative dose. Bone Joint Res. 2017; 6(8): 499–505. PubMed Abstract | Publisher Full Text | Free Full Text\n\nPujol-Nicolas A, Morrison R, Casson C, et al.: Preoperative screening and intervention for mild anemia with low iron stores in elective hip and knee arthroplasty. Transfusion. 2017; 57(12): 3049–57. PubMed Abstract | Publisher Full Text\n\nvon Elm E, Altman DG, Egger M, et al.: Strengthening the reporting of observational studies in epidemiology (STROBE) statement: guidelines for reporting observational studies. BMJ. 2007; 335(7624): 806–8. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWagner AK, Soumerai SB, Zhang F, et al.: Segmented regression analysis of interrupted time series studies in medication use research. J Clin Pharm Ther. 2002; 27(4): 299–309. PubMed Abstract | Publisher Full Text\n\nBernal JL, Cummins S, Gasparrini A: Interrupted time series regression for the evaluation of public health interventions: a tutorial. Int J Epidemiol. 2017; 46(1): 348–55. PubMed Abstract | Publisher Full Text | Free Full Text\n\nJandoc R, Burden AM, Mamdani M, et al.: Interrupted time series analysis in drug utilization research is increasing: systematic review and recommendations. J Clin Epidemiol. 2015; 68(8): 950–6. PubMed Abstract | Publisher Full Text\n\nAlthoff FC, Neb H, Herrmann E, et al.: Multimodal Patient Blood Management Program Based on a Three-pillar Strategy: A Systematic Review and Meta-analysis. Ann Surg. 2019; 269(5): 794–804. PubMed Abstract | Publisher Full Text\n\nMadrid E, Urrútia G, Roqué i Figuls M, et al.: Active body surface warming systems for preventing complications caused by inadvertent perioperative hypothermia in adults (Review). Cochrane Database Syst Rev. 2016; (4): CD009016. PubMed Abstract | Publisher Full Text\n\nBhaskaran K, Gasparrini A, Hajat S, et al.: Time series regression studies in environmental epidemiology. Int J Epidemiol. 2013; 42(4): 1187–95. PubMed Abstract | Publisher Full Text | Free Full Text\n\nVenkataramani AS, Bor J, Jena AB: Regression discontinuity designs in healthcare research. BMJ. 2016; 352: i1216. PubMed Abstract | Publisher Full Text | Free Full Text\n\nO'Keeffe AG, Geneletti S, Baio G, et al.: Regression discontinuity designs: an approach to the evaluation of treatment efficacy in primary care using observational data. BMJ. 2014; 349: g5293. PubMed Abstract | Publisher Full Text\n\nMoscoe E, Bor J, Bärnighausen T, et al.: Regression discontinuity designs are underutilized in medicine, epidemiology, and public health: a review of current and best practice. J Clin Epidemiol. 2015; 68(2): 122–33. PubMed Abstract | Publisher Full Text\n\nMunting KE, Klein AA: Optimisation of pre-operative anaemia in patients before elective major surgery - why, who, when and how? Anaesthesia. 2019; 74 Suppl 1: 49–57. PubMed Abstract | Publisher Full Text\n\nChaplin DD, Cook TD, Zurovac J, et al.: The Internal and External Validity of the Regression Discontinuity Design: a Meta-Analysis of 15 Within-Study Comparisons. J Policy Anal Manag. 2018; 37(2): 403–29. Publisher Full Text"
}
|
[
{
"id": "70571",
"date": "08 Oct 2020",
"name": "David Reeves",
"expertise": [
"Reviewer Expertise Statistics",
"Health research."
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIt is very welcome to see a statistical analysis plan for an observational study submitted for publication, as this is relatively rare. It is also quite brave for the authors to do so: unlike an RCT, the form that the analysis of an observational dataset takes is largely dictated by the data available, and a priori plans that seem good in theory frequently need a major overhaul in the light of the actual data. Publishing a plan in advance risks making oneself a hostage to fortune if one’s good ideas subsequently turn out to be not so feasible in practice. However, what we do not know in the present instance, is how much of this plan is genuinely a priori, and how much based on data exploration and analysis already undertaken, though from the precise sample sizes and details presented I suspect quite a bit. Nonetheless, publication is still very worthwhile since the paper provides a level of detail probably not possible in a paper presenting the actual findings of the analysis, given the word-length restrictions of most publications.\nThe authors present a mostly well-written and well-thought-out proposal that uses statistical methods of interrupted time-series and regression discontinuity analysis to evaluate the impact of changes in Hospital Trust policy around care for patients admitted for elective lower limb arthroplasty, on outcomes for those patients. The methods proposed are sound and it is good to see them being applied in this context. My comments below are largely concerned with improving the clarity around specifics of the analyses, issues around seasonal effects, and addressing autocorrelation.\nTable 1: Use of the terms “control cohort” and “intervention cohort” here is a little confusing, as the term “controls” is also used later under Addressing Threats to Validity, where it is applied to a sub-group of anaemic patients during the intervention period – i.e. a different control cohort. I would have preferred Table 1 to use terms such as “pre-intervention” and “post-intervention” to avoid confusion.\nIf I understand Table 1 and Figure 1 correctly, there will be 3 ITS analyses, although the paper could be clearer about this in the text. Moreover, the majority of the intervention cohort for the first ITS (TXA started) will also be part of the control cohort for the second ITS (increased TXA) – since the date ranges overlap – and the intervention cohort for ITS 2 will be identical to the control group for ITS 3 (pre-op anaemia optimisation). If this is the case (or even if it is not) the authors need to clarify the situation here. Overlapping cohorts mean that the analyses will not be independent and may have implications for interpretation of the findings.\nFor clarity I would like to have seen Figure 1 indicate the control cohort periods for each ITS, as well as the implementation and intervention periods. It took me some time work out how Table 1 related to Figure 1 in terms of the time-periods involved.\nOutcomes will be analysed in the form of monthly means or proportions. One issue here, which is not mentioned in the paper, is that the sample size will vary considerably over time. For the first ITS (TXA started) the control period covers approx 50 months and the sample size is 1500, implying a mean sample size of 30 patients per month – very small when the outcome is a proportion; whereas the intervention period is about 20 months with a total sample of 3000, indicating 150 per month. Thus outcome means/proportions will be far more variable over the control period. I haven’t checked, but the same may apply to the other ITS analyses. Ideally data-point variability should be taken into account in the analysis, and is something that the authors should at least mention and discuss the implications of, in the paper.\nEach ITS analysis will incorporate a 6-month implementation period between the pre and post periods, for which data will be dropped from the model. One concern here is the potential for an annual cycle in the data values. I cannot say if elective lower limb arthroplasty is subject to seasonal variation, but certainly hospital admissions for many other conditions are. The risk here is that 6 months can represent the time between the lowest and highest points in an annual cycle. Thus it is conceivable that at the end of the pre period, the cycle will be at it’s lowest point, but at the subsequent start of the post period, it will be at the top (or vice-versa). Particular care will need to be taken to evaluate whether any change in level or trend at this point can be explained by the presence of an annual cycle. The authors acknowledge the potential for seasonality in their discussion of autocorrelation (see below). However, I would like to see a specific sensitivity analysis designed to assess robustness against the threat of an annual cycle, regardless of the outcome of any tests for autocorrelation, given the use of a 6-month lag.\nTests for autocorrelation, using the Durbin-Watson, are planned, using a lag of up to 12 time-points. However, these tests are likely to have very low power, given the numbers of data-points and the measurement error around the individual values (which at times will be very wide). To interpret a non-significant test as implying an absence of autocorrelation would be highly questionable. The data series will almost inevitably in reality possess autocorrelation, even if undetected by the DW, and in my view it would be better to conduct analysis under the assumption that autocorrelation is present. As I have suggested above, a sensitivity test against an annual cycle should be conducted regardless.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Yes\n\nAre sufficient details of the methods provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable",
"responses": [
{
"c_id": "6499",
"date": "13 May 2021",
"name": "Ashley Scrimshire",
"role": "Author Response",
"response": "Thank you for taking the time to provide considered and insightful feedback on our article. Your comments have been addressed in the revised manuscript. A summary of responses is given below. Comment: Table 1: Use of the terms “control cohort” and “intervention cohort” here is a little confusing, as the term “controls” is also used later under Addressing Threats to Validity, where it is applied to a sub-group of anaemic patients during the intervention period – i.e. a different control cohort. I would have preferred Table 1 to use terms such as “pre-intervention” and “post-intervention” to avoid confusion. Response: Agreed, this was unclear. Table 1 has now been updated and the terms “pre-intervention” and “post-intervention” have replaced “control cohort” and “intervention cohort” to avoid confusion. This table also now outlines previously published, pre-post design cohort studies from this unit and does not outline the time periods for this analysis. A new Table 3 in the paper clearly outlines the time periods included in this analysis. Comment: If I understand Table 1 and Figure 1 correctly, there will be 3 ITS analyses, although the paper could be clearer about this in the text. Moreover, the majority of the intervention cohort for the first ITS (TXA started) will also be part of the control cohort for the second ITS (increased TXA) – since the date ranges overlap – and the intervention cohort for ITS 2 will be identical to the control group for ITS 3 (pre-op anaemia optimisation). If this is the case (or even if it is not) the authors need to clarify the situation here. Overlapping cohorts mean that the analyses will not be independent and may have implications for interpretation of the findings. Response: We agree that these figures and accompanying explanations could be clearer. The text has been updated to clarify that there will be two primary ITS analyses, plus secondary and sensitivity analyses. Figure 1 has been updated to clearly demarcate the pre- and post-intervention periods for each analysis. A new Table 3 also outlines the planned analyses and the time periods included in each. Comment: Outcomes will be analysed in the form of monthly means or proportions. One issue here, which is not mentioned in the paper, is that the sample size will vary considerably over time. For the first ITS (TXA started) the control period covers approx 50 months and the sample size is 1500, implying a mean sample size of 30 patients per month – very small when the outcome is a proportion; whereas the intervention period is about 20 months with a total sample of 3000, indicating 150 per month. Thus outcome means/proportions will be far more variable over the control period. I haven’t checked, but the same may apply to the other ITS analyses. Ideally data-point variability should be taken into account in the analysis, and is something that the authors should at least mention and discuss the implications of, in the paper. Response: Thank you for your comment. Data-point variability is expected, although not to the degree in the reviewer comment. Hopefully this is clearer now the time periods that are included in this study have been clarified in response to previous comments. Data-point variability has now been discussed in the amended text. The primary analysis will include all THR/TKR procedures in the dataset. Here the expected counts per month are 100 or more, so proportions will be used. For the secondary analyses, the data will be split into anaemic and non-anaemic sub-groups. Here, it is expected around 20-30% of patients per month will be anaemic, so the counts are expected to drop. In this instance analyses using proportions and counts will be undertaken. Comment: Each ITS analysis will incorporate a 6-month implementation period between the pre and post periods, for which data will be dropped from the model. One concern here is the potential for an annual cycle in the data values. I cannot say if elective lower limb arthroplasty is subject to seasonal variation, but certainly hospital admissions for many other conditions are. The risk here is that 6 months can represent the time between the lowest and highest points in an annual cycle. Thus it is conceivable that at the end of the pre period, the cycle will be at it’s lowest point, but at the subsequent start of the post period, it will be at the top (or vice-versa). Particular care will need to be taken to evaluate whether any change in level or trend at this point can be explained by the presence of an annual cycle. The authors acknowledge the potential for seasonality in their discussion of autocorrelation (see below). However, I would like to see a specific sensitivity analysis designed to assess robustness against the threat of an annual cycle, regardless of the outcome of any tests for autocorrelation, given the use of a 6-month lag. Tests for autocorrelation, using the Durbin-Watson, are planned, using a lag of up to 12 time-points. However, these tests are likely to have very low power, given the numbers of data-points and the measurement error around the individual values (which at times will be very wide). To interpret a non-significant test as implying an absence of autocorrelation would be highly questionable. The data series will almost inevitably in reality possess autocorrelation, even if undetected by the DW, and in my view it would be better to conduct analysis under the assumption that autocorrelation is present. As I have suggested above, a sensitivity test against an annual cycle should be conducted regardless. Response: Thank you for your advice on this. The paper has been amended and the analyses will assume autocorrelation is present and a sensitivity analysis assuming seasonality has also been incorporated."
}
]
},
{
"id": "72020",
"date": "02 Nov 2020",
"name": "Al Ozonoff",
"expertise": [
"Reviewer Expertise Statistics",
"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 authors provide a prospective statistical analysis plan for a forthcoming study of orthopedic surgical cases from the UK National Health Service (NHS). The study uses quasi-experimental Interrupted Time Series (ITS) and Regression Discontinuity (RD) designs. The statistical analysis plan (SAP) is clear and well-written although there are some aspects that could be clarified. It is understood that many details of the model development will be determined upon examination of the data and thus a prospective statistical analysis plan should not be over-specified. However, there are some important elements of the modeling process that could be further explained in terms of what available methods might be considered.\nSpecific comments follow:\nData source. There could be more added to the section on data sources. The data set includes N=20,772 patients who have undergone primary elective THR or TKR surgeries at NHCT. Are there any surgeries excluded? A brief 1-2 sentences to state explicitly and formally the inclusion and exclusion criteria would be useful.\n\nInterrupted Time Series. The exclusion of data from the six month period following each intervention seems overly conservative. Since the data are available for screening versus surgery time, the intervention can be modeled not as a binary (0/1) indicator but rather as a continuous implementation variable ranging from 0 to 1, estimated by the monthly proportion of surgeries for which patients received screening. Thus the effect of the intervention is modeled as a weighted average during the six month period following intervention which is a more efficient use of data and should provide a more precise estimate of the intervention effect.\n\nThe discussion of threats to ITS validity does not give much credit to the possibility that the patient population may change over the course of the study evaluation. While the authors note that there are no known changes in the overall population served by NHCT, it seems more plausible that there are shifts in demographics or other characteristics of the population receiving THR or TKR. Simple examinations of sex, age, and other clinical factors over the 11+ years of the study period seem warranted if only to verify that there are no major changes in the study population.\n\nThe discussion of threats to RDD validity could be sharpened. Most of the methods described involve visual inspection of graphical parameters with little formal testing planned. Comparability of groups on either side of the threshold might test formally the hypothesis of difference between groups as would be done for an RCT. It is not explained how bandwidth selection would address the threat to validity posed by incomparability, especially if an observed difference might be explained by manipulation of the assignment variable.\n\nDescribing model development, the bins for Hg will be chosen from options of 1, 2, or 5 g/L each with no explanation of what considerations are important nor how the data will drive the decision. Similarly, there should be detail provided on which ‘data driven methods’ will inform bandwidth selection.\n\nThere is no discussion of how to determine the functional form of the regression. What alternatives are considered if the relationship between Hg and outcome does not appear linear. There is a mention that non-linear models are considered without much insight into what methods are available in this case.\n\nMinor edits/corrections:\nOutcomes p3. Rates might be better specified with the appropriate denominator e.g. 30-day critical care readmission rate (per 1000 surgeries).\n\nData description p5. Typo ‘determin’ => ‘determine’.\n\nRegression discontinuity p5. Typo ‘populationas’ => ‘population as’.\n\nAddressing threats to validity p6. Typo ‘adhered to’ => ‘adhere to’.\n\nFinal phrase ‘Whereas RDD…’ is a fragment => combine with the previous sentence.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Yes\n\nAre sufficient details of the methods provided to allow replication by others? Partly\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable",
"responses": [
{
"c_id": "6500",
"date": "13 May 2021",
"name": "Ashley Scrimshire",
"role": "Author Response",
"response": "Thank you for taking the time to prove considered feedback on our article and for engaging in further discussion on your comments, this is very much appreciated. Your comments have been incorporated into the revised manuscript and a summary of our responses is given below. Comment: Data source. There could be more added to the section on data sources. The data set includes N=20,772 patients who have undergone primary elective THR or TKR surgeries at NHCT. Are there any surgeries excluded? A brief 1-2 sentences to state explicitly and formally the inclusion and exclusion criteria would be useful. Response: Thank you for your comment. This has been clarified in the text and Table 2 now presents the eligible procedure codes. Comment: Interrupted Time Series. The exclusion of data from the six month period following each intervention seems overly conservative. Since the data are available for screening versus surgery time, the intervention can be modeled not as a binary (0/1) indicator but rather as a continuous implementation variable ranging from 0 to 1, estimated by the monthly proportion of surgeries for which patients received screening. Thus the effect of the intervention is modeled as a weighted average during the six month period following intervention which is a more efficient use of data and should provide a more precise estimate of the intervention effect. Response: This is a very interesting point and thank you for engaging in further discussion on this. The paper has been updated. We now plan to include a sensitivity analysis modelling the intervention as a continuous implementation variable as suggested by the reviewer. Comment: The discussion of threats to ITS validity does not give much credit to the possibility that the patient population may change over the course of the study evaluation. While the authors note that there are no known changes in the overall population served by NHCT, it seems more plausible that there are shifts in demographics or other characteristics of the population receiving THR or TKR. Simple examinations of sex, age, and other clinical factors over the 11+ years of the study period seem warranted if only to verify that there are no major changes in the study population. Response: Thank you for highlighting this oversight, we agree with your comments. We will include comparison of key patient demographics and characteristics in the pre- and post-intervention groups. This has been included in the text. Comment: The discussion of threats to RDD validity could be sharpened. Most of the methods described involve visual inspection of graphical parameters with little formal testing planned. Comparability of groups on either side of the threshold might test formally the hypothesis of difference between groups as would be done for an RCT. Response: Thank you for your advice on these points. The manuscript has been updated to make this more robust. In particular we plan to generate tables and undertake statistical tests comparing non-outcome characteristics for groups either side of the threshold. Comment: It is not explained how bandwidth selection would address the threat to validity posed by incomparability, especially if an observed difference might be explained by manipulation of the assignment variable. Response: As detailed in the updated manuscript, manipulation of the assignment variable by patients is not considered likely in this scenario. However this will be explored within the data. We have now clarified our analysis plans in the manuscript. As such bandwidth selection is only relevant to our planned non-parametric sensitivity analysis, rather than the primary parametric analyses which will use all data. Sensitivity analyses in which the model incorporates predicted factors that may influence outcome such as age, comorbidities, will be undertaken. In addition, variables that are identified as being unbalanced between the two groups (i.e. as a result of possible manipulation of the assignment variable) will be included as covariates in further sensitivity analyses. Comment: Describing model development, the bins for Hg will be chosen from options of 1, 2, or 5 g/L each with no explanation of what considerations are important nor how the data will drive the decision. Similarly, there should be detail provided on which ‘data driven methods’ will inform bandwidth selection. Response: Agreed, we were not clear on our approach to this. The text has been updated. We intend to first plot data using a range of bin sizes and visually inspect these to rule out ones that are clearly too wide or too narrow. We will go on to conduct F-tests (using 2k dummies and interactions) to identify bin widths that over smooth the data. From the remaining choices we will pick the widest bin size that is not rejected by either F-test. As for bandwidth selection, this is only relevant to our planned nonparametric sensitivity analysis. Here we intend to use the cross-validation method to inform bandwidth selection. Comment: There is no discussion of how to determine the functional form of the regression. What alternatives are considered if the relationship between Hg and outcome does not appear linear. There is a mention that non-linear models are considered without much insight into what methods are available in this case. Response: Agreed, we had not been clear on this, the text has now been updated. Our intentions are that after bin size has been selected plots will first be inspected visually. The F-Test approach will then be used to determine the functional form of the regression. Starting with a simple linear model and adding a higher order term until the F-test is no longer statistically significant. Robustness checks for this model in which the outer most 1,5 and 10% of data points are dropped will be conducted. Comment: Outcomes p3. Rates might be better specified with the appropriate denominator e.g. 30-day critical care readmission rate (per 1000 surgeries). Response: Agreed, this has now been updated in the text Comment: Typos/grammar: Data description p5. Typo ‘determin’ => ‘determine’. Regression discontinuity p5. Typo ‘populationas’ => ‘population as’. Addressing threats to validity p6. Typo ‘adhered to’ => ‘adhere to’. Final phrase ‘Whereas RDD…’ is a fragment => combine with the previous sentence Response: These have been corrected, thank you for highlighting."
}
]
}
] | 1
|
https://f1000research.com/articles/9-224
|
https://f1000research.com/articles/10-383/v1
|
13 May 21
|
{
"type": "Research Article",
"title": "Complications and postoperative ileus in laparoscopic versus open colectomy: A retrospective cohort study",
"authors": [
"Nadim Malibary",
"Abdullah Almohaimeed",
"Abdullah Alshareef",
"Abdulkarim Alzahrani",
"Faris Siddiq",
"Mohammed Sulaimani",
"Nouf Y. Akeel",
"Ali H. Farsi",
"Mohammed O. Nassif",
"Ali A. Samkari",
"Abdulaziz M. Saleem",
"Nora H. Trabulsi",
"Abdullah Almohaimeed",
"Abdullah Alshareef",
"Abdulkarim Alzahrani",
"Faris Siddiq",
"Mohammed Sulaimani",
"Nouf Y. Akeel",
"Ali H. Farsi",
"Mohammed O. Nassif",
"Ali A. Samkari",
"Abdulaziz M. Saleem",
"Nora H. Trabulsi"
],
"abstract": "Background: Postoperative complications are a major concern after colorectal surgery, and can lead to an increased burden on patients and the healthcare system. Complications include postoperative ileus (POI) and prolonged postoperative ileus (PPOI). There are well-established risk factors and potential modifiable risk factors that affect the incidence of POI and PPOI, including invasive techniques, operative difficulty, perioperative blood loss, and delayed mobilization. We compared the incidence of POI, PPOI, and other postoperative complications between laparoscopic colectomy and open colectomy. Methods: This retrospective review investigates 120 patients who underwent either laparoscopic or open colectomy in King AbdulAziz University Hospital in Jeddah, Saudi Arabia, between January 2016 and June 2019. Data were collected from patients’ electronic medical records. Patients were classified into laparoscopic and open colectomy groups. The main outcomes of interest were POI, PPOI and the overall complication rate. These outcomes were calculated and compared between the two groups. Results: The overall incidence of POI and PPOI was 4.2% and 15%, respectively. There was a higher incidence of POI in the laparoscopic approach group (7.2% vs. 1.5%, P=0.03); however, the incidence of PPOI was higher in the open approach group (20% vs. 9.1%, P=0.03). The open surgery group showed a higher rate of overall complications (P=0.001). The mean estimated blood loss was lower in the laparoscopy group (139.09±145.83 vs. 343.85±307.78 mL; P<0.001). Significant earlier mobilization was observed in the laparoscopic group (3.12±1.77 vs. 5.39±3.48 days; P<0.001). Conclusion: The incidence of PPOI was significantly different depending on the surgical approach; however, the laparoscopy group tolerated regular diet earlier and had better outcomes regarding postoperative complications. The laparoscopic approach was associated with earlier ambulation and was more cost-effective based on the length of the hospital stay. Further randomized studies are required to confirm superiority of the laparoscopic approach in terms of postoperative recovery.",
"keywords": [
"postoperative ileus",
"postoperative complications",
"colectomy",
"laparoscopy",
"laparotomy"
],
"content": "Introduction\n\nPostoperative complications are often inevitable following abdominal surgeries. They range from altered postoperative recovery which does not require medical intervention, to life-threatening conditions requiring intensive care management and may lead to mortality.1,2 Among these complications, postoperative ileus (POI) is still the most common postoperative problem causing delays in patient discharge, while anastomotic leak is considered the most important factor that leads to readmission within 30 days.3 Along with other complications, POI and anastomotic leak contribute heavily to the economic burden on the healthcare system.3 The incidence of POI across extensive studies was found to range from 10% to 30%, leading to a 29% increase in the length of stay (LOS) in the hospital.4,5 The term ileus refers to the disability of gastrointestinal peristalsis, which is characterized by absent or decreased peristalsis that results in the accumulation of digestive secretions leading to intolerance to oral feeding, abdominal distention, abdominal pain, failure to pass flatus, absence of bowel movement, nausea, and vomiting. These complications increase the risk of aspiration pneumonia, malabsorption, and anastomosis leakage.4 Normally, the functionality of the small intestine returns within 24–48 hours postoperatively, while the colon requires 48–72 hours of recovery.6\n\nIn Saudi Arabia, data on surgical outcomes and the differences between laparoscopic and open approaches in terms of postoperative ileus are scarce. Our goal was to evaluate the incidence of POI and prolonged postoperative ileus (PPOI) as well as postoperative complication rates between the two different approaches, following colorectal surgery in our institution. This was with a view to assessing the potential contributing factors.\n\n\nMethods\n\nWe conducted a retrospective cohort study at King AbdulAziz University Hospital (KAUH), a tertiary center in Jeddah, Saudi Arabia. Data of 134 adult patients who underwent colectomy for colorectal cancer from January 2016 to June 2019 were collected from the electronic medical database and reviewed. Patients were divided into two groups, laparoscopy, and laparotomy approach. A total of 14 patients were excluded due to their conversion from laparoscopy to open surgery. The final population size was 120.\n\nThis study was approved by the Institutional Review Board of KAUH in 2019 (ref. 145-19). The need for obtaining patient consent was waived by the IRB.\n\nAll adult patients aged > 18 years that were diagnosed with non-metastatic colon or rectal cancer and who had undergone operation were extracted from the hospital’s data base and included. Key search terms were laparoscopic/open right or left colectomy, laparoscopic/open low anterior resection, laparoscopic/open total colectomy, laparoscopic/open subtotal colectomy, laparoscopic/open abdominoperineal resection and laparoscopic/open total coloproctectomy. Patients were classified into two groups according to the surgical approach used: either laparoscopic colectomy; or open colectomy. Patients who had laparoscopic conversion to open, i.e. surgeries which started with laparoscopy that ended up being laparotomy were excluded. In addition, patients with disseminated cancer, concurrent procedure, or sepsis (in the form of peritonitis) were excluded from the study to avoid confounders. Patients with incomplete records were also excluded from the analysis of that particular entity.\n\nThe data collected included demographic information (age, sex, Body Mass Index, comorbidities) as well as preoperative variables including diagnosis, neoadjuvant therapy, comorbidities, and previous abdominal surgeries. Intraoperative variables were also documented, including the American Society of Anesthesiologists (ASA) score, use of epidural anesthesia, colorectal procedure, approach (laparoscopy or open), stoma formation, estimated blood loss, blood transfusion, and procedure duration. All patients received a clear liquid diet 24 h after the operation and subsequently progressed to a regular diet. After the regular diet was tolerated and bowel movements returned to normal, the patient was discharged.\n\nPostoperative variables included the type of analgesia, vomiting, abdominal distention, time of mobilization, time until clear and regular diets were tolerated, and the day of the first bowel movement. The length of hospital stay, from the time of operation until patient discharge, was also recorded. Readmission within 30 days and postoperative complications were assessed based on the Clavien–Dindo score.7 POI was defined as the absence of first flatus and intolerance of an oral intake within three days, postoperatively, and PPOI was defined as the delayed passage of flatus with intolerance of an oral intake for more than three days, postoperative.8\n\nStatistical analysis was performed using IBM SPSS Statistics Version 21.0.Mean ± standard deviation was used to describe the numerical data. Patient treatment and outcome related variables where represented as percentages and frequencies of the total population. Comparisons and the relationships between the groups were made using independent t-test, chi-square test, and bivariate correlation. The results were considered significant where the two-tailed P value ≤ 0.05.\n\nA total of 120 patients that were diagnosed with colorectal cancer who underwent different colonic procedures were included in this study (see Underlying data23). The patients’ baseline characteristics are presented in Table 1. Patients were divided into two groups: the laparoscopic approach group, 55 patients (45.8%); and the open approach group, 65 patients (54.2%). The age of the patients ranged from 22 years to 90 years, with a mean (SD) age of 61.36 ± 13.85 years. The patients were predominantly male (60%), and most of the cohort had colon cancer (67.5%). Over half of the patients were either overweight or obese (65%), and a third had diabetes mellitus (33.3%). Most patients were of ASA class 2 or 3 (92.5%).\n\nRegarding operative variables, the majority were elective procedures (77.5%) and most had anastomoses (74.2%) (Table 2). Most patients did not require blood transfusion, and among those who did, the average number of units transfused was 1.75 (SD, 0.46).\n\nTable 3 presents the postoperative outcomes including postoperative complications, POI, and PPOI in both the laparoscopic and the open approaches. The incidence of POI and PPOI in the study group was 4.2% and 15%, respectively. There was a higher incidence of POI in the laparoscopic approach (7.2% vs. 1.5%, P = 0.03); however, the incidence of PPOI was higher in the open approach (20% vs. 9.1%, P = 0.03). The mean time of first bowel movement in the laparoscopic and open approaches were 3.13 ± 2.13 vs. 3.94 ± 2.65 days; P = 0.09). Patients with previous abdominal surgeries showed no difference in PPOI compared to those with no previous surgeries (P = 0.33). The operative duration was greater in the laparoscopy approach group (403.16 ± 133.73 vs. 277.34 ± 123.39 min; P < 0.001) along with less bleeding compared to the open approach group (139.09 ± 145.83 vs. 343.85 ± 307.78 mL; P < 0.001). Regular diet was tolerated earlier in the laparoscopy approach group than in the open approach group (5.44 ± 2.7 vs. 8.94 ± 6.64 days; P < 0.001). Mobilization was also observed earlier in the laparoscopic approach (3.12 ± 1.77 vs. 5.39 ± 3.48 days; P < 0.001).\n\na Some patients had more than one complication.\n\nb Some data are missing.\n\nRegarding the incidence of postoperative complications, 59% of patients had no complications, while 41% had varying degrees of complications. The open approach showed a higher rate of complications—37 patients (56.9%), compared to 11 patients (20%) in the laparoscopic group. According to the Clavien–Dindo score, this difference was statistically significant (Table 3).\n\nFurthermore, the LOS was longer in the open approach compared to the laparoscopic approach (14.52 ± 10.47 vs. 8.24 ± 4.29 days; P < 0.001). Patients with anastomotic leak had a longer LOS (23.86 ± 9.5 vs. 10.85 ± 8.17 days; P < 0.001). General and epidural anesthesia was used for most patients (98 [81.7%]), while the remaining patients received general anesthesia only (22 [18.3%]). No significant difference was found between patients with POI and PPOI in the use of epidural or general anesthesia (P = 0.24).\n\nAddressing the incidence of POI and PPOI is essential for determining the risk factors associated with these complications and can therefore help in decreasing their occurrence. In our study, the incidences of POI and PPOI following colorectal surgery were 4.2% and 15%, respectively, while the literature demonstrates that the incidence of POI is 10-30% and the incidence of PPOI is 2-54%.4,5,9\n\nPrevious studies have demonstrated that the risk factors for POI and PPOI include more invasive approaches, operative difficulty, older age, perioperative blood loss, and delayed mobilization.10,11 Our analysis showed that the open approach was associated with a significantly higher incidence of PPOI than the laparoscopic approach. In the literature, the open approach was identified as an independent risk factor for the development of an ileus.9 At the same time, most of the patients with POI, which is a less severe form of ileus, were in the laparoscopic group. These results are more likely explained by the inflammatory and neurological responses to surgical trauma and increased requirements for narcotics, which are more pronounced in the open approach group.12,13 It has been suggested that adherence to protocols of enhanced recovery after surgery could potentially decrease the incidence of POI. These protocols that recommend minimally invasive procedures, early ambulation, and early feeding.14\n\nPrevious studies,2,10,14 including a cross-sectional study conducted in 2013 in Isfahan, Iran,6 have found that the occurrence of ileus is directly associated with the duration of the surgical procedure. However, the Iranian study solely focused on the duration of the operation, rather than the type of surgical approach used.6 In our analysis, the duration of laparoscopic colectomy was significantly longer than that of the open procedure; however, this did not lead to an increase in the incidence of PPOI. Another study that observed 295 patients who underwent laparoscopic colectomy for colorectal cancer, also found that the duration of the operation has little impact on POI and PPOI.15 Some studies speculate that the longer duration of the laparoscopic approach is due to the limited range of motion and flexibility of instruments, in addition to the two-dimensional view and the dependence on surgeon skill.16 However, we do not agree with that statement in view of ongoing innovations, and the early exposure of trainees to laparoscopic surgery. There is the potential risk of bias, however, as it may be the case that more advanced disease that requires open surgery and multi-organ resection could contribute to prolonged operative time, POI, and PPOI.\n\nIn terms of intraoperative complications, studies have shown that the higher the estimated blood loss, the higher the risk of developing POI. This is explained by the stimulation of the sympathetic stress response and its inhibition of bowel motility.17 Many studies state that the open approach results in more blood loss and blood transfusions than the laparoscopic approach.18,19 Our results have also shown a significant difference in blood loss between open surgery and laparoscopy (343.85 vs. 152.73 mL). The significant increase in bleeding in the open approach may have occurred due to the larger surgical incision. However, this could also be influenced by the fact that more advanced disease that requires major resection would be associated with more blood loss and a higher rate of transfusion.\n\nRegarding the postoperative hospital course, our results have shown a significant earlier tolerance of regular diet in the laparoscopy group compared to the open group (5.44 vs. 8.94 days). This may be due to less trauma during the operation and the release of less amounts of stress hormones, allowing for early bowel recovery.18 Patients who underwent laparoscopy showed earlier ambulation (3.12 vs. 5.39 days) because of the small surgical incision and less pain. Early mobilization in the laparoscopy group also helped to stimulate bowel function. Similar results on early regular diet tolerance and early mobilization in the laparoscopy group were observed in other studies.12\n\nThe laparoscopic approach was associated with a significantly lower risk of overall complications and this supports our point of view.13 Furthermore, our study has shown that the Clavien–Dindo score was lower in the laparoscopy group than in the open group. A recent study showed that the most common surgical complication is surgical site infection (SSI), while POI is the third most common complication.20 In our study, the most frequent complications were POI and PPOI, followed by SSI. With regard to LOS, we found that it was shorter in the laparoscopy group compared to the open group. This was similar to the findings of a recent retrospective cohort study performed in the United States, which investigated both surgical approaches and robotic surgery, and showed that robotic and laparoscopic surgeries had shorter LOS than the open approach.21 In addition, a better quality of life was observed in patients that underwent laparoscopic colectomy in a randomized controlled trial.22\n\nThe study’s main limitations were its retrospective nature, small number of patients, and the lack of standardized definitions of POI and PPOI. These results are limited to a small population in a single tertiary center, therefore not necessarily applicable to the general population and definitive conclusions cannot be made. Further studies with a larger sample size, involving multiple colonic diseases, are required to address this issue.\n\nThe incidence of both POI and PPOI were significantly influenced by the surgical approach used. The laparoscopic approach showed better postoperative mobilization and tolerance to regular diet. However, overall complications were more frequent in the open approach. Our suggestion for future studies is to address more extensive pre-and postoperative measures aimed at decreasing the incidence of POI, PPOI, and other complications of colorectal surgeries.\n\n\nData availability\n\nZenodo: Complications and postoperative ileus in laparoscopic versus open colectomy: A retrospective cohort study. http://doi.org/10.5281/zenodo.4730346.23\n\nThis project contains the following underlying data:\n\n- raw data.xlsx\n\n- CODING FOR REASEARCH VARIABLES.docx\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "References\n\nJakobson T, Karjagin J, Vipp L, et al.: Postoperative complications and mortality after major gastrointestinal surgery. Medicina. 2014; 50(2): 111–117. PubMed Abstract | Publisher Full Text\n\nKim YW, Kim IY: Comparison of the short-term outcomes of laparoscopic and open resections for colorectal cancer in patients with a history of prior median laparotomy. Indian J Surg. 2017; 79(6): 527–533. PubMed Abstract | Publisher Full Text | Free Full Text\n\nScarborough JE, Schumacher J, Kent KC, et al.: Associations of specific postoperative complications with outcomes after elective colon resection: a procedure-targeted approach toward surgical quality improvement. JAMA Surg. 2017; 152(2): e164681. PubMed Abstract | Publisher Full Text\n\nBragg D, El-Sharkawy AM, Psaltis E, et al.: Postoperative ileus: recent developments in pathophysiology and management. Clin Nutr. 2015; 34(3): 367–376. PubMed Abstract | Publisher Full Text\n\nVenara A, Neunlist M, Slim K, et al.: Postoperative ileus: pathophysiology, incidence, and prevention. J Visc Surg. 2016; 153(6): 439–446. PubMed Abstract | Publisher Full Text\n\nFesharakizadeh M, Taheri D, Dolatkhah S, et al.: Postoperative ileus in colorectal surgery: is there any difference between laparoscopic and open surgery? Gastroenterol Rep. 2013; 1(2): 138–143. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDindo D, Demartines N, Clavien PA: Classification of surgical complications: a new proposal with evaluation in a cohort of 6336 patients and results of a survey. Ann Surg. 2004; 240(2): 205–213. PubMed Abstract | Publisher Full Text | Free Full Text\n\nVather R, Trivedi S, Bissett I: Defining postoperative ileus: results of a systematic review and global survey. J Gastrointest Surg. 2013; 17(5): 962–972. PubMed Abstract | Publisher Full Text\n\nLluis N, Biondo S: Prolonged postoperative ileus after colorectal surgery: still an unresolved problem. Minim Invasiv Appr Colorectal Dis. 2018; 138: 279–306. Publisher Full Text\n\nHarnsberger CR, Maykel JA, Alavi K: Postoperative Ileus. Clin Colon Rectal Surg. 2019; 32(3): 166–170. PubMed Abstract | Publisher Full Text | Free Full Text\n\nStory SK, Chamberlain RS: A comprehensive review of evidence-based strategies to prevent and treat postoperative ileus. Digest Surg. 2009; 26(4): 265–275. PubMed Abstract | Publisher Full Text\n\nMasoomi H, Buchberg B, Nguyen B, et al.: Outcomes of laparoscopic versus open colectomy in elective surgery for diverticulitis. World J Surg. 2011; 35(9): 2143–2148. PubMed Abstract | Publisher Full Text\n\nDelaney CP, Chang E, Senagore AJ, et al.: Clinical outcomes and resource utilization associated with laparoscopic and open colectomy using a large national database. Ann Surg. 2008; 247(5): 819–824. PubMed Abstract | Publisher Full Text\n\nGrass F, Slieker J, Jurt J, et al.: Postoperative ileus in an enhanced recovery pathway—a retrospective cohort study. Int J Colorectal Dis. 2017; 32(5): 675–681. Postoperative ileus in an enhanced recovery pathway—a retrospective cohort study\n\nPędziwiatr M, Pisarska M, Małczak P, et al.: The incidence of prolonged postoperative ileus after laparoscopic colorectal surgery—does ERAS protocol bring anything new? Indian J Surg. 2018; 80(4): 333–339.\n\nKong TW, Lee KM, Cheong JY, et al.: Comparison of laparoscopic versus conventional open surgical staging procedure for endometrial cancer. J Gynecol Oncol. 2010; 21(2): 106–111. PubMed Abstract | Publisher Full Text | Free Full Text\n\nArtinyan A, Nunoo-Mensah JW, Balasubramaniam S, et al.: Prolonged postoperative ileus—definition, risk factors, and predictors after surgery. World J Surg. 2008; 32(7): 1495–1500. PubMed Abstract | Publisher Full Text\n\nGlaser F, Sannwald GA, Buhr HJ, et al.: General stress response to conventional and laparoscopic cholecystectomy. Ann Surg. 1995; 221(4): 372–380. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSchlottmann F, Patti MG: Laparoscopic versus open surgery still an open debate. J Laparoendos Adv Surg Tech. 2017; 27(12): 1223–1224. PubMed Abstract | Publisher Full Text\n\nTolstrup MB, Watt SK, Gögenur I: Morbidity and mortality rates after emergency abdominal surgery: an analysis of 4346 patients scheduled for emergency laparotomy or laparoscopy. Langenbecks Arch Surg. 2017; 402(4): 615–623. PubMed Abstract | Publisher Full Text\n\nMcCarthy E, Gough BL, Johns MS, et al.: A comparison of colectomy outcomes utilizing open, laparoscopic, and robotic Techniques. Am Surg. 2020 [cited Dec 19]. PubMed Abstract | Publisher Full Text\n\nMcCombie AM, Frizelle F, Bagshaw PF, et al.: The ALCCaS Trial: a randomized controlled trial comparing quality of life following laparoscopic versus open colectomy for colon cancer. Dis Colon Rectum. 2018; 61(10): 1156–1162. PubMed Abstract | Publisher Full Text\n\nMalibary N: Complications and postoperative ileus in laparoscopic versus open colectomy: A retrospective cohort study [Data set]. Zenodo. 2021. Publisher Full Text"
}
|
[
{
"id": "85323",
"date": "28 May 2021",
"name": "Hefzi Alratrout",
"expertise": [
"Reviewer Expertise General",
"digestive and Colorectal surgeon."
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 is an interesting topic with nice results, however, I do have a few minor comments and suggestions:\nConcerning the article's name: I think it would be more convenient to remove postoperative ileus from the title, and just say: Complications in laparoscopic versus open... etc. Or say: postoperative morbidities in laparoscopic versus open... etc.- Because postoperative ileus is among postoperative complications, and is considered a morbidity.\n\nRegarding the results of POI and PPOI: PPOI is any POI that extends beyond 3 days, thus, logically the numbers and percentages of PPOI are less than POI because some patients will resolve their postoperative ileus. However, in this article the numbers of POI is more than PPOI. Did they inverse the numbers? or when they say PPOI what they really mean is late onset of postoperative ileus?\n\nAgain, good article and worth publishing after correction and clarification of those 2 points.\nThank 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? 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": "6815",
"date": "21 Jun 2021",
"name": "nadim malibary",
"role": "Author Response",
"response": "Dear reviewer, thank you for your time and effort. Regarding your first point, we can't argue that Ileus is not a post operative complication. The purpose of this project was comparing POI and PPOI between 2 surgical approaches, and we had to mention other morbidities too, hence the broader title. For the second point, PPOI are patients who had persistent ileus beyond 3 days, and in our tables are not considered POI. Meaning that POI patients are only the patients whose POI was resolved during the 3-day period, and if it takes longer, they are counted as PPOI. We had a bigger number of PPOI than POI in our cohort. Regards"
}
]
},
{
"id": "92062",
"date": "19 Oct 2021",
"name": "Mario Trejo-Avila",
"expertise": [
"Reviewer Expertise Colon and Rectal Surgery"
],
"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 retrospective cohort study. I have several comments to this manuscript:\nAbstract:\nThe aim of the study is lacking.\n\nIn the conclusion, I think its not appropriate to include that “the laparoscopic approach was more cost-effective”. This was not the aim of the study, it should not be part of the conclusion.\n\nMethods:\nThe aim of the study is ambiguous. It should be clear whether the aim is the incidence of postoperative ileus or postoperative complications.\n\nI suggest to add a paragraph regarding primary and secondary outcomes, with their respective definitions.\n\nRegarding the inclusion criteria, including all the procedures is misleading. One should expect higher complications rates (and higher ileus incidence) after a total colectomy or after a pelvic procedure in comparison to a right colectomy (which is by definition less invasive).\n\nResults:\nIn table 1, there are patients with colon and rectal cancers, but what patients where included as “colorectal cancer“?\n\nIncluding elective vs. emergency surgery is misleading. It is expected to have higher complications rates after emergency resections.\n\nWhy the Inclusion of an ASA-V patient that by definition is a moribund patient?\n\nIt should be explained the reason why patients after open surgery mobilize later than laparoscopic patients.\n\nIt is confusing why patients in the laparoscopic group have better tolerance of clear liquids and regular diet (less days) but the incidence of POI is higher in that group. Please explain this.\n\nIn Table 3 the percentages presented for postoperative complications are confusing. SSI rates of 87.5%? Anastomotic leaks 71.4? And 100% of DVT?\n\nDiscussion:\nThe limitation section of the study is incomplete. There are more flaws in this study that need to be mentioned.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
}
] | 1
|
https://f1000research.com/articles/10-383
|
https://f1000research.com/articles/10-32/v1
|
18 Jan 21
|
{
"type": "Study Protocol",
"title": "Epidemiological, humanistic and economic burden of dog-mediated rabies in India: a systematic review protocol",
"authors": [
"Denny John",
"Abhishek Royal",
"Omesh Bharti",
"Denny John",
"Omesh Bharti"
],
"abstract": "Background: Rabies is a neglected zoonotic disease. It is transmitted through the bite of a rabid animal and dog bites are responsible for around 95% of human cases. The disease is almost fatal after the onset of symptoms. It is an endemic and major public health problem in India with one-third of the global deaths reported from this country. Protocol: This systematic review aims to estimate the epidemiological, humanistic and economic burden of dog-mediated rabies in India. Initially the existence of controlled descriptors in MeSH terms (such as 'Epidemiology', 'Rabies', 'Cost', 'Dog bite', 'Quality of Life', 'India' etc), and their synonyms (key words) was identified in MEDLINE, and were later combined with Boolean operators 'AND' and 'OR' to develop a detailed search strategy. Two independent reviewers will screen the titles and abstracts and select the studies as per the inclusion criteria. The selected studies will be assessed for their quality and risk of bias. Data will be extracted using standardized data extraction tools and will be synthesized for analysis. Disagreements that arise between the reviewers will be resolved through discussion, or with a third reviewer. Discussion: This systematic review will be performed to critically examine relevant literature and report the epidemiological, humanistic and economic burden of dog-mediated rabies in Indian context. The findings will help in estimation of burden of the disease in India and expected to contribute in policy making and planning of the program and interventions in the country. Protocol registration: PROSPERO ID: CRD4202021326",
"keywords": [
"Rabies",
"Dog bite",
"Systematic Review",
"Protocol",
"Burden of illness",
"Epidemiology",
"Humanistic burden",
"costs"
],
"content": "Introduction\n\nRabies is a neglected zoonotic disease which results in 59,000 deaths per year across the globe1. It is nearly 100% fatal after the onset of symptoms but could be prevented through timely access to post-exposure prophylaxis (PEP) following animal bites2,3. The administration of the recommended PEP following an exposure is guided through three World Health Organization exposure categories: I (no exposure), II (exposure) and III (severe exposure)4. As dogs are responsible for more than 95% human cases, the effective strategy also includes vaccination of dogs against rabies and pre-exposure prophylaxis for high risk individuals including veterinary healthcare workers, children and adults at risk3.\n\nRabies is an endemic disease and major public health problem in India. It is prevalent across the entire country except in Andaman & Nicobar and Lakshadweep Islands. Annual human deaths due to rabies are estimated to be around 20,000 and the annual incidence of animal bites to be 1.7% (17.5 million per year) in India5. The number of deaths due to furious rabies as estimated by Million Deaths Study in 2012 was 127006. IDSP (Integrated Disease Surveillance Programme) reported an increase in animal bites from 4.2 million in 2012 to 7.4 million in 2018 and dogs are responsible for more than 95% of rabies deaths7. At these rates, India contributes approximately one third of global rabies deaths annually. The disease mainly affects people belonging to lower socio-economic categories, and children in the age group of 5–15 years in the country8.\n\nDespite presence of the National Rabies Control Programme (NRCP), incidence of rabies has remained stagnant and grossly under-reported9. The true burden of disease is not reflected in hospital data due to issues in reporting and community-based systems are considered better for rabies surveillance in India10. There is serious need of improved reporting systems to address the lack of accurate data and its verification in a number of regions in the country10,11.\n\nThis systematic review protocol attempts to measure the magnitude of the epidemiological, economic and humanistic burden of dog-mediated rabies in India. It has been planned to highlight key evidence gaps, precise measurements and utilization decisions to enable policymakers to frame the best health practice solutions. A preliminary search on PROSPERO, MEDLINE, Cochrane Database of Systematic Reviews and JBI Database of Systematic Reviews and Implementation Reports was conducted, and no current or ongoing systematic reviews on the topic were identified to the best of our knowledge.\n\n\nProtocol\n\nThe methods of this systematic review have been developed and reported in compliance with the Preferred Reporting Items for Systematic Reviews and Meta-Analysis Protocols (PRISMA-P)12 (see Reporting guidelines for a completed checklist13). In accordance with guidelines, the study protocol is registered with the International Prospective Register of Systematic Reviews (PROSPERO) with ID: CRD42020213261\n\nTo synthesize evidence on epidemiological, humanistic and economic burden of dog bites and dog-mediated rabies and its complications in India\n\nWhat is the epidemiological, humanistic and economic burden of dog bites and dog-mediated rabies and its complications in India?\n\nPopulation. This systematic review will include rabies patients and human dog-bite victims irrespective of their age and gender.\n\nOutcomes\n\nEpidemiological outcomes: Prevalence, category and socio-demographic trends of dog bites; clinical and epidemiological profile of victims, morbidity and; incidence of rabies.\n\nHumanistic outcomes: Utility and heath-related quality of life (HRQoL) measurements associated with dog bites and rabies.\n\nEconomic outcomes: Various costs including direct and indirect costs and resources utilized in association with dog-bite and rabies.\n\nThe following study designs will be included:\n\nFor epidemiological outcomes, Randomized Control Trials (RCTs) with comparator arm, cohort and cross-sectional studies will be included.\n\nFor humanistic outcomes, RCTs with comparator arm, case-control, cohort and cross-sectional studies reporting patient reported HRQoL and other utility and humanistic outcomes will be included.\n\nFor economic outcomes, partial economic evaluation such as cost, cost of illness and resource utilization analyses; and full economic evaluation such as cost-effectiveness, cost utility, cost minimization, and cost-benefit analyses studies will be included.\n\nStudies without the relevant data on the outcomes of interest, such as rabies caused due to other animals, in languages other than English, not having an Indian context, and conducted on mammals other than humans will be excluded.\n\nThe search strategy will include identification of both published and unpublished studies. A preliminary limited search of MEDLINE was conducted to identify articles on the topic. The words present in the titles and abstracts of the relevant articles, and the index terms used to describe the articles were used to develop a full search strategy. The search strategy, including all identified keywords and index terms, will be adapted for each included information source. Controlled vocabularies (e.g. Medical Subject Heading terms) to identify synonyms were used. The MEDLINE search strategy is available as Extended data13.\n\nAdditional databases to be searched include EMBASE, Cochrane Central, PROQUEST, and Shodhganga. An Advisory Board comprising of researchers and experts working in the field of rabies in India will be established for guidance on the identification of grey literature such as technical reports by the Ministry of Health and Family Welfare and other institutions, Masters/PhD thesis etc., and their opinion. Administrative data from Integrated Disease Surveillance Programme (IDSP), Health Management Information System (HMIS) and Central Bureau of Health Intelligence (CBHI) will be searched and analyzed14. The reference list of all studies selected for critical appraisal will be screened extensively for additional studies.\n\nAll identified studies will be pooled and uploaded into Rayyan QCRI software and duplicates will be first removed. Titles and abstracts will then be screened and assessed against the inclusion criteria for the review by two independent reviewers (AR & DJ) using Rayyan QCRI software15. The eligible studies after the initial screening will be retrieved in full and will be assessed in detail against the inclusion criteria by two independent reviewers (AR & DJ). Reasons for exclusion of full-text studies unable to meet the inclusion criteria will be recorded and reported in the final analysis. Any disagreements between the reviewers at any stage of the selection process will be resolved through discussion, or in consultation with a third reviewer (OB). The results of the search will be reported in full in the final systematic review and presented as per Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) guidelines16.\n\nEpidemiological burden: Eligible studies will be critically appraised for methodological quality using STROBE checklist for cohort and cross-sectional studies17,18 and; the JBI standardized critical appraisal instrument for RCTs19.\n\nHumanistic burden: The methodological quality of the eligible studies for the included HRQoL measures will be critically appraised by using Consensus-based Standards for the selection of health Measurement Instruments (COSMIN) checklist20.\n\nEconomic burden: Eligible partial economic evaluation and full economic evaluation will be critically appraised by using Consensus Health Economic Criteria (CHEC) list and Consolidated Health Economics Evaluation Reporting Standards (CHEERS) checklist respectively21,22.\n\nEpidemiological and/or mathematical modeling studies will be assessed using Optional scoring checklist for the assessment of the degree of model validation for modeling studies23.\n\nAnnexure 1 provides the extraction forms for the various checklists used for the included studies (Extended data13). The results of the critical appraisal will be reported in narrative and tabular formats.\n\nThe following data will be extracted with regards to epidemiological burden: publication date and details, authors, location, setting, study population, study period and sample size. The data extracted will also include specific details about the condition, populations, study methods and proportions of interest to the review question and specific objectives. If studies did not specify the exact years of study, the year of publication will be used. Annexure 2 provides data extraction tool for epidemiological data (Extended data13).\n\nFor the humanistic burden, different disease-specific HRQoL measures will be extracted. For each questionnaire, the dimensions of HRQoL that are assessed will be identified. Annexure 3 provides data extraction tool for humanistic burden data (Extended data13).\n\nFor the economic burden, the form will be structured based on the format and guidelines used to produce structured abstracts of economic evaluations for inclusion in the CCEMG and data items included in published studies24. Annexure 4 provides data extraction tool for economic data (Extended data13).\n\nIn cases of uncertainty or missing data, the corresponding authors will be contacted for additional information, missing or additional data. Any disagreements that arise between the reviewers will be resolved through discussion, or with a third reviewer (OB).\n\nEpidemiological burden: Data extracted from the included studies will, where possible (e.g. studies using uniform case definitions, the same measures of outcome, context and approaches), will be pooled and proportional meta-analysis will be conducted using Metafor package in R.\n\nHumanistic burden: Depending on the quantity, quality and nature of the papers identified, humanistic outcome results will be subjected to a narrative and tabulated summary.\n\nEconomic burden: Depending on quantity, quality and nature of the economic papers identified, economic results will be subjected to a narrative summary, or sorting in tables by comparisons/outcomes.\n\nIf meta-analysis is possible, data from the included studies for epidemiological burden will be transformed using a Logit transformation or double arcsine transformation to calculate the weighted summary of proportion (pooled incidence and prevalence) under a random effect model. The effect size will be expressed as a proportion with 95% confidence intervals around the summary estimate. Heterogeneity will be assessed using the Chi-squared, Tau-squared and I-squared tests. To explore potential sources of heterogeneity from the included studies, characteristics likely to modify incidence/ prevalence estimates will be considered for subgroup analysis. The following probable subgroups will be analyzed (where possible): gender, age groups, socio-economic status and region. Sensitivity analyses will be performed to explore the impact of individual studies on the overall calculated estimates. This will be performed by investigating whether dropping or adding primary studies with slightly non-standard disease definitions will make a difference. Where statistical pooling in a meta-analysis is not possible due to heterogeneity, the findings will be presented in a narrative form including tables and figures to aid in data presentation. Sources of heterogeneity and reason for which it is determined to be inappropriate to pool data will be specified in the systematic review report.\n\nData related to HRQoL and utility will be presented in narrative and tabulated summary according to the tools and measures used in the available studies as per various probable sub groups.\n\nData on costs and resources utilized will be presented in narrative summary and tabulated form to shed light on whether there are differences as per various possible subgroups including category of exposure, prophylaxis, distance from health facility, type of health facility and socio-demographic differences. The available unit cost data will be tabulated along with reporting of price year. The costs will be converted in 2020 International Dollars’ value using implicit price deflators for Purchasing Power Parities as recommended by CCEMG for greater transparency and comparability across studies24,25.\n\nThe publication bias will be assessed through generation of a funnel plot if at least 10 studies are included in meta-analysis. The symmetry of Funnel plot will be tested by Egger test26,27.\n\n\nDiscussion\n\nThis systematic review will be performed to critically examine relevant literature on epidemiological, humanistic and economic burden of dog-mediated rabies in the Indian context. The aim is to identify and report the epidemiological burden of dog bites, dog bite victims and rabies; direct and indirect costs associated with prophylaxis of dog bites and; utility and other humanistic outcomes in rabies in Indian context. Understanding these parameters could help policy makers to understand the burden of the illness in the country and will aid in proper allocation of scarce resources and funding. This will also help in proper formulation and effective implementation of the national program. This review will also help in implementation research in India. Limitation of the review, its implications and suggestions for future research will also be provided.\n\n\nData availability\n\nNo data is associated with this article\n\nFigshare: Extended Data Set: The epidemiological, humanistic and economic burden of dog-mediated rabies in India_a systematic review protocol.pdf, https://doi.org/10.6084/m9.figshare.13385474.v113.\n\nThis project contains following extended data:\n\nMEDLINE Search Strategy\n\nCritical appraisal checklist\n\nData extraction tool for epidemiological burden studies\n\nData extraction tool for humanistic burden studies\n\nData extraction tool for economic burden studies\n\nFigshare: PRISMA-P checklist for ‘The epidemiological, humanistic and economic burden of dog-mediated rabies in India: a systematic review protocol’, https://doi.org/10.6084/m9.figshare.13385474.v113.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).",
"appendix": "Acknowledgements\n\nWe acknowledge the help of Mrs Vasumathi Sriganesh, Founder, QMed Knowledge Foundation for her guidance in the development of Search Strategy for this systematic review protocol.\n\n\nReferences\n\nHampson K, Coudeville L, Lembo T, et al.: Estimating the global burden of endemic canine rabies. PLoS Negl Trop Dis. Carvalho MS, editor. 2015 [cited 2020 Jul 8]; 9(4): e0003709. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWorld Health Organization: WHO Expert Consultation on Rabies. Second report. World Health Organ Tech Rep Ser. 2013; (982): 139. Reference Source\n\nFooks AR, Banyard AC, Horton DL, et al.: Current status of rabies and prospects for elimination. Lancet. Lancet Publishing Group; 2014 [cited 2020 Jul 5]; 384(9951): 1389–99. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWorld Health Organization (WHO): Rabies vaccines and immunoglobulins: WHO position April 2018. [cited 2020 Jul 5]. Reference Source\n\nDirector General Of Health Services G of I: National Rabies Control Programme. [cited 2020 Jul 5]. Reference Source\n\nSuraweera W, Morris SK, Kumar R, et al.: Deaths from symptomatically identifiable furious rabies in India: a nationally representative mortality survey. PLoS Negl Trop Dis. 2012 [cited 2020 Dec 13]; 6(10): e1847. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSecond Draft Ministry of Health and Family Welfare 2 Draft National Action Plan for Eliminating Dog Mediated Rabies from India. [cited 2020 December 13]. Reference Source\n\nSudarshan MK, Madhusudana SN, Mahendra BJ, et al.: Assessing the burden of human rabies in India: results of a national multi-center epidemiological survey. Int J Infect Dis. 2007 [cited 2020 Jul 5]; 11(1): 29–35. PubMed Abstract | Publisher Full Text\n\nKole AK, Roy R, Kole DC: Human rabies in India: a problem needing more attention. Bull World Health Organ. World Health Organization; 2014 [cited 2020 Jul 5]; 92(4): 230. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSudarshan MK, Narayana DHA: Appraisal of surveillance of human rabies and animal bites in seven states of India. Indian J Public Health. 2019 [cited 2020 Jul 5]; 63(Supplement): S3–S8. PubMed Abstract\n\nSudarshan MK, Narayana DHA: Background paper for developing a policy for the use of rabies biologicals and vaccination of humans in India. Indian J Public Health. 2019; 63(Supplement): S51–3. PubMed Abstract\n\nMoher D, Shamseer L, Clarke M, et al.: Preferred reporting items for systematic review and meta-analysis protocols (PRISMA-P) 2015 statement. Syst Rev. 2015; 4(1): 1. PubMed Abstract | Publisher Full Text | Free Full Text\n\nRoyal A, Kumar O, John D: Extended Data Set: The epidemiological, humanistic and economic burden of dog-mediated rabies in India_a systematic review protocol.pdf. figshare. Dataset. 2020. http://www.doi.org/10.6084/m9.figshare.13385474.v1\n\nMigliavaca CB, Stein C, Colpani V, et al.: How are systematic reviews of prevalence conducted? A methodological study. BMC Med Res Methodol. 2020 [cited 2020 Dec 12]; 20(1): 96. PubMed Abstract | Publisher Full Text | Free Full Text\n\nOuzzani M, Hammady H, Fedorowicz Z, et al.: Rayyan-a web and mobile app for systematic reviews. Syst Rev. 2016 [cited 2020 Sep 29]; 5(1): 210. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMoher D, Liberati A, Tetzlaff J, et al.: Preferred reporting items for systematic reviews and meta-analyses: The PRISMA statement. PLoS Med. 2009 [cited 2020 Jul 5]; 6(7): e1000097. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSTROBE Statement-Checklist of items that should be included in reports of cohort studies. [cited 2020 Dec 10]. Reference Source\n\nSTROBE Statement-Checklist of items that should be included in reports of cross-sectional studies. [cited 2020 Dec 10]. Reference Source\n\nChecklist for Randomized Controlled Trials Critical Appraisal tools for use in JBI Systematic Reviews. [cited 2020 Dec 10]. Reference Source\n\nTerwee CB, Mokkink LB, Knol DL, et al.: Rating the methodological quality in systematic reviews of studies on measurement properties: A scoring system for the COSMIN checklist. Qual Life Res. 2012 [cited 2020 Jul 5]; 21(4): 651–7. PubMed Abstract | Publisher Full Text | Free Full Text\n\nCHEC list: Consensus Health Economic Criteria - Research - Maastricht University. [cited 2020 Dec 10]. Reference Source\n\nHusereau D, Drummond M, Petrou S, et al.: Consolidated Health Economic Evaluation Reporting Standards (CHEERS) statement. BMJ. 2013 [cited 2020 Jul 5]; 346: f1049. PubMed Abstract | Publisher Full Text\n\nKopec JA, Finès P, Manuel DG, et al.: Validation of population-based disease simulation models: a review of concepts and methods. BMC Public Health. 2010; 10: 710. PubMed Abstract | Publisher Full Text | Free Full Text\n\nShemilt I, Mugford M, Byford S, et al.: Incorporating Economics Evidence. In: Cochrane Handbook for Systematic Reviews of Interventions. Chichester, UK: John Wiley & Sons, Ltd; 2008 [cited 2020 Jul 5]; 449–79. Publisher Full Text\n\nCCEMG - EPPI-Centre Cost Converter v.1.4. [cited 2020 Sep 29]. Reference Source\n\n10.4.3.1 Recommendations on testing for funnel plot asymmetry. [cited 2020 Oct 22]. Reference Source\n\nMeta-analysis: publication bias Publication bias. [cited 2020 Oct 19]. Reference Source"
}
|
[
{
"id": "80932",
"date": "17 Mar 2021",
"name": "Koen K.A. Van Rompay",
"expertise": [
"Reviewer Expertise I work in animal models of infectious diseases (so have limited/moderate expertise in 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 article is well-written and I do not have any major comments.\nI have several minor comments/suggestions/corrections:\nIn the Abstract, Background section: The statement, \"The disease is almost fatal after the onset of symptoms\" should be corrected to indicate that it it almost always fatal.\n\nIntroduction: The word \"of\" is missing in the sentence, \"...more than 95% of human cases...\".\n\nIntroduction, last sentence: I suggest specifying that here with pre-exposure prophylaxis one means vaccination.\n\nProtocol - Eligibility criteria - Population: one can add \"India\".\n\nUnder Eligibility criteria, in the section \"Outcomes\", fix the spelling error in \"health-related\".\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Yes\n\nAre sufficient details of the methods provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable",
"responses": [
{
"c_id": "6574",
"date": "12 May 2021",
"name": "Abhishek Royal",
"role": "Author Response",
"response": "Thanks a lot for providing your valuable comments for this articles. We have incorporated following changes as per your suggestions: Rabies has been mentioned as an ‘almost always fatal’ disease after the onset of symptoms. The pre-exposure prophylaxis has been mentioned in the form of vaccination for high risk individuals. The participants has been mentioned to be based in India. The grammatical and spelling errors has been corrected."
}
]
},
{
"id": "83097",
"date": "13 Apr 2021",
"name": "Sumon Ghosh",
"expertise": [
"Reviewer Expertise My research focuses on surveillance of avian influenza",
"rabies control",
"and antimicrobial resistance in Bangladesh."
],
"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 Protocol is well-written which includes all the information necessary to conduct a systematic review and I think very useful contribution to the literature. The article is detailed and written using a standard format to write systematic review protocol. This protocol clearly spelled out the magnitude of the epidemiological, economic and humanistic burden of dog-mediated rabies in a part of the world where rabies has remained stagnant and grossly under-reported.\nI have only a few minor comments:\nThe author did not mention the timeline for selection of the articles.\n\nMention about the inclusion of modelling studies reporting the outcomes of interest in Indian context conducted at international/regional level.\n\nWill the data related to dog bites be reported from the studies reporting bites from all animals?\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Yes\n\nAre sufficient details of the methods provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable",
"responses": [
{
"c_id": "6575",
"date": "12 May 2021",
"name": "Abhishek Royal",
"role": "Author Response",
"response": "Thanks a lot for providing your valuable comments to this article. We have incorporated following changes to the article as per your suggestions: The modelling studies reporting the outcomes of interest will also be searched and will be included after screening for inclusion criteria. There is no specific timeline for the literature search. All the articles identified till the last date of literature search will be subjected to screening for inclusion criteria in this systematic review. The data specific to dog-bites and dog-mediated rabies will be extracted from the studies reporting data from all animal bites."
}
]
}
] | 1
|
https://f1000research.com/articles/10-32
|
https://f1000research.com/articles/10-376/v1
|
12 May 21
|
{
"type": "Research Article",
"title": "General public’s knowledge and practices on face mask use during the COVID-19 pandemic: a cross-sectional exploratory survey from Dharan, Nepal",
"authors": [
"Kadir Alam",
"Subish Palaian",
"Pathiyil Ravi Shankar",
"Nisha Jha",
"Subish Palaian",
"Pathiyil Ravi Shankar",
"Nisha Jha"
],
"abstract": "Background:\n\nFacemasks are considered a cheap, effective, and safe method to control the spread of coronavirus disease-19 (COVID-19). This study assessed the knowledge and practice of face mask use amongst the Nepalese public during the COVID-19 lockdown.\n\nMethods:\n\nA cross-sectional study using a self-developed, validated questionnaire (Cronbach alpha 0.556) was conducted in Dharan, Nepal during May 2020. Pharmacists from ten pharmacies throughout Dharan city administered and recorded responses from a selected sample, stratified across age, gender, education, and place of residence. Completed questionnaires were entered in SPSS, coded, and normality tested using a one-sample K-S test. Demographic characteristics were described using descriptive statistics. Median scores among subgroups were compared using inferential statistics. Descriptive analyses were performed for demographic parameters and inferential statistics for outcome variables, calculating median scores among subgroups which were further compared using non-parametric tests at alpha=0.05.\n\nResults:\n\n381 individuals participated - 211 males (55.4%) and 170 females (44.6%) . 93 (24.5%) respondents were between 20-30 years of age and three (0.8%) were over 70. 200 (52.5%) participants were educated between classes VIII to XII; seven (1.8%) having postgraduate education. 129 (33.9%) participants were from hill tribes. Knowledge scores were high (median score 16; maximum score 18). Around 20% of participants had never used a face mask before the pandemic; most knew about the ongoing pandemic (80%), about washing hands before using a mask (92.6%), and covering the mouth and nose (78.7%), Under half knew to avoid touching the mask while wearing it (42.3%). Knowledge scores were higher among men (p=0.038), younger age groups (p=0.010), and those with greater education (p=0.048).\n\nConclusion:\n\nKnowledge was good, and the public were aware of the proper use of face masks. Educational interventions could be targeted to those with lesser knowledge, and steps to promote sustained face mask use could be beneficial.",
"keywords": [
"COVID-19",
"Face masks",
"General public",
"Knowledge",
"attitude and practice",
"Nepal"
],
"content": "Introduction\n\nThe World Health Organization (WHO) received information about a pneumonia of unknown cause from Chinese authorities in Wuhan, China on December 31, 2019. This was soon shown to be caused by a coronavirus temporarily named 2019-nCoV and later called Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2).1 Coronaviruses (CoV) are a large family of viruses causing illness ranging from the common cold to more severe diseases. A novel coronavirus (nCoV) is a new strain that has not been previously identified in humans.2 Due to the severity and spread, Coronavirus disease (COVID-19) was declared a global pandemic by the WHO on 11 March 2020. As per the WHO press release on 27 June 2020 at 8:18 am, globally there have been 9653048 confirmed cases of COVID-19 and 491128 deaths.3 The first case in Nepal was diagnosed and reported on 25th January 2020.4 As of 6th July, 2020, the total infected, active cases, and death toll due to COVID 19 in Nepal was 15784, 6547 and 34 respectively.5 The government of Nepal has increased the provision of isolation beds in the country, locked down the whole country, and sealed international borders including the open border with India.5,6\n\nMeasures to prevent and control coronavirus disease-19 (COVID-19) include regular handwashing, physical distancing, and covering the mouth and nose with a face mask, thereby reducing spread of droplets. It is advised to wear masks in public during this pandemic in order to reduce the risk of infection transmission.7 The disease is highly contagious and can be transmitted by respiratory droplets1 which can be released during activities like speaking, coughing, and sneezing.8\n\nCovering the face is one of the major measures recommended for prevention. It prevents the spread of droplets and helps in maintaining respiratory hygiene. Several guidelines suggest that the use of face masks reduces infection transmission. A study from Bangladesh suggested that about 72% of people strongly believed that covering the nose and mouth when coughing and sneezing prevents COVID-19 transmission.9\n\nMasks are considered as one of the important protective measures for all individuals. Masks can be made of different materials and are of various designs. These different types of masks have different filtering capacities.10 There are several types of masks, including surgical masks, cotton face masks, N-95 face masks, cloth masks and plastic lined masks. Among these, the most effective mask has been the N-95 face mask and it is recommended for use while conducting clinical procedures and for delivering clinical care for COVID-19 patients.11 There are no studies published from Nepal, hence, the study was planned to assess the knowledge and practice of the Nepalese public on face mask use during the lockdown period of the COVID-19 pandemic.\n\n\nMethods:\n\nStudy design: A cross sectional survey assessing the general public’s knowledge and practice regarding face mask use.\n\nStudy duration: Data collection was carried out during 15th May to 20th June 2020, when the country was under lockdown due to COVID-19.\n\nStudy site: The study was conducted in Dharan, a city located in the eastern part of Nepal with a population of approximately 150,000, located close to the border with India. This city was selected since it has a mixed population in terms of age, gender, ethnicity, and educational qualifications etc., who would be available at the time of lockdown as the city hosts many healthcare and educational centers.\n\nSample selection: Any individual willing to participate in the study as per the inclusion and exclusion criteria were enrolled. A mixed population with multiple knowledge levels, and from multiple professions covering both genders were enrolled.\n\nSample size calculation: The sample size was calculated using Raosoft sample size calculator using the formula below:15\n\nSample size = Z2*(p)* (1-p)/c2\n\nwhere, c = margin of error, P = Prevalence of the characteristic\n\nThus, the sample size (n) at 95% confidence interval and 5% margin of error\n\nCalculated sample size was n = 1.962 x 0.564 x 0.463/ (0.05)2 = 377.86 ∼ 378\n\nThe prevalence (p) value was taken from study conducted by Kumar J et al. in Pakistan.12\n\nThe calculated sample size was 378 and a total of 380 responses were collected.\n\nSampling Technique: Since Dharan has a mixed population it was difficult to identify a definite population at a definite locality. Ten areas spread uniformly through the city were identified and pharmacists having pharmacies in those localities were contacted to serve as data collection centers. The community pharmacists were trained by the principal investigator (KA) on aspects such as contents of the questionnaire, obtaining participants’ consent and responses from the public while maintaining social distancing, stratification of the sample, and entering the responses.\n\nInclusion and exclusion criteria: Individuals of both gender who were over 15 years of age were considered eligible for the study. Any individual visiting the pharmacies with respiratory symptoms or who were unwilling to respond to the survey were excluded.\n\nStratification of study sample: The stratification of the total sample of 378 was based on the National demographic data of Nepal- 2019.13 The gender distribution was stratified as 0.96 males per one female, age group 15-40 yrs. 50% and above 40 yrs. 50%; literate (56%) versus illiterate (44%): urban 20.2% rural: 79.8% However, due to ongoing lockdown, strict stratification could not be maintained during the study.\n\nStudy questionnaire: The study questionnaire was designed by the researchers based on their understanding and reference to the WHO guidelines on face mask use published during the COVID-19 pandemic.14 The questionnaire had two parts Part I: Demography, Part II: General public knowledge and practice on face mask use and related aspects.\n\nThis part collected information on age, gender, educational qualifications, occupation, and ethnicity.\n\nThis part had a total of 18 questions; five ‘yes or no’ questions, one right or wrong question, two open ended questions on how to dispose face masks and methods other than face masks that were effective in preventing or reducing the impact of COVID-19, and the last question examining the five steps of correct face mask use recommended by the WHO.14 There were also nine statements scored using three-point Likert type questions with responses of agree, neutral, and disagree. The final version of the study questionnaire was translated into Nepali following the back-and-forth process. Thus, the version provided to pharmacists was in Nepali language which was then subjected to pilot testing.\n\nThe study questionnaire was content validated by the researchers and a public health expert with the questionnaire themes matched with the study objectives. The validity of the questionnaire was noted by pilot testing the questionnaire on ten subjects who were later excluded from analysis in the main study. The reliability was assessed by calculating Cronbach’s alpha. The score was 0.56 upon removal of questions with poor reliability scores and this modified questionnaire was used in the final study.\n\nMethod of data collection: Since the study was conducted during lockdown it was not possible to collect the responses directly from the public. Hence trained community pharmacy practitioners were contacted to collect the data from their visitors. During the data collection process, personal hygiene and social distancing were maintained and while collecting the responses, both the respondent and the community pharmacists wore face masks. A total of ten pharmacies were identified from various areas of Dharan and the community pharmacists were trained individually by the principal investigator regarding the questionnaire and how to record the responses. The principal investigator oversaw the collection of responses and found the process adequate and appropriate.\n\nData analysis: The completed questionnaire was verified by the principal researcher and details entered in IBM SPSS Statistics for Windows, Version 26 and the normality of the data checked using one-sample Kolmogorov-Smirnov test (p < 0.05). An open- access alternative to SPPS is PSPP. The demographic parameters were analyzed descriptively and tabulated as numbers and percentages. Independent-sample median test was used to compare the scores among different subgroups of respondents, at alpha = 0.05. Further post hoc analyses were performed for statistically significant pairs using a Bonferroni correction for multiple tests at alpha = 0.05. The number (percentage) of individuals answering each question correctly was noted. The number of individuals who answered all five steps regarding the correct use of a face mask was calculated. The proportion of individuals answering all five steps correctly among different subgroups were compared using chi-square test (p < 0.05).\n\nPilot testing: A pilot study was conducted among ten individuals as mentioned previously to ascertain the feasibility of the study and to identify any technical difficulties in collecting the data. Their information was not included in the final analysis.\n\n\nResults\n\n381 individuals participated in the study. Table 1 shows their demographic characteristics. The majority of respondents were below 50 years of age. There were more males [211 (55.4%)] than females and the highest percentage overall were housewives and students [127 (33.3%)]. Most respondents [200 (52.5%)] had studied till high school (standards VIII to XII). Majority of respondents were from the hill tribes [129 (33.9%)]. The hill tribes included Rai, Limbu, Kirati, Gurung, Magar, Tamang, among others. The Hindu castes (other than Brahmin and Chettri) and Christian were included in ‘Others’.\n\nThe questionnaire used is shown in Additional file 1. The total score was obtained by adding the scores of statements/questions 1, 2, 3, 4 (with five subsections), 5 and 7 (with nine sub questions). Question 6 dealt with measures other than lockdown which can reduce the spread of the pandemic. Seventy-two respondents (18.9%) mentioned lockdown, 305 (80.1%) mentioned handwashing, 135 (35.5%) mentioned sanitization of objects and surroundings, 25 (6.6%) mentioned avoiding handshake as a form of greeting, 28 (7.3%) mentioned covering of face before sneezing, while avoiding crowds, and following social distancing measures were mentioned by 80 (21.0%) and 218 (57.2%) respondents.\n\nThe distribution of the individual and the total scores were checked for normality using one-sample Kolmogorov-Smirnov test (p < 0.05). The distribution was not normal and hence median and interquartile range were used as measures of central tendency and variation. The median total score was 16 and the interquartile range was 3. The maximum possible score was 18.\n\nFigure 1 shows the general public’s ability to mention the WHO recommended steps for using a face mask correctly. All the individual steps had over 75% correct response with Step V having 85.04% responses.\n\nStep I: Before putting on a mask, clean hands with alcohol-based hand rub or soap and water; Step II: Cover mouth and nose with mask and make sure there are no gaps between your face and the mask; Step III: Avoid touching the mask while using it; if you do, clean your hands with alcohol-based hand rub or soap and water; Step IV: Replace the mask with a new one as soon as it is damp and do not re-use single-use masks; Step V: To remove the mask: remove it from behind (do not touch the front of mask); discard immediately in a closed bin; clean hands with alcohol-based hand rub or soap and water, adopted from Reference 14.\n\nTable 2 shows the distribution of median scores according to demographic characteristics of the respondents. The scores were significantly higher among younger respondents, and more educated respondents. On doing pair-wise comparisons the scores were significantly higher among respondents between 10 to 20 years of age compared to those between 50 to 60 years (p = 0.042) and those between 60-70 years (p = 0.012). Regarding education the scores were significantly lower among illiterate respondents compared to those who had completed secondary school (p = 0.022), and among illiterate compared to respondents with professional education (p = 0.012). The median score of all individual statements was 1.\n\nTable 3 mentions the number and percentage of respondents who answered each question yes or correctly. The percentage was over 90% for most questions. The number of respondents who could mention all five steps of using a face mask properly was 201 (52.8%). The proportion of respondents who mentioned all five steps correctly was higher among younger respondents (less than 50 years of age) (p = 0.001). The proportion was also higher among those with higher education levels (p = 0.005).\n\n\nDiscussion\n\nCOVID-19 pandemic is a major public health emergency. Lack of effective drug treatments and preventive vaccines has required adoption of different non-pharmacological measures to mitigate the problem to the maximum possible extent. Various strategies such as social distancing, lock downs, and use of facemasks are considered effective interventions by many health experts and policy makers. The wearing facemasks by the public was tried even during previous pandemics, including influenza, and SARS as a viable strategy to prevent virus transmission through the respiratory route.16 During the COVID-19 pandemic several countries have emphasized wearing face masks by the public and implemented multiple measures to compel people to wear masks,17 to such an extent that some countries are imposing fines for not wearing masks in public.18 In Nepal, the government recommends use of face masks by the public in line with the WHO guidelines on face mask use.19 Face masks reduce the spread of infection through nasal and oral routes and controls the spread of COVID-19 by reducing the amount of infected saliva and respiratory droplets released into the air from individuals with subclinical or mild COVID-19 symptoms.20 SARS-CoV-2 is a large sized virus (approximately 120 nm in diameter)21 and can be filtered by face masks. Currently there are no studies in Nepal assessing the general public’s knowledge and use of face masks during the ongoing COVID-19 pandemic.\n\nIn the current research only one-fifth of the respondents have ever used facemask at the time when COVID-19 was already present in the country for about four months and the country was under lockdown during the time of conducting the research. In a similar study from Malaysia, nearly half of the public studied wore face masks22 and in Pakistan 91% of general public felt wearing facemask should be used as a preventive measure for COVID-19.23 In contrast to their practice of wearing face mask, the respondents in the current study showed a very high knowledge as demonstrated by correct response to most questions by over 90% of study respondents. Thus, as shown in the Malaysian study,22 the present research also documents that knowledge scores are not associated with face mask use behaviors. Such a situation of high knowledge linked to poor facemask use was even observed in a study from Pakistan conducted among health professionals which showed a positive attitude among health professionals, but moderate-to-poor level of knowledge and practice regarding the use of face mask.24\n\nIn the present research the respondents’ knowledge scores were significantly lower among the illiterate cohort compared to those who had completed secondary school and those with professional education. This can be attributed to the availability of digital technology,24, 25 electronic and print resources in spreading awareness to the educated people who are more likely to benefit from these resources. The telecommunication service providers in Nepal have also created awareness messages which are played while dialing any phone numbers in the country, which is a welcome effort, as most of the country now has access to mobile phones.26 Thus, it is mandatory to explore initiatives such as radio programs,27 street plays,28 art29 etc., as alternative options which could reach even illiterate and aged people.\n\nIn the present research, the knowledge scores were significantly higher among respondents between 10 to 20 years of age compared to those between 50 to 60 years and those between 60-70 years. Similar to the current study findings, the Malaysian study22 found that the wearing of face masks was associated with gender, age group, region, occupation, and income group. In general, younger people are more likely to be aware about the pandemic and its prevention strategy of using face masks. However, poor knowledge among elderly people is worrisome as the elderly are more likely to suffer from COVID-19 complications and associated mortality.30 Thus, it is mandatory to create age specific awareness programs using media which the elderly are aware of and have access to.\n\nIn the current research, only just over half of the respondents (52.8%) could correctly mention all the five steps of using a face mask properly. Face masks do not provide protection if they fit improperly and there are gaps between the surface of the mask and face.31 Of the respondents answering all steps correctly, a higher proportion was among younger respondents aged less than 50 years and those with higher education levels. Interventions are needed to demonstrate correct use of face masks which can be conducted by distributing pamphlets and information on the correct steps to be followed. The WHO has videos demonstrating correct use of face mask which could be used to educate the public.19\n\nWhile answering one of the questions on whether face mask can be made from a piece of cloth, more than half of the respondents disagreed, suggesting that public were not aware of home-made masks. Homemade face masks could be potentially beneficial, economic, and easily available at all times and can be even reused with adequate care and not be shared among others.32\n\nThis study had a few limitations. Though the study found a high knowledge among respondents and identified the factors influencing the knowledge scores, the source of knowledge among respondents was not assessed. Assessing the knowledge source would have given the researchers an opportunity to recommend more specific interventions. This study also did not evaluate any specific reasons (including myths) for not using facemask by the public, and finally the study was conducted only in one city in Nepal and hence cannot be generalized to the entire nation. This study also lacks triangulation as the information was collected only by using a questionnaire. In Nepal, currently there are two layered and three-layered face masks and this research focused on face mask as a generic and not on any of the specific types.\n\n\nConclusions\n\nThe public in Dharan, Nepal possessed a high knowledge on facemask use during COVID-19. However, the practice of face mask use was low and influenced by education, literacy, and age. Specific interventions targeting elderly and illiterate people using methods other than electronic and printed sources may be beneficial.\n\n\nList of Abbreviations\n\nCoV: Coronaviruses; nCoV: Nobel Coronavirus; WHO: World Health Organization.\n\n\nDeclarations\n\nEthical Approval and consent to participate: The research proposal was approved by the Nepal health Research Council, the National health research authority that oversees conduct of human research in the country. (Approval number 2385 dated 12th May 2020). The participants were informed about the purpose of the research and written consent from participant was obtained prior to enrolling them. In the case of participants under the age of 15, consent was taken from their parent or legal guardian. Anonymity was maintained throughout the research and no information related to individual respondents are available in the public domain.\n\nConsent for publication: Written informed consent was obtained from all participants/the participants’ parent or legal guardian.\n\n\nData availability:\n\nPilot Study\n\nFigshare. Public knowledge and practice about facemask use in Dharan, Nepal. https://doi.org/10.6084/m9.figshare.14380955.v2.33\n\nThis project contains the following underlying data:\n\n• Facemask COVID Pilot Data key.docx (a list of the questions asked in the pilot study)\n\n• Pilot data.xlsx (the results of the pilot study)\n\nFinal Study\n\nFigshare: General public’s knowledge and practices on face mask use during the COVID-19 pandemic: a cross-sectional exploratory survey from Dharan, Nepal. https://doi.org/10.6084/m9.figshare.14380883.v3.34\n\nThis project contains the following underlying data:\n\n• Facemask COVID Data key.docx (a list of the questions asked in the final study)\n\n• Face mask.xlsx (the results of the final study)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nAuthors’ contributions: KA and SP conceived and designed the study. PRS and SP finalized the methodology and tools used. KA collected the data. PRS, SP analysed the data. NJ and PRS and SP drafted the manuscript. All the authors made significant contributions to writing the manuscript and reviewing the literature. The order of authorship as placed in the manuscript is final and accepted by the coauthors. The final manuscript has been read and approved by all the authors.\n\n\nAuthors’ information:\n\n1Department of Clinical Pharmacology, B.P. Koirala Institute of Health Sciences, Dharan, Nepal. 2Department of Clinical Sciences, College of Pharmacy and Health Sciences, Ajman University, Ajman, UAE. 3IMU Centre for Education, International Medical University, Kuala Lumpur, Malaysia. 4Department of Clinical Pharmacology and Therapeutics, KIST Medical College, Lalitpur.",
"appendix": "Acknowledgements\n\nAuthors would like to acknowledge the community pharmacists for their help in data collection. We are also thankful to the study respondents who spent their valuable time in responding the survey.\n\n\nReferences\n\nWorld Health Organization: Rolling updates on coronavirus disease (COVID-19).2020. Accessed 27 Jun 2020. Reference Source\n\nNational Institute of Allergy and Infectious Disease: Overview of Coronavirus.2020. Accessed 27 Jun 2020. Reference Source\n\nWorld Health Organization: COVID-19 Dashboard.2020. Accessed 27 Jun 2020. Reference Source\n\nBastola A, Sah R, Rodriguez-Morales AJ: The first 2019 novel coronavirus case in Nepal. Lancet Infect Dis. 2020; 20: 279–80. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMinistry of health and population, Government of Nepal: Coronavirus disease (COVID-19) outbreak updates & resource materials.2020. Accessed 27 Jun 2020. Reference Source\n\nShrestha R, Shrestha S, Khanal P, et al.: Nepal's First Case of COVID-19 and public health response. J Travel Med. 2020; PubMed Abstract | Publisher Full Text | Free Full Text\n\nFeng S, Shen C, Xia N, et al.: Rational use of face masks in the COVID-19 pandemic. Lancet Respir Med. 2020; 8: 434–6. PubMed Abstract | Publisher Full Text | Free Full Text\n\nMorawska L: Size distribution and sites of origin of droplets expelled from the human respiratory tract during expiratory activities. J. Aerosol Sci. 2009; 40: 256–69. Publisher Full Text\n\nFarhana K: Knowledge and perception towards Novel Coronavirus (COVID 19) in Bangladesh. Int Res J Bus Soc Sci. 6: 76–79. Publisher Full Text\n\nBrosseau L, Ann RB: N95 respirators and surgical masks. Centers for Disease Control and Prevention. Reference Source\n\nLeung NHL, Chu DKW, Shiu EYC, et al.: Respiratory virus shedding in exhaled breath and efficacy of face masks. Nat Med. 2020; 26: 676–680. PubMed Abstract | Publisher Full Text\n\nKumar J, Katto MS, Siddiqui AA, et al.: Knowledge, Attitude, and Practices of Healthcare Workers Regarding the Use of Face Mask to Limit the Spread of the New Coronavirus Disease (COVID-19). Cureus. 2020; PubMed Abstract | Publisher Full Text | Free Full Text\n\nCentral Bureau Of Statistics, Government of Nepal: District Profile of Sunsari 2074.2018. Accessed 5 Apr 2020. Reference Source\n\nWorld Health Organization: How to wear a non-medical fabric mask safely.2020. Accessed 17th April 2020. Reference Source\n\nIsrael GD: Determining Sample Size.1992, Revised 2009. Accessed 23 Apr 2020. Reference Source\n\nBrienen NCJ, Timen A, Wallinga J, et al.: The effect of mask use on the spread of influenza during a pandemic. Risk Anal. 2010; 30: 1210–8. PubMed Abstract | Publisher Full Text | Free Full Text\n\nWhich countries have made wearing face masks compulsory? Al Jazeera News. Accessed 3 Jul 2020. Reference Source\n\nBai N: Still Confused About Masks? Here’s the Science Behind How Face Masks Prevent Coronavirus.2020. Reference Source\n\nWorld Health Organization: Coronavirus disease (COVID-19) advice for the public: When and how to use masks. Accessed 5 Jul 2020. Reference Source\n\nCheng VC, Wong SC, Chuang VW, et al.: The role of community-wide wearing of face mask for control of coronavirus disease 2019 (COVID-19) epidemic due to SARS-CoV-2. J Infect. 2020; PubMed Abstract | Publisher Full Text | Free Full Text\n\nNew Coronavirus (SARS-CoV-2) and the Safety Margins of Plasma Protein Therapies. Plasma Protein Therapeutics Association. 2020. Accessed 5 Jul 2020. Reference Source\n\nAzlan AA, Hamzah MR, Sern TJ, et al.: Public knowledge, attitudes and practices towards COVID-19: A cross-sectional study in Malaysia. PLoS ONE. 2020; PubMed Abstract | Publisher Full Text | Free Full Text\n\nMirza T, Ali R, Khan H: THE KNOWLEDGE AND PERCEPTION OF COVID-19 AND ITS PREVENTIVE MEASURES, IN PUBLIC OF PAKISTAN. PAFMJ. 30Apr.2020 [cited 20Jul.2020]; 70(2): 338-5. Reference Source\n\nTing DS, Carin L, Dzau V, et al.: Digital technology and COVID-19. Nature Med. 2020; 26: 459–61. PubMed Abstract | Publisher Full Text | Free Full Text\n\nChan AKM, Nickson CP, Rudolph JW, et al.: Social media for rapid knowledge dissemination: early experience from the COVID-19 pandemic. Anaesthesia. 2020; Publisher Full Text\n\nRise in number of mobile phone users: 2016. Accessed 2 Jul 2020. Reference Source\n\nUnited Nations: UN radio spreads Covid-19 information to remote areas. Accessed 5 Jul 2020. Reference Source\n\nPress Trust of India: Tribal women perform street play on Covid-19 to spread awareness among tea garden workers. Accessed 5 Jul 2020. Reference Source\n\nMukami M: Somali artists use art to spread COVID-19 awareness. Artists in Horn of Africa country fight misinformation, rumors and stigma surrounding coronavirus pandemic. Anadolu Agency. 2020. Accessed 5 Jul 2020. Reference Source\n\nLiu K, Chen Y, Lin R, et al.: Clinical features of COVID-19 in elderly patients: a comparison with young and middle-aged patients. J Infect. 2020; PubMed Abstract | Publisher Full Text | Free Full Text\n\nU.S. Food and Drug Administration: N95 Respirators, Surgical Masks, and Face Masks.2020. Accessed 5 Jul 2020. Reference Source\n\nCenter for disease control and prevention: Use of Cloth Face Coverings to Help Slow the Spread of COVID-19.2020. Accessed 5 Jul 2020. Reference Source\n\nAlam K, Palaian S, Shankar PR, et al.: Public knowledge and practice about facemask use in Dharan, Nepal. Figshare. 2021. Publisher Full Text\n\nAlam K, Palaian S, Shankar PR, et al.: General public’s knowledge and practices on face mask use during the COVID-19 pandemic: a cross-sectional exploratory survey from Dharan. Nepal. figshare. Dataset. 2021; Publisher Full Text"
}
|
[
{
"id": "170369",
"date": "05 May 2023",
"name": "Susumu Annaka",
"expertise": [
"Reviewer Expertise Political science",
"Public health",
"Public policy",
"Comparative political economy"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 conducted in Dharan, Nepal in May 2020. This study explored the knowledge and practice of face mask use among citizens during the COVID-19 lockdown. It seems that the study is appropriately conducted and reports that the level of education and age are correlated with respondents' answers. I think the findings are modest and descriptive but this means that the work is important because masks can effectively protect people from the disease.\nMajor point: The study shows that the levels of education and age affect respondents' knowledge of masks but it seems to me that it does not control the effects of each variable and then, for example, we cannot understand why the older get a low score. I mean that education can affect the effect of age. To test this, we can control the effect of education. However, this study does not do that.\nAnd as the authors have acknowledged, it targeted a small area in Nepal. It should be a potential limitation of this paper because new findings can be everywhere and generalisability is needed to be a scientific approach.\nMinor point: Also, I recommend that the authors add a few sentences in the conclusion which mention the results in some more detail though a little bit redundant. For example, the higher educated get a higher score and the younger do a higher score.\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": []
},
{
"id": "258348",
"date": "05 Apr 2024",
"name": "Kholis Ernawati",
"expertise": [
"Reviewer Expertise Public Health",
"Environmental Health",
"Environmental Science",
"Digital Health",
"Health in Islam"
],
"suggestion": "Approved",
"report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe study, conducted in Dharan, Nepal, in May 2020, aimed to explore the understanding and implementation of masks during the COVID-19 lockdown. Although successful in documenting the relationship between education level and age and community response to the use of masks, the weakness lies in the limited scope of the study to a small area in Nepal, resulting in limitations in the generalization of the findings. Although the primary results highlight the influence of education level and age on people's understanding of masks, this research has yet to consider the interaction between these two variables, such as how education level may influence the impact of age on mask understanding. Suggestions for researchers are to enrich the conclusions with a deeper understanding of the differences in scores based on these variables and broaden the discussion by linking relevant theories and research results related to high knowledge but low practice of using masks.\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": []
}
] | 1
|
https://f1000research.com/articles/10-376
|
https://f1000research.com/articles/10-375/v1
|
11 May 21
|
{
"type": "Research Article",
"title": "Uropathogens and their antimicrobial susceptibility pattern: A retrospective study in a district level hospital in Western Nepal",
"authors": [
"Manoj Ghimire",
"Sudeep Adhikari",
"Kalpana Ghimire",
"Bishal Tiwari",
"Soni Koju",
"Sajana Poudel",
"Sulab Khanal",
"Sudeep Adhikari",
"Kalpana Ghimire",
"Bishal Tiwari",
"Soni Koju",
"Sajana Poudel",
"Sulab Khanal"
],
"abstract": "Background: Urinary tract infection (UTI) is a common cause of hospital visits. There is an increasing trend of resistance of uropathogens to antibiotics worldwide. The aim of this study was to identify the common uropathogens, along with their antimicrobial susceptibility. Methods: This retrospective cross-sectional study was conducted from April 2018 to April 2020 at Beni hospital. All patients with urinary tract infection visiting Beni hospital during this time and who had urine culture sensitivity tests done were included in this study. Urine samples were first cultured on cystine lactose electrolyte-deficient agar by a semi-quantitative technique, and then incubated aerobically for 18–24 h at 37 °C. The identified bacterial isolates were tested for antimicrobial susceptibility by the Kirby–Bauer disc diffusion technique. Results: Of the 1173 samples, 164 (14%) samples showed significant growth. Escherichia coli (74%) was the most common causative organism. E. coli was sensitive in 113 cases (95%) out of 119. Amikacin was tested in 87 isolates that showed 99% sensitivity. Other commonly used antimicrobial agents had lower sensitivity rates: gentamicin (83%), ciprofloxacin (75%), ceftriaxone (59%), cefixime (56%), cotrimoxazole (55%), cefotaxime (41%), and ampicillin (38%). Conclusions: E.coli is the most common pathogen associated with urinary tract infection. Nitrofurantoin and amikacin can be good empirical agents for treating UTI in patients coming to Beni hospital.",
"keywords": [
"antimicrobial susceptibility",
"Escherichia coli",
"urinary tract infection",
"uropathogens"
],
"content": "Introduction\n\nUrinary tract infection (UTI) is one of the common health problems affecting people of all ages, race/ethnicity, sex, and circumcision status. It is caused mostly by bacteria, but viruses and fungi have also been implicated in rare cases.1,2\n\nSeveral studies have reported that there is an increased resistance of uropathogens to a number of common broad-spectrum antibiotics worldwide.3-5 As the resistance patterns differ across different areas, every hospital should formulate their own anti-microbiogram for common infections, so as to guide the appropriate treatment.\n\nThe objective of this study is to find the prevalence of common uropathogens and, secondly, to identify antimicrobial sensitivity and resistance patterns to those pathogens.\n\n\nMethods\n\nA retrospective cross-sectional study was carried out in Beni hospital. A convenient sampling technique was used and all patients with urinary tract infection visiting Beni hospital from April 2018 to April 2020 and had urine culture sensitivity tests done were included in this study.\n\n15–30 mL of urine was collected in a sterile leak-proof urine container. A midstream clean-catch specimen was taken. Patients were first asked to cleanse the urethral area before collecting the specimen. Specimens received in the laboratory were processed within 2 hours. Transport medium for urine specimens, such as 1.8% boric acid, sodium chloride or polyvinylpyrolidine, was used.\n\nThe sample received was inoculated in the cysteine lactose electrolyte deficient agar media with a 1-mL calibrated loop of internal diameter, 0.001 mL volume of urine specimen using a semi-quantitative method. After inoculation, it was incubated at 37°C overnight for visible growth. A growth of >105 colony forming unit/mL was considered as significant bacteriuria. Bacterial identification was done using standard bacteriological techniques. The antibiotic susceptibility tests of the isolates against different antibiotics were done using Mueller Hinton agar (MHA) by the standard disk diffusion technique of modified Kirby–Bauer method as recommended by the Clinical & Laboratory Standards Institute. In this study, if the isolates were resistant to at least one agent in three or more antimicrobial categories, they were regarded as multi-drug resistant (MDR) organisms.\n\nThis study is subject to selection bias as samples were taken conveniently and confirmation bias as observer might be familiar with common drugs that are resistant to pathogens\n\nData entry and analysis were done by using SPSS version 25.0 (RRID:SCR_019096); JASP (RRID:SCR_015823) is an open-source alternative to SPSS. Descriptive statistical methods were carried out for data analysis.\n\nEthical clearance was obtained from the national ethical review board, Nepal Health Research Council. The reference number of the ethical letter was 1886 dated 20th January, 2021.\n\nHospital data were reviewed, and patients were not directly involved in the research; approval from the hospital was taken and consent from the patient had been waived by the Nepal Health Research Council\n\n\nResults\n\nUrine samples from 1173 symptomatic patients were received for urine culture during the study period. Out of 1173 samples, 164 urine samples (14%) showed significant growth of at least one of the uropathogens tested in this study: E. coli, Staphylococcus aureus, Klebsiella spp., Acinetobacter spp. The most common pathogen isolated was E. coli (74%) followed by Klebsiella spp. as shown in Table 1.\n\nE. coli was sensitive in 113 cases (95%) out of 119. Amikacin was tested in 87 isolates that showed 99% sensitivity. Other commonly used antimicrobial agents had lower sensitivity rates: gentamicin (83%), ciprofloxacin (75%), ceftriaxone (59%), cefixime (56%), cotrimoxazole (55%), cefotaxime (41%), and ampicillin (38%). The sensitivity pattern of other microbes is shown in Table 2.\n\n\nDiscussion\n\nAs with other infections, UTIs are managed initially with empirical antibiotics till the urine culture reports become available. In Nepal, most hospitals in rural areas do not have proper microbiology laboratories performing bacterial culture, so treatment is solely empirical in such cases. Our study showed E. coli as the most common pathogen (74%) causing UTI, followed by Klebsiella spp. (13%) and Acinetobacter spp. (10%). Similar findings have also been reported in different studies conducted in Nepal and other countries.4-7 So, empirical antibiotics to treat UTI should target E. coli.\n\nAmong 119 samples of E. coli tested for nitrofurantoin, it was sensitive in 113 cases (95%). Amikacin was tested in 87 isolates that showed 99% sensitivity. Other commonly used antimicrobial agents had lower sensitivity rates: gentamicin (83%), ciprofloxacin (75%), ceftriaxone (59%), cefixime (56%), cotrimoxazole (55%), cefotaxime (41%), and ampicillin (38%). Various studies done in Nepal have also shown lower sensitivity of the pathogen to these agents.3,14 Our study suggests that nitrofurantoin would be a good first-choice oral antibiotic for managing lower UTI such as cystitis. However, in pyelonephritis or prostatitis, nitrofurantoin is not recommended as it does not attain sufficient concentration in these tissues. Based on our study results, aminoglycoside amikacin (parenteral) can be used empirically for pyelonephritis, or when a patient does not tolerate oral medicine. In a prospective cohort study conducted in Singapore from 2015 to 2016, E. coli was sensitive to amikacin in 100% of the cases.6\n\nOther commonly used oral antimicrobial agents like ciprofloxacin, cotrimoxazole and cefixime had lower sensitivity to E. coli. They had been used rampantly in Nepal in the past, mainly for typhoid fever. This explains the increase in resistance to these agents. Several studies done in Nepal and abroad have also shown higher resistance of E. coli to these antibiotics.3,4,7-10 Ceftriaxone one of the most commonly used antibiotic in hospitalized patients in Nepal, however its sensitivity to E. coli was only 59%, hence its empirical use in hospitalized UTI patients should be discouraged.\n\nKlebsellia spp. was found to be more sensitive to antimicrobrial agents as compared with E. coli. It was sensitive in all 16 samples tested for ciprofloxacin, 14 samples tested for amikacin, 17 out of 18 samples tested for cotrimoxazole (94%) and 16 out of 17 tested samples tested for gentamycin (94%). However, a study done at KIST Medical College from March 2013 to April 2014 showed that Klebsellia spp. obtained from all urine samples were multidrug resistant and extended spectrum beta lactamase producers. 15\n\nAcinetobacter spp. was more resistant compared with other microbes isolated in this study. It was resistant in all 16 cases tested for cefotaxime, 11 out of 15 samples tested for ceftriaxone (73%), 10 out of 15 samples tested for cotrimoxazole (67%), four out of seven samples for gentamycin (36%) and three out of seven samples for amikacin (30%). Similar to this study, a study published in The Pan African Medical Journal also showed Acinetobacter spp. resistant to commonly administered antibiotics with high susceptibility to amikacin.16\n\nMultidrug-resistant organisms are resistant to at least one agent in three or more classes of antimicrobial agents. The rising incidence of a multidrug resistance phenotype of extended-spectrum beta-lactamase (ESBL) genes and fluoroquinolones resistance, has become a global concern because of their potential cause of serious infections which are difficult to treat.12 In this study, MDR was isolated in 52 out of 122 cases of E. coli (43%), 13 out of 16 cases of Acinetobacter spp. (81%) and five out of 21 cases of Klebsiella spp. (24%). Significant proportions of MDR uropathogens were seen in other studies too, done in different hospitals of Nepal.5,13 Antimicrobial resistance (AMR) is a major concern in both developed and developing countries as various studies have shown its rising incidence. It has posed a major challenge for successful treatment of infectious diseases. With increased prevalence of irrational and injudicious use of antimicrobial agents and inadequate antibiotic stewardship programs, it is a major burden for Nepal.14 Even in rural areas like Beni, Myagdi, all classes of antimicrobial agents are easily available. In our experience antibiotics have been sold mostly without proper diagnostic evaluation of patients and prescription of physicians in both major cities and rural areas of Nepal.\n\nIn Beni hospital, culture and sensitivity were not routinely sent in all clinically suspicious cases of urinary tract infections. Also, sensitivity was not tested on all appropriate classes of antimicrobial agents. Had it been done, we would have a broader view of sensitivity and resistance pattern. As we are collecting more data on this matter, we will have analysis of more data in the future which would give a more accurate prospect of the antimicrobial susceptibility pattern in this hospital.\n\nThe susceptibility patterns of antimicrobial agents to microbes vary from country to country and also in different regions of the same country. The guidelines used in Western countries may not be useful in Nepal. It is necessary to identify the sensitivity pattern in a particular location and to develop the treatment protocol accordingly. Very few studies have been published regarding AMR in the Gandaki province of Nepal.14 This study will help for selection of appropriate empirical antimicrobial agents for treatment of UTI in this region.\n\nThe limitation of the study is external validity. As data were collected from a single hospital, our findings cannot be generalized and multicenter studies with larger sample size are needed to find out the real scenario of antimicrobial resistance pattern and formulation of treatment guidelines accordingly. Also patient information like genitourinary malformations, prior exposure to antibiotics, recent hospitalization or prior history of UTI were not taken into consideration, which can be important risk factors for resistant uropathogens.\n\n\nConclusions\n\nE. coli is the most common pathogen associated with urinary tract infection in Beni hospital. It is resistant to broad-spectrum penicillin, third-generation cephalosporins and fluoroquinolones. Resistance to nitrofurantoin is low and could be the antibiotic of choice for uncomplicated cystitis. Amikacin showed promise as a suitable intravenous agent but needs further studies with adequate sample size\n\n\nData availability\n\nHarvard Dataverse: Underlying data for ‘Uropathogens and their antimicrobial susceptibility pattern: A retrospective study in a district level hospital in Western Nepal’, https://doi.org/10.7910/DVN/HTQELY.\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\n\nAuthor Contributions:\n\nManoj Ghimire- Conceptualization, Data Curation, Formal Analysis, Supervision, Methodology, Writing – Original Draft Preparation\n\nSudeep Adhikari- Supervision, Writing – Original Draft Preparation, Writing – Review & Editing\n\nKalpana Ghimire- Data Curation, Project Administration, Supervision, Writing – Review & Editing\n\nBishal Tiwari- Project Administration, Supervision, Writing – Review & Editing\n\nSoni Koju- Data Curation, Writing – Original Draft Preparation\n\nSajana Poudel- Conceptualization, Project Administration, Data Curation\n\nSulab Khanal-Data Curation, Methodology",
"appendix": "References\n\nBehzadi P, Behzadi E, Yazdanbod H, et al.: A survey on urinary tract infections associated with the three most common uropathogenic bacteria. Maedica. 2010; 5(2): 111. PubMed Abstract | Free Full Text\n\nPatel HB, Soni ST, Bhagyalaxmi A, et al.: Causative agents of urinary tract infections and their antimicrobial susceptibility patterns at a referral center in Western India: An audit to help clinicians prevent antibiotic misuse. J Family Med Prim Care. 2019; 8(1): 154–9. PubMed Abstract | Publisher Full Text | Free Full Text\n\nGanesh R, Shrestha D, Bhattachan B, et al.: Epidemiology of urinary tract infection and antimicrobial resistance in a pediatric hospital in Nepal. BMC Infect Dis. 2019; 19(1): 420. PubMed Abstract | Publisher Full Text | Free Full Text\n\nSiwakoti S, Subedi A, Sharma A, et al.: Incidence and outcomes of multidrug-resistant gram-negative bacteria infections in intensive care unit from Nepal- a prospective cohort study. Antimicrob Resist Infect Control. 2018; 7: 114. PubMed Abstract | Publisher Full Text | Free Full Text\n\nBaral P, Neupane S, Marasini BP, et al.: High prevalence of multidrug resistance in bacterial uropathogens from Kathmandu, Nepal. BMC Res Notes. 2012; 5: 38. PubMed Abstract | Publisher Full Text | Free Full Text\n\nHo HJ, Tan MX, Chen MI, et al.: Interaction between Antibiotic Resistance, Resistance Genes, and Treatment Response for Urinary Tract Infections in Primary Care. J Clin Microbiol. 2019; 57(9). PubMed Abstract | Publisher Full Text | Free Full Text\n\nAhmed SS, Shariq A, Alsalloom AA, et al.: Uropathogens and their antimicrobial resistance patterns: Relationship with urinary tract infections. Int J Health Sci (Qassim). 2019; 13(2): 48–55. PubMed Abstract | Free Full Text\n\nIbrahim ME, Bilal NE, Magzoub MA, et al.: Prevalence of Extended-spectrum β-Lactamases-producing Escherichia coli from Hospitals in Khartoum State, Sudan. Oman Med J. 2013; 28(2): 116–20. PubMed Abstract | Publisher Full Text | Free Full Text\n\nIbrahim ME, Bilal NE, Hamid ME: Increased multi-drug resistant Escherichia coli from hospitals in Khartoum state. Sudan. Afr Health Sci. 2012; 12(3): 368–75. PubMed Abstract | Publisher Full Text | Free Full Text\n\nDe Francesco MA, Ravizzola G, Peroni L, et al.: Urinary tract infections in Brescia, Italy: etiology of uropathogens and antimicrobial resistance of common uropathogens. Med Sci Monit. 2007; 13(6): Br136–44. PubMed Abstract\n\nChaudhari B, Singh G, Parajuli K, et al.: Incidence and Susceptibility of Uropathogens Isolated among the Patients at Tertiary Care Hospital in Eastern Nepal. J Nobel Medical College. 2016; 5(2): 51–55. DOI: 10.3126/jonmc.v5i2.16318\n\nTenney J, Hudson N, Alnifaidy H, et al.: Risk factors for aquiring multidrug-resistant organisms in urinary tract infections: A systematic literature review. Saudi Pharm J. 2018; 26(5): 678–84. PubMed Abstract | Publisher Full Text | Free Full Text\n\nAwasthi T, Pant N, Dahal P: Prevalence of multidrug resistant bacteria in causing community acquired urinary tract infection among the patients attending outpatient department of Seti Zonal Hospital, Dhangadi, Nepal. Nepal Journal of Biotechnology. 2015; 3(1): 55–59.\n\nAcharya KP, Wilson RT: Antimicrobial Resistance in Nepal. Front. Med. 2019; 6(105). PubMed Abstract | Publisher Full Text | Free Full Text\n\nSubedi S, Maharjan J, Shrestha B: Antibiotic Susceptibility Test of Klebsiella pneumoniae and K. oxytoca Isolated from Different Clinical Samples and Perform Random Amplified Polymorphic DNA among K. pneumoniae. British Microbiol Res J. 2016; 12: 1–11. DOI: 10.9734/BMRJ/2016/23376\n\nMusyoki VM, Masika MM, Mutai W, et al.: Antimicrobial susceptibility pattern of Acinetobacter isolates from patients in Kenyatta National Hospital, Nairobi, Kenya. Pan Afr Med J. 2019; 33: 146. PubMed Abstract | Publisher Full Text | Free Full Text"
}
|
[
{
"id": "90208",
"date": "09 Aug 2021",
"name": "Gianluigi Franci",
"expertise": [
"Reviewer Expertise Microbiology",
"Clinical Microbiology",
"Host-Microorganism interaction",
"Microbioal Epigenetic"
],
"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\nSummary:\nThis retrospective study highlights an increasingly growing problem: antimicrobial resistance to antibiotics commonly used in hospitals, focusing on urinary infections. The objectives of this study were to identify the most frequent uropathogens, with their pattern of sensitivity to antibiotics, in patients with bacteriuria visiting the Beni hospital from April 2018 to April 2020. The results report an incidence of positivity equal to 14%. Escherichia coli (E. coli) was the most common isolate (74%), poly sensitive strain in 95% of cases, with high sensitivity towards Amikacin, gentamicin, ciprofloxacin but with a sensitivity of around 50% for the other antibiotics tested (ceftriaxone, cefixime, co-trimoxazole), and less than 40% to cefotaxime and ampicillin. In conclusion, E. coli is recognized as the most common pathogen associated with urinary tract infection, and indicating nitrofurantoin and amikacin as efficient antibiotics to be used in empirical therapy for the treatment of urinary tract infections in patients arriving at Beni hospital. The objectives of the study are very interesting, but the statistics and numbers of analyzed microorganisms do not fit the possibility of having a statistical analysis in terms of species isolated and antibiotic resistance profiles. Moreover, the manuscript needs a deeper reorganization and correction of the text.\nAbstract:\nThe abstract is missing some information. This is part of the low number of microorganisms isolated. Taking apart the E. coli, all the other species are so limited that no assumption and evaluation can be included.\nIntroduction:\nThe introduction should be improved with epidemiological data of similar hospitals in terms of geographical region and assisted person.\n\nThe aims and perspectives of the study should be described better.\nMethods:\nConcerning the high potential interest of people around the world to this kind of data, an international guideline in the antimicrobial resistance value should be used. Indeed in the paper, it was not possible to understand the concentration of the antibiotics that have been used. I strongly recommend the use of EUCAST lines.\nResults:\n\nIn order to have a sufficient number of isolated microorganisms requested for robust statistical analysis, I recommend increasing the period of time analysed.\n\nIn addition, in the tables, it may be more useful to report the percentages and in parentheses the total number of isolates tested. However, there is no statistical value (p-value) to confirm the significance of the information calculated and presented in the manuscript, so statistical calculations are lacking.\n\nFinally, why did the authors just evaluate the last two years? Moreover, they include a period of analysis pre-COVID-19 and during the pandemic infection. Is it possible that this variable was not 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? No\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNo\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly",
"responses": []
},
{
"id": "89329",
"date": "16 Aug 2021",
"name": "Piyush Rhajbhandari",
"expertise": [
"Reviewer Expertise Microbiology and infectious 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\nThe research article is well written, however:\nMethodology:\nAs a retrospective study, the methods describing sample collection and culture sensitivity do not change the outcome and can be omitted.\nDetailed methods on how the reports were stored in the hospital (HMIS vs hardcopy), how it was retrieved (database from server vs data entry from hardcopy), and function used in SPSS needs to be included. This will help in analyzing errors as typo or process errors.\nData analysis:\nThe authors need to be aware of the intrinsic resistance of organisms to particular drugs (eg: Klebsiella pneumoniae vs ampicillin) and CLSI guidelines.\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? Yes",
"responses": []
},
{
"id": "90903",
"date": "17 Aug 2021",
"name": "Adhi Kristianto Sugianli",
"expertise": [
"Reviewer Expertise Infectious Diseases",
"microbiology",
"antimicrobial resistance"
],
"suggestion": "Approved With Reservations",
"report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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: Interesting topic about the antimicrobial susceptibility pattern in uropathogens, which needed to establish the guideline for empirical treatment. However, there is some specific concern regarding the article, as follows:\nIntroduction\nIn the Introduction section, the authors need to show the importance of performing local antimicrobial susceptibility data, e.g elaborate with WHO surveillance program (GLASS) as the source of information. This is an important point to strengthen the rationale of the article.\nMethods\nIn the Methods section, information regarding microbiology procedures has been written properly. However, the authors need to add more about the study population, data collection, and variable definition, for example:\n(1) Describe the site of data collection, e.g Beni Hospital;\n\n(2) How do the authors collect the data retrospectively, e.g using medical records and/or laboratory information systems? If both of them are used as the source of the data, then how do the authors elaborate on both of the data? Please clarify and explain in the Methods section;\n\n(3) Lastly, the authors need to define the definition of a patient with a UTI in this study.\n\nThe important information that is also needed is the antibiotic that is used in this study. This needs to be explained and described clearly in the Methods section, as well as the quality control of the AST procedure.\n\nPlease indicate and clarify that no technical method and/or supplies (e.g reagent, instrument, etc) was changed between 2018 – 2020.\n\nPlease provide references in the Methods section, as well as the version of CLSI.\nResults\nIn the Results section, there is the statement: “out of 1173 samples, 164 urine samples (14%) showed significant growth of at least one of the uropathogens tested in this study: E. coli, Staphylococcus aureus, Klebsiella spp., Acinetobacter spp.” This might be better to provide information among 1173 specimens; how many urine specimens have shown growth of the organism? This is confusing since only 164 were included from 1173, which indicates almost half of the population was rejected. Please clarify and write more information about this in the results.\n\nThe authors need to clarify the purpose for tabulating between gender and certain isolate and might be more informative if the data are reported separately between years (looking for trends).\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": []
},
{
"id": "90902",
"date": "28 Sep 2021",
"name": "José Molina-López",
"expertise": [
"Reviewer Expertise Bacteriologist: antimicrobial drug resistant"
],
"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, \"Uropathogens and their antimicrobial susceptibility pattern: A retrospective study in a district level hospital in Western Nepal by Ghimire M, Adhikari S, Ghimire K, Tiwari B, Koju S, Poudel S and Khanal S\", is an interesting study where the authors show the identification of several bacterial species associated with urinary tract infections and determine their susceptibility to different antimicrobial agents. They concluded that Escherichia coli (E. coli) is the most common pathogen found.\nI have a lot of suggestions for the authors:\nIf E. coli is associated with urinary tract infections (UTIs) worldwide in high percentages and it's known that several serogroups (O1, O2, O4, O6, O7, O8, O15, and O25) of E. coli cause UTIs, the authors could search the main serogroups for a stronger study.\n\nThere are also a lot of publications about the virulence factors in E. coli (FimH, sat, iutA, papC, cnf1 and hlyCA) that promote the damage in the patients suffering UTIs. That information will be important to characterize the E. coli strains.\n\nOn the other hand, Clermont et al.1 published the phylogenetic classification of associated E. coli UTIs.\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/10-375
|
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