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https://f1000research.com/articles/13-753/v1	05 Jul 24	{ "type": "Research Article", "title": "Causal relationship between financial deepening, national security, ecological footprint, and economic growth in Nigeria", "authors": [ "Charles O. Manasseh", "Chine Sp Logan", "Ogochukwu C. Okanya", "Kenechukwu K. Ede", "Odidi C..O. Onuselogu", "Chi A. Ngong", "John C. Duru", "Jonathan E. Ogbuabor", "Ifeoma C. Nwakoby", "Charles O. Manasseh", "Chine Sp Logan", "Ogochukwu C. Okanya", "Odidi C..O. Onuselogu", "Chi A. Ngong", "John C. Duru", "Jonathan E. Ogbuabor", "Ifeoma C. Nwakoby" ], "abstract": "Background This study seeks to examine the causal link between financial deepening, national security, ecological footprint, and economic growth in Nigeria, in order to contribute to the contradicting evidence on economic growth drivers.\n\nMethods The dynamic ARDL model was employed as the baseline model to establish the link between the phenomena, and the FMOLS and DOLS as robust models using time series data spanning from 1995 to 2022. The FMOLS and DOLS models take into consideration the presence of endogeneity, cross-sectional dependency, and heterogeneity.\n\nResults The results demonstrate that whereas ecological footprint has positive and significant long-term relationships with economic growth, financial deepening and national security have negative and significant long-run relationships with economic growth. There was a 34% and 50% correction to the short-term to long-term adjustment speed, respectively. The findings of the Granger causality, interaction terms, marginal (ME), and threshold (TH) effects demonstrate: a) a significant bidirectional causal relationship between national security and economic growth, as well as a one-way significant causal link between financial deepening and economic growth; b) changes in national security and ecological footprint have a significant and negative impact on the financial deepening effect on economic growth; c) significant negative and marginal effects of national security on economic growth, as well as significant positive marginal effects of ecological footprints on economic growth; and d) the impact of financial deepening on economic growth becomes apparent when the increases in the marginal effect of the ecological footprint reach a critical limit over the ( TH CO 2 = 0.981) threshold.\n\nConclusions This study highlights the significant link between Nigeria’s financial deepening, national security, ecological footprint, and economic growth. It recommends that viable policies be put in place to support the development of financial institutions, increasing security infrastructure investment, and promoting renewable energy use for sustainable environment and reduced carbon emissions.", "keywords": [ "Financial Deepening", "National Security", "Ecological Footprint", "and Economic Growth" ], "content": "1. Introduction\n\nEconomic growth is crucial for national development and improving people’s lives. It increases company profitability, enables higher research and development spending, and fosters technological breakthroughs (Ndako et al. 2017). It boosts confidence and encourages firms to take risks and innovate. However, it also requires increased financial access, a secure environment, and a reduced ecological footprint for effective economic growth (Yang et al. 2021). According to the United Nations (2020) report, financial deepening promotes the supply of financial services with a broader range of options aimed at all levels of society. Similarly, Hamilton and Godwin (2013) saw financial deepening as a growth in the supply of financial assets in an economy. It depicts the entire range of financial assets accessible in the economy that promote capital accumulation, access to finance, risk management, investment promotion, improved resource allocation, consumption stimulation, production enhancement, and innovation and entrepreneurship (Kose et al. 2006). Because of the intricacy of the financial system, domestic deposits rise and a wider range of financial claims can be made (Christian 2013). Economic growth is encouraged by financial deepening, which makes the infrastructure and financial markets necessary to fulfill changing demands. In order to foster investor confidence, ensure peace, oversee regulations, safeguard infrastructure, combat illegal activities, and foster global collaboration, a stable environment is essential. However, because ecological footprints are directly related to growth, developed financial institutions and markets can help reduce the impact of environmental risks while also advancing global sustainability goals by promoting sustainable finance, encouraging green investments, and incorporating environmental considerations into financial decisions.\n\nNational security and economic growth are inextricably linked, and as such, Romm (1993) claimed that economic activity can only improve if investors’ property rights and lives are secured. As a result, a nation’s security and defense are vital in protecting assets, infrastructure, and resources from external threats such as terrorism, military aggression, and cyber-attacks (Saba, 2021). By securing these assets, security actions help to maintain the economy’s stability and resilience, assuring ongoing commercial operations, trade flows, and investment activity (Saba and Ngepah, 2020a). According to Rajan (2022), the importance of national security extends beyond sustaining domestic order to include the health and prosperity of nations. Amid, good national security measures, such as good governance, rule of law, and conflict prevention, help to foster political stability by lowering the danger of internal conflicts, civil unrest, and regime instability. It also creates a predictable business environment, which promotes investment, entrepreneurship, and economic growth (Saba and Ngepah, 2020a). Similarly, despite Africa’s inherent security constraints, security outcomes promote economic progress (Saba, 2020). Further research on the relationship between military spending and security outcome convergence by Saba and Ngepah (2021), Saba and Ngepah (2020b), and Saba (2019) highlights the significance of fortifying national security architectures. These studies also show that this relationship has a convergence security outcome on economic activities in Africa.\n\nRegardless of the importance of protecting lives and property, and national defense, studies by Yasin et al. (2019), Murshed et al. (2021), and Nathaniel et al. (2020) highlight the ecological footprint as a significant challenge that can deter growth even in a secure environment. They declare that human causes contribute to environmental deterioration (Yasin et al. 2019), and that as a country’s population grows, so does the demand for food, making it difficult to boost food production without compromising people’s wellbeing. Studies by Alexander and Klemm (2019), Yahaya and Kolapo (2020), Rajan (2022), Romm (1993), Ansari et al. (2021), Wang et al. (2020), Yang et al. (2021) and Zafar et al. (2019) have demonstrated that overuse of natural resources—such as plant-based diets, products from livestock and fish, wood, and forests—increases waste and carbon emissions. As a result, an environment that promotes output without sacrificing wellbeing is required. In light of the above discussions, this paper examines the causal link between financial deepening, national security, ecological footprint, and economic growth in Nigeria. It attempts to investigate the following: a) the impact of financial deepening on economic growth; b) the impact of national security on economic growth; c) the impact of ecological footprint on economic growth; d) the direction of the causal relationship between these factors, and e) the interactive effect of national security and ecological footprints on economic growth. Therefore, it is crucial to understand the relevance and the policy consequences of these phenomena’ linkage, as previous study in Nigeria has not looked at the synergy between them. Understanding the connections in Nigeria could help identify strategies for addressing the interrelated opportunities and challenges the nation faces. As a result, it could offer options for coordinated policy interventions that could support financial services accessibility, fight insecurity by stepping up border controls, law enforcement, intelligence sharing, and conflict resolution; protect the environment; and ultimately support socioeconomic transformation, long-term growth and development, and resilience in a rapidly changing global landscape.\n\nThis study varies from the existing literature in the following ways. The first and most crucial step was to examine the influence of national security on economic growth, specifically utilizing the global terrorism index. This measurement captures the impact of other African terrorist organizations and their resurgence, such as Islamic State in the greater Sahara (ISGS), Islamic State in the West African Province (ISWAP), Jama’at Nusrat al-Islam wal Muslimeen (JNIM), and Boko Haram in the northeast, as well as armed banditry in the northwest, which have posed serious security challenges for Nigeria. Specifically, Boko Haram has carried out multiple attacks, bombings, and kidnappings that have resulted in fatalities, population relocation, and infrastructure destruction. The continuing existence and increasing power of violent extremist groups in the Sahel regions threatens to worsen the humanitarian situation and disperse instability throughout Africa, putting neighboring nations’ security and economies at serious danger. Second, prior research in the literature neglected to evaluate the interaction between national security and financial deepening and ecological footprint in order to determine whether or not enhanced national security can significantly alter or influence the effects of these factors on Nigeria’s economic growth. Third, in order to comprehend how changes in ecological footprints or national security affect economic growth while leaving other variables constant, we take into account the threshold and marginal effects (TH) of these factors on growth. This discovery will aid in determining how interventions or modifications to policy variables affect economic growth. It will also assist decision-makers in assessing the efficacy of policy measures that can support well-informed choices about program design and resource allocation. Unlike previous studies, we used FMOLS and DOLS models to strengthen our ARDL results, addressing endogeneity and heterogeneity issues that are inherent in ARDL. The remaining sections of the research are arranged as follows: The key empirical review is covered in Section 2, whereas the study methods are presented in Section 3. The summary of the empirical findings and discussions are provided in Section 4, while Section 5 offers the conclusion and policy recommendations.\n\n\n2. Literature review\n\nThe review of empirical studies in this section focused on three key themes: national security and economic growth, ecological footprints and economic growth, and financial deepening and economic growth.\n\nThe conventional neoclassical paradigm posits that economic development is propelled by an integrated financial system, as argued by Henry (2006). According to this perspective, the financial system plays a crucial role in promoting economic growth by stimulating domestic consumption, leading to higher savings and consequently reducing capital expenses. Another perspective emphasizes that the financial system drives economic expansion through indirect mechanisms. Correspondingly, an accessible financial system fosters economic growth by facilitating an upswing in financial services, thereby stimulating the economy (King and Levine, 1993). In this context, Ndako (2017) discovered a long-term correlation between investment, development of finance, and growth in Nigeria. In this context, Paul (2017) explored the enduring impact of finance strengthening on growth. Yahaya and Kolapo (2020) assert that the banking industry is connected to the rise of finance, which in turn has a significant effect on growth. Conversely, Nguyen et al. (2019) contended that the influence of the financial system on growth is contingent upon the degree of development. According to Yang (2019), the financial development of middle-income nations promotes growth. Anachedo and Osakwe (2023) looked at how financial depth affected economic expansion between 1985 and 2021. The analysis also demonstrated a strong adverse correlation between the broad money ratio, insurance industry premiums, and economic expansion. Further information reveals a positive relationship between growth and the market value ratio as well as a connection between Nigeria’s increasing economic growth rates and an increase in loans to the private sector. Additionally, Afzal et al. (2023) discovered a bidirectional causal relationship between financial liquidity and Poland’s economic growth, both in the long and short terms.\n\nIn growing African countries, Manasseh et al. (2024) discovered a bidirectional causal association between trade openness, GDP per capita, money supply ratio, and domestic lending to the private sector. Additionally, Okafor et al. (2021) also showed that financial depth has a positive impact on economic growth. Kerimov (2021) investigated the underpinnings of the connection between financial depth and economic advancement using data from 2008 to 2019. According to the study’s findings, bank loan negatively affects GDP-based economic growth. Akintola, Oji-Okoro, and Itodo (2020) found that the long-term development of real production growth is positively and significantly impacted by the strengthening of finance, bank liquidity, and all share indexes. According Kapaya’s (2020) research, there is a short-term positive correlation between financial depth and economic growth, but a long-term negative correlation between financial system efficiency and economic growth.\n\nDefense, or national security, of a sovereign state, comprising its institutions, people, and economy, is considered the responsibility of the government. Governments employ a variety of strategies, such as diplomatic relations and their combined military, economic, and political might, to maintain a nation’s security. Research has also been done on the connection between different security measures and other macroeconomic indicators, and the results demonstrate that a nation’s ability to maintain peace is crucial to its ability to flourish. Because of this, Saleem et al. (2020) found a long-term negative correlation between investment and terrorism in Southern Asia, while Edeme and Nkalu (2019) concluded that terrorism is the reason behind Nigeria’s poor economic gain. Mehmet (2017) discovered that most countries’ economic growth was negatively impacted by terrorist acts, particularly those with low incomes. Research by Saba (2020), Chuk et al. (2017), Bezi et al. (2016), Zakaria et al. (2019), and Saba and Ngepah (2021) shows that terrorist activity makes businesses more vulnerable and hinders their potential to thrive. Further evidence show that economic growth is driven by security outcomes in six regional economic groups. The study also revealed that military spending has a significant influence on industrialization in AMU, CEN-SAD, IGAD, and SADC, while it is insignificant and inversely associated with economic growth in COMESA, ECCAS, and ECOWAS. Consequently, military spending, and industrialization have a long run association.\n\nYusuf and Mohd (2023), Ngepah and Djemo (2019), Saba (2021), Saba (2020), Saba (2019), Kabiru et al. (2023), and Aminu et al. (2023) investigate the following subjects: The degree of alignment between military spending and security implications for 34 African nations between 1990 and 2015; and the link between military expenditure and security results for 51 African countries between 2000 and 2018. These studies’ findings demonstrated that: a) different security approaches, methods, or actions produce the same or similar results throughout Africa; b) military spending has a significant negative impact on growth in the continent; c) there is no evidence or support for the hypothesis that higher military spending causes economic growth or aligns economic outcomes in Africa; d) military expenditures and their ensuing security effects differ from nation to nation with different effects on economic growth in Africa; e) the increasing level of insecurity in Nigeria has a negative impact on the economy; and f) terrorism hinders economic growth, respectively.\n\nRecent study has found that ecological footprints are increasingly influencing economic factors. According to some research, it hinders the growth of economic indicators, while other studies believe it has a favourable influence on them. For example, Yang et al. (2021) observed that the ecological footprint of the BICS economies increased GDP. Also, Ullah et al. (2021) found a significant association across all regimes when they examined the link between GDP and ecological footprint in the top fifteen clean energy economies. The amount of energy derived from biomass and the ecological footprint were shown to be significantly correlated by Wang et al. (2020). Mehmood et al.’s (2023) research on the link between environmental footprints and economic expansion in South Asia revealed a bidirectional causal association between the use of renewable energy and environmental footprints in G7 countries, as well as a causal feedback connection between GDP and the environmental footprints. Additionally, Udemba’s (2020) work demonstrates that Nigeria’s ecological footprint and economic growth are growing at the same time. Further evidence from the ARDL findings indicates a positive link between carbon emissions and economic growth; however, when the country’s income and demographic were also taken into account, a negative link was shown between carbon emissions and growth.\n\nIn contrast to past study that indicated a direct association, Ansari et al. (2021) and Obayagbona (2023) revealed an inverse connection between ecological footprints and economic growth. Ansari et al. (2021) also show that the influence of the ecological footprint on economic growth is diminished by globalization. In a similar vein, Ahmad et al. (2020) said that technological progress makes it possible to reduce the impact of the ecological footprint on growth. Furthermore, a study conducted by Obayagbona (2023) examined the link between carbon dioxide emissions and economic growth in Ghana and Nigeria. The findings indicated that ecological footprints indicators, such as GHG emissions and the use of renewable energy, enjoyed a substantial adverse effect on economic expansion in Ghana and Nigeria, while other control variables, such as openness to commerce and the use of electricity, displayed a negligible positive and negative link with economic growth, respectively.\n\n\n3. Methods\n\nThis study spanned the period 1995 – 2022. The study’s period was determined by data reliability and accessibility. The primary goal of the study was to evaluate the causal links between Nigeria’s financial deepening, national security, ecological footprint, and economic growth. Table 1 shows the study’s data, definition of acronym, and data repository links (sources).\n\nUtilizing yearly time series data from 1995 to 2022, this study used the dynamic autoregressive distributed lag approach (ARDL) created by Pesaran et al. (2001) as the baseline model to estimate the causal relationship between financial deepening, national security, ecological footprints, and economic growth in Nigeria. The output of the baseline model was carefully tested using fully modified ordinary least squares (FMOLS) and dynamic ordinary least squares (DOLS) models, taking into account the limitation of the ARDL model and the expected impacts. Endogeneity and heterogeneity concerns are taken into account in the robustness check models. Research such as Manasseh et al. (2017), Manasseh et al. (2023), Odhiambo (2009), and Al-Malkawi et al. (2012), in contrast to Johansen and Juselius (1990) and Gregory and Hansen (1996), adopted ARDL because it is appropriate and can provide asymptotically normal estimates of long-run coefficients (Pesaran and Shin, 1999). Compared to other models, the ARDL model increases the probability of determining the suitable dynamic model structure, supporting the efficacy of long-run parameters in cointegration techniques (Pesaran et al., 2001; Pesaran and Shin, 1999). However, the dynamic ARDL model is as follows.\n\nIn equation (2), εi,t=(∀i+πi,t). The fixed effect known as ∀i denotes the time-invariant or unobserved characteristics unique to Nigeria. The πi,t, also known as time-fixed effects, identifies the time-specific effects that affect country’s dataset over a given period. Hence, others remained as defined above, Interacti,t depict the interactive terms (M2/GDPCO2 & M2/GDPNSI), where δ expresses how much the interaction factors influence economic growth. The exchange rate (EXR) and inflation rate (INFL), are the study’s control variables and t is the unit of time. It is thus expected that π>0. This suggests that more financial deepening boosts economic growth, whereas rising levels of ecological footprint and insecurity are expected to have the opposite effect. For this reason, a conditional ARDL (p, q, q,,,, q) error correction term (ECT) is stated as follows after the re-parameterized ARDL (p, q) of Pesaran et al. (1999) and Pesaran et al. (2001):\n\nTo gain a thorough knowledge of the influence of a unit change in national security (NSC) and ecological footprints (CO2) on economic growth in Nigeria, while maintaining all other variables constant, we estimated the marginal (ME) impacts using equations (4) and (5). The marginal effect measures how much revenue growth is likely to vary in response to minor changes in national security and ecological footprints. This is critical now in Nigeria to comprehend the severity of insecurity and the consequences of over-reliance on natural resources such as carbon emissions on economic growth.\n\nThe coefficients (ϑ&σ) in the partial derivative equations (4) and (5) are the main focus. If (ϑ&σ) are negative i.e. (ϑ&σ<0) and (π&θ) are positive i.e. (π&θ>0), it depicts that a unit change in national security and ecological footprint have adverse effects on the economic growth respectively; while the interaction of financial deepening with the national security and ecological footprint improves economic growth in Nigeria. According to the former, as insecurity and ecological footprint (CO2) rise, their negative impacts reduce both financial deepening and economic growth in Nigeria. Following the works Muoneke et al. (2023), Okere et al. (2022), and Ofori and Figari (2023), calculating the threshold (TH) levels of the national security and ecological footprint is crucial for policymaking. This is because the coefficients (ϑ&σ)as well as (π&θ) have different signs and magnitudes. Thus, we present the threshold-level equations for the interactive variables as follows.\n\nThe possibility of estimating equations (6) means that the marginal effects (ME) must be greater than zero, thus, this is shown in equations (7) and (8) as in below.\n\nWhere ME stands for the marginal effect of national security and ecological footprint; while THCO2, THNSC and THPINS are their thresholds respectively.\n\nEven if the ARDL approach is successful and adequate in building a suitable dynamic model structure that supports the efficacy of long-run parameters and estimates variables only when they are integrated of 1(0) or 1(1), its capacity to manage sequence correlation and endogeneity is limited. We conducted a sensitivity analysis with fully modified ordinary least squares (FMOLS) and dynamic ordinary least squares (DOLS) to lessen the impact of this problem on the output. These models are very efficient in estimating long-run coefficients if the coefficients are cointegrated. While DOLS provides a parametric method that can lessen the association between explanatory variables and error terms (Pedroni, 2001), FMOLS offers a non-parametric model that has the benefit of eliminating autocorrelation and heteroskedasticity concerns (Kao & Chiang, 2001). The FMOLS and DOLS are specified as follows:\n\nZ represents the regressor’s vector (W = Xi,t−Xi′), Xi,t stands for explanatory factors, and Si,t indicates dependent variables. The DOLS estimator surprisingly outperforms the OLS, ARDL, and FMOLS estimators in limited samples when it comes to unbiased estimation based on Monte Carlo simulations. By considering endogeneity equally in a model, the robust correction for endogeneity in the explanatory variables is obtained.\n\n\n4. Empirical Results and Discussion\n\nThe study’s variables were initially subjected to pre-estimate tests, which included unit roots tests, Spearman correlation matrix tests, and descriptive statistics to give additional details about the variables, before the ARDL (p, q) estimation. We employed unit root tests such the Phillip-Perron (PP) and Augmented Dickey-Fuller (ADF) tests. The results of the unit root test indicate that none of the variables in 1∼I(2), are integrated (see Table 4). In other words, any variable being studied must be integrated of I∼I(0) or I∼I(1). The null hypothesis (H0) is rejected in light of the results. We therefore conclude that the series is stationary and devoid of unit roots. Based on the outcomes of the unit root testing, the dynamic ARDL technique is demonstrated to be a suitable baseline model for the estimation. Moreover, the results of the dynamic ARDL estimation (see Tables 6 and 7) were extensively verified by the use of FMOLS and DOLS; Table 8 presents the results of these analyses.\n\nTable 2 displays the descriptive statistic results, which reveal that the mean, median, standard deviation, skewness, and kurtosis values are not far apart. The results also revealed that the total variations in the series vary from -2.298 to 3.525, representing the series’ min and max values, and that the probability values of the Jarque-Bera statistic for each variable are statistically significant (less than 0.05).\n\nThe Spearman’s rank correlation test, as shown in Table 3, allowed us to gain insight into the direction and strength of the association between two ranking variables. It illustrates the monotony of the connection between two variables. The study discovered substantial positive correlations between financial deepening (M2/GDP), national security (NSC), ecological footprint (CO2), inflation rate (INFL), and economic growth (RGDP). Furthermore, it was shown that there is a significant negative association between economic growth (RGDP) and the exchange rate (EXR). Also, a significant negative association was found between the GDP and the exchange rate (EXR). An ARDL bound test (see Table 5) is carried out to verify the long-term cointegration of the variables, as suggested by the findings. However, Table 4 shows the results of unit tests that were run before the bound test, such as the Augmented Dickey-Fuller (ADF) and Phillip-Perron (PP) unit root tests. Since the PP test ignores serial correlation and the ADF employs parametric autoregression to imitate the error structure, the two tests are integrated.\n\nTable 3 displays unit root test results, showing that certain variables were integrated of I∼I(0) and I∼I(1). None of the variables were integrated of I∼I(2). Based on the results, the null hypothesis (H0) of unit roots is rejected. As a result, the series has no unit roots and the variables are stationary, as previously indicated. This is because the rule of thumb stipulated that if the probability values were less than 0.05, the null hypothesis would be rejected. Furthermore, based on these findings, the ARDL model adopted as the baseline model has been identified as the most effective estimating technique for the study. Also, as seen in Table 5, we conducted an ARDL bound test for cointegration in line with Pesaran et al. (2001) and Narayan (2004) since the outcomes of our unit root tests suggest that the variables are integrated of I∼I(0) or I∼I(1). The findings demonstrate a substantial long-term association among the variables. The outcomes are shown in Table 5.\n\nThe calculated F-statistic is contrasted with the 1% upper critical value proposed by Pesaran et al. (2001) and Narayan (2004) in Table 5. As a rule of thumb, we reject the null hypothesis and come to the conclusion that there is no long-term link if the calculated F-statistic is greater than the critical value at 1% (upper bound). Since the F-statistic (13.77) is higher greater than the crucial values at 1%, the results indicate that the variables have a long-run association. Therefore, we argue that there are long-term connections between Nigeria’s economic growth, ecological footprint, national security, and financial deepening. We estimate the long-run model with an OLS estimator using equation (1) since the bounds test suggests cointegration. In addition, we generate the residuals series and fitted a regular restricted error correction model (ECM) using the coefficient of the one-lagged level of the ECM using equation (3), and the results are shown in Table 7. When OLS is applied to equation 1, the residual series is utilized to create the error correction model (ECM), as seen in Table 6. Following that, we fitted the error correction model in order to obtain the results displayed in Table 7 using equation (3).\n\nThis section presents and discusses the ARDL estimated results on the causal relationships among financial deepening, ecological footprints, national security, and economic growth. Several post-estimation tests were conducted, such as the Ramsey RESET, Breusch–Godfrey serial correlation, and heteroskedasticity test. The RESET test confirms that the regression’s functional form is appropriate. The results of the heteroskedasticity and serial correlation tests show that the variables are homoscedastic and uncorrelated, and the normality test shows that the error terms are normally distributed. The ARDL findings are shown in Table 6 below.\n\nThe results displayed in the first column demonstrate that, although the ecological footprint—proxied by the amount of carbon dioxide (CO2) emitted per person—has a significant and positive effect on economic growth. Financial deepening—proxied by the money supply to GDP ratio (M2/GDP)—and national security—proxied by the global terrorism index—have a significant negative relationship with economic growth (proxy, real GDP). The significant inverse relationship between financial deepening and growth suggests that Nigeria’s financial deepening has a mitigating effect on economic growth. This outcome confirms a recent analysis that found 38 million adults in Nigeria are financially excluded, which equates to roughly 36% of the adult population in the country. This shows that in order to encourage the mobilization of savings, facilitate investment, and propel economic growth in Nigeria, it may be necessary to guarantee a strong financial infrastructure as well as better access to financing. According to Apergis et al. (2007), increasing access for individuals who lack sufficient financial resources can thereby speed up economic growth. But studies by Yang (2019), Ndako (2017), Anachedo and Osakwe (2023), Manasseh et al. (2024), and Akintola, Oji-Okoro, and Itodo (2020) held contrary few on the impact of financial depth. Moreover, a negative and significant connection has been seen between economic growth and national security and this conclusion lends credence to the research conducted by Edeme and Nkalu (2019), Saleem et al. (2020), Mehmet (2017), and Saba and Ngepah (2021). It appears from the evidence that growing levels of insecurity are impeding Nigeria’s economic progress. This outcome is consistent with the 2021 Global Terrorism Index research, which ranks Nigeria as the sixth most terrorized nation in the world due to an upsurge in violence that has claimed many lives and destroyed numerous economic assets. Therefore, it will be challenging to achieve economic growth if the Nigerian government does not prioritize measures to strengthen national security by addressing the underlying causes of insecurity, enhancing law enforcement, intelligence-sharing, border control, investing in defense capabilities, and promoting social inclusion.\n\nThe ecological footprint, a measure of the consequences of the entire process of producing energy for human use, is most notable for its positive and significant long-term association with Nigeria’s economic growth. Our results were in line with Yang et al. (2021) and Udemba (2020); however, the evidence we provided was in contrast to that of Ansari et al. (2021), Obayagbona (2023), and Obayagbona (2023). This result contradicts the a priori assumption, which maintains that ecological footprints and economic growth are inversely related. Consequently, the significant association that exists between ecological footprints and economic growth might point to an increase in manufacturing that is energy-intensive and associated with environmental degradation, climate change, and the depletion of natural resources. Therefore, the Nigerian government needs to tighten environmental laws and support green technology in order to maintain the rising growth in the face of ecological footprints, as demonstrated by our findings. This can be accomplished by implementing laws that promote climate resilience, the use of renewable energy sources, environmental preservation, and the reduction of ecological footprints. These results counter those of recent studies by Saleem et al. (2020), Mubashra and Shafi (2018), Wang et al. (2020), and Zafar et al. (2019) that shown an inverse link between growth and ecological footprints. Furthermore, after controlling for each variable’s impact on growth, we discovered a direct association between inflation (INFL) and exchange rate (EXR). This result goes against preconceived notions.\n\nThe findings in the second column are the outcome of additional research into the interaction impact between national security and ecological footprints. The goal is to acquire a better understanding of whether the impact of financial deepening on economic growth varies with changes in national security or environmental footprints in Nigeria. The interaction of financial deepening and national security (M2/GDPNSC) has a negative and significant long-term influence on economic growth. This suggests that the interaction effect of insecurity reduces the impact of financial deepening on economic growth by -0.168. As a result, insecurity erodes peace and order, reducing economic activity. These findings align with the findings of several other studies, including Rajan (2022) and Romm (1993), To find out if the level of ecological footprints (CO2) affects the link between financial deepening (M2/GDP) and economic growth, we also interact financial deepening and ecological footprints (M2/GDPCO2). The findings indicate a significant and negative long-term impact on economic growth. This demonstrates how the interaction of CO2 reduces the effect of financial deepening on Nigeria’s economic growth.\n\nThe results show that, in the short term, ecological footprints have a significant positive impact on economic growth, but financial depth and national security have a significant negative impact. In order to reach full convergence to its equilibrium level, economic growth will respond to changes in financial depth, national security, and ecological footprints at a pace of about 34.4% during the first year, according to the ECM, which is -0.344 and has the anticipated negative sign. The bound test for cointegration is validated by the ECM, which is statistically significant at the 5% level, indicating that the variables are in long-run equilibrium. The study concludes that there is a long-term association between the variables based on these findings. Lastly, it shows that the model satisfies the stability criteria using the cumulative sum of recursive residuals (CUSUM) and cumulative sum of squares (CUSUMSQ) tests from Brown et al. (1975). The fact that the CUSUM and CUSUMMSQ are within the 5% major critical bounds makes this clear (see Figure 1). This shows that the calculated parameters remain constant from 1995 to 2022. It illustrates that the estimated parameters remain constant from 1995 and 2022. The ARCH test for heteroskedasticity in the model’s error process yields an F-statistic of 0.295(χ2=0.929), which is not statistically significant (see Table 3). This suggests that heteroscedasticity is not an issue for the model. The Breusch-Godfrey serial correlation Lagrange multiplier (LM) test produces an F-statistic of 0.223(χ2=0.828), indicating no statistical significance for higher order serial correlation. This implies that we cannot reject the null hypothesis that there is no serial correlation in the residuals. We conclude that the data exhibit a normal distribution since the normality test produced a p-value of 0.198, which supports the null hypothesis. The model’s goodness-of-fit (R-square) of 82% suggests that it is appropriate.\n\nSource: Authors’ Concept.\n\nFurthermore, Table 8 presents the tests that utilized Pairwise Granger Causality to evaluate the causal link between financial deepening, national security, ecological footprints and economic growth. Table 8 shows the unidirectional/one-way causal link that we found between financial deepening and economic growth. The causal relationship runs from financial deepening to economic growth, suggesting that financial deepening the driving force behind economic growth. This evidence validates the findings of Manasseh et al. (2024). Similarly, we discovered a two-way causal relationship between national security and economic growth, as well as a one-way link between ecological footprints and economic growth. These results suggest that ecological footprints are the primary driver of Nigeria’s economic growth, and that economic growth and national security are mutually reinforcing. Consequently, ecological footprints stimulate economic growth, while economic prosperity and national security are mutually dependent. So, studies conducted by Mehmet (2017), Edeme and Nkalu (2019), Saleem et al. (2020), Saba and Ngepah (2021), Yang et al. (2021), Udemba (2020), Ansari et al. (2021), and Obayagbona (2023) indicated that ecological footprints and national security boost economic growth. Nonetheless, recent study into the causal link between other variables, such as the exchange rate (EXR) and economic growth, demonstrates a bidirectional or two-way relationship, implying that EXR and economic growth may be predicted mutually.\n\nGiven the efficacy of these models in addressing issues with heteroskedasticity, autocorrelation, and endogeneity, which could affect the outcomes derived from the baseline model (ARDL), sensitivity tests are required to verify whether the results have changed, and the results are presented in Table 9 below.\n\nThe FMOLS and DOLS results in Table 9, genuinely corroborated our previous findings using the ARDL model that financial deepening (M2/GDP), national security (NSC), and ecological footprints (C02) are important drivers of economic growth in Nigeria. The data demonstrates that there are both short- and long-term relationships between the phenomena in Nigeria. Further analysis revealed that while financial deepening and national security have negative and significant long-run relationships with economic growth, the ecological footprint (CO2), inflation rate, and exchange rate (EXR) in Nigeria have positive and significant long-run relationships with economic growth. This is indicated by the first column of results. Our earlier results were discovered to be in agreement with the interacting outcomes of the second model (Table 9). Ecological footprints improve the impact of financial deepening on Nigerian economic growth, but national security reduces this gain. The findings suggest that the interactive influence of terrorism inhibits growth, but the interactive influence of ecological footprint promotes growth. As a result, it follows that the ecological footprint is essential to halting environmental damage, climate change, and the depletion of natural resources. Robust checking with the FMOLS and DOLS models confirmed the suitability of the ARDL model for the study, indicating that the results may have implications for policy forecasts.\n\nThe findings of the estimated ARDL models (1) and (2), which are displayed in Tables 6 and 9, reveal that national security (NSC), as measured by the global terrorism index, is significant and inversely related to Nigeria’s economic growth, while ecological footprint (CO2) and financial deepening encourage economic growth. Hence, it is essential to investigate if their respective marginal effects promote or inhibit economic growth in Nigeria. Equations (4) and (5) from the baseline model findings were used to compute the marginal effects (ME) of national security (NSC) and ecological footprint (CO2), which were then reproduced in equations (11) and (12), following the studies by Muoneke et al. (2023), Okere et al. (2022), and Ofori and Figari (2023).\n\nThe study indicates that there is a negative association between the marginal effects of the interaction between M2/GDP and NSC (π = -0.168<0) and the unconditional effects of NSC (ϑ = -0.864<0). Both the 5% and 1% levels of statistical significance are reached by the effects. When every other factor remains constant, declining economic growth is associated to worsening national security conditions, as indicated by negative values (ϑ & π). Nonetheless, economic growth can be negatively impacted by a decline in Nigeria’s national security, and the growth-promoting effects of financial deepening may be compromised. This demonstrates how growing levels of insecurity hurt Nigeria’s ability to prosper economically. Further inquiry indicates that both the unconditional effect (σ = 0.841161) and the interaction’s marginal effect (θ = 0.139>0) of ecological footprint are positive. Both effects show statistical significance. A positive unconditional effect of the ecological footprint on economic growth implies that greater resource use and environmental effect result in higher levels of economic growth, whereas a positive marginal effect implies that economic growth is inextricably linked to resource mining, manufacturing, and usage. Increased economic activity, such as manufacturing, crop production, and expansion of infrastructure, may be indicated by larger ecological footprints. All of these factors influence the impact of financial deepening on economic growth. The stimulating effect of natural resources might thereby amplify the impact of financial deepening on economic growth. Furthermore, when the coefficients of the ecological footprint and national security (ϑ & σ) and (σ & θ) have opposing signs, equations (6) and (8) may be applied to estimate the threshold effect of each. So, the threshold is determined when the marginal effects (ME) are greater than zero. Beyond the threshold level, the potential benefits of economic activity and the influence of financial deepening are presumably outweighed by the environmental degradation associated with higher ecological footprints. The calculated threshold level (THCO2=0.981) indicates a critical limit above which increases in ecological footprint have a significant impact on economic growth.\n\nThe primary goal of this study is to examine the relationships between financial deepening, national security, ecological footprint, and economic growth in Nigeria. The findings below were obtained using yearly time series data from 1995 to 2022, as well as autoregressive distributed lag (ARDL) as the baseline model and fully modified ordinary least squares (FMOLS) and dynamic ordinary least squares (DOLS) as robustness check models. First, the results of the baseline model indicate, a significant long-term relationship between financial deepening, national security, ecological footprint, and economic growth. While financial deepening and national security are significant and have a negative relationship with economic growth, the ecological footprint has a direct and significant impact on Nigeria’s economic growth. While Ndako (2017), Anachedo and Osakwe (2023), and Akintola, Oji-Okoro, and Itodo (2020) support our findings, Apergis et al. (2007) argued that improving access to adequate financial resources increases economic growth. Our findings about the relationship between financial deepening and economic growth contradict their claims. Furthermore, this analysis validates previous research that has suggested that national security is inversely and strongly associated to economic growth (Edeme & Nkalu, 2019; Saleem et al., 2020; Mehmet, 2017; Saba & Ngepah, 2021). As with Yang et al. (2021) and Udemba (2020), our findings on the relationship between economic growth and ecological footprint refuted the evidence offered by Ansari et al. (2021) and Obayagbona (2023). Previous research indicate that financial deepening, national security, and ecological footprint are substantial and significant determinants of economic growth.\n\nSecond, evidence from the interaction terms using both the baseline and robust models shows that the interactive influence of financial deepening and national security (M2/GDPNSC) has a significant and negative long-term relationship with economic growth, whereas financial deepening and ecological footprints (M2/GDPCO2) have a significant and positive long-term relationship with economic growth. This suggests that, while the interactive influence of financial deepening caused by changes in ecological footprints has a significant and long-term positive impact on economic growth, the interactive influence of financial deepening caused by changes in national security conditions has a negative impact on economic growth. These results therefore align with those of a number of previous research, including Rajan (2022), Romm (1993), and Scheve and Slaughter (2017). Third, a one-way causal link was shown by the Pairwise Granger causality test results, indicating that ecological footprint and financial deepening, respectively, are the driving force of economic growth. This indicates that economic growth is boosted by both ecological footprint and financial deepening. The results of Manasseh et al. (2024), who claimed that financial deepening predicts economic growth in emerging nations, were supported by this research. In a similar vein, we found a bidirectional causal link that suggests mutual reinforcement between economic growth and national security. Fourth, we found a negative and significant correlation between the interaction’s marginal effects of national security (π = -0.168<0) and the unconditional effects of national security (ϑ = -0.864<0), after controlling for the marginal and threshold impacts of national security and ecological footprints. As a result, negative values (ϑ = -0.864 & π = -0.168) indicate an association between declining economic growth and deteriorating national security conditions. Subsequent analysis shows that ecological footprint interaction has a positive and significant relationship between its marginal effect (θ = 0.139>0) and unconditional effect (σ = 0.8412>0). As a result, the expansion of Nigeria’s economy is inextricably related to activities with an ecological impact, such as resource extraction, production and consumption.\n\nAdditionally, based on the findings explained above, no empirical research reviewed examined the synergy between financial deepening, national security, environmental footprint, and economic growth, particularly in Nigeria. Few studies in Nigeria focused on the link between financial deepening and economic growth; security and economic growth and; ecological footprint and economic growth, respectively. As a result, one of the study’s strong points is the synergy between the occurrences and the degree of gap caused in the national security measurement. Furthermore, prior empirical studies (see Rajan, 2022; Romm, 1993) were unable to adequately capture the character and implications of terrorism across African countries. The global terrorism index, which assesses the impact of Africa’s rising terrorism rate on economic growth, was employed as a proxy for national security in this study to capture the previously explained. Thus, we found that the global terrorism index and Nigeria’s economic growth were significantly and negatively correlated. This implies that terrorist organizations operating in Africa, including Islamic State in the West African Province (ISWAP), Jama’at Nusrat al-Islam wal Muslimeen (JNIM), and Islamic State in the Greater Sahara (ISGS), pose a threat to Nigeria’s economic growth. In addition, previous studies (Edeme & Nkalu, 2019; Saleem et al., 2020, Mehmet, 2017; Saba & Ngepah, 2021) have not taken into account the interaction link that exists between financial deepening and national security. The long-term evidence from the findings suggested that reducing insecurity through enhanced border protection, judicial enforcement, intelligence cooperation, and dispute resolution could support Nigeria’s economic transformation. The evidence also indicated a significant and inverse relationship between the two. Finally, we examine the marginal effects of national security (π = -0.168<0) on Nigeria’s economic growth, which have likewise received little attention in earlier research. The analysis shows that declining national security conditions also account for variations in Nigeria’s economic growth. The ability to incorporate these knowledge gaps into existing empirical literature is not without restrictions. Thus, we suggest carrying out cross-national research on the connections between national security and economic growth in the future. This would improve a comparative analysis of how the global terrorism index and its heterogeneity affect African countries’ economic growth.\n\nThese results highlight how important financial deepening is to Nigeria’s economic expansion. Given the inverse relationship between financial deepening and economic growth in Nigeria, reducing credit availability for both individuals and businesses may stifle investment in profitable ventures such as technology innovation, infrastructure development, and entrepreneurship. Also, enhancing financial accessibility, having strong financial intermediaries, and financial systems encourage saving, and economic growth, which in turn leads to resilience, equitable growth, and a decline in poverty. With this knowledge, Nigerian authorities may create and carry out concerted initiatives to strengthen the banking sector, increase customer access to financial services, encourage financial literacy, and foster financial innovation. In addition, comprehending the connection between economic growth and national security is vital in safeguarding Nigeria’s political stability, vital infrastructure, and sovereignty. The discovered inverse link between national security and growth implies economic growth and prosperity may be negatively impacted by worsening security circumstances in Nigeria. Thus, security concerns like insurgency, terrorism, and intercommunal strife endanger societal cohesiveness, investor confidence, and economic progress. The significance of these findings for Nigerian authorities stems from the fact that they highlighted the necessity of giving priority to initiatives aimed at reducing instability by bolstering law enforcement, intelligence cooperation, and conflict resolution institutions, all of which are necessary to promote economic success. Furthermore, the findings about the marginal effect of national security to economic growth in Nigeria may also be utilized by policy analysts to evaluate the effects of policy actions on employment, income, and health outcomes. The evaluation of policy efforts, resource allocation, and program development in Nigeria can all be enhanced by an understanding of marginal impacts.\n\nLastly, the significant and positive association between ecological footprint and economic growth suggests that environmental degradation is an inevitable cost of economic growth. Thus, a positive ecological footprint typically depicts the unsustainable exploitation of natural resources like timber, minerals, and fossil fuels. As such, long-term risks to economic sustainability can arise from resource depletion, ecosystem deterioration, biodiversity loss, and perturbation of biological processes. The significance of these, emphasizes how urgently we must move toward sustainable development pathways that strike a balance between social justice, environmental preservation, and economic prosperity. This calls for the implementation of resource-efficiency- and ecosystem-health-promoting policies.\n\n\n5. Conclusion and policy recommendations\n\nIn conclusion, this study investigated the causal link between financial deepening, national security, ecological footprint, and economic growth in Nigeria for the period of 1995–2022, using the ARDL estimation technique as the base model and FMOLS and DOLS as robustness-checking models. Thus, the following hypotheses were investigated in an effort to determine whether there is a link between these occurrences: a). Financial deepening has no significant effect on economic growth; b). National security has no significant effect on economic growth; c). The ecological footprint has no significant impact on economic growth; d). The interaction between national security and ecological footprint has no significant influence on the impact of financial deepening on economic growth; and e). There is no significant causal link between the phenomena. The findings thus show that: a) financial deepening has a positive and negative relationship with economic growth in Nigeria; b) national security has a positive and negative relationship with economic growth; c) ecological footprint has a positive and significant correlation with economic growth; d) changes in national security and ecological footprint have a significant and negative relationship with the effect of financial deepening on economic growth; and e) there is a significant unidirectional causal link as well as a significant bidirectional causal link between financial deepening, ecological footprint, and economic growth.\n\nBased on the findings explained above, the following policy recommendations were made. First, we advocate for a mix of policy actions to improve access to finance, strengthen the financial services sector, and promote long-term economic expansion. These policy measures include: a) policies that can facilitate the availability of financial services, especially for those with limited incomes and neglected rural populations; b) policies that can strengthen the legal structure to support financial security, safeguarding consumers, and market ethical conduct; c) making sure that policies that may encourage creativity and rivalry in the financial industry to drive efficiency, reduce costs, and boost access to finances are implemented; and d); and d) policies that promote credit operations, lower transaction costs, and enhance the evaluation of credit risk through boosting spending on the building of financial structures, such as payment networks, and bureaus of credit. Second, we endorse policies that support Nigeria’s border surveillance, intelligence, and enforcement agencies, among other security infrastructure components. It is possible to foster unity in society and support efforts to promote peace in Nigeria by giving priority to dealing with the underlying causes of dispute. Discussion with all parties involved, leaders in the community, and disadvantaged populations can be utilized to handle complaints, settle conflicts, and establish confidence between neighborhoods. Lastly, an integrated approach that incorporates ecological sustainability into growth plans and economic initiatives should be given top priority. This can be done by: a). putting policies in place that support conservation, organic, and other sustainable agricultural practices; b). enforcing stricter environmental laws and regulations to safeguard ecosystems; c). quickening the switch to clean energy sources like solar, wind, hydro, and biomass to lessen reliance on crude oil and reduce carbon dioxide emissions; and d). giving precedence to expenditures in environmentally friendly building projects that lessen environmental harm, improve adaptability to global warming, and contribute to economic growth in Nigeria.\n\n\nEthical approval\n\nThe paper is original and has not been published elsewhere in any form or language (partially or in full). There is no ethical approval for this work since it is a social science research. We utilized an annual time series data obtained from the World Bank’s World Development Indicator which has been widely used for research in social science studies which we are ready to make available at the request of the journal.\n\nWe consent that our paper titled “Causal relationship between Financial Deepening, National Security, Ecological Footprint, and Economic Growth in Nigeria” should be published in this journal.", "appendix": "Data availability\n\nData for each of the variables such as real GDP, money supply (% of GDP), CO2 emissions (in metric tons per person), GDP deflator, and exchange rates, for the period 1995-2022 used in this study were sourced from the World Bank: https://databank.worldbank.org/source/world-development-indicators#.\n\nThe data for global terrorism index for the period 1995 – 2022 used for the study were sourced from institute for economics and peace (https://www.economicsandpeace.org/reports/) and reliefweb (https://reliefweb.int/report/world/global-terrorism-index-2022) reports for various years.\n\nAccess to the source data is free of charge subject to the terms and conditions set by the World Bank (https://data.worldbank.org/summary-terms-of-use), and the average score of various years’ global terrorism index reports has already been published and made accessible for use.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgments\n\nWe appreciate the authors of this work for their valuable contributions and the reviewers for their numerous innovative suggestions that help to improve the quality of the research.\n\n\nReferences\n\nAfzal A, Firdousi SF, Mahmood K: The links between financial depth and economic variables: evidence from Poland. 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Publisher Full Text" }	[ { "id": "303565", "date": "19 Aug 2024", "name": "Murat Cetin", "expertise": [ "Reviewer Expertise economic growth", "energy economics", "environmental economics" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis study explores the causal link between financial deepening, national security, ecological footprint, and economic growth in Nigeria, in order to contribute to the contradicting evidence on economic growth drivers. It is possible to improve the study if the following changes are made in the study: 1. In the introduction, the research questions should be created. 2. The contribution of the research to the literature should be emphasized in detail. 3 It should be explained why the 1995-2022 period was chosen 4. There are very few new studies in the literature. Please strengthen the literature with 5-8 new studies 5. Adding the following studies to the literature will contribute to the improvement of the study:\n1. https://dergipark.org.tr/en/download/article-file/2650339 2. https://dergipark.org.tr/en/download/article-file/2674319 3. https://doi.org/10.3389/fpubh.2022.1050550 4. https://www.ibaness.org/bnejss/2022_08_special_issue/18_Cetin_and_Kapcak.pdf 5. https://dergipark.org.tr/en/download/article-file/1546010 6. https://dergipark.org.tr/en/download/article-file/2151955 7. https://www.uludag.edu.tr/dosyalar/iibfdergi/genel-dokuman/2012_1/ASL04.pdf\n\nIs the work 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": "303563", "date": "26 Aug 2024", "name": "Shah Zaman", "expertise": [ "Reviewer Expertise Climate Change", "Energy Economics", "Environmental Economics", "World Economy", "Western Economics", "International Economics and Trade", "Financial Economics", "Managerial Economics", "Resource Economics", "Business Administration", "Renewable Energy Policy", "Urban Environmental Management", "Human Resource Management", "Policy and Planning", "Project Management and Evaluation" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nNote for the editor Thank you for providing me opportunity to review the paper, titled \"Causal relationship between financial deepening, national security, ecological footprint, and economic growth in Nigeria.\" The paper offers a thorough and insightful analysis of these key variables within the Nigerian context, but there are several aspects in the form of comments for the authors, where the paper excels and areas where it could benefit from further refinement. I recommend the paper for indexing, subject to minor revisions. The authors should address the areas for improvement outlined above to strengthen the clarity, depth, and impact of their work. With these enhancements, the paper has the potential to make a significant contribution to the understanding of the complex relationships between financial deepening, national security, ecological footprint, and economic growth in developing economies, particularly Nigeria. Comments for the authors Comment 1. - The introduction could benefit from a clearer articulation of the specific research questions or hypotheses being tested. While the general objectives are clear, more precise research questions would help guide the reader through the study. - It would be beneficial to include a brief discussion on the broader theoretical framework guiding the study. This would provide readers with a better understanding of how the study contributes to existing economic theories on growth, security, and sustainability. Comment 2. - While the literature review is extensive, it could be more critical. The authors should aim to identify specific gaps in the literature more explicitly and demonstrate how their study addresses these gaps. - The review could also benefit from a discussion of the limitations of existing studies. This would help justify the methodological choices made in this study, particularly the use of the ARDL model and robustness checks with FMOLS and DOLS. Comment 3. - The paper could provide more detail on the data sources and the justification for the time period selected (1995-2022). Specifically, the authors should discuss any potential insufficiency or limitations associated with the data. - The authors might consider providing more information on how they addressed potential multicollinearity among the independent variables, as this is a common issue in econometric analyses involving multiple related predictors. - Additionally, the paper could benefit from a discussion on the potential limitations of the ARDL model itself and how these limitations are mitigated by the use of FMOLS and DOLS. Comment 4. - The discussion of the results could be enhanced by linking the findings more explicitly to the broader literature. For instance, when discussing the negative impact of financial deepening on economic growth, it would be useful to compare this with findings from other studies in different contexts. - The authors should consider discussing the policy implications of their findings in more detail. While some recommendations are provided, a more thorough discussion of how these findings can inform specific policy decisions in Nigeria would strengthen the paper. Comment 5. - The conclusion could benefit from a more forward-looking perspective, considering potential future research directions based on the findings of this study. This would help position the paper as a catalyst for further research in this area. - The policy recommendations, while sound, could be expanded with more specific examples or case studies from other countries that have successfully implemented similar strategies. This would provide a more concrete basis for the recommendations.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] } ]	1	https://f1000research.com/articles/13-753
https://f1000research.com/articles/13-465/v1	09 May 24	{ "type": "Research Article", "title": "Mapping Vulnerability to Potential Crisis Events in Surabaya City: A GIS-Based Approach", "authors": [ "Ali E. M. Jarghon", "Nyoman Anita Damayanti", "Inge Dhamanti", "Hari Basuki Notobroto", "Atik Choirul Hidajah", "Anas M. M. Awad", "Ali E. M. Jarghon", "Inge Dhamanti", "Hari Basuki Notobroto", "Atik Choirul Hidajah", "Anas M. M. Awad" ], "abstract": "Background This study aims to develop a vulnerability map for Surabaya using GIS-based Multi-Criteria Decision Analysis (MCDA) to assess the city’s vulnerability to COVID-19.\n\nMethods Six key factors influencing vulnerability were identified and their relative importance determined through the Analytic Hierarchy Process (AHP) pairwise comparison matrix. GIS was utilized to classify Surabaya’s vulnerability into five levels: very low, low, medium, high, and very high.\n\nResults The resulting vulnerability map provides essential insights for decision-makers, healthcare professionals, and disaster management teams. It enables strategic resource allocation, targeted interventions, and formulation of comprehensive response strategies tailored to specific needs of vulnerable districts.\n\nConclusions Through these measures, Surabaya can enhance its resilience and preparedness, ensuring the well-being of its residents in the face of potential emergency outbreaks.", "keywords": [ "Vulnerability mapping", "Disaster management", "AHP", "Public health preparedness", "GIS-based analysis", "GIS" ], "content": "Introduction\n\nIn early 2020, countries worldwide faced susceptibility to the SARS-CoV-2 and COVID-19 coronaviruses.1 The COVID-19 virus spread uncontrollably across the globe, evolving into a pandemic with severe health implications.2 The COVID-19 outbreak had far-reaching effects on various aspects of daily life in numerous countries across the world.3,4\n\nThe initial COVID-19 case in China, specifically in Wuhan, was identified.5 Nonetheless, the virus propagated swiftly, and within a few months, confirmed cases had emerged in most countries worldwide.1\n\nPopulation may be at the greatest danger in the event of any crisis (such as the COVID-19 outbreak).6,7 The city of Surabaya is the capital city of East Java Province, Indonesia, as well as the largest metropolitan city in the province. Surabaya is the second largest city in Indonesia after Jakarta.8\n\nThe distribution of societal susceptibility to the impacts of a disaster is often spatial.9,10 However, it’s essential to recognize that social vulnerability is a dynamic process significantly shaped by government initiatives and mitigation strategies.11 Consequently, communities already facing vulnerability may experience an exacerbation of their situation due to an inadequate or delayed government response.11\n\nThe term “vulnerability” describes a situation in which there is a potential for increased exposure to a community’s hazards.12 Vulnerability mapping is a commonly utilized approach that suggests utilizing multiple determining factors to classify a particular community into various health vulnerability groups.13\n\nThe concept of epidemic prediction mapping using multiple criteria analysis has been explored in several studies.14 These studies often employ the multi-criteria decision analysis (MCDA) approach, considering numerous criteria in the vulnerability mapping of COVID-19.15 Various factors, encompassing demographic (e.g., population), epidemiological (e.g., chronic diseases), and ecological/physical aspects (e.g., temperature), typically drive the mapping of COVID-19.10,16–18 One of the most commonly employed MCDA strategies in these studies is the Analytic Hierarchy Process (AHP).19 The AHP offers a systematic approach to assigning equitable weights to various influential criteria.\n\nA professional approach to mapping epidemic vulnerability and conducting risk assessment, such as for COVID-19 vulnerability, involves utilizing Geographic Information Systems (GIS) based Multi-Criteria Decision Analysis (MCDA).20–24 In this study, the COVID-19 Vulnerability Index (CVI) was developed through the application of GIS-based Multi-Criteria Decision Analysis (MCDA). This index was then utilized to classify the governorates of Surabaya into different COVID-19 vulnerability categories.\n\nThis study aims to assess community vulnerability in emergency situations based on COVID-19 data. By establishing a COVID-19 vulnerability map for Surabaya city.which is extremely valuable in helping decision-makers identify potential COVID-19 outbreaks and, in turn, implement appropriate mitigating strategies to protect public health, particularly in the governorates that are most at risk.\n\n\nMethods\n\nSurabaya is a city located in Indonesia. It is also the capital of the Jawa Timur province. The city is one of the most significant financial hubs in the country. As of the 2015 Census, the population of the city is 2.880.000. It is the second most populous city in Indonesia. The city proper contains a total surface area of 350.5 km2 (135.3 sq mi). The metropolitan area however sprawls out to 5,925 km2 (2,288 sq mi). The population density reaches upward of 9,900/km2 (26,000/sq mi) in the city proper, and drops toward 2,200 per square kilometer (5,700 per square mile) as one moves toward the edge of the metropolitan area. The area of Surabaya City is divided into 5 regions (East, North, South, West, and Center) divided into 31 sub-districts and 163 villages see Figure 1 (Surabaya City Statistics Center, 2022).\n\nThe COVID-19 vulnerability map in this study was constructed using the compiled CVI map. The design of the CVI map considered six crucial factors, as outlined in Table 1. These criteria were selected due to their capacity to increase COVID-19 vulnerability (P, PD, HB, D, N, and ICU) see Table 1.\n\nThe overall methodological approach for developing of COVID-19 vulnerability map is as follows:\n\n1. Identify the criteria and assign weight for each criteria using AHP (consistency ratio must be ≤0.1).\n\n2. Later on, identify the sub-criteria within scale of 1-9.\n\n3. Input data to GIS and overlay summation process assigned\n\n4. Covid-19 vulnerability index (CVI)\n\n5. CVI through natural breaks (Jenks) in GIS was used to develop the COVID-19 vulnerability map.\n\n\nResult\n\nThe AHP pairwise comparison matrix approach, presented in Table 2, was employed to allocate weights for the various CVI criteria.26 Afterward, the consistency of these assigned weights was assessed by calculating a consistency ratio (CR) as follows.26\n\nCI: consistency index, RI: random consistency index that depends on the number of criteria, λ: maximum eigenvector of the matrix, and n: the number of criteria.\n\nTable 2 presents the Analytic Hierarchy Process (AHP) pairwise comparison matrix used to allocate weights for the various criteria related to the COVID-19 Vulnerability Index (CVI). The table showcases the relative importance of each criterion in assessing vulnerability, aiding in the prioritization and decision-making process for strategic interventions and resource allocation.\n\nThe permissible CR value must not surpass 0.1, in this research, a CR value of 0.06 was attained, indicating that the CVI criteria matrix demonstrates consistency.27\n\nIn the CVI map, every criterion was categorized into nine value classes, and each class was assigned a score ranging from 1 less important to 9 highly important.26 The chosen criteria were then converted into raster format and reclassified using various GIS tools (see Figure 2).\n\nGIS was utilized to calculate the CVI by employing the weighted overlay summation process.27 This involved aggregating the weighted cell values of various selected criteria. Each criterion’s input layer was multiplied by its respective weight, and the outcomes were combined through summation. In the end, the comprehensive CVI was computed using the natural breaks (Jenks) method in GIS. This CVI value was then employed to create the COVID-19 vulnerability map covering the entirety of the Surabaya city.\n\nThe COVID-19 vulnerability map for the Surabaya was designed (see Figure 3). This map classified the Surabaya districts into five distinct COVID-19 vulnerability categories, ranging from very low to very high. Additionally, Table 3 provides the population counts for each COVID-19 vulnerability class in the Surabaya city.\n\n\nDiscussion\n\nOngoing and resurging diseases that have the potential to become pandemics remain a persistent challenge for nations and healthcare systems, resulting in significant human and economic tolls. This underscores the importance of prioritizing global health readiness in the face of emerging epidemics. Enhancing healthcare infrastructure stands as the most effective safeguard against disease outbreaks and other health-related risks, making it a vital component of health security for all countries.28\n\nIn terms of demographic factors, districts like Simokerto, Wonokromo, Gubeng, Sawahan, Tambaksari, Bubutan, Tegalsari, Semampir, and Kenjeran are identified as being in very high to high vulnerability zones. These districts share a high population density. The study specifically selected districts with scores ranging from 7 to 9, which revealed that approximately 47% of Surabaya’s inhabitants are in a high vulnerability zone. On the other hand, related to nurse number to population indicates district of Sambikerep, Sawahan, Kenjeran, Rungkut, Jambangan, Bubutan, Gunung Anyar, Karang Pilang, Asemrowo, Bulak, and Krembangan are under high to very high vulnerable zone. More ever, related to number of doctors to population indicates districts of Jambangan, Sambikerep, Sukomanunggal, Sawahan, Bubutan, Rungkut, Kenjeran, Krembangan, Gunung Anyar, Karang Pilang, Asemrowo, and Bulak are under high to very high vulnerable zone. The criteria of nurses and doctors play a crucial role in responding to an emergency outbreak. However, these factors suffer from a shortage of doctors and nurses to effectively manage any outbreak.\n\nMeanwhile, districts of Dukuh Pakis, Tandes, Semampir, Lakarsantri, Sambikerep, Jambatan Bubutan, Karang Pilang, Gunugng Anyar, Rungkut, Sawahan, Asemrowo, Krembangan, Kenjeraan, and Bulak are under high to very high vulnerable zone because of bed hospital to population in districts. The study selected districts with scores ranging from 7 to 9 only. This revealed that 15 districts, accounting for 47.8% of the total population, have a shortage of hospital beds. This highlights a high vulnerability for the city of Surabaya in the event of a potential emergency outbreak.\n\nHowever districts of Pakal, Tegalsari, Tenggilis Mejoyo, Lakarsantri, Dukuh Pakis, Karang Pilang, Jambangan, Gunung Anyar, Rungkut, Bulak, Kenjeran, Semampir, Krembangan, Bubutan Asemrowo, Tandes, and Sambilerep are in a highly vulnerable zone due to the ICU capacity in relation to the district’s population. The study selected districts with scores ranging from 7 to 9, revealing that 17 districts have an ICU shortage. This highlights a high vulnerability for the city of Surabaya in the event of a potential emergency outbreak.\n\nThe vulnerability map of Surabaya, as depicted in Figure 3 plays a crucial role in assessing the city’s preparedness for a potential emergency outbreak. By identifying districts within Surabaya that exhibit high vulnerability, especially those with high population density and other relevant criteria, this map serves as an essential tool for understanding where vulnerabilities are most pronounced. In the context of a potential emergency outbreak, such as a public health crisis or a natural disaster, areas with high vulnerability, as indicated on the map, may face greater challenges in responding to and managing the crisis effectively. These challenges could include a shortage of healthcare facilities, limited access to medical resources, overcrowding, and socioeconomic factors that hinder residents’ ability to cope with emergencies.\n\n\nConclusion\n\nIn this research, a vulnerability map was created for the Surabaya using CVI values derived through GIS-based MCDA. Six significant factors were chosen, Weightings for these factors were determined using the AHP pairwise comparison matrix. The GIS was employed to categorize Surabaya’s CVI values into five COVID-19 vulnerability levels: very low, low, medium, high, and very high.\n\nThe information provided by this map empowers decision-makers, healthcare professionals, and disaster management teams to allocate resources strategically, implement targeted interventions, and develop comprehensive response strategies tailored to the specific needs of vulnerable districts. By doing so, Surabaya can enhance its resilience and preparedness, ultimately safeguarding the well-being of its residents in the face of potential emergency outbreaks.", "appendix": "Data availability statement\n\nThe data for this study owned by the Ministry of Health Republic Indonesia, it can be obtained through the following link; https://sirs.kemkes.go.id/fo/home/profile_rs/1171015.\n\nFighshare: STROBE Checklist for “Mapping vulnerability to potential crisis events in Surabaya city: A GIS-based approach”, https://doi.org/10.6084/m9.figshare.25598073.v1. 29\n\nLicence: CC BY 4.0.\n\n\nAcknowledgements\n\nThe authors would like to thank the health district office in the City of Surabaya for insightful suggestions and advice.\n\n\nReferences\n\nWHO: Coronavirus Disease 2019 (COVID-19): Situation Report-72.2020.\n\nWHO: Coronavirus Disease 2019 (COVID-19): Situation Report-91.2020.\n\nShadeed S, Alawna S: GIS-based COVID-19 vulnerability mapping in the West Bank, Palestine. Int. J. Disaster Risk Reduct. 2021; 64(January): 102483. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGralinski LE, Menachery VD: Return of the coronavirus: 2019-nCoV Viruses.2020; 12: 135.\n\nWHO: Novel Coronavirus (2019-nCoV): Situation Report-1.2019.\n\nPalaiologou P, Ager AA, Nielsen-Pincus M, et al.: Social vulnerability to large wildfires in the western USA. Landsc. Urban Plan. 2019; 189: 99–116. Publisher Full Text\n\nRufat S, Tate E, Burton CG, et al.: Social vulnerability to floods: a review of case studies and implications for measurement. Int. J. Disaster Risk Reduct. 2015; 14(4): 470–486. Publisher Full Text\n\nSurabaya Municipality: Surabaya Municipality in Statistics 2022.Reference Source\n\nRamchand R, Seelam R, Parks V, et al.: Exposure to the Deepwater Horizon Oil Spill, associated resource loss, and long-term mental and behavioral outcomes (2019). Disaster Med. Public Health Prep. 2019; 13: 889–897. PubMed Abstract \| Publisher Full Text\n\nAcharya R, Porwal A: A vulnerability index for the management of and response to the COVID-19 epidemic in India: an ecological study. Lancet Glob. Health. 2020; 8: e1142–e1151. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLancet T: Redefining vulnerability in the era of COVID-19 (2020). Lancet. 2020; 395: 1089. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHoland IS, Lujala P, Rød JK: Social vulnerability assessment for Norway: a quantitative approach. Nor. Geogr. Tidsskr. 2011; 65(1): 1–17. Publisher Full Text\n\nFlanagan BE, Hallisey EJ, Adams E, et al.: Measuring community vulnerability to natural and anthropogenic hazards: the centers for disease control and prevention’s social vulnerability index. J. Environ. Health. 2018; 80: 34–36. PubMed Abstract\n\nChretien JP, George D, Shaman J, et al.: Influenza forecasting in human populations: a scoping review. PLoS One. 2014; 9(4): e94130. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSangiorgio V, Parisi F: A multicriteria approach for risk assessment of Covid-19 in urban district lockdown. Saf. Sci. 2020; 130: 104862. Publisher Full Text\n\nSchoeman D, Fielding BC: Coronavirus envelope protein: current knowledge. Virol. J. 2019; 16(1): 69. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMacharia PM, Joseph NK, Okiro EA: A vulnerability index for COVID-19: spatial analysis at the subnational level in Kenya. BMJ Public Heal. 2020; 5.\n\nMeraj G, Farooq M, Singh SK, et al.: Coronavirus pandemic versus temperature in the context of Indian subcontinent: a preliminary statistical analysis. Environ. Dev. Sustain. 2021; 23(4): 6524–6534. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSaaty T: A scaling method for priorities in hierarchical structures. J. Math. Psychol. 1977; 15: 234–281. Publisher Full Text\n\nCox R, Sanchez J, Revie CW: Multi-Criteria Decision Analysis Tools for Prioritising Emerging or Re-Emerging Infectious Diseases Associated with Climate Change in Canada. PLoS One. 2013; 8(8): e68338. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPaul MC, Goutard FL, Roulleau F, et al.: Quantitative assessment of a spatial multicriteria model for highly pathogenic avian influenza H5N1 in Thailand, and application in Cambodia. Sci. Rep. 2016; 6(August): 1–10. Publisher Full Text\n\nKanga S, Sudhanshu MG, Farooq M, et al.: Reporting the management of COVID-19 threat in India using remote sensing and GIS based approach. Geocarto Int. 2020; 37: 1337–1344. Publisher Full Text\n\nRanga V, Pani P, Kanga S, et al.: National Health-GIS Portal-A Conceptual Framework for Effective Epidemic Management and Control in India.2020.\n\nKanga S, Meraj G, Singh SK, et al.: Analyzing the Risk to COVID-19 Infection using Remote Sensing and GIS. Risk Anal. 2021; 41(5): 801–813. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nIndonesian Ministry of Health: Annual Indonesian Health Profile.2021. Reference Source\n\nSaaty TL: The Analytic Hierarchy Process: Planning, Priority Setting, Resource Allocation. McGraw-Hill International Book Co.; 1980.\n\nMalczewski J: GIS and Multi-Criteria Decision Analysis. Wiley; 1999; 392.\n\nIhekweazu C, Agogo E: Africa’ s response to COVID-19.2020; 18–20.\n\nJarghon A: Vulnerability mapping. Dataset. figshare. 2024. Publisher Full Text" }	[ { "id": "276920", "date": "30 May 2024", "name": "Peiman Ghasemi", "expertise": [ "Reviewer Expertise Disaster 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\nHow did the COVID-19 outbreak evolve into a pandemic, and what were its severe health implications globally? Where was the initial COVID-19 case identified, and how quickly did the virus spread to other countries? In the introduction, you need to connect the state of the art to your paper goals. Please follow the literature review by a clear and concise state of the art analysis. This should clearly show the knowledge gaps identified and link them to your paper goals. Please reason both the novelty and the relevance of your paper goals. Clearly discuss what the previous studies that you are referring to. What are the Research Gaps/Contributions? Please note that the paper may not be considered further without a clear research gap and novelty of the study. Literature Review has the chance to be further improved: it seems that the authors have made the retrospection. However, via the review, what issues should be addressed? What is the current specific knowledge gap? What implication can be referred to? The above questions should be answered. Authors need to propose their study and compare your study with efficient crisis management by selection and analysis of relief centers in disaster integrating GIS and multicriteria decision methods, evaluating the efficiency of relief centers in disaster and epidemic conditions using multi-criteria decision-making methods and GIS: A case study, evaluating the performance of emergency centers during coronavirus epidemic using multi-criteria Decision-making methods, data-driven modeling using system dynamics simulation to provide relief in earthquake based on different scenarios What role does population vulnerability play in crisis situations like the COVID-19 outbreak? How does social vulnerability contribute to the impact of disasters, and how can government responses exacerbate or alleviate these vulnerabilities? What methods are commonly used for vulnerability mapping, especially concerning health-related crises like COVID-19? How does Geographic Information Systems (GIS) aid in assessing vulnerability, particularly in the context of epidemic prediction mapping? What factors were considered in developing the COVID-19 Vulnerability Index (CVI) for Surabaya, and how were weights assigned to these factors? How does the vulnerability map of Surabaya help decision-makers identify and address potential COVID-19 outbreaks, especially in high-risk areas?\n\nIs the work clearly and accurately presented and does it cite the current literature? No\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNo\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "11920", "date": "05 Jul 2024", "name": "Ali Jarghon", "role": "Author Response", "response": "Author response: Thank you so much for your comments, I have corrected/ added upon your request. How did the COVID-19 outbreak evolve into a pandemic, and what were its severe health implications globally? Author response: Thank you so much for your comment, I have corrected/ added upon your request from line 2-4 in red font Where was the initial COVID-19 case identified, and how quickly did the virus spread to other countries? Author response: Thank you so much for your comment, I have corrected/ added upon your request from line 6-8 What are the Research Gaps/Contributions?/ Clearly discuss what the previous studies that you are referring to. Author response: Thank you so much for your comment, I have corrected/ added upon your request from line 43- 49 What role does population vulnerability play in crisis situations like the COVID-19 outbreak? Author response: Thank you so much for your comment, I have corrected/ added upon your request from line 21-27 How does social vulnerability contribute to the impact of disasters, and how can government responses exacerbate or alleviate these vulnerabilities? Author response: Thank you so much for your comment, I have corrected/ added upon your request from line 21-27 What methods are commonly used for vulnerability mapping, especially concerning health-related crises like COVID-19? Author response: Thank you so much for your comment, I have corrected/ added upon your request from line 33-37 How does Geographic Information Systems (GIS) aid in assessing vulnerability, particularly in the context of epidemic prediction mapping Author response: Thank you so much for your comment, I have corrected/ added upon your request from line 50- 53 What factors were considered in developing the COVID-19 Vulnerability Index (CVI) for Surabaya, and how were weights assigned to these factors? Author response: Thank you so much for your comment, I have corrected/ added upon your request from line (78-81), (116-121) How does the vulnerability map of Surabaya help decision-makers identify and address potential COVID-19 outbreaks, especially in high-risk areas? Author response: Thank you so much for your comment, I have corrected/ added upon your request from line 163-171 Authors need to propose their study and compare your study with efficient crisis management by selection and analysis of relief centers in disaster integrating GIS and multicriteria decision methods, evaluating the efficiency of relief centers in disaster and epidemic conditions using multi-criteria decision-making methods and GIS: A case study, evaluating the performance of emergency centers during coronavirus epidemic using multi-criteria Decision-making methods, data-driven modeling using system dynamics simulation to provide relief in earthquake based on different scenarios Author response: Thank you so much for your comment, I have corrected/ added upon your request from line 173- 183" } ] }, { "id": "276913", "date": "07 Jun 2024", "name": "Subham Roy", "expertise": [ "Reviewer Expertise Spatial analysis", "GIS", "Remote Sensing" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nClearly state why Surabaya was chosen for this study. For instance, mention the specific challenges Surabaya faces that make it a critical area for vulnerability mapping. Highlight the expected outcomes of the study, such as identifying high-risk areas for targeted interventions. Add overall methodological flowchart for better understanding to the readers. Provide specific details on the selection criteria for the six key factors influencing vulnerability. Mention the tools and techniques used in the GIS analysis and how the Analytic Hierarchy Process (AHP) was applied. Include specific data points or notable trends found in the results. For example, state the percentage of the city classified as high vulnerability and the key factors contributing to this classification. Expand the literature review to include a broader range of studies related to vulnerability mapping and GIS-based MCDA. Discuss different methodologies and their findings, and how they relate to your study. Clearly identify the gaps in the existing literature that your study aims to fill. Articulate the novelty and significance of your research objectives. For instance, if previous studies have not focused on the integration of certain criteria or regions, highlight this as a gap your study addresses. Include more studies that have used similar methodologies or have focused on similar objectives (Add the literature in table format). Discuss the strengths and limitations of these studies to provide a comprehensive background for your research. Critically analyze the existing literature by highlighting the methodologies, findings, and gaps. Explain how your study builds on or diverges from these studies. For example, compare the use of different GIS techniques or criteria in vulnerability mapping. Provide a detailed explanation of how the AHP process was applied, including the steps taken to ensure the consistency ratio was ≤0.1. Describe how the pairwise comparison matrix was constructed and used to assign weights. Clearly describe the sources of your data, including any databases, surveys, or other sources. Explain how the data was collected and any limitations or biases that may affect the results. Elaborate on the GIS techniques used in your study. Explain the weighted overlay summation process and the natural breaks (Jenks) method in more detail. Provide a step-by-step description of how these techniques were applied to create the vulnerability map. Present the results with detailed explanations of the tables and figures. For example, explain what Table 2 and Figure 2 show and how they contribute to the overall findings. Provide context for the data presented in these tables and figures. Try to validate the results using statistical methods like R2, MAE, RMSE, ROC Curve etc. Ensure the statistical analysis is robust and clearly interpreted. Provide more details on the consistency ratio calculation and its significance. Explain how the weights were validated and the implications of the statistical findings. Discuss the practical implications of your findings for disaster management and public health preparedness. Provide specific recommendations for policymakers, healthcare professionals, and emergency responders based on your findings. Summarize the main findings of the study, highlighting the key contributions to the field. For example, state how the vulnerability map can be used to improve emergency preparedness in Surabaya. Emphasize the practical implications of the findings for policymakers and emergency preparedness. For example, discuss how the findings can inform resource allocation and strategic planning\n\nIs the work clearly and accurately presented and does it cite the current literature? No\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? No", "responses": [ { "c_id": "11921", "date": "05 Jul 2024", "name": "Ali Jarghon", "role": "Author Response", "response": "Author response: Thank you so much for your comment, I have corrected/ added upon your request. 1. Clearly state why Surabaya was chosen for this study. For instance, mention the specific challenges Surabaya faces that make it a critical area for vulnerability mapping. Highlight the expected outcomes of the study, such as identifying high-risk areas for targeted interventions. Author response: Thank you so much for your comment, I have corrected/ added upon your request from line 57- 60 in red font 2. Add overall methodological flowchart for better understanding to the readers. Author response: Thank you so much for your comment, I have corrected/ added upon your request. Figure 2. 3. Provide specific details on the selection criteria for the six key factors influencing vulnerability. Mention the tools and techniques used in the GIS analysis and how the Analytic Hierarchy Process (AHP) was applied. Author response: Thank you so much for your comment, I have corrected/ added upon your request from line78-81 4. Include specific data points or notable trends found in the results. For example, state the percentage of the city classified as high vulnerability and the key factors contributing to this classification. Author response: Thank you so much for your comment, I have corrected/ added upon your request from line1(39-142), (153-156) 5. Expand the literature review to include a broader range of studies related to vulnerability mapping and GIS-based MCDA. Discuss different methodologies and their findings, and how they relate to your study. Author response: Thank you so much for your comment, I have corrected/ added upon your request from line 36- 49 6. Clearly identify the gaps in the existing literature that your study aims to fill. Articulate the novelty and significance of your research objectives. For instance, if previous studies have not focused on the integration of certain criteria or regions, highlight this as a gap your study addresses Author response: Thank you so much for your comment, I have corrected/ added upon your request from line 36-49 7. Include more studies that have used similar methodologies or have focused on similar objectives (Add the literature in table format). Discuss the strengths and limitations of these studies to provide a comprehensive background for your research. Author response: Thank you so much for your comment, I have corrected/ added upon your request from line 36-49 8. Critically analyze the existing literature by highlighting the methodologies, findings, and gaps. Explain how your study builds on or diverges from these studies. For example, compare the use of different GIS techniques or criteria in vulnerability mapping. Author response: Thank you so much for your comment, I have corrected/ added upon your request from line 36-49 9. Provide a detailed explanation of how the AHP process was applied, including the steps taken to ensure the consistency ratio was ≤0.1. Describe how the pairwise comparison matrix was constructed and used to assign weights. Author response: Thank you so much for your comment, I have corrected/ added upon your request from line 93-110 10. Clearly describe the sources of your data, including any databases, surveys, or other sources. Explain how the data was collected and any limitations or biases that may affect the results. Author response: Thank you so much for your comment, I have corrected/ added upon your request from line 82 11. Elaborate on the GIS techniques used in your study. Explain the weighted overlay summation process and the natural breaks (Jenks) method in more detail. Provide a step-by-step description of how these techniques were applied to create the vulnerability map. Author response: Thank you so much for your comment, I have corrected/ added upon your request Summarized in Figure2 12. Present the results with detailed explanations of the tables and figures. For example, explain what Table 2 and Figure 2 show and how they contribute to the overall findings. Provide context for the data presented in these tables and figures. Author response: Thank you so much for your comment, I have corrected/ added upon your request from line 101-110 13. Try to validate the results using statistical methods like R2, MAE, RMSE, ROC Curve etc. Author response: Thank you so much for your comment, This study utilizes spatial analysis and GIS to predict areas at risk based on collected data. Our approach identifies weaknesses by geographical location, ranking areas from most to least vulnerable according to the weighted results of each parameter. Ultimately, the findings are presented in the form of a map. 14. Ensure the statistical analysis is robust and clearly interpreted. Provide more details on the consistency ratio calculation and its significance. Explain how the weights were validated and the implications of the statistical findings. Author response: Thank you so much for your comment, I have corrected/ added upon your request from line 106 15. Discuss the practical implications of your findings for disaster management and public health preparedness. Provide specific recommendations for policymakers, healthcare professionals, and emergency responders based on your findings. Author response: Thank you so much for your comment, I have corrected/ added upon your request from line 173- 183 16. Summarize the main findings of the study, highlighting the key contributions to the field. For example, state how the vulnerability map can be used to improve emergency preparedness in Surabaya. Author response: Thank you so much for your comment, I have corrected/ added upon your request from line 163- 172 17. Emphasize the practical implications of the findings for policymakers and emergency preparedness. For example, discuss how the findings can inform resource allocation and strategic planning Author response: Thank you so much for your comment, I have corrected/ added upon your request from line173-183" } ] } ]	1	https://f1000research.com/articles/13-465
https://f1000research.com/articles/11-913/v1	08 Aug 22	{ "type": "Systematic Review", "title": "Probiotic effect in preterm neonates with sepsis - A systematic review protocol", "authors": [ "Faiza Iqbal", "N Siva", "Manasa Kolibylu Raghupathy", "Leslie Edward S Lewis", "Apurv Barche", "Jayashree Purkayastha", "Baby S Nayak", "Faiza Iqbal", "N Siva", "Manasa Kolibylu Raghupathy", "Leslie Edward S Lewis", "Apurv Barche", "Baby S Nayak" ], "abstract": "Background: The microbiota in the intestine is made up of trillions of living bacteria that coexist with the host. Administration of antibiotics during neonatal infection causes depletion of gut flora resulting in gut dysbiosis. Over the last few decades, probiotics have been created and promoted as microbiota management agents to enrich gut flora. Probiotics decrease the overgrowth of pathogenic bacteria in the gut of preterm neonates, reducing the frequency of nosocomial infections in the Neonatal Intensive Care Unit (NICUs). Methods: The systematic review will include randomized control trials (RCTs) of premier neonates with sepsis. Studies will be retrieved from global databases like Cochrane CENTRAL, CINAHL Plus via EBSCO host, MEDLINE via PubMed, EMBASE, SCOPUS, Ovid, Web of Science, ProQuest Medical Library, Microsoft academic, and DOAJ by utilizing database-specific keywords. Screening, data extraction, and critical appraisal of included research will be carried out separately by two review writers. Findings will be reported in accordance with the PRISMS-P 2020 guidelines. Conclusions: The findings of this systematic review will help to translate the evidence-based information needed to encourage the implementation of potential research output in the field of neonatal intensive care, guide best clinical practise, assist policy making and implementation to prevent gut dysbiosis in neonates with sepsis by summarising and communicating the evidence on the topic. PROSPERO registration number: This systematic review protocol has been registered in PROSPERO (Prospective Register of Systematic Reviews) on 10th March 2022. The registration number is CRD42022315980.", "keywords": [ "Probiotics", "Preterm", "Neonatal Sepsis", "Gut health", "Mortality", "Morbidity", "Growth" ], "content": "Introduction\n\nAccording to the Global Burden of Disease (GBD), there are 1.3 million yearly incident cases of neonates sepsis and associated infections (about 937 instances per 100,000 live births) and 203,000 sepsis-related neonatal deaths.1 A preterm infants’ immature intestine predisposes it to infection and inflammation, as it has immature immunity, barrier function, and peristalsis resulting in gut dysbiosis.2 Co-morbidities like c-section deliveries, antenatal and post-natal antibiotic exposure, parenteral nutrition and prolonged stays in a neonatal intensive care unit (NICU), lead to a rapid decrease in taxonomic richness and diversity of good commensal gut bacteria contributing to the loss of colonization resistance.3,4\n\nThe gut is the centre of microbial activity; it is essential to address neonatal microbiota dysbiosis as many of the events like period of gestation, method of delivery, dietary patterns, weaning and antibiotic administration play an important role in framing gut flora and may have an impact on long term health outcomes.5,6 The host and gut microbiota have unique and cryptic interlinkage; the formation of an individual’s gut microbiota starts right from birth and is shaped by various factors. Starting from birth, the gut microbiota plays three critical roles: protective, metabolic, and trophic.5 Gut flora carries out their effects by modulating immunologic, endocrine, and neurological pathways.7\n\nThe gut also serves as a significant source of noninflammatory immune stimulators in healthy people throughout their lives. However, these beneficial health-promoting factors of the gut microbiota are not infallible and can be altered due to dysbiosis or neonatal infection. Numerous studies have shown that antibiotic consumption causes dysbiosis and disturbance of the gut microbiome in infants, children and adults.8,9 Probiotics have been shown to improve the gut health of preterm infants.9–11 Probiotics are defined by the World Health Organization as “live microorganisms that give a health benefit to the host when supplied in sufficient concentrations”.12 Probiotics can enhance your immune system while preventing the formation of pathogenic gut bacteria.13\n\nA shift in the composite microbiota system has increased disease risk.6 The use of probiotics facilitates the restoration of the gut microbial profile. It may protect high-risk neonates by preventing the movement of microbes and microbial metabolites across the mucosa, elimination of pathogenic organisms, modifying host reactions to microbial supplements and enhancing nutrition by upregulation of immune response.14,15 A relative reduction in the Bifidobacteriaceae counts and an increase in Enterobacteriaceae and Clostridiaceae may be a good criterion to define dysbiosis in the initial months of life.11,16 It can also explain gut colonization between birth, which can serve as the basis for introducing nutritional strategies targeted at the microbiota.\n\nThese nutritional interventions, based mainly on probiotics, may be used for favourably altering the gut microbiome and preventing neonatal sepsis. Dysbiosis of the gut microbiome invites the expansion of the pathobiont population, leading to sepsis in neonates.17 Probiotic supplementation aims to rebuild the gut bacteria, preventing necrotizing enterocolitis (NEC), infection and other problems. The initial days of life are crucial for an adequate microbiome that facilitates gut maturation and neonatal health. Therefore, strategies focused primarily on establishing microbiota and consuming probiotic supplements that can help balance the gut microbiota composition, improve well-being, and lower disease risk in neonates.\n\nProbiotics supplements help revive the disrupted gut microbiota and prevent gut inflammation and other intestinal diseases.18 Probiotics decrease the overgrowth of pathogenic bacteria in the gut of preterm neonates, reducing the frequency of nosocomial infections in the Neonatal Intensive Care Unit (NICU).19 According to systematic evaluations of randomized controlled trials (RCT), probiotics have substantial potential to lower mortality and morbidity in premature neonates. A systematic assessment of RCT narrated the benefits of probiotics in low- and middle-income countries.11 The supplements may restore the composition of the gut microbiome and introduce beneficial functions to gut microbial communities. According to recent randomized controlled research, early probiotic use may have the capacity to alter the gut flora during antibiotic treatment recovery.20\n\nProbiotics are becoming more well acknowledged as a valuable tool for promoting health and preventing adverse health outcomes in premature neonates.21,22 They may protect high-risk neonates by increasing the barrier for migration of bacteria and their products across the mucosa, by elimination of potential pathogens, by modifying host response to microbial products, and enhancing nutrition by upregulation of the immune response.23 This study aims to evaluate the effect of probiotics on the gut health and growth of preterm infants in neonates with sepsis. We hypothesized that the administration of specific probiotics could improve the gut microbiota of preterm neonates by lowering the risk of morbidity and mortality with sepsis.\n\nOver the last few decades, probiotics have been created and promoted as microbiota management agents to enrich gut flora. Early life is a crucial time for the gut of neonates to be gradually colonised with different species of bacteria that collectively promote initial gut maturation. Bacterial diversity in preterm neonates is low and comparatively different from term neonates.18 Probiotic supplements may help to restore the gut microbiome composition and introduce beneficial functions to gut microbial communities, resulting in the improvement or prevention of inflammation of the gut and other phenotypes of systemic or intestinal diseases.24\n\nProbiotic supplement in preterm has been proven to decrease pathogen overgrowth and promote the maturation of the intestinal mucosa by facilitating the growth and proliferation of probiotic bacteria in the intestinal tract.25 Antibiotic exposure was observed to significantly alter gut microbiota, with a considerable reduction in Bifidobacterium and Lactobacillus, according to Zhong et al., 2021.20 The administration of probiotics concurrently with antibiotics was more advantageous to the gut microbiota than waiting until after antibiotic therapy to use probiotics, especially in terms of increasing Bifidobacterium abundance.20 Pneumonia and sepsis accounted for 46% of all admission diagnoses and were attributed to 29% of the overall death rate, compared to 26% globally.26\n\nThe mode of delivery influences the gut microbial pattern. Several high-quality studies suggest that bacterial diversity differs among babies based on the mode of delivery. Neonates born by vaginal delivery swallow the vaginal bacteria on their way down the birth canal, which results in the primary source for initial seeding of microbiota to the neonatal gut. Over the initial year of life, there is an abundance of Bifidobacterium spp. and a decrease of Enterococcus spp. and Klebsiella spp.27 Microbiota of caesarean section neonates show distinctly different gut flora than vaginally delivered infants and are more likely to have skin, breastmilk, oral and environmental bacteria.28\n\nInfections spread rapidly in preterm infants, resulting in severe disease and death; therefore, infection prevention directly reduces neonatal morbidity and mortality. In a systematic review conducted by Balasubramanian et al. among preterm infants in India, metanalysis showed a significantly lower risk in blood culture positive Late-Onset Sepsis (LOS) after 48 hours of birth in the probiotic group (p < 0.001).22 A double-blinded, placebo-randomized controlled trial was conducted using Bacillus clausii to prevent LOS in 244 preterm infants. Of that, 120 were extremely preterm neonates, of which 59 received a placebo and 61 received probiotics. On other hand, 124 babies were stratified as preterm, 61 neonates received a placebo and 61 received probiotics. The study concluded that prophylactic administration of B. clausii to preterm neonates did not result in a significant difference in LOS incidence compared with placebo.29\n\nThe gut microbiome is a complex and dynamic population of hundreds of bacteria responsible for transporting nutrition, controlling intestinal epithelial maturation, and building an innate immune defence in neonates. An RCT was conducted by Panigrahi et al. to prevent sepsis among rural Indian neonates. Researchers used Lactobacillus plantarum plus fructooligosaccharide as a probiotic on 4,556 neonates of birthweight < 2000 grams, gestational age ≥ 35 weeks with no sign of sepsis and morbidity and were recruited and monitored for 60 days; a significant decrease in neonatal sepsis (culture-positive sepsis, culture-negative sepsis) and lower respiratory tract infections were observed. The study’s findings suggested that neonatal sepsis in developing countries could be effectively prevented using a symbiotic containing L. plantarum ATCC-202195.30 The findings of this systematic review would definitively answer whether early administration of specific probiotics could improve the gut microbiota of preterm neonates by lowering the risk of infant morbidity and mortality in neonates with sepsis, and assist healthcare providers and policymakers in developing a probiotic supplement guideline for sepsis neonates.\n\n\nMethods\n\nAs this is a systematic review protocol, ethical approval is not required as we will not be directly involving human participants.\n\nHow effective is probiotics on gut health, lowering the risk of morbidity and mortality among preterm neonates with sepsis?\n\nTo identify the effect of probiotics on improving gut health of preterm neonates with sepsis.\n\nTo determine the impact of probiotics on lowering the risk of morbidity and mortality among preterm neonates with sepsis.\n\nWe will systematically review existing randomized and non-randomized control trial studies and execute a meta-analysis when acceptable data is available. This protocol follows the recommendations of the Preferred Reporting Items for Systematic Review and Meta-Analyses of Protocols (PRISMA-P) 2015.40 The Participants, Interventions, Comparators and Outcomes elements used for the systematic review are listed in Table 1.\n\nNICU: Neonatal Intensive Care Unit; NRCT’s: Non- randomized controlled trials.\n\nA comprehensive search would be conducted in global databases like Cochrane CENTRAL, CINAHL Plus via EBSCO host, MEDLINE via PubMed, EMBASE, SCOPUS, Ovid, Web of Science, ProQuest Medical Library, Microsoft academic, and DOAJ. by utilizing the stated search keywords: “Premature neonates”, “Preterm birth”, “Very low birth weight”, “Low birth weight”, Preterm, “Preterm infants”, “extremely low birth weight”, “Neonates”, “Neonatal infection”, Infection, “Late-onset sepsis”, “Early-onset sepsis”, Sepsis, “Neonatal period”, “intestinal infection”, “Nosocomial infection”, septicaemia, Bacteraemia, “septic shock”, probiotic, “Probiotic supplement”, Lactobacilli, Lactobacillus, Bifidobacterium, “Lactic acid bacteria”, Bacillus OR “Probiotic therapy”, “Randomized Controlled Trial”, and “Non- randomized controlled trial” (Extended data38).\n\nAdditional references will be found in the reference lists of all primary research and review papers. To get necessary supplementary information, we will reach out to relevant field experts and researchers from the included papers. For data management, records will be exported to EndNote X7.\n\nTwo review authors (FI, SN) shall execute independent searches of the study titles and abstracts of the indicated study sources. We shall exclude the articles which do not meet the inclusion criteria. If there is a disagreement among those reviewers, it will be resolved through conversation, and the complete text will be examined. Two reviewers will independently assess the included abstracts as “include” or “exclude” after obtaining the whole manuscript. If required, we will work with a supervisory review author (LEL) to address any disagreements. We will keep track of why the articles were refused. We will look for and eliminate duplicates and compile numerous reports from the same research.\n\nData will be extracted by examining general features such as gestational age, research participants, setting, identifiers, type of pathogen isolated, LOS, early-onset sepsis (EOS), type of probiotic, study selection criteria, and results. To organize the list of intervention parameters to assist intervention replication and research comparability, we will use the TIDier checklist (Template for Intervention Description and Replication).31 Additionally, we will extract data of specific characteristics such as type of probiotic used, dosage, antibiotic exposure, gestational age, type of delivery and trend of weight gain. Two review authors will independently use the data extraction templates to abstract the data from included articles in the review. The included studies will have the following data collected: research title and authors, sample size, study setting, intervention features, assessment procedures, outcomes, findings, conclusions, and year of publication. If there is a disagreement, we will discuss it until we reach an agreement, or we will handle it with the assistance of a third reviewer (MKR).\n\nWe will assess the quality of included randomized controlled trials using the Revised Cochrane Risk of Bias Tool (RoB 2.0). The RoB 2.0 tool considers the following factors: a) The randomization method, b) deviation from the planned intervention, c) outcome measurement, d) missing outcomes, and e) selective reporting. Two authors will independently evaluate each paper. RCT risk will be assessed and classified into three categories: low risk, high risk, and some concerns.32 To assess the quality of the included non-randomized controlled trials, we will use the Joanna Briggs Institute (JBI) Critical Appraisal Checklist. If there is any disagreement, we will solve it by contacting a methodology expert (BSN).\n\nWe will contact the primary authors whenever possible to obtain the missing data. The most important empirical data, including screening, randomization, intention-to-treat, as-treated, and per-protocol groups, will be investigated thoroughly. The article will be excluded from the review if the authors do not respond within two weeks after communicating through email. If this is not possible, we will consider the missing data a major bias, and the article will be removed from consideration.\n\nIf possible, sub-group analysis will be carried out based on the neonatal gestational age (extremely preterm, very preterm, moderate preterm and late preterm) and study period.\n\nTwo independent reviewers (FI and SN) will extract the data from each study and enter it into a Microsoft Excel file Version 16.61. Preferred Reporting Items for Systematic Review and Meta-analysis (PRISMA) standards will be used to provide evidence regarding the effect of probiotics on the gut health of preterm neonates with sepsis (Extended data39).33 The GRADE (Grading of Recommendations Assessment, Development, and Evaluation) approach will be employed to assess the quality of evidence in the included articles. The quality of the information is rated as a four-point scale, high, moderate, low, and very low. If there is sufficient homogeneity in study design and study subjects among the selected studies, meta-analyses will be conducted.34 As a result, continuous and dichotomous outcomes will be integrated for meta-analysis purposes. Statistical analyses will be conducted with the help of the Cochrane Review Manager (RevMan 5).\n\nSensitivity analysis will be performed to investigate the robustness of the results by examining the effects of including and excluding studies with a high risk of bias and studies with missing data. The results’ robustness will be evaluated using a variety of impact size measures, such as risk ratio and odds ratio, and various statistical models, such as fixed effects and random-effects models.\n\n\nDiscussion\n\nThe microbiota in the intestine is made up of trillions of living bacteria that coexist with the host. Depleting gut microflora in neonates, especially in vulnerable preterm neonates, may elevate the risk of neonatal infections resulting in administration of antibiotics.35 Although antibiotics are targeted to kill only pathogens, they may adversely affect commensals by destroying them or inhibiting their activity, resulting in gut dysbiosis. Probiotic supplementation has become increasingly popular in the fight against gut microbiota depletion.16,20,21\n\nA randomized control trial was conducted by Zhong et al. to assess the impact of probiotic supplements on 90 neonates with gestational age ≥ 37 weeks. The study concluded that antibiotics cause a decrease in the microbial richness and variety of the gut microbiota in neonates and the attenuation of several bacteria, especially Bifidobacterium and Lactobacillus.20 A significant reduction in newborn sepsis has been reported in randomized controlled trials (RCTs) of various probiotic strains and combinations given to preterm infants of different gestational ages and birth weights. Panigrahi et al., in their randomized control trial, examined the effect of probiotics in neonatal sepsis and showed a significant reduction in neonatal sepsis cases when supplemented with Lactobacillus plantarum.36 Costeloe et al. evaluated the effect of Bifidobacterium breve strain BBG-001 on the development of sepsis or NEC in very low birth weight neonates. At two weeks postnatal age, he observed B. breve colonisation in 1186 (94%) survivors. There were 85% in the probiotic group and 37% in the placebo group.37\n\nThis systematic review will include randomized controlled trials and all types of non-randomized control trials. Meta-analysis will be carried out with the results of RCTs, and narrative description will be used to analyse non-randomized control trials regarding the effect of probiotics among preterm neonates with sepsis. This review includes only the use of probiotics in preterm infants, excluding the studies that assessed the effect of prebiotics and synbiotics among preterm neonates. Only studies published in English will be included; thus, eligible studies published in other languages will be excluded.\n\n\nData availability\n\nNo underlying data are associated with this article\n\nFigshare: supplementary_file1.docx. https://doi.org/10.6084/m9.figshare.19839604.38\n\nThis project contains the following extended data:\n\n• Supplementary_File1.docx (Appendix 1- Search Strategy; Appendix 2 – Search Terms)\n\nFigshare: Supplementary file 2. https://doi.org/10.6084/m9.figshare.19839964.39\n\nThis project contains the following extended data:\n\n• Supplementary_file2.pdf (PRISMA flow chart of Systematic review)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nFigshare: PRISMA-P checklist for ‘Probiotic effect in preterm neonates with sepsis - A systematic review protocol’, https://doi.org/10.6084/m9.figshare.19839241.40\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).", "appendix": "References\n\nFleischmann C, Reichert F, Cassini A, et al.: Global incidence and mortality of neonatal sepsis: a systematic review and meta-analysis. 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Publisher Full Text\n\nZhong H, Wang XG, Wang J, et al.: Impact of probiotics supplement on the gut microbiota in neonates with antibiotic exposure: an open-label single-center randomized parallel controlled study. World J. Pediatr. 2021 Aug 1; 17(4): 385–393. PubMed Abstract \| Publisher Full Text\n\nNavarro-Tapia E, Sebastiani G, Sailer S, et al.: Probiotic Supplementation during the Perinatal and Infant Period: Effects on gut Dysbiosis and Disease. Nutrients. 2020 Jul 27; 12(8): 2243. PubMed Abstract \| Publisher Full Text\n\nBalasubramanian H, Ananthan A, Rao S, et al.: Probiotics for Preterm Infants in India – Systematic Review and Meta-Analysis of Randomized Controlled Trials. Indian J. Pediatr. 2020 Oct 1; 87(10): 817–825. PubMed Abstract \| Publisher Full Text\n\nBelkaid Y, Hand T: Role of the Microbiota in Immunity and inflammation. Cell. 2014 Mar 27; 157(1): 121–141. PubMed Abstract \| Publisher Full Text\n\nHemarajata P, Versalovic J: Effects of probiotics on gut microbiota: mechanisms of intestinal immunomodulation and neuromodulation. Ther. Adv. Gastroenterol. 2013 Jan; 6(1): 39–51. PubMed Abstract \| Publisher Full Text\n\nSeghesio E, De Geyter C, Vandenplas Y: Probiotics in the Prevention and Treatment of Necrotizing Enterocolitis. Pediatr. Gastroenterol. Hepatol. Nutr. 2021 May; 24(3): 245–255. Publisher Full Text\n\nBryce J, Boschi-Pinto C, Shibuya K, et al.: WHO Child Health Epidemiology Reference Group. WHO estimates of the causes of death in children. Lancet Lond Engl. 2005 Apr 26; 365(9465): 1147–1152. Publisher Full Text\n\nBäckhed F, Roswall J, Peng Y, et al.: Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life. Cell Host Microbe. 2015 May 13; 17(5): 690–703. PubMed Abstract \| Publisher Full Text\n\nKorpela K: Impact of Delivery Mode on Infant Gut Microbiota. Ann. Nutr. Metab. 2021 Aug 30; 1–9.\n\nTewari VV, Dubey SK, Gupta G: Bacillus clausii for Prevention of Late-onset Sepsis in Preterm Infants: A Randomized Controlled Trial. J. Trop. Pediatr. 2015 Oct; 61(5): 377–385. Publisher Full Text\n\nPanigrahi P, Parida S, Nanda NC, et al.: A randomized synbiotic trial to prevent sepsis among infants in rural India. Nature. 2017 Aug 24; 548(7668): 407–412. Publisher Full Text\n\nHoffmann TC, Glasziou PP, Boutron I, et al.: Better reporting of interventions: template for intervention description and replication (TIDieR) checklist and guide. BMJ. 2014 Mar 7; 348: g1687. PubMed Abstract \| Publisher Full Text\n\nSterne JAC, Savović J, Page MJ, et al.: RoB 2: a revised tool for assessing risk of bias in randomised trials. BMJ. 2019 Aug 28; 366: l4898. Publisher Full Text\n\nPage MJ, McKenzie JE, Bossuyt PM, et al.: The PRISMA 2020 statement: an updated guideline for reporting systematic reviews. BMJ. 2021 Mar 29; 372: n71. Publisher Full Text\n\nGuyatt GH, Oxman AD, Kunz R, et al.: What is “quality of evidence” and why is it important to clinicians? BMJ. 2008 May 3; 336(7651): 995–998. PubMed Abstract \| Publisher Full Text\n\nMadan JC, Salari RC, Saxena D, et al.: Gut microbial colonisation in premature neonates predicts neonatal sepsis. Arch Dis Child Fetal Neonatal Ed. 2012 Nov; 97(6): F456–F462. PubMed Abstract \| Publisher Full Text\n\nPanigrahi P, Parida S, Nanda NC, et al.: A randomized synbiotic trial to prevent sepsis among infants in rural India. Nature. 2017 Aug 24; 548(7668): 407–412. PubMed Abstract \| Publisher Full Text\n\nCosteloe K, Bowler U, Brocklehurst P, et al.: A randomised controlled trial of the probiotic Bifidobacterium breve BBG-001 in preterm babies to prevent sepsis, necrotising enterocolitis and death: the Probiotics in Preterm infantS (PiPS) trial. Health Technol. Assess. (Winch. Eng.). 2016 Aug; 20(66): 1–194. PubMed Abstract \| Publisher Full Text\n\nIqbal F, Siva N, Raghupathy MK, et al.: supplementary_file1.docx. figshare.2022 [cited2022Jun2]. Publisher Full Text\n\nIqbal F, Siva N, Raghupathy MK, et al.: Supplementary file 2. figshare.2022 [cited2022Jun2]. Publisher Full Text\n\nIqbal F, Siva N, Kolibylu Raghupathy M, et al.: PRISMA-P Checklist.docx. figshare.2022 [cited2022Jun2]. Publisher Full Text" }	[ { "id": "198892", "date": "14 Sep 2023", "name": "Cecile Leah T Bayaga", "expertise": [ "Reviewer Expertise My area of expertise is on clinical nutrition specifically chemical and microbiological composition of human milk." ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nGeneral Observation From my perspective, the paper is unfished. There are no results of the systematic review. The tense used is in the future; hence it will still be implemented.\nSpecific Observation Abstract Following the PRISMA guidelines, the abstract lacks the following details:\nExplicitly stated objective\n\nInclusion/Exclusion criteria\n\nMethods on how bias was lessened\n\nMethods on how data were synthesized\n\nNo major results and discussion\n\nNo mention of funding agency\nIntroduction First, majority of the systematic reviews published do not have subsections under this portion. Having sub sections probably is beneficial when the author writes the Introduction. However, reading is made smooth if there were no sub sections. Second, the specific objective which was supposed to be in this section was found in the Methods section. Last, the stated objective of the study does not jive with the stated hypothesis. The premise “growth of preterm infants” was included in the objective but absent in the hypothesis.\nMethods There is a need to refine the methods to indicate it has been implemented, make the connection seamless, and revise the statements to make them clearer.\nDiscussion There was no discussion as there were no results presented.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Partly\n\nAre sufficient details of the methods and analysis provided to allow replication by others? No\n\nIs the statistical analysis and its interpretation appropriate? No\n\nAre the conclusions drawn adequately supported by the results presented in the review? No", "responses": [ { "c_id": "10230", "date": "16 Nov 2023", "name": "Faiza Iqbal", "role": "Author Response", "response": "Dear Reviewer, Thank you for taking the time to review our systematic review protocol. We appreciate your feedback and would like to address your observation that the paper appears unfinished due to the absence of results and the use of future tense. It's essential to clarify that a systematic review protocol is a prelude to the actual systematic review. Protocols are written before the systematic review and data extraction phases commence, and they serve as a comprehensive plan that outlines the steps and procedures that will be followed during the review process. The use of future tense in the protocol is intentional and necessary because, protocols are typically written before starting the search and data extraction process. At this stage, the review team has not yet gathered and analyzed the data, so it would be premature to present any results. Instead, the protocol serves as a blueprint for the systematic review, detailing the research questions, eligibility criteria, search strategy, data extraction methods, and analysis plan. Rest assured that once the systematic review is completed, we will publish the results in a separate paper or report, where we will present and discuss our findings based on the data collected and analyzed during the review process. This follow-up publication will provide a comprehensive overview of the results and their implications. We hope this clarifies the purpose and scope of our systematic review protocol. We value your input and appreciate your understanding of the process. If you have any further questions or suggestions, please feel free to share them. Sincerely, Faiza Iqbal" } ] } ]	1	https://f1000research.com/articles/11-913
https://f1000research.com/articles/11-1085/v1	22 Sep 22	{ "type": "Review", "title": "The one-humped camel: The animal of future, potential alternative red meat, technological suitability and future perspectives", "authors": [ "Djamel Djenane", "Mohammed Aider", "Mohammed Aider" ], "abstract": "Camel meat is an ethnic food consumed across the arid regions. For these medicinal and nutritional benefits, it can be a great option for sustainable meat worldwide supply. Consumers can be benefit from the subtle taste of camel meat, flavored with aromatic and medicinal herbs from the arid regions. Research on the camel meat from both an economic and technological aspects is quite recent, which explains the limited information available on this area. Nevertheless, developing new preservation techniques as well the development of various products from camel meat through optimum processing constitute an axis of fu-ture scientific research in order to valorize this product. The camel meat as an alternative source to red meats is also discussed as well as the challenges of its acceptance by consumers. In light of the enthusiasm for this meat, to which many beneficial health effects are attributed, it seemed interesting to conduct this review.", "keywords": [ "Camelus dromedarius", "future food", "health claims", "alternative red meat", "Comprehensive review", "Health food" ], "content": "Introduction\n\nThe current enthusiasm for the consumption of camel meat as red meat is based in part on the therapeutic or medicinal virtues that are attributed to it. It is considered lean because it comes from animals fed on natural pastures, and responds to the strong “health claim” trend, which consists of limiting the consumption of red meats and animal fats.\n\nToday, multidisciplinary research is carried out on camel meat for the adoption of efficient production systems, the improvement of its transformation as well as its marketing. In recent years, various researchers have introduced new alternative preservation techniques applicable to all meats to maintain their quality (Djenane et al. 2020). This strategy would extend shelf life while ensuring product safety during distribution and subsequent retail display.\n\nThe camel sector is currently facing a gradual opening of borders to animal products. This come from countries where technical and regulatory developments have made it possible to promotion the camel meat industry and improve product quality. The camel sector must adapt to the transition towards a competitive economy to design and implement liberalization reforms in a context marked by agreements concluded between the countries. In arid regions, veterinary control focuses more on animal health compliance for healthy consumption. Despite the efforts made by the veterinary services to ensure safe meat, hygiene conditions remain insufficient (Yehia et al. 2021).\n\nThis review discusses the nutritional and qualitative properties of camel meat, explains its versatility and positive effects on human health. The current “health claims” situation of this product and the development prospects through a few technological suitability in progress, and future perspectives are also discussed. In addition, this review brings additional elements which we aim to summarize here. In addition to the knowledge acquired on camel meat, in the view of the most recent works, the current market situation for this product and development prospects will be presented.\n\n\nCamel populations (numbers) and distribution\n\nCamel is a polygastric animal, but it is often referred to as “pseudo-ruminant”. Because camels are migratory animals, the number of dromedaries is not known with precision given the drought episodes and the population movements that accompanied it. The world camel population exceeds 35 million heads (Faye, 2020). Camelus dromedarius is the most frequent and widespread domestic camel species composing 90% of the total camel population, whereas the two-humped Bactrian camel (Camelus bacterium) represents the remainder (10%).\n\nAustralia plays a special role, as much of the camel herds are kept in the wild. An environmental problem has arisen because of an abundant population that is continuously growing. To solve the problem, the Australian authorities opted for the mass destruction of feral camels. However, another suggested route was the promotion of the meat of this species on local and international markets (https://www.nintione.com.au).\n\n\nCamel meat specifications and consumer perception\n\nFor long periods, camel meat was considered a powerful marker of social, ethnic, and religious identities (Baba et al. 2021). Adopted from the beef specifications, the Central Australian Camel Industry Association Inc., presents the camel meat specifications at its website (http://www.australiancamelindustry.com.au), and some authors have claimed that the adoption of these specifications greatly facilitates the international trade of camel meat (https://www.nintione.com.au). Many traditional camel meat products characterize Africa and the Middle East regions. However, only a few of them have been reported and characterized scientifically.\n\nSWOT analysis was conducted to identify the camel meat commodity’s strengths, weaknesses, opportunities and threats. The results of this analysis showed that one of the identified weaknesses is the lack of consumer awareness towards camel meat (Mbaga, 2013). Often, consumers are unaware that camel meat is a healthy product. As a general rule, consumers will not buy any product unless they have heard of it before. Therefore, consumer awareness remains a very important factor. Consumers tend dislike camel meat because they associate meat with the camel itself, and this is often one of the reasons for this disapproval. Under these circumstances, it would be ideal for manufacturers to avoid the use of promotional labels that show the image of the camel itself. The Australian meat industry has been successfully promoted kangaroo meat and lessons can also be drawn from the same approaches (https://www.awe.gov.au/biosecurity-trade/export/controlled-goods/kangaroo).\n\nConsumer motivations and barriers for buying camel meat were further investigated via the survey approach. A previous study is available in the literature regarding small ruminants’ meat consumer preferences (Brahimi et al. 2020). This study was designed to deepen understanding of consumers' perceptions of different meats, as well as the motivations and barriers consumers face when approaching these products. Consumers often mentioned price as an important quality attribute. The health aspect also emerged among participants. Some consumers believed that camel meat had lower fat content compared to other meats, and was particularly suitable for people with diseases.\n\n\nBioactive compounds in camel meat\n\nCamel meat is characterized by a considerable amount of conjugated linoleic acid (CLA) and monounsaturated fatty acids (MUFAs) (Popova et al. 2021). Scientists found that CLA appeared to reduce tumor growth in several types of cancer and against atherosclerosis (Kim et al. 2016). For this reason, the main objective of new animal feeding strategies is to increase the concentration of polyunsaturated fatty acids (PUFAs) and the levels of CLA in forages. Importantly, the ω6/ω3 ratio in camel meat was lower (≈3) (Maqsood et al. 2015a) than the recommended values of human health diets (≤4.0) by British Department of Health (BDH 1994). Ayyash et al. (2019) claim that camel meat was traditionally used as a remedy for some diseases such as pneumonia, hypertension, hyperacidity, and respiratory disease as well as an aphrodisiac (Figure 1). Recently, an in vitro comparative study, investigated the health-promoting benefits (anticancer) of semi-dry fermented camel sausages fortified by two novel probiotic Lactiplantibacillus plantarum compared with fermented beef sausage (Ayyash et al. 2019). Fermented camel sausages showed greater anticancer activity than beef sausages. The same authors found that the antihypertensive via inhibition of angiotensin-converting enzyme (ACE), greater cytotoxicity capacities and antioxidant activities in fermented camel sausages were more pronounced than in beef sausages.\n\nKnowledge about camels was traditionally restricted to limited geographical areas, particularly Middle East, Asia, and Africa, but the use of camel’s products as a nutrient for health benefits is currently known worldwide. However, during the 20th century, when intercultural migration of people became very important, knowledge about camels and their products began to reach countries beyond Middle East, Asia and Africa. Scientific efforts continue around the world to identify more therapeutic constituents.\n\nMejri et al. (2017a) identified several bioactive molecules in some fermented camel products. The results showed that identified peptides below 3 kDa have an antioxidant and antihypertensive effects. Gheisari and Motamedi (2010) studied the antioxidant enzymes activity in refrigerated camel meat and confirmed its catalase stability. However, glutathione peroxidase (GSH-Px) activity decreased in camel meat during refrigerated storage. L-carnitine (β-hydroxy-γ-trimethyl amino butyric acid) plays a crucial biological role. A study evaluated the concentrations of free carnitine, acylcarnitine and total carnitine from camel meat (Alhomida et al. 1995), and found 5.17, 2.60 and 7.77 μmol/g fresh weight of free carnitine, acylcarnitine and total carnitine, respectively. Similarly, Kadim and Sahi (2018) indicated that camel meat could be a significant source of carnitine. However, a higher proportion of acyl carnitine in plasma and skeletal muscle of the camel than other animal species suggests an adaptive mechanism that could be common to camelids, which may provide energy to various tissues during scarcity of water and feed for long periods.\n\nAn important dipeptides such as carnosine (β-alanyl-L-histidine) and its derivative anserine (β-alanyl-L-methyl-L-histidine) are found in high concentration in the muscle of mammalian species. Dromedary camel meat contains 164.9 mg carnosine/100 g and 236.9 mg anserine/100 g fresh weight (Kadim and Sahi 2018). Carnosine has been proven to act as antioxidant in various meat systems (Sánchez-Escalante et al. 2001; Djenane et al. 2004), and also as anticancer actions in various model systems by the restoration of normal cellular homeostasis (Turner et al. 2021). The average levels of carnosine and anserine in camel muscles has 182 and 269 mg/100 g fresh weight, respectively. Little has been known about antioxidant enzymes in camel meat. Chafik et al. (2020) suggested a new carbonic anhydrase enzyme that was purified and differentiated from camel liver for atmospheric CO2 sequestration. Other endogenous antioxidants enzymes were found in camel muscles such as superoxide dismutase (SOD), coenzyme Q10, catalase and GSH-Px (selenium-containing enzyme) contribute to oxidative defense and stimulates the reduction of harmful free radicals (Gheisari and Motamedi 2010).\n\n\nOrganoleptic properties of camel meat\n\nTo enhance the image of camel meat, and the search for new outlets for this meat, the camel sector must promote these organoleptic qualities in the same way as other red meats (Halagarda and Wójciak 2022), but also, strengthen its image with additional nutritional benefits.\n\nThe ultimate pH (pHu) of camel muscles (5.5 to 6.6) is a consequence of lactic acid accumulation via glycolysis and is considered one of the main factors determining the organoleptic characteristics of meat. Soltanizadeh et al. (2008) found that the pH decline was faster in beef meat than camel. A more rapid pH decline may inactivate protease activity, meaning a reduction in the proteolysis and subsequent post mortem tenderization. Therefore, there is a possibility that the higher myofibril fragmentation index (MFI) observed in camel meat was due to its higher post mortem pH values, and consequently for higher protease activity (Kadim et al. 2006).\n\nThe importance of moisture in camel meat is in its marked effects on its processing potential, quality characteristics and shelf life optimization during storage. Meat cuts with low water holding capacity (WHC) are drier and would lose more weight during refrigeration, storage, transportation and marketing. Result of this, loss of minerals, salts and vitamins (Kadim et al. 2013). In meat, juiciness and tenderness are closely correlated. The more tender the meat, the faster the juice is released by chewing it. Meat with higher pH value has a greater WHC than that with a low pH value; often referred to as: dark, firm and dry (DFD), and pale, soft, exudative (PSE) meats, respectively (Liu et al. 2021).\n\nMeat tenderness is often determined by muscle characteristics, collagen content and its solubility, post mortem glycogen concentration, proteolytic enzymes content and more likely in the enzyme/inhibitor ratio, a parameter reflecting the efficiency of the proteolytic systems (Nair et al. 2019). Reports that camel meat is less tender than other animals are likely due, at least in part, to the higher average age of slaughtered animals, mainly obtained from old animals (aged >10 years). A number of studies have shown that Warner–Bratzler–Shear Force (WB-SF) values increase with animal age. The values reported in the literature, indicate higher values than those reported for beef.\n\nKadim et al. (2006) suggested that the shear-force value from aged camels (8 years) was 48% higher than that from young camels (1–5 years). The WB-SF values for various camel muscles were determined by Kadim et al. (2013). The infraspinatus, triceps brachii, longissimus thoracis muscles have significantly lower shear-force (6.3–6.7 kg) values than semitendinosus, semimembranosus, and biceps femoris muscles (9–12.9 kg), which might be due to less connective tissue. Suliman et al. (2019) reported a similar result.\n\nConsumer acceptance of identified individual muscles should be assessed with the aim of developing positive marketing strategies towards consumer perception of camel meat. However, evidence suggests that camel meat tenderness is not significantly different from beef if it is slaughtered at the same ages (Kadim et al. 2011). Many exogenous enzymes have the capacity to degrade muscle proteins, leading to this effect, a significant degradation of the miofibrillary system, and consequently, a better sensory qualities of obtained meat (Bagheri Kakash et al. 2019). The MFI of old camels (6 years) was lower than youngers (<3 years) (Al-Owaimer et al. 2014). The authors observed a strong relationship between physical disruptions of the myofibrils and the tenderness. MFI is one of the most widely used methods to determine post mortem proteolysis in meat of various species. This index is a very useful indicator of meat tenderness. Smili et al. (2022) reported that MFI of Algerian Sahraoui dromedary meat was significantly affected by both slaughter age and post mortem period. The same authors confirmed that the 30-kDa band is a proteolytic product of Troponin-T in camel longissimus lumborum muscles. Soltanizadeh et al. (2008) observed the appearance, on the third day of storage, of a 30-kDa band in camel meat which was linked to the higher degree of proteolysis. Therefore, various methods have been developed for tenderizing camel meat. Abdel-Naeem and Mohamed (2016) found that addition of Zingiber officinale extract in camel meat burgers resulted in higher MFI. The tenderness of meat can also be improved by the use of exogenous enzymes which break down muscle proteins including connective tissue. Nevertheless, the action of proteolytic enzymes on collagen is limited, which makes them less useful for old camels’ muscles with high collagen content. Recently, plant proteases have been used as a sustainable manner to improve the texture of tough camel meat and to develop functional meat products that contain bioactive molecules with antioxidant activities (Gagaoua et al. 2021). From another perspective and to overcome the problem of toughness in camel meat, Smith et al. (2016) showed that whatever the age of the animal or the sex, electrical stimulation (ES) could drastically decrease the hardness of camelid meat. ES of carcasses at 20 to 100 V is a proven method to prevent fibers cold shortening and thus to improve tenderness of meat (Polidori and Vincenzetti, 2017). The effects of post mortem ES (90 V)/20 min was assessed by Kadim et al. (2009), authors found that muscles from young camel were not affected by cold shortening and ES had a significant effect on meat quality attributes. Muscles from electrically non-stimulated carcasses have a higher WB-SF value (9.47 kg/cm2) compared to those of stimulated carcasses (6.97 kg/cm2) (Kadim et al. 2009).\n\nCarcass suspension methods can also have a direct effect on meat tenderness. Indeed, the “tenderstretching” mode favored the tenderness of camel meat (Smith et al. 2016). The combination of ES/tenderstretching further promotes tenderness of camel meat (Biffin et al. 2020). The key mechanism by which ES improves tenderness is by rapidly decreasing the concentration of adenosine triphosphate (ATP), which reduces the potential for myofibrils to contract and cold shortening if post mortem carcasses are immediately refrigerated.\n\nCamel meat is described as “raspberry red” and sometimes brown in older animals (due to a higher concentration of myoglobin: Mb) (Kadim et al. 2013). Abdelhadi et al. (2013) reported that there are differences in the color of camel meat with a seasonal effect linked to the diversity of animal feeding throughout the year. It was significantly darker red in autumn compared with summer and less yellow in autumn than in summer and winter. In addition to season’s differences, storage temperatures were reported to affect muscle biochemical characteristics and color. The color characteristics of camel meat can be influenced by the post mortem storage period and the type of muscle (Suliman et al. 2019). A high redness (a) color component was associated with a lower lightness (L), which might be due to an increase in Mb content (Maqsood et al. (2015a). However, meat from older camels have lower L* (darker) and higher a* (redder) than that of younger camels (Kadim et al. 2006). Post mortem proteolysis increases light scattering properties of meat and thereby affects L, a and b* (yellowness) values (Hughes and Anderson 2020), which is also directly related to the pHu. Meat proteins have an isoelectric pH (pHi) of 5.5. This results in open muscle structure and as a result lighter scattering between the myofibrils, which makes the surface of the meat lighter. It is obvious that during the retail display, the meat surface color is unstable. This phenomenon is due to several factors such as, post mortem biochemical changes in protein and lipid fractions of the meat, surface microbial overgrowth, oxidation of lipids and Mb and finally, the phenomenon of photo oxidation due to the fluorescent tube installed in the refrigerated display cases (Djenane et al. 2001, 2003). In the USA, an average of 2.55% of total red meats sold are discarded annually due to discoloration (13.4 million kg, the equivalent of USD 3.73 billion loss) (Ramanathan et al. 2022).\n\nStrategies for preserving color of camel meat were the application of post mortem low voltage ES. Abhijith et al. (2020) reported that meat from electrically stimulated carcasses, have a brighter red color than meat from -non-stimulated carcasses. Using appropriate packaging and cold storage conditions (vacuum, modified atmosphere packaging (MAP) and active packaging) can play a major role in color enhancement of meat during storage (Nerin et al. 2006; Camo et al. 2011; Lammi et al. 2018; Ait Ouahioune et al. 2022a). Maqsood et al. (2015b) reported that camel meat total haem content expressed as haematin was 92.3 mg/g which is higher than what was found in beef (76.16 mg/g). However, the presence of a high haem content could contribute to fast meat pigment oxidation during its refrigerated storage. Average Mb contents in camel meat was found to be 7.16 mg/g (Maqsood et al. 2015a). In contrast, Gheisari (2011) reported 3.64 mg/g. This difference could be due to several experimental factors such as part of the carcass, solvents and extraction conditions. In general, the quality of camel meat has been assessed using traditional conventional methods, and it will be important for the camel sector to take into account the new technologies already applied to beef.\n\n\nTechnological aspects of camel meat\n\nCamel meat has been processed into burgers, cured or cooked ham, kebabs, meatballs, patties, mortadella, merguez, sausages, and shawarma to add value (http://www.australiancamelindustry.com.au). Australian processed camel meat has been accepted as international traded meat products (Wu et al. 2011). It is now exported to Canada, China, Europe, Saudi Arabia and the USA. The potential of camel meat has received increased attention in recent times. In this context, Kargozari et al. (2014) compared the fatty-acid and volatile-compound profiles, sensory qualities and the physicochemical of dry sausages (Sucuk) made from camel meat and hump fat with sausages made from beef and beef fat and from a mixture of both. The authors suggest that the physicochemical properties and some textural attributes of camel meat sausages were comparable to those of beef. Nerveless, the flavor components were quantitatively much higher in camel sausages. The same authors concluded that camel meat can successfully replace beef in sausage manufacture.\n\nThe growing concern of consumers regarding the food health and safety issues has led to the development of products that promote health and well-being beyond its nutritional effect. Fermented meat products can be considered as relevant matrix for the delivery of bioactive molecules with potential health benefits (Mejri et al. 2017b; Ayyash et al. 2019). In a comparative study, Kargozari et al. (2014) found that fermented camel sausages exhibited greater resistance to lipid oxidation (lower thiobarbituric acid reactive substances: TBA-RS) during storage compared to beef sausages. These authors obtained an ω-6/ω-3 ratio of 6.22 for beef sausages and 2.95 for camel sausages. This indicates that camel sausages fit perfectly into the recommendations for this ratio (BDH, 1994). Abdel-Naeem and Mohamed (2016) found that addition of ginger (Zingiber officinale) and papain (Carica papaya) extracts in camel burger resulted in improvement of the lipid stability and significant increase of sensory scores of treated burgers during storage. Gagaoua et al. (2021) showed that marinade with plant proteases has been used to improve the texture of tough camel meat. This can be a valuable strategy to develop locally tender camel and healthier products. Maqsood et al. (2015b) studied the effect of phenolic compounds such as tannic acid and catechin on sensory quality and fatty acid profile of camel meat during storage, and found that incorporation of these compounds improved sensory scores and fatty acid profile. Furthermore, authors suggest that tannic acid and catechin could prevent protein breakdown in chilled ground camel meat, which was most likely due to their antimicrobial and antioxidant activity. Despite the low cholesterol content of camel meat, the salt curing process can induce significant amounts of cholesterol in the final products (Mamani-Linares et al. 2014). To avoid this problem, solar drying under the open sky of camel meat without salting was carried out by Chaouch et al. (2018).\n\nThe growing demand for Halal gelatin, and the rejection of gelatin from a mainly porcine source have encouraged scientists to search for alternative sources such as camel skin (Asif Ahmed et al. 2020). Recently, Al-Hassan (2020) demonstrated that gelatin could be extracted from camel skin as a promising source of Halal gelatin.\n\nThe evolution of modern retail outlets with better packaging, labeling, and cold chain facilities will address the drawbacks of the current situation in the camel meat sector. Referring to packaging technologies, very little data are available on the application of innovative techniques in camel sector (Table 1). Microbial spoilage associated with color change and lipid oxidation are the critical factors limiting shelf-life and consumer acceptability of stored camel meat (Maqsood et al. 2015b). Haem pigment is known to be potent catalyst of lipid oxidation in muscle foods. With increasing storage time, damage to haem pigment results in the release of ferrous (Fe+2), which can accelerate lipid oxidation (Gheisari, 2011). Its role as catalyst of lipid oxidation is because is capable of catalyzing the production of reactive oxygen species (ROS) such as superoxide anion (O2•−). This process is frequently explained by the Fenton reaction. Alkyl radicals can be formed as a result of the reaction of O2•− with fatty acids and hence the onset of lipid oxidation. Moreover, O2•− could be transformed into hydrogen peroxide (H2O2) by dismutation, which react with ferrous iron (Fe+2) to produce the hydroxyl radical (OH•).\n\nDjenane et al. (2020) reported that high oxygen (80%) modified atmospheres associated with olive leaf extracts (Olea europaea Subsp. laperrinei) and nisin, a polycyclic antibacterial peptide produced by Lactococcus lactis can be used as a strategy to retain the redness of camel meat during retail display. Jouki and Khazaei (2012) found the lowest lipid oxidation degrees for vacuum packaged camel meat compared to anoxic MAP (60% CO2; 40% N2) and air packaged meat during chilled storage, and concluded that vacuum packaging can be used as an effective strategy against deleterious consequences of lipid oxidation. In this same perspective, Maqsood et al. (2016) reported that the shelf life of chilled vacuum stored camel meat could be extended to 18 days compared to wrapped samples.\n\nModern food packaging provides a way to make food safe, reliable, shelf-stable and clean. However, the packaging, without departing from its irreplaceable role in food preservation, is accused today of polluting food and polluting the environment (Ncube et al. 2020). Unfortunately, most food packaging is designed to be single use and is not recycled. The world's population continues to grow and so do natural resources demand. Consumers not only care more and more about what they eat, they are also more concerned with the packaging of the food they buy. This increased focus on environmentally friendly consumption leads to the development of more sustainable business practices and a low-cost circular economy (Baghi et al. 2022). Because of the inability of plastics to degrade, the environmental pollution it causes is a major global concern (Chamas et al. 2020). To overcome this serious problem of plastic waste, the modern food industry requires new and effective approaches to preserving perishable food products. The ideal packaging should have a lower carbon and water footprints, be biodegradable and/or compostable, uses waste or by-products, is eco-designed and safe, and has the right preservation properties to minimize food waste (Moshood et al. 2022; Ait Ouahioune et al. 2022b). The incorporation of bioactive molecules (antimicrobial and antioxidant) in packaging materials can remarkably help extend the shelf-life of perishable foods by retarding microbial growth and reducing oxidation (Djenane et al. 2016). Nanotechnology can also play a fundamental role in the meat industry, from processing, preservation to packaging of fresh or processed meat products (Lamri et al. 2021).\n\nOver the past decade, meat products commercialization strategies have notably changed all over the world (Juárez et al. 2021). However, as a result of increasing demand for fresh and ready-to-use meats, a need has emerged for adequate preservation techniques to maintain their quality and safety. These technologies include chilled storage, vacuum and MAP, biopreservation, active and biodegradable packaging, and their combination (Figure 2).\n\nCamel meat is rich in Mb (haem protein) and several authors have reported the pro-oxidant effect of this protein in its oxidized state on lipid oxidation (Maqsood et al. 2015a,b). This makes camel meat more susceptible to oxidation of lipids and therefore to the development of unpleasant odors (off odor) and can limit its shelf life during storage. To overcome this problem, the use of antioxidants is one of the main strategies to extend the shelf life of camel meat (Djenane et al. 2020). Nowadays, frozen storage of meat is broadly utilized to extend its shelf life over one year (Dang et al. 2021). Additionally, most previous studies do not consider the impact of freezing and cooking on varying nutrient amounts in camel meat. The most important phenomenon observed, when cooking meats, is the thermal denaturation of muscle proteins (Sayd et al. 2016), that may cause loss of juice displaying a direct impact on the nutrient content of cooked meats.\n\nRecently, novel strategies are directed towards the use of natural bio preservatives ingredients, which can minimize lipid and pigment oxidation, and off odor development with increase of the color stability and consequently the acceptability of camel meat. Therefore, the use of natural plant-based antioxidants, especially phenolic compounds, could be an effective way to extend the shelf life of stored camel meat (Djenane et al. 2020). Thus, plant extracts not only possess antioxidant activity, but also antimicrobial activity against spoilage bacteria and harmful pathogens (Djenane et al. 2012a,b).\n\nIt has been reported that camel meat treated with tannic acid and catechin had lowest TBA-RS value, indicating strong inhibitory effect on lipid oxidation during nine days of storage (Maqsood et al. 2015b). Gheisari and Motamedi (2010) found that the presence of high activities of endogenous antioxidant enzymes such as catalase and GSH-Px could lead to a significant decrease in lipid oxidation during camel meat storage. The PUFAs content in camel meat is still desirable for human consumption; unfortunately, these FAs are likely to be susceptible to rapid oxidation. It has been shown that a level of lipid oxidation in the range of 1.5 to 2 mg/kg of malondialdehyde in camel meat caused its rejection by a trained panel for the unpleasant off odors (Djenane et al. 2020). Studies have shown that in some camelids, the level of lipid oxidation remains low (Smith et al. 2019). This is due to the probably high levels in fat soluble vitamins such as vitamin E and other antioxidants reported in camel meat, which is the result of its supply of aromatic and medicinal herbs from arid regions. Maqsood et al. (2015b) investigated the effect of phenolic compounds on microbial quality of camel meat during refrigerated storage. The authors suggested that phenolic compounds were effective in inhibiting microbial growth in meat by chelating specific metal ions essential for microbial growth. In previous study, Djenane et al. (2020) found that higher oxygenated MAP (80% O2) associated with Olea europaea extracts treatment combined with nisin can be a promising tool and constitute a relevant strategy to control microbial growth and oxidation phenomena in camel meat. Similarly, Jouki and Khazaei (2012), using an anoxic MAP (60% CO2 + 40% N2) combined with refrigeration storage (4°C) have obtained significant improvement in physicochemical and sensory properties of camel meat within three weeks of storage. Recently, Yehia et al. (2021) reported that the use of combined natural biopreservative agents (Citrox and chitosan) can be a promising tool to control Campylobacter jejuni growth and to preserve packaged camel meat even at abuse refrigeration (10°C) storage. A combination of essential oils (EOs) components like carvacrol, thymol or cinnamaldehyde with the yogurt-based marinade exerts a lethal effect against Escherichia coli O157: H7 and Salmonella spp. without significant changes in the sensory characteristics of the cooked camel (Osaili et al. 2020b). Mentha spicata EO was incorporated at different concentrations (0.5 to 1.5% v/w) into camel meat to evaluate its antibacterial activity at refrigerated storage. The final microbial population decreased until 4 log cfu/g. Moreover, during storage, peroxide value (PV), total volatile basic nitrogen (TVBN) remained lower in treated compared to control samples. Similarly, Khezrian and Shahbazi (2018) incorporated of Ziziphora clinopodioides EO in combination with Ficus carica extract into active packaging films, and found that packed meats exhibited better safety against Listeria monocytogenes and E. coli O157: H7. Sensory attributes were significantly enhanced in treated camel meat samples.\n\nCamel meat remains an essential source of protein for arid region populations. Nonetheless, various traditional meat products have long been known in the region and prepared for family or religious feasts. For example, during the “Al Adha feast”, Muslim families ought to slaughter a whole camel to be shared equally between seven families. Surplus meat was then transformed into more stable products. This was achieved by combined treatments in an empirical application. However, the sanitary and hygienic importance, and the perishable nature of these products prompted public authorities to establish controlled slaughter structures. Strict compliance with good hygiene practices in slaughterhouses is therefore essential to prevent bacterial contamination of carcasses, with the aim of maintaining optimal meat quality, thus protecting consumer health.\n\n\nCamel meat as a substitute for other red meats\n\nOne of the major challenges for global food security is the high demand for meat products. For these medicinal and nutritional benefits, camel meat can be a great option for sustainable meat supply (Baba et al. 2021). In addition, the price of camel meat is often lower than that of cattle and sheep, due to lower transaction costs and circuits with fewer intermediaries, for a production that also remains very extensive and therefore with few inputs. This allows access to meat proteins for the often most disadvantaged populations and ensures that camel meat has a certain competitiveness. Hence, the one-humped camel as a meat source seems to present a viable alternative to cattle (Figure 3). The general qualitative characteristics of camel meat are very similar to those of beef. Moreover, it is difficult for an uninformed consumer to tell the difference (Suliman et al. 2020).\n\nDuring the last decades, the world consumption of camel meat is increasing and the main “camel meat eaters” with more than 3 kg/habitant/year are in Emirates, Mauritania, Mongolia, Oman, Somalia and Western Sahara (Faye and Bonnet, 2012). The cholesterol content of camel meat (50 mg/100 g) is lower than that of other farm animals (Raiymbek et al. 2015). It appears that camel meat can be used as a substitute for beef due to its reduced cholesterol content and is a strong commercial argument for emphasizing the healthy character of this product.\n\nThe growing demand for meat cannot be met by conventional meat production alone, because 80% of all arable land is already used directly or indirectly for livestock production (https://ourworldindata.org/environmental-impacts-of-food), and this is unsustainable as it is, due to its large ecological footprint. By 2050, the world's population will reach around 10 billion people, according to a new report published by the United Nations Department of Economic and Social Affairs (https://population.un.org). A great challenge awaits policy makers and ensuring food security without compromising the main pillars of sustainability is one of the main objectives of the United Nations for sustainable development. In this optical, the camel sector must adopt sustainable practices in order to become more competitive (Faye, 2013). Compared to other species such as goats, cattle and sheep, camel is less destructive for the fragile pasturelands. Camel meat is therefore an ecologically friendly food. Camels also have a very efficient feed conversion rate. Nowdays consumers, especially in rich civilizations, tend to favor produces that are environmentally friendly; as a result, this is a very important attribute that needs to be promoted in favor of camel meat.\n\nIn arid regions, camel herds are often dispersed over large areas rather than clustered like cattle and sheep. However, camels eat only small amounts at a time and are considered one of the least overgrazing ruminants, unlike sheep and goats. Camel meat can consequently be produced economically compared with other competing meats. According to FAOSTAT, the worldwide meat production has been projected to be double by 2050 (http://faostat3.fao.org), due mainly to the increase in production and consumption, which is likely to intensify the freshwater crisis in the future. The virtual water content (VWC) for camel production has not been well investigated. Quantification of VWC for the camel production plays an important role in understanding the aspects of national water footprint (WFP) in arid regions and is highly needed to guide the allocation of livestock farming and optimize water use (Qasemipour and Abbasi 2019). However, the current changes in camel farming practices (the Bedouin system based on camel mobility called “H’mil” versus semi or intensive systems) based on intensification of the management could modify this conception. According to Chowdhury et al. (2017), the unit VWC of camel is 3.5- and 1.7-times the VWC for sheep and cow, respectively. One kg of cow and camel meat required 19.7 and 14.6 kg of feed supply, respectively. To my knowledge, there are no works on the carbon footprint and on the water consumption required for the production of 1 kg of camel meat. However, Faye (2013) found that the water consumption for producing 1 L of camel milk was multiplied by nine passing from 938 to 8601 liters of water per liter of produced milk. However, all these results remain to be confirmed by future other studies in different arid and semi-arid regions.\n\nGenerally, in developed countries, meat production has significant impact on nearly all aspects of the environment, including climate change (https://ourworldindata.org/environmental-impacts-of-food). Beef is the most popular meat widely produced in the world. Unfortunately, it is also the most inefficient animal to produce meat in terms of the amount of input needed to produce it (Paris et al. 2022). Camel is considered a fundamental pillar of the national economy and food security for many countries in arid regions (Faye, 2013). Meat professionals see the still virgin camel market as a sure opportunity to do good business and participate in the development of rapidly changing agricultural and agri-food sectors. Camel meat has reduced production costs because camels are usually reared in arid regions. In these harsh environments, poor quality feed is the only source for camels and is not utilized by other domesticated species. As a result, camels can produce meat at a lower cost compared to cattle, goats and sheep. FAO projects the global meat production to more than double from 229 million tons in 1999 to 465 million tons in 2050 (http://faostat3.fao.org). The average meat consumption worldwide during 2015 was 42.14 kg per capita/year, while in 2019 it was 43.16 kg per capita/year. Thus, the increase in consumption between these years was 2.42%. In the total meat consumption was added beef, sheep, pig, goat, poultry and then other meats (camels, rabbits…). Meanwhile, the global population is also expected to further increase. This will drive up total worldwide meat consumption. Producing more meat to meet the problem of population growth means more animal feed will have to be produced, which also means more land and water will be needed. On the basis of these expected challenges, camel meat is presented as a potential substitute for other red meats because, among other things, camels require fewer resources in terms of land and water.\n\nRecently, more attention has been paid to the nutritional value of camel meat, with the aim of creating additional value for various camel meat products. Although the marketing systems for camel meat are not well organized. This causes failure in appreciating the importance of these products in contributing to the development of the camel sector. Camel milk, on the other hand, has been marketed and used as a processing aid in several European countries, in particular the Netherlands, Denmark and England. This culminated in 2013 when the European Community authorized the import of camel milk from the United Arab Emirates. This great popularity of camel milk is probably due to the prior knowledge of its nutritional value and human health benefits compared to the more widely consumed cow's milk.\n\nThe world’s Muslim population is expected to increase by about 35% in 20 years (2010–2030), by 2030, the global Muslim population is expected to reach 2.2 billion people compared with 1.6 billion in 2010. This huge increase in the Muslim population, coupled with the recent increase in popularity of camel meat in Australia and China, creates an unprecedented potential for camel meat.\n\n\nRecommendations\n\nA valid alternative to beef and other red meats could be the camel meat. North African countries are the largest African producer of camel meat and derivatives. The high nutritional properties of camel meat make it suitable for inclusion in the Mediterranean diet in order to adapt it to the needs and conditions of the population. Consumers tend dislike camel meat because they associate meat with the camel itself, and this is often one of the reasons for this disapproval. Under these circumstances, it would be ideal for manufacturers to avoid using promotional labels that show the image of the camel itself. This problem could be addressed through commercial advertising and education. It empowers consumers, helping them acquire the skills and attitudes they need to be able to gear the choices they make to their economic and health interests. Australians have succeeded in promoting kangoro meat and lessons can also be drawn from the same approaches. Consumers describe camel meat as tough even though they agree that it is no different from beef in terms of flavor. The meat consumption behavior by consumers will contribute to the development of livestock camel sector. However, almost all research has proven that the older a camel, the tougher the meat. Research has established, however, that it is generally accepted that younger animals produce more tender meat than older animals. Therefore, age is an important factor in determining the quality of camel meat. There are potential opportunities for camel meat industry through brand development. Future camel research should focus on exploiting its meat potential in the same way as dairy through interdisciplinary research on efficient production systems, improved meat technology and marketing. Finally, the consumer dietary for lower or no meat consumption (e.g. vegetarian or vegan diets) or for cultured meat are assumed to expand slowly and to be adopted by a small part of population concentrated mainly in rich countries, and therefore hardly affect meat consumption over the next decade (Chriki and Hocquette, 2020).\n\n\nConclusions\n\nCamel is the animal of the future. Without a doubt, the camel can be a tool to fight against the future challenges of climate change and their consequence on the earth. For these medicinal and nutritional benefits, camel meat can be a great option for sustainable meat worldwide supply, which represents a strong commercial argument to confirm the healthy nature of this product (Figure 4). Knowledge about camels was traditionally restricted to limited geographical areas, particularly Middle East, Asia, and Africa, the use of camel’s products as a nutrient and for its health benefits is now known worldwide. From an economic profitability point of view, camel meat has a competitive advantage over other meats due to low production costs. However, in camel meat, the information on bioactive compounds is limited and this needs further study to identify other bioactive compounds of interest and compare them with those of other red meats. Camel meat has been processed into limited camel products to add value. It is also interesting to draw the attention of researchers from arid and semi-arid countries as well as stakeholders including decision-makers in these countries to the urgency of assessing or identifying the health risks associated with consumption of camel products and thus take the necessary measures to reduce these risks. In the light of this review, the need to implement a control strategy is obvious. The dynamics of infectious diseases in camels are highly variable. Veterinary laboratories should be provided with accurate diagnostic tools in order to detect infected animals that represent potential reservoirs of infection at an early stage and especially during seasons with abundant vectors.\n\nCamel meat, which is produced naturally and biologically, would occupy important place on the global market. Though the scientific research achievements are modest, they open new up horizons for the modernization of the sector in order to improve the productive performances of camels in arid regions. Suitable chilling and innovative packaging technologies, are required to augment hygienic meat production and could lead to the development of expanded markets for camel meat not only in the Middle East and North Africa but also globally. Slaughterhouse solid waste management and effluent treatment are some of the parts that need better technological involvement.\n\n\nData availability\n\nThere are no underlying data associated with this article.", "appendix": "References\n\nAbdelhadi OMA, Babiker SA, Hocquette JF, et al.: Effect of ageing on meat quality of the one humped camel (Camelus dromedarius). Emir J Food Agric. 2013; 25: 150–158. Publisher Full Text\n\nAbdel-Naeem HH, Mohamed HM: Improving the physico-chemical and sensory characteristics of camel meat burger patties using ginger extract and papain. Meat Sci. 2016; 118: 52–60. PubMed Abstract \| Publisher Full Text\n\nAbhijith A, Dunshea FR, Warner RD, et al.: A meta-analysis of the effectiveness of high, medium, and low voltage electrical stimulation on the meat quality of small ruminants. Foods. 2020; 9: 1587. 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Publisher Full Text\n\nMbaga MThe economic potential of camel meat. Camel meat and meat products. Kadim IT, Mahgoub O, Faye B, et al., editors.Wallingford, Oxfordshire, UK, Cambridge, MA:CABI©;2013; 2013. .\n\nMejri L, Vásquez-Villanueva R, Hassouna M, et al.: Identification of peptides with antioxidant and antihypertensive capacities by RP-HPLC-Q-TOF-MS in dry fermented camel sausages inoculated with different starter cultures and ripening times. Food Res. Int. 2017a; 100: 708–716. PubMed Abstract \| Publisher Full Text\n\nMejri L, Ziadi A, El Adab S, et al.: Effect of commercial starter cultures on physicochemical, microbiological and textural characteristics of a traditional dry fermented sausage reformulated with camel meat and hump fat. J Food Measure Charact. 2017b; 11: 758–767. Publisher Full Text\n\nMoshood TD, Nawanir G, Mahmud F, et al.: Sustainability of biodegradable plastics: New problem or solution to solve the global plastic pollution? 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Publisher Full Text\n\nOsaili TM, Al Nabulsi AA, Dhanasekarane DK, et al.: Growth behaviour and thermal inactivation of Escherichia coli O157:H7 and Salmonella spp. in ground lean camel meat. Int J Food Microbiol .2020b; 316: 108423. PubMed Abstract \| Publisher Full Text\n\nOsaili TM, Hasan F, Dhanasekarane DK, et al.: Effect of Youghourt-based marinade combined with essential oils on the behaviour of Listeria monocytogenes, Escherichia coli O157:H7 and Salmonella spp. in camel meat chunks during storage. Int J Food Microbiol .2021a; 343: 109106. PubMed Abstract \| Publisher Full Text\n\nOsaili TM, Hasan F, Al-Nabulsi AA, et al.: Effect of essential oil and vacuum packaging on spoilage-causing microorganisms of marinated camel meat during storage. Foods. 2021b; 10: 2980. PubMed Abstract \| Publisher Full Text\n\nParis B, Vandorou F, Tyris D, et al.: Energy use in the EU livestock sector: A review recommending energy efficiency measures and renewable energy sources adoption. Appl. 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Publisher Full Text\n\nRamanathan R, Lambert LH, Nair MN, et al.: Economic loss, amount of beef discarded, natural resources wastage, and environmental impact due to beef discoloration. Meat Muscle Biol. 2022; 6: 1–8. 13218.\n\nRitchie H: UN Food and agriculture organization.2017.Reference SourceReference Source\n\nRitchie H, Roser M: Environmental Impacts of Food Production.2020. [Online Resource].Reference SourceReference Source\n\nSánchez-Escalante A, Djenane D, Torrescano G, et al.: The effects of ascorbic acid, taurine, carnosine and rosemary powder on color and lipid stability of beef patties packaged in modified atmosphere. Meat Sci .2001; 58: 421–429. PubMed Abstract \| Publisher Full Text\n\nSayd T, Chambon C, Sante-Lhoutellier V: Quantification of peptides released during in vitro digestion of cooked meat. Food Chem. 2016; 197 Pt B: 1311–1323. PubMed Abstract \| Publisher Full Text\n\nShahbazi Y, Karami N, Shavisi N: Effect of Mentha spicata essential oil on chemical, microbial, and sensory properties of minced camel meat during refrigerated storage. J Food Saf. 2018; 38: e12375.\n\nSmili H, Becila S, Della Malva A, et al.: Postmortem muscle protein changes as a tool for monitoring Sahraoui dromedary meat quality characteristics. Foods. 2022; 11: 732. PubMed Abstract \| Publisher Full Text\n\nSmith MA, Bush RD, van de Ven RJ, et al.: Effect of electrical stimulation and ageing period on alpaca (Vicugna pacos) meat and eating quality. Meat Sci. 2016; 111: 38–46. PubMed Abstract \| Publisher Full Text\n\nSmith MA, Nelson CL, Biffin TE, et al.: Vitamin E concentration in alpaca meat and its impact on oxidative traits during retail display. Meat Sci. 2019; 151: 18–23. PubMed Abstract \| Publisher Full Text\n\nSoltanizadeh N, Kadivar M, Keramat J, et al.: Comparison of fresh beef and camel meat proteolysis during cold storage. Meat Sci. 2008; 80: 892–895. PubMed Abstract \| Publisher Full Text\n\nSuliman GM, Al-Owaimer AN, Hussein E, et al.: Meat quality characteristics of the Arabian camel (Camelus dromedarius) at different ages and post-mortem ageing periods. Asian-Austr J Anim Sci. 2020; 33: 1332–1338. PubMed Abstract \| Publisher Full Text\n\nSuliman GM, Alowaimer AN, Hussein EOS, et al.: Chemical composition and quality characteristics of meat in three one-humped camel (Camelus dromedarius) breeds as affected by muscle type and post-mortem storage period. Animals. 2019; 9: 834. PubMed Abstract \| Publisher Full Text\n\nThe Central Australian Camel Industry Association Inc:2022. (accessed 27 March 2022).Reference Source\n\nTurner MD, Sale C, Garner AC, et al.: Anti-cancer actions of carnosine and the restoration of normal cellular homeostasis. Biochim Biophys Acta Mol Cell Res. 2021; 1868: 119117. 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Publisher Full Text" }	[ { "id": "187921", "date": "26 Jul 2023", "name": "Waleed Al-Marzooqi", "expertise": [ "Reviewer Expertise Research Interests:· Animal responses to nutrients· Assessment of nutritional value of feedstuffs.· Quantification the impact of anti-nutritional factors together with processing conditions.· Meat production 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\nThe manuscript requires substantial reworking due to the presence of repetitive sentences, particularly between the recommendation and conclusion sections. To improve the clarity and quality, the recommendation should be condensed into a concise paragraph that highlights the primary assumptions and limitations. On a positive note, the language and style meet the required standards.\nMoreover, it is crucial to ensure a clear and concise statement of the objective in the abstract to provide readers with a comprehensive understanding of the study's focus. Furthermore, the authors should dedicate more attention to elaborating and discussing the points mentioned below. These crucial pieces of information are currently absent from the manuscript and their inclusion through thorough examination is necessary to enhance the overall quality of the article.\n\nVariation in nutritional composition of camel meat such as effect of Age at which the camel is slaughtered plays a significant role in determining the meat's composition and in turn, affects consumer acceptance. Also, the nutritional composition of camel meat shows considerable diversity based on the specific muscle being studied. Different muscle portions have distinct compositions, influencing the overall nutritional profile of the meat. In addition, variations in the chemical composition of camel meat have been observed due to differences in breeds. Different breeds of camels may exhibit varying nutritional properties in their meat.\nUnderstanding these variations is essential for researchers, meat processors, and consumers to make informed decisions regarding camel meat consumption and utilization. By considering these factors, stakeholders can optimize the production and marketing of camel meat products, meeting the preferences and demands of consumers while ensuring the meat's overall quality and nutritional value.\n\nMain constraints of camel production such as presence of camel disease, poor overall knowledge of producer, lack or insufficient market infrastructure, lack of market information and lack or insufficient overall support. Addressing these constraints through targeted interventions, such as disease control programs, capacity-building initiatives, improved market linkages, and policy support, can help to enhance the sustainability and profitability of camel production systems.\n\nCamel rearing and production and slaughtering and processing. Both camel rearing and production, as well as slaughtering and processing, play pivotal roles in determining the overall quality, safety, and value of camel meat in the market.\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? Partly", "responses": [ { "c_id": "10629", "date": "09 Jan 2024", "name": "djamel djenane", "role": "Author Response", "response": "Responses to Reviewer Comments The authors appreciated the careful review and greatly acknowledge the comments and manuscript overall evaluation provided. The authors made the recommended changes and responded in detail to the questions raised by the reviewer. Reviewer#1: The manuscript requires substantial reworking due to the presence of repetitive sentences, particularly between the recommendation and conclusion sections. To improve the clarity and quality, the recommendation should be condensed into a concise paragraph that highlights the primary assumptions and limitations. On a positive note, the language and style meet the required standards. Response: Many thanks for your consideration and valuable comments. The recommendation has been modified according to the reviewer suggestions. Reviewer#1: Moreover, it is crucial to ensure a clear and concise statement of the objective in the abstract to provide readers with a comprehensive understanding of the study's focus. Response: We have carefully considered comments and revised the manuscript. We add more information about main objectives of the paper. Reviewer#1: Furthermore, the authors should dedicate more attention to elaborating and discussing the points mentioned below. These crucial pieces of information are currently absent from the manuscript and their inclusion through thorough examination is necessary to enhance the overall quality of the article. Response: We have carefully considered your comments and revised the manuscript. We hope that you will be pleased with this revision. New references were added to the text regarding the points added. Reviewer#1: Variation in nutritional composition of camel meat such as effect of Age at which the camel is slaughtered plays a significant role in determining the meat's composition and in turn, affects consumer acceptance. Also, the nutritional composition of camel meat shows considerable diversity based on the specific muscle being studied. Different muscle portions have distinct compositions, influencing the overall nutritional profile of the meat. In addition, variations in the chemical composition of camel meat have been observed due to differences in breeds. Different breeds of camels may exhibit varying nutritional properties in their meat. Response: Thank you. Additional data on the chemical composition of camel meat and its variation factors have been added to the manuscript. Reviewer#1: Main constraints of camel production such as presence of camel disease, poor overall knowledge of producer, lack or insufficient market infrastructure, lack of market information and lack or insufficient overall support. Addressing these constraints through targeted interventions, such as disease control programs, capacity-building initiatives, improved market linkages, and policy support, can help to enhance the sustainability and profitability of camel production systems. Response: We appreciate your good comments. We have carefully revised the manuscript by introducing the main constraints of camel production such as camel disease, poor overall knowledge of the producer, lack or insufficiency of market infrastructure, lack of information on the market and the lack or insufficiency of overall support. Effectively addressing these constraints can help improve the sustainability and cost-effectiveness of camel production systems. Reviewer#1: Camel rearing and production and slaughtering and processing. Camel rearing and production, as well as slaughtering and processing, play pivotal roles in determining the overall quality, safety, and value of camel meat in the market Response: The discussion regarding these issues was improved. Thank you very much Pr Dr Djenane Djamel" } ] }, { "id": "153807", "date": "25 May 2024", "name": "Mounir Hassani Zerrouk", "expertise": [ "Reviewer Expertise Food science" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nNotes: This particular article offers an interesting insight on the possible applications and consideration of the camel meat as a potential source for meat production. The article discusses in great detail the important compounds contained in camel meat which could represent a significant source for healthy active principals, therefore proving the beneficial aspects of the camel meat consumption, as well as highlighting several properties of the mentioned product in order to further support the claims and validity of the use of this product as a healthier alternative. The authors have equally ensured to support the data mentioned in the article with relative and recent research as references to the statements made. Another interesting aspect of the offered study is the technological aspects section which represents the potential strategies for the exploitation of camel meat as an environment friendly substitute to red meats as well as potential methods for its storage/shelf life extension.\nThe following list contains minor corrections which need to be taken into consideration:\nAbstract\nReplace: \"the arid regions\" with \"arid regions\".\n\nReplace: \"can be benefit\" with \"can benefit\".\n\nReplace: \"Research on the camel meat\" with \"Research on camel meat\".\n\nReplace: \"the limited information available on this area\" with \"the limited information available in this area\".\n\nReplace: \"developing new preservation techniques as well the development of various products\" with \"as well as the development of various products\".\n\nThe word 'future' should be represented without a hyphen.\n\nReplace: \"The camel meat as an alternative source to red meats\" with \"Camel meat as an alternative source to red meats\".\nIntroduction:\nReplace: \"This come from countries where technical and regulatory developments have made it possible to promotion the camel meat industry and improve product quality\" with \"This comes from countries where technical and regulatory developments have made it possible to promote the camel meat industry and improve product quality\".\n\nReplace: \"This review discusses the nutritional and qualitative properties of camel meat, explains its versatility and positive effects on human health….., in the view of the most\" with \"This review discusses the nutritional and qualitative properties of camel meat, and explains its versatility and positive effects on human health…….., in view of the most...\"\n\nReplace: \"Consumers tend dislike camel meat because they associate meat with the camel itself\", with \"Consumers tend to dislike camel meat because they associate meat with the camel itself\".\n\nReplace: \"The Australian meat industry has been successfully promoted\" with \"The Australian meat industry has successfully promoted\".\n\n\"Bioactive compounds in camel meat Camel meat is characterized by a considerable amount\": the word camel meat seems to be repeated twice at the beginning of the sentence.\n\nReplace: \"by British Department of Health (BDH 1994). Ayyash et al. (2019) claim that camel meat was traditionally used\" with \"by the British Department of Health (BDH 1994). Ayyash et al. (2019) claim that camel meat was traditionally used\".\n\nReplace: \"particularly Middle East, Asia, and Africa, but the use of\" with \"particularly the Middle East, Asia, and Africa, but the use of\".\n\nReplace: \"However, during the 20th century, when intercultural migration of people became very important, knowledge about camels and their products began to reach countries beyond Middle East, Asia and Africa\" with \"However, during the 20th century, when the intercultural migration of people became very important, knowledge about camels and their products began to reach countries beyond the Middle East, Asia and Africa\".\n\nReplace: \"a higher proportion of acyl carnitine in plasma and skeletal muscle of the camel than other animal species suggests an adaptive mechanism that\" with \"a higher proportion of acyl carnitine in plasma and skeletal muscle of the camel than in other animal species suggests an adaptive mechanism\".\n\nReplace: \"that may cause loss of juice displaying a direct impact on the nutrient content of cooked meats\" with \"which may cause loss of juice displaying a direct impact on the nutrient content of cooked meats\".\n\nReplace: \"Camels also have a very efficient feed conversion rate. Nowdays consumers\" with \"Camels also have a very efficient feed conversion rate. Nowadays consumers\".\nIn general, this article offers a concise and complete study around the use and application of camel meat as a novel source of meat products and their derivatives while respecting the appropriate steps to introducing a review article and offering an open invitation towards potential studies with clear and relevant perspectives and 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": "11875", "date": "29 Jun 2024", "name": "djamel djenane", "role": "Author Response", "response": "Abstract Replace: \"the arid regions\" with \"arid regions\". It's done Replace: \"can be benefit\" with \"can benefit\". It's done Replace: \"Research on the camel meat\" with \"Research on camel meat\". It's done Replace: \"the limited information available on this area\" with \"the limited information available in this area\". It's done Replace: \"developing new preservation techniques as well the development of various products\" with \"as well as the development of various products\". It's done The word 'future' should be represented without a hyphen. OK, the hyphen is removed. Replace: \"The camel meat as an alternative source to red meats\" with \"Camel meat as an alternative source to red meats\". It's done Introduction: Replace: \"This come from countries where technical and regulatory developments have made it possible to promotion the camel meat industry and improve product quality\" with \"This comes from countries where technical and regulatory developments have made it possible to promote the camel meat industry and improve product quality\". It's done Replace: \"This review discusses the nutritional and qualitative properties of camel meat, explains its versatility and positive effects on human health….., in the view of the most\" with \"This review discusses the nutritional and qualitative properties of camel meat, and explains its versatility and positive effects on human health…….., in view of the most...\". It's done Replace: \"Consumers tend dislike camel meat because they associate meat with the camel itself\", with \"Consumers tend to dislike camel meat because they associate meat with the camel itself\". It's done Replace: \"The Australian meat industry has been successfully promoted\" with \"The Australian meat industry has successfully promoted\". It's done \"Bioactive compounds in camel meat Camel meat is characterized by a considerable amount\": the word camel meat seems to be repeated twice at the beginning of the sentence. it's corrected Replace: \"by British Department of Health (BDH 1994). Ayyash et al. (2019) claim that camel meat was traditionally used\" with \"by the British Department of Health (BDH 1994). Ayyash et al. (2019) claim that camel meat was traditionally used\". It's done Replace: \"particularly Middle East, Asia, and Africa, but the use of\" with \"particularly the Middle East, Asia, and Africa, but the use of\". It's done Replace: \"However, during the 20th century, when intercultural migration of people became very important, knowledge about camels and their products began to reach countries beyond Middle East, Asia and Africa\" with \"However, during the 20th century, when the intercultural migration of people became very important, knowledge about camels and their products began to reach countries beyond the Middle East, Asia and Africa\". It's done Replace: \"a higher proportion of acyl carnitine in plasma and skeletal muscle of the camel than other animal species suggests an adaptive mechanism that\" with \"a higher proportion of acyl carnitine in plasma and skeletal muscle of the camel than in other animal species suggests an adaptive mechanism\". It's done Replace: \"that may cause loss of juice displaying a direct impact on the nutrient content of cooked meats\" with \"which may cause loss of juice displaying a direct impact on the nutrient content of cooked meats\". It's done Replace: \"Camels also have a very efficient feed conversion rate. Nowdays consumers\" with \"Camels also have a very efficient feed conversion rate. Nowadays consumers\". It's done" } ] } ]	1	https://f1000research.com/articles/11-1085
https://f1000research.com/articles/11-1293/v1	11 Nov 22	{ "type": "Research Article", "title": "Clinical spectrum and short-term outcome of post-COVID multisystem inflammatory syndrome in children after the 2019 pandemic: a longitudinal cohort study", "authors": [ "Sudesh Kumar", "Piyali Bhattacharya", "Nikhil Arya", "Anamika Kumari", "Nandita Chattopadhyay", "Sudesh Kumar", "Piyali Bhattacharya", "Nikhil Arya", "Nandita Chattopadhyay" ], "abstract": "Background As a post-COVID complication in children, multisystem inflammatory syndrome in children (MIS-C) is important because of its varied and life-threatening manifestations. With this background, this study attempts to focus on MIS-C cases in an underprivileged rural setting in north-eastern India, with most patients being treated with methylprednisolone rather than intravenous immunoglobulin due to financial constraints.\nMethods\nIn this prospective longitudinal cohort study at MGM Medical College, 27 MIS-C cases diagnosed following WHO criteria were included. Laboratory and radiological investigations, including echocardiography, were performed as required for diagnosis and to assess prognosis. Most patients were treated with methylprednisolone. A follow-up assessment was done six weeks after discharge for any residual impairment. Results\nThe most frequently affected age group was 5–10 years (59.28%), while respiratory (48.14%) and cardiac (40.74%) were the most commonly involved systems. Logistic regression studies established a significant association between serum ferritin level and prolonged hospital stay (coefficient 0.0674, p=0.0041), possibly due to greater complications in cases with high ferritin levels. Organ impairment was found to increase the need for inotrope use (coefficient 3.8797, p=0.00584). Most cases were treated with methylprednisolone alone (85.18%) with a favourable response and no death occurred.\nConclusion The favourable response in cases treated with methylprednisolone only affirms the effectiveness of the drug as a cheaper alternative in a resource-poor setting. The study highlights that higher ferritin levels in complicated cases leads to prolonged hospitalisation and the increased need for inotropes in cases with organ impairment.", "keywords": [ "Ferritin", "Methylprednisolone", "MODS", "SARS-COV-2 infection" ], "content": "Introduction\n\nStudies on COVID-19-related complications in children were first reported in April 2020 when healthy children presented with either cardiogenic shock or a Kawasaki disease (KD)-like condition associated with severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) infection.1–3 Subsequently, the World Health Organization (WHO) and Center for Disease Control and Prevention (CDC) proposed a case definition for multisystem inflammatory syndrome in children (MIS-C).4–6 MIS-C occurs due to dysregulation of the innate immune system 4–6 weeks following severe acute respiratory syndrome (SARS) infection.7–9 The clinical spectrum varies from mild disease to multi-organ dysfunction syndrome (MODS) which leads to death.10–12 In the largest case series of MIS-C from the USA, the mortality rate was 2%.13 Coronary artery abnormalities developed in 8–24% of cases.14 Most cases were treated with either intravenous immunoglobulin (IVIG) alone or along with methylprednisolone (MP).15,16 As in many other bacterial and viral infections, serum ferritin levels were significantly raised in COVID and post-COVID, along with other inflammatory mediators including tumour necrosis factor alpha (TNFa), interleukin-1 (IL-1), interleukin-8 (IL-8), and type I interferon (IFN). Ferritin plays a crucial role in decreasing iron availability, intracellular sequestration, taming inflammatory reactions, and protecting host cells from oxidative damage.\n\nThe affordability of IVIG is an issue in this remote, underprivileged area in North-Eastern India, prompting us to perform this study with the objectives to study the different clinical presentations across age groups, immediate and short-term outcomes and parameters associated with disease severity.\n\n\nMethods\n\nThis was a prospective longitudinal cohort study conducted at MGM Medical College and LSK Hospital, Bihar, India. From 1st June 2021 to 30th April 2022, the study included recruitment, follow-up, and data collection. Informed consent was taken from participant attendants and ethical clearance was obtained by Ethical committee of institute. IEC No. MGM/PRI-880/22.\n\nChildren up to the age of 18 years admitted to MGM Medical College & Hospital with a clinical diagnosis of MIS-C, in accordance with the WHO criteria, were included in the study.17 Infections including dengue, scrub typhus, and bacterial sepsis and active covid infection (diagnosed by nasopharyngeal rapid antigen test) were excluded by appropriate investigations. COVID-19 antibody IgG and IgM qualitative testing was done in all cases (method: Enzyme Linked Fluorescent Assay Technique on instrument of the VIDAS family). Data collection was done by trained resident doctors in a preformed abstraction form during the hospital stay and on follow-up after six weeks of discharge.\n\nA detailed clinical history and examination were conducted to determine precipitating factors for the illness and reach a clinical diagnosis. Necessary investigations for the diagnosis of MIS-C and evaluation of organ impairment at the time of discharge & follow-up were conducted. Laboratory markers including erythrocyte sedimentation rate, C-reactive protein, neutrophil/lymphocyte ratio, serum ferritin, D-dimer, liver and renal function tests, prothrombin time, and activated partial thromboplastin time (APTT) were done at the time of admission before starting immune-modulator therapy. Creatinine phosphokinase (CPK-MB) and troponin-1 were not included as they were not done routinely at this hospital. Chest X-rays, high-resolution chest computed tomography (CT) scans, electrocardiogram (ECG), and echocardiography were performed where indicated at the time of admission and at the time of follow-up. After six weeks, the children were reassessed with a clinical evaluation and lab tests.\n\nDemographics, clinical signs and symptoms, laboratory parameters, echocardiography, and coronary findings (at admission and at six-week follow-up), duration of ICU stay, medication (with special emphasis on immunomodulators and inotropes), mechanical ventilation, and mortality were all collected using a pre-designed proforma.\n\nThe choice of immunomodulators for treatment was decided by the treating team based on affordability for the patient and guidelines for the management of COVID-19 provided by the Ministry of Health and Family Welfare, Government of India.18 Echocardiography was done in all patients with shock at admission and again six weeks after discharge in case of residual cardiac impairment. Left ventricular ejection fraction (LVEF), coronary artery abnormality with a Z-score of >2.5, and other features like myocarditis, dilated cardiomyopathy, pericardial effusion, and arrhythmia were assessed.19 A person was thought to be in shock if they needed more than 20 mL/kg of IV fluid or an inotrope to keep their blood pressure above the 5th centile.\n\nPatients who were treated with methylprednisolone received a pulse dose of 30 mg/kg/day for three days, followed by 2 mg/kg/day for a week or until their CRP value normalised. Steroids were tapered off over the next 2–3 weeks. Children treated with IVIG received 2 gm/kg as a continuous infusion over 8–12 hours. Recovery with residual organ impairment was defined on the basis of clinical features and laboratory findings or echocardiographic findings at the time of discharge.\n\nThe patients were categorized into three groups according to age: <5 years, 5–10 years, and >10 years for subgroup comparison. All patients were further categorised based on hospital stay (duration) and organ impairment (fully recovered or partial recovery).\n\nSamples were taken using a simple random sampling method technique.\n\nBased on a 95% confidence interval, a 5% alpha error, and the fact that MIS-C occurs in 2% of cases,2 the sample size was calculated to be 32 by online Epi Info software.\n\nWe used R software, version 3.4 (RRID:SCR_001905), for statistical analysis. All continuous variables were summarised using the mean (SD) or median (IQR). Categorical variables were expressed in counts (%). Age group and laboratory findings and complication mean were compared by ANOVA test and categorical frequency were compared by Chi squared test. Logistic regression analysis was used to assess the significant association between complications and laboratory findings. P value less than 0.05 was considered significant.\n\n\nResults\n\nA total of 42 participants were enrolled in the study, but 10 individuals had active cases of COVID-19 (rapid antigen test positive) and 5 were serologically negative and hence were excluded. Among the 27 patients with confirmed MIS-C, 14 (51.9%) were male and 13 (48.1%) were female. The median age of patients was 8 years (range 2–16 yrs.). The most common age group of MIS-C was 5–10 years (59.28%). Three (11.11%) patients had comorbidities such as cerebral palsy, seizure disorder, and pulmonary tuberculosis. A temporal association with COVID-19 infection was identified with serological testing of COVID-19 IgG and IgM. All patients were serologically IgG positive and four (14.81%) were IgM positive.\n\nA fever was present in 26 (96.29%) cases, and one patient was afebrile (Table 1). The most common system involved was the respiratory system, with 13 patients displaying complications of this kind (48.14%). Dyspnea (100%) and cough (38.4%) were the most common symptoms of the respiratory system. Table 1 gives the demographic, clinical characteristics, and the outcome of MIS-C cases across age groups.\n\nThe second most common organ involvement was the cardiac system, which was affected in 11 patients (40.74%). Shock and hypotension were noted in all cases and one patient suffered from cardiac arrhythmia in the form of sinus tachycardia. The incidence of shock was highest in the age group of 5–10 years (81.18%). Mucocutaneous involvement was seen in seven (25.92%) children, among whom a macula-papular rash over the trunk and extremities was evident in six of them (85.71%). Two patients (28.57%) had non-purulent conjunctivitis, and one each had petechia and oropharyngeal congestion. Cervical lymphadenopathy was seen in one child. Seven (25.92%) patients had CNS affection, including six (85.71%) with altered sensorium, four (57.14%) with seizures, and two (28.57%) with headaches. Gastrointestinal involvement was seen in five (18.51%) children, of which diarrhoea was reported in four (80%), followed by abdominal pain in three (60%), and nausea and vomiting in two (40%). Two patients (7.4%) suffered from hepatitis C.\n\nAt the time of admission, anaemia (below 2 standard deviations for age and sex) was found in 14 (51.85%) children. Four (14.8%) had thrombocytopenia (1.5 lakh/mm3) and four (14.8%) had leucopenia (5000 mm3).\n\nAmong inflammatory markers, C-reactive protein (CRP) and erythrocyte sedimentation rate (ESR) were raised in all cases, with an average mean value of 15.89 and 25.59, respectively. Serum ferritin (mean value of 942.04 ng/mL) and dimer (3255 ng/mL) levels were also raised in all cases. Prothrombin time/activated partial thromboplastin time (PT/APTT) was abnormal in two (7.4%) cases and transaminase values were raised in three (11.11%) patients (Table 2).\n\nEchocardiography (ECHO) was done in 11 patients in which myocarditis (54.54%), global hypokinesia (18.18%), severely decreased left ventricular ejection fraction (LVEF) less than 30% was 18.18%, moderately decreased LVEF [30–55%] was 45.45%, and one patient pulmonary embolism were noted.\n\nTwenty-four (88.88%) patients required intensive care, and the median duration of PICU stay was 6.5 days (range 2–15). Four patients (16.66%) required mechanical ventilation and 11 (45.83%) required inotropic support.\n\nTwenty-three patients (85.18%) were treated with methylprednisolone, and four (14.8%) patients were treated with IVIG. Of the patients treated with IVIG, one patient had a complete recovery and three had residual organ impairment at the time of discharge (95% CI, 25–75%; p=0.239). One patient who suffered from a pulmonary embolism was given anticoagulant therapy.\n\nAt the time of discharge, 14 (51.85%) children had fully recovered, and 13 (48.14%) patients suffered from organ impairment, of which 10 had cardiovascular involvement (76.9%), two had CNS involvement (15.38%), and one had respiratory involvement (7.6%). The average median hospital stay duration was 13.5 days (range 7–34). No patients had expired.\n\nAll discharged patients remained clinically stable, and no new symptoms or deterioration were noted. In patients with partial recovery, improvement in terms of increased LVEF, Z scores, and respiratory findings was noted. However, hemiparesis and facial palsy persisted in children with CNS involvement. Multiple logistic regression was done to predict the effect of laboratory markers on the likelihood of occurrence of organ impairment and prolongation of hospital stay in which only serum ferritin level [Coefficient 0.00674; p = 0.0041] was significant for prolongation of hospitalization possibly due to its positive association with greater organ impairment (Tables 3, 4, 5 and Figure 1).\n\nCVS (cardiovascular system), CNS (central nervous system), RESP (respiratory system).\n\n\nDiscussion\n\nThe present study shows a favourable outcome in MIS-C treated with methylprednisolone therapy. In this study, the median age was 8 years old and the most common age group was 5–10 years. Fever was a universal symptom (96.29%). The most common systems of involvement were respiratory (48.14%) and cardiac (40.74%). Shock mainly occurred in the age group of 5–10 years. Mucocutaneous involvement occurred in 25.92% of cases and CNS involvement in 25.92% of cases.\n\nIn a recent multicentre observational study of 134 cases, Nayak S et al. have shown that fever was a universal finding. In 50.7% and 39.6% of the cases, gastrointestinal and respiratory symptoms were observed, respectively. Shock was noted in 35% of cases.20 Sugnan S et al. found that the median age of patients with MIS-C was 7.5 years and the most common symptoms were gastrointestinal (84%) and cardiac (91%).21 In our study gastrointestinal symptom was not such a common presentation as GI cases with relatively milder symptoms, did not come to the tertiary center and commonest age presentation similar to the study by Sugnan S et al.\n\nLaboratory parameters showed a trend toward lower lymphocytes and a high N/L(neutrophil/lymphocyte) ratio. Inflammatory markers such as CRP, ESR, D-dimer, and serum ferritin were high in all cases in our study population. Lacuna–Rangel found an association with having a high white blood cell count, low lymphocyte count, low platelet count, and elevated CRP with increased mortality and severity of disease.22 Tiwari Arun et al. showed that inflammatory markers (CRP, ESR, D-dimer, and ferritin) were elevated in all cases.23 In our study, as in the study by Tiwari et al., these inflammatory markers were elevated.\n\nIn our study, cardiac evaluation by echocardiography revealed myocarditis (54.54%) as a prominent finding, which is higher than a Brazilian study which reported myocarditis in only 27% of cases and a Turkish study that found that a 22.4% incidence of myocardial dysfunction in MIS-C may be due to the fact that mostly referral patients were included in the study.24,25 Thrombosis was not reported in any Indian study but was observed in our studies, and was also documented in studies conducted in the United States and the United Kingdom.26,27\n\nIn our study, 88.88% of cases required intensive care, and the median duration of pediatric intensive care unit (PICU) stay was 6.5 days; 16.66% of PICU patients required MV. In our study, the PICU admission rate was high compared with the subsequently discussed literature due to patients who were critically ill and mostly referred from other hospital.\n\nNayak S et al. reported that 55.2% of patients required intensive care and the median PICU stay was four days. MV was required in 27.38% of cases and the median stay in a hospital was 8.09 days.20\n\nIn our study, most patients were treated with methylprednisolone. At the time of discharge, 51.85% had recovered completely and there was no mortality. The remaining 48.15% went home with some residual impairment. In earlier studies, mortality due to MIS-C was reported to be 1.2–2%.27,28 Godfred-Cato S et al. reported a favourable short-term outcome response to IVIG and steroids.28\n\nIn our study multiple logistic regression showed high serum ferritin level was significantly associated with longer duration of hospital stay which is consistent with study of Mercks J et al. Clinically, it was evident that no systemic complications were seen in cases within one week of hospital stay, though in most cases, greater organ impairment was the underlying cause of the prolonged hospital stay. So, it may be inferred that higher ferritin levels were associated with organ impairment, which led to a prolonged hospital stay. A study by Merck J et al. showed that age and high ferritin were associated with more severe MIS-C.29\n\nIn binary logistic regression, another significant finding was that organ impairment necessitated a greater requirement for inotropes.\n\nIt is thus observed that our patients, mostly treated with methylprednisolone, had a similar outcome compared with studies from other parts of the country and abroad. In a resource-poor setting, this was an effective and affordable mode of treatment.\n\n\n\n1. Being a tertiary center, only patients in more serious condition were admitted, and hence the overall clinical spectrum of MIS-C may not have been truly reflected in the study population.\n\n2. Due to the small sample size, the results may not be representative of the general population.\n\n\n\n1. Use of pulse methylprednisolone therapy as a first-line treatment for MIS-C had favourable immediate and short-term outcomes.\n\n2. High serum ferritin levels are associated with severe systemic complications leading to prolonged hospitalisation.\n\n3. Greater organ infliction, as reflected by residual organ impairment, is associated with increased use of inotropes.\n\n\nConclusions\n\nIn patients with MIS-C with severe organ impairment, IV methylprednisolone pulse therapy was associated with favourable immediate and short-term follow-up outcomes. High serum ferritin can predict severe systemic complications and hence prolonged hospitalisation. This study demonstrates that cases with eventual residual organ impairment require greater use of inotropes. Further studies and longer follow-ups of patients diagnosed with MIS-C are required to improve treatment and follow-up criteria.\n\n\nInformed consent\n\nWritten informed consent was obtained from the parents of all participants under the age of 18 years old.\n\n\nEthical approval\n\nEthical clearance was obtained by the Institutional Ethics Committee. IEC No: MGM/PRI-880/22.", "appendix": "Data availability\n\nFigshare: MISC. https://doi.org/10.6084/m9.figshare.21523530.v1. 30\n\nThe project contains the following underlying data:\n\n- MISC Data Entry.xlsx (raw data).\n\n- MISC questionnaire.docx (raw questionnaire).\n\nFigshare: STROBE checklist for ‘[Clinical spectrum and short-term outcome of post-COVID multisystem inflammatory syndrome in children after the 2019 pandemic: a longitudinal cohort study.]’. https://doi.org/10.6084/m9.figshare.21523530.v1. 30\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\nNYC Health: 2020 Health alert 13: pediatric multi-system inflammatory syndrome potentially associated with covid -19.May 4, 2020.\n\nRiphagen S, Gomez X, Gonzalez-Martinez C, et al.: Hyperinflammatory Shock in Children during COVID-19 Pandemic. Lancet. 2020; 395(May): 1607–1608. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nVerdoni L, Mazza A, Gervasoni A, et al.: An Outbreak of Severe Kawasaki-like Disease at the Italian Epicentre of the SARS-CoV-2 Epidemic: An Observational Cohort Study. Lancet. 2020; 395(June): 1771–1778. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWorld Health Organization (WHO): Multisystem inflammatory syndrome in children and Adolscent with COVID-19: scientific Brief2020.Reference Source\n\nCenters for Disease Control and Prevention: Emergency preparedness and response: a multisystem inflammatory syndrome in children (MIS-C) associated with coronavirus disease 2019 (COVID-19). Health advisory2020 May 14.Reference Source.\n\nRoyal College of Paediatrics and Child Health: Guidance: Paediatric multisystem inflammatory syndrome temporally associated with COVID-19. RCPCH;2020 May 1.\n\nLiu J, Li S, Liu J, et al.: Longitudinal Characteristics of Lymphocyte Responses and Cytokine Profiles in the Peripheral Blood of SARS-CoV-2 Infected Patients. EBioMedicine. May 2020; 55: 102763. PubMed Abstract \| Publisher Full Text\n\nLi H, Liu L, Zhang D, et al.: SARS-CoV-2 and Viral Sepsis: Observations and Hypotheses. Lancet. 2020; 395(May): 1517–1520. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJiang L, Tang K, Levin M, et al.: COVID-19 and Multisystem Inflammatory Syndrome in Children and Adolescents. Lancet Infect. Dis. 2020; 20(November): e276–e288. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHoste L, Van Paemel R, Haerynck F: Multisystem Inflammatory Syndrome in Children Related to COVID-19: A Systematic Review. Eur. J. Pediatr. 2021; 180(February): 2019–2034. PubMed Abstract \| Publisher Full Text\n\nBagri NK, Deepak RK, Meena S, et al.: Outcomes of Multisystem Inflammatory Syndrome in Children Temporally Related to COVID-19: A Longitudinal Study. Rheumatol. Int. 2021; 42(October): 477–484. PubMed Abstract \| Publisher Full Text\n\nTang Y, Li W, Baskota M, et al.: Multisystem Inflammatory Syndrome in Children during the Coronavirus Disease 2019 (COVID-19) Pandemic: A Systematic Review of Published Case Studies. Transl. Pediatr. 2021; 10(January): 121–135. PubMed Abstract \| Publisher Full Text\n\nSon MBF, Murray N, Friedman K, et al.: Multisystem Inflammatory Syndrome in Children — Initial Therapy and Outcomes. N. Engl. J. Med. June 2021; 385: 23–34. Publisher Full Text PubMed Abstract \|\n\nValverde I, Singh Y, Sanchez-de-Toledo J, et al.: Acute cardiovascular manifestations in 286 children with multisystem inflammatory syndrome associated with COVID-19 infection in Europe. Circulation. 2021 Jan 5; 143(1): 21–32. PubMed Abstract \| Publisher Full Text\n\nVerdoni L, Mazza A, Gervasoni A, et al.: An Outbreak of Severe Kawasaki-like Disease at the Italian Epicentre of the SARS-CoV-2 Epidemic: An Observational Cohort Study. Lancet. 2020; 395(June): 1771–1778. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAbrams JY, Godfred-Cato SE, Oster ME, et al.: Multisystem Inflammatory Syndrome in Children Associated with Severe Acute Respiratory Syndrome Coronavirus 2: A Systematic Review. J. Pediatr. November 2020; 226: 45–54.e1. PubMed Abstract \| Publisher Full Text\n\nWorld Health Organisation: Multisystem Inflamatory Syndrome in Children and adolescents with COVID-19.Published May 15, 2020.Reference Source\n\nwww.mohfwgov.in/pdf/guidelines for Management of Covid 19 in children. (18th June 2021)\n\nMcCrindle BW, Rowley AH, Newburger JW, et al.: Diagnosis, Treatment, and Long-Term Management of Kawasaki Disease: A Scientific Statement for Health Professionals From the American Heart Association. Circulation. 2017; 135(April): e927–e999. PubMed Abstract \| Publisher Full Text\n\nNayak S, Panda CP, Biswal B, et al.: Eastern India Collaboration on Multisystem Inflammatory Syndrome in Children (EICOMISC): A Multicentre Observational Study of 134 Cases. Front. Pediatr. 11 March 2022. Publisher Full Text\n\nSugunan S, Bindusha S, Geetha S, et al.: Clinical Profile and Short-Term Outcome of Children With SARS-CoV-2 Related Multisystem Inflammatory Syndrome (MIS-C) Treated With Pulse Methylprednisolone. Indian Pediatr. 2021; 58(April): 718–722. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLagunas-Rangel, Alejandro F: Neutrophil-to-lymphocyte Ratio and Lymphocyte-to-C-reactive Protein Ratio in Patients with Severe Coronavirus Disease 2019 (COVID-19): A Meta-analysis. J. Med. Virol. 2020; 92(April): 1733–1734. PubMed Abstract \| Publisher Full Text\n\nTiwari A, Balan S, Rauf A, et al.: COVID-19 Related Multisystem Inflammatory Syndrome in Children (MIS-C): A Hospital-Based Prospective Cohort Study from Kerala, India. BMJ Paediatrics Open. 2021; 5(October): e001195. PubMed Abstract \| Publisher Full Text\n\nAntúnez-Montes OY, Escamilla MI, Figueroa-Uribe AF, et al.: COVID-19 and Multisystem Inflammatory Syndrome in Latin American Children. Pediatr. Infect. Dis. J. 2020; 40(October): e1–e6. PubMed Abstract \| Publisher Full Text\n\nLima-Setta F, Clara M, de Magalhães-Barbosa G , et al.: Multisystem Inflammatory Syndrome in Children (MIS-C) during SARS-CoV-2 Pandemic in Brazil: A Multicenter, Prospective Cohort Study. J. Pediatr. 2021; 97(May): 354–361. PubMed Abstract \| Publisher Full Text\n\nDavies P, Evans C, Kanthimathinathan HK, et al.: Intensive Care Admissions of Children with Paediatric Inflammatory Multisystem Syndrome Temporally Associated with SARS-CoV-2 (PIMS-TS) in the UK: A Multicentre Observational Study. Lancet Child Adolesc. Health. 2020; 4(September): 669–677. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFeldstein LR, Rose EB, Horwitz SM, et al.: Multisystem Inflammatory Syndrome in U.S. Children and Adolescents. N. Engl. J. Med. 2020; 383(July): 334–346. PubMed Abstract \| Publisher Full Text\n\nGodfred-Cato S, Bryant B, Leung J, et al.: COVID-19–Associated Multisystem Inflammatory Syndrome in Children — United States, March–July 2020. MMWR Morb. Mortal. Wkly. Rep. 2020; 69(August): 1074–1080. PubMed Abstract \| Publisher Full Text\n\nMerckx J, Cooke S, El Tal T, et al.: Predictors of Severe Illness in Children with Multisystem Inflammatory Syndrome after SARS-CoV-2 Infection: A Multicentre Cohort Study. Can. Med. Assoc. J. 2022; 194(April): E513–E523. PubMed Abstract \| Publisher Full Text\n\nKumar S, Bhattacarya P, Arya N, et al.:MISC Data Entry.xlsx. figshare. Dataset.2022. Publisher Full Text" }	[ { "id": "231102", "date": "24 Jan 2024", "name": "Anita Dhanrajani", "expertise": [ "Reviewer Expertise My areas of research include Kawasaki disease", "MISC and Pediatric Lupus" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nI am not seeing a section for aims of the study. Methods are very vaguely described. Specifically need to include detailed descriptions of the control group and intervention group along with treatment protocols used for this group. Not sure what the section \"Procedure\" means. Typically study methodology needs to be described under following sections: Population Intervention Control Outcome\nAlso unclear what was the maximum dose used for both steroids and IVIG.\n\nAlso encourage to use a separate table to show outcomes in the two groups (IVIG only vs Steroids only) assuming that this is the primary aim for the study.\n\nOverall, encourage the authors to rewrite the manuscript to follow a standard format and include more detailed description of methodology for reproducibility.\n\nIs the work 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?\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": "10969", "date": "22 Mar 2024", "name": "sudesh kumar", "role": "Author Response", "response": "Thanks for guiding and promoting me." }, { "c_id": "11938", "date": "05 Jul 2024", "name": "sudesh kumar", "role": "Author Response", "response": "Respected Sir/Ma'am, I have tried to correct your queries." } ] }, { "id": "261166", "date": "05 Jun 2024", "name": "Dr Jigna N Bathia", "expertise": [ "Reviewer Expertise PEDIATRIC RHEUMATOLOGY" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nI appreciate your work; however, I don’t find it suitable for approval. Following are my observations: 1) Aims and Objectives not mentioned. 2) Methods, Procedure not very clear. 3) Outcome measures are vague, clear cut outcome measures need to be defined. Total recovery, partial recovery, residual impairment, organ impairment to be defined 4) There is a sentence “thought to be in shock”; definitions should be clear , “thought “ is not the right way to define in manuscripts. 5) How many had coronary artery abnormalities? 6) In one table lymph nodes seems to be kept under mucocutaneous category. Lymph nodes does not come under mucocutaneous. Lymph nodes fall under lymphoreticular system. 7) What kind of rashes were seen? 8) How many had liver and spleen enlargement? 9) Liver function test may also be included. 10)Ig G and IgM mentioned is in one table. I assume it is Covid IgG and IgM, however it should be written in full. 11) Distribution of patients with regards to how many received what dose needs to be clear. 12) Use of steroids in MIS-C is well reported by now. Even lower doses have been used. 13) to rectify errors in grammar.\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?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [ { "c_id": "11937", "date": "05 Jul 2024", "name": "sudesh kumar", "role": "Author Response", "response": "Respected Sir/Ma'am, I have tried to correct your queries." } ] } ]	1	https://f1000research.com/articles/11-1293
https://f1000research.com/articles/11-1486/v1	12 Dec 22	{ "type": "Case Report", "title": "Case Report: Wellens syndrome in acute total occlusion saved by collateral", "authors": [ "Mochamad Yusuf Alsagaff", "Tony Santoso Putra", "Bagus Putra Dharma Khrisna", "Ricardo Adrian Nugraha", "Tony Santoso Putra", "Bagus Putra Dharma Khrisna", "Ricardo Adrian Nugraha" ], "abstract": "Background: It is important and challenging to distinguish between acute myocardial infarction and Wellens syndrome due to its time to intervention. Difficulties in differentiating between subtypes could mean the patients are overtreated or receive undertreatment. Case report: A 57-year-old man was referred to our emergency ward with acute onset of chest pain. Electrocardiographic (ECG) changes were suggestive of Wellens syndrome type A. Nitroglycerin was administrated, the patient's chest pain disappeared, and we planned an early invasive strategy. He had a previous documented ECG before he went for catheterization and based on the second ECG changes were suggestive of an ST elevation. As the result of the invasive strategy, it was found that there was single-vessel disease, near total occlusion in the middle of the left anterior descending artery (LAD) with collateral from the right coronary artery. After two days of observation in the Intensive Cardiovascular Care Unit (ICCU), the patient improved and was transferred to the Low Care Unit. Conclusions: The case highlights Wellens syndrome in acute total occlusion with collateral artery.", "keywords": [ "acute myocardial infarction", "acute coronary syndrome", "percutaneous coronary intervention", "Wellens syndrome" ], "content": "Introduction\n\nWellens syndrome is characterized by specific ECG profiles in the precordial lead, especially in the T-wave segment, which is associated with critical stenosis of the proximal left anterior descending (LAD) coronary artery.1 The incidence rate is 10–15% of all patients with acute coronary syndrome.2 Moreover, the presence of coronary collateral circulation can change an ECG picture that should be an ST-elevated myocardial infarction due to total or near total occlusion of the left anterior descending artery, turning into an ECG picture of Wellens syndrome.\n\nIn this case, we present Wellens syndrome in acute total occlusion saved by collateral. Significant collateral circulation is believed to improve clinical outcomes, especially in patients with acute coronary syndrome.\n\n\nCase report\n\nA 57-year-old man presented at Dr. Soetomo General Hospital, Surabaya, Indonesia, with sudden chest pain. He had a history of uncontrolled type 2 diabetes mellitus, uncontrolled hypertension, hypercholesterolemia, and a recent history of angina three years prior without undergoing a revascularization procedure. There was no history of cocaine use. He was brought to the emergency department with acute onset of substernal chest pain and diaphoresis. The chest pain started two hours before he was brought to the emergency ward. His chest pain score was four on the visual analogue scale (VAS). Nitroglycerin was administrated then the patient's chest pain disappeared. On physical examination on the emergency ward, he was afebrile with a heart rate of 99, blood pressure of 170/100 mmHg, respiratory rate of 22 breaths per minute, and oxygen saturation of 95% in room air. He was overweight with a pained grunt and he occasionally clutched his chest. Physical examination was unremarkable.\n\nOn day one, the patient was admitted to our emergency ward due to abrupt and sudden onset chest pain with VAS 4/10, that was not relieved by nitroglycerin. ECG showed a biphasic T wave in V2–V4 (Wellens A) (Figure 1). The patient was diagnosed with non-ST elevation myocardial infarction. On day two, transthoracic echocardiography revealed regional wall motion abnormality with reduced ejection fraction. ECG changed into an anterior acute ST-elevation myocardial infarction. Then, we planned to perform early invasive strategy. Coronary angiography revealed a total occlusion in the middle left anterior descending coronary artery. We performed percutaneous coronary intervention and stenting in the lesion. On day four, the patient improved significantly during the critical period and was transferred to low care. On day five, ECG revealed an inverted T wave in V2–V6 (Wellens B) (Figure 2), and then the patient was discharged without any sequelae.\n\nSignificant laboratory findings suggested elevated troponin I levels 2,058 ng/ml (<0.02), HbA1c 8.5% (<6.5%), and complete blood count, renal function test, liver function test and serum electrolyte were within normal limits. ECG in the emergency department (Figure 1) showed an ST segment of less than 1 mm, and there was a biphasic T wave in V2–V4 (Wellens type A) (Figure 2); echocardiography was therefore performed showed ejection fraction was 48%, there was LV dilatation (LVIDd 6.1cm) and eccentric left ventricular hypertrophy (LVdMI: 132.62 g/m2; RWT: 0.320); from segmental analysis, it was found that there was hypokinetic in the anteroseptal (B–M) region, septal (A) region; others regions were within normal limits.\n\nBefore the invasive strategy was done, the patient had another ECG eight hours after the first ECG, based on the second (Figure 2). The ECG showed ST-segment elevation changes that were greater than 1 mm. The early invasive strategy (Figure 3 and Figure 4; Extended data: Video 1 and Video 2)3,4 showed that the left anterior descending artery (LAD) had total occlusion of 100% in the middle LAD (Figure 3). The left circumflex artery (LCx) had non-significant stenosis of 40% proximal and 65% distal, and right coronary artery (RCA) had non-significant stenosis of 55% distal. The RCA had grade 2 collateral arteries that supply blood to the mid LAD (Figure 4).\n\nThe left circumflex artery (LCx) had non-significant stenosis of 40% proximal and 65% distal LCx.\n\nIt is revealed that there is grade II collateral from distal RCA to distal LAD. (Notes: RAO CRA = right anterior oblique + cranial view, a radiographic projection).\n\nRight Bundle Branch Block (RBBB): the ECG shows an inverted T wave, RsR’ in lead V1–V3, QRS duration is >130 ms.\n\nPulmonary embolism has symptoms of chest pain, but the ECG shows S1Q3T3. It means the presence of an S wave in lead I (indicating a rightward shift of the QRS axis) with a Q wave and T inversion in lead III.\n\nCocaine users have ECG patterns like Wellens, called “pseudo-Wellens syndrome”, due to vasospasm of the coronary arteries.\n\nIn accordance with the 2020 European Society of Cardiology Guidelines for Acute Coronary Syndrome,5 our patient received an acetylsalicylic acid loading dose of 300 mg followed by 100 mg once daily, high dose statin with Atorvastatin 40 mg once daily at night, Bisoprolol 2.5 mg once daily, Ramipril 5 mg once daily in the morning, Fondaparinux injection 2.5 mg subcutaneous once daily, IV nitroglycerin 20 mcg/minute for hypertension; the patient’s angina subsided. He was also receiving basal insulin bolus for his diabetes. An early invasive strategy was carried out and the patient was then moved to the ICCU.\n\nOur patient improved significantly during the critical period. After two days in the ICCU, he had no complaints. Based on physical examination, he was afebrile. His heart rate was 70 beats per minute, with blood pressure 123/70 mmHg, respiratory rate 18 breaths per minute, and peripheral oxygen saturation was 95% with a nasal cannula of three litres per minute. Our patient was no longer using nitroglycerin pumps and anticoagulants, and he was transferred to the low-care unit. After three days in the hospital, the results of the ECG examination showed an inverted T wave in V2–V6, and then the patient was discharged without any sequelae. After one month, the patient was controlled for the disease without any sequelae.\n\n\nDiscussion\n\nWellens ECG pattern is commonly found in a patient with total or near total occlusion in the proximal left anterior descending coronary artery. It is commonly associated with NSTE-ACS, followed by new onset angina CCS III-IV or crescendo angina, without increased cardiac markers.6 The spontaneous transformation from Wellens type A ECG pattern into Wellens type B ECG pattern is a rare case. It reflects a pattern of electrocardiography (ECG) that sometimes changes due to occlusion and spontaneous reperfusion from the collateral coronary artery. Wellens type A and type B are particular for critical, proximal stenosis of the left anterior descending (LAD) coronary artery.7 Criteria for diagnosing Wellens syndrome include all of the following8,9:\n\n• Wellens type A describes a pattern of ECG that shows biphasic T wave in the lead V2–V4\n\n• Wellens type B describes a pattern of ECG that shows T inverted in the lead V2–V4\n\n• History of angina\n\n• ECG without Q wave\n\n• Normal or minimally elevated troponin levels\n\n• ST segment isoelectric or minimally elevated (<1 mm)\n\nIn this case, the first ECG showed a biphasic T wave in lead V1–V4 (Wellens type A) and it was minimally elevated (<1 mm). After a few hours before the invasive procedure, the second ECG showed a change in ST-segment elevation of more than 1 mm. In this case, the patient's ECG and troponin level showed Wellens syndrome. However, after a few hours the patient's ECG showed changes, namely an increase in elevation in the ST segment (>1 mm). An abnormal T wave ischemic pattern may persist, remaining between hours to weeks, even when the patient is asymptomatic without chest pain.7 T wave abnormalities can be normalized or evolved into ST-segment elevation in the symptomatic patient with Wellens syndrome. The mechanism responsible for these ECG findings is repolarization heterogeneity resulting from reperfusion of a briefly occluded LAD. This could explain the evolution of T-wave modifications.10,11 In this case, there was complete occlusion in the middle LAD, but the patient received collateral artery supply from the RCA so that the ECG feature mimicked the critical occlusion picture in the proximal LAD.\n\nThe collateral of the coronary artery is classified into five grades. Collateral grade 0 reveals no flow between the collateral of the coronary artery. This condition can occur when several collateral arteries are visible yet not angiographically apparent at any other time. Collateral grade 1 flow reveals a barely apparent collateral coronary artery. Sometimes, there might be an unclear connection with the significant epicardial coronary artery. Collateral grade 2 flow reveals a moderately opaque collateral coronary artery but it was only present through 75% of the cardiac cycle. Collateral grade 3 flow reflects a well-opacified collateral coronary artery while the column of dye is well defined (i.e., >0.5 mm in diameter), but it was <0.7 mm wide throughout most of its length. Collateral grade 4 flow mimics collateral grade 3. The collateral is very well opacified, fills antegrade, and is very large. It was >0.7 mm in diameter throughout its length.12,13\n\nThe cardiac catheterization results found that a collateral artery originating from the right coronary artery (RCA) supplied the mid-distal LAD. Therefore the heart muscle that should have been severely damaged due to not getting blood supply from the LAD could still survive due to the presence of the collateral artery. Previous data has established that enough collaterals can prevent ischemia and directly induce spontaneous reperfusion in one-third of NSTE-ACS patients. Spontaneous reperfusion with well-developed coronary collateral circulation is associated with a better prognosis in cardiovascular mortality reduction.14\n\nIn ischemic conditions, collateral circulations are a good predictor of prognosis. Collateral circulation may support cardiac function and decrease cardiac mortality and morbidity rate. Collateral circulations are inter arterial anastomoses that exist neonatally and grow more significant because of many mechanisms like cytokines and growth factors induced by shear stress and ischemia and pressure gradient changes.15 The collateral circulation artery may appear several weeks after occlusion.14\n\nThe patient felt that his treatment at the hospital was excellent and fast, especially when he felt chest pain. After the medication was taken, his chest pain gradually disappeared. The patient was also very grateful for the direct action of inserting a catheter into the heart in less than 24 hours. The patient hopes that the publication of cases of diseases like his will help paramedics handle them in the future.\n\n\nConclusions\n\nThis case shows Wellens syndrome, which can change into ST-elevation myocardial infarction. Wellens can also occur in the left anterior descending artery that is in total occlusion but gets its blood supply from a branch of the right coronary collateral artery. Based on this case report, an early invasive strategy is recommended, with favorable clinical outcomes.\n\n\nConsent\n\nWritten informed consent for publication of their clinical details and clinical images was obtained from the patient.", "appendix": "Data availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\nFigshare: Extended data for ‘Case Report: Wellens syndrome in acute total occlusion saved by collateral’.\n\nThis project contains the following extended data:\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgments\n\nThe authors would like to express enormous gratitude to all staff, residents, fellows, and nurses in the Intensive Cardiovascular Care Unit and Catheterization Unit that allowed us to collect the data on this patient.\n\n\nReferences\n\nArisha MJ, Hallak A, Khan A: A Rare Presentation of a Rare Entity: Wellens Syndrome with Subtle Terminal T Wave Changes. Case Rep Emerg Med. 2019; 2019: 1–4. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWillim HA, Agustyana A, Arilaksono DG, et al.: A Case Report of Wellens’ Syndrome: An Ominous Sign of Left Anterior Descending Artery Critical Stenosis and Impending Anterior Myocardial Infarction. Indones J Med. 2020; 5: 246–252. Publisher Full Text\n\nNugraha RA, Santoso T: Video 1: Angiography revealed total occlusion at mid LAD. figshare. [Media].2022. Publisher Full Text\n\nNugraha RA, Santoso T: Video 2: Angiography revealed collateral from distal RCA to distal LAD. figshare. [Media].2022. Publisher Full Text\n\nCollet JP, Thiele H, Barbato E, et al.: ESC Scientific Document Group, 2020 ESC Guidelines for the management of acute coronary syndromes in patients presenting without persistent ST-segment elevation: The Task Force for the management of acute coronary syndromes in patients presenting without persistent ST-segment elevation of the European Society of Cardiology (ESC). Eur. Heart J. 2021; 42(14): 1289–1367. PubMed Abstract \| Publisher Full Text\n\nTorelli E, Sardeo F, Nuzzo E, et al.: Wellens Syndrome without chest pain, is it possible? Eur. Rev. Med. Pharmacol. Sci. 2020; 24: 7718–7721. PubMed Abstract \| Publisher Full Text\n\nMiner B, Grigg WS, Hart EH: Wellens Syndrome. Treasure Island (FL): 2021.\n\nZin S, Win M, Oo H, et al.: revisited.2016; 1: 4–7.\n\nRhinehardt J, Brady WJ, Perron AD, et al.: Electrocardiographic manifestations of Wellens’ syndrome. Am. J. Emerg. Med. 2002; 20: 638–643. PubMed Abstract \| Publisher Full Text\n\nRamires TG, Sant’Anna J, Pais J, et al.: Wellens’ syndrome: a pattern to remember. BMJ Case Rep. 2018; 2018: 1–2. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTzimas G, Antiochos P, Monney P, et al.: Atypical Electrocardiographic Presentations in Need of Primary Percutaneous Coronary Intervention. Am. J. Cardiol. 2019; 124: 1305–1314. PubMed Abstract \| Publisher Full Text\n\nTraupe T, Gloekler S, De Marchi SF, et al.: Assessment of the human coronary collateral circulation. Circulation. 2010; 122: 1210–1220. Publisher Full Text\n\nGibson CM, Ryan K, Sparano A, et al.: Angiographic methods to assess human coronary angiogenesis. Am. Heart J. 1999; 137: 169–179. PubMed Abstract \| Publisher Full Text\n\nSeiler C, Stoller M, Pitt B, et al.: The human coronary collateral circulation: Development and clinical importance. Eur. Heart J. 2013; 34: 2674–2682. Publisher Full Text\n\nChilian WM, Penn MS, Pung YF, et al.: Coronary collateral growth—Back to the future. J. Mol. Cell. Cardiol. 2012; 52: 905–911. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "263011", "date": "13 Apr 2024", "name": "Zahid Khan", "expertise": [ "Reviewer Expertise Intervention cardiology and General internal 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\nThe introduction should provide some more information about Wellens syndrome and why early intervention is important. Please exclude any patient identifiable information such as location of the patient/hospital provided in the case report section. Please use the term poorly controlled rather uncontrolled for both hypertension and diabetes. I would suggest to use either recent history or history of angina three years ago rather than using both. There was no history of cocaine use (This is not required and it should be part of the social history along with smoking and drinking) On physical examination on the emergency ward (in the emergency ward , oxygen saturation of 95% on room air)\nThe trop rise of this level does not really fit with Wellens syndrome. Wellens syndrome patients tend to have mild trop rise\nThe differential diagnosis are poorly constructed and please include more relevant differential diagnosis.\nGeneral comments. The case report is about a patient presenting with chest pain and the authors claim that the patient had wellens syndrome. The case report has significant grammatical errors that need rectifying. The presentation lacks flow and is disjointed. The high level of trop does not really fit with wellens syndrome type picture. Please remove all patient's identifiable information from the case report. The introduction and case presentation sections need significant revision.\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": "11632", "date": "28 Jun 2024", "name": "Ricardo Adrian Nugraha", "role": "Author Response", "response": "The introduction should provide some more information about Wellens syndrome and why early intervention is important. Authors response: thank you for your suggestion. We have provided some more information about Wellens syndrome in the Introduction section. We have provided the reason why early intervention is important in the Conclusion section. Please exclude any patient identifiable information such as location of the patient/hospital provided in the case report section. Authors response: thank you for your constructive feedback. We have removed any patient identifiable information In our 2 videos. Please use the term poorly controlled rather uncontrolled for both hypertension and diabetes. Authors response: thank you for your suggestion. We have used the term poorly controlled hypertension and diabetes. I would suggest to use either recent history or history of angina three years ago rather than using both. Authors response: thank you for your suggestion. We have used the term history of angina three years ago. There was no history of cocaine use (This is not required and it should be part of the social history along with smoking and drinking) Authors response: thank you for your suggestion. We have used the term social history of smoking or drinking. On physical examination on the emergency ward (in the emergency ward , oxygen saturation of 95% on room air) Authors response: thank you for your suggestion. We have used the term as you have suggested. The trop rise of this level does not really fit with Wellens syndrome. Wellens syndrome patients tend to have mild trop rise Authors response: thank you for your suggestion. Unfortunately, our case has significant raised of troponin level which may be unsuitable for Wellens syndrome. We have tried to search for any literatures regarding cardiac enzyme among Wellens syndrome, and found that troponin may be falsely reassuring in patients with Wellens syndrome. Only 12% of patients with Wellens syndrome had elevated cardiac enzymes, and these elevations were less than twice the upper limit of normal. Increase of cardiac enzymes in our case may indicates that cardiac myonecrosis have already been occurred at the time of diagnosis. The differential diagnosis are poorly constructed and please include more relevant differential diagnosis. Authors response: thank you for your suggestion. We have added several differential diagnosis: Hyperacute T-waves, de Winter T-waves, Isolated posterior MI, T waves upright in V1, Persistent juvenile T-wave pattern, Digitalis toxicity, Acute myocarditis, Preexcitation syndromes, Later stages of pericarditis, and Central nervous system disorders. General comments. The case report is about a patient presenting with chest pain and the authors claim that the patient had wellens syndrome. The case report has significant grammatical errors that need rectifying. Authors response: thank you for your suggestion. We tried to correct several grammatical errors in our literatures. The presentation lacks flow and is disjointed. The high level of trop does not really fit with wellens syndrome type picture. Authors response: thank you for your suggestion. Unfortunately, our case has significant raised of troponin level which may be unsuitable for Wellens syndrome. We have tried to search for any literatures regarding cardiac enzyme among Wellens syndrome, and found that troponin may be falsely reassuring in patients with Wellens syndrome. Only 12% of patients with Wellens syndrome had elevated cardiac enzymes, and these elevations were less than twice the upper limit of normal. Increase of cardiac enzymes in our case may indicates that cardiac myonecrosis have already been occurred at the time of diagnosis. Please remove all patient's identifiable information from the case report. Authors response: thank you for your constructive feedback. We have removed any patient identifiable information In our 2 videos. The introduction and case presentation sections need significant revision. Authors response: thank you for your suggestion. We have provided some more information about Wellens syndrome in the Introduction section." } ] }, { "id": "263004", "date": "09 May 2024", "name": "Dhan Bahadur Shrestha", "expertise": [ "Reviewer Expertise General Cardiology", "Arrythmia and electrophysiology", "Sudden cardiac death/Cardiac arrest" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThank you for offering this opportunity to review the manuscript by Alsagaff et al. titled \"Case Report: Wellens syndrome in acute total occlusion saved by collateral.\" It is an interesting topic, and I carefully reviewed the manuscript. General Comments 1. As a rule of writing, it is recommended not to abbreviate if the abbreviation is not used more than once. The abstract and manuscript sections are separate sections; the abbreviations/acronyms need the same consideration. The use of LAD/ICCU in the abstract is unnecessary. However, in the manuscript body, ECG is not abbreviated on its first use. Authors need to be careful in considering the same principle throughout the manuscript 2. Some written statements are contradictory. The abstract mentions \"...near total occlusion in the middle of the left anterior descending artery (LAD) with collateral from the right coronary artery. \" However, the case report section mentions total occlusion. For uniformity, authors need to consider the same principle throughout the manuscript. 3. I agree with general comments in terms of writing, as suggested by another reviewer. The authors need more background discussion about Wellen syndrome and its equivalent STEMI and perhaps consideration of a new MI classification considering vascular occlusion (OMI vs. N-OMI). It seems the authors are more so focused on collateral circulation in the discussion, which may be less relevant in mentioning detailed classifications of collaterals in half of the discussion section. 4. It's unclear to me whether the authors reported HS-troponin or just troponin. The AHA 2021 chest pain guideline recommends an HS-troponin assay.\n\n5. The relevance of this paragraph \"The patient felt that his treatment at the hospital was excellent and fast, especially when he felt chest pain. After the medication was taken, his chest pain gradually disappeared. The patient was also very grateful for the direct action of inserting a catheter into the heart in less than 24 hours. The patient hopes that the publication of cases of diseases like his will help paramedics handle them in the future.\" is uncertain to me, rather more objective mention of patient care timeline (door to cath lab/balloon) and its alignment with recent 2018 ESC or 2021 AHA/ACC revascularization guideline would be more 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": "11633", "date": "28 Jun 2024", "name": "Ricardo Adrian Nugraha", "role": "Author Response", "response": "1. As a rule of writing, it is recommended not to abbreviate if the abbreviation is not used more than once. The abstract and manuscript sections are separate sections; the abbreviations/acronyms need the same consideration. The use of LAD/ICCU in the abstract is unnecessary. However, in the manuscript body, ECG is not abbreviated on its first use. Authors need to be careful in considering the same principle throughout the manuscript Authors response: thank you for your very constructive feedback. We have replaced any abbreviations with the full words. 2. Some written statements are contradictory. The abstract mentions \"...near total occlusion in the middle of the left anterior descending artery (LAD) with collateral from the right coronary artery. \" However, the case report section mentions total occlusion. For uniformity, authors need to consider the same principle throughout the manuscript. Authors response: thank you for your critical observation. We have reviewed again the angiography video and found it was critical occlusion (99% stenosis). 3. I agree with general comments in terms of writing, as suggested by another reviewer. The authors need more background discussion about Wellen syndrome and its equivalent STEMI and perhaps consideration of a new MI classification considering vascular occlusion (OMI vs. N-OMI). It seems the authors are more so focused on collateral circulation in the discussion, which may be less relevant in mentioning detailed classifications of collaterals in half of the discussion section. Authors response: thank you for your feedback. We have added several background of Wellens syndrome in the Introduction section. We have added the reason to a new MI classification considering vascular occlusion (OMI vs. N-OMI) in the Discussion section. 4. It's unclear to me whether the authors reported HS-troponin or just troponin. The AHA 2021 chest pain guideline recommends an HS-troponin assay. Authors response: thank you for your questions. It was HS-troponin I. 5. The relevance of this paragraph \"The patient felt that his treatment at the hospital was excellent and fast, especially when he felt chest pain. After the medication was taken, his chest pain gradually disappeared. The patient was also very grateful for the direct action of inserting a catheter into the heart in less than 24 hours. The patient hopes that the publication of cases of diseases like his will help paramedics handle them in the future.\" is uncertain to me, rather more objective mention of patient care timeline (door to cath lab/balloon) and its alignment with recent 2018 ESC or 2021 AHA/ACC revascularization guideline would be more appropriate. Authors response: after reviewing it carefully, we decided to delete this irrelevant paragraph." } ] } ]	1	https://f1000research.com/articles/11-1486
https://f1000research.com/articles/13-750/v1	05 Jul 24	{ "type": "Research Article", "title": "Tuberculosis Case Finding Using Self-Assessment Paradigm Through the E-TIBI Application in HIV Patients", "authors": [ "Erwin Astha Triyono", "Merita Arini", "Feriawan Tan", "Lilis Masyfufah", "Merita Arini", "Feriawan Tan", "Lilis Masyfufah" ], "abstract": "Background The goal of eliminating tuberculosis has not yet shown a bright spot. Specifically for HIV patients (PLHIV), WHO has made it a special category as a pillar for eliminating tuberculosis. The tuberculosis screening has not yet reached the national target because it is carried out manually by health workers, requiring optimization following technological developments. This study aims to determine the effectiveness of tuberculosis case finding using a self-assessment paradigm in HIV patients.\n\nMethods This research was cross-sectional. The data obtained from HIV patients before and after using the E-TIBI application for 3 months each was analyzed using the compare mean independent t-test. Then the Chi-squared test was carried out on the E-TIBI screening characteristic variables.\n\nResult In total, there were 921 respondents with 148 (16%) presumptive TB. It was found that there was a significant difference (p<0.05) in the number of presumptive TB cases found in HIV patients before and after using the E-TIBI application. The person with presumptive TB showed 20 of 24 characteristic variables that were statistically significant (p<0.05).\n\nConclusion E-TIBI can increase the tuberculosis case finding in HIV patients so it has the potential to be implemented as a screening tool in the PLHIV community.", "keywords": [ "Tuberculosis", "HIV", "Case Finding", "Self-Assessment", "Digital Health" ], "content": "Introduction\n\nThe goal of eliminating tuberculosis (TB) by 2030 by WHO has not shown bright spots. This infectious disease is still a major health problem in the world. This disease is caused by Mycobacterium tuberculosis that very easily transmitted through air droplets released by sufferers. The risk of transmission increases many times in individuals with chronic immune problems such as in patients with HIV.1,2 The group of people living with HIV (PLHIV) is specifically categorized by WHO as a pillar for eliminating tuberculosis because of the strong relationship of both.3\n\nThe tuberculosis epidemic has claimed more human lives than any other infectious disease. Globally, a total of 10.6 million people in the world are infected with tuberculosis, with an estimated 1.6 million deaths each year and the PLHIV group causes 200,000 deaths.3 HIV disease is also a global health burden with a total of 70 million sufferers worldwide and 35 million reported dead. Tuberculosis infection in this population can increase the progression of disease to death.4\n\nCurrently, TB-HIV case detection is mostly done manually by taking anamnesis from health workers, TB-HIV cadre approaches, and community.5,6 Manual case finding is still not effective due to limited personnel, lack of training, and lack of health officer motivation. Therefore, finding TB-HIV cases requires a more modern system following current developments in digital technology.7,8\n\nThe advanced development of digital technology can be utilized to optimize self-assessment-based disease case findings. Through the self-assessment paradigm, people can effectively and efficiently carry out screening independently and proceed to medical examinations if necessary.9 Therefore, this research aims to determine the effectiveness of tuberculosis case finding using on self-assessment paradigm through the E-TIBI application in HIV patients (PLHIV) at Dr. Soetomo General Hospital, Surabaya so that it can reduce morbidity and mortality in TB-HIV patients.\n\n\nMethods\n\nThis research method was cross-sectional with the population were all HIV patients undergoing outpatient therapy at Dr. Soetomo General Academic Hospital in Surabaya. The data were collected from the period October – December 2023 for data before (using medical record data filled in by health workers) and January – March 2024 for data after using the E-TIBI application. To assess the effectiveness of pre and post tuberculosis case findings among PLHIV tested using the compare means independent t-test. Then, the characteristic variables were tested using crosstab with a Chi-squared test.\n\nE-TIBI application was a website-based application that can be accessed freely at https://dinkes.jatimprov.go.id/assesment-tbc/public/. After accessing the link an informed consent will appear. There were three main section of this screening. First the respondent must fill in the initial identity (determine the screening for her/him or someone else) and second the identity details (age, gender, occupation, and address). Next the screening question section that’s contain 21 questions. After completing and submitting the form a result come out showing whether presumptive TB or Not. On the E-TIBI application, there was also a filling guide and video education.\n\nPresumptive TB were determined according to the following criteria: Main symptom (Cough for more than two weeks) with or without additional symptoms, there were main symptoms or additional symptoms with a contact history, major symptoms or additional symptoms associated with risk factors. The questionnaire in this application was obtained from the Tuberculosis Symptom Screening from the Indonesian Ministry of Health 2022.10\n\nE-TIBI application was manufactured by utilizing an information technology development standard that involves database connections with Hypertext Preprocessor (PHP)11 and HTML based programming. The stylesheet language using CSS (Cascading style sheets) with Asynchronous JavaScript and XML (AJAX). Additional tools used was Vue.js, PostgreSQL, VueX, and Vite. The prototype design using Figma and Sketch. The device used in manufacturing this application was a laptop with processor Core i5-7th gen, 8GB RAM with Windows 10 Operating System, 64-bit, SSD 128GB.\n\nThis website-based application has been registered as copyright of the Ministry of Law and Human Rights of the Republic of Indonesia with number EC00202365785.\n\n\nResult\n\nThe total number of HIV patients (PLHIV) who accessed the E-TIBI application was 921 people with 148 (16%) presumptive tuberculosis. In Table 1 it was found that there was a significant difference (p<0.05) with difference means -43.000 in the number of presumptive TB case findings in HIV patients (PLHIV) before and after using the E-TIBI application. Table 2 shows the characteristics of the E-TIBI screening results, the person with presumptive tuberculosis showed 20 of 24 characteristic variables that were statistically significant (p<0.05).\n\n\nDiscussion\n\nSince 2011, WHO has recommended that people living with HIV (PLHIV) undergo routine tuberculosis screening. If 4 cardinal symptoms are found consisting of cough, fever, night sweats and weight loss, PLHIV must undergo a molecular diagnostic examination such as Xpert MTB/RIF/Ultra11.12 This research is an investigative effort towards a new paradigm to increase TB case finding in key populations. As far as researchers’ best research is concerned, this research is the first to be conducted in Indonesia. In general, this research illustrates the potential benefits of technology as a new approach to finding a person with presumptive TB.\n\nIn Indonesia, the tuberculosis case findings still rely on health workers who are assisted by trained cadres in health facilities. The Ministry of Health, through active and passive approaches, is trying to increase the acceleration of case finding. Active case finding is carried out by tracking contact, epidemiological investigations and mass screening of at-risk groups, while passive case finding is by examining patients who come to health facilities.13 Through E-TIBI a new paradigm is formed by emphasizing public participation as the main actor who initiates the initial examination. It is believed that this public participation can increase the tuberculosis case findings, especially in the PLHIV group. Health facilities will also receive notification and be given the authority to follow up if there is presumptive TB in their working area. Apart from that, E-TIBI is also a medium for information and education about tuberculosis and its management.\n\nIn this study, from the screening results, 148 (16%) presumptive TB were found. This result compared with other studies was quite varied. Gersh (2021) found 48 (12.6%) participants with TB symptom, Santos (2020) found 15.4% patients with three symptoms WHO screening, Owiti’s research (2019) found 4160 (0.7%) patients with presumptive symptoms of tuberculosis, Bjerrum (2016) found 12.6-20% tuberculosis suspicion, and Burmen (2016) found 96 (16%) PLHIV patients needed further examination.14–17 The use of E-TIBI shows a significant relationship with the number of presumptive TB in PLHIV patients who undergo TB screening. The number of presumptive TB from the E-TIBI self-assessment results is seven-fold higher when compared to manual screening. This is possible because the use of electronic screening is much simpler and can reduce delay by answering questions that are available on the website application, while manual screening must be carried out at the clinic, this is also found in Woliansky (2024) and Blink (2022) study.18,19\n\nThe result found cough, weight loss, decreased appetite, fever, fatigue, night sweats, dyspnea, chest pain, and lumps in the neck were statistically significant with presumptive tuberculosis. Based on current research these signs and symptoms are often found in TB patients.17 In HIV patients (PLHIV) these symptoms become more varied depending on the severity and immunosuppression of the patient.20\n\nOur study indicated that BMI or body mass index is quite influential in combined TB-HIV infection. Several studies state that patients with a BMI below normal have a three-fold higher risk of being infected with TB than HIV patients compared to those with a normal BMI.21 Apart from that, a low BMI also has a worse prognosis, increasing the risk of death up to three-fold higher.22 This is because patients with a BMI below normal are assumed to experience malnutrition which aggravates their immunocompromised condition and leads to death.23\n\nHistory of contact with TB sufferers is important in TB screening, as this study shows. Household contact research by Karbito (2022) said that spending five hours or more with active TB patients increases the risk of latent TB infection by three-fold higher compared to less than five hours a day.24 Laghari’s research (2019) states that household contact increases the risk of TB infection by up to fifteen-fold higher.25\n\nIn the result found Diabetes mellitus (DM) was statistically significant with presumptive tuberculosis. The risk of TB in patients with DM increases to three-fold higher.26 Diabetes mellitus has also been shown to increase the risk of multi-drug-resistant TB. Uncontrolled diabetes mellitus as assessed by high HbA1c and GDP is closely related to TB susceptibility and worsens treatment prognosis.27 This is also exacerbated by Indonesia being in the top three countries with the highest TB burden in the world and the top 10 countries with DM sufferers in the world. Pathophysiologically, DM itself worsens TB infection through many mechanisms ranging from increasing the risk of infection, increasing the risk of latent TB reactivation, increasing the risk of relapse, and worsening treatment to death.28 TB infection also often causes temporal hyperglycemia, which is caused by stress, prolonged inflammation, changes in glucose and lipid metabolism, and insulin resistance syndrome.29\n\nA history of TB treatment or infection is a risk factor that also has an influence, especially in the HIV population, as found in this study. Based on several works of literature, it is stated that the risk of latent TB reactivation becoming active TB in PLHIV is up to twenty-fold higher.30 Other research states that tuberculosis infections in PLHIV are more likely to be caused by reactivation than by new infections.31 This is mainly caused by the depletion of CD4+ cells in untreated PLHIV patients. Apart from that, it was also reported that functional disruption of TB-specific T cells, increased regulation of TB receptors on macrophages, manipulation of macrophage bactericidal pathways, deregulation of chemotaxis, and deregulation of macrophage apoptosis by TNF were the reasons why reactivation increased.32\n\nSmoking is also a risk factor that has a significant relationship with TB-HIV infection. These results are supported by research which states that smoking increases the risk of TB up to three-fold higher and people who have ever smoked up to two-fold higher compared to those who have never smoked in PLHIV.33 Exposure to cigarette smoke also significantly increases the risk of transmitting TB to family or close contacts. In addition, the prevalence of smoking has doubled in TB patients compared to the general population.34 Apart from that, smoking also worsens TB symptoms, increases the risk of drug resistance, increases the risk of cardiovascular disease, worsens treatment outcomes and even death.35\n\nIn the future, the research team plans to develop this application not only limited to screening but into a complete TB-HIV management system, through an account application that is used to carry out TB screening in PLHIV, update patient data, namely the results of diagnosis confirmation, drug taking visits and evaluation until completion of treatment. And then this application is also expected to be implemented in all tuberculosis key populations and the wider community.\n\nThe tuberculosis case finding using self-assessment through the E-TIBI application is a new paradigm of disease screening conducted in Indonesia. With the help of technological advances through E-TIBI, tuberculosis screening can be done easily and quickly by anyone, anytime and wherever they are. This research has limitations, not all HIV patients (PLHIV) can access the E-TIBI service because some patients do not bring cellphones that have an internet connection and some of them cannot use internet technology.\n\n\nConclusion\n\nE-TIBI has the potential to be a tuberculosis screening tool because the number of TB case findings in HIV patients (PLHIV) before and after using the E-TIBI application was a significant increase (p<0.05). The presumptive tuberculosis showed 20 of 24 characteristic variables that were statistically significant (p<0.05). It is hoped that this application can be implemented widely as a screening tool in the PLHIV community.\n\nThis research was registered at the Ethical Committee in Health Research Dr. Soetomo General Academic Hospital, Surabaya, Indonesia (0920/KEPK/II/2024 dated February 19, 2024).\n\nConsent: In this study, before the participant undergo screening, written informed consent will appear in the website application and if participants agree, they must click “willing” before they can carry out screening.", "appendix": "Data availability\n\nFigshare: Tuberculosis Case Finding Using Self-Assessment Paradigm Through the E-TIBI Application in HIV Patients_Raw Data E-TIBI. https://doi.org/10.6084/m9.figshare.25953712.v2 36\n\nThis project contains the following underlying data:\n\n• Raw Data Spss E-TIBI.xlsx (Anonymised answers to questionnaire, correct answer +1 incorrect answer 0)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0)\n\nFigshare: Tuberculosis Case Finding Using Self-Assessment Paradigm Through the E-TIBI Application in HIV Patients_Screening form, https://doi.org/10.6084/m9.figshare.26082367.v3 37\n\nThis project contains the following extended data:\n\n• Screening form.docx (Blank Indonesian version of questionnaire.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nFigshare: Tuberculosis Case Finding Using Self-Assessment Paradigm Through the E-TIBI Application in HIV Patients_STROBE.docx, https://doi.org/10.6084/m9.figshare.25991857.v2 38\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0)\n\n\nAcknowledgments\n\nThe researchers would like to thank the East Java Provincial Health Office, Indonesia and the Department of Internal Medicine, Dr. Soetomo General Academic Hospital Surabaya, Indonesia\n\n\nReferences\n\nDarsino AM: Risk factors in pulmonary tuberculosis patients undergoing hospitalization: a literature review. Indonesia. J. Biomed. Sci. 2022; 16(2).\n\nVan Woudenbergh E, Irvine EB, Davies L, et al.: HIV Is Associated with Modified Humoral Immune Responses in the Setting of HIV/TB Coinfection. Imperiale MJ, editor. mSphere. 2020 Jun 24; 5(3): e00104–e00120. Publisher Full Text\n\nWHO: Global Tuberculosis Report. WHO; 2022.\n\nTan F, Triyono EA, Wahyunitisari MR: Microbial Patterns of Hospitalized HIV Positive Patients Admitted in Dr. Soetomo General Hospital, Surabaya, Indonesia. J. Vocat. Heal. Stud. 2021 Jul 31; 5: 1.\n\nAbeid R, Mergenthaler C, Muzuka V, et al.: Increasing TB/HIV Case Notification through an Active Case-Finding Approach among Rural and Mining Communities in Northwest Tanzania. Wang M, editor. J. Trop. Med. 2022; 2022: 1–11. Publisher Full Text\n\nOhene SA, Bonsu F, Adusi-Poku Y, et al.: Case finding of tuberculosis among mining communities in Ghana. Quinn F, editor. PLoS One. 2021 Mar 18; 16(3): e0248718. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nIswari AP, Porusia M: Faktor Kinerja Kader Community TB-HIV Care Aisyiyah Terhadap Penemuan Suspek TB di Surakarta.2018.\n\nKusumawati PK, Saraswati LD, Martini M, et al.: Gambaran Pengetahuan Petugas TB-HIV Dalam Penemuan dan Akses Pengobatan (Studi di Layanan Komprehensif Berkesinambungan di Puskesmas Kota Semarang). Jurnal Kesehatan Masyarakat (Undip). 2021 Aug 1; 9(4): 497–503. Publisher Full Text\n\nTriyono EA, Mahanani M, Anggraini SD, et al.: Early Detection of Tuberculosis Application (E_TIBI): A New Paradigm To Detetct New Case of Tuberculosis. Aplikasi Deteksi Dini Tuberkulosis (E-TIBI): Paradigma Baru untuk Menemukan Kasus Baru Tuberkulosis. JBE. 2023 Sep 15; 11(3): 267–276. Publisher Full Text\n\nKemenkes.: Standar Prosedur Operasional (SPO) Gerakan Optimalisasi Kasus Tuberkulosis (TBC). Tahun. 2022; 2022.\n\nLerdorf R: PHP on Hormones.Reference Source\n\nDhana A, Hamada Y, Kengne AP, et al.: Tuberculosis screening among HIV-positive inpatients: a systematic review and individual participant data meta-analysis. Lancet HIV. 2022 Apr; 9(4): e233–e241. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKemenkes: Strategi Nasional Penanggulangan Tuberkulosis di Indonesia 2020-2024.2020.\n\nBjerrum S, Bonsu F, Hanson-Nortey NN, et al.: Tuberculosis screening in patients with HIV: use of audit and feedback to improve quality of care in Ghana. Glob. Health Action. 2016 Dec 1; 9(1): 32390. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nOwiti P, Onyango D, Momanyi R, et al.: Screening and testing for tuberculosis among the HIV-infected: outcomes from a large HIV programme in western Kenya. BMC Public Health. 2019 Dec; 19(1): 29. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGersh JK, Barnabas RV, Matemo D, et al.: Pulmonary tuberculosis screening in anti-retroviral treated adults living with HIV in Kenya. BMC Infect. Dis. 2021 Dec; 21(1): 218. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSantos ML, Batista JdAL, Braga C, et al.: Effectiveness of screening for tuberculosis in HIV: a pragmatic clinical trial. Rev Saúde Pública. 2021 Jul 23; 55: 45. Publisher Full Text\n\nWoliansky M, Lee K, Tadakamadla S: The effectiveness of electronic screening and brief intervention for alcohol-related maxillofacial trauma: a randomized controlled trial. Oral Surg. Oral Med. Oral Pathol. Oral Radiol. 2024 May; 137(5): 451–462. PubMed Abstract \| Publisher Full Text\n\nVan Den Blink A, Janssen LMJ, Hermanides J, et al.: Evaluation of electronic screening in the preoperative process. J. Clin. Anesth. 2022 Nov; 82: 110941. Publisher Full Text\n\nHamada Y, Getahun H, Tadesse BT, et al.: HIV-associated tuberculosis. Int. J. STD AIDS. 2021 Aug; 32(9): 780–790. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKufa T, Chihota V, Mngomezulu V, et al.: The incidence of tuberculosis among hiv-positive individuals with high CD4 counts: implications for policy. BMC Infect. Dis. 2016 Dec; 16(1): 266. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTola A, Mishore KM, Ayele Y, et al.: Treatment Outcome of Tuberculosis and Associated Factors among TB-HIV Co-Infected Patients at Public Hospitals of Harar Town, Eastern Ethiopia. A five-year retrospective study. BMC Public Health. 2019 Dec; 19(1): 1658. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKegne T, Anteneh Z, Bayeh T, et al.: Survival Rate and Predictors of Mortality Among TB-HIV Co-Infected Patients During Tuberculosis Treatment at Public Health Facilities in Bahir Dar City. Northwest Ethiopia. IDR. 2024 Apr; 17: 1385–1395. Publisher Full Text\n\nKarbito K, Susanto H, Adi MS, et al.: Latent tuberculosis infection in family members in household contact with active tuberculosis patients in Semarang City, Central Java, Indonesia. J. Public Health Afr. 2022 Jul 27 [cited 2024 Apr 27]; 13(2). PubMed Abstract \| Publisher Full Text \| Free Full Text Reference Source\n\nLaghari M, Sulaiman SAS, Khan AH, et al.: Contact screening and risk factors for TB among the household contact of children with active TB: a way to find source case and new TB cases. BMC Public Health. 2019 Dec; 19(1): 1274. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBisht MK, Dahiya P, Ghosh S, et al.: The cause–effect relation of tuberculosis on incidence of diabetes mellitus. Front. Cell. Infect. Microbiol. 2023 Jun 26; 13: 1134036. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHarries AD, Kumar AMV, Satyanarayana S, et al.: Diabetes mellitus and tuberculosis: programmatic management issues. Int. J. Tuberc. Lung Dis. 2015 Aug 1; 19(8): 879–886. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nVan Crevel R, Critchley JA: The Interaction of Diabetes and Tuberculosis: Translating Research to Policy and Practice. TropicalMed. 2021 Jan 8; 6(1): 8. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRestrepo BI: Diabetes and Tuberculosis. Schlossberg D, editor. Microbiol Spectr. 2016 Dec 23; 4(6): 4.6.48. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPawlowski A, Jansson M, Sköld M, et al.: Tuberculosis and HIV Co-Infection. Hobman TC, editor. PLoS Pathog. 2012 Feb 16; 8(2): e1002464. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWinter JR, Smith CJ, Davidson JA, et al.: The impact of HIV infection on tuberculosis transmission in a country with low tuberculosis incidence: a national retrospective study using molecular epidemiology. BMC Med. 2020 Dec; 18(1): 385. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYang Q, Han J, Shen J, et al.: Diagnosis and treatment of tuberculosis in adults with HIV. Medicine. 2022 Sep 2; 101(35): e30405. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBronner Murrison L, Martinson N, Moloney RM, et al.: Tobacco Smoking and Tuberculosis among Men Living with HIV in Johannesburg, South Africa: A Case-Control Study. Oni T, editor. PLoS One. 2016 Nov 28; 11(11): e0167133. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTeshima A, Shatnawi AA, Satyanarayana S, et al.: High prevalence of current tobacco smoking among patientswith tuberculosis and people living with HIV in Jordan: Across-sectional survey. Tob. Induc. Dis. 2023 Oct 20; 21(October): 1–13. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKumar SR, Pooranagangadevi N, Rajendran M, et al.: Physician’s advice on quitting smoking in HIV and TB patients in south India: a randomised clinical trial. Public Health Action. 2017 Mar 21; 7(1): 39–45. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTriyono EA: Tuberculosis Case Finding Using Self-Assessment Paradigm Through the E-TIBI Application in HIV Patients_Raw Data E-TIBI. [Dataset]. figshare. 2024. Publisher Full Text\n\nTriyono EA: Tuberculosis Case Finding Using Self-Assessment Paradigm Through the E-TIBI Application in HIV Patients_Screening form. [Journal contribution]. figshare. 2024. Publisher Full Text\n\nTriyono EA: Tuberculosis Case Finding Using Self-Assessment Paradigm Through the E-TIBI Application in HIV Patients_STROBE.docx. [Preprint]. figshare. 2024. Publisher Full Text" }	[ { "id": "301074", "date": "07 Aug 2024", "name": "Srinath Satyanarayana", "expertise": [ "Reviewer Expertise All aspects related to TB service delivery." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nMajorly, the target population (the denominator) for the screening services is unclear.\nHow many PLHIV were there, how many of them were informed about the new E-TIBI, what was the uptake, what were the mechanisms that were adopted by the researchers for educating the PLHIV about the new method of screening? Need more details about how the intervention was rolled. In addition, there is hardly any gap between pre-and post-periods. Without these details it is not possible to assess the data and the appropriateness of the results in table 1. Table 2 presents data on bi-variable analysis. Recommend the researchers to conduct a multivariable analysis to find out the independent variables that are associated with the outcome of interest.\nOther issues: In the introduction, it is mentioned that globally 10.6 million people are infected with this. This is incorrect. An estimated ~10.6 million develop the disease every year and disease is not the same as infection. In the introduction, no details are provided about TB and HIV disease burden of Indonesia and the levels of TB-HIV co-disease burden. Overall, the contents of the manuscript need to be significantly enhanced to get a clear understanding of what was done and to get a better sense of 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? 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	https://f1000research.com/articles/13-750
https://f1000research.com/articles/13-748/v1	05 Jul 24	{ "type": "Review", "title": "A Pharmacist Perspective on Optimizing Pharmacotherapy among Older Adults – A Review", "authors": [ "Priya Manirajan", "Palanisamy Sivanandy", "Priya Manirajan" ], "abstract": "Multimorbidity and the associated consumption of multiple medications are common among the older population, posing a significant health concern. This leads to an increased incidence of side effects, adverse drug reactions, and higher healthcare costs for the individual, their family, and the country’s overall healthcare expenditure. Older adults experience complications due to the natural aging process and polypharmacy. The pharmacokinetic and pharmacodynamic variables of medications play a crucial role in their recovery and overall health. While many studies have highlighted the rising incidence of multimorbidity among older adults, they often overlook the importance of optimizing medication therapy to reduce complications, side effects, adverse drug reactions, falls, and improve medication adherence. This narrative review focuses on the impact of polypharmacy on older adults, age-related pharmacokinetic changes, pharmacodynamics in this population, and various methods to optimize pharmacotherapy. The findings of this review aim to provide healthcare providers with a better understanding of how to optimize pharmacotherapies and reduce drug-related complications in older adults.", "keywords": [ "Complications", "medications", "older adults", "optimization", "polypharmacy" ], "content": "Introduction\n\nOlder adults, also known as seniors or elders, are individuals who are 65 years and older. The advancements in healthcare globally have helped increase longevity, resulting in a growing aging population worldwide. It is estimated that the percentage of individuals aged 65 and older will increase from 10% in 2022 to 16% in 2050.1–3 Additionally, the report predicts that by 2050, the ratio of the elderly population to children under the age of five will be 2:1.3 This increase in the elderly population is primarily attributed to lower mortality and higher survival rates. Figure 1 and Figure 2 illustrate the top 50 countries with the highest percentage of older population,2 as well as the distribution of the world’s oldest populations by country or territory in 2022 and 20503 respectively.\n\nOne of the main health concerns among older adults is the presence of multimorbidity. Multimorbidity is defined as the presence of two or more non-communicable diseases, for example, hypertension,4 diabetes,5,6 depression, and so on.7 A recent study reported a global prevalence of multimorbidity of 37.2%.8 The same study pointed out that 51% of adults aged 60 years and above have multimorbidity. This finding is similar to an Indian study, which reported an increasing prevalence of multimorbidity from 48.31% in those aged 45 years and above to 73.86% in those aged above 75 years.9 Similarly, a study from Malaysia reported that 40.6% of the country’s older adults have multimorbidity.10 Multimorbidity is common among older adults due to declining physiological function and the presence of shared risk factors such as smoking, a sedentary lifestyle, and an unhealthy diet which lead to the onset and progression of chronic diseases.\n\nPharmacotherapy treatment is the mainstay for many non-communicable diseases. The increasing prevalence of multimorbidity leads to older adults being prescribed a higher number of medications, resulting in polypharmacy and hyperpolypharmacy. Polypharmacy is when a patient uses five or more medications, while hyperpolypharmacy is when they use ten or more medications.11–13 The reported prevalence of polypharmacy in the literature varies widely, ranging from 2.6% to 86.6%.14,15 Despite the benefits of managing multimorbidity, increased medication consumption can have unwanted effects on older adults. This article aims to guide healthcare providers (HCPs) in optimizing pharmacotherapy for older adults taking into consideration the unique physiological changes and challenges that come with aging.\n\n\nImpact of polypharmacy on older adults\n\nPolypharmacy significantly increases the risk of medication-related problems among older adults. These problems include drug interactions, inappropriate prescribing, prescribing cascade, medication non-adherence, and more.16,17 Drug interactions are more common among older adults with polypharmacy and can manifest in various ways, such as drug-drug interactions, drug-disease interactions, or drug-food interactions.\n\nDrug-drug interactions typically decrease the effectiveness of medication by either inhibiting drug metabolism or increasing clearance. For instance, an elderly patient with hypertension who takes non-steroidal anti-inflammatories (NSAIDs) for knee pain may experience a drug interaction with an ACE inhibitor, leading to elevated serum potassium levels and reduced kidney function.\n\nIn the case of drug-disease interactions, chronic NSAID use in a heart failure patient can exacerbate their condition. Additionally, drug-food interactions can impact the outcome of pharmacotherapy by altering the drug’s pharmacokinetics. One common example is warfarin, a vitamin K antagonist, taken with green leafy vegetables high in vitamin K content, which can affect the anticoagulation stability of warfarin.\n\nInappropriate prescribing is common among older adults ranging from 45.3% to 51%.18 One of the leading causes of polypharmacy besides comorbidities is overprescribing. Overprescribing refers to prescribing medications more than necessary for patients. Overprescribing tends to increase with age and higher prevalence was reported among older people near the end of life in some studies up to 76%.19 A study conducted in the United States, reported that antidepressants, thyroid hormones, proton pump inhibitors, H2 receptor blockers, and analgesics were commonly overprescribed medications among older adults.20 In addition to overprescribing, underprescribing can also be an issue. Underprescribing or underprescription is defined as the failure to prescribe a drug that is indicated for the management of a condition or illness, despite the absence of a valid basis for doing so.21 Underprescribing can also occur to avoid polypharmacy among older adults. A study reported that the prevalence of underprescribing ranges from 22% to 70% among the older population.22 Numerous factors, such as multimorbidity, polypharmacy, dementia, frailty, risk of adverse pharmacological events, lack of specific clinical trials for older patients, and economic concerns, are linked to under-prescription.23,24 Underprescribing leads to negative outcomes such as an increased risk of cardiovascular events, deteriorating disability, hospitalisation, and mortality.25,26\n\nMedication adherence refers to the extent to which a person follows a doctor’s instructions for taking medications.27 This includes taking the right medication, at the right dose, at the right frequency, and at the right time. Medication adherence can be challenging for older adults with multimorbidity and polypharmacy thus, leading to non-adherence. There are several risk factors identified for non-adherence among older adults with multimorbidity and polypharmacy. Cognitive decline is observed among the aging population which leads to unintentional omission of medications.28,29 Moreover, the complexity of pharmacotherapy prescribed for such patients does not help with adherence levels either.30,31 Other reported factors include sex, medication cost, lack of social support, health literacy, and self-administration of drugs.32–34\n\nAdverse drug reactions (ADRs) are common and widely reported among older adults with polypharmacy and multimorbidity.35,36 This is due to age-related changes in pharmacokinetics and pharmacodynamics, such as decreased hepatic and renal function, longer elimination half-lives, and higher sensitivity to medications. Older adults are more susceptible to ADRs compared to younger adults. ADRs often lead to increased hospital admissions with stays of up to 6 days and a mortality rate of 0.34%.37 Medications commonly associated with ADRs include analgesics, antithrombotics, proton pump inhibitors, antihypertensives, antidepressants, antipsychotics, and bisphosphonates.38–40 Drug-drug interactions have also been identified as a significant factor in ADRs development. Specific drugs that are known to cause ADRs due to interactions include warfarin, aspirin, heparin, and other antithrombotic agents.41,42 These drugs can interact with proton pump inhibitors, antidepressants, and antiplatelets leading to gastrointestinal or cerebral haemorrhagic events.\n\nMultimorbidity and polypharmacy increase the likelihood of prescribing cascade events in older adults. A prescribing cascade is when an adverse drug event (ADE) is mistaken for a new medical condition, leading to the unnecessary addition of another medication.43 For example, a diuretic may be prescribed to reduce edema caused by calcium channel blockers used for hypertension. Another common prescribing cascade involves prescribing an antiparkinsonian agent to address extrapyramidal symptoms caused by antipsychotic agents. These cascades not only worsen the effects of an unrecognized ADR but also contribute to the development of chronic polypharmacy.11\n\n\nAge-related pharmacokinetic changes\n\nWhen prescribing pharmacological agents to older adults, it is crucial to consider pharmacokinetic changes such as absorption, distribution, metabolism, and elimination. The pharmacokinetics of medications can be affected by age-related pharmacologic changes as well as sex-related changes and multimorbidity, which are more common in the elderly. Additionally, pharmacokinetic changes in older adults can be affected by geriatric syndromes as well.44\n\nAgeing affects all organ systems including the gastrointestinal system which is responsible for the absorption of medicated oral preparations. The gastrointestinal system plays a crucial role in motility, enzyme and hormone secretion, and the digestion of food. One common complaint among older adults is xerostomia or dry mouth. Xerostomia can be caused by systemic diseases like Sjogren’s syndrome, pharmacological agents such as atropine, and radiation therapy that damages the salivary glands. Salivary gland hypofunction may impair drug absorption through the oral mucosa, such as sublingual glyceryl trinitrate, reducing clinical efficacy.45\n\nThe walls of the small and large intestines reduce in size among older adults leading to a reduced surface area, and impaired absorption.46 Additionally, an aging-related decrease in hydrochloric acid production can lead to impaired absorption of certain drugs such as aspirin, and early release of drugs from enteric-coated oral formulations.47 The passage of medications from the stomach into the small intestine can be prolonged by age-related delay in gastrointestinal motility or the consumption of anticholinergic medications.48 Delayed motility can impair absorption, onset of action, peak drug concentration, and clinical effects of medications like paracetamol, which is absorbed in the upper small intestine.\n\nAs a person ages, body fat increases while total body water, blood, and plasma volume decline. These changes result in an increased volume of distribution and half-life of lipophilic drugs like diazepam. Therefore, when the same medication dose is prescribed to older adults and young people, it can lead to higher levels of free drugs and greater effectiveness in older adults, potentially causing toxicity. Additionally, it can decrease the distribution of hydrophilic drugs like digoxin and lithium. In addition to changes in plasma volume, older adults also experience decreases in plasma proteins such as albumin and lean tissue as they age. Drugs with high protein binding, like warfarin and phenytoin, may become unbound when albumin levels are reduced, especially during illness, leading to an increased risk of toxicity.49 On the other hand, α-1-acid glycoprotein increases with age, resulting in decreased free concentrations of basic drugs such as amoxicillin, potentially leading to inadequate dosing.\n\nThe impact of first-pass metabolism by the liver decreases with age. The decline in hepatic metabolism is characterized by a decrease in liver mass, blood flow, and hepatic enzymes such as cytochrome P-450, flavine monooxygenases, and UDP glucuronosyl transferases.49 A study in Japan stated that hepatic unbound clearance fell by 32% at age 80 and 40% at age 90 compared to age 40, implying a 0.80% annual decline with age.50 Hence, older adults may have higher circulating drug concentrations for a given oral dose. Drugs such as nitrate, propranolol, phenobarbital, and nifedipine are some examples of medications with an increased risk of toxic effects due to a decline in physiological function. The hepatic metabolism of drugs can also be impacted by smoking, reduced hepatic blood flow in heart failure patients, and the use of medications that activate or inhibit the cytochrome P-450 metabolic enzymes.\n\nThe aging process not only affects the absorption, distribution, and metabolism of drugs but also alters the renal elimination of drugs. The size of the kidney decreases by 20-30% between the age of 30 to 80 years.49 Besides structural changes, the glomerular filtration rate (GFR), renal plasma flow, and tubular function also decrease with age.51 More often, the serum creatinine level is maintained within the normal range despite reduced GFR due to less muscle mass.52 Therefore, drug doses should be tailored according to the measured renal clearance of the patient using equations such as CKD Epidemiology Collaboration, Berlin Initiative Study, and Full Age Spectrum which are more accurate than Cockcroft–Gault.53 Drugs that rely heavily on renal elimination such as sildenafil, clozapine, amoxicillin, and others require a reduction in dose and/or frequency to avoid toxic plasma concentrations of drugs.54\n\n\nPharmacodynamics in older adults\n\nPharmacodynamics as opposed to pharmacokinetics examines the drug’s action on the body. It can be affected by receptor binding and sensitivity, post-receptor effects, chemical interactions, and physiological changes due to disease, genetic mutations, aging, or other drugs.55 Therefore, older adults may have a different physiological response to the same drug dosing compared to younger patients. Increasing age can increase sensitivity to most drugs such as digoxin, warfarin, opioids, antipsychotics, and diuretics. However, β-adrenoceptor responsiveness decreases with age due to decreased activation of adenylyl cyclase and reduced production of cAMP.56 This means that β-blocker doses may need to be increased to achieve an adequate response.\n\nIn addition, older adults also have increased sensitivity to anticholinergic drugs. The side effects of these drugs include dry mouth, constipation, delirium, blurred vision, and urinary retention. Commonly consumed medications with anticholinergic effects include antipsychotics, tricyclic antidepressants, and sedative antihistamines. Taking multiple medications with anticholinergic effects can result in an anticholinergic burden, which, when combined with aging, may lead to cognitive decline and a loss of functional capacity.57 Furthermore, older adults with a moderate to high anticholinergic burden are at an increased risk of falls.58 Therefore, it is highly encouraged to regularly review medications and consider deprescribing drugs with anticholinergic effects.\n\n\nOptimizing pharmacotherapy in older adults\n\nDespite the challenges associated with pharmacotherapy management in older adults, there are practical ways to resolve these issues. The following steps can be taken to overcome pharmacotherapy challenges in older adults:\n\n\nMedication review\n\nA medication review is a routine practice conducted in healthcare settings by doctors, pharmacists, and nurses.59 This process can be valuable in identifying medications with anticholinergic burden, potentially inappropriate medications (PIMs), and prescribing cascade events that are commonly observed in older adults. When performed correctly and regularly, medication reviews can help detect many drug-related issues early on, such as side effects, adverse effects, interactions, or missed doses.60 The primary goal of a medication review is to ensure that medications are functioning as intended and addressing the patient’s health concerns. Additionally, it can simplify medication regimens and promote adherence in older adults with polypharmacy. The medication review process can take place in various settings, including nursing homes, hospitals, primary care facilities, community pharmacies, and during home visits.\n\nFrom a patient’s perspective, a medication review provides an opportunity for older adults and their caregivers to discuss any concerns or questions they have about their medications with a HCP. This open communication can lead to better medication management and improved overall health.\n\nIn recent years, the National Health Service in England has introduced a comprehensive medication review called Structured Medication Review (SMR). SMRs are evidence-based and thorough reviews of a patient’s medication, taking into account all aspects of their health. The SMRs are intended for patients with hyperpolypharmacy, severe frailty, and potentially addictive pain management medications, which are commonly found in older adults.61 These SMRs can be implemented by healthcare facilities in different countries to improve the optimization of prescribed medications.\n\nBy addressing medication errors, improving adherence, and ensuring optimal medication use, medication reviews can significantly improve health outcomes for older adults. This can lead to fewer hospitalisations, improved quality of life, and a reduction in healthcare costs. In addition to this, medication reviews can also help prevent falls and related injuries.62 Figure 3 describes the optimization of pharmacotherapy in older adults.\n\n\nDeprescribing\n\nDeprescribing has recently gained popularity due to an aging society with an increasing number of individuals living with various chronic diseases. Deprescribing is defined as the process of tapering, withdrawing, discontinuing, or stopping medications to reduce potentially problematic polypharmacy, ADE, and inappropriate or ineffective medicine use.63 Deprescribing is a practical approach to reducing ADRs, improving adherence, reducing pill burden, lowering fall risk, and enhancing quality of life.64,65\n\nA multicenter controlled trial conducted in Australia found that a deprescribing strategy significantly decreased the number of medications prescribed to older adults with polypharmacy, with no adverse events reported.66 The most frequently deprescribed medication classes were supplements, gastric acid suppressants, statins, oral hypoglycemics, and diuretics. Deprescribing medications like diuretics can potentially prevent the prescribing cascade. Furthermore, deprescribing reduces exposure to high-risk anticholinergics, thus decreasing the anticholinergic burden in older adults and avoiding unwanted side effects such as dry mouth, constipation, urinary retention, cognitive impairment, and dementia.67 Similarly, a randomized controlled trial in Ireland reported that deprescribing significantly reduced polypharmacy and medication costs in frail older adults.68\n\nDeprescribing can be accomplished in five simple steps69,70;\n\nStep 1: Obtain a comprehensive medication history and assess adherence.\n\nStep 2: Identify any PIMs.\n\nStep 3: Decide if the dosage can be lowered or if the medication can be discontinued.\n\nStep 4: Develop a plan for tapering and withdrawing the medication.\n\nStep 5: Monitor the outcomes, including improvements in clinical parameters, and ADRs.\n\nThere are numerous tools available to assist clinicians in deprescribing medication. A popular tool is the STOPP/START (Screening Tool of Older Persons’ Prescriptions/Screening Tool to Alert to Right Treatment) criteria. It is a physiological systems-based explicit set of criteria that aims to define clinically important prescribing problems related to PIMs and potential prescribing omissions.71 Other useful tools that can be used in clinical settings include the Medication Appropriateness Index, Good Palliative-Geriatric Practice, Current medicines, Elevated risk, Assess, Sort, Eliminate algorithm, and Beers Criteria.72 Identifying prescribing cascades in clinical practice can be challenging for clinicians. Therefore, the ThinkCascades tool was recently developed through a modified Delphi process with an international multidisciplinary expert panel to identify clinically important prescribing cascades affecting older adults, which helps prevent and manage polypharmacy.73\n\n\nIndividualized treatment approach\n\nDue to the complex interplay of age-related physiological changes, multimorbidity, and declined cognitive function, individualized treatment approaches are crucial for older adults. A one-size-fits-all approach is not sufficient, as health heterogeneity increases to varying degrees with age.74,75 Therefore, prescribers need to consider older adults’ comorbidities, and physiological functions such as renal function, cognitive function, functional status, and life expectancy before prescribing any medications.\n\nWhen it comes to prescribing medications for older adults, a key principle that HCPs need to remember is ‘start low, go slow’. Initiating medications with low doses and titrating up the dosage until a desirable treatment outcome has been achieved including the absence of adverse effects, is important. Tools like STOPP/START and Beers Criteria can be used when prescribing medications for older adults. Prescribing combination medications such as felodipine and enalapril in a single formulation, can reduce polypharmacy and improve adherence among older adults.\n\nIndividualized treatment recognises the unique life experiences and challenges older adults face, such as loss, retirement, or changes in living situations. This fosters a more empathetic and relatable therapeutic environment. For instance, frail older adults may have difficulties in managing complex insulin therapy, so simplifying or de-escalating the treatment would benefit them greatly.76 Treatment plans can be adjusted as needed to accommodate changes in health or preferences, ensuring the approach remains safe and effective over time. Overall, individualized treatment empowers older adults to take charge of their well-being and achieve a higher quality of life.\n\n\nDevelopment of geriatric specific guideline\n\nThe development of geriatric-specific guidelines is crucial for improving the care of older adults. The need for population-specific guidelines arises from the unique challenges faced by older adults. These challenges include physiological changes, polypharmacy, and cognitive decline. General clinical guidelines available in most healthcare facilities might not address these complexities, potentially leading to poorer health outcomes. One of the major challenges in developing guidelines is determining best practices or recommendations based on available evidence. This is because the majority of clinical trials may not include older adults in the study, so the outcomes may not be generalised for this population. Clinical trials need to consider the inclusion of older adults as the population is expected to grow in the future. Pharmacy-related geriatric guidelines should be developed in hospitals, primary care clinics, nursing homes, and community pharmacies to provide optimal prescribing. Some of the pharmacy-related geriatric guidelines include the Pharmacist’s Comprehensive Geriatric Assessment in France, the Medication Therapy Adherence Clinic for Geriatrics and the Geriatric Pharmacy Pocket Book in Malaysia.77 These guidelines not only help clinical pharmacists but also other HCPs in making treatment decision.\n\n\nPatient education\n\nPatient education plays a critical role in optimizing pharmacotherapy for older adults. Understanding their medications helps older adults take them correctly, at the right times, and for the intended duration. This reduces the risk of missed doses or misuse, leading to better treatment outcomes. Educated patients are more likely to identify potential problems like drug interactions or side effects and medications that potentially increase the risk of falls.78 They can then communicate these concerns to their HCPs, preventing complications. Knowledge about medications empowers older adults to manage their conditions more effectively. They can recognise signs of improvement or worsening health, allowing for timely adjustments to their treatment plan. Understanding their medications fosters a sense of control and autonomy in older adults. This can lead to greater satisfaction with their healthcare and a more active role in their treatment decisions.\n\nThere are some practical ways to provide patient education in daily practice. Firstly, tailored communications are key. Older adults typically experience sensory loss, memory decline, and slower processing of information. Therefore, it is important to use clear, concise language and address individual needs and learning styles. Speak slowly, clearly, and loudly enough for them to understand the information being conveyed. Visual aids or written information can also be helpful as a reference for older adults.79 Emphasize potential side effects of prescribed medications, proper medication administration, and when to seek medical attention. It is crucial to create a comfortable environment where older adults can ask questions and express concerns without fear of judgment. Patient education should also be extended to family members or caregivers who assist with medication management. In addition to verbal communication, patient education handouts, either physical or electronic, can be provided to patients and their caregivers for Ref. 40. This will undoubtedly improve the care provided to older adults.\n\n\nCollaborate with a multidisciplinary team\n\nA multidisciplinary approach is beneficial for optimizing pharmacotherapy. The team can include geriatricians, physicians, pharmacists, nurses, dieticians, physiotherapists, and other specialists. By combining expertise from various disciplines, the team can gain a holistic understanding of the patient’s health, including medical conditions, cognitive function, and social circumstances. This allows for a more individualized medication plan. Collaboration among team members helps identify and prevent potential medication errors, minimizing the risk of ADRs. A study conducted in the United States reported that a multidisciplinary team consisting of clinical pharmacists has led to significantly more deprescribing of PIMs.81 Through education and support from various HCPs, patients are more likely to understand and adhere to their medication regimens. Open communication within the team ensures everyone involved is on the same page about the patient’s treatment plan and avoids overlapping medical records and prescriptions. The collaborative effort exhibited by the multidisciplinary team can optimize medication use to improve the older adult’s health, quality of life, and functional ability.\n\n\nPromote patient autonomy & shared decision-making\n\nPrescribing medications for older adults involves a unique set of ethical considerations, especially regarding patient autonomy and shared decision-making. Older adults cherish their independence and their ability to take charge of their healthcare. HCPs must respect this autonomy by offering clear information about medications, possible side effects, and treatment objectives in a way that is easy to comprehend, taking into account any cognitive limitations. Patients should feel empowered to ask questions and voice any concerns they may have. Ultimately, the decision to accept or decline medication lies with the patient, even if it contradicts the doctor’s advice.\n\nHowever, patient autonomy can be compromised by a few factors. Older adults with cognitive impairment have difficulties comprehending complex medication information and making informed decisions. In addition to cognitive impairment, polypharmacy dampers autonomy by creating adherence issues. When autonomy is challenged, shared decision-making becomes crucial. This involves including the patient in discussions but may also involve incorporating input from trusted family members or caregivers. Family members can provide valuable insights into the patient’s medical history, daily functioning, and preferences. The patient’s level of understanding and decision-making ability should always be prioritised. If the patient lacks capacity, a healthcare proxy or legal guardian may need to be involved. Clear communication with both the patient and family is essential to ensure everyone understands the treatment plan and its potential benefits and risks. Overall, the goal is to find a balance between respecting patient autonomy and ensuring their well-being. This can involve a flexible approach that adapts to the individual needs and circumstances of each older adult.\n\n\nConclusion\n\nThe older adult population is heterogeneous, with differences in physiology due to aging altering pharmacokinetics and pharmacodynamics, functional disabilities, cognitive impairment, and multimorbidity to varying degrees. This leads to an increased incidence of polypharmacy and ADRs. Therefore, optimizing pharmacotherapy for the growing older adult population will greatly benefit their health.", "appendix": "Data availability\n\nNo data are associated with this article.\n\n\nReferences\n\nUnited Nations Population Division: World Population Prospects 2022: Summary of Results. New York: United Nations Population Division; 2019. [cited 2024 Mar 03]. Reference Source\n\nFelix Richter: The world’s oldest populations.Updated Feb 20, 2024. [cited 2024 Mar 03]. Reference Source\n\nThe top 50 countries with the largest percentage of population aged 65 and up. 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Publisher Full Text" }	[ { "id": "319107", "date": "25 Sep 2024", "name": "Ayaka Matsumoto", "expertise": [ "Reviewer Expertise Polypharmacy in Rehabilitation Medicine", "Clinical Nutrition" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 believe this paper is important as it reviews the key considerations for optimizing drug therapy in the older adults. However, I have several concerns and would like to propose the following revisions:\n\nNovelty and Differentiation: While the paper provides a comprehensive review, it would benefit from a clearer emphasis on what makes it unique compared to other similar reviews. Highlight specific angles or methods that distinguish this paper from the existing literature. Focus on True Health Outcomes: While the paper acknowledges the benefits of medication optimization in reducing the number of drugs, PIMs, and anticholinergic load, it should go further by discussing outcomes directly affecting the elderly's quality of life. It would be useful to include data on physical function, ADL (activities of daily living), quality of life, and mortality in elderly populations. Studies like the one in reference(PMID: 35633757) that show the impact of medication reviews on optimizing therapy and health outcomes could be cited. Insufficient Citations: The paper lacks references in critical sections, such as the one on \"Promote patient autonomy & shared decision-making.\" Adding recent systematic reviews and relevant research will strengthen the paper's academic depth. Consider citing the latest studies that discuss optimizing drug therapy outcomes in the elderly, particularly those focused on shared decision-making models.\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? No\n\nIs the review written in accessible language? Yes\n\nAre the conclusions drawn appropriate in the context of the current research literature? Partly", "responses": [] }, { "id": "359202", "date": "22 Jan 2025", "name": "Demetra Antimisiaris", "expertise": [ "Reviewer Expertise Polypharmacy", "geriatrics" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 is important but it depends on the audience. The topic of optimization of pharmacotherapy is so vast that what this paper presents is a primer that is suitable for novice learners (like new pharmacy students or nursing students). The algorithm is presented as if it is accepted science but in reality, the experts in the field do not reduce optimization of pharmacotherapy for older adults to this simplistic level. Also, the terminology in the algorithm requires a lot of explanation not present in the paper.\n\nSome of the early content is a nice review, but then later the citations do not support the statements adequately. And there are several statements that are not comprehensive nor explanatory as to why, but just a statement. Like \"clear communication with both patient and family is essential to ensure everyone understands....\" the reader might ask why is everyone understanding important?\n\nAging population, PK sections are all conventional geriatric pharmacy review topics, and the authors wrote those sections well. PD section includes B receptors and anticholinergic, but there are so many other PD changes with age that at minimum that section should refer to those as examples of PD concerns. The authors could possibly list more PD examples and review some of the mechanisms of increased sensitivity to some or all of the drugs listed in the sentence “Increasing age can increase sensitivity to most drugs such as digoxin, warfarin, opioids, antipsychotics, and diuretics”\nIn this section, optimizing pharmacotherapy in older adults: the following sentence is too definitive and simplistic and could mislead readers. “The following steps can be taken to overcome pharmacotherapy challenges in older adults:- unless the evidence explaining step by step (with cited research) is provided, that sentence sounds too definitive.\n\nMedication Review Section:\n\nthe SMR presented is nothing more than what the paper’s title infers- “A Pharmacist Perspective”. The SMR is presented as if the algorithm presented is validated under validated clinical science and study yet is in reality a pharmacist’s perspective or rather the author's creation not through validated expert opinion methods nor through a study but just the author's perspective and the algorithm should probably be framed as such. That said, I agree with the components that should be considered in optimizing pharmacotherapy in older adults but there is so much more to it from a biomedical and clinical science perspective.\n\nWhen reviewing the steps in the presented algorithm, the reader asks in their mind about the exigence of each step (the details, how to, or what about). For example, I may have missed it earlier, but I think the first mention of the prescribing cascade is in this diagram.\n\nSome of the citations do not seem to match the statement. For example, citation #61 is in support of this section ending in sentence “The SMRs are intended for patients with hyperpolypharmacy, severe frailty, and potentially addictive pain management medications, which are commonly found in older adults.” …when the actual publication reports a focus group reporting gaps in stake holders training and perspectives in SMR implementation. Beyond this section there are a lot of similar issues with citations.\nAlso there are statements not supported by robust explanations nor citations to support. For example: “A multidisciplinary approach is beneficial for optimizing pharmacotherapy. The team can include geriatricians, physicians, pharmacists, nurses, dieticians, physiotherapists, and other specialists. By combining expertise from various disciplines, the team can gain a holistic understanding of the patient’s health, including medical conditions, cognitive function, and social circumstances. This allows for a more individualized medication plan.” Where is the explanation of how and why a multidisciplinary approach is beneficial and what citations support this idea?\n\nSUGGESTION: This paper could be more viable as an opinion article or brief report (but as brief report it would even need more fine tuning).\n\nI truly appreciate the topic, and that people care to write about it. So, I don't mean to be discouraging to the authors and hope to offer this feedback in the spirit of encouraging robustness or framing in alignment with the existing content. I commend the authors for doing this work- and especially as polypharmacy grows globally and with an aging population, we need more of this type of content!\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? No\n\nIs the review written in accessible language? Yes\n\nAre the conclusions drawn appropriate in the context of the current research literature? Partly", "responses": [] } ]	1	https://f1000research.com/articles/13-748
https://f1000research.com/articles/13-683/v1	24 Jun 24	{ "type": "Research Article", "title": "Evaluation of positioning accuracy, radiation dose and image quality: artificial intelligence based automatic versus manual positioning for CT KUB", "authors": [ "Souradip Kundu", "Kaushik Nayak", "Rajagopal Kadavigere", "Saikiran Pendem", "Priyanka .", "Souradip Kundu", "Kaushik Nayak", "Rajagopal Kadavigere", "Saikiran Pendem" ], "abstract": "Background Recent innovations are making radiology more advanced for patient and patient services. Under the immense burden of radiology practice, Artificial Intelligence (AI) assists in obtaining Computed Tomography (CT) images with less scan time, proper patient placement, low radiation dose (RD), and improved image quality (IQ). Hence, the aim of this study was to evaluate and compare the positioning accuracy, RD, and IQ of AI-based automatic and manual positioning techniques for CT kidney ureters and bladder (CT KUB).\n\nMethods This prospective study included 143 patients in each group who were referred for computed tomography (CT) KUB examination. Group 1 patients underwent manual positioning (MP), and group 2 patients underwent AI-based automatic positioning (AP) for CT KUB examination. The scanning protocol was kept constant for both the groups. The off-center distance, RD, and quantitative and qualitative IQ of each group were evaluated and compared.\n\nResults The AP group (9.66±6.361 mm) had significantly less patient off-center distance than the MP group (15.12±9.55 mm). There was a significant reduction in RD in the AP group compared with that in the MP group. The quantitative image noise (IN) was lower, with a higher signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR) in the AP group than in the MP group (p<0.05). Qualitative IQ parameters such as IN, sharpness, and overall IQ also showed significant differences (p< 0.05), with higher scores in the AP group than in the MP group.\n\nConclusions The AI-based AP showed higher positioning accuracy with less off-center distance (44%), which resulted in 12% reduction in RD and improved IQ for CT KUB imaging compared with MP.", "keywords": [ "Artificial Intelligence", "Computed Tomography", "Image quality", "Positioning accuracy", "Radiation dose" ], "content": "Introduction\n\nComputed Tomography (CT) is a valuable imaging modality for the diagnosis of various pathologies. However, CT scans use X-rays, which involve exposure to ionizing radiation. Therefore, the radiation exposure in CT must be kept “As Low as Reasonably Achievable (ALARA)”.1–3 In recent years, several dose optimization tools have been introduced, such as “deep learning image reconstruction (DLIR)”, “iterative reconstruction (IR)”, “automatic tube current modulation (ATCM),” and “automatic tube voltage selection (ATVS)”.4–9 In addition, proper patient positioning is crucial for obtaining higher image quality with an optimized radiation dose.10\n\nRadiology medical technologists can utilize laser lights to visually evaluate the patient’s central placement in CT imaging; however, this approach is user-dependent, and patient miscentering is common and well-documented problem that can have detrimental consequences.11 If the patient is placed away from the gantry isocenter (i.e., the table is too up or down), the localizer image will be either enlarged or reduced in width. Furthermore, the use of ATCM along with patient miscentering could lead to an unacceptable Image quality (IQ) with an increase in the radiation dose (RD).12–14 For manual positioning, the interaction between the radiographers and the patient poses a risk of cross-infection in patients with infectious diseases.14\n\nRecently, an artificial intelligence (AI)-based positioning camera, which works based on an AI algorithm that uses intelligence (a body contour detection algorithm) to detect a patient’s body using a three-dimensional (3D) camera.15 Various companies have introduced AI-based contactless positions for patients. A 3D camera equipped with a visible light camera, an infrared light source, and a sensor was installed above the patient. It adjusts the height of the table and maintains the patient within the isocenter of the gantry. It also detects body contours and automatically positions the patient for CT examination according to the selected protocol.14–18 Hence, this study aimed to evaluate and compare the positioning accuracy, IQ, and RD of AI-based automatic and manual positioning for CT Kidney Ureter and Bladder (KUB) imaging.\n\n\nMethods\n\nThis is a prospective study. Ethical approval was obtained from the Institutional ethical committee (IEC 168/2023) of Kasturba Medical College and Hospital, Manipal, India on 7th June 2023, and then the study was registered on Clinical Trial Registry- India (CTRI/2023/06/054173) on 20th June 2023. Written informed consent was obtained from all participants for publication and participation in the data collection for the study.\n\nThe study included a total of 286 patients, with 143 patients in each group referred for CT KUB Imaging for various clinical indications such as evaluation of renal calculi, flank pain, kidney masses, and traumatic injury to the kidneys. Patients who were uncooperative and those with CT KUB images with artifacts (movement and metal) were excluded. Patient age and BMI were noted, and only patients with normal BMI were included. All patients underwent CT using a Philips Incisive 128 Slice CT Scanner.\n\nPatients in group 1 Manual positioning (MP group) underwent CT KUB imaging using manual positioning. The patient was positioned supine on a scan table with the feet first towards the gantry, and the arms were extended and supported above the head. The table height was adjusted by the gantry-mounted adjustment button such that the horizontal laser beam coincided with the mid-coronal plane of the patient and to the gantry isocenter by visual inspection. The area covered the dome of the diaphragm immediately below the symphysis pubis.\n\nGroup 2 Automatic Positioning (AP group) patients underwent CT KUB imaging by AI-based automatic patient positioning, which included an AI-enabled camera mounted on the ceiling above the patient table.\n\nAn AI-based camera automatically detected the patient’s orientation in the supine position with the feet first into the gantry. After selecting the CT KUB protocol, the area of interest (from the diaphragm to the symphysis pubis) to be scanned was automatically detected using an AI – based camera, and the table height was adjusted to the gantry isocenter.\n\nThe image acquisition parameters were kept the same for both groups such as use of ATCM, tube voltage of 120 kVp, rotation time of 0.75s, pitch 1.0, matrix 512*512, slice thickness and increment 3 mm. The MP group patient images was reconstructed with IR technique – iDose4- level 4 (Philips Health Care ®,TM). The AP group patient images were reconstructed with DLIR technique (Precise Image; Philips Health Care ®,TM). The axial CT images from both the groups were reconstructed to extended field of view (FOV) of 500 mm.\n\nThe off-center distance was measured to evaluate the accuracy of patient positioning. To calculate the off-center distance, an axial slice of the CT KUB image at the level of the fourth lumbar vertebra, with an Field of View (FOV) of 500 mm, was selected. A straight line was drawn that joins the anterior and posterior margins of the complete FOV, and the midpoint of this line was determined, which represents the gantry isocenter. Another straight line that joined the anterior and posterior surfaces of the patient was drawn, and the midpoint of this line was determined to represent the patient’s center. The distance between the gantry isocenter and the patient’s center was measured using a measuring tool to evaluate the off-center distance12 (Figure 1). The scan length was noted in both the groups.\n\nRadiation dose descriptors such as “Volumetric Computed Tomography Dose Index (CTDIv) in mGy,” “Dose Length Product (DLP) in mGy.cm”, “Size Specific Dose Estimate (SSDE) in mGy” was noted from the CT scanner and the “effective dose (ED)” was calculated using the following formula: E=DLPXConversion factor(K) (K= 0.015 mSv/mGy. cm).19\n\nQuantitative IQ was assessed by calculating “signal to noise ratio (SNR),” “contrast to noise ratio (CNR)” and “image noise (IN).” 3 mm slice thickness axial CT KUB images were selected, and six circular regions of interest (ROI) measuring 4-5 mm2 in diameter were drawn in the following regions: upper poles of the kidneys, lower poles, subcutaneous fat, and psoas muscle (Figure 2A and 2B).\n\nThe IN was calculated as the standard deviation (SD) of the ROI, and the attenuation value was the mean value of the ROI. SNR and CNR were calculated using the following formula20:\n\nQualitative analysis of IQ was performed by two radiologists with > 10 years of experience in CT KUB reporting who were blinded to the patient positioning and image reconstruction technique. They assessed “image noise (IN)”, “image sharpness (IS)”, “image artifacts (IA)”, and “overall image quality (OIQ)” using a five-point Likert scale, as shown in Figure 3.\n\nStatistical analysis of the data was performed using Jamovi -2.3.28.0 (https://www.jamovi.org/download.html). An independent t-test was used to compare RD (CTDIvol, DLP, SSDE, and ED), scan length, quantitative IQ (attenuation, image noise, SNR, and CNR), and off-center distance between the MP and AP positioning groups. The Chi-square test was used to compare the qualitative analysis of IQ. Statistical significance was set at p< 0.05. Kappa value (k-value) was calculated to assess the interobserver agreement of qualitative IQ analysis and the scores as follows: almost perfect (0.81-0.99)”, “substantial (0.60 – 0.79)”, “moderate (0.40 – 0.59)”, “fair (0.21 – 0.39), “and “< 0.20, none to slight agreement”.21\n\n\nResults\n\nThe study included 286 patients referred for CT KUB imaging, 143 patients underwent CT KUB imaging using manual positioning, and the remaining 143 patients underwent automatic positioning. Patient details are summarized in Table 1.\n\nThe mean off-center distance in the MP group and AP group was 15.12 ± 9.55 cm and 9.66 ± 6.361 cm. A statistically significant difference in the off-center distance (p < 0.05) was noted between the MP and AP group. The AP group showed 44% less off-center distance compared to the MP group. Scan length also showed a significant difference (p < 0.05) between the AP (56.0 ± 1.75 cm) and MP group (58.2 ± 3.55 cm).\n\nThe mean and standard deviation (SD) of the radiation dose indices for both groups are shown in Table 2. There was a statistically significant difference in the measured CTDIvol (p < 0.05), DLP (p < 0.05), SSDE (p < 0.05), and effective dose (p < 0.05) between the MP and AP groups. The AI based AP group showed 8.38%, 12.32%, 10.32%, 12.42% reductions in CTDIvol, DLP, SSDE, and ED, respectively, compared with MP group.\n\nThe mean and SD of the quantitative IQ parameters for both groups are shown in Table 3. Quantitative IQ parameters, such as attenuation of the right kidney (p = 0.740), left kidney (p = 0.570), psoas muscle (p = 0.157), and subcutaneous fat (p = 0.053), did not show significant differences between the MP and AP group. However, other parameters such as IN and SNR of the right kidney, left kidney, psoas muscle, and subcutaneous fat showed statistically significant differences (p < 0.05), with lower IN and higher SNR in the AP group than in the MP group. The AP group showed 46.42% total IN reduction compared to MP group Similarly, the CNR of right and left kidney was higher in AP group compared MP group with significant difference (p < 0.05).\n\nThe qualitative IQ scores of both readers in the MP and AP groups are shown in Table 4. IN, IS, and OIQ showed a statistically significant difference (p < 0.05) between the two groups, with higher scores in the AP group than in the MP group for both readers (Figure 4). There was no significant difference in IA scores (p = 0.652) between the MP and AP group. However, none of the images were rated as suboptimal or unacceptable (score < 4) by the two readers. IN (MP, k = 0.98; AP, k = 0.88), IA (MP and AP, k = 1), IS (MP, k = 0.97; AP, k = 0.92), and OIQ (MP, k = 0.97; AP, k = 0.94) showed almost perfect inter-observer agreement between the two readers.\n\n\nDiscussion\n\nIn this study, we evaluated the positioning accuracy, IQ, and RD of artificial intelligence (AI)-based automatic and manual positioning for CT Kidney Ureter Bladder (KUB) imaging. A closer look at off-center distances showed that the off-center positions were significantly lower in the AI-based AP group than in the MP group. The mean off-center distances for the AP and MP groups were 9.662±6.36 mm. and 15.117±9.55 mm. Similar findings were observed in a study by Yadong et al., in which the off-center distance was significantly higher in the MP group (4.05 ± 2.40 cm) than in the AP group (1.56 ± 0.83 cm) for CT thorax imaging.14 The study was performed by Ronald et al. on pediatric patients with and without immobilization devices. They found that utilizing the 3D camera for positioning pediatric patients, without an additional immobilization device, resulted in more precise positioning compared to manual methods employed by radiographers, which is similar to the findings of adults. Notably, there was no difference in the positioning accuracy between the 3D camera and radiographers for patients placed with an immobilization device.15 Saltybaeva et al. evaluated the accuracy of the 3D camera algorithm for AP and compared the results with those of MP for both chest and abdominal CT. For chest CT, the average difference in off-center was 7 ± 4 mm when using AP and 19 ± 9 mm when the table height was selected manually by technologists. For the abdomen, the average vertical off-centering was 4 ± 2 mm and 18 ± 11 mm for the automatic and MP respectively.18\n\nAEC techniques are perhaps the most important innovations in terms of dose reduction. When using an AEC, the tube current is adjusted automatically based on the size and attenuation of the anatomy.22–24 Off-center anatomy can result in suboptimal exposure settings, which affect IQ and increase RD.25,26 In our study, there were notable reductions in radiation dose metrics such as CTDIv (8.38%), DLP (12.32%), ED (12.42%), and SSDE (10.32%) in AI-based AP group compared to MP group. Yadong et al. observed 16% dose reduction for AP in CT thorax examinations compared to MP.14 Dane et al. showed 23.8%, 22.8%, 17.2 %, and 20.5 % reductions in radiation dose for CT chest without contrast, abdominal pelvis enterography, chest with contrast, and abdomen pelvis contrast studies, respectively, for 3D camera-based positioning.13 Similar findings were noted in a study by Aly et al., who showed a higher off-center distance in the MP group than in the AP group. Due to the higher off-center distance, the radiation dose parameters such as CTDIv (abdomen: 10.2±4.3, 9.8 ±5.5 mGy; thorax: 8.6±4.3, 8.5 ±3.9 mGy), DLP (abdomen: 485.8±221.9, 492.2 ± 293.6 mGy.cm; thorax: 310.80±221.5, 319.0 ± 188.9 mGy.cm) and SSDE (abdomen: 13.1 ± 4.1, 12.9 ± 4.3 mGy; thorax: 10.5 ± 4.1, 10.7 ± 3.7 mGy) was higher in MP group compared to AP group.12\n\nThe AI-based AP group CT images showed lower IN quantitatively and qualitatively than the MP group because of the higher positioning accuracy with less off-center distance in the AP group, and the images were reconstructed using the DLIR algorithm. SNR and CNR were also higher in the AP group than in the MP group. The qualitative IQ parameters, such as IS (MP: 4.86 ± 0.34; AP: 4.97 ± 0.17) and OIQ (MP: 4.08 ± 0.26, AP: 4.97 ± 0.19), showed higher mean scores in the AP group than in the MP group. Similar findings were reported by Yadong et al., in which the IN was lower in the AP group than in the MP group.14,27\n\nOur study had some limitations. First, we did not measure and compare patients positioning time in automatic and manual positions. Second, we could not assess whether the off-center distance observed in the study during manual patient positioning was below or above the gantry isocenter. Third, we enrolled patients with a normal BMI in this study. However, we did not specifically address how variations in patient weight may affect the accuracy of patient positioning.\n\n\nConclusion\n\nAI-based patient positioning is a touchless system that is operated by a single switch. The AI-based automatic positioning technique aligns the patient to the isocenter of the gantry with less off-center alignment and increases positioning accuracy. Hence, the study concludes that AI-based automatic positioning improves the overall image quality with noise reduction and reduced RD in patients undergoing CT KUB imaging. Further research in this area will improve the role of AI in healthcare optimization and patient care.\n\n\nEthics and consent\n\nEthical approval was obtained from the Institutional ethical committee (IEC 168/2023) of Kasturba Medical College and Hospital, Manipal, India on 7th June 2023, and then the study was registered on Clinical Trial Registry- India (CTRI/2023/06/054173) on 20th June 2023. Written Informed consent was obtained from all participants for publication and participation in the data collection for the study.", "appendix": "Data availability\n\nFigshare: AI based AP and MP CT KUB, https://doi.org/10.6084/m9.figshare.25641063.v3. 28\n\nThis project contains the following underlying data:\n\n• Data_AP_MP (demographic details of patients, Qualitative and Quantitative analysis, radiation dose metrics, and off-center distance – Excel sheet)\n\n• AP KUB Images, MP KUB Images\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nPower SP, Moloney F, Twomey M, et al.: Computed tomography and patient risk: Facts, perceptions and uncertainties. World J. Radiol. 2016 28; 8(12): 902–915. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSchmidt CW: CT scans: balancing health risks and medical benefits. Environ. Health Perspect. 2012; 120(3): A118–A121. 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PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAly A, Ebrahimian S, Kharita MH, et al.: Effect of technologist and patient attributes on centering for body CT examinations: Influence of cultural and ethnic factors. PLoS One. 2022; 17(8): e0273227. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDane B, O’Donnell T, Liu S, et al.: Radiation dose reduction, improved isocenter accuracy and CT scan time savings with automatic patient positioning by a 3D camera. Eur. J. Radiol. 2021; 136: 109537. PubMed Abstract \| Publisher Full Text\n\nGang Y, Chen X, Li H, et al.: A comparison between manual and artificial intelligence-based automatic positioning in CT imaging for COVID-19 patients. Eur. Radiol. 2021; 31(8): 6049–6058. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBooij R, van Straten M , Wimmer A, et al.: Automated patient positioning in CT using a 3D camera for body contour detection: accuracy in pediatric patients. Eur. 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PubMed Abstract \| Publisher Full Text\n\nZhang X, Zhang G, Xu L, et al.: Application of deep learning reconstruction of ultra-low-dose abdominal CT in the diagnosis of renal calculi. Insights Imaging. 2022; 13(1): 163. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMcHugh ML: Interrater reliability: the kappa statistics. Biochem. Med. 2012; 22(3): 276–282.\n\nFavazza CP, Yu L, Leng S, et al.: Automatic exposure control systems designed to maintain constant image noise: effects on computed tomography dose and noise relative to clinically accepted technique charts. J. Comput. Assist. Tomogr. 2015; 39(3): 437–442. PubMed Abstract \| Publisher Full Text\n\nInoue Y, Nagahara K, Kudo H, et al.: CT dose modulation using automatic exposure control in whole-body PET/CT: effects of scout imaging direction and arm positioning. Am. J. Nucl. Med. Mol. Imaging. 2018; 8(2): 143–152. PubMed Abstract\n\nEffectiveness of Low Dose Over Standard dose CT for Detection of Urolithiasis: A Systematic Review. Indian J. Forensic Med. Toxicol. 2020; 14(4): 4447–4451. Publisher Full Text\n\nZheng X, Gutsche L, Al-Hayek Y, et al.: Impacts of Phantom Off-Center Positioning on CT Numbers and Dose Index CTDIv: An Evaluation of Two CT Scanners from GE. J. Imaging. 2021; 7(11): 235. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAkin-Akintayo OO, Alexander LF, Neill R, et al.: Prevalence and Severity of Off-Centering During Diagnostic CT: Observations From 57,621 CT scans of the Chest, Abdomen, and/or Pelvis. Curr. Probl. Diagn. Radiol. 2019; 48(3): 229–234. Publisher Full Text\n\nGang Y, Chen X, Wang H, et al.: Accurate and efficient pulmonary CT imaging workflow for COVID-19 patients by the combination of intelligent guided robot and automatic positioning technology. Intell. Med. 2021; 1: 3–9. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPriyanka: F1000 Data AI based AP and MP for CT KUB. [Dataset]. figshare. 2024. Publisher Full Text" }	[ { "id": "296056", "date": "01 Jul 2024", "name": "Chandrasekhar Priyanka", "expertise": [ "Reviewer Expertise Computed Tomography", "Magnetic Resonance Imaging", "Radiation dose", "Mammography and Fetal MRI" ], "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 interesting and innovative in exploring the advantages of AI-based positioning camera which detects the patients contour and allows for automatic positioning in CT KUB examination. Major comments The article highlights the AI-based positioning ability of accurately positioning the patient with respect to the isocenter of gantry. It explains the benefits of reduced radiation dose by positioning the patient to isocenter in CT. The improvement in image quality with AI-based deep learning reconstruction algorithm (DLR) with automatic positioning such as precise image compared to iterative reconstruction (iDose4) with manual positioning for CT KUB examinations was presented well in the article using qualitative and quantitative image quality analysis. Radiation is an important concern while performing CT scans. The present study also highlights the 12% reduction in radiation dose which is a substantial improvement, contributing to safer imaging practices. Minor comments: A small typographic error was noted in the units of off-center distance between abstract (mm) and results section (cm) which can be corrected. The study focused on CT KUB, requires exploration in other body parts for comprehensive understanding and realizing the full potential of AI-based positioning techniques in CT.\nOverall, I feel the article is excellent in the current era of utilizing the advantages of artificial intelligence-based technologies for optimizing the workflow, improving the patient care and comfort in CT.\n\nIs the work 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": "296053", "date": "01 Jul 2024", "name": "Tasleem Shaikh", "expertise": [ "Reviewer Expertise Medical Imaging Technology." ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nMajor comments: The article highlights the advantages of AI-based automatic positioning using precise images in terms of positioning accuracy, radiation dose, and image quality compared to manual positioning for CT KUB examination. The introduction highlights the importance of reducing radiation dose in CT examinations using AI-based automatic positioning, which improves positioning accuracy and image quality with adherence to the ALARA principle. The methodology is well explained. Inclusion criteria for patient selection, measurement of radiation dose parameters, image quality (quantitative and qualitative) parameters, off-center distance, and standardized protocols for both AI-based and manual positioning enhance the study's reproducibility. Appropriate statistical methods were used to analyze the data. The results section presents the findings clearly and organized, using appropriate tables and figures to illustrate the data. The significant improvements in positioning accuracy and reduction in radiation dose with AI-based positioning are well-documented. The 44% reduction in off-center distance suggests a substantial improvement in patient positioning accuracy, which is essential for optimal imaging. The statistically significant reductions in CTDIvol (8.38%), DLP (12.32%), SSDE (10.32%), and ED (12.42%) for the AP group compared to the MP group are noted. Higher qualitative IQ scores support the benefits of AI-based positioning in producing better diagnostic image quality. The almost perfect interobserver agreement suggests that these results are reliable and reproducible. The discussion effectively summarizes the results and implications of improved positioning accuracy and reduced radiation dose for clinical practice. AI's potential to enhance consistency and efficiency in CT KUB scans is well-articulated, and the limitations of the study are well-addressed. The conclusion highlights the potential of AI-based automatic positioning to improve clinical outcomes and reduce radiation exposure for CT KUB examinations. Minor comments: Ensure all the abbreviations are clearly defined when first used in the manuscript. Include a section on future research directions of the study. Suggest how the findings of this study could be applied or expanded in future research. Check for typographic errors in the units. The study is well structured, with clear comparisons and statistically significant results that highlight the potential of AI in CT imaging procedures, leading to better patient outcomes and improved workflow in radiology.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] } ]	1	https://f1000research.com/articles/13-683
https://f1000research.com/articles/13-744/v1	04 Jul 24	{ "type": "Research Article", "title": "Teacher attributes as predictors of assessment practices in public universities of Ethiopia", "authors": [ "Million Yilma", "Menna Olango", "Samuel Assefa", "Menna Olango", "Samuel Assefa" ], "abstract": "Background Higher education teachers dwell on various classroom assessment practices. Their assessment practices play a significant part of the teaching learning process and in determining student achievement. In this respect, their different attributes determine the nature of their classroom assessment practices. This cross-sectional survey study aimed to examine differences in assessment practices among public university teachers with respect to their academic status, teaching experience, assessment training and specializations.\n\nMethods The study adopted Assessment Practices Inventory (API) which was distributed to a sample of 380 randomly selected teachers from four public universities. The majorities (93.4%) of questionnaires which were properly completed were entered to SPSS version 25 software and used for analysis. Multivariate analysis of variance (MANOVA) was used for analysis and Pillai’s Trace was utilized for interpretation of the results.\n\nResults The results showed that academic status (P= .000); teaching experience (P = .000); and assessment training (P =.030) had significant differences for the combined dependent variables (assessment practice). However, field of specialization (P =.130) did not show significant difference in the overall assessment practice although differences were observed in assessment design and interpretation.\n\nConclusion Academic status, teaching experience, and assessment training are important attributes of teachers that shape their assessment practices. Therefore, as teachers hold the sole responsibility of classroom assessment, training and development courses in assessment, experience sharing and learning opportunities are necessary regardless of their specializations, academic status, and teaching experience.", "keywords": [ "classroom assessment", "academic status", "assessment training", "teaching experience" ], "content": "Introduction\n\nAssessment is a process of getting information about learners’ performance, using clearly defined assessment criteria to determine what the learners know or can do and then using that information as evidence for making judgments about learners’ achievements (Department of Basic Education, 2012). The roles of assessment are a critical aspect of ensuring quality education and student development in any academic institution (Brown, et al., 2019). In fact, according to Brown et al. (2019), no factor influences a learning environment as much as assessment. Teachers are actively engaged on various classroom assessment practices as part of making the learning process as effective as it could possibly be. These assessment practices entail a wide range of dimensions such as assessment design, assessment administration, scoring and interpretation, assessment grading, and assessment data utilization or evaluation (Koloi-Keaikitse & Traynor, 2023). Thus, teachers’ assessment practices are a very important aspect of the learning process and they are directly related to students’ learning achievement (Crichton & McDaid, 2016) and key components to effective teaching and learning (Pastore & Andrade, 2019).\n\nHigher education assessment practices play a crucial role of ensuring the achievement of student learning outcomes by providing feedback for improvement. They are the cornerstones of informing instructional decision-making teachers have to rely on (Moss & Brookhart, 2019). In this regard, assessment in Ethiopian universities is one of the major components of the teaching learning process throughout the academic year. Teachers engage themselves on various assessment activities that range from devising an assessment technique to practically putting that in to practice and giving feedback to students. This requires the teachers to make appropriate decisions related to for example, what sorts of assessments are suitable for students, when and how to carry out assessments, what sorts of resources are required to conduct assessments, and how to utilize the information obtained from the assessments effectively. This indicates that teachers are the key drivers of the classroom assessment process from start to end. Therefore, as teachers’ classroom assessment practices are a means by which student learning outcomes are ensured, they need to be sufficiently taken care of Hunduma et al. (2023).\n\nStudies such as Bailey and Garner (2010) found that teachers play a critical role in designing and implementing assessments, and their academic levels influence the quality and effectiveness of their assessment practices. Holmboe et al. (2010) also argued that teachers with higher academic levels demonstrate a deeper understanding of assessment principles and are more likely to employ effective assessment strategies in their teaching. Moreover, Furtak et al. (2016) indicated that teachers with higher academic qualifications and specialized training in formative assessment demonstrated greater proficiency in implementing effective formative assessment strategies. Similarly, students under the guidance of academically qualified teachers demonstrated higher levels of academic achievement through improved self-assessment practices (Yan, 2019). Other studies also outlined the importance of teachers’ level of academic status in designing and implementing assessment tools that effectively measure students’ skills and knowledge (Paiva et al., 2022; Brown et al., 2019; Yan & Brown, 2021).\n\nOn the other hand, teaching experience was found to play a crucial role in shaping teachers’ approaches to assessing student learning (Popham, 2011). It is reported that more experienced and academically qualified teachers provide more comprehensive and constructive assessment feedback compared to their less experienced counterparts (Bailey & Garner, 2010). Moreover, other studies (such as Gamage et al., 2020; Susan & Catherine, 2017; Moss & Brookhart, 2019; Black and Wiliam, 2018) argue that experienced teachers demonstrate a deeper understanding of assessment principles and are adept at implementing formative and summative assessment techniques more effectively.\n\nThe other attribute having a profound effect on teachers’ assessment practice differences is the assessment training received by teachers. In this regard, Jacob, Hill, and Corey (2017) indicated that training programs can significantly improve teachers’ knowledge and instructional practices, which could also extend to assessment practices. Similarly, Brookhart (2011) provided insights into the educational assessment knowledge and skills for teachers and indicated that teachers who have undergone specific trainings in assessment exhibit more confidence and competence in designing and implementing appropriate assessment techniques. Some aspects of the assessment practices of the academic staff may be explained in relation to subject specializations (DeLuca et al., 2016) but the importance of educational assessment knowledge and skills for teachers acquired through objective training is emphasized (Brookhart, 2011; DeLuca et al., 2016; Yan & Brown, 2021). Therefore, regardless of a teacher’s field of specialization, there definitely is a need to put an emphasis on assessment literacy in teacher training programs to ensure that educators are equipped with the necessary assessment skills and preparedness.\n\nIn different levels of academic institutions including universities, although teachers play a key role in the overall classroom assessment process, there are disparities among them. This is supported by researchers such as Bruggeman et al. (2021) and Matovu and Zubairi (2015) who found out that assessment practices vary among teachers of different higher education institutions as well as in their departments, faculties, and universities. As a result, they suggested consistency of assessment policies and strategies among institutions and within their constituent departments and faculties. Moreover, other studies reported inconsistencies in the factors influencing teachers’ assessment practices (Boud & Associates, 2010; Zhang & Burry-Stock, 2003; Koloi-Keaikitse & Traynor, 2023; Popham, 2009; Koloi-Keaikitse, 2017; Borghouts, et al., 2016). However, many of these studies have been done in primary and secondary schools although a few (such as Postareff et al., 2012; Xu, & Liu, 2009) have been done in universities.\n\nIn Ethiopia, a few researchers (Soromessa, 2015; Mekonnen, 2014; Chalchisa, 2014; Belay, 2017; Abera et al., 2017; Moges, 2018) investigated some aspects of assessment such as implementation and challenges of continuous assessment. Tulu and Tolosa (2018) studied classroom assessment in secondary schools but it was limited to the techniques used and the challenges faced by the teachers during their assessment works. Hunduma et al. (2023) investigated perceptions and practices of continuous assessment in government higher learning institutions. However, no research exists regarding the differences in assessment practices of teachers with respect to their attributes in public universities of Ethiopia. Thus, understanding assessment practices of university teachers serves as a way of finding out whether they adopt or use quality assessment practices to meet the learning needs of students and the varying needs of other stakeholders. Therefore, this research was aimed to investigate the relationship of teachers’ academic status, years of teaching experience, field of specialization, and levels of assessment training with their classroom assessment practices. Thus, the study formulated the following basic research questions and hypotheses.\n\n• What is the relationship of teachers’ academic status, years of teaching experience, field of specialization, and levels of assessment training with their classroom assessment practices?\n\n• Are there significant differences in teachers’ assessment practices due to their academic status, years of teaching experience, levels of assessment training and types of specializations?\n\n• H0a: There is no significant relationship among teachers’ academic status, years of teaching experience, field of specialization, and levels of assessment training with their classroom assessment practices.\n\n• H0b: There is no significant difference in teachers’ assessment practice due to their academic status, years of teaching experience, levels of assessment training and types of specializations.\n\n\nMethods\n\nHawassa University, College of Education, Research Ethics Review Committee (RERC) has approved the implementation of the research on June 03, 2023; with reference number COE- REC-007/2023 (Letter of Research Ethics Review Committee). The Committee confirmed that the research met the criteria that subject risk is minimized; subjects are selected equitably; respect for person-informed consent is determined and has been documented appropriately and privacy and confidentiality are maintained. Written informed consent was obtained from all participants.\n\nThis study employed a quantitative cross-sectional survey research design which entails collecting quantitative data at a specific point in time in the lives of respondents. Surveys are a powerful and useful tool for collecting data on human characteristics, such as their beliefs, attitudes, thoughts, and behavior (Creswell, 2012). Moreover, it is asserted that for large-sample studies, survey research is more objective and appropriate (Choy, 2014).\n\nThe populations for this study were teachers in public universities of Ethiopia. According to the ministry of education of Ethiopia, there are around 40000 teachers in the universities. There are around 42 public universities in the country. These universities are grouped by the Ministry of Science and Higher Education (MoSHE) under four categories (research, applied, comprehensive, and specialized universities). First, four universities were chosen by simple random sampling from their respective categories (one from each category). Thus, Hawassa, Bulehora, Wolkite, and Addis Ababa Science and Technology universities were selected (Hawassa from research, Bulehora from comprehensive/general, Wolkite from applied, and Addis Ababa Science and Technology University from the specialized universities). Then, six specializations (Engineering and technology, Natural and computational sciences, Agricultural science, Computing and informatics, Social science and humanities, and Education and behavioral sciences) were selected using simple random sampling. Using simple random sampling from the different stratum aggregated by gender, academic status, and specializations, teachers (n=380) were included from the four randomly selected public universities. This ensured that samples were representative of the relevant subgroups (see Table 1). The number of samples was determined considering the teacher population of public universities in Ethiopia based on the sample table of Krejcie and Morgan (1970). Samples from each of the academic statuses were included carefully because they also relate to teaching experience and assessment training. With regard to participants, all active teachers during the data collection were eligible for being included in the study. This means teachers who were engaged in professional development programs elsewhere during data collection and those non-Ethiopian citizens were not included. The difference in the number of male and female samples was due to the persistent gap in the number of male and female teachers in public universities of Ethiopia.\n\nFor the purpose of this study, the API- Assessment Practices Inventory (Zhang & Burry-Stock, 2003) was adopted and used for data collection. It consisted of 67 items measured on two rating scales: “Use” and “Skill”. The use scale ranged from 1 (not at all used) to 5 (used very often), the skill scale from 1 (not at all skilled) to 5 (very skilled). This instrument was selected because it covered a relatively wider range of issues by providing a larger pool of items that fit to the objective of this research. This study incorporated 58 API and 5 demographic items giving a total of 63 items. Based on the pilot study, 6 items were adapted to suit to the purpose and context of the study (public universities of Ethiopia), while 43 items were adopted from API and 9 items were dropped due to validity and reliability issues, or not being applicable at the university level in the Ethiopian context. From the questionnaires distributed to 380 respondents, 360 of them were returned. However, 355 were used for analysis because 5 were not completed properly.\n\nWith regard to reliability, in the API in Zhang & Burry-Stock (2003), the Cronbach’s alpha values of the scales ranged from .89 to .77 for assessment practices (use scale) and from .91 to .85 for self-perceived assessment skills (skill scale). A pilot study was conducted prior to the actual study from which the ‘skill’ scale had an overall Cronbach’s alpha value of.94, and the ‘use’ scale had an overall value of α = .96 indicating a strong internal consistency of the items. On the final data, the overall Cronbach’s alpha value for the ‘skill’ scale was .97 and for the ‘use’ scale was.95 indicating a strong internal consistency. The Cronbach alpha value of the components varied from .94 to .82 for the ‘skill’ scale and from .90 to.80 for the ‘use’ scale. All the items in the scales as well as within the factors were reliable as they were all above the required minimum standard .70.\n\nConstruct validity is about how well a test measures the concept it was designed to measure. It’s crucial to establishing the overall validity of an instrument. For ensuring construct validity of an instrument, a factor analysis utilizing Principal Component Analysis (PCA) with varimax rotation method can be conducted (Taherdoost, 2016). This is because the Principal Component Analysis (PCA) method is capable of reducing and eliminating factors that are less dominant or relevant in influencing a certain performance. Therefore, for this study, PCA was used to determine the construct validity of the instrument. Thus, items loading above 0.40 (the minimum recommended value in research) were considered for further analysis but items cross loading above 0.40 were deleted as recommended. In this way, the factor analysis results will satisfy the criteria of both of the construct validity types including discriminant validity (loading of at least 0.40, no cross-loading of items above 0.40) and convergent validity (eigenvalues of 1, loading of at least 0.40). As a result, 9 items which were loading below the minimum recommended value (0.40) and which were cross-loading above 0.40 were removed. Finally, 58 items were retained for use in the final data collection. In addition, face validity and content validity of the instrument was ascertained by subject specialists in the area of assessment.\n\nDuring data collection, all the necessary procedures were given due attention starting from getting permission from respective bodies. Thus, the researchers obtained support and approval letters from Hawassa University’s School of Graduate Studies before beginning the data collection activities. The letters were given to the representatives of the selected universities and permission to contact teachers was solicited from deans of sampled colleges from the selected universities. All participants signed an informed consent and agreed to the processing of data for research purposes. Participants’ names were made anonymous. The data collectors were briefed in advance on some important points with respect to the study such as its objectives, the nature of the questionnaire and the respondents and what they should do before, during and after the data collection. Respondents were accessed physically based on their convenience by travelling to their respective universities (Hawassa, Wolkite, Bulehora, and Addis Abeba science and technology universities) and were provided with the questionnaire to fill in, through department heads and college deans in most cases. The data collection was completed in 25 days from June 5 to 30, 2023. Emphasis was given to every step of the way in order to minimize non-response rate. During the data collection and data analysis period all reasonable care was employed to ensure that the confidentiality of the data was maintained. Codes were used to identify universities and participants in the study. Identifiable and sensitive information linking to universities and participants were withheld to ensure that the integrity of the study was not compromised.\n\nMultivariate analysis of variance (MANOVA) was employed to examine the differences in assessment practices among teachers with respect to their different academic status, teaching experience, assessment training and specializations. MANOVA was used to determine whether or not two or more categorical grouping variables (and/or their combinations) significantly affect optimally weighted linear combinations of two or more normally distributed outcome variables. As there were four continuous dependent variables out of the assessment practices scale and four independent categorical variables, MANOVA was the best option for the analysis.\n\nWith respect to MANOVA assumptions, all the dependent variables are continuous and the four independent variables included in the MANOVA are categorical and have more than two groups. There was independence of observations. Moreover, this study has made sure that adequate sample size was incorporated. The Box’s M test of 533.849 indicates that the homogeneity of covariance matrices across groups is not fulfilled (F(220, 6968.646) = 1.78, p = 0.000) since the p-value for the Box’s Test is.000, which is lower than the commonly used value of α = .001. In such cases, it is recommended to utilize a more robust MANOVA test statistic, Pillai’s Trace, when interpreting the MANOVA results (Tabachnick and Fidell, 2007). Finally, the dependent variables are moderately correlated (not greater than 0.9) indicating no effect of multicollinearity with a maximum value of.816 in this study.\n\nThe four categorical independent variables included in the study are teachers’ academic status, years of teaching experience, field of specialization, and levels of assessment training received. Academic status has five categories (graduate assistant, lecturer, assistant professor, associate professor, and professor). Teaching experience, although a continuous variable, was categorized for convenience in the analysis and interpretation with five years range (1-5 years, 6-10, 11-15, 16-20, and 21 and above years). Field of specialization has six categories (Engineering and technology, Natural and computational science, Agricultural science, Computing and informatics, Social science and humanities, and Education and behavioral sciences). Finally, assessment training received has four categories (no assessment training at all, training on some topics of assessment, a course dedicated to assessment, and more than one course of assessment). Moreover, the combined dependent variable for the analysis was assessment practice which included four specific variables that were dealt with the MANOVA analysis. These are designing assessment (Usedesign); administering, scoring and interpreting assessments (AdmnScorInterp); grading assessments (UseGrading); and application of assessment results (UseApplication).\n\n\nResults\n\nPillai’s Trace was used for interpretation of results because it is recommended to be a more robust test statistic for interpreting the MANOVA results when the covariance matrices are not homogeneous (Tabachnick and Fidell, 2007). Moreover, when groups differ along more than one variate, Pillai’s trace is most powerful and Roy’s root is least (Field, 2009). Therefore, Pillai’s trace was used in the analysis instead of Wilk’s Lambda which is the most common.\n\nThe MANOVA results of the main effects for the combined dependent variables (see Table 2) indicate that academic status/level has- Pillai’s Trace = .306, F (16, 984) = 5.09, P = .000, η2 = .076; Teaching experience- Pillai’s Trace = .259, F (16, 984) = 4.27, P = .000, η2 = .065; Field of specialization- Pillai’s Trace = .108, F (20, 984) = 1.37, P = .130, η2 = .027; Assessment training- Pillai’s Trace = .091, F (12, 735) = 1.91, P = .030, η2 = .030. These outcomes depict that academic status, teaching experience and assessment training had significant differences with respect to the combined dependent variable (assessment practices) but field of specialization was not significant here. However, significant interaction effects of academic status and specialization was observed on the combined dependent variable at P = .027.\n\n* p < .05.\n\n p <.01.\n\n* p <.001.\n\nAnalysis of variance (ANOVA) was conducted on each dependent variable as a follow-up test to MANOVA (see Table 3). Thus, significant differences were observed in academic status for three of the dependent variables, i.e. assessment design, assessment grading, and assessment application. For assessment design F (4, 246) = 3.22, P = .013, η2 = .050; for assessment grading F (4, 246) = 17.33, P = .000, η2 = .220; for assessment application F (4, 246) = 12.84, P = .000, η2 = .173. Academic status had not revealed significant difference for assessment administration, scoring and interpretation. In teaching experience, significant differences were observed for two of the dependent variables, i.e. assessment grading and assessment application. For assessment grading F (4, 246) = 9.77, P = .000, η2 = .137; for assessment application F (4, 246) = 13.81, P = .000, η2 = .183. Teaching experience did not reveal significant differences for two of the dependent variables, i.e. assessment design; and assessment administration, scoring and interpretation. In the contrary, field of specialization of teachers revealed significant differences in assessment design only, F(5, 246) = 2.82, P = .017, η2 = .054. Assessment training received by teachers showed significant differences in all of the dependent variables. For assessment design F (3, 246) = 2.59, P = .020, η2 = .031; for assessment administration, scoring and interpretation F (3, 246) = 4.10, P = .007, η2 = .048; for assessment grading F (3, 246) = 3.43, P = .018, η2 = .040; for assessment application F (3, 246) = 3.82, P = .011, η2 = .045. Lastly, no significant interaction effects of the independent variables were observed in all of the dependent variables.\n\n* p < .05.\n\n p <.01.\n\n* p <.001.\n\nPost Hoc tests were conducted to find out which groups are significantly different for the dependent variables for which significant univariate significance was found. Thus, academic status of teachers showed differences with respect to the four assessment practices dependent variables. For example, in designing assessments, graduate assistants and lecturers were significantly different from all the other groups at p < .001. Assistant professors, associate professors and professors significantly differed in assessment design with graduate assistants and lecturers at p < .001 but not with each other. In administration, scoring and interpretation of assessments, graduate assistants and lecturers significantly differed from all the other groups at p < .001. Assistant professors and associate professors were significantly different from graduate assistants and lecturers at p < .001 and the former differed significantly with professors at.035 while the latter didn’t show significant difference. In assessment grading, graduate assistants and lecturers significantly differed from all the other levels at p < .001. Assistant professors, associate professors and professors were significantly different from graduate assistants and lecturers at p < .001 but not significantly with each other. Similarly, in application of assessment results, assistant professors, associate professors and professors had significant differences with graduate assistants and lecturers at p < .001 but not with each other (see Table 4 of underlying data).\n\nMoreover, differences were observed within years of teaching experience with respect to the assessment practices dependent variables. For example, in designing assessments, teachers with teaching experience of below 10 years were significantly different from all the other groups above 10 (i.e., 11-15, 16-20, 21 and above) at p < .001. similarly, in administering, scoring and interpreting assessments, teachers having below 10 years of experience had significant differences with all the other groups having 11 and above years at p < .001. Teachers with 11 to 15 years of experience had significant differences with 1 to 5, 6-11 and 21 and above years of experience at p < .001 but they did not have significant differences with 16-20 years of experience. Teachers with 16 to 20 years of experience had significant differences with those groups below 10 years of experience at p < .001 but not significantly with the other groups. Lastly, teachers with 21 and above years of experience had significant differences with those groups having experience of below 15 years at p < .001 but not significantly with those 16 to 20 years of experience. In grading assessments, the groups below 10 years of experience had significant differences with those groups having experience of 16 years and above at p < .001. This scenario was similar in application of assessments as well. Generally, this results show that teaching experience matters with respect to teachers’ assessment practices (see Table 5 of underlying data).\n\nSignificant differences were also observed in the different levels of assessment training teachers received with respect to the assessment practices dependent variables. For example, in designing assessments, teachers who received no assessment training at all had significant differences from all the other groups at p < .001. Those who received training on some topics of assessment had significant differences with all the other groups p < .001 but not significantly with those who had a course in assessment. Those who received more than one course of assessment had significant differences from all the other groups at p < .001. In assessment administration, scoring and interpretation, teachers who received no assessment training at all and teachers who received training on only some topics of assessment had significant differences from all the other groups at p < .001. Those teachers who received one course dedicated to assessment had significant differences from all the other groups at p < .001 except with those who took some topics of assessment with which significant difference was not observed. Lastly, those teachers who received training on more than one course of assessment had significant differences with all the other groups at p < .001. In relation to grading of assessments, teachers who received no assessment training at all and those who received training on only some topics of assessment had significant differences with all the other groups at p < .001. This scenario was similar for those who received training on one course of assessment and also more than one courses of assessment as well. In the same way, in application of assessment results, all the groups having any level of assessment training had significant differences with those having no training at all at p < .001 (see Table 6 of underlying data).\n\nLastly, from the Post Hoc Test results, it is seen that significant differences were observed in assessment design between education and behavioral sciences and the other specializations at p < .001. In administering, scoring and interpreting assessments also education and behavioral sciences had significant differences with all specializations at p < .05.\n\n\nDiscussion\n\nThe study revealed that level of academic status, years of teaching experience and assessment training teachers received depicted significant differences in teachers’ assessment practices. Moreover, significant interaction effects of academic status and specialization was observed on the assessment practices of teachers. In a more detailed analysis, the different levels of each of the independent variables (academic status, teaching experience, field of specialization, and assessment training) were compared on the basis of the four dependent variables of assessment practices (designing assessments; administering, scoring and interpreting assessments; grading assessments; and application of assessment results).\n\nAcademic status (graduate assistants, lecturers, assistant professors, associate professors, and professors) was compared against each of the dependent variables and significant differences were observed among the different levels among them. For instance, in designing assessments, graduate assistants and lecturers were significantly different from all the other higher academic statuses and with each other as well. Higher academic statuses (assistant professors, associate professors, professors) were significantly different from the relatively lower academic statuses (graduate assistants and lecturers) but not with each other.\n\nIn administering, scoring, and interpreting assessments, graduate assistants and lecturers significantly differed from all the other higher academic statuses and with each other as well. Assistant professors were significantly different from graduate assistants, lecturers, and professors but not with associate professors. Associate professors were significantly different from graduate assistants and lecturers but not from assistant professors and professors. Lastly, professors were significantly different from graduate assistants, lecturers and with assistant professors. However, significant difference was not observed with associate professors.\n\nIn assessment grading, graduate assistants and lecturers were significantly different from all the other levels. Assistant professors were significantly different in assessment grading form graduate assistants and lecturers but not from associate professors and professors. Similarly, associate professors and professors were significantly different in assessment grading form graduate assistants and lecturers but not with assistant professors. Lastly, in application of assessment results, graduate assistants and lecturers were significantly different from all the other academic levels. However, assistant professors, associate professors and professors had significant differences with graduate assistants and lecturers in a similar way but not significantly with each other.\n\nOverall, the findings revealed that academic status of university teachers is significantly related to their assessment practices. This is supported by Park et al. (2016) who revealed that the academic level of teachers is a sole contributor to their assessment practices because teachers with higher academic levels demonstrate a more nuanced understanding and use of assessment practices. Gable et al. (2012) also found that teachers with higher academic levels and academic status exhibited greater preparedness to implement evidence-based assessment practices. Other studies also suggested that teachers with a higher academic levesl demonstrate a deeper understanding of assessment principles and are more likely to employ effective assessment strategies in their teaching (Bailey and Garner, 2010; Scarino, 2013; Holmboe et al., 2010).\n\nDifferences were observed among university teachers with different years of teaching experience (1 to 5, 6 to 10, 11 to 15, 16-20, 21 and above years) with respect to the different assessment practices dependent variables. For example, in designing assessments, teachers with 1 to 5 and 6 to 10 years of teaching experience were significantly different from all the other groups with more than 10 years of teaching experience. Teachers with more than 10 years of experience had significant differences from those with below 10 years of experience, but were not significantly different from one another.\n\nIn administering, scoring and interpreting assessments, teachers having below 10 years of teaching experience had significant differences with all the other groups with more than 10 years of experience. Teachers with 11 to 15 years of experience had significant differences from those with below 10 years and 21 and above years of experience but not from those with 16 to 20 years of experience. Teachers with 16 to 20 years of experience had significant differences with those less than 10 years of experience but not from the other groups with more than 10 years of experience. Lastly, those teachers with 21 and above years of experience had significant differences with those less than 15 years of experience but not from those with 16 to 20 years. In grading assessments, the groups below 10 years of experience had significant differences with those groups having experience of 16 years and above. Similarly, those with 21 and above years of experience had significant differences from all the other groups except from those with 16 to 20 years of experience which were not significant. This scenario in grading was similar in application of assessments as well.\n\nOverall, these findings revealed that teaching experience matters in classroom assessment practices of teachers and has practical implications for institutional administrators who work with both inexperienced and experienced teachers. In this respect, studies found that teaching experience significantly influences teachers’ assessment practices and that experienced teachers demonstrate a deeper understanding of assessment principles and are adept at implementing formative and summative assessment techniques (Berendonk et al., 2012; Gamage et al., 2020; Cook and Ellaway, 2015). Similarly, other studies emphasized the dynamic nature of assessment practices and the need for teachers to develop multifaceted assessment literacy through training and practical experiences to develop their confidence to adapt to changing educational landscapes (Willis et al., 2013; Brookhart, 2011). As it has been shown that teachers with more teaching experience gain more confidence in using different assessment practices, they can therefore be asked to mentor the novice teachers in their institutions, departments etc.\n\nIn the different levels of assessment training (no assessment training at all, training on only some topics of assessment, training on one course dedicated to assessment, and training on more than one courses of assessment), significant differences were observed when compared on the basis of the four assessment practices dependent variables. For example, in designing assessments, teachers who received no assessment training at all depicted significant differences from all the other groups. Teachers who received training on some topics of assessment had significant differences with all the other groups except from those who had a course dedicated to assessment. Those who received a course dedicated to assessment had significant differences from all the other groups except from those with training on some topics of assessment. Those who received more than one course of assessment had significant differences from all the other groups.\n\nIn assessment administration, scoring and interpretation, teachers who received no assessment training at all had significant differences from all the other groups. Those teachers who received training on only some topics of assessment had significant difference with all the other groups except with those who took a course dedicated to assessment which showed no significant difference. Those teachers who received one course dedicated to assessment had significant differences from all the other groups except those who took some topics of assessment which significant difference was not observed. Lastly, those teachers who received training on more than one course of assessment had significant differences with all the other groups.\n\nIn relation to grading of assessments, those who received no assessment training at all and those who received training on only some topics of assessment had significant differences with all the other groups. This scenario was similar for those who received training on one course of assessment and also more than one courses of assessment as well. Lastly, in application of assessment results, those teachers who received no assessment training at all had significant differences with all the other groups. This scenario was also similar for the other groups as well. Therefore, the findings of this study clearly depict that assessment training teachers acquire fundamentally influences their assessment practices and have implications for teacher educators.\n\nWith training, it is noted that the quality of assessment training attained by the academic staff can determine the effectiveness of assessments they use in any learning institution (Yan and Brown, 2021). For this reason, delivering assessment training courses are some of the ways institutions can equip their academic staff with the required assessment competencies and skills (DeLuca et al., 2016; Livingston, & Hutchinson, 2016). Similarly, Shernoff et al. (2017) emphasized the necessity of integrating a course in assessment with an appropriate text to provide beginning teachers with a more comprehensive understanding of assessment.\n\nGenerally, no significant differences were observed among different specializations with respect to teachers’ overall assessment practices. However, significant interaction effects of teachers’ academic status and specialization was observed in this case. This meant that teachers of different specializations with different academic levels were different in their assessment practices. Moreover, significant differences were observed in assessment design between education and behavioral sciences and the other specializations (engineering and technology, agricultural sciences, computational sciences, computing and informatics, and social sciences and humanities). In administering, scoring and interpreting assessments also education and behavioral sciences had significant differences with all the other specializations. Similarly, Matovu and Zubairi (2015) reported statistically significant differences in the interpretation of assessment results in the specializations of Education and Arts. This difference is attributed to the fact that teachers from the education discipline are provided with assessment trainings as part of their university course works. This highlights the importance of developing teachers’ general assessment knowledge and skills that are applicable across different disciplines. This is because assessment skills and practices are not limited to subject-specific knowledge, but rather require a broader understanding of the assessment process, which is not heavily influenced by the teacher’s field of specialization (Brookhart, 2011; Scarino, 2013; Matovu and Zubairi, 2015; Popham, 2011). Therefore, prospective teachers need to be equipped with sufficient assessment knowledge and expertise that would make it possible for them to undertake effective assessments irrespective of their specializations.\n\nAs teachers play a pivotal role in the classroom assessment process, understanding how their attributes such as academic status, teaching experience, assessment training they received and specializations relate to their classroom assessment practices is very important. Therefore, findings from this study may provide valuable insights for understanding teachers’ personal attributes with respect to their classroom assessment practices in Ethiopia and elsewhere. This helps to adequately emphasize teachers’ readiness during their training to adequately conduct classroom assessments relative to the significant amount of time they spend on assessment-related activities.\n\nThis study revealed some important findings that can inform both assessment policy and practice especially in the context of higher education institutions. However, the findings were limited by the use of a self-reported survey questionnaire only. The study would have benefited from analysis of relevant documents or having some important interviews with teachers. The gender disparity in the respondent pool was also one of the constraints faced by the study. Future studies may use multiple methods of data collection including classroom observation, document analysis such as analysis of teacher-made assessments, and interviews to validate teacher self-report data.\n\n\nConclusions\n\nAs teachers are primarily responsible for conducting classroom assessment, their classroom assessment practices are fundamental to the education process. Therefore, this study examined differences in assessment practices of public university teachers of Ethiopia with respect to their different academic status, teaching experience, assessment training and specializations. The study concluded that different levels of academic status, teaching experience and assessment training have significant relationships with assessment practices and that they trigger significant differences in the overall assessment practices of teachers. There are significant differences in the different assessment practice variables between teachers with higher academic statuses and those with relatively lower ones. This scenario works in a similar way for years of teaching experience as well as levels of assessment training they received. There are significant differences in the different levels of experience and assessment training teachers received with respect to the specific assessment practices dependent variables. Therefore, the null hypothesis that there is no significant difference in assessment practices of teachers with respect to their different academic status, teaching experience, and assessment training is rejected. The claim that there is no relationship between these variables is also rejected. Moreover, significant differences were observed among some specializations with respect to some specific assessment practices dependent variables although significant differences were not observed with respect to the combined dependent variable (assessment practice).\n\nTherefore, the findings from this study indicate that professional development programs having practical implications for classroom assessment should be devised and provided to university teachers based on appropriate needs. Real time assessment experiences and training opportunities for teachers should be arranged according to the curriculum needs and existing gaps in assessment irrespective of their fields of specializations. The content of teacher education course requirements should be analyzed based on the curriculum needs and ensure the inclusion of assessment courses. In addition, any form of in-service workshop offerings should consider teachers’ needs based on the curriculum requirements to narrow persistent assessment practice gaps among teachers of different academic status, experiences and specializations. Training targeted directly towards critical assessment skills that teachers are required to have with respect to their specializations and the academic level of their students. This is fundamental in ensuring that all learners are assessed appropriately. Future studies who wish to study teachers’ classroom assessment practices should be able to corroborate findings from appropriate qualitative methods to complement findings from quantitative analyses. In future studies, besides the teacher related factors, considering other variables which are potentially related to assessment practices in universities would be appropriate.\n\nHawassa University, College of Education, Research Ethics Review Committee (RERC) has approved the implementation of the research on June 03, 2023; with reference number COE- REC-007/2023 (Letter of Research Ethics Review Committee). The Committee confirmed that the research met the criteria that subject risk is minimized; subjects are selected equitably; respect for person-informed consent is determined and has been documented appropriately and privacy and confidentiality are maintained. Written informed consent was obtained from all participants.", "appendix": "Data availability statement\n\nThe datasets used in our analysis are available from:\n\nZenodo: Teacher attributes as predictors of assessment practices in public universities of Ethiopia, https://doi.org/10.5281/zenodo.12518529 (Yilma et al., 2024).\n\nThe study contains the following underlying data:\n\n• Table 1.xlsx: depicts demographic characteristics of the respondents.\n\n• Table 2.xlsx: depicts multivariate tests for the combined dependent variables.\n\n• Table 3.xlsx: depicts the follow-up analysis using univariate ANOVA\n\n• Table 4.xlsx: depicts multiple comparisons among different academic status of teachers.\n\n• Table 5.xlsx: depicts multiple Comparisons for teaching experience.\n\n• Table 6.xlsx: depicts multiple comparisons for assessment training teachers received.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0)\n\nZenodo: Teacher attributes as predictors of assessment practices in public universities of Ethiopia, https://doi.org/10.5281/zenodo.12518529 (Yilma et al., 2024).\n\nThe study contains the following extended data:\n\n• Items used for pilot study.xlsx: depicts the original sets of items used in the pilot study.\n\n• Modified items.xlsx: depicts items retained with some modifications based on the pilot study.\n\n• Items excluded.xlsx: depicts items excluded based on results from the pilot study.\n\n• Items used for final data collection.xlsx: depicts the final sets of items used for the final data collection.\n\n• STROBE Checklist.xlsx: depicts STROBE checklist for cross-sectional study.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nAbera G, Kedir M, Beyabeyin M: The implementations and challenges of continuous assessment in public universities of Eastern Ethiopia. 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Publisher Full Text\n\nGamage K, Wijesuriya D, Ekanayake S, et al.: Online delivery of teaching and laboratory practices: continuity of university programs during COVID-19 pandemic. Educ. Sci. 2020; 10. Publisher Full Text\n\nHolmboe ES, Sherbino J, Long DM, et al.: The role of assessment in competency-based medical education. Med. Teach. 2010; 32(8): 676–682. Publisher Full Text\n\nHunduma CM, Abo GB, Gursha AN: Perceptions and practices of continuous assessment in government higher learning institutions in Ethiopia. Res. Humanit. Soc. Sci. 2023; 13: 7. Publisher Full Text\n\nJacob R, Hill H, Corey D: The Impact of a Professional Development Program on Teachers’ Mathematical Knowledge for Teaching, Instruction, and Student Achievement. J. Res. Educ. Effect. 2017; 10(2): 379–407. Publisher Full Text\n\nKoloi-Keaikitse S: Assessment of teacher perceived skill in classroom assessment practices using IRT Models. Cogent Educ. 2017; 4(1): 1281202. Publisher Full Text\n\nKoloi-Keaikitse S, Traynor A: Discrepancies between teachers’ self-reported perceived skills and use of classroom assessment practices: The case of Botswana. Cogent Educ. 2023; 10(2). Publisher Full Text\n\nKrejcie RV, Morgan DW: Determining sample size for research activities. Educ. Psychol. Meas. 1970; 30(3): 607–610. Publisher Full Text\n\nLivingston K, Hutchinson C: Developing teachers’ capacities in assessment through career-long professional learning. Assess. Educ.: Princ. Policy Pract. 2016; 24(2): 290–307. Publisher Full Text\n\nMatovu M, Zubairi AM: Assessment practices in the developing world: Predictors of assessment practices in Ugandan institutions of higher learning. IIUM J. Educ. Stud. 2015; 3(2): 75–112. Publisher Full Text\n\nMekonnen GT: EFL classroom assessment: Teachers’ practice and teaching techniques adjustment in Ethiopia. Educ. Res. Rev. 2014; 9(20): 1071–1089. Publisher Full Text\n\nMoges B: The implementations and challenges of assessment practices for students’ learning in public selected universities, Ethiopia. Univ. J. Educ. Res. 2018; 6(12): 2789–2806. Publisher Full Text\n\nMoss CM, Brookhart SM: Advancing formative assessment in every classroom: A guide for instructional leaders. 2nd ed.ASCD; 2019.\n\nPaiva JC, Leal JP, Figueira L: Automated Assessment in Computer Science Education: A State-of-the-Art Review. ACM Trans. Comput. Educ. 2022; 22(3): 1–40. Publisher Full Text\n\nPark H, Byun SY, Sim J, et al.: Teachers’ Perceptions and Practices of STEAM Education in South Korea. Eurasia J. Math., Sci Tech. Ed. 2016; 12(7). Publisher Full Text\n\nPastore S, Andrade HL: Teacher assessment literacy: A three-dimensional model. Teach. Teach. Educ. 2019; 84: 128–138. Publisher Full Text\n\nPopham WJ: Assessment Literacy for Teachers: Faddish or Fundamental? Theory into Practice, Digital/Theory Into Practice. 2009; 48(1): 4–11. Publisher Full Text\n\nPopham WJ: Assessment literacy overlooked: A teacher educator’s confession. Teach. Educ. 2011; 46: 265–273. Publisher Full Text\n\nPostareff L, Virtanen V, Katajavuori N, et al.: Academics’ conceptions of assessment and their assessment practices. Stud. Educ. Eval. 2012; 38(3): 84–92. Publisher Full Text\n\nScarino A: Language assessment literacy as self-awareness: Understanding the role of interpretation in assessment and in teacher learning. Lang. Test. 2013; 30: 309–327. Publisher Full Text\n\nShernoff DJ, Sinha S, Bressler DM, et al.: Assessing teacher education and professional development needs for the implementation of integrated approaches to STEM education. Int. J. STEM Educ. 2017; 4(1): 13. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSoromessa T: The practice of student assessment: The case of college of natural science, Addis Ababa University, Ethiopia. J. Educ. Pract. 2015; 6(25): 141. Reference Source\n\nSusan JD, Catherine B: Staff student partnership in assessment: enhancing assessment literacy through democratic practices. Assess. Eval. High. Educ. 2017; 42(3): 463–477. Publisher Full Text\n\nTabachnick BG, Fidell LS: Using multivariate statistics. 5th ed.New York: Allyn and Bacon; 2007.\n\nTaherdoost H: Validity and Reliability of the Research Instrument; How to Test the Validation of a Questionnaire/Survey in a Research. Soc. Sci. Res. Netw. 2016. Publisher Full Text\n\nTulu G, Tolosa T; J.-F: The nature of classroom assessment in Ethiopian public secondary schools: Subject teachers’ views. J. Educ. Soc. Behav. Sci. 2018; 26(3): 1–11. Publisher Full Text\n\nWillis J, Adie L, Klenowski V: Conceptualizing teachers’ assessment literacy in an era of curriculum and assessment reform. Aust. Educ. Res. 2013; 40: 241–256. Publisher Full Text\n\nXu Y, Liu Y: Teacher assessment knowledge and practice: A narrative inquiry of a Chinese College EFL teacher’s experience. TESOL Q. 2009; 43: 493–513. Publisher Full Text\n\nYan Z, Brown GT: Assessment for learning in the Hong Kong assessment reform: A case of policy borrowing. Stud. Educ. Eval. 2021; 68: 100985. Publisher Full Text\n\nYan Z: Self-assessment in the process of self-regulated learning and its relationship with academic achievement. Assessment and Evaluation in Higher Education/Assessment & Evaluation in Higher Education. 2019; 45(2): 224–238. Publisher Full Text\n\nYilma M, Olango M, Assefa S: Teacher attributes as predictors of assessment practices in public universities of Ethiopia. [Data set]. Zenodo. 2024. Publisher Full Text\n\nZhang Z, Burry-Stock JA: Classroom assessment practices and teachers’ self-perceived assessment skills. Appl. Meas. Educ. 2003; 16(4): 323–342. Publisher Full Text" }	[ { "id": "302850", "date": "30 Jul 2024", "name": "Richelle Marynowski", "expertise": [ "Reviewer Expertise Assessment practices", "mathematics teaching and learning", "teacher professional development." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe paper reports on a quantitative study designed to report on the assessment practices of public university teachers in Ethiopia. The survey results identified that there were relationships between teachers' academic status, levels of training and teaching experience and assessment practices. There were no differences noted between specialization and assessment practices.\nThe paper is clearly written and includes the appropriate supporting data and analysis to ensure that results follow the data gathered. There could be more literature incorporated in the discussion regarding professional development and implications for assessment practices at the post-secondary level. In particular, what kinds of programs have been shown to be effective, if any.\n\nThe discussion was a bit repetitive from the results and I would have liked to see more contextual implications for Ethiopia's public universities as well as more context about Ethiopia's post-secondary system to give more background to interpret the results.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? 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": "314796", "date": "05 Sep 2024", "name": "Abraham Gyamfi", "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\nareas of suggestions 1. The focus of the research questions and the hypotheses are the same. Stick to the one but the hypothesis is ideal. 2. present the results based on the hypothesis (research hypothesis by research hypothesis)\nstrengths 1. good methodology, statistical tools and conclusion. 2. the work is clearly and accurately presented except for the presentation of results\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] } ]	1	https://f1000research.com/articles/13-744
https://f1000research.com/articles/13-742/v1	04 Jul 24	{ "type": "Systematic Review", "title": "Physical activity implementation in the curricula of healthcare professions: a systematic review", "authors": [ "Reena Patel", "Sophie Lane", "Petros C. Dinas", "Ian M. Lahart", "George S. Metsios", "Reena Patel", "Sophie Lane", "Petros C. Dinas" ], "abstract": "Background The objective was to investigate the impact of physical activity (PA) teaching and learning approaches in healthcare professionals (HCPs) education on PA-related knowledge, confidence, and behaviour.\n\nMethods Eligible experimental studies investigated the effect of interventions that incorporate PA in to the undergraduate and postgraduate education, and continuous professional development of any HCP (medical doctors, nurses, physiotherapists, etc.) on PA-related outcomes including knowledge, perceptions, and confidence to prescribe PA. Six databases (Cochrane Central Register of Controlled Trials, CINAHL, Embase, ERIC, Medline, and SPORTDiscus) were searched from inception to October 2022. Risk of bias was assessed using the Joanna Briggs Institute critical appraisal tools. A narrative data synthesis was undertaken to assess the overall effectiveness of the reviewed educational interventions: knowledge, perceptions, confidence, attitudes, beliefs, and changes in behaviour/practice.\n\nResults A total of 32 studies comprising 3,256 participants fulfilled the eligibility criteria. The most frequently employed learning approach in eligible studies was training workshops (n=13), followed by experiential learning (n=4). Half of the studies included knowledge as an outcome (n=16) and 10 studies each included a measure of confidence and changes in behaviour/practice. Randomized controlled trials (RCTs) (n=7), showed no improvement in any measure of knowledge, confidence, or behaviour. Two RCTs reported beneficial effects of experiential learning on confidence and perceived behavioural control. In non-randomised studies, training workshops and didactic input with and without simulated e-learning led to statistical improvements in knowledge, confidence, perceived competence, and attitudes.\n\nDiscussion Most of the eligible studies lacked an adequate sample size, and, in many cases, there was a high loss to follow up which represents a threat to the internal validity of the studies. We found that a blended approach to teaching and learning supported with experiential or simulated experiences to improve the knowledge, perceived competence, and confidence to prescribe PA.", "keywords": [ "healthcare professionals", "education", "learning and teaching approaches" ], "content": "Introduction\n\nPhysical inactivity is a risk factor for the development of non-communicable diseases (NCDs),1 and is the fourth leading cause of premature mortality (7.2% of all early deaths)2 on a global scale.3 Furthermore, physical inactivity is responsible for 15.74 million disability-adjusted life years (DALYs) globally, which constitutes a significant burden on national health care systems.4 Summing across five major NCDs (heart disease, stroke type 2 diabetes, and breast and colon cancer), the estimated the global health-care costs of physical inactivity was $53.8 billion in 2013.5 In the United Kingdom (UK), physical inactivity is associated with one in six deaths, and is estimated to cost the UK £7.4 billion annually.6 On the other hand, regular physical activity (PA) can both help prevent and treat symptoms of several NCDs, such as heart disease, stroke, diabetes, and breast and colon cancers, and improve mental health.7 Despite the widely reported benefits of PA, only 66% of men and 58% of women meet the current PA recommendations.8 According to the World Health Organization (WHO), those who are physically inactive have a 20% to 30% increased risk of all-cause mortality in comparison with those who participate in at least 30 minutes per day of moderate intensity PA.9\n\nTo meet the WHO target for a 15% relative reduction in the global prevalence of physical inactivity in adults and in adolescents by 2030, there is a call to strengthen current workforce capabilities regarding promoting and prescribing PA. With a global shift in preventative medicine, it is increasingly important to ensure that the requisite knowledge, skills, and attitudes are embedded within healthcare curriculum. For instance, there is a reported lack of PA promotion in medical schools,10 with one study reporting that only 56% of medical schools in the UK teach the Chief Medical Officer’s guidance for PA to future doctors.11 This may also be the case for other healthcare professionals (HCPs).\n\nIndeed, there is currently, no standardised approach to deliver PA promotion in the training of HCPs. Lectures on PA promotion along with independent learning activities and the use of self-directed educational tools may be effective in improving the exercise prescription skills of undergraduate medical students.8 Previous research has also suggested that PA counselling skills could be improved by curricular features, such as personal PA behaviour, a strong conceptual base, practice experience, and integration of PA training into existing curriculum.12 Studies on the key determinants of the effectiveness and long-term sustainability of PA interventions from the perspective of HCPs are required and highlights the need for a systematic assessment and synthesis of current research on this topic. Such a review can help identify gaps in the literature and give direction for future research.\n\nConsidering these objectives and the need to explicitly appraise and synthesize current evidence on the key determinants of effective PA promotion, a systematic review was deemed the most suitable approach for reviewing the literature. Therefore, the aim of the current systematic review is to investigate PA teaching and learning approaches in HCPs education and the impact it can have on their knowledge, confidence, and behaviour with regards to PA interventions in their practice. The systematic review was designed to take a whole educational system approach, including the upstream integration in undergraduate education as well as the downstream capability development with qualified healthcare practitioners.\n\n\nMethods\n\nWe conducted a unregistered systematic review in line with the Centre for Reviews and Dissemination recommendations for undertaking systematic reviews13 and the Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) statement.14 Inclusion criteria were determined utilising the PICOS (Population, Interventions, Comparison, Outcomes, Study design) format (Table 1).\n\n\n\n• Any intervention that incorporates PA education into existing/new curricula in HCPs education,\n\n• Any educational mode of delivery (e.g., online, taught, group or individual),\n\n• Interventions published in English,\n\n• Undergraduate, postgraduate, and continuous professional development.\n\n\n\n• Curriculum change: any new additions would be reflected in the new curriculum of HCPs\n\n• Knowledge\n\n• Perceptions\n\n• Confidence (ability of prescribing PA)\n\nThe systematic review was limited to the publications written in the English language. We excluded studies based solely on PA interventions without an educational component. Interventions that combined PA with other health behaviours (e.g., healthy eating) were also excluded if outcomes were not available for PA knowledge, behaviour, and confidence.\n\nPICOS inclusion informed the selected search terms. Searches were performed by a specialist librarian of the following databases: Cochrane Central Register of Controlled Trials (Issue 9 of 12, September 2020), CINAHL (1982-present), Embase (1974-2020), ERIC (1966-2020), Medline (1946-2020) and SPORTDiscus. Examples of search terms (abstract, keyword’s, MeSH term, subject heading, title) were ‘students’, ‘education’, ‘curriculum’, ‘exercise’, ‘physical activity’, ‘professional’, ‘medical’ ‘nursing’ or ‘allied health’, ‘lifestyle’, ‘systematic review’ and ‘randomised controlled trial’. Reference lists of included articles returned from the database search were scanned for relevant publications. No time limit was specified, original search was completed in 2020 and an updated search was conducted in Oct 2022. The search algorithm can be found in Appendix 1.54\n\nAll records generated by the searches were imported onto Rayyan15 and duplicate records were removed. Two reviewers (RP and IML) independently screened the titles and abstracts from the literature search according to the eligibility criteria (Table 1). Full texts of articles which were consistent with study eligibility, were obtained and assessed independently by three reviewers (RP, IML and SB). Full-text articles that met the eligibility criteria were included in the review. Disagreement on selection of articles was solved by discussion until consensus was reached, another author (GM) was available to arbitrate if needed. Reasons for exclusion of non-eligibility studies were recorded, see Appendix 2.54\n\nAfter full-text screening, RP and SB extracted data using the 2016 Guideline for Reporting Evidence-based practice Educational interventions and Teaching (GREET).16 The GREET checklist includes items recommended for reporting educational interventions for facilitating foundation knowledge and skills in evidence-based practice. Specifically, questions are asked to address the why, what, who, how, where and the how well of the educational intervention. For each eligible study, information on the characteristics of studies, study population, PA educational intervention and outcomes were extracted. Characteristics of studies included study design, country of origin and year of publication. Characteristics of study population included sample size, pre-registration/post-registration, and professional background. Characteristics of PA intervention included content, mode of delivery and duration. Data was also extracted on outcomes assessed, statistical analysis and effect of intervention on outcomes. The data extracted from the eligible studies are in line with the PRISMA guidelines, summarised in the characteristics of eligible studies Table 2.\n\n\n\nA. 3-h Nutrition and PA for childhood overweight in-person training (n=16)\n\nB. Nutrition and PA for childhood overweight web-based training over a 3-week period (n=17)\n\n\n\nA. In-person, 1-d, 7-h seminar (n=49)\n\nB. Web-based delivery, 7-h over a 4-week period (n=43)\n\n\n\n- 1-h knowledge test.\n\n\n\n- Self-reported change in practice survey\n\n\n\n- 15-item behaviour checklist during an observed structured clinical examination (OSCE)\n\n- 16-item questionnaire self-reported perceived skill for each of the 5A items\n\n\n\nA. Students were assigned by facilitators to either face-to-face or virtual attendance (n=27)\n\nB. Students had the option to attend, either face to face or virtually (n=31).\n\n\n\n- Survey of clinical confidence\n\n\n\n- Summative, observed structured clinical examination using a standardised patient\n\n\n\n- Adapted TPB questionnaire\n\nThe purpose of the risk of bias assessment was to assess the methodological quality of the eligible studies and to determine the extent to which they have addressed the possibility of bias in its design, conduct and analysis. Two authors (SB and RP) independently assessed risk of bias using Joanna Briggs Institute critical appraisal tools.17 Any disagreements were resolved through discussion, with a third reviewer (IML) acting as an arbitrator when necessary.\n\nMeta-analysis was not possible due to the variation in quantitative study designs and the widely varying methods of measurement and analysis employed by the analytical studies, and/or insufficient data reported. Consequently, a narrative synthesis was undertaken because it can be used in systematic reviews focusing on a range of questions, not only those relating to the effectiveness of a particular intervention.18 To assess the overall effectiveness of the reviewed educational interventions, we first evaluated each study’s design and then we assessed the strength of evidence of measured outcomes: knowledge, perceptions, confidence, attitudes, beliefs, and changes in behaviour/practice (where available).\n\n\nResults\n\nA PRISMA checklist is provided in an online depository.54\n\nIn total 1,542 articles were identified and screened. Following title and abstract screening, 1,411 articles were excluded. After full-text screening of 57 articles, 25 studies were included in the systematic review. An updated search was undertaken in Oct 2022, a total of 863 articles were retrieved across various databases; 67 duplicates were removed, 796 were abstract screened, 743 were excluded which left 53 articles for full-text screening. Of the 53, seven additional articles were eligible for inclusion. Therefore, the total eligible number of studies was 32. The screening process and reasons for exclusion of full text articles are shown in Figure 1 using the PRISMA 2020 flow diagram for new systematic reviews. Reference to excluded studies and reasons can be found in Appendix 2.\n\nThe characteristics of the included studies are reported in Table 2. The eligible studies included the following populations: medical students (n=12), medical doctors (n=8), pharmacy students (n=2), physiotherapy students (n=1), physician assistant students (n=1), nursing students (n=1), nurses (n=1), and a mixed cohort (n=6). The sample size by profession included, medical students (n=1801), medical doctors (n=452), pharmacy students (n=160), physiotherapy students (n=32), PA students (n=40), nursing students (n=50), nurses (n=117), and mixed cohorts (n=717).\n\nOf the included studies, 11 were held in the United States of America (USA), six in Australia four in the UK and Canada, two in Ireland and one study in each of the following countries: Brazil, Mexico, Israel, India and Spain. All studies were published in a range of academic journals between 1999-2022. Seven of the studies had a randomised controlled trial (RCT) design, eight were non-randomised controlled trials, and 17 were single group pre-post-test designs. All trials included a single publication except for Jadczak et al. (2018)19 which included two publications. Total size of sample was 3,256 participants, pre- and post-registration learners accounted for 2370 and 844, respectively.\n\nDuration of the PA education interventions varied and ranged from a two-hour lecture to a 16-hour intervention over an eight-month period. Overview of commonly used learning pedagogical approaches are presented in Table 3.\n\n\n\n• Case studies\n\n• Pre-reading material\n\n• Lecture-based teaching\n\n\n\n• Theory and practical content\n\n• Interactive teaching\n\n\n\n• Interactive quizzes\n\n• Web-based discussions\n\n• Asynchronous self- learning module\n\n• Web course\n\n\n\n• Simulated patients\n\n• Lab based simulation\n\n• Web patient encounter\n\n• Lifestyle assessment write up\n\n\n\n• Theory and practical content\n\n• Pedometer use\n\n\n\n• Clinical practice\n\n• Pedometer use\n\n• Physical activity engagement\n\n\n\n• E-learning (asynchronous)\n\n• In-person activities\n\n\n\n• Flexible implementation of resources\n\nWhere a control group existed, no intervention, traditional intervention (i.e. delivery of existing curriculum), or usual practice were the most common types. In most cases they were from the same population as the study sample except for Kotecki and Calyton (2003),20 who compared pharmacy students with practising pharmacists.\n\nThe eligible studies used a variety of outcome measures. The most reported educational outcomes were knowledge (n=16), perceptions (n=3), confidence (n=10), attitudes (n=3), beliefs (n=1), and changes in behaviour/practice (n=10). Most of the outcome measures were self-developed, some were based on theoretical models such as Theory of Planned behaviour, and the only validated measure used was Kirkpatrick’s model of training evaluation. Two of the studies used structured clinical examination using a standardised patient to assess changes in practice.21,22\n\nReporting of the studies was generally good with all studies clearly stating their research aims and appropriately describing methodology. Recruitment and data collection were described by all studies, convenience sampling was the most used sampling technique, and 11 studies adequately described loss to follow up.\n\nNone of the studies described a relationship between the participants and the researchers, making it impossible to establish what relationship, if any, existed. Eight of the studies lacked detail on who delivered the educational intervention making it difficult to establish if there may be a risk of bias introduced through professional association. Most of the outcome measures were self-developed and therefore, a key limitation of the studies, appropriate statistical tests were applied for all the studies.\n\nFor most of the eligible studies, PA specific content was adequately described, and frequency and duration of sessions were often well described, what was less clear was the scheduling of sessions and time in between them.\n\nFor the seven eligible RCTs, only two23,24 reported “true randomization”, while only one23 reported “concealment” of the allocation to groups. Two RCTs21,25 reported no “similarity of treatment groups at baseline”, while all RCTs reported: a) blinding of participants to the treatment assignment, b) blinding of those delivering the treatment assignment, and c) blinding of outcomes assessors to the treatment assignment. Also, all RCTs reported that treatment groups treated identically other than the intervention of interest and that participants analysed in the groups to which they were randomized. Finally, three RCTs23,26,27 reported complete follow-up or adequately described the differences between groups adequately, while the latter information was missing from the remaining four RCTs. The outcomes of the risk of bias assessment of the eligible RCTs can be found in Table 4, while a summary of them can be found in Figure 2.\n\nN: No; Y: Yes.\n\nOnly two22,28 out of the 25 eligible quasi-experimental and single-arm design studies did not report the “cause” and the “effect” of interest in their research question. Six studies reported similar participant characteristics in comparison groups,29–34 one study28 reported differences in participants across groups, and in three studies22,35,36 this information was unclear. In the remaining 15 single group studies this risk of bias component was not applicable.\n\nSix studies22,29,32,34–36 reported that apart from the allocated intervention all participants received similar treatment, one study28 reported differences in received, in two studies30,31 this information was unclear, while in the remaining 16 this risk of bias component was not applicable.\n\nAlso, there was a control group in nine20,28–31,33–36 out of the 25 studies, while all studies reported multiple measurements of outcome (pre-post). In follow up completeness and adequately description component, nine studies20,22,29–32,34,37,38 reported yes, in one study28 this information was unclear, while the remaining 10 studies reported no. Regarding the component of outcomes of participants to be included in same way, in two studies31,35 this information was unclear, nine studies20,22,28–30,32–34,36 reported yes, while in the remaining 14 studies this risk of bias component was not applicable. In the outcomes measurements reliability component, two studies39,40 reported no, in seven studies20,22,28–31,35 this information was unclear, while the remaining 16 studies reported yes. Finally, all studies reported appropriate statistical analysis. The outcomes of the risk of bias assessment of the e eligible quasi-experimental and single arm design can be found in Table 5, while a summary of them can be found in Figure 3.\n\nN: No; Y: Yes; N/A: Not applicable.\n\nDidactic input\n\nOf the three studies21,35,41 which reported a solely didactic approach to education delivery, two35,41 reported statistical improvements in confidence and knowledge in students’ ability to assess and counsel about PA as well as students’ beliefs regarding the importance of PA in managing disease. Maloney et al 2011,21 was the only RCT and reported no statistical difference in the knowledge and change in practice between the intervention and the control group.\n\nTraining workshops\n\nInteractive training workshops were the most common method of educational delivery. Of the 13 eligible studies, four (of which one was a RCT and two were non-randomised control trials) did not reach statistically significant findings in relation to knowledge, behaviour, and perceptions. The remainder were single group pre-post-test design and statistical improvements in confidence, attitudes, beliefs, knowledge, and behaviour were observed.\n\nSelf-directed e-learning\n\nSelf -directed on-line learning was exclusively used in three of the studies, all of which were single group pre-post-test design.8,38,40 Raj, Khan and Nair (2020) study40 did not reach statistical significance in knowledge scores, Pugh et al (2020) did achieve statistical improvements in relation to students’ knowledge and confidence and Webb et al.38 revealed a statistical increase in the frequency of discussion on PA.\n\nDidactic with Simulation-based learning\n\nDidactic with simulation-based learning was used in three of the studies, of which two20,30 were non-randomised control trials and the remaining study42 was a single group pre-post-test design. Of the three studies, Jadczak, Tam and Visvanathan (2018)30 reported a statistical improvement in perceived competence, Kotecki and Clayton (2003)20 reported statistical improvements in confidence and Bass iii et al (2004)42 noted a statistical improvement in knowledge and self-efficacy for exercise prescription.\n\nDidactic with experiential learning\n\nExperiential learning for Hasson et al (2018)39 was in the form of pedometer use and whilst the intervention did not impact knowledge amongst public health nurses it did result in statistically significant positive changes in attitudes and behaviours when compared to baseline data.\n\nExperiential learning\n\nOf the four studies that included interventions comprising experiential learning, three were RCTs (Cooke; Marques-Sule; Shields 2010), and one was a single group pre-post-test design (Jadczak et al., 2017). Marques-Sule and colleagues (2022) found a statistical within-group improvement in Physiotherapists PA knowledge in the intervention group but no change in the control group, while Cooke et al. (2015) found improvements in UK medical students perceived behavioural control in both intervention and control groups. Another RCT found that contact with adolescents with Down syndrome during a physiotherapy clinical placement statistically improved students’ attitudes towards exercise for people with Down syndrome.27 In a single-group study, Jadczak, and colleagues (2017) observed that an intervention consisting of medical student-led interviews of older people participating in a community-based exercise class led to statistical improvements in students perceived competence in counselling older people about exercise.\n\nFlipped classroom\n\nOf the three eligible studies that used a flipped classroom approach, only Ockene et al (2021)26 was a RCT, Pasarica and Kay (2020)22 was a non-randomised control trial and Mattison and Nemec (2014)43 was a single group pre-post-test design. In relation to perceived skill, Ockene et al.’s study revealed no statistical difference between the intervention and control group. Pasarica and Kay (2020) revealed no statistical difference in perceived confidence and Mattison and Nemec (2014) noted a statistically significant improvement in knowledge following the intervention.\n\nOther\n\nFreene et al. (2022) found that the use of PA champions to encourage access to a PA resource across 13 health disciplines in one Australian university, resulted in no statistical changes in PA promotion preparedness, PA knowledge, or the amount of PA content delivered, despite a statistical increase in the use of teaching resources.\n\n\nDiscussion\n\nThis systematic review explored and synthesised physical activity teaching and learning approaches in HCPs education and the impact it can have on HCPs knowledge, confidence, and behaviour relating to PA counselling in their practice. This review has highlighted that no single educational approach used in isolation has been shown to provide effective and enduring changes among healthcare professionals. However, consistent positive outcomes were reported for education which is delivered in an interactive format (i.e., training workshops) using a mixed approach to delivery (e.g., classroom-based with simulation-based learning). These findings corroborate with the conclusions of other studies.12,44 For example, Netherway, Smith, and Monforte44 indicated that employing blended learning approaches was welcomed by medical students, indicated that employing blended learning approaches was welcomed by medical students, including peer mentoring activities. This was further reiterated by Dacey et al.12 who concluded that positive outcomes were associated with programs that provide both didactic approaches and counselling practice experience.\n\nPrevious research45 has suggested that conceptual frameworks that illuminate the complexity of behaviour change could increase the likelihood of improving PA counselling skills. Within the current review, theoretical frameworks used included Stages of Change behavioural model,29 Theory of Planned Behaviour,33 and Social Cognitive Theory.26 In some studies behaviour change was included within the content but there was insufficient detail on underpinning theoretical frameworks. Ten studies included theoretical concepts based in behavioural science, concepts such as PA counselling, motivational interviewing, adherence21,29,31,42,46 and the 5 ‘As’ (Ask, Advise, Assess, Assist, and Arrange)33,41 were commonly used. 15 of the studies included sufficient description of the educational content and eight of the studies detailed the pedagogical approach that would allow for replication.\n\nHealthcare programmes should implement current educational theory/principles in order to maximise the development of professional expertise.47 A limited number of studies (n=8) provided an underpinning educational theory for the teaching and learning strategy that was employed. Experiential learning featured in six20,23,26,42,48 of the studies, and this took the form of an educational intervention (seminar or lectures) followed by use of a pedometer to review step count data23 or a simulated patient experiences in physical activity counselling. Kotecki and Clayton20 and Bass iii et al.42 both used simulated standardised patient opportunities (2 hours and 15 minutes respectively). Similarly, Marques-Sule et al.48 implemented a service-learning programme for physiotherapy students with real patients (4h) with heart transplantation and acute coronary syndrome. Greater consideration needs to be given to evidence based pedagogical approaches that support learners to achieve a deeper level of learning.\n\nSimulated and peer evaluation have both been reported as positive learning experiences for physiotherapy students.49 Seven of the studies provided enhanced learning opportunities via experiential modes of learning. In Shields et al. study50 physiotherapy students completed a 10 week twice weekly progressive resistance training programme with an adolescent living with Down’s Syndrome. Participants in Cooke et al.23 and Pasarica and Kay22 studies used a pedometer and participants were required to set step count goals. Jadczak, Tam and Visvanathan30 followed a 1.5-hour PA module with a 30-minute counselling session with an older adult. Similarly, Keyes and Gardner37 and Kotecki and Clayton20 also provided a simulated 1:1 mock patient consultation. These additional learning opportunities provide students with opportunities to safely apply their learning within a simulated environment. The potential benefit from using these learning approaches is that self-reflection and feedback can be used to improve performance and better prepare the learner for practice.\n\nThere is a call for embedding sports and exercise medicine into the medical curriculum.51 In 11 of the 32 studies, PA education was taught alongside other lifestyle interventions mainly nutrition25,35,42,52 or in combination with multiple lifestyle factors such as smoking, alcohol, and stress management.23,37 Whereas 21 studies were exclusively related to PA educational interventions within specific modules. PA and behaviour change span patient pathways and clinical specialities, and therefore there is a call for PA to be integrated or spiralled throughout the curriculum.\n\nAlthough various e-learning approaches were used in the appraised studies, such as online self-learning modules, interactive exercises, and web-based discussion forums, they could have been developed further to include virtual consultations. The interventions that did compare in-person versus web-based approaches produced similar outcomes, suggesting that from a time and cost efficiency perspective, e-learning approaches may form e a growing evidence base.\n\nInstructors involved in the delivery of the educational interventions included research study teams, strength and conditioning specialist, medical doctors, academics, pharmacist, exercise physiologists and nurses, calling for a multi-disciplinary team approach to teaching and learning.\n\nThe current systematic review sheds light on the teaching and learning approaches used in delivering PA education for health care professionals. Whilst this review has captured teaching and learning approaches for pre- and post-registration provision across all health care professions, this review does have several limitations. First, this review built exclusively on published studies, whereas unpublished studies, grey literature and non-peer-reviewed literature were excluded. Although including unpublished, grey, and non-peer-reviewed literature has potential benefits in terms of comprehensiveness, it can introduce greater bias in the results of the systematic review. Unpublished studies are usually of lower methodological quality than published studies. The educational intervention studies within this review generally have design limitations which limit the ability to support replication and draw any firm conclusions.\n\nGiven the heterogeneity and reliance on self-developed, self-report survey measures, caution must be applied to the validity of the reported outcomes due to the risk of response bias.53 Most of the studies lacked an adequate sample size, and, in many cases, there was a high loss to follow up which will result in selection bias representing a threat to the internal validity of the studies. Similar design limitations have been reported elsewhere.12\n\n\nConclusion\n\nTo develop the next generation of health care professionals to deliver effective PA intervention, the literature advocates for a blended approach to teaching and learning supported with experiential/simulated experiences. Although the available evidence had limitations, there was some evidence to support simulation-based learning as it encourages learners to participate in real world problem solving while reflecting on their learning experiences. Interventions that combined theoretical concepts with practical application in an active learning environment also tended to result in more favourable outcomes.\n\nRecommendations based on this review include the development of blended learning approaches that integrate the cognitive and behavioural domains of clinical competence. Where experiential learning does exist, to apply it through the framework of simulation-based learning pedagogy to support consolidation and transferability of learning. There was a paucity of evidence from RCTs to support each learning approaches, but for some of the approaches there was no available RCTs (e.g., self-directed e-learning and didactic with simulation-based or experiential learning). Development of a validated outcome measures would considerably enhance the methodological validity and credibility of research findings. Finally, there is a need for longitudinal studies in this area that would better represent the longer-term impact of PA education intervention. This review highlights the need for more robust research in this area to fully realise the impact that PA education intervention for HCPs can have on the health and quality of life of the populations they serve.", "appendix": "Data availability\n\nNo data are associated with this article.\n\nFigshare: PRISMA checklist and flow chart for Physical activity implementation in the curricula of healthcare professions. A systematic review, https://doi:10.6084/m9.figshare.25816216. 54\n\nThis project contains:\n\n• Figure 1.tiff\n\n• Appendices.docx\n\n• PRISMA checklist.docx\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\n\nReferences\n\nBull FC, Bauman AE: Physical inactivity: the “Cinderella” risk factor for noncommunicable disease prevention. J. Health Commun. 2011; 16 Suppl 2: 13–26. 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Publisher Full Text" }	[ { "id": "302072", "date": "07 Aug 2024", "name": "Andrew Kweku Conduah", "expertise": [ "Reviewer Expertise § Population Estimates and Projections.§ Population Health and Mortality- Health Emergencies & Preparedness", "Ageing & Intergeneration Relations", "and Non-Communicable Disease & Health Projection (Physical Activity", "Obesity", "Tobacco Control", "etc.)§ Business Demography§ Business Policy and Strategy§ Business Management§ Public Administration§ Entrepreneurial 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 systematic review investigates the integration of physical activity (PA) into the curricula of healthcare professions. It highlights the significance of PA in preventing and managing non-communicable diseases (NCDs) and improving mental health. The review examines current PA teaching and learning approaches in healthcare education, assessing their impact on healthcare professionals' knowledge, confidence, and behaviour regarding PA interventions. It identifies effective strategies, gaps, and global variations in PA curriculum implementation, emphasising the need for standardized training approaches. The review also evaluates both undergraduate and ongoing training programs, offering recommendations for enhancing PA education in healthcare settings.\nIntroduction The introduction establishes physical inactivity as a significant risk factor for non-communicable diseases (NCDs) and premature mortality. It highlights the global and national burden of physical inactivity, including economic costs and health impacts. The evidence presented underscores the importance of physical activity (PA) in preventing and managing NCDs and improving mental health. However, the introduction could benefit from additional context on global variations in PA promotion within healthcare curricula. Including data on PA curriculum integration from various countries would strengthen the argument for the review's relevance.\nProblem Statement The problem statement is well-articulated, capturing the need for integrating PA into healthcare curricula. It effectively identifies the gap in current PA promotion practices among healthcare professionals (HCPs) and highlights the lack of standardised approaches in HCP training. Enhancing the statement with specific examples of how current PA promotion efforts fall short in different regions and healthcare professions would add depth.\nObjectives of the Review The review's objectives are to investigate PA teaching and learning approaches in HCP education and their impact on knowledge, confidence, and behaviour regarding PA interventions. The aim to evaluate both undergraduate and ongoing training in HCPs is well-founded, addressing a critical gap in the literature.\nRationale for the Paper The rationale for the systematic review is vital. It highlights the need to comprehensively evaluate current PA curricula and teaching methods in HCP education to identify effective strategies and gaps. Examining upstream (undergraduate) and downstream (qualified practitioners) aspects aligns well with the global call for improved PA promotion.\nGlobal Context Incorporating examples and data from various countries would offer a more comprehensive view of the global landscape of PA implementation in healthcare curricula. This would strengthen the case for the review by demonstrating the widespread relevance of the issue and highlighting variations in PA promotion practices across different healthcare systems.\nStrengths of the Approach The systematic review exhibits several notable strengths. Firstly, the systematic screening and removal of duplicates, along with independent screening by multiple reviewers, enhances the reliability of the inclusion process. This rigorous methodology ensures that each record is considered only once and that multiple perspectives are included in the screening process.\nSecondly, the review employs clear criteria and guidelines for study inclusion, which are well-defined and cover populations, interventions, comparisons, outcomes, and study designs. Standardised data extraction tools, such as the GREET checklist and alignment with PRISMA guidelines, ensure comprehensive and consistent data extraction.\nThirdly, the bias assessment is conducted using Joanna Briggs Institute critical appraisal tools, which adds rigour to the methodological quality assessment of the studies. This systematic approach helps to identify and mitigate potential biases in the included studies.\nLastly, the narrative synthesis approach is appropriate given the variability in study designs and outcome measurements. This qualitative assessment allows for a comprehensive data evaluation when a meta-analysis is not feasible.\nAreas for Improvement The review methodology could be improved by summarising the findings from the narrative synthesis and discussing how the results align or diverge across studies, which would enhance the synthesis's rigour.\nAnalysis The review's comprehensive analysis reflects variability in intervention effectiveness and methodological rigour. The process of selecting studies is clearly outlined, and the characteristics of eligible studies are thoroughly described, aiding in understanding the generalisability and context of the findings. The risk of bias assessment identifies areas of concern such as randomisation, blinding, and follow-up completeness. However, the lack of blinding and incomplete follow-up descriptions in some studies raise potential concerns about the validity of the results. The synthesis of results across different learning approaches is well-organised but shows mixed results regarding statistical significance. The analysis identifies strengths in educational interventions like training workshops and experiential learning while highlighting inconsistencies and limitations in other approaches.\nDiscussion Section The discussion section effectively summarises the review's findings, emphasising the effectiveness of interactive and blended learning approaches for PA education. However, it could benefit from more specific studies that demonstrated these positive outcomes to illustrate the findings better. The mention of theoretical frameworks is appropriate, but the discussion lacks depth in explaining their application and specific impact on learning outcomes. More detailed examples of influential educational theories used in the reviewed studies would strengthen the discussion.\nThe limitation section appropriately identifies the exclusion of unpublished, grey, and non-peer-reviewed literature as a potential bias. More detail on how this might have affected the review's conclusions would be beneficial. A more critical analysis of how design limitations such as small sample sizes and high dropout rates specifically impact the validity and reliability of the findings would enhance the discussion. Further elaboration on how reliance on self-report measures impacts the validity of the outcomes and suggestions to mitigate this issue in future research would be valuable.\nRecommendations The recommendations provided are sound but could be more detailed. The call for blended learning approaches is well-founded. Still, more explicit guidance on integrating cognitive and behavioural domains in practical terms and specific strategies or frameworks for implementation would be helpful. The support for simulation-based learning is well-argued, but elaborating on how this approach can be effectively implemented in various educational settings, including potential challenges and solutions, would strengthen the recommendations.\nThe call for more randomised controlled trials (RCTs) and validated outcome measures is appropriate. Still, it lacks specific recommendations on what future studies should focus on and how they should be designed to address current gaps. Detailed suggestions on structuring longitudinal studies and particular aspects of PA education to be investigated over the long term would enhance the recommendations.\nConclusion The review report effectively highlights the importance of integrating physical activity into healthcare curricula and comprehensively evaluates current PA teaching and learning approaches. While the methodology and analysis are rigorous, there are areas for improvement regarding transparency, detailed findings, and practical recommendations. The review can provide a stronger foundation for future research and practical implementation in healthcare education by addressing these aspects.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Partly\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Partly\n\nIs the statistical analysis and its interpretation appropriate? Not applicable\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes\n\nIf this is a Living Systematic Review, is the ‘living’ method appropriate and is the search schedule clearly defined and justified? (‘Living Systematic Review’ or a variation of this term should be included in the title.) Not applicable", "responses": [] } ]	1	https://f1000research.com/articles/13-742
https://f1000research.com/articles/13-740/v1	04 Jul 24	{ "type": "Study Protocol", "title": "Protocol for scoping review: Instruments for assessing vision-specific health-related quality of life in children and adolescents with visual impairment.", "authors": [ "Tshubelela Sello Simon Magakwe", "Rekha Hansraj", "Sphamandla Josias Nkambule", "Zamadonda Nokuthula Queen Xulu-Kasaba", "Rekha Hansraj", "Sphamandla Josias Nkambule", "Zamadonda Nokuthula Queen Xulu-Kasaba" ], "abstract": "Childhood visual impairment (VI) is less common than in adults, but research has demonstrated that it can have significant long-term negative impacts on the health-related quality of life (HR-QoL) of children and adolescents. Unfortunately, there is currently a lack of vision-specific instruments available for accurately assessing HR-QoL in children and adolescents with VI, particularly in resource-limited settings. The objective of this scoping review is to methodically evaluate the evidence pertaining to (1) the accessibility and usage of instruments specifically designed to assess HR-QoL in children and adolescents who have VI, (2) summarise studies on HR-QoL in children and adolescent with VI, and (3) describe the psychometric properties of vision-specific instruments used for assessing HR-QoL in children and adolescents with VI. The review will be conducted in accordance with the Joanna Briggs Institute (JBI) guideline (2020) for scoping reviews, utilizing frameworks by Arksey and O’Malley, and methodological enhancements suggested by Levac (2010). A systematic search will be performed through various databases, including PubMed, Science Direct, Scopus, Web of Science, and EBSCOhost, to identify peer-reviewed articles published in English from inception until 31 December 2023. The EBSCOhost platform will include several databases, such as Academic Search Complete, APA PsycINFO, Health Source-Consumer Edition, Health Source: Nursing/Academic Edition, and Open Dissertations. The extracted data will be analysed narratively using QualCoder 1.9 version, and the study’s findings will be reported in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews (PRISMA-ScR). The researchers anticipate that the literature will assist in exploring and relating various types of HR-QoL tools used globally. This review’s conclusion will help researchers ascertain research gaps in vision-related QoL instruments based on different economies, countries, and environments. This will further aid researchers in planning and developing tools suitable for African contexts and languages.", "keywords": [ "Visual impairment", "vision-related quality of life instruments", "health-related quality of life", "children's eye health", "adolescents" ], "content": "1. Introduction\n\nThe Classification of Diseases, injuries, and Causes of Death, of the World Health Organization (WHO) defines visual impairment (VI) as having a best-corrected visual acuity (VA) that is less than 0.30 LogMAR but better than 1.00 LogMAR.1 It is recommended to include low vision, which is defined as VA worse than 0.50 LogMAR but better than or equal to 1.30 LogMAR, or corresponding visual field loss of 10 degrees in the better eye, with the best correction, as well as blindness, which is defined as the VA of worse than 1.30 LogMAR and/or visual field restrictions where the widest diameter is 20 degrees or less in the better-seeing eye with the best correction, in the definition of VI.2 Moreover, VI can be further categorized as mild, moderate, or severe.3 Visual impairment can significantly impact a child’s performance in school, as 85% of learning depends on vision.4 Children with VI also face limitations in participating in sporting activities that require good vision.5 The negative effects of VI extend beyond academic and athletic performance to the socio-economic security of affected individuals.2,4 Thus, not suprisingly, VI has been shown to impact children’s quality of life (QoL).4\n\nGlobally, there are approximately 19 million children with visual impairments,2 12.8 million of whom suffer from uncorrected refractive error (URE),6 with eight million children classified as blind due to URE.7 It is noteworthy that 90% of these children reside in low to middle-income countries.8,9 The impact of VI is significantly greater when it occurs before or during school-going age, as these children are likely to carry these conditions for a greater number of years.10 It has been reported that visual impairment affects the quality of life (QoL) of the affected individuals.2,4 According to the WHO, QoL can be defined as the state of complete physical, mental, and social well-being, and not merely the absence of disease.11 The WHO group that focuses on the QoL of individuals elaborates further by indicating that QoL is also concerned with the personal perception of an individual’s position in life in the context of the culture and value systems in which they live, and concerning personal goals, expectations, standards, and concerns.12,13 Therefore, the vision-related QoL can be defined in the context of uncorrected refractive error and visual impairment.14\n\nThe assessment of HR-QoL is currently an important expansion that is used to evaluate the impact of any disease or health condition on an individual’s QoL and the effectiveness of treatment on those individuals, moreover, it can also be used to determine the effectiveness of treatment on the affected individuals.15,16 These self-reporting instruments have been accepted as important tools in ophthalmic research too,17 and are considered better than the traditional way of relying on the signs, symptoms, morbidity, and mortality.18 Moreover, studies have shown that children can answer any HR-QoL questionnaire reliably if their reading skills, cognitive capacity, and emotional development were considered during the development of those questionnaires.19,20 Many vision-specific instruments for assessing HR-QoL in adults have been reviewed,21 yet despite the high prevalence of VI due to URE among children in recent years, very few similar instruments for children and adolescents have undergone review.\n\nFurthermore, there is a notable absence of clear understanding regarding the accessibility and implementation of specialized tools designed to evaluate the HR-QoL in visually impaired children and adolescents. These instruments are currently developed using English and utilised by individuals whose first language is not English, and these instruments have been developed amongst individuals primarily in developed countries with varying social, economic, and cultural backgrounds. Therefore, this review will aim to map the availability of the vision-specific HR-QoL instruments that measure the QoL of children and adolescents with visual impairment (VI) taking the aforementioned gaps into account.\n\nWe conducted the preliminary search on three different platforms, namely the Open Science Framework, the Cochrane Database of Systematic Reviews, and JBI Evidence Synthesis. No systematic or scoping reviews related to the topic were found at present.\n\nThis scoping review aims to accomplish three main objectives. Firstly, it will involve a systematic mapping of available evidence on the use and accessibility of vision-specific instruments that assess the Health-Related Quality of Life (HR-QoL) in children and adolescents with VI. Secondly, it will synthesize the findings of studies that focus on HR-QoL in children and adolescents with VI. Lastly, it aims to provide a description of the psychometric properties of the currently available vision-specific instruments that evaluate HR-QoL in children and adolescents with VI.\n\n\n2. Methods\n\nA scoping review study uses systematic methods to examine literature and evidence related to a specific research subject, with the ultimate goal of informing practice in a given field. This particular review is part of a larger study that aims to create a context-specific HR-QoL instrument for children in an African setting, utilizing existing data. Using the scoping review framework guidelines established by Arksey and O’Malley (2005),22 and recommended methodological enhancements by Levac et al. (2010),23 this scoping review will consist of five steps. According to Arksey and O’Malley (2005), conducting a scoping review involves five distinct stages as follows: (1) defining the review question and establishing criteria for selecting studies, (2) searching for studies that address a particular review question, (3) selecting studies that meet specific inclusion criteria for the review, (4) charting data from included studies, and ultimately (5) collating, summarizing, and reporting all findings. Thereafter, review results will be aligned with the PRISMA extension for scoping reviews (PRISMA-ScR) checklist and explanation24 in the final report. This review protocol was registered on the Open Science Framework, reference (9hw8c-v1) and access link https://archive.org/details/osf-registrations-9hw8c-v1 (https://doi.org/10.17605/OSF.IO/9HW8C). This protocol adhered to the PRISMA-ScR checklist.35\n\nWhat is the evidence regarding the availability and usage of vision-specific instruments to assess health-related quality of life in children and adolescents with visual impairment?\n\nSub-questions:\n\n1. What are the findings of studies examining HR-QoL in children and adolescents with visual impairments?\n\n2. What are the psychometric properties of current vision-specific instruments for assessing HR-QoL in children and adolescents with visual impairments?\n\nThe main research question was determined using the PCC nomenclature framework, recommended by the JBI Manual for Evidence Synthesis: 2020 Edition as outlined in Table 1.25\n\nTo ensure a thorough and replicable search for relevant studies, a systematic search will be conducted in reputable bibliographic databases, including PubMed, Science Direct, Scopus, Web of Science, and EBSCOhost. The EBSCOhost platforms will encompass various databases, such as Academic Search Complete, APA PsycInfo, Health Source-Consumer Edition, Health Source: Nursing/Academic Edition, and Open Dissertations. These databases and platforms will be explored to identify peer-reviewed articles published in English from the date of inception up to 31 December 2023, as well as other supplementary information sources like Google Scholar. The primary and supplementary systematic searches will be performed by TSS, the principal investigator, according to a pre-defined search strategy developed in collaboration with two subject librarians from the University of KwaZulu Natal and the University of Free State.\n\nThe comprehensive search strategy was co-developed by the first author and the two subject specialists. The draft was reviewed by all authors to ensure the appropriate use of indexing terminology and Medical Subject Headings (MeSH) descriptors before it was tested on a subset of records from the PubMed database. The search strategy descriptors and truncation details are presented in appendix I and II, and are deposited on Zenodo,36 while Table 2 shows the number of records returned from the consulted PubMed database.\n\nThis scoping review will include all studies conducted worldwide that report on the development of vision-related quality-of-life assessment tools for children and adolescents between 5 and 18 years of age as outlined in Table 3.\n\nTypes of sources\n\nThe scope of this review encompasses a range of study designs, both experimental and epidemiological. This includes randomized controlled trials, non-randomized controlled trials, quasi-experimental studies, before and after studies, prospective and retrospective cohort studies, case-control studies, and analytical cross-sectional studies. To avoid any duplication of data, we will exclude HR-QoL instruments/questionnaires utilized in reviews and conference abstracts. Similarly, we will not be including gray literature in this review, as it is outside the scope of our focus, which is on quantitative questionnaires and instruments that have been psychometrically tested and validated for use on children and adolescents living with VI.\n\nStudy/source of evidence selection\n\nAfter conducting the search, all citations that are identified will be compiled and uploaded into Mendeley version 2.76.0/2023, and any duplicates will be removed. The titles and abstracts of these citations will be independently screened by TSS and HC to determine their relevance to the review’s inclusion criteria. Any sources deemed potentially relevant will be retrieved in full, and their citation details will be imported into the JBI System for the Unified Management, Assessment, and Review of Information (JBI SUMARI) (JBI, Adelaide, Australia).27 The full text of the selected citations will be thoroughly assessed against the inclusion criteria by two or more independent reviewers. Any sources not meeting the inclusion criteria will be excluded, with reasons for their exclusion, and will be recorded in this scoping review. In the event of any disagreements between the reviewers during any stage of the selection process, they will be resolved through discussion or with the help of an additional reviewer/s.\n\nTwo independent reviewers will utilize a data extraction tool, which was created via google form, and includes authors and year of study, title, country, ages of the participants, ethnicity, sample sizes, concept measured, domains, rating scales, list of items, outcome measurers, conclusion, and recommendations. This tool has been developed by the PI and pretested for compatibility to extract data from the papers included in the scoping review. A draft extraction form is provided represented in Appendix III, which can be found in Zenodo.36 Zenodo The data extraction tool will be modified as needed for each source. Any changes or alterations made during the scoping review process will be clearly outlined. Any discrepancies or conflicts that arise between the reviewers will be resolved through open discussion and, if needed, with the assistance of an additional reviewer. If any information is missing or incomplete in a paper, the authors will be contacted to provide any necessary data.\n\nThe complete findings of the literature search and study selection process will be fully disclosed in the final scoping review, accompanied by a PRISMA-ScR flow diagram as depicted in Figure 1.24 The extracted data will be analysed using Qualcoder 1.9 computer software in a narrative format. A comprehensive table will be presented, detailing the frequency of usage and components assessed for each narrative account of the existing literature. Furthermore, each questionnaire will be summarized narratively to provide additional context.\n\nQuality assessment\n\nWe will evaluate the quality of the included studies to ensure that the study design aligns with our research objectives and that studies are accurately reported to minimize bias, we will use the Mixed Methods Appraisal Tool (MMAT) version 201828 to assess the appropriateness of the aim, methodological and study design accuracy, recruitment strategies, data collection, data analysis, findings, discussions, and conclusions of the authors. Additionally, we will use the Grading of Recommendations, Assessment, Development and Evaluation (GRADE) tool29 to assess the confidence in each finding of the study.\n\n\n3. Discussion\n\nIncreasingly, health services are focusing on capturing patient perceptions of their vision status.30 Even in ophthalmic research, quality of life measurement is being recognized as a key supplemental indicator.17 Traditionally, eye care professionals have relied on the results of clinical examinations to determine the impact of vision problems on children, or sometimes from the observations of parents (proxies) or teachers.31 This has been an important method to rely on since it has always been difficult for the child to express their vision problems.32 However, it is questionable whether measurements like visual acuity, contrast sensitivity, visual field, etc. can accurately represent the child’s perspective.29 Quality-of-life tools have been reported to serve as reliable, relevant, and cost-effective methods to assess, to an extent, the impact of vision problems on children.33 It is self-reported, and it is better than the proxy. Moreover, studies have shown that children can answer any HR-QoL questionnaire reliably if their reading skills, cognitive capacity, and emotional development were considered during the development of those questionnaires.19,33\n\nSeveral instruments to measure the quality of life (QoL) in adults have been developed and validated elsewhere and found to exhibit good reliability. However, not enough has been done to develop these instruments for school-aged children.30 In most cases, these tools designed for adults need to be modified first before being used in children, and the process of modifications may compromise the already established reliability and validity. The WHO QoL group recommended that ideally, each country should develop its own instrument to measure the impact on any disease and treatment, which is culture-sensitive and age-appropriate.13 This will help the learner to honestly evaluate himself, rather than be evaluated by the test results from the eye care practitioner. The QoL instrument can also be used in assessing the effectiveness of management strategies or even disease progression. Therefore, this review aims to map all available vision-specific HR-QoL instruments used for children.\n\n\n4. Conclusion\n\nThe literature analysed in this study will assist in developing quality-of-life tools tailored to specific contexts, including Africa. Furthermore, the results of this study will be critical to guiding practice, informing social security policies, and guiding practices related to children.\n\n\nAuthor contributions\n\nTSS, RH, and ZXK conceptualized the project, TSS and SJN developed the methodology, ZXK administered the project, and TSS and SJN drafted and edited the manuscript. All authors have reviewed and approved the final manuscript.\n\n\nEthics and consent\n\nWhile ethical clearance is not mandatory for this study, we have obtained it from the Biomedical Research Ethics Committee of the University of KwaZulu Natal under the reference BREC/00003939/2022, which covers the larger study of which this review is a part. The findings of this scoping review and meta-analysis will be shared through various channels, including electronic and print media, conference presentations, and key stakeholder meetings.", "appendix": "Data availability\n\nNo data are associated with this article.\n\nOSF: Vision-specific instruments for the assessment of Health-Related Quality Of Life (HR-QOL) for children and adolescents with visual impairment: A Scoping Review. https://doi.org/10.17605/OSF.IO/9HW8C. 34\n\nZenodo: PRISMA-ScR checklist for ‘Protocol for scoping review: instruments for assessing vision-specific health-related quality of life in children and adolescents with visual impairment’. https://zenodo.org/doi/10.5281/zenodo.11485472. 35\n\nZenodo: Supplementary Documents instruments for assessing vision-specific health-related quality of life in children and adolescents with visual impairment. Scoping review protocol. https://zenodo.org/doi/10.5281/zenodo.11642275. 36\n\nThis project contains the following extended data:\n\n- MeSH terms\n\n- Search strategies with MeSH descriptors and truncation\n\n- Data extraction instrument\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\n\nAcknowledgments\n\nThis study would like to express its gratitude to two librarians, namely Elma Van Der Merwe, Chief Officer of Library & Information Services at the University of Free State, and Pravina Laljeeth, Information Specialist & Senior Research librarian at the University of KwaZulu Natal. They provided invaluable assistance with the search strategies used in this study.\n\n\nReferences\n\nWHO: International statistical classification of diseases and related health problems - 10th revision.2011. (accessed 25 May 2022). Reference Source\n\nResnikoff S, Pascolini D, Mariotti SP, et al.: Global magnitude of visual impairment caused by uncorrected refractive errors in 2004. Bull. World Health Organ. 2008; 86: 63–70. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWHO: International Statistical Classification of Diseases and Related Health Problems (ICD) Classification.2022. (accessed 05 May 2022). Reference Source\n\nFalkenberg HK, Langaas T, Svarverud E: Vision status of children aged 7-15 years referred from school vision screening in Norway during 2003-2013: A retrospective study. BMC Ophthalmol. 2019; 19: 180. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKhadka J, Ryan B, Margrain TH, et al.: Development of the 25-item Cardiff Visual Ability Questionnaire for Children (CVAQC). Br. J. Ophthalmol. 2010; 94: 730–735. PubMed Abstract \| Publisher Full Text\n\nNaipal S, Rampersad N: A review of visual impairment. Afr. Vis. Eye Health. 2018; 77: 4.\n\nWHO: Prevention of Blindness and Deafness. Available data on blindness, update 2006.2021. (accessed 07 April 2022). Reference Source\n\nDandona R, Dandona L, Srinivas M, et al.: Refractive error in children in a rural population in India. Invest. Ophthalmol. Vis. Sci. 2002; 43: 615–622. PubMed Abstract\n\nAdeoti CO: Beliefs and attitude towards spectacles. Niger. J. Clin. Pract. 2009; 12: 359–361. PubMed Abstract\n\nRahi JS, Dezateux C: Epidemiology of visual impairment in Britain. Arch. Dis. Child. 1998; 78: 381–386. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCai T, Verze P, Bjerklund Johansen TE: The Quality of Life Definition: Where Are We Going? Uro. 2021; 1: 14–22. Publisher Full Text\n\nWHOQOL Group: Study protocol for the World Health Organization project to develop a Quality of Life assessment instrument. Division of Mental Health, World Health Organization; 1994; vol. 2. : 153–159.\n\nThe World Health Organization Quality of Life assessment (WHOQOL): position paper from the World Health Organization. Soc. Sci. Med. 1995; 41: 1403–1409. PubMed Abstract \| Publisher Full Text\n\nKumaran SE, Balasubramaniam SM, Kumar DS, et al.: Refractive Error and Vision-Related Quality of Life in South Indian Children. Optom. Vis. Sci. 2015; 92: 272–278. PubMed Abstract \| Publisher Full Text\n\nTadić V, Cooper A, Cumberland P, et al.: Measuring the quality of life of visually impaired children: first stage psychometric evaluation of the novel VQoL_CYP instrument. PLoS One. 2016; 11: 1–15.\n\nDe Civita M, Regier D, Alamgir AH, et al.: Evaluating health-related quality-of-life studies in paediatric populations: Some conceptual, methodological and developmental considerations and recent applications. PharmacoEconomics. 2005; 23: 659–685. Publisher Full Text\n\nBirch EE, Cheng CS, Felius J: Validity and reliability of the Children’s Visual Function Questionnaire (CVFQ). J. AAPOS. 2007; 11: 473–479. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPesudovs K, Burr JM, Harley C, et al.: The development, assessment, and selection of questionnaires. Optom. Vis. Sci. 2007; 84: 663–674. Publisher Full Text\n\nRiley AW: Evidence that school-age children can self-report on their health. Ambul. Pediatr. 2004; 4: 371–376. Publisher Full Text\n\nRavens-Sieberer U, Erhart M, Wille N, et al.: Generic health-related quality-of-life assessment in children and adolescents: Methodological considerations. PharmacoEconomics. 2006; 24: 1199–1220. Publisher Full Text\n\nMargolis MK, Coyne K, Kennedy-Martin T, et al.: Vision-specific instruments for the assessment of health-related quality of life and visual functioning: A literature review. PharmacoEconomics. 2002; 20: 791–812. Publisher Full Text\n\nArksey H, O’Malley L: Scoping studies: Towards a methodological framework. Int. J. Soc. Res. Methodol. 2005; 8: 19–32. Publisher Full Text\n\nLevac D, Colquhoun H, O’Brien KK: Scoping studies: advancing the methodology. Implement. Sci. 2010; 5: 69–78. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTricco AC, Lillie E, Zarin W, et al.: PRISMA extension for scoping reviews (PRISMA-ScR): Checklist and explanation. Ann. Intern. Med. 2018; 169: 467–473. PubMed Abstract \| Publisher Full Text\n\nAromataris E, Munn Z: Introduction to Scoping reviews. JBI Manuals Evid Synth. 2020. (Accessed 12 April 2022). Reference Source\n\nBerk L: The field of child development. Child Development New York, NY, USA: Pearson; 9th ed.2013; pp. 4–6.\n\nPiper C: System for the unified management, assessment, and review of information (SUMARI). J. Med. Libr. Assoc. 2019; 107: 634–636. Publisher Full Text\n\nHong QN, Fàbregues S, Bartlett G, et al.: The Mixed Methods Appraisal Tool (MMAT) version 2018 for information professionals and researchers. Educ. Inf. 2018; 34: 285–291. Publisher Full Text\n\nGRADE Welcome to the GRADE working group: From evidence to recommendations – transparent and sensible. (accessed 08 April 2022). Reference Source\n\nTadić V, Cooper A, Cumberland P, et al.: Measuring the quality of life of visually impaired children: First stage psychometric evaluation of the novel VQoL - CYP instrument. PLoS One. 2016; 1: 11.\n\nAngeles-Han ST, Griffin KW, Harrison MJ, et al.: Development of a vision-related quality of life instrument for children ages 8-18 years for use in juvenile idiopathic arthritis-associated uveitis. Arthritis Care Res. 2011; 63: 1254–1261. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGothwal V, Lovie-Kitchin JE, Nutheti R: The development of the LV Prasad-Functional Vision Questionnaire: a measure of functional vision performance of visually impaired children. Invest. Ophthalmol. Vis. Sci. 2003; 44: 4131–4139. PubMed Abstract \| Publisher Full Text\n\nMisajon RA, Hawthorne G, Richardson J, et al.: Vision and quality of life: The development of a utility measure. Invest. Ophthalmol. Vis. Sci. 2005; 46: 4007–4015. Publisher Full Text\n\nMagakwe TSS, Masemola HC, Nkambule SJ, et al.: Vision-Specific Instruments For The Assessment Of Health-Related Quality Of Life (HR-QOL) For Children And Adolescents With Visual Impairment: A Scoping Review.2023. (accessed 05 June 2024). Publisher Full Text\n\nMagakwe TSS, Hansraj R, Nkambule SJ, et al.: Protocol for scoping review: instruments for assessing vision-specific health-related quality of life in children and adolescents with visual impairment. PRISMA-ScR Checklist. Zenodo. 2024. (accessed 05 June 2024). Publisher Full Text\n\nMagakwe TSS, Hansraj R, Xulu-Kasaba ZN: Supplementary Documents instruments for assessing vision-specific health-related quality of life in children and adolescents with visual impairment. Scoping review protocol. Zenodo. 2024. (accessed 13 June 2024). Publisher Full Text" }	[ { "id": "308968", "date": "19 Aug 2024", "name": "Ellen B M Elsman", "expertise": [ "Reviewer Expertise Systematic reviews of PROMs/instruments", "children/adolescents/young adults with visual impairment", "scale construction and validation" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is a protocol for a scoping review that aims to identify vision-specific instruments for health-related quality of life in children with visual impairment. The protocol is well written, but I have some concerns about the search strategy and methodology.\nThe aim is threefold. First, the use and accessibility of vision-specific instruments that assess the HRQoL in children and adolescents with VI will be mapped. This seems to be the main aim. However, it is unclear from the methods how exactly the accessibility will be evaluated. Second, studies that focus on HRQoL in children and adolescents with VI will be synthesized. But it is unclear what exactly will be synthesized, and what studies will be included. For example, will the authors also include qualitative studies focusing on HRQoL of children with VI? Looking at the eligibility criteria, this indeed seems the case. I'm wondering how this relates to the first and third objective, that mainly focus on instruments used in children with VI. This second objective seems a lot broader and potentially out of place. Third, a description of the psychometric properties of the instruments will be given. What psychometric properties will be considered, and how will the authors describe the psychometric properties? Will for example tools from the COSMIN initiative be used?\nThe search strategy seems very limited. For example, if I look for some of the search terms at blocks.bmi-online, larger search blocks can be found. I question whether all relevant publications will be found using this search strategy. Focusing the research aim might also give options for optimizing the search strategy.\nA risk of bias assessment and grading of the quality of evidence is planned. However, these are not usual steps in a scoping review, but seem more relevant for a systematic review. I advise the authors to take a critical look whether these are indeed applicable to their aims.\nAlso, some literature seems to be omitted. For example Rainey, Khadka, Elsman and Adhikari have done important work in the field of low vision of children and adolescents in recent years, including scale development.\n\nAll in all, although the protocol is well written, the research aim lacks focus, and the methods are not specific enough. Improving the research aim could result in a clearer description of the methods, although the search strategy needs to be improved as well based on the improved aim, to make sure all relevant studies are included.\n\nIs the rationale for, and objectives of, the study clearly described? Partly\n\nIs the study design appropriate for the research question? Partly\n\nAre sufficient details of the methods provided to allow replication by others? No\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable", "responses": [] }, { "id": "308974", "date": "19 Aug 2024", "name": "Ekemiri Kingsley", "expertise": [ "Reviewer Expertise Low Vision", "Pediatric eye care", "Visual Impairment", "and Public Health." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe article outlines a scoping review aimed at creating a context-specific HR-QoL instrument for children in an African setting, using existing data. The review follows Arksey and O’Malley’s framework (2005) and the PRISMA extension for scoping reviews (PRISMA-ScR). It involves five stages: defining the review question, searching for studies, selecting studies, charting data, and summarizing findings. The methodology includes detailed steps for searching and selecting studies, data extraction, and analysis but has some gaps that affect its replicability and the clarity of the datasets presented.\n1. Details of the Methods for Replication: Partly Adequate\nIssue: The article provides an overview of the search strategy, eligibility criteria, data extraction tool, data analysis approach, and quality assessment methods. However, several critical details necessary for full replication are missing.\n- Eligibility Criteria: The criteria for excluding gray literature are not sufficiently detailed or justified. The authors should clarify why gray literature is excluded and how this aligns with the study’s objectives. Consider including some gray literature if it contributes significantly to the research question. -Offer a detailed rationale for excluding gray literature. - Consider including gray literature if it provides significant insights.\n-Data Extraction Tool: While the data extraction tool is mentioned, there is no information on how it was pretested or validated. The methodology should detail the development, pretesting, and validation of the tool, and document any modifications with justifications. - Describe how the tool was developed, pretested, and validated. Document any changes to the tool and provide justifications.\n- Data Analysis: The approach to data analysis using Qualcoder 1.9 is outlined but lacks specifics on how themes will be identified, coded, and reported. Provide a step-by-step process and examples of coding to enhance clarity. - Include a detailed process for data analysis using Qualcoder. -Provide examples or a coding framework to illustrate how themes will be generated and analyzed. Outline Quality Assessment Methods:\n- Quality Assessment: The application of MMAT and GRADE tools is mentioned without clear criteria or processes. The authors should outline specific criteria for each tool and describe how discrepancies in quality assessment will be resolved. - Detail the criteria for applying MMAT and GRADE tools. - Explain the process for resolving discrepancies in quality assessment.\nQuality Assessment: The application of MMAT and GRADE tools is mentioned without clear criteria or processes. The authors should outline specific criteria for each tool and describe how discrepancies in quality assessment will be resolved. - Ensure datasets are clear, organized, and available in accessible formats. - Include comprehensive metadata and documentation for clarity and usability.\n2. Datasets Presentation: Not Adequate The datasets are not clearly presented in a usable and accessible format. The details on how data will be organized and shared are insufficient.\n-Include detailed documentation on how data was extracted, organized, and any modifications made during the review process.\n\n- Provide tables of the articles selected, this should include. Study Characteristics, Population, Characteristics, descriptions of any interventions, tools, or instruments, The outcomes measured in the studies, Themes or Concepts, Methodological Details:\n- Lack of detail on inter-rater reliability assessment and resolution of disagreements. Include a plan for assessing inter-rater reliability and a protocol for resolving disagreements.\n\n- The PRISMA-ScR fillable checklist is incomplete, the author should make effort to complete this form.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Yes\n\nAre sufficient details of the methods provided to allow replication by others? Partly\n\nAre the datasets clearly presented in a useable and accessible format? No", "responses": [] } ]	1	https://f1000research.com/articles/13-740
https://f1000research.com/articles/13-739/v1	04 Jul 24	{ "type": "Research Article", "title": "Parents’ satisfaction with physiotherapy services for neuropediatric outpatients in government and private hospitals in the United Arab Emirates: a cross-sectional study", "authors": [ "Hanadi Ahmed AlNaqbi", "Meeyoung Kim", "Nabeel Al-Yateem", "Fatma A. Hegazy", "Hanadi Ahmed AlNaqbi", "Meeyoung Kim", "Nabeel Al-Yateem" ], "abstract": "Background Healthcare, like other industries, emphasizes performance, quality, and consumer experience while also attempting to reduce costs. However, high-quality healthcare remains paramount for vulnerable and ill patients. This study aimed to investigate parents' and caregivers' level of satisfaction with physiotherapy services provided to neuropediatric outpatients on the United Arab Emirates (UAE).\n\nMethods This descriptive cross-sectional study included 103 parents/caregivers of children with neurological disabilities that were randomly selected from different Emirates Health Services Hospitals in the UAE. Data was collected using the long-form Patient Satisfaction Questionnaire (PSQ-III).\n\nResults The overall mean satisfaction was 159±7.73 (out of 250 points). Communication (20.36/25), interpersonal factors (20.17/35), and doctor-patient time (20.17/35) had the highest mean satisfaction scores (8.06/10). The lowest mean satisfaction scores were for access/availability/convenience (34.60/60), technical quality (33.17/50), and economic elements (23.83/40).\n\nConclusion Despite participants’ overall satisfaction scores being positive, some service domains require improvement to improve satisfaction, specifically the access/availability/convenience, technical quality, and economic elements. These areas should be prioritized by service providers and managers to improve patients’ experiences and clinical outcomes.", "keywords": [ "Parents satisfaction", "Physiotherapy", "Pediatric rehabilitation", "Neurological disabilities" ], "content": "Introduction\n\nMany industries worldwide, including healthcare, have increasingly prioritized performance, quality, and user satisfaction while simultaneously attempting to reduce costs. Healthcare providers deliver vital services to vulnerable and critically ill patients, along with essential preventative and health promotion services. Several healthcare organizations worldwide have launched quality improvement initiatives to improve patient satisfaction and prevent negative experiences, but it is becoming increasingly important to implement effective strategies to provide quality care that is also cost-efficient.1,2\n\nSatisfaction is known as a belief and attitude regarding certain or specific services provision of an institution.3,4 Patient satisfaction is considered the most important indicator for health service quality assessment.5 Parental and patient satisfaction become a well-established outcome indicator for assessing the quality of healthcare system.4,6 Parental satisfaction is determined by how effectively parents ‘expectations of ideal care are balanced with how they actually feel about real available care.7,8 According to the numerous studies, poor communication and lack of information are the most serious parent/patient complaint.9,10 Even when therapists try to explain the patient condition, their terminology is often misunderstood. So, Listening to parents is very important in process of communication.11\n\nAmong the most widely used patient satisfaction tool is the Hospital Consumer Assessment of Healthcare Providers and Systems (HCAHPS) survey. Many organizations use the HCAHPS as a key performance indicator.12 However this tool is general and nature and is of limited use for specific and specialized services like the physiotherapy service.13 Consistent with global trends, the United Arab Emirates (UAE) has prioritized the development of a world-class healthcare system to serve its population. To achieve this, the UAE government introduced new quality criteria and mandated that all healthcare institutions receive accreditation from national and international agencies.14\n\nFurthermore, healthcare organizations in the UAE consistently undergo evaluation against comprehensive quality outcomes to assess their efficiency and determine funding and reimbursement. For example, the Department of Health in Abu Dhabi uses a healthcare quality index called “Muashir” to measure the performance of healthcare organizations against pre-set key performance indicators. Distinguished facilities receive a rating from one to five domains, which is made public and used to allocate funding to these institutions.15 This system means that the operation of these healthcare organizations depends on their achievement of quality outcomes, which results in competition among organizations to perform better and attract more funding. This approach is not implemented universally across the UAE, as healthcare services are managed federally through the Ministry of Health and Prevention (MOHAP) or locally by local health authorities. However, many local health authorities have recognized the successful implementation of Muashir and are considering rolling out this approach across their healthcare institutions.\n\nTo support physiotherapists to make a maximum contribution to developing healthcare services for their patient population in the UAE, elements of their practice that contribute to patient satisfaction need to be identified. Identifying these elements can form the basis for planning and implementing relevant measures to improve available services. At the clinical level, physiotherapy patients who are satisfied with their treatment tend to interact well with their therapist, remain loyal to them, and seek further treatment when necessary.16\n\nWhen initiating treatment, physiotherapists meet with their patients (and patients’ parents/caregivers in pediatric cases) for a consultation to develop an appropriate treatment plan.17 The fulfilment of this plan should lead to patient satisfaction; however, many systemic, process, and outcome factors could affect the execution of the treatment plan and thereby affect patient satisfaction. This means it is essential to clarify aspects that impact patient satisfaction in these services. Therefore, the present study explored patient satisfaction in the context of rehabilitation healthcare (physiotherapy) services in the UAE, as the principal investigator is a clinician working in pediatric rehabilitation services. This study was conducted to determine parents’/caregivers’ level of satisfaction with the physiotherapy services provided to their children in the physiotherapy departments of private and government hospitals in the UAE.\n\n\nMethods\n\nThis study used a cross-sectional correlational design. Participants completed self-report questionnaires that assessed the satisfaction of parents/caregivers of children attending rehabilitation services and other relevant variables.\n\nWe included Parents or caregivers of children that had physical disabilities and neurological problems who were receiving rehabilitation sessions in physiotherapy departments in government and private hospitals in the UAE. Parents/caregivers were invited to participate if they were able to read and understand English and had a child aged between 5 months and 16 years that was a neuropediatric patient who had received at least 12 physiotherapy sessions. Parents and caregivers of patients who were admitted to hospital (inpatients) were excluded from this study. In addition, we did not include patients from all physiotherapy specialties as their needs may differ, which would impact their satisfaction.\n\nConvenience sampling was used to recruit parents/caregivers of children receiving rehabilitation services. All major hospitals for children’s rehabilitation governed by the Emirates Health Services authority were contacted to obtain approval to conduct this study. Those settings that responded and approved this study were approached to assist with recruitment and all eligible parents/caregivers in these settings were invited to participate. Data were collected from 103 parents/caregivers of children with various neurological disabilities attending rehabilitation services at different Emirates Health Services facilities.\n\nThe sample size was calculated depending on the proportion (78%) stated in a previous study addressing the same research question [48]. The appropriate sample size with sufficient power of 80% (alpha= 0.05) was calculated by the Epi Info, a program developed by the Centers for Disease Control and Prevention.\n\nThe long form of the Patient Satisfaction Questionnaire (PSQ-III) was used in this study (English language version), which was validated in previous studies.18,19 The scale is open access and available for researchers use through the authors website.20 The scale was found to be reliable, with Cronbach’s alpha coefficients of 0.92 for the whole scale and 0.74–0.89 for the subscales.17 The PSQ-III is a 50-item survey that measures global satisfaction with medical care as well as satisfaction with seven specific aspects of care: general satisfaction, technical quality, interpersonal manner, communication, financial aspect of care, time spent with doctor, and accessibility of care.\n\nRespondents are asked to rate their satisfaction with the medical care they received, with responses on a scale from 1 to 5 (strongly agree to strongly disagree) that indicate to what extent they agreed with each statement.18 An open-ended comments option was added at the end of the structured questionnaire to accommodate qualitative information from participants regarding their suggestions for service improvements. We also collected information on the children’s age, gender, and the duration they had received physiotherapy treatment.\n\nParticipants were parents or caregivers who usually accompanied children to their physiotherapy session. They were selected following contact with the heads of the physiotherapy departments in different government and private hospitals via electronic communications that explained the study purpose. A link to the electronic questionnaire (PSQ-III) was distributed to eligible parents/caregivers through their preferred communication channel.\n\nEthical approval was obtained from the Research Ethics Committee of the University of Sharjah [approval no: REC-21-04-28-02-S], and the ethical committee of the Ministry of Health and Prevention [Approval Reference No: MOHAP/DXB-REC/JJJ/No. 57/2021] on April 2021. Before recruiting participants, written informed consent which included information of the study’s purpose, was obtained from all eligible participants. Each parent who expressed interest to participate in this study was instructed to read, understand, and sign the consent form. Furthermore, the integrity and confidentiality of all data collected during the study were assured by local institutional policies. Participants were informed that they had their right to withdraw at any time without prejudice and no incentives were offered at any point in the study.\n\nData were analyzed using SPSS Software. Descriptive statistics were used to describe participants’ demographics and levels of satisfaction. Continuous variables were expressed as means and standard deviation, while categorical variables were expressed as counts and percentages. Correlational analysis was performed to assess the association between demographic variables and the satisfaction score.\n\n\nResults\n\nBefore proceeding with data analysis, the reliability of the study questionnaire was assessed to ensure valid and reliable results. The reliability of the scale used in this study was assessed and returned a Cronbach’s alpha value of 0.7, which is considered acceptable reliability value.\n\nIn total, 103 parents/caregivers participated in this study, of which 44.7% (n=46) had female children receiving rehabilitation and the remaining (55.3%, n=57) had male children receiving rehabilitation. The majority of participants had children that were scheduled for a long duration of physiotherapy treatment (i.e., >12 sessions). The mean age of the children was 57±48 months (4.75 years). Table 1 presents sociodemographic details of participants’ children.\n\nThe mean satisfaction score for the sample was 159±7.73 (out of 250 points). The highest levels of satisfaction were found for communication (20.36/25), followed by interpersonal aspects (20.17/35) and time spent with the doctor (8.06/10). The lowest mean satisfaction scores were recorded for access/availability/convenience (34.60/60, SD=3.08), technical quality (33.17±1.97/50) and financial aspects (23.83±2.66/40). Table 2 presents the descriptive statistics for the survey items.\n\nTable 3 shows the level of satisfaction with each PSQ-III item. In the general satisfaction domain, most (97.1%) participants agreed that some aspects of the medical care that they received could be improved. However, most (94.2%) participants were satisfied that their child was treated by medical staff who were aware of the latest medical developments. Regarding the interpersonal aspect domain, most (90%) participants indicated that the doctors always tried to prevent them worrying. In terms of communication, most (89.3%) participants reported that when they visited the doctor, they were always free to express concerns and believed that this was important. A majority (68.9%) of participants sometimes worried about having to pay a large medical bill. In addition, most (88.3%) participants reported that the doctors usually spent plenty of time with their children, and 88.3% noted that they could easily get hospital care without any trouble.\n\nWe also assessed the correlations between the child's age and parents' /caregivers' satisfaction scores. These variables showed a significant, negative, and weak correlation, which indicated that satisfaction tended to decrease as the child’s age increased. A nonparametric Mann-Whitney U test was used to assess differences in parents’/caregivers’ satisfaction scores by the child’s sex and physiotherapy duration. This analysis showed that there were no significant differences between these groups in terms of their satisfaction scores.\n\n\nDiscussion\n\nParents' and caregivers' satisfaction with their child’s rehabilitation intervention is necessary for the sustainability of services. Conducting patient satisfaction surveys can help enhance clinical practice, and can also provide relevant data for the marketability of healthcare services and quality of care delivered.19,21 Patients are considered users of healthcare services, meaning patient satisfaction is an important tool to evaluate the quality of services provided. In this study, the overall level of satisfaction with neuropediatric rehabilitation services was high, but a lower level of satisfaction was observed when specific aspects of care were assessed. This suggested that it is not possible to assess the level of patient satisfaction by simply asking patients if they were happy with the services that they received.\n\nWe found no significant differences in parents’/caregivers’ satisfaction by the child’s sex and physiotherapy duration. However, this finding may be because our sample size was insufficient to allow these comparisons. Similarly, a previous study revealed patient satisfaction was not affected by their age, educational status or occupation.22 In contrast, other studies showed that age, sex, ethnicity, education, and occupation were the main predicators of overall patient satisfaction. For example, a study from Nigeria reported that the communication and access/availability/convenience domains were strongly associated with sex; however, there was no sex-based difference in satisfaction with the time spent with doctor, technical quality, interpersonal financial, and general satisfaction domains.23\n\nHowever, we found that age was the best predictor of satisfaction in the majority of satisfaction dimensions, whereas the Nigerian study reported patients’ age was not a determinant of their satisfaction with services they received.23\n\nIn the present study, the satisfaction of parents\\caregivers differed across various areas examined in the questionnaire. The mean total satisfaction score (63.8%, 159.49/250) showed that the majority of participants had a good level of satisfaction with the physiotherapy treatment that their children received at the government and private hospitals run by Emirates Health Services. A previous study reported the mean overall score for patient satisfaction with physiotherapy care was 68.2%, which was consistent with our results.24 However, other studies reported lower levels of satisfaction for various reasons. A study from Nepal found that patients’ general satisfaction was relatively low (39%), although this was attributed to the unavailability of certain desired facilities.25 Participants in our study were satisfied with the time the therapist spent with their child (80.6%) in each session. This finding was expected because therapists in the participating services typically spend 45–60 min in one treatment session with their patients. Our participants indicated that their satisfaction was increased when the therapist spent a long time with their child and explained the treatment plan.\n\nIn contrast to our results, a study from Dubai reported that 40% of parents/caregivers were dissatisfied with the time that their children spent with the therapist. Those authors suggested that this dissatisfaction could be explained by the therapists’ heavy workloads or the patients’ condition not requiring a long time for treatment.26\n\nAnother study conducted in Katsina State, Nigeria, found patients reported low satisfaction with the time spent with the doctor because there was a large number of surgeries completed and patients felt they did not receive proper interaction.23\n\nPrevious studies focused on psychological issues related to pediatric practice revealed that parents/caregivers were interested in knowing more about their children’s psychological problems and good communication was a powerful predictor of satisfaction. Good communication during medical visits was reported to significantly influence parents’/caregivers’ satisfaction, functional status, and patient compliance.27 This was consistent with our finding that most (81.4%) participants were satisfied with the therapist because there was good communication between the therapist and parents/caregivers. This was consistent with the results of other studies that found the highest level of satisfaction was reported for the communication domain.28 One study suggested that communication had the highest mean satisfaction score because patients appreciated their therapists’ listening ability.24\n\nThe interpersonal and access/availability/convenience domains had the lowest scores in our study (57.6% and 57.7%, respectively). This was consistent with a previous study that also showed these two domains had the lowest mean satisfaction scores.23 Financial aspects also had a low satisfaction score in our study (59.6%) Some of our participants were not satisfied with the financial domain because they felt that they were not protected from financial hardship. Others noted they were required to pay for services from their own pocket, which could expose them to future financial issues.\n\nWe faced some challenges that might have affected this study, particularly parents’/caregivers’ reluctance to complete the questionnaire and the small sample size because of the COVID-19 pandemic (Coronavirus disease of 2019). In addition, the questionnaire was not translated into Arabic, which makes it difficult to generalize the findings and might have contributed to the small sample size. However, a reasonable number of parents/caregivers completed the survey, and our findings may help in identifying reasons for dissatisfaction with neuropediatric rehabilitation services, as well as which domains require improvement and what improvement they may need.\n\n\nConclusions\n\nIn conclusion, this study sheds light on the crucial aspect of parents' satisfaction with physiotherapy treatment for neuropediatric outpatients in the UAE. The findings underscore the overall positive satisfaction reported by parents and caregivers regarding various aspects of physiotherapy services, particularly in communication, interpersonal factors, and doctor-patient time. However, it is evident that there are areas in need of improvement, notably access/availability/convenience, technical quality, and economic elements. These findings emphasize the importance of continuous assessment and enhancement of healthcare services to meet the evolving needs of patients and their families. Addressing the identified areas of concern is paramount to enhancing patient experiences and ultimately improving clinical outcomes. Therefore, it is imperative for service providers and managers to prioritize these domains in their efforts to optimize the quality of care provided to neuropediatric outpatients and ensure the delivery of patient-centered healthcare in the UAE.", "appendix": "Data availability statement\n\nHarvard Dataverse: “Replication Data for: Parents’ satisfaction with physiotherapy services for neuropediatric outpatients in Government and Private Hospitals in the United Arab Emirates: a cross-sectional study” https://doi.org/10.7910/DVN/QBANIG. 29\n\nThe data set contains the underlying data:\n\n• Satisfaction data - with items recoded.tab: This file contains the socio-demographic and QoL variables.\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\n\nAcknowledgments\n\nThe researchers would like to thank all patients who participated in this study. Also, the authors acknowledge the hospitals which facilitated this study on their premises.\n\n\nReferences\n\nAl-Yateem N, Docherty C, Rossiter R: Determinants of Quality of Care for Adolescents and Young Adults With Chronic Illnesses: A Mixed Methods Study. J. Pediatr. Nurs. 2016; 31(3): 255–266. PubMed Abstract \| Publisher Full Text\n\nMacias CG: Quality Improvement in Pediatric Emergency Medicine. Acad. Pediatr. 2013; 13(6, Supplement): S61–S68. Publisher Full Text\n\nHagen IH, Iversen VC, Nesset E, et al.: Parental satisfaction with neonatal intensive care units: a quantitative cross-sectional study. BMC Health Serv. Res. 2019; 19(1): 37. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSharew NT, Bizuneh HT, Assefa HK, et al.: Investigating admitted patients’ satisfaction with nursing care at Debre Berhan Referral Hospital in Ethiopia: a cross-sectional study. BMJ Open. 2018; 8(5): e021107. 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PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGannotti ME, Law M, Bailes AF, et al.: Comparative Effectiveness Research and Children With Cerebral Palsy: Identifying a Conceptual Framework and Specifying Measures. Pediatr. Phys. Ther. 2016; 28(1): 58–69. Publisher Full Text\n\nMyrhaug HT, Jahnsen R, Østensjø S: Family-centred practices in the provision of interventions and services in primary health care: A survey of parents of preschool children with cerebral palsy. J. Child Health Care. 2016; 20(1): 109–119. PubMed Abstract \| Publisher Full Text\n\nBetiku AO, Folashade AB, Aribaba OT, et al.: Comparison of patients’ satisfaction with eye care and family medicine services at a primary health centre in Ogun State, Nigeria. Int. J. Commun. Med. Public Health. 2021; 8(12): 5687–5695. Publisher Full Text\n\nRabiu MM, Taryam MO, Bashir E, et al.: Assessment of patients satisfaction with cataract surgical services in katsina state. Invest. Ophthalmol. Vis. Sci. 2022; 7(1): 1–6.\n\nOjeniweh O, Mariere U, Rotifa S, et al.: Patient satisfaction with physical therapy care in a tertiary healthcare facility: an evaluation of quality of physical therapy services provided in Federal Medical Centre, Yenagoa, Bayelsa State. Yen. Med. J. 2021; 3(2): 116–123.\n\nAdhikari M, Paudel NR, Mishra SR, et al.: Patient satisfaction and its socio-demographic correlates in a tertiary public hospital in Nepal: a cross-sectional study. BMC Health Serv. Res. 2021; 21(1): 135. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAl-Yateem N: Replication Data for: Parents’ satisfaction with physiotherapy services for neuropediatric outpatients in Government and Private Hospitals in the United Arab Emirates: a cross-sectional study. Harvard Dataverse. 2024; V1. UNF:6:Xi+hkuwus7MBMEgHNzqnKw== [fileUNF]. Publisher Full Text" }	[ { "id": "300265", "date": "12 Jul 2024", "name": "Bhamini Krishna Rao", "expertise": [ "Reviewer Expertise Pediatric neurorehabilitation", "Neonatal intensive care unit", "pelvic floor dysfunction and physiotherapy" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe manuscript titled \"Parents’ satisfaction with physiotherapy services for neuropediatric outpatients in government and private hospitals in the United Arab Emirates: a cross-sectional study\" presents a valuable exploration of parental satisfaction with physiotherapy services for children with neurological disabilities in the UAE. The study design, which utilizes a cross-sectional correlational approach, is appropriate for the research objectives and provides a comprehensive overview of the satisfaction levels among parents and caregivers.\n\nThe methods section is detailed and well-structured, clearly outlining the study design, participant recruitment, data collection, and analysis procedures. The choice of the Patient Satisfaction Questionnaire (PSQ-III) is justified and its reliability is well-documented, making it a suitable tool for this study. The ethical considerations are thoroughly addressed, ensuring the integrity and ethical soundness of the study. However, providing more details on the sampling process, including the selection criteria and any potential biases, would enhance the transparency and replicability of the methodology.\nThe results are presented clearly and concisely, with comprehensive tables that effectively illustrate the key findings. The analysis is robust, and the interpretation of the data is logical and consistent with the study's objectives. The sociodemographic characteristics of the participants are well-documented, providing important context for understanding the results. The correlation analysis between demographic variables and satisfaction scores is particularly useful, highlighting the factors that influence parental satisfaction. Including more detailed subgroup analyses could provide additional insights into these factors.\nThe discussion effectively interprets the results in the context of existing literature, highlighting both the strengths and areas needing improvement in the physiotherapy services. The identification of areas requiring improvement, such as access, technical quality, and economic elements, is particularly valuable for informing future service enhancements. The discussion could be further enriched by exploring potential strategies for addressing these areas and by discussing the implications of the findings for policy and practice in more detail. Additionally, a comparison with similar studies in other regions could provide a broader perspective on the findings and underscore the study's relevance in a global context.\nIn conclusion, this study sheds light on the crucial aspect of parents' satisfaction with physiotherapy treatment for neuropediatric outpatients in the UAE. The findings underscore the overall positive satisfaction reported by parents and caregivers regarding various aspects of physiotherapy services, particularly in communication, interpersonal factors, and doctor-patient time. However, it is evident that there are areas in need of improvement, notably access, technical quality, and economic elements. These findings emphasize the importance of continuous assessment and enhancement of healthcare services to meet the evolving needs of patients and their families. Addressing the identified areas of concern is paramount to enhancing patient experiences and ultimately improving clinical outcomes. Therefore, it is imperative for service providers and managers to prioritize these domains in their efforts to optimize the quality of care provided to neuropediatric outpatients and ensure the delivery of patient-centered healthcare in the UAE.\nSuggestions for Improvement: The abstract can be reorganized to suit the title of the study by giving importance to parents whose children receive long term rehabilitation services. The introduction can emphasize more on how caregiving is difficult in neuropediatric population rather than giving too much importance to general aspects of patient satisfaction\nProvide more details on the sampling process and potential biases in the methods section. Include more detailed subgroup analyses in the results section to provide additional insights into factors influencing satisfaction. The results section can highlight parents' or caregivers' characteristics and then compare it with the patient satisfaction scores. Explore potential strategies for improving areas of low satisfaction in the discussion. Compare findings with similar studies in other regions to provide a broader context. Include specific recommendations for future research and practice in the conclusion. Recommendation: Approve for indexing with minor 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? 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": "300260", "date": "30 Jul 2024", "name": "Ehab Mohamed Abd El-Kaf", "expertise": [ "Reviewer Expertise Professor of Physical Therapy." ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis manuscript makes a valuable contribution to understanding parental satisfaction with physiotherapy services for children with neurological disabilities in the UAE. The study highlights the local importance and relevance of this issue and provides useful insights for healthcare providers seeking to improve service quality. Overall, this manuscript provides a comprehensive overview of parental satisfaction with physiotherapy services for children with neurological disabilities in the UAE. Enhancing the introduction with additional references, clarifying secondary objectives, and providing more details on the sampling process and subgroup analyses would further improve the manuscript. Here are a detailed review of the sections. 1. The introduction is clear and effectively sets the stage for the study, emphasizing the importance of patient satisfaction in healthcare within the UAE's evolving landscape. While the background information on patient satisfaction is comprehensive, adding recent studies on similar settings would enhance this section. 2. The goals and objectives of the study are well-stated and align with the introduction. The aim to investigate parents' satisfaction with physiotherapy services for neuropediatric patients is clear. However, clarifying any secondary objectives would provide a more complete picture of the study's scope. 3. The methods section is detailed and well-organized, outlining the study design, participant recruitment, data collection, and analysis procedures. The use of the Patient Satisfaction Questionnaire (PSQ-III) is well-justified, and ethical considerations are thoroughly addressed. More details on the sampling process, including selection criteria and potential biases, would improve transparency and replicability. 4. Results are presented clearly with tables that effectively illustrate key findings. The mean satisfaction scores for different service domains are well-documented, and the statistical analysis is sound. Including more detailed demographic data and subgroup analyses would provide additional context and highlight factors influencing parental satisfaction. 5. The discussion interprets the results well, relating them to existing literature and emphasizing the study's local significance. Identifying areas for improvement, such as access, technical quality, and economic elements, is valuable. The discussion could be enriched by exploring strategies for addressing these areas and discussing the implications for policy and practice in more detail. 6. Comparing the findings with similar studies in other regions would offer a broader perspective. 7. The conclusion succinctly summarizes the main findings and their implications, emphasizing the need for ongoing assessment and improvement of physiotherapy services. Including specific recommendations for future research and practice would strengthen the conclusion.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? 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/13-739
https://f1000research.com/articles/13-3/v1	03 Jan 24	{ "type": "Systematic Review", "title": "COVID-19 and the need for special care for women with polycystic ovary syndrome: A systematic review", "authors": [ "Warda A. Alrubasy", "Shams Khalid Sameer", "Mohammad J. J. Taha", "Mohammad T. Abuawwad", "Abdalla Abu-Zeinh", "Marwa Mahmood", "Hebatullah Humeidan", "Ahmad J. Taha", "Abdulqadir J. Nashwan", "Warda A. Alrubasy", "Shams Khalid Sameer", "Mohammad J. J. Taha", "Mohammad T. Abuawwad", "Abdalla Abu-Zeinh", "Marwa Mahmood", "Hebatullah Humeidan", "Ahmad J. Taha" ], "abstract": "Objective The study investigates the association between coronavirus disease 2019 (COVID-19) and polycystic ovary syndrome (PCOS) and assess whether women with PCOS are at a higher susceptibility and risk for COVID-19 complications.\n\nMethods This review analyzes articles indexed in PubMed, Scopus, Google Scholar, and the Cochrane Library, focusing on the onset of the COVID-19 pandemic in December 1, 2019, until November 1, 2022. The quality of the evidence was assessed using the NIH quality assessment tool. The study was registered on PROSPERO (CRD42023371956) on January 12, 2023.\n\nResults A total of 11 observational studies were identified, totaling 22,155 PCOS patients. Despite the heterogeneity of the included studies, the findings of most of the studies were similar in terms of increased susceptibility and severity of COVID-19 infection in PCOS patients. PCOS patients were reported to have a 51% higher risk of COVID-19 infection than non-PCOS women (HR =1.51). Many causes have been identified to play a role, most notably the overactivation of the renin-angiotensin system (RAS) and elevated levels of RAS-associated proteins, decreased serum levels of neuropilin-1 (sNRP1), elevated serum biomarkers such as platelet degranulation and coagulation cascade markers increased acute phase response, and lower levels of vitamin D could render PCOS patients susceptible to a chronic inflammatory state, which can also lead to difficulties and severe consequences, when impacted by COVID-19. Furthermore, the COVID-19 pandemic also influenced psychological well-being, with an increase in the incidence and severity of depression and anxiety among PCOS patients in the COVID-19 pandemic era compared to healthy individuals.\n\nConclusions Patients with PCOS are more likely to get infected with COVID-19 and display a higher affinity to severe infections and complications due to overlapping and confounding factors. These findings suggest that PCOS patients may need more medical attention when infected with COVID-19.", "keywords": [ "Polycystic Ovary Syndrome (PCOS)", "COVID-19 complications", "Susceptibility to infection", "Chronic inflammatory state", "Renin-Angiotensin System (RAS)" ], "content": "Introduction\n\nCoronavirus disease 2019 (COVID-19), caused by the severe acute respiratory distress syndrome coronavirus 2 (SARS-CoV-2), first originated in Wuhan, China in 2019 and has been declared as a global pandemic by the World Health Organization in March 2020.1 Since then, data from medical studies has grown addressing the risk factors that contribute to the infection’s susceptibility, severity, and outcomes. COVID-19 illness has a large clinical spectrum, with people infected with COVID-19 presenting with a wide range of symptoms ranging from mild fatigue to severe respiratory distress.2 Symptoms predominantly affect the respiratory system, including fever or chills, cough, and shortness of breath. Human-to-human transmission mainly occurs through respiratory droplets.3\n\nPolycystic ovary syndrome (PCOS) is the most common endocrine disorder among women of reproductive age, with a prevalence of 4–20% and a wide range of signs and symptoms.4 Emerging evidence suggests that COVID-19 and PCOS share several risk factors.5,6 PCOS is associated with several comorbidities, including type 2 diabetes and an enhanced prothrombotic state, which may eventually lead to an increased risk of cardiovascular events and consequences.7,8 Furthermore, women with PCOS have chronic low-grade inflammation which could contribute to the infection.9 COVID-19 has also been associated with similar clinical issues, including thromboembolic events and inflammatory environment.10 In light of these PCOS-related comorbidities, these patients may experience significant consequences from COVID-19 infection.\n\nThe majority of COVID-19 infections are characterized by mild to moderate symptoms.11 Severe COVID-19 infections, on the other hand, have been associated with immunocompromise, advanced ages, diabetes, hypertension, and other cardiovascular comorbidities.12,13 As a result, identifying high-risk COVID-19 groups is critical for making early choices on suitable care. PCOS patients are sometimes required to seek consultation from different medical disciplines due to the complicated nature of the syndrome in addition to its reproductive and metabolic symptoms.14 This could be an extra burden for PCOS patients since they may go untreated and mismanaged in the era of the COVID-19.\n\nThe purpose of this study is to summarize the findings of relevant studies that investigated the association between COVID-19 and PCOS in order to highlight the possible risk factors that may render PCOS patients more liable for morbidity and mortality in cases of COVID-19 infection.\n\n\nMethods\n\nThis systematic review is reported following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) checklist,15,53 with and pre-registered protocol on PROSPERO [CRD42023371956] on January 12, 2023. It investigates available evidence regarding the relationship between COVID-19 and PCOS.\n\nWe included papers that investigated the relationship between PCOS and COVID-19 infection and complications. The interest of the investigation is the main impact of PCOS disease on the infection, course, complications, and outcome of COVID-19 disease. The inclusion criteria of this study were: 1) Papers investigating the underlying factors between PCOS and COVID-19 disease, 2) Studies comparing normal and PCOS patients, 3) in vivo studies, 4) English language papers, and 5) Free access papers. Information sources included PubMed, Scopus, Web of Science, Cochrane library, and Google Scholar.\n\nThe search for relevant literature was conducted on PubMed, Scopus, Cochrane Library, and Google Scholar, with date restrictions from the beginning of the COVID-19 pandemic December 1, 2019, until November 1, 2022. A detailed overview of the systematic search is provided in Table 1. It is important to note that the search strategy adhered to recent recommendations for systematic reviews.16 The first 200 records on Google Scholar were searched, as the relevance of the results significantly decreased beyond this point. We also researched related systematic reviews published in the field to identify potentially relevant full-text articles. After completing the searches, we exported the retrieved references to an EndNote X9® (Alternatively, Zotero could be used as an open-access which can perform the same function) file and removed duplicates. Two independent reviewers (WA, SK) screened the titles and abstracts and assessed potential full texts for eligibility. Studies that met our eligibility criteria were included in our review. Any discrepancies between reviewers were resolved by a third reviewer (MJJT, MTA).\n\nEach paper was independently extracted by two authors to avoid any bias. Characteristics and outcome data from the included papers and any discrepancies were resolved by a third reviewer. Characteristics extracted from trials included: study design, country of participants, main outcome, sample characters, and key findings of the papers. A separate section was also added for quality assessment of the papers.\n\nThe quality of the retrieved papers was assessed according to the National Institutes of Health (NIH) quality assessment tool.17 Each type of research was assessed to the suitable tool from NIH quality assessment tools. The score of each paper is illustrated in Table 2.\n\n\n\n- PCOS patients struggled during lockdowns.\n\n- Pandemic worsened their pre-existing mental health issues.\n\n- Affected mental-health by inability to access exercise facilities.\n\n- Positive impacts of the disruption of daily lives routines.\n\n\n\n- 50% of PCOS patients gained weight during the COVID-19 isolation.\n\n- 46% of controls had an increase in their weight.\n\n\n\n- Majority of PCOS patients reported negative impact of the lock down measures on their sleep.\n\n- Increasing levels of insomnia.\n\n- Elevated levels of stress and depression.\n\n\n\n- PCOS patients had significantly lower Vitamin D levels.\n\n- Increased levels of inflammatory markers PCOS women.\n\n\n\n- Studying level of Proteins and inflammatory markers altered in COVID-19 disease in both PCOS and controls.\n\n\n\n- Biomarkers of platelet degranulation, coagulation cascade, are elevated in PCOS.\n\n\n\n- Measuring levels of sNRP1 to assess the reflection of severe COVID-19 infection.\n\n\n\n- Decreased sNRP1 levels in PCOS patients.\n\n\n\n- Measuring levels of RAS-related proteins in both PCOS and controls.\n\n\n\n- Increased RAS activation in PCOS patients.\n\n- RAS overactivity seen as; High renin and angiotensin levels.\n\n\n\n- RAS-related proteins might be related to insulin resistance present in PCOS patients.\n\n\n\n- PCOS patients have reduced ACE-2 levels which leads to increased COVID-19 severity.\n\n\n\n- SCARFs were downregulated in PCOS patients.\n\n- Less risk of ovarian SARS-CoV-2 infection in PCOS.\n\n\n\n- Decreased level of BMI reduction in PCOS women from 6.8% before the pandemic to 3.7% during COVID-19 lockdown.\n\n\n\n- PCOS patients struggled during lockdowns.\n\n- Pandemic worsened their pre-existing mental health issues.\n\n- Affected mental-health by inability to access exercise facilities.\n\n- Positive impacts of the disruption of daily lives routines.\n\n\n\n- 50% of PCOS patients gained weight during the COVID-19 isolation.\n\n- 46% of controls had an increase in their weight.\n\n\n\n- Majority of PCOS patients reported negative impact of the lock down measures on their sleep.\n\n- Increasing levels of insomnia.\n\n- Elevated levels of stress and depression.\n\n\n\n- PCOS patients had significantly lower Vitamin D levels.\n\n- Increased levels of inflammatory markers PCOS women.\n\n\n\n- Studying level of Proteins and inflammatory markers altered in COVID-19 disease in both PCOS and controls.\n\n\n\n- Biomarkers of platelet degranulation, coagulation cascade, are elevated in PCOS.\n\n\n\n- Measuring levels of sNRP1 to assess the reflection of severe COVID-19 infection.\n\n\n\n- Decreased sNRP1 levels in PCOS patients.\n\n\n\n- Measuring levels of RAS-related proteins in both PCOS and controls.\n\n\n\n- Increased RAS activation in PCOS patients.\n\n- RAS overactivity seen as; High renin and angiotensin levels.\n\n\n\n- RAS-related proteins might be related to insulin resistance present in PCOS patients.\n\n\n\n- PCOS patients have reduced ACE-2 levels which leads to increased COVID-19 severity.\n\n\n\n- SCARFs were downregulated in PCOS patients\n\n- Less risk of ovarian SARS-CoV-2 infection in PCOS.\n\n\n\n- Decreased level of BMI reduction in PCOS women from 6.8% before the pandemic to 3.7% during COVID-19 lockdown.\n\n\n\n- No evidence for an increased risk of COVID-19 infection increased risk of COVID-19 infection, hospitalization or mortality in women with PCOS, acne vulgaris ar hirsutism.\n\n- Management with common medications (spironolactone, estradiol, metformin) was not associated with COVID-19 infection risk\n\nPCOS: Polycystic ovary syndrome, SCARFs: coronavirus-associated receptors and factors\n\nThe collected data from the included studies was qualitatively synthesized. No quantitative evaluations were performed due to heterogeneity of the data. In the qualitative synthesis, summarizing was done. Next, the dangers of COVID-19 on PCOS were examined in relation to baseline parameters (age, gender, body mass index (BMI), presenting symptoms, signs and complications).\n\n\nResults\n\nWe retrieved 361 records from our search, 200 duplicates were removed, and the remaining 66 titles and abstracts were screened. Then, 29 potential full texts were assessed, and 11 studies were included in this review.18–28 The flow of studies is illustrated in Figure 1.\n\nAll included studies are observational studies with a total of 22,155 PCOS patients, from four countries (United Kingdom, India, Slovenia, and Turkey). A retrospective cohort study discussed the susceptibility of COVID-19 in PCOS patients.27 A total of four papers discussed the biomarkers that were elevated in both PCOS and COVID-19.21–24 A retrospective cohort study discussed both biomarkers and COVID-19 susceptibility.25 A cross sectional study discussed the expression of the SARS-Co-V-2 receptors on the ovarian granulosa cells.26 In total, four papers, two cohorts20,28 and two cross sectionals,18,19 discussed the psychological aspect such as depression and anxiety. Despite the heterogeneity of the included studies, they all tend to agree upon the predisposition of PCOS patients to a more severe form of COVID-19 infection.\n\nThe overall quality of the included studies was high (9.25 ±1.75). The characteristics and details of the papers included in the systematic review are summarized in Table 2.\n\nThe effect of PCOS on the course of COVID-19 infection is reported in only two clinical studies only; Subramanian et al.26 conducted a retrospective cohort study on 21,292 PCOS patients in the UK, compared to their age-matched 78,310 women without PCOS, to assess the risk of COVID-19 infection in PCOS patient. The study revealed a 51% higher risk of COVID-19 infection in women with PCOS compared to controls (HR =1.51). However, the hazard ratio was reduced to 1.36 after adjustment for BMI, and it was further reduced to 1.28 in the fully adjusted model.27\n\nContrary to these observations, Yale et al. conducted a study on 1590 PCOS women who tested positive for COVID-19 infection and concluded no evidence for an increased risk of COVID-19 infection, hospitalization, or mortality in women with PCOS compared to controls.29\n\nThe COVID-19 quarantine had both positive and negative consequences on the mental health of PCOS patients. Atkinson et al. conducted a cross sectional study on 12 PCOS patients in the UK and found that the lockdown caused a detrimental impact on PCOS women’s weight reduction in a variety of ways, including the inability to use exercise facilities such as gyms, pools, and classes, as well as decreased physical activity, which was reported as a major concern of PCOS patients.18 A cohort study conducted by Sustarsic et al., also reported that women achieved a 6.8% weight loss before the lockdown, which was decreased to 3.7% during the lockdown.28 Furthermore, another cohort study on 333 PCOS patients in the UK conducted by Kite et al. discovered increased levels of sleep disruption and insomnia, which correlates with findings of higher levels of stress and despair in these patients during the lockdown.20\n\nOn the other hand, some patients reported positive impact during the quarantine as it breaks the work routine allowing these individuals to adopt new exercise and eating habits, as described by Atkinson et al.18\n\nMoin et al. conducted a series of studies investigating the levels of the inflammatory markers and proteins that are characteristically altered in COVID-19 disease in both PCOS and non-PCOS patients.21–25 PCOS patients demonstrated an overactivation of the renin-angiotensin-aldosterone system (RAAS) and elevated levels of RAAS-associated proteins. These include renin, angiotensin, and vascular endothelial growth factor (VEGF), together with reduced Angiotensin-converting enzyme 2 (ACE-2) levels, which may lead to more complications and severe outcomes of infection. Furthermore, a study suggests there may be a possible increased susceptibility of COVID-19 in PCOS patients due to decreased serum levels of soluble neuropilin-1 (sNRP1), elevated levels of membrane bound neuropilin-1 and RAAS hyperactivity.25 A total of 21 out of 60 serum biomarkers of platelet degranulation and coagulation cascade markers and acute phase response proteins were altered in PCOS women when compared to the control group.23 A similar study reported that 12 out of 34 protein biomarkers contained within the platelet degranulation and coagulation cascades had different levels between PCOS women and controls.22\n\nNaigaonkar et al. found a lower expression of SARS-CoV-2 receptors; Angiotensin converting enzyme 2 (ACE-2), Basigin (BSG), C-type lectin domain family four member M (CLEC4M) and Dipeptidyl peptidase 4 (DPP4), in the ovarian granulosa cells of PCOS patients.26 In addition, similar or higher expressions of the following proteases: Transmembrane protease serine 2 (TMPRSS2), Furin, Cathepsin B (CTSB), and Cathepsin L (CTSL) was found. The ACE-2 receptor was downregulated in the granulosa cells of PCOS women compared to the control group. The BSG receptor was downregulated in the cells but had a higher expression in the granulosa cells of PCOS women. Additionally, Furin was downregulated in the oocytes and upregulated in the granulosa cells of PCOS women. CTSB was elevated in both the oocytes and granulosa cells of women with PCOS. TMPRSS2 receptor was not expressed in the ovarian granulosa cells.26\n\nThe relationship between vitamin D and macrophage-derived cytokines was revealed in a study by Moin,21 who discovered that PCOS patients had lower vitamin D levels than controls, which is related with noticeably greater levels of baseline macrophage activation markers, such as chemokine CXC ligand 5 (CXCL5), CD163, and matrix metalloproteinase-9 (MMP9), in addition to lower levels of the protective CD200, CD80, and IL12. These findings correlated negatively with the BMI, as when the data was adjusted for BMI, none of these indicators were substantially different between the two groups, implying that the vitamin-D associated rise in inflammatory markers may be accounted for by elevated BMI.\n\nThis systematic review shows the relationship between polycystic ovarian syndrome PCOS and COVID-19 infection, complications, and severity. This paper found that BMI was the most important risk factor for COVID-19 susceptibility in PCOS women as it had the highest impact on the hazard ratio of COVID-19 infection in these patients.27 Furthermore, vitamin D deficiency in these women was linked with increased levels of macrophage derived inflammatory markers.21\n\nIn addition, the study revealed an association between PCOS and COVID-19 in terms of higher serum levels of characteristic biomarkers common between the two.22,23 Moreover, the study found that PCOS patients suffer from hyperactivity of the RAAS system, which is associated with reduced levels of both sNRP1 and ACE2 in their serum,23,24 consequently resulting in an increased susceptibility to COVID-19 infection as well as a more severe form of the disease.\n\nThe findings of Naigaonkar et al. stated that the ovarian granulosa cells had decreased expression of SARS-CoV-2 receptors.26 The majority of findings concerning the impact of the COVID-19 pandemic on the lifestyle and mental health of women with PCOS indicated adverse effects as well.\n\nThis systematic review aims to report the relationship between polycystic ovarian syndrome PCOS and COVID-19 infection, complications, and severity. Our search yielded 11 papers investigating the relationship between COVID-19 infection and PCOS. All included papers were observational studies that describe the overlapping risk factors for both diseases.\n\nStarting by susceptibility of PCOS patients to COVID-19 disease, we found that PCOS patients are more prone to COVID-19 infection. A relationship which is attributed to many factors reported by Subramanian et al., who found that BMI had the highest impact on the hazard ratio of severe COVID-19 in PCOS patients.27 This could be explained by the fact that high BMI levels are associated with increased insulin level, which has been shown to stimulate ovarian androgen production.30 Additionally, BMI is associated with overexpression of ACE-2 in adipocytes, chronic systemic inflammation, and overactivation of the immune system.31 However, it is noteworthy to mention that Kyrou et al. reported that hyperandrogenism was the main risk factor that could render PCOS patients prone to COVID-19 infection as it increased the ACE-2 expression which could increase the COVID-19 entry into the cell.6\n\nHyperandrogenism is a common disorder in PCOS patients, and it has been linked to increased severity of SARS-CoV-2 infection. Evidence from literature supports the fact that hyperandrogenism favors COVID-19 infection by causing upregulation of its receptors, increasing the viral entry into host’s cells.32 One of these receptors is the TMPRSS2 enzyme, which interacts with the viral spike protein facilitating its entry to the pneumocytes. This receptor is controlled by testosterone levels in blood. Another enzyme that is upregulated by the high androgen levels is ACE-2, which acts as a key mediator for the viral entry to the cells.6,31 After the viral entry, degradation of ACE-2 by SARS-CoV-2 takes place, strengthening the positive feedback loop of inflammation, and enhancing the acute inflammation observed in severe COVID-19.33 On a different note, the findings of Naigaonkar’s study25 were of importance. The ovarian granulosa cells had decreased expression of SARS-CoV-2 receptors, which could operate as a protective factor against COVID-19 infection to PCOS women’s ovaries. These findings are supported in literature by several studies.34,35\n\nThe development of an inflammatory cytokine storm causing multisystem failure, and possibly death, is one of the main complications of COVID-19 illness.36 PCOS has been linked to higher serum levels of biomarkers and proteins such as platelet degranulation, vascular injury, and acute phase response proteins, all of which are common in both conditions and can introduce patients to a chronic inflammatory state.6 Vitamin D deficiency was reported in nearly 75% of women with PCOS which is connected to increased underlying inflammation and a higher probability of catastrophic COVID-19 outcomes.37,38 This could be explained by vitamin D’s role in modulating and regulating cytokine release during inflammation and reducing the severity of infection.39\n\nThese inflammatory and biochemical interactions between PCOS and COVID-19 are of great importance. Novel research suggests a multifactorial relationship between menstrual cycle and COVID-19, especially when considering the systemic hormonal effect of both the hypothalamic-pituitary axis, and the ovarian-endometrial axis. Of these effects, the anti-inflammatory effect of ovarian progesterone is of interest. In normal settings, an inflammatory state such as COVID-19 infection would alter the effect of progesterone on the endometrial shedding resulting in decreased menstrual volume and a prolonged cycle.40,41 However, these symptoms can cause confusion in the setting of PCOS for two main reasons: The first is that these symptoms resemble those of PCOS, which might suggest that COVID-19 predisposes to a PCOS-like state, the second is that PCOS patients, being subjected to endometrial progesterone resistance, are at risk of more severe effects of COVID-19 induced inflammation.32 These findings are of significant importance, but further research is yet to be conducted to confirm and understand these associations between menstrual or ovulatory disorders (such as PCOS) and COVID-19.\n\nThrombotic events were one of the major complications linked to COVID-19 illness. According to literature, they are linked to specific risk factors such as endothelial injury, obesity, inflammation, complement activation, microvascular damage, and inflammatory mediators.42,43 Many of these markers have been found to be higher in PCOS patients, potentially increasing the risk of thrombotic events if COVID-19 infection develops.23,27\n\nSeveral treatment modalities exist for PCOS, and in the setting of COVID-19, these modalities can alter the course of COVID-19 or be altered by it. One of the commonly administered drugs for COVID-19 patients is Metformin, which helps regulate insulin resistance and moderate BMI and androgen excess.44 Fortunately, Metformin could help reduce COVID-19 severity in patients, due to its anti-viral and anti-inflammatory effects, as shown in a study conducted by Chan et al.45 An interesting study by Jerzak and Szafarowska investigated personalized therapy protocols for pregnant PCOS patients positive for COVID-19.46 Due to the complexity of cases, individualized modalities have been applied, with main components of anti-coagulants as Aspirin and Low Molecular Weight Heparin (LMWH), anti-inflammatory drugs as N-acetylcysteine (NAC), and Metformin. The overall outcome was promising, with little to no symptoms of infection, allowing for preservation of health.46 This points towards the possibility of protecting vulnerable PCOS patients from severe COVID-19 consequences using simple yet effective treatment regimes.\n\nIn terms of mental health and lifestyle, the negative effect of COVID-19 pandemic on PCOS patients was the most prevalent. Studies reported that the overall impact of the COVID-19 pandemic on lifestyle and mental health of the PCOS patients was negative, with the exception of better sleep quality.47 In contrast to the previous finding, evidence from cohort research conducted by Kite et al. revealed that restricting measures used during the COVID-19 pandemic had a negative impact on sleep quality, with an increased amount of daytime sleeplessness in PCOS patients.20 Furthermore, depression is one of the main hazards that threaten PCOS patients, as reported by Wang et al.48 Wang et al. found that women with PCOS had a high prevalence of anxiety and depression. Depression and anxiety levels were elevated during the COVID-19 pandemic as found by a systematic review conducted by Deng et al.49 Deng and his team had gathered information on 5153 COVID-19 patients and found that 45% of COVID-19 patients experienced depression and 47% experienced anxiety. Despite similar conclusions, depression and anxiety levels measurements were dependent on population surveys that can be subjective and may lack standard measurement rules. Another important finding in the present review shows that the COVID-19 pandemic disrupted weight-loss programs, potentially escalating the risks and complications of obesity, as well as increasing BMI, which is the main reason for the increase in severity of COVID-19 complications in PCOS patients, as stated previously. Similarly, weight gain has been reported in numerous investigations on people of various ages and occupations as a global complication of the COVID-19 pandemic lockdown.50–52\n\nThe overall COVID-19 complications that are exaggerated in PCOS patients, render these patients vulnerable to true risks, and shed the light on the importance of giving these patients a treatment priority, with more medical attention, thorough management and close follow up when they develop COVID-19. An illustration of the factors intertwining between COVID-19 and PCOS is provided in Figure 2.\n\nThe key strength of this review is the ability to cumulatively assess the interaction between PCOS and COVID-19 at both the clinical and molecular levels and evaluate their impact on the severity of the COVID-19. In addition, this review handled both psychological and pathophysiological aspects of the PCOS disease impact on the COVID-19 course, complications and outcomes. Nevertheless, the findings of this review were subject to some limitations, as all included papers were observational studies, risking higher bias and confounding. Moreover, the heterogeneity in diagnosis, measurement of the outcome, and lacking data about mortality and hospitalization emphasize the need for more in-depth investigation to clarify the significance of each contributing factor to this association. Further focused analysis of PCOS patients in the scope of COVID-19 infection is needed to ensure the assessment of all relevant aspects of this risky interaction.\n\n\nConclusion\n\nThe current study’s major purpose was to determine if women with PCOS need special medical management and care if they become infected with COVID-19. One of the more important findings of this study is that PCOS patients should be closely monitored and receive a higher level of medical attention and management if they are infected with COVID-19 because they are prone to more severe infection and complications due to many overlapping and contributing factors. However, more research is needed to study the relationship between the factors that may make PCOS patients more susceptible to serious infections, with a focus on PCOS cohort individuals to assess the COVID-19 disease course. Also, more studies are needed to assess the impact of early and higher medical intervention on the course of COVID-19 when infecting PCOS patients.\n\n\nAuthor’s contribution\n\n\n\n- Warda A. Alrubasy: Conceptualization, Data Curation, Formal Analysis, Methodology, Supervision, Writing – Original Draft Preparation, Writing – Review & Editing\n\n- Shams Khalid Sameer: Conceptualization, Data Curation, Formal Analysis, Methodology, Supervision, Visualization, Writing – Original Draft Preparation, Writing – Review & Editing\n\n- Mohammad J. J. Taha: Conceptualization, Data Curation, Formal Analysis, Methodology, Supervision, Visualization, Writing – Original Draft Preparation, Writing – Review & Editing\n\n- Mohammad T. Abuawwad: Conceptualization, Data Curation, Formal Analysis, Methodology, Supervision, Visualization, Writing – Original Draft Preparation, Writing – Review & Editing\n\n- Abdalla Abu-Zeinh: Conceptualization, Data Curation, Methodology, Writing – Original Draft Preparation, Writing – Review & Editing\n\n- Marwa Mahmood: Conceptualization, Data Curation, Methodology, Writing – Original Draft Preparation, Writing – Review & Editing\n\n- Hebatullah Humeidan: Conceptualization, Data Curation, Methodology, Writing – Original Draft Preparation, Writing – Review & Editing\n\n- Ahmad J. Taha: Data Curation, Writing – Original Draft Preparation, Writing – Review & Editing\n\n- Abdulqadir Nashwan: Visualization, Writing – Original Draft Preparation, Writing – Review & Editing\n\nAll authors have read and agreed to the published version of the manuscript.", "appendix": "Data availability\n\nNo data are associated with this article.\n\nFigshare: PRISMA checklist for ‘COVID-19 and the Need for Special Care for Women with Polycystic Ovary Syndrome: A Systematic Review’. https://doi.org/10.6084/m9.figshare.24660270. 53\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgments\n\nThe authors would like to thank Dr. Nadine Alaa Sherif for her guidance and support.\n\n\nReferences\n\nWHO: WHO Director-General’s opening remarks at the media briefing on COVID-19-11 March 2020.2020.\n\nParasher A: COVID-19: Current understanding of its Pathophysiology, Clinical presentation and Treatment. Postgrad. Med. 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PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nEyupoglu ND, Aksun S, Ozturk M, et al.: Impact of social isolation during COVID-19 pandemic on health behaviors and weight management in women with polycystic ovary syndrome. Eat. Weight Disord. 2022; 27(7): 2407–2413. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKite C, Atkinson L, McGregor G, et al.: Sleep Disruption and Depression, Stress and Anxiety Levels in Women With Polycystic Ovary Syndrome (PCOS) During the Lockdown Measures for COVID-19 in the UK. Front. Glob. Womens Health. 2021; 2: 649104. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMoin ASM, Sathyapalan T, Butler AE, et al.: Vitamin D Association With Macrophage-Derived Cytokines in Polycystic Ovary Syndrome: An Enhanced Risk of COVID-19 Infection? Front. Endocrinol (Lausanne). 2021; 12: 638621. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMoin ASM, Nandakumar M, Sathyapalan T, et al.: Biomarkers of COVID-19 severity may not serve patients with polycystic ovary syndrome. J. Transl. Med. 2021; 19(1): 63. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMoin ASM, Sathyapalan T, Atkin SL, et al.: COVID-19 biomarkers for severity mapped to polycystic ovary syndrome. J. Transl. Med. 2020; 18(1): 490. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMoin ASM, Sathyapalan T, Atkin SL, et al.: Renin-Angiotensin System overactivation in polycystic ovary syndrome, a risk for SARS-CoV-2 infection? Metabol. Open. 2020; 7: 100052. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMoin ASM, Sathyapalan T, Atkin SL, et al.: The relationship of soluble neuropilin-1 to severe COVID-19 risk factors in polycystic ovary syndrome. Metabol. Open. 2021; 9: 100079. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNaigaonkar A, Patil K, Joseph S, et al.: Ovarian granulosa cells from women with PCOS express low levels of SARS-CoV-2 receptors and co-factors. Arch. Gynecol. Obstet. 2022; 306(2): 547–555. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSubramanian A, Anand A, Adderley NJ, et al.: Increased COVID-19 infections in women with polycystic ovary syndrome: a population-based study. Eur. J. Endocrinol. 2021; 184(5): 637–645. PubMed Abstract \| Publisher Full Text\n\nŠuštaršič A, Vrtačnik Bokal E, Burnik Papler T: The Impact of COVID-19 Lockdown on Weight Loss Program in Infertile Polycystic Ovary Syndrome Women with Obesity. Obes. Facts. 2021; 14(6): 650–657. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYale K, Elsanadi R, Ghigi A, et al.: Androgens and women: COVID-19 outcomes in women with acne vulgaris, polycystic ovarian syndrome, and hirsutism.2021; 60(7): e267.\n\nBarber TM, Franks S: Obesity and polycystic ovary syndrome. Clin. Endocrinol. 2021; 95(4): 531–541. Publisher Full Text\n\nde Medeiros SF , Yamamoto MMW, de Medeiros MAS , et al.: Polycystic ovary syndrome and risks for COVID-19 infection: A comprehensive review. Rev. Endocr. Metab. Disord. 2022; 23: 251–264. Publisher Full Text\n\nMoradi F, Enjezab B, Ghadiri-Anari A: The role of androgens in COVID-19. Diabetes Metab. Syndr. 2020; 14(6): 2003–2006. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBastolla U, Chambers P, Abia D, et al.: Is Covid-19 severity associated with ACE2 degradation?2022; 1: 789710.\n\nBlauschmidt S, Greither T, Lampe K, et al.: Dipeptidyl peptidase 4 serum activity and concentration are increased in women with polycystic ovary syndrome. Clin. Endocrinol. 2017; 87(6): 741–747. Publisher Full Text\n\nGao Q, Zhang W, Li T, et al.: Interrelationship between 2019-nCov receptor DPP4 and diabetes mellitus targets based on protein interaction network. Sci. Rep. 2022; 146(1): 1–11. Publisher Full Text\n\nZanza C, Romenskaya T, Manetti AC, et al.: Cytokine storm in COVID-19: immunopathogenesis and therapy. Medicina. 2022; 58(2): 144. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nIslam MB, Chowdhury UN, Nashiry MA, et al.: Severity of COVID-19 patients with coexistence of asthma and vitamin D deficiency. Inform. Med. Unlocked. 2022; 34: 101116. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLin MW, Wu MH: The role of vitamin D in polycystic ovary syndrome. Indian J. Med. Res. 2015; 142(3): 238–240. PubMed Abstract \| Publisher Full Text\n\nHayakawa K, Wang X, Lo EH: CD200 increases alternatively activated macrophages through cAMP-response element binding protein–C/EBP-beta signaling. J. Neurochem. 2016; 136(5): 900–906. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLebar V, Laganà AS, Chiantera V, et al.: The Effect of COVID-19 on the Menstrual Cycle: A Systematic Review. J. Clin. Med. 2022; 11(13). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDellino M, Vimercati A, D’Amato A, et al.: \"GONE WITH THE WIND\": The Transitory Effects of COVID-19 on the Gynecological System. J. Pers. Med. 2023; 13(2). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTaha MJ, Abuawwad MT, Alrubasy WA, et al.: Ocular manifestations of recent viral pandemics: A literature review.2022; 9.\n\nPage EM, Ariëns RA: Mechanisms of thrombosis and cardiovascular complications in COVID-19. Thromb. Res. 2021; 200: 1–8. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFruzzetti F, Perini D, Russo M, et al.: Comparison of two insulin sensitizers, metformin and myo-inositol, in women with polycystic ovary syndrome (PCOS). Gynecol. Endocrinol. 2017; 33(1): 39–42. PubMed Abstract \| Publisher Full Text\n\nChan LE, Casiraghi E, Laraway B, et al.: Metformin is associated with reduced COVID-19 severity in patients with prediabetes. Diabetes Res. Clin. Pract. 2022; 194: 110157. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJerzak M, Szafarowska M: Preliminary Results for Personalized Therapy in Pregnant Women with Polycystic Ovary Syndrome During the COVID-19 Pandemic. Arch. Immunol. Ther. Exp (Warsz). 2022; 70(1): 13. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKocevska D, Blanken TF, Van Someren EJ, et al.: Sleep quality during the COVID-19 pandemic: not one size fits all. Sleep Med. 2020; 76: 86–88. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWang Y, Ni Z, Li K: The prevalence of anxiety and depression of different severity in women with polycystic ovary syndrome: a meta-analysis. Gynecol. Endocrinol. 2021; 37(12): 1072–1078. Publisher Full Text\n\nDeng J, Zhou F, Hou W, et al.: The prevalence of depression, anxiety, and sleep disturbances in COVID-19 patients: a meta-analysis. Ann. N. Y. Acad. Sci. 2021; 1486(1): 90–111. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAghili SMM, Ebrahimpur M, Arjmand B, et al.: Obesity in COVID-19 era, implications for mechanisms, comorbidities, and prognosis: a review and meta-analysis. Int. J. Obes. 2021; 45(5): 998–1016. Publisher Full Text\n\nChang T-H, Chen Y-C, Chen W-Y, et al.: Weight gain associated with COVID-19 lockdown in children and adolescents: A systematic review and meta-analysis. Nutrients. 2021; 13(10): 3668. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLa Fauci G, Montalti M, Di Valerio Z, et al.: Obesity and COVID-19 in children and adolescents: reciprocal detrimental influence—systematic literature review and meta-analysis. Int. J. Environ. Res. Public Health. 2022; 19(13): 7603. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAbuawwad M: PRISMA 2020 checklist. Figshare. 2023. Publisher Full Text" }	[ { "id": "283179", "date": "06 Jun 2024", "name": "Ioannis Ilias", "expertise": [ "Reviewer Expertise Clinical Endocrinology" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 aimed to investigate the association between COVID-19 and Polycystic Ovary Syndrome (PCOS) and determine if women with PCOS had a higher susceptibility and risk for COVID-19 complications. A total of 11 observational studies were identified, with 22,155 PCOS patients. The findings suggested that PCOS patients had a higher risk of COVID-19 infection than non-PCOS women. Factors such as overactivation of the renin-angiotensin system, decreased serum levels of neuropilin-1, elevated serum biomarkers, and lower levels of vitamin D could contribute to a chronic inflammatory state in PCOS patients, leading to difficulties and severe consequences when affected by COVID-19. Additionally, the COVID-19 pandemic had negatively impacted the psychological well-being of PCOS patients, with an increase in depression and anxiety. The authors concluded that PCOS patients may have required more medical attention when infected with COVID-19.\nTwo main concerns [1]. The objective in the abstract is different from the objective in the article's main text [2]. The authors state that they used an NIH tool to assess the quality of the papers which were scrutinized. However, the reference that they quote is not relevant to this tool.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? No\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? Yes\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes\n\nIf this is a Living Systematic Review, is the ‘living’ method appropriate and is the search schedule clearly defined and justified? (‘Living Systematic Review’ or a variation of this term should be included in the title.) Not applicable", "responses": [ { "c_id": "11732", "date": "12 Jun 2024", "name": "Abdulqadir Nashwan", "role": "Author Response", "response": "Dear reviewer, Both objectives in the abstract and text aim for the same points: associations between PCOS and COVID-19 infection and the higher liability of COVID-19 complications in PCOS patients. However, they are written in different ways. In abstract: The study investigates the association between coronavirus disease 2019 (COVID-19) and polycystic ovary syndrome (PCOS) and assesses whether women with PCOS are at a higher susceptibility and risk for COVID-19 complications. In the text: This study aims to summarize the findings of relevant studies investigating the association between COVID-19 and PCOS to highlight the possible risk factors that may render PCOS patients more liable for morbidity and mortality in cases of COVID-19 infection. We will replace the citation with “Study Quality Assessment Tools.” National Heart Lung and Blood Institute, U.S. Department of Health and Human Services, www.nhlbi.nih.gov/health-topics/study-quality-assessment-tools. Accessed 7 June 2024. Both are from the same website, but this one is for the whole website." } ] } ]	1	https://f1000research.com/articles/13-3
https://f1000research.com/articles/12-1263/v1	04 Oct 23	{ "type": "Case Report", "title": "Case Report: Masseter hypertrophy: A case and review", "authors": [ "Prasanna R. Sonar", "Aarati S. Panchbhai", "Aarati S. Panchbhai" ], "abstract": "Masseter muscle hypertrophy is a rare condition with no known etiology that has become more prevalent due to growing aesthetic concerns. It is distinguished by either unilaterally or bilaterally enlarged masseter muscles. Its origin is still unknown. This study discusses a clinically confirmed case of unilateral masseter muscle hypertrophy and provides an outline of the condition's etiology, prevalence, diagnosis, and course of treatment.", "keywords": [ "computed tomography", "magnetic resonance imaging", "masseter muscle hypertrophy" ], "content": "Introduction\n\nAnatomically, the masseter muscle is a robust, two-layered quadrate muscle. It originates from the inferior and deep surface of the zygomatic arch and mostly enters into the inferior lateral side of the mandibular ramus.1 Unilateral or bilateral masseter muscle expansion is known as masseter hypertrophy. It may be asymptomatic or frequently accompanied by discomfort, which can occasionally be mistaken for parotid gland swelling.2–4 For the functional, aesthetic, and differential diagnosis of head and neck pathology, it is an uncommon condition with an unknown cause. However, the most common reason patients with masseteric hypertrophy seek treatment is because of their facial appearance.5 The case report's objectives are to outline the signs and symptoms of idiopathic masseter hypertrophy, offer a differential diagnosis, and recommend a course of action.\n\n\nCase report\n\nA 19-year-old male visited the dental hospital's oral medicine department. Due to unilateral facial swelling, the patient complained of an unattractive appearance (Figure 1). The patient explained that the enlargement, which had been asymptomatic until now, had gradually increased since birth. Additionally, he had never before experienced trouble opening his mouth or temporomandibular symptoms. There was no family history of any such swelling, no history of face injuries, dental anomalies, or clicking in the temporo-mandibular joint.\n\nA soft to firm unilateral tissue mass was discovered during a clinical examination over the left body, close to the mandibular angle, which became prominent when the patient clenched their jaws (Figure 2). When the left masseter was palpated, the inferior portion of the muscle showed increased size. The masseter on the left side was broader than on the right side. Due to the increase in muscle size and stress, there was compensatory hypertrophy at the insertion of muscle. Bone spur growth and the prominence of the mandibular angle were felt (Figure 2).\n\nThe jaws moved normally as they opened and closed. During the occlusion, there was no midline deviation seen. Both an intra-oral and extra-oral examination revealed no abnormalities or possible etiological factors. There was no indication of a para-functional habit.\n\nAn orthopantomogram (OPG) was performed to look for any pathology (Figure 3). Compared to the right side, the antagonial notch on the OPG scans was slightly more pronounced. Other anomalies were not found in OPG.\n\nWhen we informed the patient about the masseter hypertrophy in this case, the patient declined further therapy. As a result, there was no treatment given in this asymptomatic patient.\n\n\nDiscussion\n\nAsian Americans are more likely to be involved.6,7 Without regard to gender, the second and third decades of life have the highest incidence rates. In their analysis of 108 instances, Baek et al. showed that the average patient age was 30 years old, 60% of them had bilateral involvement, and 57% of them were men.7\n\nAccording to some authors, the word “hypertrophy” may be deceptive because it refers to an increase in fiber count rather than cell size.8\n\nThe cause of the majority of instances is unknown, despite the fact that numerous potential culprits, including malocclusion, bruxism, clenching, and abnormalities of the temporo-mandibular joint, have been proposed.4,8\n\nIn addition to being crucial for proper mastication, the masseter muscle is also crucial for facial aesthetics. Asymptomatic chronic expansion of one or both masseter muscles, known as masseteric hypertrophy, is typically the main complaint in cases of this condition.\n\nThe mandibular angle's bone spurs are frequently present observations. Bloem and Hoof asserted that this finding cannot be used as a diagnostic tool because 20% of healthy individuals have it. According to Guggenheim and Cohen,9 bone spurs are brought on by periostal irritation and new bone formation in response to the muscles bundles' elevated pressures.\n\nIt is important to correctly diagnose idiopathic masseter muscle hypertrophy because it can be mistaken for other conditions. Among these are masseter tumor, salivary gland disease, parotid tumor, parotid inflammatory disease, and intrinsic masseter muscle myopathy (caused by hypotrophy or hypoplasia on the contralateral side).10-12\n\nA sialography is necessary to rule out this option since the correct diagnosis is more challenging in unilateral cases and necessitates a differential diagnosis with parotid gland abnormalities.13,14\n\nClinical examination, medical history, imaging modalities' findings, and muscle palpation can all be used to diagnose masseter hypertrophy. Visual inspection and palpation revealed a consistent muscle mass in masseteric hypertrophy, and the patient's forced bite could be felt to compress the muscle. Other benign and malignant neoplasms, on the other hand, are characterized by irregular and nodular development. The size and position of bucco-masseteric masses can be determined by sonography, computed tomography (CT), and magnetic resonance imaging (MRI).5 For the examination of hyperostosis at the point of muscle attachment in benign masseteric hypertrophy, CT scanning is essential.5 The panoramic radiograph is the most feasible diagnostic to support the clinical diagnosis when the physical examination points to masseteric hypertrophy.5 Ultrasonography of the region confirmed the uniform increased muscle mass with characteristics of normal musculature without any cystic, nodular or irregular foci.5\n\nThe use of CT is a well-established technique for delivering a wealth of details about nearby buildings and notable landmarks. Due to its high-quality imaging of bone structures and direct bone imaging, which is not achievable with MRI since cortical bone produces no detectable signal, CT scanning is essential in cases with masseter muscle hypertrophy with bone flaring. However, in this case report, the hypertrophied area and the border between the medial and lateral pterygoid could not be limited by CT. However, because muscle structural signals from the damaged side of the body are stronger than those from the unaffected side, MRI made it easier to diagnose the condition.9\n\nThere have been several reported treatments for masseter hypertrophy, ranging from non-invasive medical procedures to invasive surgical procedures. Some examples of conservative treatment include occlusal correction, relaxation therapy, botulinum therapy, spasmolytics, tranquilizers, and antidepressant therapy. Compared to surgical treatments, conservative techniques have both benefits and drawbacks.15,16 Despite being an intrusive treatment, surgical therapy is nevertheless favored for more dependable and long-lasting results. Masseteric enlargement typically doesn't require treatment. Reassurance, tranquilizers or muscle relaxants, psychiatric care, and injection of extremely modest dosages of botulinum toxin type A are examples of non-surgical therapeutic techniques.17 To fix malocclusions and premature contacts, dental restorations and occlusal modifications are crucial. Habits that are dysfunctional must be avoided. Patients may choose to have cosmetic surgery in this situation to lessen the prominence of the mandibular angle bone.18\n\nA benign ailment called masseter muscle hypertrophy normally doesn't require surgery.\n\nDue to improper diagnosis in these circumstances, needless biopsies, exploratory surgeries, and even radiotherapy for parotid tumors may be performed. To rule out other disorders, conventional radiography examinations, CT scans, and MRI scans are useful.19\n\n\nConclusion\n\nMasseter hypertrophy can have a substantial impact on the aesthetics and functionality of the face, changing the jaw's appearance and function. To choose the best course of treatment, it is crucial to precisely evaluate the underlying problem.\n\nWritten informed consent for publication of their clinical details and clinical images was obtained from the patient.", "appendix": "Data availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\nZenodo: CARE checklist for ‘Case Report: Masseter hypertrophy: A case and review’. https://doi.org/10.5281/zenodo.8307408.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nRoncevic R: Masseter muscle hypertrophy. J. Maxillofac. Surg. 1986; 14: 344–348. Publisher Full Text\n\nNishida M, Iizuka T: Intrac oral removal of the enlarged mandibular angle associated with masseteric hypertrophy. J. Oral Maxillofac. Surg. 1995; 53: 1476–1479. PubMed Abstract \| Publisher Full Text\n\nNewtom JP, Cowpe JG, Mc Clure IJ: Masseteric hypertrophy preliminary report. Br. J. Oral Maxillofac. Surg. 1999; 37: 405–408. PubMed Abstract \| Publisher Full Text\n\nBaş B, Özan B, Muğlali M, et al.: Treatment of masseteric hypertrophy with botulinum toxin: a report of two cases. Med. Oral Patol. Oral Cir. Bucal. 2010; 15(4): e649–e652. PubMed Abstract \| Publisher Full Text\n\nMittal HC: Management of Acquired Bilateral Masseteric Hypertrophy-A Case Report. Journal of Oral Health & Community Dentistry. 2015 Apr 1; 9(2): 92–95. Publisher Full Text\n\nWhitaker LA, Kim SS, Bindiger A: Prominent mandibular angle: preoperative management, operative technique and results in 42 patients (Discussion). Plast. Reconstr. Surg. 1989; 83(2): 272–280.\n\nRispoli DZ, Camargo PM, Pires JL Jr, et al.: Benign masseter muscle hypertrophy. Rev. Bras. Otorrinolaringol. 2008; 74(5): 790–793. Publisher Full Text\n\nAddante RR: Masseter muscle hypertrophy: report of case and literature review. J. Oral Maxillofac. Surg. 1994; 52(11): 1199–1202. PubMed Abstract \| Publisher Full Text\n\nSannomya EK, Gonçalves M, Cavalcanti MP: Masseter muscle hypertrophy: case report. Braz. Dent. J. 2006; 17: 347–350. Publisher Full Text\n\nCruz RL, Nunes MM, Radwanski HN: Hipertrofia idiopática do masseter: considerações terapêuticas e revisão de literatura. Rev. Bras. Cir. 1994; 84(1): 35–43.\n\nTeixeira VC, Mejia JES, Estefano A: Tratamento cirúrgico da hipertrofia benigna do masseter por abordagem intra-oral. Rev. Bras. Cir. 1996; 86(4): 165–170.\n\nBlack MJ, Schloss MD: Masseteric muscle hypertrophy. J. Otolaryngol. 1985; 14(3): 203–205.\n\nSchellas KP: MR imaging of muscles of mastication. Am. J. Roentgenol. 1989; 153: 847–855. Publisher Full Text\n\nDa Silva K, Mandel L: Bilateral temporalis muscle hypertrophy: a case report.2006; 102: 1–3.\n\nShetty N, Malaviya RK, Gupta MK: Management of unilateral masseter hypertrophy and hypertrophic Scar- a case report. Case Rep. Dent. 2012; 2012: 1–5. Publisher Full Text\n\nPeretta R, Melison M, Meneghello R, et al.: Unilateral masseter muscle hypertrophy: morphofunctional analysis of relapse after treatment with botulinum toxin. Cranio. 2009; 27(3): 200–210. PubMed Abstract \| Publisher Full Text\n\nAl-Ahmad HT, Al-Qudah MA: The treatment of masseter hypertrophy with botulinum toxin type A. Saudi Med. J. 2006; 27: 397–400.\n\nWaldhart E, Lynch JB: Benign hypertrophy of the masseter muscles and mandibular angles. Arch. Surg. 1971; 152: 115.\n\nTrujillo JR, Fontão FNG, Kiatake SSMG: Unilateral masseter muscle hypertrophy. Quintessence Int. 2002; 33: 776–779. PubMed Abstract" }	[ { "id": "246352", "date": "24 Feb 2024", "name": "Nabeel Ayappali Kalluvalappil", "expertise": [ "Reviewer Expertise Oral Medicine", "Maxillofacial Radiology", "Dental Radiology", "Head and Neck Ultrasonography", "CBCT", "Forensic Odontology", "Red and White Oral lesions", "Intentional Replantation", "Modern technologies in Dentistry", "Lasers", "Implants", "Oral cancer", "Precancerous lesions and conditions" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nSummary: The article provides a detailed examination of unilateral masseter muscle hypertrophy, presenting a case report of a 19-year-old male with unilateral facial swelling attributed to this condition. The patient's history, clinical examination findings, diagnostic tests, treatment options, and outcomes are thoroughly discussed. Additionally, the article offers insights into the prevalence, etiology, differential diagnosis, and management of masseter muscle hypertrophy, contributing to the understanding and treatment of this rare condition.\nSuggestions: 1. To facilitate better understanding for the readers, it would be helpful to present the imaging findings more clearly.\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": "11497", "date": "30 May 2024", "name": "Prasanna Sonar", "role": "Author Response", "response": "Respected Sir/ Maam, Photos of imaging modalities are not available. Kindly consider. thankyou." } ] }, { "id": "265347", "date": "16 May 2024", "name": "Vini Mehta", "expertise": [ "Reviewer Expertise Public health" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nPlease elaborate the introduction and discussion.\n\nRemove sub headings from the discussion.\n\nIs a review of the literature included with your case?\n\nThe references used in the case report are very old. Kindly update the references and ensure that 70% of the references are used from last 5 years.\n\nIs the background of the case’s history and progression described in sufficient detail? No\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Yes\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? No\n\nIs the case presented with sufficient detail to be useful for other practitioners? No", "responses": [] } ]	1	https://f1000research.com/articles/12-1263
https://f1000research.com/articles/12-234/v1	02 Mar 23	{ "type": "Research Article", "title": "The open field assay is influenced by room temperature and by drugs that affect core body temperature", "authors": [ "Jessica A. Jimenez", "Eric S. McCoy", "David F. Lee", "Mark J. Zylka", "Jessica A. Jimenez", "Eric S. McCoy", "David F. Lee" ], "abstract": "Background: The open field assay is used to study anxiety-related traits and anxiolytic drugs in rodents. This assay entails measuring locomotor activity and time spent in the center of a chamber that is maintained at ambient room temperature. However, the ambient temperature in most laboratories varies daily and seasonally and can differ between buildings. We sought to evaluate how varying ambient temperature and core body temperature (CBT) affected open field locomotor activity and center time of male wild-type (WT, C57BL/6) and Transient Receptor Potential Subfamily M Member 8 (Trpm8) knock-out (Trpm8-/-) mice. TRPM8 is an ion channel that detects cool temperatures and is activated by icilin. Methods: Mice were placed in the open field at 4°C and 23°C for 30 minutes. Distance traveled and time spent in the center were measured. Mice were injected with icilin, M8-B, diazepam, or saline, and changes in activity level were recorded. Results: The cooling agent icilin increased CBT and profoundly reduced distance traveled and center time of WT mice relative to controls. Likewise, cooling the ambient temperature to 4°C reduced distance traveled and center time of WT mice relative to Trpm8-/- mice. Conversely, the TRPM8 antagonist (M8-B) reduced CBT and increased distance traveled and center time of WT mice when tested at 4°C. The TRPM8 antagonist (M8-B) had no effect on CBT or open field behavior of Trpm8-/- mice. The anxiolytic diazepam reduced CBT in WT and Trpm8-/- mice. When tested at 4°C, diazepam increased distance traveled and center time in WT mice but did not alter open field behavior of Trpm8-/- mice. Conclusions: Environmental temperature and drugs that affect CBT can influence locomotor behavior and center time in the open field assay, highlighting temperature (ambient and core) as sources of environmental and physiologic variability in this commonly used behavioral assay.", "keywords": [ "open field assay", "Trpm8", "Temperature" ], "content": "Introduction\n\nDrugs used to treat neurological and neuropsychiatric disorders are typically evaluated in rodent models for safety and efficacy prior to use in humans.1 Characterizing animal models of neuropsychiatric disorders often relies on behavioral traits such as motor function, social interactions, anxiety-like and depressive-like behavior, substance dependence, and various forms of cognitive function.2 Due to the complexity of most behavior tests, researchers must carefully consider the sources of variability introduced by experimenters, testing environments, and intraspecies differences.\n\nRodent physiology and behavior are influenced by environmental temperature.3,4 For example, an innocuous cold stimulation at 15°C altered sleeping, rearing, climbing, and eating behavior in wild-type (WT) mice.5 This cold stimulation did not alter these behaviors in mutant mice lacking the Transient Receptor Potential Subfamily M Member 8 (TRPM8) cation channel, which is a receptor for menthol and icilin (mint-derived and synthetic cooling compounds, respectively) and plays an important role in thermosensation.5,6 Additionally, mice deficient in uncoupling protein 1 (UCP-1), a key metabolic regulator highly expressed in brown adipose tissue, were reported to display selective enhancement of anxiety-related behavior exclusively under thermogenic conditions (23°C), but not at thermoneutrality (29°C).7\n\nEnvironmental temperature sensation and perception is also influenced by core body temperature (CBT). Alterations to CBT can be a consequence of physiological changes associated with disease state, exercise, metabolic function, and hormonal changes. Further, numerous drugs can affect body temperature including barbiturates, cyclic antidepressants, hypoglycemic agents, opioids, antihistamines, and anticholinergic drugs.8–11 It is currently unclear if drugs such as these, which are used to treat neurological and neuropsychiatric disorders, affect CBT directly or indirectly, and if the behavioral tasks that are commonly used to study these drugs are influenced by changes in CBT.\n\nHere we sought to evaluate how ambient temperature and changes in CBT influence locomotor activity and center time in the open field assay—an assay that is commonly used to study anxiolytic drugs and animal models of anxiety. In addition to using WT mice, we also used Trpm8-/- mice, which lack the primary receptor for cool temperature sensation in mammals, as well as drugs that activate (icilin) or antagonize (M8-B) this receptor. Diazepam was also evaluated as a model anxiolytic drug. By precisely controlling environmental temperature and TRPM8 activity (genetically and pharmacologically), we found that commonly used measures associated with the open field assay are profoundly sensitive to ambient temperature and CBT. To enhance rigor and reproducibility, we recommend that ambient and core temperature be precisely controlled when performing the open field assay. Moreover, drugs that increase activity and center time in the open field test may do so via thermoregulatory mechanisms, independent of effects on anxiety.\n\n\nMethods\n\nAnimal protocols in this study were approved by the Institutional Animal Care and Use Committee at the University of North Carolina at Chapel Hill and were performed in accordance with these guidelines and regulations at the University of North Carolina at Chapel Hill (NIH/PHS Animal Welfare Assurance Number D16-00256 A3410-01, expiration April 30, 2025; USDA Animal Research Facility Registration Number 55-R-0004; AAALAC Institutional Number #329, re-accreditation November 2020). All data presented in this study are from mice obtained from crossing Trpm8+/- male with Trpm8+/- female mice. Trpm8 mutant mice were obtained from Jackson Laboratories (B6.129P2-Trpm8tm1Jul/J; stock #008198). Mice were raised in a facility with a 12 h:12 h light:dark cycle with ad libitum access to food (Teklad 2020X, Envigo, Huntingdon, UK) and water. All mice were tested at 8-12 weeks of age. Mice were excluded if they showed signs of distress or lethargy. Genomic DNA was isolated from tail clips using Proteinase K. Genotyping was performed by polymerase chain reaction (PCR) amplification of genomic DNA with primers: WT Forward 5′-CCT TGG CTG CTG GAT TCA CAC AGC-3′, Mutant Reverse 5′-CAG GCT GAG CGA TGA AAT GCT GAT CTG-3′, WT Reverse 5′-GCT TGC TGG CCC CCA AGG CT-3′. Premade buffers along with the platinum Taq were used for amplification (Invitrogen) to amplify DNA in a BioRad DNA Engine (PTC-200). Nucleotides were obtained from Qiagen. Amplification cycle was as follows: 94°C for 3 min, 36 cycles of 94°C for 30 s, 68°C for 60 s and 72°C for 60 s. A final incubation was performed at 72°C for 2 min.\n\nDrugs or control (saline or DMSO) were administered intraperitoneally (i.p.). Icilin (I9532-50MG, Sigma) was dissolved in DMSO and administered at 50 mg/kg body weight (bw). Diazepam (RXDIAZEP5-10, Shop Med Vet) was diluted in saline to 1 mg/mL administered at 2 mg/kg bw. M8-B hydrochloride (SML0893-25MG, Sigma) was dissolved in DMSO to 6 mg/ml and administered at 12 mg/kg bw.\n\nCBT was assessed using a Digi-Sense Thermocouple Meter (Fisher 13-245-293). Mice were acclimated to the procedure 2x each day for one week prior to testing. Temperature was measured 30, 60 and 90 minutes post drug administration for diazepam and M8-B. To assess the effects of icilin on CBT, measures were taken every 15 minutes.\n\nExploratory activity in a novel environment was assessed by a 1 h trial in an open-field chamber (45 cm × 45 cm × 40 cm) 30 minutes post icilin or diazepam administration, and 1 h following M8-B administration. The total distance moved by each mouse in the open arena, and time spent in the center region of the open-field, were recorded by camera (Sony) connected to the EthoVision software (Noldus Wageningen). Testing was performed at room temperature (23°C) or in the cold room (4°C).\n\nData were graphed using GraphPad Prism (v9.5.0) and analyzed with a paired t-test approach. All studies were randomized, double blind, and vehicle-controlled consisting of 6-14 mice. All animals were group housed.\n\nAn earlier version of this article can be found on bioRxiv (doi: https://doi.org/10.1101/2022.10.17.512128).\n\n\nResults\n\nWe found that the ambient temperature varied throughout the day (data not shown, can be found as Underlying data14), week, and season in a room that we previously used for behavioral studies (Figure 1A-C, Building 1).14 Temperature fluctuations are presumably common in laboratory settings because building heating, ventilation, and air conditioning are set to maximize human comfort during the work day and minimize energy use during off-peak hours, like evenings and on weekends. Moreover, room temperature was over 4°C warmer in the winter months and 2°C warmer in the summer months in a different laboratory located in a different building (Building 2; Figure 1B and C). Temperature differences over days, seasons, and buildings represent a major source of variability, especially for behavioral experiments that are carried out at “room temperature” and that could be influenced by temperature. To address this source of uncontrolled variability, we worked with the university to custom engineer the heating, ventilation, and air conditioning within our behavioral room so that the temperature could be precisely maintained at a set temperature (we chose 23°C) without fluctuations over the course of the day and seasons (Figure 1B and C). This temperature-controlled room, and a cold room set at 4°C, were used for all subsequent behavioral studies.\n\n(A) The average temperature in a semi-temperature controlled room for each month of one year (n=11-14). Temperature during the (B) winter and (C) summer measured every 20 minutes for one week within lab space, located in two different buildings and in a room that was specifically engineered to maintain temperature with minimal fluctuations over hours, days, weeks, and years (n=3-4). Temperature monitored with a La Crosse Technologies weather station.\n\nTRPM8 is a principal sensor of cold temperatures in mammalian primary sensory neurons.12,13 To explore the impact of TRPM8 stimulation on open field behavior, we administered (i.p.) 50 mg/kg bw icilin, a TRPM8 agonist, or DMSO control to WT mice. Icilin led to a significant increase in CBT beginning at 90 minutes post injection (Figure 2A). To assess the impact of increased CBT on open field behavior, we administered 50 mg/kg bw icilin, waited 10 minutes, and then measured distance traveled and time spent in the center (Figure 2B and C). Icilin administration significantly reduced activity in the open field, suggesting that an increase in CBT led to a reduction in open field behavior.\n\n(A) CBT was measured every 15 minutes following 50 mg/kg bw i.p. administration of icilin (n=14) or vehicle (n=11). (B) Distance traveled and (C) time spend in the center in the open field at 23°C was measured 10 minutes post-icilin administration for one hour. Data represent means ± SEM. CBT, core body temperature; WT, wild-type; bw, body weight; i.p., intraperitoneally.\n\nStimulation of TRPM8 channels with icilin impacts the behavior of WT mice in the open field (Figure 2). Thus, we hypothesized that cold stimulation of TRPM8 channels would similarly impact open field behavior and that mice lacking TRPM8 channels would resist the effect of cold stimulation on open field behavior. We found that WT and Trpm8-/- mice display similar distance traveled and time spent in the center when tested at 23°C (Figure 3A and B). When mice were tested at 4°C, an effect of genotype was revealed, in which the WT mice display reduced distance traveled and center time compared to Trpm8-/- mice (Figure 3C and D).\n\n(A) Distance traveled and (B) center time were assessed in WT and Trpm8-/- mice at room temperature (23°C). (C-D) Open field behavior was reassessed in the cold room, at 4°C. Data represent means ± SEM. n=8-15 mice. WT, wild-type; Trpm8, Transient Receptor Potential Subfamily M Member 8.\n\nWe next used a TRPM8 antagonist (M8-B) to block cold-induced stimulation of TRPM8 channels in WT mice. Administration (i.p.) of M8-B at 12 mg/kg bw decreased the CBT of WT but not Trpm8-/- mice at >1 h post injection at room temperature (Figure 4A). Thus, mice were placed in the open field chamber 1 h following M8-B administration. We found that TRPM8 antagonist administration partially recovered the reduction in open field behavior at 4°C in WT mice (Figure 4B and C, Figure 5A and B). These data suggest that environmental temperature sensation influences open field behavior in mice.\n\nEffect of 12 mg/kg bw M8-B on WT (n=8) and Trpm8-/- mice (n=8) CBT. (A) Total distance traveled and (B) center time at 4°C 1 h following 12 mg/kg bw M8-B administration. Data represent means ± SEM. n=8-10 mice. Trpm8, Transient Receptor Potential Subfamily M Member 8; WT, wild-type; bw, body weight; CBT, core body temperature.\n\n(A) Distance traveled and (B) center time in WT mice. (C) Distance traveled and (D) center time in Trpm8-/- mice. Data represent means ± SEM. n=6-8 mice. WT, wild-type; Trpm8, Transient Receptor Potential Subfamily M Member 8. Data in this figure are also shown in Figures 4B and 4C and 6B and 6C.\n\nBenzodiazepines, such as diazepam, are commonly prescribed to reduce anxiety in humans. Diazepam functions to increase gamma-aminobutyric acid (GABA) in the brain and is used to treat anxiety. To investigate whether the anxiolytic effect of diazepam was associated with a reduction in CBT in mice, WT and Trpm8-/- mice were administered 2 mg/kg bw of the drug at room temperature. Diazepam exposure led to a reduction in CBT at 30–90 minutes post injection (Figure 6A). This reduction in CBT was associated with a near-significant increase in distance traveled and center time displayed by WT but not Trpm8-/- mice, when tested at 4°C (Figure 6B and C, Figure 5).\n\n(A) CBT measured at 30, 60 and 90 minutes post 2 mg/kg bw diazepam in WT (n=8) and Trpm8-/- mice (n=8). (B) Total distance traveled and (C) time spent in center at 4°C, 30 minutes post 2 mg/kg bw diazepam administration. Data represent means ± SEM. N=8-10 mice. CBT, core body temperature; bw, body weight; WT, wild-type; Trpm8, Transient Receptor Potential Subfamily M Member 8.\n\n\nDiscussion\n\nIn this study we compared the behavioral effects of the anxiolytic drug diazepam, with the effects of other drugs that alter cool temperature sensation and CBT, including icilin and M8-B in WT and Trpm8-/- mice. We observed CBT and open field behavioral effects of icilin and M8-B in WT mice, but not Trpm8-/- mice.\n\nThe effect of drugs on core body temperature may be mediated by acting on any component of the thermoregulatory system. These components include heat production, heat conservation, and thermosensing-related pathways within the nervous system that coordinate thermoregulation.8 Clark et al.,8 present a thorough study of drug-induced changes in body temperature and provide a source of information on interactions between certain drugs and the thermoregulatory system. The data present an extensive review of the magnitude of body temperature changes induced by psychoactive compounds while taking into account the species, administration route, dose, and environmental temperature differences. Considering the effects of drug-induced changes on body temperature and the impact of CBT on behavior, studies using rodent models of psychological disorders should consider potential alterations to the perception of environmental temperatures.\n\nThe spontaneous behavior of animal models is often used to evaluate the efficacy of drugs used to treat neuropsychiatric disorders. One main concern with animal models is the lack of standardization between laboratories, which can lead to results that are not reproducible. We suggest that stricter testing protocols include assessment of room temperature and control for drug-induced alterations to CBT.\n\nBy providing greater understanding of the relationship between body temperature and behavior in mice, our data highlight the importance of assessing CBT, environmental temperature, and drug-induced changes to thermoregulation. Thus, consideration of ambient and CBT is a straightforward approach to enhance rigor and reproducibility in studies of neuropsychiatric disorders.", "appendix": "Data availability\n\nFigshare: The open field assay is influenced by room temperature and by drugs that affect core body temperature. https://doi.org/10.6084/m9.figshare.21954539. 14\n\nThis project contains the following underlying data:\n\n- csv. files containing the data for each individual graph represented in the paper. Each file has been named according to the experiment performed.\n\n- Completed ARRIVE checklist\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nKumar V, Bhat ZA, Kumar D: Animal models of anxiety: a comprehensive review. J. Pharmacol. Toxicol. Methods. 2013; 68(2): 175–183. Publisher Full Text\n\nHånell A, Marklund N: Structured evaluation of rodent behavioral tests used in drug discovery research. Front. Behav. Neurosci. 2014; 8: 252.\n\nHankenson FC, Marx JO, Gordon CJ, et al.: Effects of Rodent Thermoregulation on Animal Models in the Research Environment. Comp. Med. 2018; 68(6): 425–438. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nŠkop V, Xiao C, Liu N, et al.: The effects of housing density on mouse thermal physiology depend on sex and ambient temperature. Mol. Metab. 2021; 53: 101332. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKasuga R, Shiraki C, Horikawa R, et al.: Role of TRPM8 in cold avoidance behaviors and brain activation during innocuous and nocuous cold stimuli. Physiol. Behav. 2022; 248: 113729. PubMed Abstract \| Publisher Full Text\n\nReimúndez A, Fernández-Peña C, García G, et al.: Deletion of the Cold Thermoreceptor TRPM8 Increases Heat Loss and Food Intake Leading to Reduced Body Temperature and Obesity in Mice. J. Neurosci. 2018; 38(15): 3643–3656. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSideromenos S, Gundacker A, Nikou M, et al.: Uncoupling Protein-1 Modulates Anxiety-Like Behavior in a Temperature-Dependent Manner. J. Neurosci. 2022; 42(40): 7659–7672. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nClark WG: Changes in body temperature after administration of amino acids, peptides, dopamine, neuroleptics and related agents. Neurosci. Biobehav. Rev. 1979; 3(4): 179–231. PubMed Abstract \| Publisher Full Text\n\nDavid DJP, Nic Dhonnchadha BÁ, Jolliet P, et al.: Are there gender differences in the temperature profile of mice after acute antidepressant administration and exposure to two animal models of depression? Behav. Brain Res. 2001; 119(2): 203–211. PubMed Abstract \| Publisher Full Text\n\nBelknap JK, Mitchell MA: Barbiturate physical dependence in mice: effects on body temperature regulation. J. Pharmacol. Exp. Ther. 1981; 218(3): 647–652. PubMed Abstract\n\nRosow CE, Miller JM, Pelikan EW, et al.: Opiates and thermoregulation in mice. I. Agonists. J. Pharmacol. Exp. Ther. 1980; 213(2): 273–283. PubMed Abstract\n\nDhaka A, Murray AN, Mathur J, et al.: TRPM8 is required for cold sensation in mice. Neuron. 2007; 54(3): 371–378. Publisher Full Text\n\nMcKemy DD, Neuhausser WM, Julius D: Identification of a cold receptor reveals a general role for TRP channels in thermosensation. Nature. 2002; 416(6876): 52–58. Publisher Full Text\n\nMcCoy E, Jiménez JA, Lee DF, et al.: The open field assay is influenced by room temperature and by drugs that affect core body temperature. [Dataset]. figshare. 2023. Publisher Full Text" }	[ { "id": "165350", "date": "13 Oct 2023", "name": "Fiona Hollis", "expertise": [ "Reviewer Expertise Behavioral neuroscience" ], "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 have examined Open Field behavior in different temperatures to better understand the effects of temperature fluctuations on behavior. This is an important topic that should be better explored. Here, the experiments, as described, do not appear rigorous enough to support the conclusions. Moreover, the discussion does not situate the manuscript within the wider context of the literature, nor discuss the limitations or alternative interpretations of these experiments. Main concerns are detailed below:\nThe authors show temperature variations that are within 2-4C between seasons/rooms/buildings. However, experiments were conducted at vastly different temperatures (4C and 23C) and the conclusion drawn that “it is important to consider temperature fluctuations”. The authors do not show such wild temperature fluctuations in Figure 1, so what is the rationale for examining behavior at 4C – a temperature that nearly every laboratory building will not be near (except cold rooms)? A more logical experiment (particularly in light of the authors’ temperature-controlled environment) would be to measure behavior at the differing temperatures that they observe across seasons or buildings. This would better reflect the variation in the literature between universities and provide insight into conflicting data. If there was no effect of those temperatures on behavior, then it could be concluded that fluctuations within 2-4C do not affect this particular behavior.\nCan the authors please discuss the rationale for their drug doses. The diazepam dose in particular has been found to be anxiogenic and potentially sedative in mice1.\nPeripheral DMSO injections can be toxic to mice above 10%. The methods suggest that drugs were dissolved in pure DMSO and then injected i.p. Can the authors please verify that the DMSO levels were not at toxic or noxious levels? Peripheral DMSO has been shown to be painful and if drugs are administered in pure DMSO, then behavioral interpretations may be limited.\nOpen Field behavior is highly influenced by lighting conditions. The authors should indicate the lighting conditions of the test in lux.\nIn Figure 3, the authors compare the effects of temperature on open field, but present the data in separate graphs. Are the same animals tested at both temperatures? If so, the data should be analyzed by repeated measures ANOVA and the temperature considered as an additional factor to genotype. This will allow the authors to make the claim of more or less effects of cold temperature on OF behavior.\nIn Figure 4, are these the same groups of animals as in Figure 3? The authors should specify whether each experiment used naïve animals or those from previous experiments. The authors injected a TRPM8 antagonist but do not include vehicle-injected groups. As this drug is diluted in DMSO, this group is necessary. Moreover, the authors are making comparisons to non-injected animals in Figure 3. Statistically and experimentally, that is inappropriate unless Figure 3 animals were injected with vehicle (in which case, this needs to be properly stated and the statistics performed on all groups).\nFigure 5, saline is used as the vehicle for diazepam, but again, there is no vehicle for M8-B (which the authors state is diluted in DMSO). This is inappropriate as DMSO injections evoke different reactions than saline injections. The results state that the reduction in CBT was associated with a near-significant increase in OF behavior in WT but not mutant mice, however, there are no correlations shown between behavior and temperature (did behavior change across time as CBT decreased?). Moreover, in this case, the OF was performed 30min after Diazepam administration for 1h, per the methods. Was CBT measured during the OF then? How did the authors confirm that behavior was not disrupted by this measurement? Was CBT measured at a separate time point from behavior? In which case, were the animals naïve or repeatedly injected? Finally, diazepam appears to have no effect on behavior at 4C – the authors should verify that their dose is working well at 23C to ensure that there are no confounding sedative or anxiogenic effects.\nThe discussion is incredibly brief and does not do anything to discuss potential limitations, explanations, or situate the manuscript within the literature. There is mention of a single review. There are other publications that discuss the pitfalls of temperature fluctuations that should be included here. The authors need to also consider the literature of Trpm8’s function and role.\nMinor: Figure 4 figure legend is mislabeled.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? No\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [ { "c_id": "10622", "date": "07 Dec 2023", "name": "Mark Zylka", "role": "Author Response", "response": "The authors have examined Open Field behavior in different temperatures to better understand the effects of temperature fluctuations on behavior. This is an important topic that should be better explored. Here, the experiments, as described, do not appear rigorous enough to support the conclusions. Moreover, the discussion does not situate the manuscript within the wider context of the literature, nor discuss the limitations or alternative interpretations of these experiments. Main concerns are detailed below: The authors show temperature variations that are within 2-4C between seasons/rooms/buildings. However, experiments were conducted at vastly different temperatures (4C and 23C) and the conclusion drawn that “it is important to consider temperature fluctuations”. The authors do not show such wild temperature fluctuations in Figure 1, so what is the rationale for examining behavior at 4C – a temperature that nearly every laboratory building will not be near (except cold rooms)? A more logical experiment (particularly in light of the authors’ temperature-controlled environment) would be to measure behavior at the differing temperatures that they observe across seasons or buildings. This would better reflect the variation in the literature between universities and provide insight into conflicting data. If there was no effect of those temperatures on behavior, then it could be concluded that fluctuations within 2-4C do not affect this particular behavior. >While the testing environments used in this study (23C and 4C) represent a wider temperature range than is observed between laboratories, this proof of principle study demonstrates that temperature can have an influence on behavior. More importantly, in this study we demonstrate that the body temperature changes induced following drug administration could lead to similar physiological responses induced by normal room temperature fluctuations. We have included in the discussion this limitation in interpretation. Can the authors please discuss the rationale for their drug doses. The diazepam dose in particular has been found to be anxiogenic and potentially sedative in mice1. >The drug doses were chosen based on those commonly used in the literature to study open field behavior. While we cannot eliminate the influence the drugs have on the entire body, the end goal was to make an association between behavior and body temperature. This limitation has been included in the discussion. Peripheral DMSO injections can be toxic to mice above 10%. The methods suggest that drugs were dissolved in pure DMSO and then injected i.p. Can the authors please verify that the DMSO levels were not at toxic or noxious levels? Peripheral DMSO has been shown to be painful and if drugs are administered in pure DMSO, then behavioral interpretations may be limited. >DMSO did not exceed 2mL/kg. Studies show that mice can tolerate 10mL/kg. This limitation has been included in the discussion. (Gad SC, Cassidy CD, Aubert N, Spainhour B, Robbe H. Nonclinical Vehicle Use in Studies by Multiple Routes in Multiple Species. International Journal of Toxicology. 2006;25(6):499-521.) Open Field behavior is highly influenced by lighting conditions. The authors should indicate the lighting conditions of the test in lux. >The lighting conditions in the room temperature and cold room studies were measured at 660 lux and 400 lux, respectively. This measurement has been added to the methods section. In Figure 3, the authors compare the effects of temperature on open field, but present the data in separate graphs. Are the same animals tested at both temperatures? If so, the data should be analyzed by repeated measures ANOVA and the temperature considered as an additional factor to genotype. This will allow the authors to make the claim of more or less effects of cold temperature on OF behavior. >Yes the same animals were tested in both temperatures. The data has been analyzed using a mixed effects analysis with multiple comparisons, Sidak. Figure 3 has been updated. In Figure 4, are these the same groups of animals as in Figure 3? The authors should specify whether each experiment used naïve animals or those from previous experiments. The authors injected a TRPM8 antagonist but do not include vehicle-injected groups. As this drug is diluted in DMSO, this group is necessary. Moreover, the authors are making comparisons to non-injected animals in Figure 3. Statistically and experimentally, that is inappropriate unless Figure 3 animals were injected with vehicle (in which case, this needs to be properly stated and the statistics performed on all groups). >Yes, the same animals are used throughout the study except for Figure 2. The tests were conducted with a 1 week recovery period in between. This statement is included in the methods. The vehicle saline injected group is included in figure 5 for comparison. Comparison was not made to DMSO injected mice. This limitation is included in the discussion. Figure 5, saline is used as the vehicle for diazepam, but again, there is no vehicle for M8-B (which the authors state is diluted in DMSO). This is inappropriate as DMSO injections evoke different reactions than saline injections. The results state that the reduction in CBT was associated with a near-significant increase in OF behavior in WT but not mutant mice, however, there are no correlations shown between behavior and temperature (did behavior change across time as CBT decreased?). Moreover, in this case, the OF was performed 30min after Diazepam administration for 1h, per the methods. Was CBT measured during the OF then? How did the authors confirm that behavior was not disrupted by this measurement? Was CBT measured at a separate time point from behavior? In which case, were the animals naïve or repeatedly injected? Finally, diazepam appears to have no effect on behavior at 4C – the authors should verify that their dose is working well at 23C to ensure that there are no confounding sedative or anxiogenic effects. >The rectal temperatures were not measured during the same time as the open field tests. The temperature and behavior tests were conducted one week apart. DMSO injected mice were not included in the study. This limitation has been included in the discussion. The discussion is incredibly brief and does not do anything to discuss potential limitations, explanations, or situate the manuscript within the literature. There is mention of a single review. There are other publications that discuss the pitfalls of temperature fluctuations that should be included here. The authors need to also consider the literature of Trpm8’s function and role. Minor: Figure 4 figure legend is mislabeled." }, { "c_id": "11021", "date": "13 Apr 2024", "name": "Mark Zylka", "role": "Author Response", "response": "We addressed minor comments regarding interpretation of results and limitations in the Discussion section." } ] } ]	1	https://f1000research.com/articles/12-234
https://f1000research.com/articles/13-737/v1	03 Jul 24	{ "type": "Research Article", "title": "The impact of death priming on climate change denial: a preliminary investigation", "authors": [ "Zach Gerber", "David Anaki", "David Anaki" ], "abstract": "Background Climate change denial (CCD) has been found to be more pronounced among individuals with a conservative political orientation. Terror Management Theory posits that an individual’s worldview serves as a primary defense mechanism in coping with existential threats, such as the reality of climate change. Drawing on these premises, we conducted preliminary research investigating the impact of death priming on CCD from the Terror management theory perspective.\n\nMethods and results We administered a death priming task and measured CCD in its immediate wake or following a delay task. We confirmed among 219 Amazon’s MTurk participants that immediately following death priming, CCD was reduced among all participants. In the delayed death priming condition, we acquired preliminary evidence that CCD was heightened among Republican participants.\n\nConclusions These findings demonstrate the relevance of death priming to CCD tendencies and potentially spawn future research regarding CCD as a particular form of coping with existential threats.", "keywords": [ "Climate Change Denial", "Terror Management Theory", "Political Orientation." ], "content": "Method\n\nThe study was approved by the Bar Ilan University Psychology Department ethics committee on November 7th, 2022 (approval number 31\\2022). For this preregistered study (https://osf.io/7ny2g), we recruited 219 participants on Amazon’s MTurk (129 men, M age = 42.52 years, SD = 10.60). Participation was restricted to United States residents who defined their political inclination as either Democrat or Republican (for additional details regarding demographics, see Table 1). To eliminate unreliable data, we removed from the data set entries with 50% and above of missing values. Other flags for eliminating data included clear response set patterns as well as unreasonably short durations of survey completion. While this process may have resulted in the removal of some genuine participants, we erred on the side of caution given the importance of data quality. Considering the sample size and an estimated effect size of 0.25, we had the power of 0.76 as determined by an a priori power analysis (GPower; Faul et al., 2007, https://www.psychologie.hhu.de/arbeitsgruppen/allgemeine-psychologie-und-arbeitspsychologie/gpower).\n\n p<.05.\n\n** p<.01.\n\nMortality salience. We used a 15-item true/false questionnaire to prime thoughts of death (Templer, 1970). This approach has been utilized successfully in a previous TMT studie conducted via the Amazon’s MTurk (Boyd et al., 2020). Participants were randomly assigned to answer questions about dying (e.g., “I am very much afraid to die”) or parallel questions about experiencing pain (e.g., “I am very much afraid of being in pain”), which served as the control. As in other research, merely responding to the questions related to death (in contrast to pain) constitutes the mortality salience prime. Therefore, responses to the prompts were not examined.\n\nClimate change denial (CCD). We measured climate change denial with an established 16-item scale (Häkkinen & Akrami, 2014). The scale captures mainly the denial of climate change’s seriousness and the denial of human involvement (e.g., “Warming of the Earth’s climate is natural and does not depend on human influence”). Responses are on a 6-point scale (1 = do not agree to 6 = agree). After reversing the scale of five items, a total score was computed by averaging the 16 items, with higher scores reflecting higher CCD. In the current sample, Cronbach’s α was 0.85.\n\nAfter signing the consent form participants completed the priming task. Then they filled the CCD scale immediately after the prime task or after a five-minute delay task consisting of a word puzzle. Following the CCD, participants filled out a demographic questionnaire, probing their age, gender, political orientation and activeness (self-report from zero to seven), education, employment, and income. Overall, the session lasted between 5 and 10 minutes, depending on whether participants completed the delay task. All research conditions were administered and randomized with the Qualtrics software platform (Qualtrics XM: The Leading Experience Management Software).\n\n\nResults\n\nWe conducted a three-way ANOVA with prime type (mortality or pain), delay task (with or without) and political orientation (Democrat or Republican) as factors. CCD score was the independent measure.\n\nResults indicated a main effect regarding political orientation, F (1,211) = 41.45, p = 0. 000, η2 = 0.16; as documented in previous CCD research, in the current sample CCD was significantly higher among Republican participants (M = 3.70; 95% CI [3.53, 3.86], SD = 0.93) in contrast to Democrat participants (M = 2.89; 95% CI [2.70, 3.07], SD = 0.95).\n\nA significant two-way interaction between the prime type and the delay task was also found; F (1,211) = 4.95, p = 0. 027, η2 = 0.02. According to our hypotheses, we conducted follow-up analysis for each task condition (with or without a delay task corresponding to distal and proximal defenses, respectively). These analyses indicated that the interaction source was from the no delay group, F (1, 107) = 4.64, p = 0.033, η2 = 0.04). CCD scores in the death condition were lower (M = 3.37; 95% CI [3.16, 3.57], SD = 0.71) than in the pain condition (M = 3.69; 95% CI [3.47, 3.90], SD = 0.85), indicating a reduction in CCD due to death priming in the proximal defense condition.\n\nThe three-way interaction was insignificant (p = 0.359). However, as can be seen in Figure 1, following the death prime in the distal condition Republican participants displayed a distinct CCD increase in accordance with our hypothesis. Therefore, we conducted among Republican participants an additional two-way ANOVA with prime type and the delay task as independent variables and CCD as the dependent variable. Only when adding political activeness (r = -.31 with CCD, see Table 1) as a covariate did this analysis achieve significance. F (1,109) = 9.20, p = 0. 003, η2 = 0.08. In the proximal group, the prime effect, although similar to the overall proximal effect reported above, did not achieve significance; F (1, 62) = 2.42, p = 0.125). However, the distal effect was significant; F (1, 46) = 5.99, p = 0.018, η2 = 0.115). CCD scores in the death condition were higher (M = 4.01; 95% CI [3.62, 4.41], SD = 0.68) than in the pain condition (M = 3.41; 95% CI [3.08, 3.73], SD = 1.08), indicating an increase in CCD due to death priming within the distal defense mode among Republican participants.\n\nFigure 1 alt text: Among republican participants while in the proximal condition death priming reduced CCD, in the distal condition it increased it.\n\nNotably, political activeness (PA) was overall higher among Republican participants (M = 3.86, SD = 2.00), in contrast to Democratic participants (M = 3.05, SD = 1.90, t(208) = 2.97, p = 0.003, d = 0.41). In turn, undermining the randomness of participant distribution regarding political orientation (see Table 2 for descriptive statistics regarding CCD and political activeness among Republican participants).\n\n\nDiscussion\n\nThree main findings were observed in the current study. First, as documented in previous research, beyond the prime type and the delay task variables CCD was higher among Republican participants than Democrat participants. Furthermore, in the immediate wake of mortality priming CCD was reduced among all participants (the proximal defense effect). Finally, following death priming and a delay task, CCD increased among Republican participants when controlling for PA (the distal defense effect).\n\nIndeed, the proximal effect suggests that death priming operates as a tool for CCD reduction when existential threat is in focal attention. Accumulating TMT research has underscored that while individuals attentionally avoid existential threat when it is abstract and does not pose an immediate threat, their focal attention gravitates toward it when perceived to pose an immediate threat (Hirschberger et al., 2010; Gerber & Anaki, 2018; Gerber et al., 2023). Applying this dynamic to CCD, as the climate crisis transforms from a futuristic abstract threat into an occurring reality, death priming may be an effective tool for facilitating climate action tendencies accordingly. Notably, the CCD scale used in the current study was a rather abstract perception of climate change, as the nature of self-report scales tends to be. Future research should investigate whether the impact of death priming on CCD is more pronounced when the perception of climate change is based on more concrete stimuli such as visceral images.\n\nFinding a preliminary distal effect among Republicans (only when controlling for PA) sheds an important light on the general tendency for CCD among conservative individuals. Seemingly, this tendency, has been considered primarily to reflect conservative individuals’ benefit from maintaining the economic status quo and existing institutional order (Norgaard, 2019; Clarke et al., 2019). The distal effect finding that the tendency for CCD among Republican participants was facilitated by death priming, supports a differential understanding; Rather than a general anthropocentric attitude of dominance over nature (Jylhä & Akrami, 2015), CCD reflects conservative individuals need to cope with an existential threat, reflected in the ramifications of climate change, to their worldview and way of life. This line of investigation is warranted and should be pursued in future research to affirm mutual recognition and common ground for promoting climate change mitigation and adaptation.\n\nBefore concluding, one must consider the overall limitations of the current study which is preliminary and exploratory in its nature. Notably, this study was conducted among US residents only, reflecting a particular political environment in time and place. Therefore, its convergence with CCD investigations conducted among samples from other world regions is limited. Moreover, although theoretically sound, the distal effect found among Republicans only when controlling for PA should be treated only as a warrant for future, more powered research. Notably, increased PA levels among Republicans in contrast to Democrats may be attributed in part to it’s being measured following mortality salience. Indeed, mortality salience has been shown to arouse PA among conservative individuals as an expression of their distal defenses (Schindler et al. 2023). Finally, PA’s mean differences patterns among Republicans (Table 2) as well as its overall covariance with CCD (Table 1), indicate that PA should be theoretically considered regarding the impact of mortality priming on CCD in future studies. To conclude, the value of the current research is primarily in being conducive to additional research regarding the psychological aspects of CCD. Indeed, the dynamics of coping with existential threats should be an additional perspective in examining CCD tendencies.\n\nThe study was approved by the Bar Ilan University Psychology Department ethics committee on November 7th, 2022 (approval number 31\\2022).\n\nA written and informed consent was obtained from each participant prior to participation.", "appendix": "Data availability\n\nThe research data set is publicly available at the OSF depository (https://osf.io/v9g7s; Gerber, 2024; DOI 10.17605/OSF.IO/V9G7S).\n\nThis project contains following dataset:\n\nOSF _ Climate Change Denial\n\nThis is in accordance with the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication) (http://creativecommons.org/publicdomain/zero/1.0/).\n\nThe research questionnaires and an example of the word puzzle delay task are publicly available at the OSF depository (https://osf.io/v9g7s).\n\nThis is in accordance with the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication) (http://creativecommons.org/publicdomain/zero/1.0/).\n\n\nReferences\n\nBurke BL, Kosloff S, Landau MJ: Death goes to the polls: A meta-analysis of mortality salience effects on political attitudes. Polit. Psychol. 2013; 34: 183–200. Publisher Full Text\n\nBoyd P, Goldenberg JL, Morris KL, et al.: Shutting the door on death: Low openness individuals become less open (to death) following mortality reminders. J. Pers. 2020; 88: 161–173. PubMed Abstract \| Publisher Full Text\n\nClarke EJ, Ling M, Kothe EJ, et al.: Mitigation system threat partially mediates the effects of right-wing ideologies on climate change beliefs. J. Appl. Soc. Psychol. 2019; 49: 349–360. Publisher Full Text\n\nFaul F, Erdfelder E, Lang AG, et al.: G* Power 3: A flexible statistical power analysis program for the social, behavioral, and biomedical sciences. Behav. Res. Methods. 2007; 39: 175–191. PubMed Abstract \| Publisher Full Text\n\nGerber Z: The impact of death priming on climate change denial: a preliminary investigation. [Data Set]. OSF. 2024. Publisher Full Text\n\nGerber Z, Gez L, Anaki D: Self-compassion facilitates responsiveness to existential threat: A brief report. Mental Health Sci. 2023; 1: 157–162. Publisher Full Text\n\nGerber Z: Self-compassion as a tool for sustained and effective climate activism. Integr. Environ. Assess. Manag. 2023; 19: 7–8. PubMed Abstract \| Publisher Full Text\n\nGerber Z, Anaki D: Self-compassion as a buffer against concrete but not abstract threat. Death Stud. 2018.\n\nGreenberg J, Pyszczynski T, Solomon S: The causes and consequences of a need for self-esteem: A terror management theory.Baumeister RF, editor. Public self and private self. Springer; 1986; pp. 189–212. Publisher Full Text\n\nHäkkinen K, Akrami N: Ideology and climate change denial. Personality and Individual Differences, 70, 62-65. J. Pers. 2014; 88: 161–173.\n\nHirschberger G, Ein-Dor T, Caspi A, et al.: Looking away from death: Defensive attention as a form of terror management. J. Exp. Soc. Psychol. 2010; 46: 172–178. Publisher Full Text\n\nJylhä KM, Akrami N: Social dominance orientation and climate change denial: The role of dominance and system justification. Personal. Individ. Differ. 2015; 86: 108–111. Publisher Full Text\n\nJylhä KM, Cantal C, Akrami N, et al.: Denial of anthropogenic climate change: Social dominance orientation helps explain the conservative male effect in Brazil and Sweden. Personal. Individ. Differ. 2016; 98: 184–187. Publisher Full Text\n\nJylhä KM, Stanley SK, Ojala M, et al.: Science denial: A narrative review and recommendations for future research and practice. Eur. Psychol. 2022.\n\nLewis SL, Maslin MA: Defining the Anthropocene. Nature. 2015; 519: 171–180. Publisher Full Text\n\nMoser SC: The work after “It’s too late”(to prevent dangerous climate change). Wiley Interdiscip. Rev. Clim. Chang. 2020; 11: e606. Publisher Full Text\n\nNorgaard KM: Making sense of the spectrum of climate denial. Crit. Policy Stud. 2019; 13: 437–441. Publisher Full Text\n\nPyszczynski T, Solomon S, Greenberg J: Thirty years of terror management theory: From genesis to revelation. Advances in experimental social psychology. Academic Press; 2015; Vol. 52. : pp. 1–70. Publisher Full Text\n\nPyszczynski T, Lockett M, Greenberg J, et al.: Terror management theory and the COVID-19 pandemic. J. Humanist. Psychol. 2021; 61(2): 173–189. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRoutledge C, Arndt J, Goldenberg JL: A time to tan: Proximal and distal effects of mortality salience on sun exposure intentions. Personal. Soc. Psychol. Bull. 2004; 30: 1347–1358. PubMed Abstract \| Publisher Full Text\n\nSmith LK, Ross HC, Shouldice SA, et al.: Mortality management and climate action: A review and reference for using Terror Management Theory methods in interdisciplinary environmental research. Wiley Interdiscip. Rev. Clim. Chang. 2022; 13: e776. Publisher Full Text\n\nSchindler S, Hilgard J, Fritsche I, et al.: Do salient social norms moderate mortality salience effects? A (challenging) meta-analysis of terror management studies. Personal. Soc. Psychol. Rev. 2023; 27: 195–225. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTempler DI: The construction and validation of a death anxiety scale. J. Gen. Psychol. 1970; 82: 165–177. Publisher Full Text\n\nWolfe SE, Tubi A: Terror Management Theory and mortalityawareness: A missing link in climate response studies? Wiley Interdiscip. Rev. Clim. Chang. 2019; 10: e566.\n\nWullenkord MC: From denial of facts to rationalization and avoidance: Ideology, needs, and gender predict the spectrum of climate denial. Personal. Individ. Differ. 2022; 193: 111616. Publisher Full Text" }	[ { "id": "314222", "date": "20 Aug 2024", "name": "Bablu Kumar Dhar", "expertise": [ "Reviewer Expertise Environmental Management" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe manuscript makes a valuable contribution to the understanding of how existential threats influence climate change denial, particularly in relation to political orientation. The study’s design is robust, and the results offer intriguing insights that warrant further investigation. However, as a preliminary study, the conclusions should be viewed as tentative, and the need for additional research is clear. Recommendations for the Authors:\nClarify the Generalizability of Findings: Emphasize the preliminary nature of the findings more explicitly in the conclusion, and discuss the limitations in terms of sample size and generalizability more thoroughly. Expand on the Implications: While the discussion of the results is solid, consider expanding on the broader implications of these findings for climate change communication strategies and political psychology. Consider Additional Analyses: Given the exploratory nature of the study, additional post-hoc analyses or robustness checks could strengthen the conclusions drawn from the data.\n\nThe manuscript is well-executed and provides a strong foundation for future research on the psychological mechanisms underlying climate change denial. With some revisions and further research, the study has the potential to significantly contribute to the field.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] }, { "id": "317847", "date": "11 Sep 2024", "name": "Lauren Keira Marie Smith", "expertise": [ "Reviewer Expertise Interdisciplinary climate communication", "Climate emotions", "Pro-environmental behaviour change" ], "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 tackle an important challenge with facing climate change – that of climate deniers. The existential, life-threatening nature of climate change is explored regarding its influence on worldview reinforcement among climate deniers and those with conservative political orientation. The authors found that CCD decreases as a proximal mortality defense – a very interesting and necessary finding given the unavoidability of threatening climate reminders in today’s world – and our pressing need to act on climate change. For Republican participants, CCD increased in the distal priming and delay. The role of political activeness and its covariance with CCD is another interesting contribution to the literature. This combination of findings is particularly useful for strategizing around how to communicate existentially threatening issues, like climate change, to those least inclined to believe the threat and perhaps most reluctant to act in pro-environmental ways.\nRecommendations: Specify US participants in the abstract. It would also be useful to know if participants were required to have a certain MTurk approval rating (to avoid bots and improve reliability, for example) and, if not, to discuss this dynamic in limitations. Including how these findings may influence or can be useful for climate communicators or those hoping to minimize climate change denial would be a useful, practical inclusion.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] } ]	1	https://f1000research.com/articles/13-737
https://f1000research.com/articles/12-254/v1	09 Mar 23	{ "type": "Research Article", "title": "The effect of Vitamin D levels on the course of COVID-19 in hospitalized patients – a 1-year prospective cohort study", "authors": [ "Darko Siuka", "Rajko Saletinger", "Jure Uršič", "Kristina Jevnikar", "Rado Janša", "David Štubljar", "Joško Osredkar", "Darko Siuka", "Rajko Saletinger", "Jure Uršič", "Kristina Jevnikar", "Rado Janša", "David Štubljar" ], "abstract": "Background: The aim of the current study was to assess the patients with COVID-19 and the impact of vitamin D supplementation on the course of COVID-19. Methods: This prospective cohort study included patients hospitalized due to COVID-19 between December 2020 and December 2021. Patients' demographic, clinical, and laboratory parameters were analysed.\n\nResults: 301 participants were enrolled in the study. 46 (15,3%) had moderate, and 162 (53,8%) had severe COVID-19. 14 (4,7%) patients died, and 30 (10,0%) were admitted to the ICU due to disease worsening. The majority needed oxygen therapy (n=224; 74,4%). Average vitamin 25(OH)D3 levels were below optimal at the admittance, and vitamin D deficiency was detected in 205 individuals. More male patients were suffering from vitamin D deficiency. Patients with the more severe disease showed lower levels of vitamin 25(OH)D3 in their blood. The most severe group of patients had more symptoms that lasted significantly longer with progressing disease severity. This group of patients also suffered from more deaths, ICU admissions, and treatments with dexamethasone, remdesivir, and oxygen. Conclusion: Patients with the severe course of COVID-19 were shown to have increased inflammatory parameters, increased mortality, and higher incidence of vitamin D deficiency. The results suggest that the vitamin D deficiency might represent a significant risk factor for a severe course of COVID-19.", "keywords": [ "vitamin D", "COVID-19", "severity", "supplementation" ], "content": "Introduction\n\nPast pandemic waves of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) led to many critical cases and, consequently, deaths of high-risk patients. However, previous studies have shown fluctuations in coronavirus disease 2019 (COVID-19) severity throughout the year, especially during different seasons. Notably, seasons also play a role in immunity variation demonstrated by significant differences in the circulating immune cells such as lymphocytes and neutrophils.1,2 Moreover, studies have shown a strong correlation between low levels of serum vitamin D3 (25-hydroxyvitamin D3, 25(OH)D3) and the incidence of COVID-19,1,2 which coincides with most viral respiratory infections occurring during the winter season.3 Previous studies have shown a positive correlation between COVID-19 severity and vitamin D deficiency. Furthermore, vitamin D supplementation was shown to improve the clinical outcome of COVID-19 patients.4,5 Vitamin D deficiency is a global health problem as many healthy individuals have suboptimal serum vitamin D levels.1–3 Vitamin D has an immunomodulatory role as it decreases the proliferation of Th1 cells and stimulates the proliferation of Th2 cells, enables the secretion of anti-inflammatory cytokines, and thus lowers the production of pro-inflammatory cytokines.6 In addition to immunomodulatory and anti-inflammatory effects, vitamin D can also reduce the risk of respiratory tract infections, especially viral infections, such as COVID-19.7–17 Several studies confirmed the beneficial role of vitamin D in reducing the risk of susceptibility to acute respiratory infection, a protective effect of vitamin D against viral and bacterial respiratory pathogens in healthy, hospitalized, or critically ill patients.8,18–23 Moreover, a positive correlation was found between low levels of vitamin 25(OH)D3 and worse clinical outcomes (increased hospital stay, readmission to hospital, severity, sepsis, and mortality).22–37 Individuals with lower vitamin 25(OH)D3 levels were shown to have an increased risk of SARS-CoV-2 infection, admission to intensive care unit (ICUs), and increased mortality.38–40\n\nBased on these studies, vitamin D supplementation during the period of respiratory infections and in individuals with COVID-19 was recommended by our group in October 2020, after the first wave of COVID-19. The ad hoc Slovenian recommendations for supplementation were as follows: for the healthy adult population, 800 IE to 2000 IE/day from October to the end of April; for high-risk individuals for vitamin D deficiency and respiratory infections 1000 to 2000 IE/day or 10 000 to 14 000/week. This group included patients with chronic diseases, individuals 70 years of age and older, individuals who live with COVID-19 patients in the same household, individuals with high-risk contact with COVID-19 patients, and healthcare workers. Pregnant women were recommended to take of 1500 IE to 2000 IE/day. Newly diagnosed COVID-19 patients were recommended a loading dose of 14 000 IE/day for four days followed by 2000 IE/day onwards. For hospitalized COVID-19 patients, the measurement of 25(OH)D3 was recommended and supplementation according to the measured serum levels was advised.41\n\nPrior to the publication of Slovenian recommendations, many studies were published, where factors that contributed to low vitamin 25(OH)D3 levels and deficiency, including higher age, positive smoking status, obesity with higher body mass index (BMI), lack of sun exposure, and the presence of chronic illnesses (diabetes, malignancies, high blood pressure, gastrointestinal disorders, etc.) were identified. Most people with these risk factors have been shown to be at an increased risk regarding both severity of the disease and mortality from COVID-19.42 Thus, it was hypothesized that optimal levels of vitamin 25(OH)D3 in the early phase of SARS-CoV-2 infection could prevent progression to severe or critical COVID-19 and reduce mortality.3,43 Besides the recommendations, considerable public awareness campaigns and educational interventions have been conducted with the objective to increase individual vitamin D supplementation in Slovenia, especially during the second COVID-19 lockdown in December 2020.44 Therefore, the purpose of our study was to assess the severity of COVID-19 patients, who were admitted to our department and determine the impact of Vitamin D supplementation at the admittance on the clinical course of COVID-19.\n\n\nMethods\n\nWe designed a prospective cohort study of COVID-19 patients, hospitalised in the COVID-19 unit of the University medical centre Ljubljana between December 2020 and December 2021. The study was approved by the Slovenian Medical Ethics Committee (Protocol ID: 0120-60/2021/5) and adhered to the tenets of the Declaration of Helsinki. Written informed consent was obtained from all participants enrolled in the study.\n\nConsecutive patients aged 18 or older, in the acute phase of COVID-19, with a PCR confirmed SARS-CoV-2 were included in the study, and their clinical charts were prospectively reviewed to collect the following relevant demographic, clinical, and laboratory parameters: age, sex, presence of comorbidities (diabetes, arterial hypertension, hyperlipidemia, coronary artery disease, history of stroke), history of smoking, alcohol consumption, the presence of COVID-19 related symptoms (fever, chest pain, cough, anosmia, dyspnoea, diarrhoea, and headache), time from the symptom’s onset or positive PCR to hospitalisation, laboratory parameters, COVID-19 related treatment and outcome. All patients underwent chest X-ray imaging in order to confirm the scale of COVID-19 infection and exclude or confirm COVID-19 associated pneumonia. Patients were divided into four groups based on the COVID-19 disease severity classification: (1) asymptomatic (positive PCR, no symptoms), (2) mild (the presence of symptoms but no shortness of breath, dyspnoea, or abnormal chest imaging), (3) moderate (evidence of lower respiratory disease during clinical assessment or imaging and who have an oxygen saturation (SpO2) ≥94% on room air at sea level) and (4) severe disease (SpO2 <94% on room air at sea level, a ratio of arterial partial pressure of oxygen to fraction of inspired oxygen (PaO2/FiO2) <300 mm Hg, respiratory frequency >30 breaths/min, or lung infiltrates >50%).\n\nCOVID-19 infection was determined by RT-PCR during this initial visit. A nasopharyngeal swab specimen for the identification of SARS-CoV-2 was taken and sent to Institute of Microbiology and Immunology to confirm the infection. The patients’ blood pressure was measured at admission and 72 hours after admission. Blood samples were collected on a day of admission to the hospital and transported to the laboratory at the University Medical Centre in Ljubljana, where they were stored at minus 80 °C until analysis. Determination of inflammatory biomarkers, C-reactive-protein (CRP), interleukin-6 (IL-6), procalcitonin (PCT), D-dimer and 25(OH)D3 have been carried out according to a routine protocol using standard laboratory procedures. Patients received COVID-19 specific treatment consisting of oxygen supplementation, dexamethasone, and/or remdesivir according to the treatment guidelines.\n\nSerum 25(OH)D3 concentration was measured in human serum with the chemiluminescence immunoassay vitamin D total (25-hydroxy-vitamin D). Vitamin D status was assigned with consideration of serum 25(OH)D3 concentration according to the literature: Deficient below 30 nmol/L, insufficient below 50 nmol/L, non-optimal between 50-75 nmol/L and optimal >75 nmol/L.43,45\n\nThe statistical analysis was performed using SPSS 21.0 (IBM Inc., Chicago, USA). Normally distributed variables were expressed as arithmetic mean and standard deviation, and One-Way ANOVA test was used for comparisons between variables. In case of abnormally distributed variables the differences between continuous variables were analysed by the nonparametric Mann-Whitney test. Binary logistic regression model was used to identify risk factors for moderate-to-severe COVID-19 course of the disease. Statistical significance for all tests was determined as p-value below 0.05.\n\n\nResults\n\nOverall, 301 participants were included in the analysis. The baseline demographic and clinical characteristics of patients are presented in Table 1. There was a similar distribution of female and male patients. The average age was 65 years. Laboratory parameters showed systemic inflammation with increased proinflammatory factors such as CRP, PCT, IL-6. Most patients (77%) had COVID-19 pneumonia detected by chest X-ray imaging. One case of acute respiratory insufficiency (ARI) was determined. 46 (15,3%) patients had moderate, and 162 (53,8%) patients had a severe course of COVID-19. Most patients were admitted to the hospital during winter season. 14 (4,7%) patients died during the follow-up, 30 (10,0%) were admitted to the ICU due to the disease worsening. A vast majority needed oxygen supplementation (n=224; 74,4%).\n\nDVT, deep vein thrombosis; PE, pulmonary embolism; LDH, lactate dehydrogenase; CRP, C reactive protein, RDW, red cell distribution width.\n\nAverage vitamin 25(OH)D3 levels were below optimal, and vitamin D deficiency and insufficiency was detected in 205 (68.1%) individuals. Approximately one third of patients had optimal 25(OH)D3 levels above 75 nmol/L. Serum vitamin 25(OH)D3 levels were significantly lower in winter months (November-April) (p<0.001) (Figure 1). Higher levels of serum vitamin 25(OH)D3 were present in the summer months (Figure 2).\n\nPatients were divided into four groups based on their serum vitamin 25(OH)D3-deficient, insufficicient, sufficient and optimal. The difference is clinical characteristics between the groups are presented in Table 2. Vitamin D deficiency was more common in males. A shorter duration of symptoms before hospitalisation was seen in the most deficient group. Fever and cough were more frequent with the optimal group of patients. In addition, severe course of COVID-19 was more common in groups with higher levels of serum vitamin 25(OH)D3 Group of patients with optimal vitamin 25(OH)D3 levels have experienced more frequent pneumonia so they needed dexamethasone and oxygen therapy.\n\nTable 3 presents the distribution of patients according to the severity of COVID-19. There were notable differences in proinflammatory markers between the groups for LDH, ferritin, CRP, PCT. Patients with more severe disease had increased levels of proinflammatory markers, and significantly lower levels of serum vitamin 25(OH)D3. However, the lowest levels of vitamin 25(OH)D3 were detected in the asymptomatic group (Figure 3). Patients with severe COVID-19 exhibited more symptoms, had a higher rate of ICU admissions and mortality.\n\n\nDiscussion\n\nThis study aimed to assess the severity of COVID-19 among our patients and potential effect of serum levels of vitamin D levels on the course of COVID-19. Previous studies have speculated about the role of vitamin D supplementation and COVID-19 but have been inconclusive. However, it is known that vitamin D plays an important role in immune system and can improve natural resistance to acute viral respiratory infections and moderate their course by inhibiting an excessive inflammatory response. A high prevalence of vitamin D deficiency especially pronounced in the autumn and winter months was reported in Slovenia, with up to 80% of adults exhibiting serum vitamin D levels <50 nmol/L, and severe deficiency with serum vitamin D levels <30 nmol/L was found in 40%.43 Therefore, our group advised vitamin D supplementation to mitigate the course of the COVID-19 disease, especially in patients at risk for a severe course. Our results show that most enrolled patients were still vitamin D deficient despite the recommendations which were published prior to the conduction of this study. It is noteworthy that vitamin D deficiency was predominantly observed during the winter months from November till April, which confirms our previous findings.43 These results could be explained by increased sun exposure in the summer, which is known to be an important source of natural vitamin D. It has been established that in the absence of UVB-induced vitamin D biosynthesis, vitamin D supply can be maintained in healthy adults with a dietary intake of between 600 and 800 IU of vitamin D.46,47 At the same time, it should be pointed out that this does not apply to individuals who already have vitamin D deficiency, and that such doses are sufficient to reach the threshold value for skeletal and muscle functions (50 nmol/L), but not to reach higher concentrations of serum level, e.g. 75 nmol/L. The results of our study show, that the Vitamin D deficiency is more prevalent in males. Interestingly, the duration of symptoms was the shortest in the most Vitamin D deficient group. Furthermore, fever and cough were more frequent within the group with optimal serum Vitamin D levels. In addition, the severe course of COVID-19 was also more common in groups with higher concentration of serum vitamin 25(OH)D3 levels. These results do not support the protective role of vitamin D in viral infections suggested in the previous studies, where vitamin D supplementation was shown to significantly lower the incidence of acute respiratory infections (ARIs) in subjects with severe vitamin D deficiency.48 Our results can be explained by several hypotheses. First, previous studies have shown that higher serum levels of vitamin D are required for beneficial effects on the immune system than for skeletal and muscle effects.49 This is further supported by a study in which patients with levels of vitamin D below 75 nmol/L were shown to 58% more likely to suffer from ARI.50 Most of our patients admitted they only started supplementing Vitamin D after they had already developed the symptoms, which could explain our results, as the immunomodulatory effects of Vitamin D have not yet started. Previous studies have shown a correlation between lower average vitamin D levels and a higher incidence of SARS-CoV-2 infections and higher mortality (Italy, France, Spain, Switzerland).51 For instance, in Chicago, those with vitamin 25(OH)D3 levels below 50 nmol/L had a 1.77 times greater risk of testing positive for the infection. Their vitamin 25(OH)D3 was determined up to a year before they fell ill or were tested.52 In our case unfortunately we did not measure levels of vitamin 25(OH)D3 at several time points. Similar differences in the vitamin D levels between positive and negative subjects was also noted in a Swiss study, where those with a positive test had an average level of only 27 nmol/L,53 and those with a negative test had an average level of 61 nmol/L. Also in Israel, it was shown that a lower level of vitamin D increases the risk of infection with SARS-CoV-2.54 In observational studies in Iran,55 Germany, and Italy, those patients with COVID who had lower levels of vitamin D had worse outcomes.56 Moreover, an almost 15-fold increased risk of death was observed in patients with vitamin D deficiency compared with those with higher vitamin 25(OH)D3 levels; similar relationships were also evident when the vitamin 25(OH)D3 cut-off was set at 50 nmol/L.56 Our results show that patients with more severe disease showed higher levels of inflammatory markers and significantly lower levels of serum vitamin 25(OH)D3. Interestingly however, again the lowest levels of vitamin 25(OH)D3 were detected in the asymptomatic group. This can be explained by the same reason as above those patients who had symptoms started taking high concentrations of vitamin D prior to their admission to the hospital as our recommendations were published over several media and in a public campaign. Patients with asymptomatic course of the disease were not aware of infection and were not supplementing vitamin D, which explains the lower levels. In addition, the majority of cases were detected during the winter months, during which the baseline serum Vitamin D levels are lower, which could have influenced the results. Nevertheless, the most severe group of patients exhibited more symptoms, a higher rate of ICU admission and a higher mortality rate which is in line with previous reports. The results of a previous study indicate that vitamin D supplementation decreases the rate of ICU admissions as well as mortality.57 The favourable outcome of vitamin D supplementation and increased serum levels can be explained by the fact that vitamin D moderates the excessive inflammation in the lungs (cytokine storm) that can have detrimental effects in some patients with COVID-19. Inconsistency in the effect of vitamin D supplementation has been shown previously and attributed to different dosing regimens, duration of supplementation, and methodology in published reports. Murai et al.58 did not detect differences in hospital stay of patients with COVID-19 who received vitamin D dose and those who did not receive vitamin D.\n\nOur study had several limitations. No clear data about the length of vitamin D supplementation prior to hospitalisation could be obtained. Our largest limitation is that no follow-up was performed, as in the following period the severity of the disease might be lower due to higher level of serum vitamin 25(OH)D3. In addition, we did not measure the levels of vitamin 25(OH)D3 in several time points of hospitalisation to confirm its effect over time.\n\n\nConclusion\n\nVitamin D levels showed a reasonable effect in the prevention of SARS-CoV-2 morbidity and mortality. Our results show the association between lower levels of serum vitamin 25(OH)D3 and COVID-19 severity. Patients with the severe course of COVID-19 were shown to have increased inflammatory parameters, increased mortality, and higher incidence of vitamin D deficiency. The results suggest that the vitamin D deficiency might represent a significant risk factor for a severe course of COVID-19. Therefore, we recommend vitamin D supplementation in high-risk patients and hospitalised COVID-19 patients. Further, prospective longitudinal studies are warranted to assess the long-term effects of Vitamin D supplementation.\n\nD.Si. and J.O. conceived of the idea for the project; D.Si. and J.O. wrote the draft version of the manuscript, R.S. supervised the patients invited to participate in the study; J.U. and K.J. compiled the clinical data on the patients involved; O.J. and D. St were responsible for completing laboratory data, and D.St. and R.J. performed the statistical calculations. All authors reviewed and agreed with the manuscript, and final approval was given by D.Si. and J.O. All authors have read and agreed to the published version of the manuscript.", "appendix": "Data availability\n\nZenodo: Siuka, Darko, Saletinger, Rajko, Uršič, Jure, Jevnikar, Kristina, Janša, Rado, Štubljar, David, & Osredkar, Joško. (2023). The effect of Vitamin D levels on the course of COVID-19 in hospitalized patients – a 1-year prospective cohort study (1.0) [Data set]. Zenodo. DOI: https://doi.org/10.5281/zenodo.7679129. 59\n\nData are available under the terms of the Creative Commons Attribution 2.0 Generic.\n\n\nReferences\n\nSiuka D, Fabjan T, Osredkar J: The COVID-19 Pandemic, Seasons and the Vitamin D Laboratory Strategy. International Journal of Sciences: Basic and Applied Research (IJSBAR). 2021; 56(2): 182–189.\n\nFares A: Factors influencing the seasonal patterns of infectious diseases. Int. J. Prev. Med. 2013; 4(2): 128–132. PubMed Abstract\n\nJordan T, Siuka D, Kozjek Rotovnik N, et al.: COVID-19 and Vitamin D- a Systematic Review. Zdr. Varst. 2022; 61(2): 124–132. PubMed Abstract \| Publisher Full Text\n\nJolliffe DA, Griffiths CJ, Martineau AR: Vitamin D in the prevention of acute respiratory infection: Systematic review of clinical studies. J. Steroid Biochem. Mol. Biol. 2013; 136: 321–329. 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Publisher Full Text" }	[ { "id": "210758", "date": "11 Oct 2023", "name": "Giulia Vivaldi", "expertise": [ "Reviewer Expertise Cohort study 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\nSiuka and colleagues report findings from a prospective cohort study assessing the effect of vitamin D supplementation on people hospitalised with SARS-CoV-2 infection. The authors assessed vitamin D deficiency in 301 participants, who were hospitalised with varying levels of COVID-19 severity. The majority (68%) of participants had some level of vitamin D deficiency. Key strengths of this study are detailed data on disease course and laboratory measures, as well as inclusion of participants with varying disease severity. However, there are some limitations.\nMajor The general statistical approach seems suitable. However, I have doubts about the binarisation of disease severity in order to use logistic regression. People who were asymptomatic had the lowest levels of vitamin D; as the authors note, this is likely to be an artefact of the guidance around vitamin D supplementation at the time. However, by combining the vitamin D levels of people with asymptomatic disease and those with mild disease, the authors create a mean value that is unlikely to be representative. This leads to a contradiction in the results, whereby analysis by vitamin D level suggests that severe disease is more common among people with higher levels of vitamin D, but analysis by disease severity appears to give the opposite result.\nAs the disease severity outcome is ordered, I believe it would make more sense to use ordered logistic regression (or, failing that, multinomial regression with a trend test). As the asymptomatic group appears to be an outlier, the authors should then consider doing sensitivity analyses excluding asymptomatic participants to see whether they can observe a difference in vitamin D level between the three remaining severity groups.\nThe authors say they do not have data on the length of vitamin D supplementation before hospitalisation, but they do not clarify whether they have any information at all on vitamin D supplementation (ie, whether or not someone was taking supplements). Any information they do have should be adjusted for in the model if at all possible.\nMinor General: One participant with ARI is included: it is unclear whether this participant had SARS-CoV-2 infection or not. If not, why were they included?\nMethods: The first paragraph of the Methods says that participants were hospitalised in the COVID-19 unit of the medical centre, but it's unclear why asymptomatic participants or those with mild disease would have been hospitalised. Were they in hospital for another reason? Please clarify.\nResults, paragraph 4: This paragraph would benefit from a more careful rewrite. Sometimes the authors are comparing each group individually, and sometimes they appear to be grouping them together.\nEg, the authors say that fever and cough were more common in the optimal group of patients, but actually fever was most common in the sub-optimal group. So are they comparing the optimal group with an average of all the other groups? The authors also say that severe disease was more common in groups with higher levels of serum vitamin 25(OH)D3, but given that the percentage dips in the 'optimal' group, it might be more accurate to say that severe disease was least common in patients who were vitamin D deficient.\nConclusion: The first two sentences of the conclusion are too strong, as I am not sure they are supported by the data. Firstly, there do not appear to be any statistical differences in mortality by vitamin D level. Secondly, as mentioned in the major comment, the combination of the asymptomatic and mild groups introduces problems in the analysis that make it difficult to state that vitamin D levels prevent disease morbidity as well.\nFigure 1: Please add a note to the figure legend explaining what the asterisk for observation 193 represents.\nTables: Female and male sex should be presented in separate rows, with percentages.\nTables: Can the authors please clarify whether the duration of symptoms is duration in total, or time between symptom onset and hospitalisation? At the moment, it is difficult to interpret.\nTable 3: It is surprising that people in the asymptomatic group report symptoms (ie, four participants reported cough). This would suggest that they were not asymptomatic. The authors should clarify whether asymptomatic means asymptomatic up to hospitalisation, or asymptomatic during the course of the disease. If the latter, the presence of symptoms in table 3 suggests there has been a mistake.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [ { "c_id": "11924", "date": "28 Jun 2024", "name": "David Stubljar", "role": "Author Response", "response": "Dear Giulia Vivaldi, thank you for your valueble review, which has established for us to create even better report of our results and bring much more quality to the final manuscript. We have managed to address all your questions and comments, so we are resbumiting new version of the manuscript and hope you will take another opportunity to check it again. Thank you in advance. David Stubljar" } ] }, { "id": "288273", "date": "25 Jun 2024", "name": "Radek Kučera", "expertise": [ "Reviewer Expertise immunochemistry", "pharmacology" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nAuthors report the results of a prospective study comparing the effect of vitamin D status on severity of SARS-CoV-2 infection. The authors evaluated vitamin D status in 301 hospitalized patients with varying severity of COVID-19 infection and different level of vitamin D. The main strengths of this study are detailed data on symptoms and course of the disease, enough amount of measured laboratory parameters and inclusion of the patients with varying COVID-19 infection severity. The results suggest that the vitamin D deficiency might represent a significant risk factor for a severe course of COVID-19 disease. To the article I have one Major and few Minor comments.\n\nMajor Conclusion The conclusion is better to rewrite because the authors observed the lowest level of vitamin D in the asymptomatic group of patients. Figure 3 is demonstrated a bit different facts that are concluded. The exact mechanism of action of vitamin D in viral infection is not yet fully understood. Although the presented study suffers from gaps in the history of vitamin D use before hospitalization, this can serve as a learning tool for future studies. The authors report that the lowest value of vitamin D was measured in asymptomatic patients. This finding is not necessarily in opposition to the findings of other studies. If we consider that the receptor for vitamin D is in every immune cell, a decrease in 25(OH)D3 in the serum may occur with good immune function, but due to a good immune function, a serious course of infection may not occur.\nMinor Determination of serum vitamin D (25(OH)D3) concentration Please add the manufacturer of the chemiluminescence immunoassay vitamin D total (25-hydroxy-vitamin D).\nFigures 1) Please change the description of y axis. Use 25(OH)D3 instead of D3. 2) I don't know what the numbers in the graphs above the columns near the wheels and stars mean. I couldn't find an explanation anywhere.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [ { "c_id": "11887", "date": "03 Jul 2024", "name": "David Stubljar", "role": "Author Response", "response": "Dear reviewer, thank you for your valuable insight and comments. We have applied all suggestions, hence we have improved our manuscript significantly and are returning corrected version. We would appreaciate of you will be able to take another look a the corrrected text. Thank you in advance. Kind regards, David Stubljar, corresponding author" } ] } ]	1	https://f1000research.com/articles/12-254
https://f1000research.com/articles/12-1256/v1	02 Oct 23	{ "type": "Research Article", "title": "Antibacterial and anti-virulence potential of plant phenolic compounds against Vibrio parahaemolyticus", "authors": [ "F. Javier Vazquez-Armenta", "M. Olivia Aros-Corrales", "M. Lizeth Alvarez-Ainza", "A. Thalia Bernal-Mercado", "J. Fernando Ayala-Zavala", "Adrian Ochoa-Leyva", "A. Alexis Lopez-Zavala", "F. Javier Vazquez-Armenta", "M. Olivia Aros-Corrales", "M. Lizeth Alvarez-Ainza", "A. Thalia Bernal-Mercado", "J. Fernando Ayala-Zavala", "Adrian Ochoa-Leyva" ], "abstract": "Background: Vibrio parahaemolyticus is a pathogenic bacterium that affects shrimp aquaculture; its infection can lead to severe production losses of up to 90%. On the other hand, plant phenolic compounds have emerged as a promising alternative to combat bacterial infections. The antibacterial and anti-virulence activity of the plant phenolic compounds quercetin, morin, vanillic acid, and protocatechuic acid against two strains of V. parahaemolyticus (Vp124 and Vp320) was evaluated.\nMethods: The broth microdilution test was carried out to determine phenolic compounds' antibacterial activity. Moreover, the biofilm-forming ability of V. parahaemolyticus strains in the presence of phenolic compounds was determined by total biomass staining assay using the cationic dye crystal violet. The semisolid agar displacement technique was used to observe the effect of phenolic compounds on the swimming-like motility of V. parahaemolyticus.\nResults: Results showed that phenolic compounds inhibited both strains effectively, with minimum inhibitory concentrations (MICs) ranging from 0.8 to 35.03 mM. Furthermore, at 0.125 – 0.5 × MIC of phenolic compounds, V. parahaemolyticus biofilms biomass was reduced by 63.22 – 92.68%. Also, quercetin and morin inhibited the motility of both strains by 15.86 – 23.64% (Vp124) and 24.28 – 40.71% (Vp320).\nConclusions: The results suggest that quercetin, morin, vanillic, and protocatechuic acids may be potential agents for controlling V. parahaemolyticus.", "keywords": [ "anti-virulence", "natural compounds", "vibriosis", "food safety" ], "content": "Introduction\n\nAccording to the Food and Agriculture Organization of the United Nations (FAO), shrimp farming represents 53% of world aquaculture production.1 In recent years, stocking densities have increased, which has led to the proliferation of diseases and the appearance of new pathologies that directly affect the profitability of shrimp production systems. Twenty percent of the diseases that appear during shrimp farming are related to bacteria, including the genus Vibrio.2 Vibrio parahaemolyticus stands out as the causal agent of Acute Hepatopancreatic Necrosis Disease (AHPND), initially defined as Early Mortality Syndrome (EMS).3 This disease has been responsible for losses of about 90% of production and, in some cases, up to 100%, threatening seafood safety and human health.3,4 The increasing prevalence of antibiotic-resistant strains has made the control of V. parahaemolyticus infections progressively challenging.\n\nOnce effective in controlling these infections, traditional antibiotics are now facing limitations due to the emergence of resistant strains and the negative environmental impacts resulting from their extensive use in aquaculture.5 Moreover, the complex and dynamic nature of aquatic environments makes preventing the spread of bacterial infections in these systems difficult. Waterborne pathogens, such as V. parahaemolyticus, can quickly disseminate throughout aquaculture facilities, contaminating water sources and other organisms.\n\nIn addition, the biofilm-forming capacity of V. parahaemolyticus further complicates the control measures, as biofilms provide protection against antimicrobial agents and enable the bacteria to persist in the environment.6 Biofilms are communities of microorganisms attached to biotic or abiotic surfaces embedded in a self-produced matrix consisting of polysaccharides, proteins, and nucleic acids.7 In the inner part of the biofilms, the oxygen concentration is lower. Hence, an anaerobic atmosphere with a low pH develops, which causes a decrease in the activity of some antibiotics.8 Other phenomena caused by these altered microenvironment conditions are decreased bacterial metabolism and dropped replication times.9 Therefore, once the biofilm is formed, its eradication becomes complicated. This challenge requires the development of novel strategies and compounds capable of effectively inhibiting bacterial growth, biofilm formation, and motility, without causing significant environmental harm or promoting antibiotic resistance.\n\nThe use of natural compounds, such as phenolic compounds, offers a promising alternative due to their antimicrobial properties and potential to address the limitations of traditional antibiotics.10 Phenolic compounds, which are secondary metabolites produced by a wide variety of plants, have shown antibacterial activity against Gram-negative (Escherichia coli, Salmonella spp., Vibrio spp.) and Gram-positive (Listeria monocytogenes and Staphylococcus aureus) pathogenic bacteria.11–13 They are widely distributed in plants as defense mechanisms against microbial pathogens. Owing to their structural diversity and biological activity, phenolic compounds have gained increasing interest as potential antibacterial agents in various applications, including food preservation, agriculture, and human health.14,15 For example, the flavonoids quercetin and myricetin showed a minimum inhibitory concentration (MIC) against V. parahaemolyticus of 0.125 and 0.25 mg/mL, respectively.16 In comparison, catechin and isorhamnetin showed MIC values of 0.05 and 0.025 mg/mL, respectively, against V. cholerae.17 Moreover, some of them, such as quercetin, catechin, ferulic acid, vanillic acid, and protocatechuic acid, have been shown to disrupt biofilm formation of pathogenic bacteria through different mechanisms of action, including inhibition of motility and EPS synthesis or/and disruption of intercellular communication.18–21 However, the effect of these phenolic compounds on V. parahaemolyticus virulence factors, such as motility and biofilm formation capacity is unknown. Therefore, the present study aimed to evaluate (quercetin, morin, vanillic acid, and protocatechuic acid) phenolic compounds’ antibacterial and anti-virulence activity against a V. parahaemolyticus reference strain (CAIM 320; Vp320), and a strain isolated from white shrimp samples (Vp124). It is hypothesized that the selected phenolic compounds will significantly inhibit the growth, biofilm formation, and motility of V. parahaemolyticus strains, thus highlighting their potential as alternative agents for controlling infections and the persistence of this pathogen. Furthermore, the flavonoids (quercetin and morin) are expected to exhibit different mechanisms of action compared to the phenolic acids (vanillic and protocatechuic acids), which may offer unique advantages in tackling V. parahaemolyticus.\n\n\nMethods\n\nThe human pathogenic reference strain CAIM 320 (Vp320) harboring the virulence genes tlh (thermolabile haemolysin), tdh (thermostable direct haemolysin), trh (TDH-related haemolysin), T3SS1: VP1680 (type III secretion system 1) and VPI and a strain isolated from shrimp, designated as Vp12422 were donated by the Laboratory of Clinical Microbiology of the University of Sonora. The studied strains were seeded on Thiosulfate Citrate Bile Sucrose agar (TCBS), reseeded in Trypticase Soy Broth (TSB) with 3% NaCl, and incubated at 37°C during the assays.\n\nStandards (purity >95%) of gallic acid (G7384), vanillic acid (94770), protocatechuic acid (03930590), rutin (R5143), morin (M4008), and quercetin (Q4951) were purchased from Sigma-Aldrich.\n\nTo determine the antibacterial capacity of phenolic compounds against V. parahaemolyticus, an inoculum of each strain (Vp124 and Vp320) was prepared from exponential phase cultures (16 h in TSB + NaCl 3% at 37 °C), adjusting the optical density (600 nm) to 0.1 absorbance units, which is equivalent to 1 × 108 CFU/mL. Concentrations of 0.8 mM - 40 mM of each compound (quercetin, morin, vanillic acid, protocatechuic acid, gallic acid, and rutin) were prepared in TSB + NaCl 3% at 37°C from dimethyl sulfoxide (DMSO) stocks. Subsequently, 5 μL of the adjusted inoculum and 295 μL of each concentration of the compounds were taken and placed in microplate wells (Costar 96) and incubated for 24 h at 37°C. The positive control was the same bacterial inoculum in TSB + NaCl 3% + DMSO 5%. As negative controls, each concentration of the tested compound and TSB + NaCl were placed in microplate wells without bacterial inoculum. The lowest compound concentration at which no visible growth was observed was considered the minimum inhibitory concentration (MIC). In addition, each compound's minimum bactericidal concentration (MBC) was determined by placing 50 μL aliquots from wells with three concentrations above the MIC on Mueller-Hinton agar + NaCl 3% plates. The MBC was considered the minimum concentration of each compound where no growth of V. parahaemolyticus was observed on the plate.23\n\nThe biofilm-forming ability of V. parahaemolyticus strains in the presence of phenolic compounds was determined by total biomass staining assay using the cationic dye crystal violet.24 An inoculum of each strain at an optical density of 0.1 units at 600 nm was prepared from exponential phase cultures. Each compound was dissolved in DMSO (5% of final volume) and added to TSB at 0.125, 0.25, and 0.5 × MIC. Subsequently, 5 μL of the inoculum and 295 μL of each concentration were taken, placed in microplate wells, and incubated for 24 h at 37 °C.\n\nAt the end of the incubation, the culture medium was removed from the microplate wells by aspiration. Three consecutive washes were performed with distilled water to remove weakly adherent cells, and then the microplate was allowed to dry at 50°C. After that, 300 μL of a 0.1% crystal violet (Sigma-Aldrich) solution was added to each well and allowed to stand for 45 min to stain the biomass of the formed biofilms. The crystal violet solution was then carefully removed, and three consecutive washes were carried out to remove the excess dye with distilled water, followed by drying at 50°C. Finally, 300 μL of 20% acetic acid was added to each well to solubilize the crystal violet for 15 min, and the absorbance of the solution was read at 594 nm. The absorbance of the solubilized violet crystal is proportional to the total biomass of the biofilms formed in each well. Each experiment was performed in triplicate, and the results were expressed as a percentage of the reduction of total biomass compared to the positive control (biofilms formed without the presence of phenolic compounds) according to the following equation:\n\nThe semisolid agar displacement technique was used to observe the effect of phenolic compounds on the swimming-like motility of V. parahaemolyticus.24 Phenolic compounds were added to TSB + NaCl 3% medium at a final concentration of 0.5 × MIC. An inoculum of each V. parahaemolyticus strain from exponential phase cultures (18 h at 37°C in TSB + NaCl 3%) was prepared at a final 1 × 108 CFU/mL concentration. Subsequently, 10 μL of bacterial suspension were taken and placed in the center of a Petri dish with semi-solid TSB + NaCl 3% agar (0.42% agar) and incubated for 16 h at 37°C. Finally, the diameter of motility halos was measured. The experiment was performed in triplicate, and cultures of each V. parahaemolyticus strain on TSB + NaCl 3% without phenolic compounds were used as positive controls.\n\nA complete randomized experimental design was used for all experiments. In the biofilm formation assay, the factors were the type of compound (quercetin, morin, vanillic acid, and protocatechuic acid) and the tested concentration (0.125, 0.25, and 0.5 × MIC), and the response variable was biomass reduction (%). In the motility assay, the factors were also the type of compound and concentration, and the response variable was motility inhibition (%). An analysis of variance (ANOVA) was performed, and where differences were found, multiple comparisons of means were performed by the Tukey-Kramer method at 95% confidence using the statistical software NCSS 2007.\n\n\nResults\n\nThe MICs of the assessed compounds are shown in Table 1, where four of the six compounds were able to inhibit the growth of both Vibrio strains. The flavonoid quercetin was the most effective, presenting the lowest MIC (0.8 mM for both strains). The flavonoid morin and protocatechuic acid showed the same effect on both Vibrio strains, with MICs of 1.6 and 28.43 mM, respectively. On the other hand, vanillic acid presented a MIC equal to 32.73 mM for the Vp124 strain and 35.03 for the Vp320 strain. In contrast, rutin and gallic acid did not inhibit the growth of V. parahaemolyticus at the evaluated concentrations, 0 - 4 mM and 0-41.12 mM, respectively. For this reason, they were discarded in the following determinations. The minimum bactericidal concentration was also evaluated; however, this effect was not observed at any tested concentrations. The observed MICs of quercetin, morin, protocatechuic acid, and vanillic acid against both Vibrio strains support our hypothesis that certain phenolic compounds can effectively inhibit the growth of V. parahaemolyticus.\n\nTo determine the effect of phenolic compounds on V. parahaemolyticus biofilm formation, sub-inhibitory concentrations of each compound were selected based on the MIC (0.125, 0.25, and 0.5 × MIC). Figure 1 shows the percentage of total biomass of V. parahaemolyticus biofilms formed at different concentrations of quercetin and morin. Both compounds were able to interfere with the biofilm formation process. For quercetin at 0.125 × MIC, a 71.97% reduction (p<0.05) was observed on the Vp124 strain, while no significant differences were found between 0.25 and 0.5 × MIC, achieving a reduction of 77.97-80.85% (p<0.05) respect to control. A similar pattern was observed in strain Vp320, where quercetin at 0.125 × MIC reduced 48.44% of the total biomass of V. parahaemolyticus biofilms, and for 0.25-0.5 × MIC, total biomass reduction was 85.31 – 91.66%. Regarding the effectiveness of morin, a reduction (p<0.05) in the total biomass of biofilms of strain Vp124 of 73.39%, 84.08%, and 89.07% was observed at concentrations of 0.125, 0.25, and 0.5 × MIC, respectively. While in the Vp320 strain, no differences were observed in the percentages of reduction at the evaluated concentrations (p>0.05), showing a reduction of 88.84-89.93 % compared to the control. The significant decrease of V. parahaemolyticus biofilm formation observed at sub-inhibitory concentrations of quercetin and morin supports our hypothesis that certain phenolic compounds can effectively disrupt biofilm formation processes.\n\nValues represent mean ± standard error (n = 3). Different literals represent differences (p<0.05) between the evaluated concentrations for each strain.\n\nFigure 2 shows the total biomass of biofilms formed by V. parahaemolyticus in the presence of vanillic and protocatechuic acids. Both phenolic acids inhibited the biofilm formation capacity of both strains compared to the control. However, no differences were found (p>0.05) between the evaluated concentrations. Vanillic acid reduced the total biomass of Vp124 biofilms by 85.92% to 92.68% and 89.55% - 90.27%for Vp320 strain. In comparison, protocatechuic acid inhibited 91.61% - 93.12% and 91.04% - 92.82% of the biofilm formation of Vp124 and Vp320 strains, respectively.\n\nValues represent mean ± standard error (n = 3). Different literals represent differences (p<0.05) between the concentrations evaluated for each strain.\n\nTable 2 shows the effect of quercetin, morin, vanillic and protocatechuic acids on the motility of Vp124 and Vp320 strains. At the tested concentrations, the flavonoids quercetin and morin inhibited the motility of both strains on soft agar (0.42% agar). In this assay, differences (p<0.05) were observed in the inhibition percentages of each strain. For the Vp124 strain, quercetin inhibited 15.86% of the displacement of the bacteria on soft agar; while an inhibition of 23.63% was observed for the Vp320 strain. In the presence of morin, a similar trend was observed, where Vp320 showed the highest (p<0.05) percentage of motility inhibition (40.71%), while for the Vp124 strain, the percentage of inhibition was 24.28%. However, phenolic acids at the evaluated concentration did not show the capacity to interfere with the motility of V. parahaemolyticus strains (p>0.05). These results demonstrated that the flavonoids quercetin and morin effectively inhibited the motility of V. parahaemolyticus strains Vp124 and Vp320, following the hypothesis that certain phenolic compounds can impact bacterial motility. On the other hand, phenolic acids, such as vanillic and protocatechuic acids, did not exhibit the same inhibitory effect on motility, highlighting the varying impacts of different phenolic compounds on V. parahaemolyticus motility.\n\nValues are mean ± standard error (n = 3).\n\n\nDiscussion\n\nPhenolic compounds are known for their antimicrobial activity against various pathogenic bacteria, including Gram-negative and Gram-positive species.10,11 In this study, vanillic and protocatechuic acids, along with the flavonoids quercetin and morin, effectively inhibited the growth of V. parahaemolyticus. Notably, flavonoids exhibited 20-40 times stronger antibacterial activity than phenolic acids, as evidenced by their lower MICs, which aligns with findings from previous research. Abuga et al.16 demonstrated that quercetin and myricetin inhibited V. parahaemolyticus, with MICs of 0.4 and 0.8 mM, respectively. Similarly, Tinh et al.12 evaluated the antibacterial activity of phenolic compounds against 96 V. parahaemolyticus isolates from Pacific white shrimp (L. vannamei) in Thailand. Among the tested compounds, vanillic acid displayed significant bactericidal activity, with MICs and MBCs ranging from 6.09 to 12.18 mM. Pyrogallol, however, exhibited the strongest antibacterial properties, with MICs and MBCs between 0.25 and 2.02 mM. Wu et al.25 also investigated the MIC of 3-p-trans-coumaroyl-2-hydroxyquinic acid against various pathogenic bacteria, including V. parahaemolyticus. Their results showed MICs ranging from 7.06 to 28.24 mM for all evaluated pathogenic bacteria, with a MIC of 14.12 mM for V. parahaemolyticus. In conjunction with our current research findings, the outcomes of these earlier studies underscore the potential of phenolic compounds as effective antibacterial agents against V. parahaemolyticus. Our study contributes to the growing body of evidence by demonstrating the comparative effectiveness of flavonoids and phenolic acids, highlighting the promising role of these natural compounds in combating V. parahaemolyticus infections.\n\nOne notable aspect of these results is the direct comparison between flavonoids and phenolic acids regarding their antibacterial activity against V. parahaemolyticus. While previous research has separately investigated various phenolic compounds for their antimicrobial properties, our study offers a unique contribution by evaluating and contrasting the effectiveness of both flavonoids and phenolic acids. The results of our study emphasize that flavonoids, such as quercetin and morin, demonstrated 20-40 times stronger antibacterial activity than phenolic acids, as evidenced by their lower MICs. This novel finding highlights the potential advantages of using flavonoids over phenolic acids in developing new strategies to control and prevent V. parahaemolyticus infections in aquaculture systems. Additionally, our study contributes to the growing body of evidence supporting using natural compounds as alternatives to traditional antibiotics, which is particularly important in increasing antibiotic resistance.\n\nThe antibacterial activity of phenolic compounds is closely related to their physicochemical properties and the ability to interact with the lipid membrane and intracellular targets. Phenolic acids can alter the morphology of treated cells and cause hyperpolarization of the lipid membrane with its consequent loss of integrity.25,26 While flavonoids can intercalate in different regions of lipid bilayers, causing changes in their fluidity, this effect depends on the number and position of hydroxyl groups.27 Wu et al.28 found a strong and positive correlation (r = 0.921) between the antimicrobial activity of flavonoids against E. coli and their ability to reduce the fluidity of lipid membranes. Furthermore, flavonoids can inhibit essential enzymes for bacterial growth, e.g., quercetin, kaempferol, luteonin, galangin, and myricetin are inhibitors of DNA gyrase (IC50 = 0.037-1.18 mg/mL).29 Also, quercetin and apigenin can inhibit d-alanine:d-alanine ligase, the enzyme responsible for the binding of alanine residues during the assembly of peptidoglycan precursors.30\n\nBiofilms enable pathogenic bacteria to survive in adverse environments, such as nutrient scarcity and exposure to antimicrobial agents.7,31 V. parahaemolyticus can form biofilms on various surfaces in aquaculture-related settings, acting as a reservoir that compromises the safety of aquaculture products.6 Our study reveals that vanillic and protocatechuic acids and the flavonoids quercetin and morin can effectively interfere with V. parahaemolyticus biofilm formation (Figures 1 and 2), contributing new insights into the potential of these compounds. Liu et al.21 demonstrated that vanillic acid reduced the total biomass of V. alginolyticus biofilms by approximately 65% at a concentration of 2.9 mM. Additionally, 2,6-di-tert-butyl-4-methylphenol, found in garlic, green algae, and cyanobacteria, inhibited the biofilm formation of V. harveyi, V. parahaemolyticus, and V. vulnificus by 80%, 83%, and 80%, respectively.32 Moreover, ethanolic extracts of ginger and its major compounds, 6-gingerol, 8-gingerol, and 6-shogaol, effectively inhibited V. parahaemolyticus biofilm formation, with 6-shogaol exhibiting the highest efficacy by reducing biofilm biomass by up to 80% at a concentration of 0.15 mM.33 This study breaks new ground by assessing the anti-biofilm activity of selected flavonoids and phenolic acids against V. parahaemolyticus, demonstrating their potential as anti-biofilm agents in combating infections in aquaculture systems. This research significantly expands on prior findings, offering a deeper and more extensive understanding of phenolic compounds' capabilities in mitigating biofilm-associated risks within the aquaculture industry.\n\nMotility is a key virulence factor in the Vibrio genus, essential in the initial adhesion to abiotic surfaces and subsequent biofilm formation.34,35 Our study reveals that flavonoids quercetin and morin inhibited V. parahaemolyticus swimming motility, while vanillic and protocatechuic acids did not exert any inhibitory effects (Table 2). V. parahaemolyticus exhibits swimming motility in aquatic environments, driven by a single polar flagellum,36 which relies on the expression of approximately 60 genes organized in at least 11 operons.37,38 Roy et al.39 reported that quercetin (0.09-0.36 mM) repressed flaA and flgL genes encoding flagellin, inhibiting V. parahaemolyticus motility and biofilm formation on shrimp and crab tissues. Our results corroborated these findings and further suggested that quercetin and morin may impair biofilm formation due to their motility-inhibiting effects. Notably, Vp124 (shrimp isolate) and Vp320 (clinical isolate) exhibited differential responses to flavonoids, with Vp124 being more resistant. Previous studies have indicated that mutations in sodium-type flagellar motor genes (motX and motY) confer resistance to known bacterial motility inhibitors, such as phenamil and amiloride.40 Investigating a potential similar resistance mechanism in these strains could be worthwhile. In contrast, the lack of inhibitory effects of vanillic and protocatechuic acids on V. parahaemolyticus motility suggests that they may interfere with biofilm formation through alternative mechanisms, such as modifying the physicochemical properties of the bacterial surface.18,20 This study provides insights into the potential role of phenolic compounds as motility inhibitors and enhances our understanding of biofilm disruption strategies in the aquaculture industry.\n\nThe different responses observed with flavonoid treatments between the Vp124 strain (isolated from shrimp), and the reference strain (clinical isolate) warrant further investigation to elucidate the underlying resistance mechanisms. It is plausible that genetic or phenotypic differences between the two strains may contribute to their varying susceptibilities to the tested compounds. The disparity in response could also be attributed to differences in gene expression profiles, metabolic pathways, or the presence of specific efflux pumps that confer resistance to these flavonoids.41 Further research employing genomic, transcriptomic, and proteomic approaches could help to identify the key genetic determinants and molecular pathways responsible for these differential responses. By understanding the resistance mechanisms in play, it may be possible to tailor more targeted and effective interventions for controlling V. parahaemolyticus infections in different settings, such as aquaculture and clinical environments. Despite the valuable insights gained from this study, some limitations should be acknowledged. Investigating a broader range of phenolic compounds and additional strains, including environmental isolates, would help to create a more complex panorama. In addition, the specific mechanisms exerted by phenolic compounds in motility and biofilm formation could go deeper into exploring the molecular targets and pathways involved in the observed inhibitory effects. Additionally, the potential synergistic or antagonistic interactions between the tested compounds and their combination with other antimicrobial agents should be investigated to identify more effective biofilm disruption and motility inhibition strategies. Future studies should incorporate in vivo and field experiments to evaluate the efficacy and feasibility of implementing these phenolic compounds. Addressing these limitations will deepen our understanding of the potential applications of phenolic compounds in controlling V. parahaemolyticus infections and mitigating biofilm-associated risks in the aquaculture industry.\n\n\nConclusions\n\nThis study provides valuable insights into the potential of phenolic compounds, particularly quercetin and morin, in controlling V. parahaemolyticus infections by inhibiting biofilm formation and motility. Quercetin and morin exhibited strong antibacterial activity compared to vanillic and protocatechuic acids. Moreover, both flavonoids effectively reduced biofilm formation and motility, supporting the hypothesis that these compounds can interfere with key virulence factors in V. parahaemolyticus. Finally, further research should address the study's limitations and focus on the underlying molecular mechanisms, synergistic or antagonistic interactions between the tested compounds, and in vivo efficacy to fully harness the potential of these phenolic compounds in combating V. parahaemolyticus infections.", "appendix": "Data availability\n\nFigshare: Underlying data supporting the results of the manuscript “Antimicrobial and Anti-Virulence Potential of Plant Phenolic Compounds Against Vibrio parahaemolyticus” https://doi.org/10.6084/m9.figshare.24123315.v4. 42\n\nData are available under the terms of the CC BY 4.0 Attribution International license (CC BY 4.0).\n\n\nAcknowledgments\n\nThe authors thank Q.B. Cesar Otero-Leon for technical support.\n\n\nReferences\n\nFAO: The State of World Fisheries and Aquaculture 2018 - Meeting the Sustainable Development Goals. Rome, Italy: 2018.\n\nPeña-Navarro N, Varela-Mejías A: Prevalencia de Las Principales Enfermedades Infecciosas En El Camarón Blanco Penaeus Vannamei Cultivado En El Golfo de Nicoya, Costa Rica. Rev. Biol. Mar. Oceanogr. 2016; 51(3): 553–564. Publisher Full Text\n\nSantos HM, Tsai C-Y, Maquiling KRA, et al.: Diagnosis and Potential Treatments for Acute Hepatopancreatic Necrosis Disease (AHPND): A Review. Aquac. Int. 2020; 28(1): 169–185. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNguyen T v, Alfaro A, Arroyo BB, et al.: Metabolic Responses of Penaeid Shrimp to Acute Hepatopancreatic Necrosis Disease Caused by Vibrio Parahaemolyticus. Aquaculture. 2021; 533: 736174. Publisher Full Text\n\nAdenaya A, Berger M, Brinkhoff T, et al.: Usage of Antibiotics in Aquaculture and the Impact on Coastal Waters. Mar. Pollut. Bull. 2023; 188: 114645. PubMed Abstract \| Publisher Full Text\n\nArunkumar M, LewisOscar F, Thajuddin N, et al.: In Vitro and in vivo Biofilm Forming Vibrio Spp: A Significant Threat in Aquaculture. Process Biochem. 2020; 94: 213–223. Publisher Full Text\n\nFlemming H-C, Wingender J, Szewzyk U, et al.: Biofilms: An Emergent Form of Bacterial Life. Nat. Rev. Microbiol. 2016; 14(9): 563–575. Publisher Full Text\n\nLee L-H, Ab Mutalib N-S, Law JW-F, et al.: Discovery on Antibiotic Resistance Patterns of Vibrio Parahaemolyticus in Selangor Reveals Carbapenemase Producing Vibrio Parahaemolyticus in Marine and Freshwater Fish. Front. Microbiol. 2018; 9: 9. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAshrafudoulla M, Mizan MFR, Ha AJ, et al.: Antibacterial and Antibiofilm Mechanism of Eugenol against Antibiotic Resistance Vibrio Parahaemolyticus. Food Microbiol. 2020; 91: 103500. PubMed Abstract \| Publisher Full Text\n\nNik Mohamad Nek Rahimi N, Natrah I, Loh J-Y, et al.: Phytocompounds as an Alternative Antimicrobial Approach in Aquaculture. Antibiotics. 2022; 11(4): 469. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nVazquez-Armenta FJ, Bernal-Mercado AT, Lizardi-Mendoza J, et al.: Phenolic Extracts from Grape Stems Inhibit Listeria Monocytogenes Motility and Adhesion to Food Contact Surfaces. J. Adhes. Sci. Technol. 2018; 32(8): 889–907. Publisher Full Text\n\nTinh TH, Elayaraja S, Mabrok M, et al.: Antibacterial Spectrum of Synthetic Herbal-Based Polyphenols against Vibrio Parahaemolyticus Isolated from Diseased Pacific Whiteleg Shrimp (Penaeus Vannamei) in Thailand. Aquaculture. 2021; 533: 736070. Publisher Full Text\n\nSkroza D, Šimat V, Smole Možina S, et al.: Interactions of Resveratrol with Other Phenolics and Activity against Food-borne Pathogens. Food Sci. Nutr. 2019; 7(7): 2312–2318. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDias R, Oliveira H, Fernandes I, et al.: Recent Advances in Extracting Phenolic Compounds from Food and Their Use in Disease Prevention and as Cosmetics. Crit. Rev. Food Sci. Nutr. 2021; 61(7): 1130–1151. PubMed Abstract \| Publisher Full Text\n\nAlbuquerque BR, Heleno SA, Oliveira MBPP, et al.: Phenolic Compounds: Current Industrial Applications, Limitations and Future Challenges. Food Funct. 2021; 12(1): 14–29. PubMed Abstract \| Publisher Full Text\n\nAbuga I, Sulaiman SF, Abdul Wahab R, et al.: In Vitro Antibacterial Effect of the Leaf Extract of Murraya Koenigii on Cell Membrane Destruction against Pathogenic Bacteria and Phenolic Compounds Identification. Eur. J. Integr. Med. 2020; 33: 101010. Publisher Full Text\n\nBhattacharya D, Bhattacharya S, Patra MM, et al.: Antibacterial Activity of Polyphenolic Fraction of Kombucha Against Enteric Bacterial Pathogens. Curr. Microbiol. 2016; 73(6): 885–896. PubMed Abstract \| Publisher Full Text\n\nBernal-Mercado A, Vazquez-Armenta F, Tapia-Rodriguez M, et al.: Comparison of Single and Combined Use of Catechin, Protocatechuic, and Vanillic Acids as Antioxidant and Antibacterial Agents against Uropathogenic Escherichia Coli at Planktonic and Biofilm Levels. Molecules. 2018; 23(11): 2813. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nVazquez-Armenta FJ, Bernal-Mercado AT, Tapia-Rodriguez MR, et al.: Quercetin Reduces Adhesion and Inhibits Biofilm Development by Listeria Monocytogenes by Reducing the Amount of Extracellular Proteins. Food Control. 2018; 90: 266–273. Publisher Full Text\n\nLemos M, Borges A, Teodósio J, et al.: The Effects of Ferulic and Salicylic Acids on Bacillus Cereus and Pseudomonas Fluorescens Single- and Dual-Species Biofilms. Int. Biodeterior. Biodegradation. 2014; 86: 42–51. Publisher Full Text\n\nLiu H, Xiao M, Zuo J, et al.: Vanillic Acid Combats Vibrio Alginolyticus by Cell Membrane Damage and Biofilm Reduction. J. Fish Dis. 2021; 44(11): 1799–1809. PubMed Abstract \| Publisher Full Text\n\nGuardiola-Avila I, Martínez-Vázquez V, Juárez-Rendón K, et al.: Prevalence and Virulence of Vibrio Species Isolated from Raw Shrimp from Retail Markets in Reynosa, Mexico. Lett. Appl. Microbiol. 2020; 71(3): 280–286. PubMed Abstract \| Publisher Full Text\n\nAlvarez Mv, Ortega-Ramirez LA, Gutierrez-Pacheco MM, et al.: Oregano Essential Oil-Pectin Edible Films as Anti-Quorum Sensing and Food Antimicrobial Agents. Front. Microbiol. 2014; 5: 5. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBeltran-Torres M, Sugich-Miranda R, Santacruz-Ortega H, et al.: Synthesis and Characterization of Bismuth (III) Complex with an EDTA-Based Phenylene Ligand and Its Potential as Anti-Virulence Agent. PeerJ Inorganic Chemistry. 2022; 4: e4. Publisher Full Text\n\nWu Y, Bai J, Zhong K, et al.: Antibacterial Activity and Membrane-Disruptive Mechanism of 3-p-Trans-Coumaroyl-2-Hydroxyquinic Acid, a Novel Phenolic Compound from Pine Needles of Cedrus Deodara, against Staphylococcus Aureus. Molecules. 2016; 21(8): 1084. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTinh TH, Elayaraja S, Mabrok M, et al.: Antibacterial Spectrum of Synthetic Herbal-Based Polyphenols against Vibrio Parahaemolyticus Isolated from Diseased Pacific Whiteleg Shrimp (Penaeus Vannamei) in Thailand. Aquaculture. 2021; 533: 736070. Publisher Full Text\n\nTsuchiya H: Structure-Dependent Membrane Interaction of Flavonoids Associated with Their Bioactivity. Food Chem. 2010; 120(4): 1089–1096. Publisher Full Text\n\nWu T, He M, Zang X, et al.: A Structure–Activity Relationship Study of Flavonoids as Inhibitors of E. Coli by Membrane Interaction Effect. Biochim. Biophys. Acta Biomembr. 2013; 1828(11): 2751–2756. PubMed Abstract \| Publisher Full Text\n\nWu T, Zang X, He M, et al.: Structure–Activity Relationship of Flavonoids on Their Anti-Escherichia Coli Activity and Inhibition of DNA Gyrase. J. Agric. Food Chem. 2013; 61(34): 8185–8190. PubMed Abstract \| Publisher Full Text\n\nWu D, Kong Y, Han C, et al.: D-Alanine:D-Alanine Ligase as a New Target for the Flavonoids Quercetin and Apigenin. Int. J. Antimicrob. Agents. 2008; 32(5): 421–426. PubMed Abstract \| Publisher Full Text\n\nGloag ES, Fabbri S, Wozniak DJ, et al.: Biofilm Mechanics: Implications in Infection and Survival. Biofilm. 2020; 2: 100017. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSanthakumari S, Jayakumar R, Logalakshmi R, et al.: In Vitro and in vivo Effect of 2,6-Di-Tert-Butyl-4-Methylphenol as an Antibiofilm Agent against Quorum Sensing Mediated Biofilm Formation of Vibrio Spp. Int. J. Food Microbiol. 2018; 281: 60–71. PubMed Abstract \| Publisher Full Text\n\nSoowannayan C, Boonmee S, Puckcharoen S, et al.: Ginger and Its Component Shogaol Inhibit Vibrio Biofilm Formation in vitro and Orally Protect Shrimp against Acute Hepatopancreatic Necrosis Disease (AHPND). Aquaculture. 2019; 504: 139–147. Publisher Full Text\n\nWang L, Ling Y, Jiang H, et al.: AphA Is Required for Biofilm Formation, Motility, and Virulence in Pandemic Vibrio Parahaemolyticus. Int. J. Food Microbiol. 2013; 160(3): 245–251. PubMed Abstract \| Publisher Full Text\n\nWatnick PI, Lauriano CM, Klose KE, et al.: The Absence of a Flagellum Leads to Altered Colony Morphology, Biofilm Development and Virulence in Vibrio Cholerae O139. Mol. Microbiol. 2001; 39(2): 223–235. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFreitas C, Glatter T, Ringgaard S: The Release of a Distinct Cell Type from Swarm Colonies Facilitates Dissemination of Vibrio Parahaemolyticus in the Environment. ISME J. 2020; 14(1): 230–244. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLu R, Sun J, Qiu Y, et al.: The Quorum Sensing Regulator OpaR Is a Repressor of Polar Flagellum Genes in Vibrio Parahaemolyticus. J. Microbiol. 2021; 59(7): 651–657. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWang Q, Wang P, Liu P, et al.: Comparative Transcriptome Analysis Reveals Regulatory Factors Involved in Vibrio Parahaemolyticus Biofilm Formation. Front. Cell. Infect. Microbiol. 2022; 12: 12. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRoy PK, Park S-H, Song MG, et al.: Antimicrobial Efficacy of Quercetin against Vibrio Parahaemolyticus Biofilm on Food Surfaces and Downregulation of Virulence Genes. Polymers (Basel). 2022; 14(18): 3847. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJaques S, Kim Y-K, McCarter LL: Mutations Conferring Resistance to Phenamil and Amiloride, Inhibitors of Sodium-Driven Motility of Vibrio Parahaemolyticus. Proc. Natl. Acad. Sci. 1999; 96(10): 5740–5745. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nStephen J, Lekshmi M, Ammini P, et al.: Membrane Efflux Pumps of Pathogenic Vibrio Species: Role in Antimicrobial Resistance and Virulence. Microorganisms. 2022; 10(2): 382. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nVazquez-Armenta FJ, Aros-Corrales MO, Alvarez-Ainza ML, et al.: Underlying data supporting the results of the manuscript “Antimicrobial and Anti-Virulence Potential of Plant Phenolic Compounds Against Vibrio parahaemolyticus”. figshare. Dataset. 2023. Publisher Full Text" }	[ { "id": "272299", "date": "15 May 2024", "name": "Saharuetai Jeamsripong", "expertise": [ "Reviewer Expertise antimicrobial resistance", "aquaculture", "epidemiology", "food safety" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nAntibacterial and anti-virulence potential of plant phenolic compounds against Vibrio parahaemolyticus\nThis study investigated antibacterial and anti-virulence effects of the plant phenolic compounds quercetin, morin, vanillic acid, and protocatechuic acid on two strains of V. parahaemolyticus (Vp124 and Vp320). Major concerns\nNo reference protocols and equations are provided in the materials and methods section. Details of media and reagents used, including company, city, and country should be included. Why did the authors choose to test only two strains of V. parahaemolyticus? Testing only two isolates of V. parahaemolyticus is a major limitation due to the small sample size, which may affect the accuracy and generalizability of the study. This limitation should be addressed. How many replicates were used in the experiments? The rationale for selecting phenolic compounds over other chemicals should be explained. The antibiotics and their concentrations used for treatment of Vibrio infection comparison with phenolic compounds should be specified. Additionally, the challenges of using plant phenolic compounds, including quantity of phenolic compounds and field application feasibility, should be discussed.\nMinor concerns\nPlease verify the unit of MIC in the abstract. There is an inconsistency in the results for vanillic acid in the table (31.73) and the text (32.73). This discrepancy needs to be corrected. Data regarding the antibacterial activity of quercetin and morin, which is 20-40 times higher than that of phenolic acids, is redundant in discussion and should be revised.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? 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?\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": "11903", "date": "26 Jun 2024", "name": "Francisco Javier Vázquez Armenta", "role": "Author Response", "response": "Dear reviewer, We want to express our gratitude for your constructive comments, which have significantly helped us improve the quality and clarity of our manuscript. Here, we provide a point-by-point response to major and minor concerns. Major concerns No reference protocols and equations are provided in the materials and methods section. Response: we appreciate your observations. The materials and methods section was improved, including the reference in the first sentence of each section. Details of media and reagents used, including company, city, and country should be included. Response: Details of media and reagents were included in the materials and method section. Why did the authors choose to test only two strains of V. parahaemolyticus? Testing only two isolates of V. parahaemolyticus is a major limitation due to the small sample size, which may affect the accuracy and generalizability of the study. This limitation should be addressed. Response: we appreciate your feedback and acknowledge the limitation regarding the sample size of V. parahaemolyticus strains tested in our study. We selected two strains with distinct phenotypic and genotypic profiles to provide a starting point for understanding the potential variability within this species. However, we agree that the small sample size limits the generalizability of our findings. We plan to expand our study to include a larger and more diverse set of V. parahaemolyticus isolates to address this. This will allow us to validate our preliminary results and enhance the accuracy and applicability of our conclusions. We will also explicitly mention this limitation in the discussion section of our manuscript and outline our future research plans to address this issue. By doing so, we aim to provide a more comprehensive understanding of V. parahaemolyticus and contribute to the broader body of knowledge in this field. How many replicates were used in the experiments? Response: All experiments were done in triplicate. The rationale for selecting phenolic compounds over other chemicals should be explained. Response: thank you for your observation. We appreciate the opportunity to clarify our rationale for selecting phenolic compounds for this study. The selection of phenolic compounds was driven by the proven antimicrobial properties, safety profile, natural origin, and the potential for synergistic effects. Phenolic compounds exert antimicrobial effects by disrupting cell membranes, inactivating essential enzymes, and interfering with microbial metabolism, enhancing their inhibitory potential against bacteria. Their natural occurrence in plants and presence in the human diet generally make them safer than synthetic chemicals, aligning with the trend toward plant-based antimicrobials. Previous research has demonstrated their efficacy against various Vibrio species, and the current study aims to confirm their effectiveness specifically against V. parahaemolyticus. Additionally, phenolic compounds can work synergistically with other antimicrobial agents, suggesting their potential in developing more effective treatment strategies. We will incorporate this rationale into the manuscript to provide a clearer understanding of our choice and strengthen the context of our research. Thank you again for your insightful feedback. The antibiotics and their concentrations used for treatment of Vibrio infection comparison with phenolic compounds should be specified. Additionally, the challenges of using plant phenolic compounds, including quantity of phenolic compounds and field application feasibility, should be discussed. Response: we appreciate the opportunity to address these important points and provide additional clarity in our study. We recognize the significance of discussing the concentration of antibiotics used in aquiculture and the challenges of using plant-derived phenolic compounds to treat Vibrio infections. Accordingly, we have included a detailed paragraph in the discussion section to address these issues comprehensively. Minor concerns Please verify the unit of MIC in the abstract. Response: the MIC unit in the abstract was verified. There is an inconsistency in the results for vanillic acid in the table (31.73) and the text (32.73). This discrepancy needs to be corrected. Response: we appreciate your observation; the correct value of MIC is 31.73 mM. Data regarding the antibacterial activity of quercetin and morin, which is 20-40 times higher than that of phenolic acids, is redundant in discussion and should be revised. Response: we appreciate your observation; this issue was addressed. Thank you again for your comments. Sincerely, The authors" } ] }, { "id": "260789", "date": "21 May 2024", "name": "Chumporn Soowannayan", "expertise": [ "Reviewer Expertise Fish and shrimp diseases" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe work is interesting and could be helpful to aquatic animal and human health research or bacteria disease research in general. The comments and questions are posted in the attached main manuscript file which can be viewed here.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "11905", "date": "26 Jun 2024", "name": "Francisco Javier Vázquez Armenta", "role": "Author Response", "response": "Dear reviewer, We appreciate your valuable feedback, which has greatly enhanced the quality and clarity of our manuscript. Below, we address each of your major and minor concerns point-by-point. Please check if this sentence is correct. If I'm not wrong, the world cultured shrimp production in 2023 was around 6 million tons, but the total aquaculture production of that year was around 96 million tons. Response: We appreciate your observations. The sentence was modified to indicate that this percentage is relative to crustacean production. Also, the reference was updated to the last published report. Many Vibrio species can cause AHPND, not just V. parahaemolyticus. Response: We appreciate your observations and agree that many AHPNDs are caused by vibrio and non-vibrio species carrying the pVA-1 plasmid, which expresses the PirAB toxin. The paragraph was modified as follows: “Vibrio parahaemolyticus is considered of veterinary importance in shrimp farming, as some strains can infect shrimp, causing various diseases such as vibriosis. Strains that have acquired the pVA-1 plasmid, encoding the PirAB toxin, are of special concern because they cause Acute Hepatopancreatic Necrosis Disease (AHPND), initially known as Early Mortality Syndrome (EMS)3. This atypical vibriosis has been responsible for losses of about 90% of production and, in some cases, up to 100%.” Are the bacteria causing AHPND the same as those causing disease in humans? If I'm right, they are different. Response: The bacteria causing Acute Hepatopancreatic Necrosis Disease (AHPND) in shrimp are typically strains of Vibrio parahaemolyticus, which are different from the strains that usually cause disease in humans. The paragraph was restructured to mention only the consequences of V. parahaemolyticus infections in shrimp farming. What was the concentration of each compound in DMSO? What were the final concentrations of the DMSO left in the final cultures? Response: The concentration of the DMSO stocks varies based on the evaluated compound, and the final cultures (both treatments and controls) had a 5% DMSO concentration. How many replicates were performed for each compound and each concentration? Response: MIC and MBC were made in triplicate. Is this the correct reference? Response: The correct reference was included. How many replicates? Response: Each experiment was performed in triplicate. Why use standard error, not standard deviation? Response: We have chosen to display the standard error on the graphs to show the accuracy of the estimate of the population mean, thereby providing a clear indication of the precision of our results. Additionally, using standard error helps readers visualize the differences among treatments, facilitating an intuitive comparison of the variability and significance between different groups. How do we know if these two are the cause or the effect? Response: Vibrio parahaemolyticus has two types of motilities: swimming and swarming. The former uses a polar flagellum in liquid media, and the latter uses lateral flagella in solid media or viscous environments. In our study, we focused on swimming motility since this kind of movement is related to the initial attachment of Vibrio to solid surfaces to start biofilm development (Zhang et al. 2023, Lu et al. 2021). Thank you again for your comments. Sincerely, The authors References: Lu, Renfei, Junfang Sun, Yue Qiu, Miaomiao Zhang, Xingfan Xue, Xue Li, Wenhui Yang, Dongsheng Zhou, Lingfei Hu, and Yiquan Zhang. 2021. \"The quorum sensing regulator OpaR is a repressor of polar flagellum genes in Vibrio parahaemolyticus.\" Journal of Microbiology 59 (7):651-657. doi: 10.1007/s12275-021-0629-3. Zhang, Yiquan, Tingting Zhang, Yue Qiu, Miaomiao Zhang, Xiuhui Lu, Wenhui Yang, Lingfei Hu, Dongsheng Zhou, Bo Gao, and Renfei Lu. 2023. \"Transcriptomic Profiles of Vibrio parahaemolyticus During Biofilm Formation.\" Current Microbiology 80 (12):371. doi: 10.1007/s00284-023-03425-7." } ] } ]	1	https://f1000research.com/articles/12-1256
https://f1000research.com/articles/10-1105/v1	02 Nov 21	{ "type": "Research Article", "title": "New incidence or recurrence hepatocellular carcinoma (HCC) in genotype 4 hepatitis C virus treated with sofosbuvir/daclatasvir with or without ribavirin", "authors": [ "Aya Essawy", "Mai Mehrez", "Sara M. Shaheen", "Hassan El Garem", "Nagwa A. Sabri", "Mai Mehrez", "Sara M. Shaheen", "Hassan El Garem", "Nagwa A. Sabri" ], "abstract": "Background: Several studies have resulted in controversial data about the recurrence or new incidence of hepatocellular carcinoma (HCC) in patients with hepatitis C who were treated with direct-acting antivirals (DAAs).\n\nAim: This observational study aimed to assess the occurrence rate of HCC in patients who developed a sustained virological response (SVR).. METHOD: A six-month prospective study was done at the National Hepatology and Tropical Medicine Research Institute [NHTMRI] in Cairo, Egypt on 150 chronic hepatitis C (CHC) patients treated with sofosbuvir and daclatasvir with or without ribavirin. Patients were assigned into two groups according to their laboratory values to either receive sofosbuvir/daclatasvir and ribavirin (S/D/R) or receive only sofosbuvir/daclatasvir (S/D). The main outcome measure was the occurrence of HCC. Results: SVR-12 was 100%. 8.5% of patients developed HCC in the S/D/R group, while 0% in the S/D group. Conclusion: New incidence or recurrence of HCC may occur in CHC genotype 4 cirrhotic patients receiving sofosbuvir/daclatasvir and ribavirin (difficult to treat) although achieving SVR. The cause of HCC development in this study is cirrhosis, not the administered DAAs.", "keywords": [ "Chronic hepatitis C", "Direct-acting antivirals", "Hepatocellular carcinoma", "Hepatitis c virus", "Sofosbuvir." ], "content": "Introduction\n\nHepatitis C virus (HCV) is a major public medical condition. A quarter of infected patients have cirrhosis and associated complications, such as hepatocellular carcinoma. Treatment aims to remove the virus and prevent the development of cirrhosis and its complications. The treatment target for HCV has been identified in terms of a sustained virologic response (SVR), which is the absence of detectable levels of viral RNA in the blood 24 weeks after the end of the drug course.1\n\nThe prevalence of hepatitis C virus (HCV) infection is the highest in the world in Egypt. It became clear that HCV infection was widespread among Egyptians and that it was the main cause of liver disease in the region. Before the HCV epidemic became evident, schistosomiasis was Egypt’s most significant public health issue.2\n\nWorldwide, 180 million people develop chronic HCV infections. While genotype 1 accounts for approximately 48% of HCV infections, the distribution of the seven genotypes varies geographically. Genotype 4 infections are around 20% of all HCV infections worldwide but accounts for nearly 93% of all HCV cases in Egypt.3\n\nGlobally, hepatocellular carcinoma (HCC) is known to be a severe malignancy with an approximate incidence of 5.6%. The second most common cause of all cancer-related deaths is also considered. Infection with HCV, studies have indicated that in approximately 30%of patients with chronic hepatitis C, the liver progresses towards cirrhosis of the liver. HCV functions as carcinogenic by many causes, direct viral oncogenic effects, or chronic inflammation and fibrosis.4\n\nThe pegylated interferon routine has long been a lonely potent regulation of chronic hepatitis C with moderate efficacy. The first appearance of boceprevir and telaprevir protease inhibitors was considered a significant breakthrough, but the potency of both drugs was limited to genotype 1. Currently, direct antiviral drugs have started a new era to effective control of HCV, undoubtedly following the approval by the FDA of medication that have further lead to a complete removal of HCV.5\n\nEvaluation of HCC prevalence and hazard factors following a sustained virological response (SVR) is necessary to give priority to HCC surveillance patients during the DAA period. Evidence is especially restricted on the HCC risk of presenting SVR among people with superior fibrosis to support the most effective SVR follow-up for HCC.6\n\nPatients with HCV-associated cirrhosis who have been treated with DAAs do not tend to minimize the occurrence of HCC over a limited time. Cirrhotic patients must also be closely monitored during and after antiviral therapy by applying or persevering with HCC monitoring, regardless of HCV infection treatment.7\n\nBerge et al. reported one of the above-mentioned mechanisms of HCC induced by DAAs. As they cause a rapid decrease in HCV RNA levels leading to a fast decline in natural killer cells (NK) activity.8\n\nThe study aimed to examine new-onset or relapse of HCC in patients receiving Sofosbuvir and Daclatasvir both with and without Ribavirin.\n\n\nEthical approval\n\nThe study protocol was accepted by the Ethics Committee of the National Hepatology and Tropical Medicine Research Institute [NHTMRI 6-2017], approval date:18/2/2017 in Cairo, Egypt. This research was reported on ClinicalTrials.gov with ID number: NCT03247296. This research was performed following the criteria set out in the Norms of Good Clinical Practice and the Helsinki Declaration. Before enrollment, all patients have been informed of the study methodology and they signed detailed written consent.\n\n\nMethods\n\nThis observational study was a six-month observational Prospective study that included 150 adults to detect HCC occurrence in HCV patients treated with SOF, DAC with or without RIB. Patients were recruited from the outpatient clinic of the National Hepatology and Tropical Medicine Research Institute (NHTMRI), Cairo, Egypt.\n\nThe study was performed on those who implemented the criteria of inclusion of the National Committee for Control of Viral Hepatitis, Ministry of Health and Population (MOHP), Egypt, and included male and female patients aged 18 to 75 years old, easy to treat group [treatment-naïve patients with PCR positive serum HCV RNA, total serum [bilirubin ≤1.2 mg/dL, albumin ≥3.5 g/dL, INR ≤1.2, and platelet count ≥150,000/mm3]. And difficult-to-treat group [interferon treatment-experienced, total serum bilirubin <1.2mg/dL, serum albumin <3.5 g/dL, INR >1.2, and/or platelet count <150,000/mm3]. For an ethical reason, there was no control group for this study because it was immoral to allocate an infected group without care. Also excluded were individuals with inadequately managed diabetes mellitus (HbA1c >9 %), total serum bilirubin, serum albumin, INR, platelet count> 3 mg/dL, >2.8 g/dL, ≥1.7, and <50,000/mm3 respectively. co-infection with HIV, HBV, any chronic liver disease other than hepatitis C, poorly controlled hypothyroidism, hepatocellular carcinoma with exception of 4 weeks after treatment with no proof of dynamic imaging activity (CT or MRI), extra-hepatic malignancy except after two years of disease-free interval, patients with Child's Paugh C.\n\nPatients’ demographics, laboratory test results, and abdominal ultrasounds reports were collected. Verbally communicated information, via phone or directly from the patients, about the drug side effects were included. Medical records were screened for evidence of medication error and interaction occurrence taking into consideration that all the medication orders were handwritten. 150 patients were allocated into two groups according to their physical examination and lab parameters: difficult-to-treat group taking sofosbuvir/daclatasvir/ribavirin(S/D/R) and easy-to-treat group taking sofosbuvir/daclatasvir (S/D). Figure 1 shows the methodology and primary results in a graphical image.\n\nLab parameters of the study participants were tested three times. At baseline, all participants were subjected to medical assessment, lab tests as well as quantitative HCV-RNA, fasting blood sugar levels or HbA1C if diabetes present as comorbidity, serum creatinine, CBC, AST, ALT, concentration of prothrombin or INR, total bilirubin, serum albumin, a test of pregnancy (childbearing aged females), alfa fetoprotein (AFP) as an HCC biomarker. Any participants who were men >40 years old, or women >50 years old underwent abdominal ultrasonography and electrocardiogram before start of the treatment.\n\nVirological response to treatment was evaluated using quantitative HCV RNA assessment, by PCR. Laboratory tests for the participants including, serum creatinine, ALT, AST, CBC, HbA1C if diabetic, INR, serum total bilirubin, albumin, AFP. Abdominal ultrasonography was repeated and any suspected focal lesion of the liver was examined with a triphasic CT scan or MRI to investigate the occurrence or the recurrence of HCC at the antiviral treatment end (12 weeks from the start) and SVR 12 (24 weeks from the start).\n\nEnrolment was dependent on the clinical need for medication rather than on statistical factors.\n\nData were obtained, reviewed, and entered, processed, and statistically analyzed using SPSS Version 21 (RRID:SCR_002865); an open-access alternative is JASP (RRID:SCR_015823). The statistical significance of the difference between the two-study mean sample was analyzed by Mann–Whitney's U-test. For categorical results, a Chi-squared test was used. For the analysis of repeated measurements, the Kruskal–Wallis test was implemented to determine the statistical significance of the discrepancy between more than two study group means. The Dunn test was chosen as a post hoc test. P-values of less than 0.05 were considered statistically significant. A Kaplan–Meier estimator was used to determine the occurrence rate or recurrence of HCC, the log-rank (Mantel–Cox) test was used to test the difference between classes.\n\nThe sample size was estimated considering a 10% improvement in AFP between treatment groups as clinically significant. Assuming a standard deviation of 42, a total of 65 patients will be expected to detect a 10% improvement in AFP with a power of 80% at a significance level of 0.05. However, despite the possible drop-out or lack of follow-up, a total of 150 patients were enrolled.\n\n\nResults\n\nThe current prospective research included 150 treatment-naïve chronic hepatitis C patients. Out of 150 patients, 145 accomplished the 12 weeks of protocol regimen with no reported clinically significant side effects. Four patients were eliminated from the study due to non-compliance and one patient died of non-medication-related cause in the (S/D/R) group. There remained 71 patients (30 males and 41 females) with mean age 53 ± 11.17 in the S/D/R group and 74 patients (29 males and 45 females) with mean age 46.1 ± 12.6 in the S/D group. Ribavirin dose modification was done for two patients who suffered from low hemoglobin (9.5 and 9 g/dL respectively for the two patients) during the treatment course. The study participants were assessed at end of treatment (EOT) and SVR12 after cessation of therapy. Basic demographic data and biochemical parameters are shown in Table 1.\n\nSix patients (three males and three females) from the S/D/R group were diagnosed with HCC although all of them achieved sustained virological response (SVR-12). All with a single HCC lesion detected by triphasic CT scan. Four (66.66%) patients were diagnosed with HCC at the EOT followup, while two (33.33%) patients were diagnosed at the SVR12 follow up. All six patients were cirrhotic from the beginning of the study. The two patients who were diagnosed with HCC at SVR12 follow-up had a history of treated HCC before the start of the study. As all the six patients were cirrhotic, and cirrhosis plays a vital role in developing HCC, cirrhosis and different DAA regimens against HCC development were evaluated using the Chi-squared test to evaluate either the resulted HCC was a consequence of cirrhosis or the used DAA regimens P-value was >0.05 for the DAA regimens, on the other hand, P-value was <0.05 for the relation of cirrhosis with HCC. Using Kaplan–Meier analysis (Figure 2), the cumulative rate of HCC at SVR12 was 30% for the cirrhotic patients who received S/D/R, P<0.001 by log-rank test.\n\nAnd the difference between the two groups was evaluated using Log-rank (Mantel-Cox) test P value < 0.05 (significant difference)\n\nAs the great deviation in HCC patients’ lab values, they were studied separately as shown in Table 2. Analysis and comparison of the biochemical values (baseline, EOT, and SVR12) revealed that values of bilirubin, platelet, and INR were significantly different from the baseline with (P-value <0.05)\n\nThe child score and AFP levels of those patients were significantly different (P-values <0.05).\n\n\n\n▪ Sustained virological response (SVR):\n\nAll 145 patients who completed the study achieved SVR, including six patients diagnosed with HCC.\n\n▪ Biochemical lab values\n\nLaboratory data of the two groups excluding the patients who developed HCC. at EOT and SVR12 weeks, follow-up was collected and statistically analyzed as shown in Table 3.\n\nAt the EOT follow-up, the S/D group showed significantly lower values than the S/D/R group in child score, bilirubin, INR, and AFP with P-values <0.05. On the contrary, the S/D/R group showed significantly lower values than the S/D group in albumin, WBCs, hemoglobin, platelet, and glycated hemoglobin levels with P-values <0.05. The previous results changed at SVR12 follow up as the S/D group keeps its place in significantly lower values than S/D/R group in bilirubin and AFP with P-values <0.05 in both. On the other hand, the S/D/R group showed significantly lower values in albumin, WBCs, hemoglobin, platelets, and INR, with p values <0.05.\n\n\nDiscussion\n\nDirect-acting antivirals (DAA) have effectively produced a new HCV-eradication era. The involvement of DAAs in developing HCC in these patients is still questionable.9 More than one study has documented different findings of the relationship between therapy by the DAAs and emerging HCC.10 The findings of those studies were as follows, the previous one from Barcelona stated the HCC relapse in 27.6% of the studied patients after a median follow-up of 5.7 months. While they achieved sustained virological response and had a negative residual HCC before treatment.11\n\nThe rates of 28.8% of HCC recurrence and 3.16% of HCC incidence were the result of an Italian study that included 59 patients with HCC history and 295 patients negative for HCC.7 Another research from France12 which included 6000 patients who were treated with interferon (IFN)-free regimens had rebutted both Spanish11 and Italian reports. Researchers found no raise in the development of HCC and an approximately low risk of recurrence of HCC.13\n\nConcerning HCC incidence in the current study, six patients out of 71 from the SOF/DAC/RIB group had developed HCC with an incidence rate of 8.5% in a mean time 18 weeks from starting the DAAs treatment. These results came in agreement with those reported by Conti et al. who reported HCC incidence of 7.6% in DAA-treated patients.7\n\nOn the other hand, Calvaruso et al. found that the incidence of HCC was only 3.5% and this contrary can be attributed to different DAAs regimens used in both studies.14\n\nIn the present study, the explanation of different outcomes in developing hepatocellular carcinoma between the two groups is that patients in the S/D/R group had more advanced liver disease as shown by their biochemical data. The mean age of patients in the S/D/R group was 53 years old, which was significantly different from those in the S/D group. It is confirmed by the statistical analysis of this study results that the cirrhosis of the six patients is the main cause of their HCC development. This study's point of strength is the regimen detailing in the two groups and accurately illustrating the HCC development in the difficult-to-treat group patients, not the easy-to-treat group which can be a unique finding in Egyptian genotype 4 patients.\n\nUpon studying the follow-up parameters of the patients who developed HCC in the current study it was found that there was an increase in Child scores, ALT, AST, bilirubin, WBCs, INR, and AFP values while there was a decrease in albumin, hemoglobin, and platelets levels, those results came in agreement with those detected by Rewisha et al.13\n\nConcerning the virological response, patients in this study achieved 100% SVR which is greater than the percentages of both Mann et al. (84.9%) and Pariente et al. (91.1%); this difference in results may be attributed to the genotype difference of the patients and their response to the Sof/Dac regimen.15,16\n\nConcerning the biochemical parameters of the patients in the two groups, the comparison resulted in significantly lower values in SOF/DAC group than SOF/DAC/RIB group in child score, bilirubin, INR, and AFP with P values <0.05. On the contrary, the SOF/DAC/RIB group showed significantly lower values than the SOF/DAC group in albumin, WBCs, hemoglobin, platelet, and glycated hemoglobin levels with P values <0.05. Those biochemical values were comparable to those reported by Welzel et al. but, the bilirubin values between the two groups were equal. The drop in hemoglobin levels can be attributed to the fact that Ribavirin resulted in hemolytic anemia through direct oxidative damage followed by a decreased lifespan of the RBC.17,18\n\nA significant outcome of this research was the discovery of reduced AFP levels following treatment with DAAs; similar to those observed by Stine et al. and, as a result of their findings, they proposed a future study that AFP could be considered as a biomarker for the probability of SVR and indicated that AFP should be collected earlier than planned during therapy (e.g. week 4) rather than a viral load.18\n\nSerum creatinine didn’t show any significant change between groups which confirming the safe use of sofosbuvir-based regimens on kidney function and consequently their use in patients with chronic kidney disease patients as mentioned by Sise et al.19\n\nIt’s worth mentioning a case reported by Ahmed M. who reported that harvoni (which also contains sofosbuvir) induced kidney function deterioration in a patient with normal kidney function, which keeps monitoring kidney functions while treating HCV patients an important issue.20\n\n\nConclusion\n\nAfter analyzing the data resulted in this study, we concluded that DAAs don’t raise the risk of developing new incidence or recurrence HCC. The developing HCC risk is increased with cirrhosis, So close monitoring of cirrhotic patients receiving DAAs is required. Other different studies from different geographical areas reported conflicting conclusions about the relation of incidence or recurrence of HCC after DAAs treatment although the SVR achievement in some of those patients. So the close monitoring of patients who will be assigned to the difficult-to-treat group is becoming mandatory.\n\n\nFunding\n\nThis research received no specific grant from any funding agency in the public, commercial, or not-for-profit sectors.\n\n\nDeclarations\n\nThis study was conducted in accordance with the principles outlined in the Good Clinical Practice standard and the Declaration of Helsinki. Prior to participation, all patients were informed about the study protocol and they signed written informed consent.\n\nNo, the results/data/figures in this manuscript have not been published elsewhere nor are they under consideration from any of the contributing authors by another publisher.\n\n\nData availability\n\nDryad: Underying data for New incidence or recurrence hepatocellular carcinoma (HCC) in genotype 4 hepatitis C virus treated with sofosbuvir/daclatasvir with or without ribavirin.\n\nProject data, https://doi.org/10.5061/dryad.x0k6djhk9. This project contains the following underlying data:\n\n▪ Data file 1: Demographic data of the S/D group\n\n▪ Data file 2: Demographic data of the S/D group\n\n▪ Data file 3: Basal data of the S/D group\n\n▪ Data file 4: Basal data of the S/D/R group\n\n▪ Data file 5: Basal data of the HCC patients\n\n▪ Data file 6: Comorbidities of the S/D/R group\n\n▪ Data file 7: Comorbiditis of the S/D group\n\n▪ Data file 8: Diabetic patients of the S/D group with their basal glycated values\n\n▪ Data file 9: Diabetic patients of the S/D/R group with their basal glycated values\n\n▪ Data file 10: EOT glycated Hgb value for both groups\n\n▪ Data file 11: EOT data for S/D group\n\n▪ Data file 12: EOT data for S/D/R group\n\n▪ Data file 13: EOT data for HCC patients\n\n▪ Data file 14: SVR 12 data for S/D group\n\n▪ Data file 15: SVR 12 data for S/D/R group\n\n▪ Data file 16: SVR 12 data for HCC patients\n\n▪ Readme file\n\nZenodo: Protocol, ethics approvals, informed consent, inclusion and exclusion criteria, https://doi.org/10.5281/zenodo.5534899.\n\nThis project contains the following:\n\n▪ Data file 1: plain form of data collection sheet\n\n▪ Data file 2: trial protocol\n\n▪ Data file 3: Informed consent\n\n▪ Data file 4: Ethics committee approval of the NHTMRI\n\n▪ Data file 5: enrollment method with inclusion and exclusion criteria\n\nZenodo: STROBE checklist for ‘New incidence or recurrence hepatocellular carcinoma (HCC) in genotype 4 hepatitis C virus treated with sofosbuvir/daclatasvir with or without ribavirin’, https://doi.org/10.5281/zenodo.5534899.\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).", "appendix": "Acknowledgment\n\nWe would like to express our deepest appreciation to our advisor Prof. Abd El Rahman El Naggar for the great support to this study completion.\n\n\nReferences\n\nJazwinski AB, Muir AJ: Direct-acting antiviral medications for chronic hepatitis C virus infection. Gastroenterol Hepatol. 2011; 7(3): 154–162.\n\nGomaa A, Allam N, Elsharkway A: Hepatitis C infection in Egypt: prevalence, impact and management strategies. Hepatic Med Evid Res. 2017; 9: 17–25. Publisher Full Text\n\nWaked I, Shiha G, Qaqish RB, et al.: Ombitasvir, paritaprevir, and ritonavir plus ribavirin for chronic hepatitis C virus genotype 4 infection in Egyptian patients with or without compensated cirrhosis (AGATE-II): a multicentre, phase 3, partly randomised open-label trial. Lancet Gastroenterol Hepatol. 2016; 1(1): 36–44. PubMed Abstract \| Publisher Full Text\n\nAbdelaziz AO, Nabil MM, Abdelmaksoud AH, et al.: De-novo versus recurrent hepatocellular carcinoma following direct-acting antiviral therapy for hepatitis C virus. Eur J Gastroenterol Hepatol. 2018; 30(1): 39–43. Publisher Full Text\n\nElbaz T, El-Kassas M, Esmat G: New era for management of chronic hepatitis C virus using direct antiviral agents: A review. J Adv Res. 2015; 6(3): 301–310. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJanjua NZ, Chong M, Kuo M, et al.: Long-term effect of sustained virological response on hepatocellular carcinoma in patients with hepatitis C in Canada. J Hepatol. 2017; 66(3): 504–513. Publisher Full Text\n\nConti F, Buonfiglioli F, Scuteri A, et al.: Early occurrence and recurrence of hepatocellular carcinoma in HCV-related cirrhosis treated with direct-acting antivirals. J Hepatol. 2016; 65(4): 727–733. PubMed Abstract \| Publisher Full Text\n\nBerge E, Arencibia A, Otón E, et al.: Clinical outcomes of direct-acting antiviral therapy in patients with compensated hepatitis C virus-related cirrhosis. Hepatoma. 2017; 3: 209–214. Publisher Full Text\n\nSessa A, Maria Guarino FM: HCC and DAA: Open Issue or Closed Wrangling?. Annals of Digestive and Liver Disease. 2019: 2.\n\nÖrmeci N: HCC incidence and recurrence after DAAs: new insights. Hepatoma Res. 2019 [cited 2020 Jan 7]; 2019(11). Publisher Full Text\n\nReig M, Mariño Z, Perelló C, et al.: Unexpected high rate of early tumor recurrence in patients with HCV-related HCC undergoing interferon-free therapy. J Hepatol. 2016; 65(4): 719–726. Publisher Full Text\n\nAnrs T, Co A, Cirvir CO: Lack of evidence of an effect of direct-acting antivirals on the recurrence of hepatocellular carcinoma: Data from three ANRS cohorts The ANRS collaborative study group on hepatocellular carcinoma. J Hepatol. 2016; 65(4): 734–740. PubMed Abstract \| Publisher Full Text\n\nRewisha EA, Elsabaawy MM, Elshaarawy O, et al.: Hepatocellular carcinoma following direct anti-viral for hepatitis C treatment: a report of an Egyptian case series. Hepatoma Res. 2017; 3(8): 178. Publisher Full Text Reference Source\n\nCalvaruso V, Cabibbo G, Cacciola I, et al.: Incidence of Hepatocellular Carcinoma in Patients With HCV-Associated Cirrhosis Treated With Direct-Acting Antiviral Agents. Gastroenterology. 2018; 155(2): 411–421.e4. Publisher Full Text PubMed Abstract \|\n\nMaan R, van Tilborg M , Deterding K, et al.: Safety and Effectiveness of Direct-Acting Antiviral Agents for Treatment of Patients With Chronic Hepatitis C Virus Infection and Cirrhosis. Clin Gastroenterol Hepatol. 2016; 14(12): 1821–1830.e6. Publisher Full Text PubMed Abstract \|\n\nPariente A, Arpurt JP, Rémy AJ, et al.: Hepatitis C treatment with all-oral direct-acting antivirals: Effectiveness and tolerance in a multicenter, prospective, observational study from French general hospitals (APROVVIE, ANGH). Press Medicale. 2019; 48(3): e101–e110. Publisher Full Text\n\nWelzel TM, Petersen J, Herzer K, et al.: Daclatasvir plus sofosbuvir, with or without ribavirin, achieved high sustained virological response rates in patients with HCV infection and advanced liver disease in a real-world cohort. Gut Journal. 2016; 65: 1861–1870. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nStine JG, Wynter JA, Niccum B: Effect of Treatment with Direct Acting Antiviral on Glycemic Control in Patients with Diabetes Mellitus and Chronic Hepatitis C Jonathan. Ann Hepatol. 2017; 16(2): 215–220. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSise ME, Backman E, Ortiz GA, et al.: Article Effect of Sofosbuvir-Based Hepatitis C Virus Therapy on Kidney Function in Patients with CKD. Clinical Journal of the American Society of Nephrology Materials. 2017; 12: 1615–1623. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAhmed M: Harvoni-Induced Deterioration of Renal and Liver Function. Advanced Research in Gastroenterology & Hepatology. 2017; 1(3): 4–5. Publisher Full Text" }	[ { "id": "100963", "date": "20 Dec 2021", "name": "Asmaa Gomaa", "expertise": [ "Reviewer Expertise Viral hepatitis and HCC" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address 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 observational study including 150 HCV patients treated with SOF, DAC with or without RIB for 12 weeks and followed for 12 weeks to detect HCC occurrence or recurrence.\nThe authors stated \"The study aimed to examine new-onset or relapse of HCC in patients receiving Sofosbuvir and Daclatasvir both with and without Ribavirin\". We can not combine the incidence of new cases with the recurrence. The recurrence of HCC is not considered a relapse.\nThe authors need to separate patients with no history of HCC from patients with previous HCC.\nThere are few typo errors. eg, recurrence of HCC is not a relapse.\nI can approve this manuscript for indexing if the authors can make the required changes.\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? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] }, { "id": "116741", "date": "08 Feb 2022", "name": "Chia-Yen Dai", "expertise": [ "Reviewer Expertise My areas of expertise are the natural course", "treatment", "and outcome of hepatitis and HCC." ], "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\nEssawy et al. have reported the retrospective study to assess the occurrence rate of HCC in patients with genotype 4 hepatitis C virus treated with sofosbuvir/daclatasvir with or without ribavirin developing a sustained virological response (SVR). With SVR-12 of 100%, the authors concluded that the cause of HCC development in this study is cirrhosis, not the administered DAAs. Some concerns are raised:\nThe present study enrolled 150 patients treated by sofosbuvir/daclatasvir with or without ribavirin and got 100% of SVR-12. The case number is small. Without a control group, the results of the current study seem to be untested. It is recommended to enroll an untreated or treatment failure group (even if the SVR indeed is very high).\n\nIt is difficult to make sure the occurrence of the HCC is new with the exclusion of the pre-existing HCC before and during treatment. Also, the follow-up period is quite short.\n\nCan the authors provide the patients' characteristics more in detail such as the HCV viral load and the fibrosis status (ex. The FIB-4 scores)?\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? No\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] } ]	1	https://f1000research.com/articles/10-1105
https://f1000research.com/articles/11-441/v1	20 Apr 22	{ "type": "Research Article", "title": "Analysis on short-term outcomes of patients with thoracic trauma at dr. Zainoel Abidin General Hospital in Banda Aceh", "authors": [ "Yopie Afriandi Habibie", "Widya Anisa", "Nurkhalis Nurkhalis", "Azharuddin Azharuddin", "Muhammad Ridwan", "Widya Anisa", "Nurkhalis Nurkhalis", "Azharuddin Azharuddin", "Muhammad Ridwan" ], "abstract": "Background: Thoracic trauma is defined as a trauma that hits the chest wall directly or indirectly, either as a result of blunt or penetrating trauma. Thoracic trauma can occurred in any age or genders, and become a life-threatening if the treatment isn’t immediate and appropriate. Methods: This research was an observational study with a cohort retrospective design using secondary data in the form of thoracic trauma patients at The Zainoel Abidin General Hospital, Banda Aceh, Indonesia in the period January 2019- December 2020. The statistical analysis used were chi square for bivariate and multivariate analysis, spesifically logistic regression analysis was conducted to know which risk factor influences the most. Result: There were 141 medical records used in this study, thoracic trauma was more common in men compared to women. The age group of 46-55 is the age group with the highest percentage of thoracic trauma patients, road traffic are the leading cause of thoracic trauma where the most common diagnosis is rib fractures. Significant factors that associated with the short outcome of thoracic trauma are thoracic trauma diagnosis (p=0,00), management of thoracic trauma (p=0,00), ventilator (p=0,04), duration of ventilator (p=0.01), sepsis (p=0,00), qSOFA score (p=0,00) and injury severity score (p=0,00). Conclusions: Motorbike accidents contributed to a considerable number of traumatic chest injuries in this study. Diagnosis, management of trauma, days of ventilation, qSOFA score, injury severity score, and development of sepsis were associated with the short-term outcome among thoracic trauma patients. Injury severity score seems to be the most influential variable in this study, the lower the better it is. Road safety intervention is urgently needed to control the underlying problems in this study.", "keywords": [ "thoracic trauma", "short-term outcome", "injury severity score", "management of chest trauma" ], "content": "Introduction\n\nThoracic trauma, located on the chest, is an occurrence or incident of an injury that can disturb daily life activities.1 Trauma will remain as one of the main health problems in the world due to its high mortality and morbidity in both developed and developing countries, in which the number of deaths in the world caused by trauma reached around a total of 5.8 million people every year.2 There are 53% of deaths caused by trauma that happened where the accident occurred, 7.5% of the cases that happened in the emergency room, and a total of 39.5% that happened in the hospitals,3 of deaths, hospitalizations, and long term disability in the first four decades of life.2\n\nIn Indonesia, the number of trauma occurrences is still high. Basic Health Research (Riskesdas) of The Ministry of Health of The Republic of Indonesia in 2018 indicates that there is an increasing number of trauma occurrences in Indonesia in which has been recorded in the amount of 8.2% that increased to 9.2% in 2018. The number of thoracic trauma occurrences in the province of Aceh is 4.1%.1 More than 90% of deaths caused by trauma occurred in the countries with the lowest income. This is related to the fact that they have a larger population compared to countries with higher income.4\n\nThoracic trauma comprises 20-25% of cases of all trauma cases worldwide and is the third most common cause of death after abdominal injury and head trauma in polytrauma patients.2 According to the ATLS protocol, early diagnosis and management of thoracic trauma cases are very important, treatment in the first hours of trauma is the gold standard, it is associated with a greater probability of reducing morbidity and mortality. Thoracic trauma is classified into open (penetrating) and closed (blunt). According to the type of trauma, lesions can be divided into four groups, namely lesions on the thoracic wall, lesions of the lungs, mediastinum, and diaphragm. The most common lesions are rib fractures, injury to the heart, aorta, and diaphragm.5 This research was carried out at the The Zainoel Abidin General Hospital Banda Aceh which is the top referral hospital in the Aceh province. This study aims to see what factors can affect the short-term outcome of trauma patients thorax at The Zainoel Abidin General Hospital Banda Aceh.\n\n\nMethods\n\nThis research has received ETHICAL APPROVAL from Health Research Ethics Commision of faculty of medicine of University of Syiah Kuala- DR Zainoel Abidin Hospital (KEPPKN Registrastion Number: 117101P) by number: 301/FK-RSUDZA/2021. Written informed consent was received from the patients.\n\nThis study is an analytic observational study with a retrospective cohort method, data collection was carried out at the Medical Record Installation of The Zainoel Abidin General Hospital Banda Aceh. The time of data collection occurred August 20th to October 20th, 2020. Sampling used a total technique that meets the inclusion criteria, namely patients who are diagnosed with thoracic trauma and are willing to be interviewed by the researcher. The exclusion criteria are all those patients diagnosed with thoracic trauma who have incomplete, not found and broken data in the medical records files according to the research variables. This study used multivariate data analysis using logistic regression to assess the factors that influence the short-term outcome of thoracic trauma patients. All data analysis was done using IBM SPSS, Statistics standard 25.\n\n\nResults\n\nResearch on short-term outcome analysis of thoracic trauma patients at The Zainoel Abidin General Hospital Banda Aceh in the 2019-2020 period recorded 260 patients. During data collection at the Medical Record Installation, 169 medical records were obtained and 91 data were not found. The obtained data recorded a total of 144 patients experiencing thoracic trauma, but three of them did not meet the inclusion and exclusion criteria of the study. The sample in this study amounted to 141 medical records (Figure 1). Based on Table 1 the number of thoracic trauma patients on males is dominating, namely 101 (71.63%) cases. Furthermore, the majority of the length of stay for thoracic trauma patients was less than 7 days with an average length of stay of 9 days, where there were 63 (44.68%) cases during 2 years of observation. As many as 58 (41.13%) cases were recorded for 7-14 days and 20 (14.19%) were recorded for >14 days. Regarding thoracic trauma type, 138 (97.87%) were blunt in which the blunt trauma was caused by traffic accidents on motorcycle users, which recorded as many as 83 (58.7%) cases. In 3 (2.13) patients experience the penetrating trauma, mostly caused by being stabbed with iron (Table 1).\n\nMV: Mechanical Ventilation.\n\nTable 2 shows that the majority of thoracic trauma patients do not use a ventilator, which consists of 122 (86.52%) cases, while those who use a ventilator are recorded as 19 (13.48%) cases. Most of the patients, exactly as many as 18 (12.77%), use less than 96 hours duration and 1 (0.71%) patient was recorded to use for more than 96 hours duration. There are 139 (98.58%) thoracic trauma patients who had no complications of sepsis, but 2 (1.42%) thoracic trauma patients were diagnosed with sepsis during hospitalization (Table 3). The qSOFA score in the majority of thoracic trauma patients was 0 in 117 (82.98%) cases, followed by 1 in 19 (13.48%) cases, and 2 in 5 (3.55%) cases. Moreover, the injury severity score in the majority of thoracic trauma patients was in the <16 (low) group, namely 87 (61.70%) cases, followed by the 16-30 (moderate) group, which was 54 (38.30%) cases.\n\nThe majority of patients with thoracic trauma were diagnosed with rib fractures (fracture costae) as 42 (29.77%) cases, followed by rib and clavicle fractures in 23 (16.31%) cases, clavicle fractures in 18 (12.77%), pulmonary contusion were recorded in 7 (4.96%) cases, rib fractures with hematothorax in 10 (7.09%) cases, hematothorax and pneumothorax in 5 (3.55%) and 2 (1.42%) cases respectively. In addition, there were 1 (0.71%) cases of each flail chest and cardiac tamponade (Table 3).\n\nIn our study 16 (11.35%) out of 141 patients only needed conservative treatment including chest physiotherapy and analgesics, while 125 (88.65%) patients need operative treatment where open reduction internal fixation (ORIF) with chest tube insertion was the common modality to treat thoracic trauma victims, followed by thoracotomy and video assisted thoracic surgery (VATS). In addition, decompression thoracic vertebrae was found in 1 (0.71%) cases (Table 4).\n\n\nDiscussion\n\nOur study shows the highest incidence of thoracic trauma occurred in patients with male gender, research conducted by Christoporus et al. stated that the reason for the male gender experiencing chest trauma more often was because the level of activity carried out by men was higher than women, male occupations are mostly done outside the home. In addition to that, men also tend to pay less attention to safety when driving a motorized vehicle.6 Based on Table 1, the majority of thoracic traumas occur due to blunt objects, the increasing incidence of blunt trauma is caused by an increase in population and high traffic flow. The study of Jigar et al. in India stated that the type of injury faced by a geographical area depends on civilization, society, culture and industrialization.7 Meanwhile, penetrating trauma is usually determined by the level of crime and violence that occurs in the community in the area itself. Furthermore, the causes of thoracic trauma with the type of blunt trauma are caused by traffic accidents on motorcycle users, which is recorded as many as 83 (58.7%) cases. During the 2015-2019 period the number of traffic accidents increased by 4.87% per year. In the report by the National Police Traffic Corps, it is stated that motorcycle accidents still dominate in Indonesia, this is because the majority of Indonesian people use motorcycles. This can occur due to non-compliance of motorcyclists to traffic signs and speed when driving a motorized vehicle.\n\nThe length of stay for chest trauma patients depends on the severity of the trauma and other additional injuries. Many factors affect the length of stays such as the type of injury, complications that occur during treatment, and the treatment in the intensive care unit.8 The study of Eray et al. said that there was a relationship between oxygen saturation and length of stay, namely the lower the oxygen saturation of trauma patients, the longer the length of stay. In addition, deaths that occur early in treatment are the reason for shorter hospital stays.9 in this study length of stay of patients with chest trauma were less than sevem days. A study in Sri Lanka said that the presence of flail chest and injury to the trachea was associated in length of stay patients with chest trauma.10\n\nAccording to Table 2, the presence of pulmonary contusions with or without flail chest is usually associated with a high incidence of ventilator use.11 The presence of pulmonary contusions can injure small airways and damaged capillaries and epithelial cells. These conditions can cause an increase in pulmonary capillary permeability which will cause alveolar edema. The previous study shows significantly that severe rib fractures were associated with a long mechanical ventilation period. Hence, the assessment of the extent of rib fractures could estimate the requirement of mechanical ventilation and prolong ICU days.12 In this study, patients who required the use of a ventilator and had access to it tended to have a high probability of getting a good outcome or living. This is in line with the research conducted by Niloofar et al. in Canada.13 Moreover, there is a significant relationship between the duration of the ventilator and the short-term outcome of thoracic trauma patients. In this study, patients who did not require the use of a ventilator tended to have a fairly good short-term outcome. Our study reported that 2 out of 141 patients with chest trauma fell into the septic condition. Patients falling into the septic condition is usually caused by open wounds and chest tube insertion. Otherwise, a study in Tanzania revealed that sepsis is the most common complication in chest trauma patients, this difference is caused by the quality of attention provided to patients between the two countries.14\n\nThere was a significant relationship between qSOFA scores and short-term outcomes of thoracic trauma patients. This is in line with the research conducted by Wenjuang et al. in Taiwan in 2021 where the study stated that the higher the qSOFA score of trauma patients, the worse the outcome (Table 2).15 Furthermore, there is a significant relationship between ISS scores and short-term outcomes of thoracic trauma patients. This is in line with the research conducted by Monafisha et al. in Tanzania which showed that there was a significant relationship between ISS scores and the outcome of thoracic trauma patients.14 In addition, the study conducted by Sadiye et al. in Turkey also shows the same thing.16 Based on Table 3, there is a significant relationship between the diagnosis and the short-term outcome of thoracic trauma patients. This is different from the research from Ethiopia in 2020 that stated that there was no significant relationship between the diagnosis and the outcome of thoracic trauma patients. The difference probably because the study only used primary diagnoses of thoracic trauma patients.17 Meanwhile, a study in Germany, which examined the outcome of thoracic trauma patients, said that rib fractures indicate death at an advanced age and the number of rib fractures correlates with poor outcomes. Bilateral flail chest is associated with increased mortality and injury to intrathoracic vessels and cardiac lacerations are associated with high mortality and prolonged ventilation also causes significant morbidity in chest trauma patients.18 Based on Table 4, there is a significant relationship between management and short-term outcomes of thoracic trauma patients. This is in line with research conducted by Ararso et al. in Ethiopia in 2020 which stated that there was a significant relationship between treatment and outcome of thoracic trauma patients. The study divided the management into conservative and operative which consisted of insertion of a chest tube and thoracotomy.17 a study conducted by Hafiz in the UK said that surgery performed within the first 48 hours resulted in shorter ICU stays, reduced risk of complications such as pneumonia, shorter hospital stays and shorter use of intensive ventilation overall.19 Research conducted by Christian et al in Switzerland stated that the return to work rate for 6 months after chest trauma was higher in the open reduction internal fixation (ORIF) group. Symptoms such as subjective dyspnea, chest pain, and chest stiffness were common in the nonoperative group 6-12 months after the trauma.20\n\nBased on Table 5, the variable that has a greater influence on the short-term outcome of thoracic trauma patients is the ISS score, in which patients that have lower ISS score have 11 times greater chance compared to the patients with the higher ISS score. This is in line with research conducted by Monafisha et al. in Canada where research shows that patients who have a high ISS score have a six times risk of producing a poor outcome.14 The same thing was also stated by Sadiye et al. In Turkey, where the ISS score is an important prognostic factor in the outcome of thoracic trauma patients, the higher the ISS score, the more severe the trauma.16\n\nThe limitation of this study is we only used data from Dr. Zainoel Abidin General Hospital, which represent a chest trauma population with a majority of blunt trauma. Furthermore, this study was conducted in the tertiary care hospital, hence, the patients with less severe trauma who have been managed in primary care are underrepresented. Also, patients who had died at the accident scene or at the emergency room were not assessed in our study.\n\n\nConclusion\n\nIn summary, thoracic trauma is a public health problem among all trauma admissions at Dr. Zainoel Abidin General Hospital. The majority of chest traumas are caused by road traffic accidents especially motorbikes due to the population of motorbike users being still high. Injury severity score is the most influential factor to the short-term outcome of patients with thoracic trauma, where the lower the ISS score, the greater chance of survival compared to a higher score.\n\n\nData availability\n\nData cannot be shared due to ethical and security concerns, nevertheless, a dataset with all the details can be shared with reviewer or readers at reasonable request to corresponding author.\n\n\nAuthor's contributions\n\nAll authors have read and approved the final manuscript. The requirements for authorship have been met, and each author believes that the manuscript represents honest work.", "appendix": "References\n\nKementrian Kesehatan Republik Indonesia: Riset Kesehatan Dasar. Badan Penelitian dan Pengembangan Kesehatan; 2018; p. 198. Reference Source\n\nBeshay M, Mertzlufft F, Kottkamp HW, et al.: Analysis of risk factors in thoracic trauma patients with a comparison of a modern trauma centre: A mono-centre study. World J. Emerg. Surg. 2020; 15(1): 1–10.\n\nKisat M, Villegas CV, Onguti S, et al.: Predictors of sepsis in moderately severely injured patients: An analysis of the national trauma data bank. Surg. Infect. 2013; 14(1): 62–68. PubMed Abstract \| Publisher Full Text\n\nWorld Health Organization (WHO): Injuries violance the facts The magnitude and causes of injuries. Geneva: World Health Organization; 2014; vol. 20. Reference Source\n\nZanette GZ, Waltrick RS, Monte MB: Epidemiological profile of thoracic trauma in a reference hospital of Foz do Rio Itajai. Rev. Col. Bras. Cir. 2019; 46(2): e2121. PubMed Abstract \| Publisher Full Text\n\nHandoyo CN: Profil Trauma Toraks di Ruang Rawat Inap Bedah RSUD Gambiran Periode Maret 2017 – Maret 2018. J. Ilm. Kedokt. Wijaya Kusuma. 2018; 7(2): 178. Publisher Full Text\n\nShah JV, Solanki MI: Analytic Study of Chest Injury. IJSS J. Surg. 2015; 01(01): 5–9.\n\nKhursheed SQ, Ashraf W, Rather AA: Clinical profile and outcome of chest trauma: a four year retrospective analysis at a tertiary care centre. Int. Surg. J. 2019; 6(7): 2519. Publisher Full Text\n\nÇinar E, Yildiz ÖÖ, Çelik IA, et al.: Retrospective analysis of thoracic trauma and evaluation of the factors affecting the duration of stay in the hospital. Disaster. Emerg. Med. J. 2020; 5(3): 159–163. Publisher Full Text\n\nMathangasinghe Y, Pradeep IHDS, Rasnayake D: Demographic, Clinical Features and Outcome Determinants of Thoracic Trauma in Sri Lanka: A Multicentre Prospective Cohort Study. Can. Respir. J. 2020; 2020: 1–6. PubMed Abstract \| Publisher Full Text\n\nRichter T, Ragaller M: Ventilation in chest trauma. J. Emerg. Trauma Shock. 2011; 4(2): 251–259. Publisher Full Text\n\nBayer J, Lefering R, Reinhardt S, et al.: Thoracic trauma severity contributes to differences in intensive care therapy and mortality of severely injured patients: Analysis based on the TraumaRegister DGU®. World J. Emerg. Surg. 2017; 12(1): 1–9.\n\nDehghan N, De Mestral C, McKee MD, et al.: Flail chest injuries: A review of outcomes and treatment practices from the national trauma data bank. J. Trauma Acute Care Surg. 2014; 76(2): 462–468. Publisher Full Text\n\nLema MK, Chalya PL, Mabula JB, et al.: Pattern and outcome of chest injuries at Bugando Medical Centre in Northwestern Tanzania. J. Cardiothorac. Surg. 2011; 6(1): 1–7.\n\nHuang W, Yang P, Xu F, et al.: Predictive value of qSOFA score for death in emergency department resuscitation room among adult trauma patients:a retrospective study. BMC Emerg. Med. 2021; 21(1): 1–11.\n\nEmircan Ş, Özgüç H, Akköse Aydin Ş, et al.: Factors affecting mortality in patients with thorax trauma. Ulus Travma ve Acil Cerrahi Derg. 2011; 17(4): 329–333. PubMed Abstract \| Publisher Full Text\n\nBaru A, Weldegiorgis E, Zewdu T, et al.: Characteristics and outcome of traumatic chest injury patients visited a specialized hospital in Addis Ababa, Ethiopia: A one-year retrospective study. Chinese J. Traumatol. - English Ed. 2020; 23(3): 139–144. PubMed Abstract \| Publisher Full Text\n\nHuber S, Biberthaler P, Delhey P, et al.: Predictors of poor outcomes after significant chest trauma in multiply injured patients: A retrospective analysis from the German Trauma Registry (Trauma Register DGU®). Scand. J. Trauma Resusc. Emerg. Med. 2014; 22(1): 1–9.\n\nIqbal HJ, Alsousou J, Shah S, et al.: Early surgical stabilization of complex chest wall injuries improves short-term patient outcomes. J. Bone Jt. Surg. - Am. Vol. 2018; 100(15): 1298–1308. PubMed Abstract \| Publisher Full Text\n\nMichelitsch C, Acklin YP, Hässig G, et al.: Operative Stabilization of Chest Wall Trauma: Single-Center Report of Initial Management and Long-Term Outcome. World J. Surg. 2018; 42(12): 3918–3926. PubMed Abstract \| Publisher Full Text" }	[ { "id": "239500", "date": "16 Feb 2024", "name": "Misauq Mazcuri", "expertise": [ "Reviewer Expertise thoracic pathologies benign", "malignant", "trauma" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 Background: can occur ( not occurred) or to any gender a life-threatening condition Result: mention % of males , thoracic trauma diagnosis , management of thoracic trauma cannot be variables to tabulate. If management to be considered need to discuss which form of management. Conclusion : Motorbike as common mode where is it mentioned in abstract result ?? What supports the statement injury severity score as most influential as many others also have similar P value. Introduction : Paragraph 1: Need to use connecting words , last line creating confusion Paragraph 2 : grammatical errors Method : need to abbreviate and maybe briefly introduce readers to ISS score and qSOFA score Result : It is not important to mention how many total patient were there etc. Directly mention 141 cases as you have mentioned your inclusion and exclusion criteria already. Avoid repetition of all results mentioned in table again in text. Eg most common length of stay was less than 7 , mentioning all not necessary (2.13 %) Similar advice for the rest of the result do not repeat all findings , mention only the most common finding Hematothorax ??? 1 case not cases Discussion : seven not sevem Paragraph 3 : you have not tabulated any factor with ventilatory support there fore cannot state you first line. Table 5 is from your own paper ?? , if yes why not mentioned in result Sepsis is not related to short term outcome\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? Yes", "responses": [ { "c_id": "11133", "date": "13 Apr 2024", "name": "Yopie Afriandi Habibie", "role": "Author Response", "response": "Background: can occur ( not occurred) or to any gender a life-threatening condition : Thank you for the correction. Result: mention % of males , thoracic trauma diagnosis , management of thoracic trauma cannot be variables to tabulate. If management to be considered need to discuss which form of management : Table 1 shows the diagnosis information, while table 3 shows the diagnosis results. Conclusion : Motorbike as common mode where is it mentioned in abstract result ?? : Yes, we will make the correction and include the vehicle that is commonly the cause of accidents. What supports the statement injury severity score as most influential as many others also have similar P value. : already described in table 5 Introduction : Paragraph 1: Need to use connecting words, last line creating confusion : \"I appreciate your correction. Thank you for pointing out the mistake. Paragraph 2 : grammatical errors : \"I appreciate your correction. Thank you for pointing out the mistake.\" Method : need to abbreviate and maybe briefly introduce readers to ISS score and qSOFA score Result : It is not important to mention how many total patient were there etc. Directly mention 141 cases as you have mentioned your inclusion and exclusion criteria already. : \"I appreciate your correction. Thank you for pointing out the mistake.\" Avoid repetition of all results mentioned in table again in text. Eg most common length of stay was less than 7 , mentioning all not necessary (2.13 %) Similar advice for the rest of the result do not repeat all findings , mention only the most common finding Hematothorax ??? : \"I appreciate the correction you gave me. Thank you.\" 1 case not cases : Thank you Discussion : seven not sevem : Thank You Paragraph 3 : you have not tabulated any factor with ventilatory support there fore cannot state you first line : Already mentioned on Table 2 Table 5 is from your own paper ?? , if yes why not mentioned in result : Yes, from my own paper. Thank you Sepsis is not related to short term outcome Is the work clearly and accurately presented and does it cite the current literature? : Yes, it cite the current literature" } ] } ]	1	https://f1000research.com/articles/11-441
https://f1000research.com/articles/13-735/v1	03 Jul 24	{ "type": "Research Article", "title": "Effect of Elderly School Policy on Quality of Life among Thailand’s Senior Citizens: A Propensity Score Matching Approach", "authors": [ "Worapath Kratoo", "Nuchanad Hounnaklang", "Worapath Kratoo" ], "abstract": "Background As Thailand’s population ages, promoting senior citizens’ quality of life (QoL) is crucial. In 2017, the Ministry of Social Development and Human Security launched the “elderly school” initiative to foster lifelong learning and enhance the QoL among senior citizens. However, comprehensive evaluations of its impact on QoL remain limited.\n\nMethods This cross-sectional survey aimed to assess the policy’s effect on QoL in Phetchabun province, Thailand. Using quota and systematic sampling, 1,374 senior citizens aged 60-80 participated. Propensity score matching (PSM) with a 1:1 match was employed to estimate the average treatment effect (ATE) of attending the elderly school on QoL. Additionally, multiple linear regression was analyzed to assess the association between QoL and its associated factors.\n\nResults PSM were matched successfully, the standardized difference was less than 10 percent, and the baseline after matching indicated balances with 687 elderly people in each group. The mean QoL score of the non-attending group was 44.40 (SD = 7.11), and that of the attending group was 57.50 (SD = 7.53). The ATE for elderly people attending school was 10.67 scores (95% CI: 9.67 – 11.67 scores) higher than those unattended. Being female, having monthly income higher than 20,000, having employment, having a caregiver, and attendance at elderly school were positively associated with QoL, and the standardized beta coefficients were 0.078, 0.059, 0.094, 0.066, and 0.550, respectively. Additionally, higher education was positively associated with higher QoL.\n\nConclusion The elderly school policy significantly enhanced the QoL of the attending senior citizens. Findings suggest continued collaboration among stakeholders to sustain and optimize this policy for improved seniors’ QoL, which has the potential to utilize lifelong learning to create an inclusive framework for healthy aging among senior citizens.", "keywords": [ "Elderly school", "Health policy", "Quality of life", "Propensity score matching" ], "content": "Introduction\n\nA global surge in the elderly population, defined as those aged 60 and above, presents a major challenge and opportunity for healthcare systems worldwide. From 2015 to 2050, the proportion of elders is projected to nearly double, from 12% to 22%1, with 80% residing in middle-income countries.2 This trend is particularly evident in Thailand, where the elderly population is expected to reach 17 million by 2040, exceeding one-quarter of the national total.3,4 This necessitates immediate attention to preparing and evolving healthcare systems to adequately support the QoL of senior citizens.\n\nThailand, with its rapidly aging population, stands at the forefront of this global challenge. By acknowledging the urgency of the situation and proactively adapting its healthcare systems, Thailand can not only serve as a model for other countries but also ensure the health and QoL of its senior citizens, paving the way for a brighter future for all.5,6\n\nThe concept of QoL encompasses an individual’s or population’s overall QoL, integrating both positive and negative experiences over a defined timeframe.7 The World Health Organization (WHO) defines QoL as an individual’s subjective perception of their life position, influenced by cultural and value systems.8,9 This multidimensional concept, as outlined by the WHO, encompasses four key domains: physical health, mental health, social relationships, and the environment.10 QoL serves as a crucial indicator for achieving Sustainable Development Goals (SDGs), particularly for the elderly population, with relevance to SDG 3: Good Health and Well-being.11\n\nDespite achieving a moderate average QoL amongst senior citizens nationwide, Thailand faces disparities in urban-rural QoL, with literature suggesting consistently lower QoL for rural older adults12–14 which is similar to Myanmar, and South India15,16 This presents a significant challenge for Lomkao district, Phetchabun province, a rural area boasting a 24.8% elderly population and exhibiting moderate QoL scores for elder residents.17,18 Research points beyond individual characteristics such as age, income, education, and chronic health conditions as sole determinants of QoL for older adults. Living arrangements and social interactions have also emerged as crucial factors deserving consideration in an effort to enhance elderly QoL.19–21 Therefore, a comprehensive approach addressing both individual and environmental factors is essential to effectively improve QoL for Thailand’s rural elderly population.\n\nIn response to the crucial role of health promotion interventions in improving and maintaining QoL for older adults, numerous such programs have been implemented globally.22–24 These interventions typically share three core objectives: enhancing functional capacity, promoting self-care behaviours, and preventing or delaying chronic illness onset.25 Implementation often involves collaboration among social welfare organizations, healthcare professionals, and educational systems.26,27 Thailand exemplifies this trend with the 2017 establishment of the elderly school initiative by the Department of Older Persons, Ministry of Social Development and Human Security.28 This program, grounded in the concepts of awareness, empowerment, and lifelong learning, aims to equip older adults with the knowledge and skills necessary to achieve optimal QoL.29,30\n\nIn 2018, Lomkao district was identified as one of 73 districts in Thailand by the District Health Board for the implementation of specific programs to address the challenges posed by an aging population. Recognizing the district’s demographic shift, the Board selected Lomkao as a priority area due to the prevalence of older adults residing within its boundaries. One of the key initiatives implemented in Lomkao to address this demographic trend is the “Elderly School” program. This program represents a targeted intervention aimed at improving the well-being and QoL for older adults in the district.31,32 As of 2022, Thailand boasts a network of 2,370 elderly schools established through partnerships with local administrative organizations (LAOs), private entities, and community groups.33 These schools offer a core curriculum encompassing four key modules: health, social, economic, and environmental education, in which the officers invite elderly people in communities to attend through voluntary participation.28,34,35 Program adaptations cater to specific regional contexts, aligning with the curriculum framework developed by the Department of Older Persons (DOP), Ministry of Social Development and Human Security. Annual budgetary allocations for elderly school support have ranged from $283,700 to $425,687 USD over the past five years. Notably, the 2021 allocation fell below the minimum due to the COVID-19 pandemic necessitating online instruction in some areas where there is hardly any regular class.33,36–39\n\nRecognizing the program’s value, alternative funding avenues through LAOs, the Community Health Security Fund, and the Thai Health Promotion Foundation have been established to bolster implementation initiatives.40 Beyond budgetary considerations, elderly schools demonstrably contribute to active aging, improved QoL, and ongoing learning among senior citizens. They provide valuable social interaction, alleviating loneliness and fostering a sense of community. Moreover, they empower older adults to productively utilize their free time, contributing to a sense of agency and QoL.41,42\n\nThe establishment of the Elderly School initiative in Thailand in 2017 aimed to address the growing needs of the nation’s aging population. However, despite its implementation across various districts, a comprehensive and dedicated assessment of its impact on senior citizens’ QoL remains elusive. This lack of evaluation presents a significant gap in understanding the effectiveness of the program and its potential for improvement. Existing research has primarily focused on the program’s development and limitations of design, which could not control the influence of covariates. This might lead to a selection bias, leaving a critical gap in understanding its effectiveness.43–46 To address this void, the present study employs PSM to evaluate the initiative’s causal effect on QoL within an aging society. Through PSM, we compare the QoL of two groups: senior citizens not attending and attending elderly schools. This approach facilitates the creation of comparable groups in real-world settings, mimicking an experimental study while mitigating selection bias and strengthening the robustness of regression analyses. In addition, investigating the association between various factors and QoL. Our findings aim to contribute to the existing body of literature, providing valuable guidance for the future implementation and refinement of lifelong learning initiatives for senior citizens in Thailand.\n\n\nMethods\n\nThis cross-sectional study was conducted in Lomkao, Phetchabun province, Thailand between December 2022 to June 2023.\n\nThe study population consisted of 11,254 elderly individuals aged 60–80 years in Lomkao district, Phetchabun province, Thailand.17 The sample size was calculated for the continuous data since this study analyzed multiple linear regression. A pilot test comparing the QoL between elderly individuals who attended and did not attend elderly school indicated a small effect size of 0.02, a power of 0.8, 13 predictors, and a significance level of 0.05.47 There are 901 elderly people, with a minimum of 451 participants in each group. Inclusion criteria were 1) age between 60 and 80 years 2) residency in Lomkao, Phetchabun province, for at least one year and 3) literacy and proficiency in Thai communication (listening and speaking). The exclusion criteria focused on individuals with mental health illnesses that include anxiety disorders, mood disorders, and physical disabilities that would significantly impede their ability to participate in the study activities.\n\nIn this study, researchers utilized a combination of quota and systematic sampling techniques. The quota sampling was based on a 1:1 matching model, comparing elderly people who attended an elderly school with those who did not. For systematic sampling, the sampling interval was determined using the formula I = N/n, where “I” represents the sampling interval, “N” is the total population (11,254), and “n” is the sample size (901). This calculation resulted in a sampling interval of approximately 13 (I = 11,254/901 ≈ 12.5 ≅ 13). Therefore, we included every 13th elderly person in the population who met the eligibility criteria.\n\nData were collected through face-to-face interviews conducted from December 2022 to June 2023. Prior to data collection, the research team, composed of the lead investigator and five experienced healthcare workers in geriatric care, underwent one week comprehensive training. This training covered the study protocol, interview techniques, and participant selection criteria. During data collection, the research team rigorously adhered to inclusion and exclusion criteria for each potential participant.\n\nAll participants were provided with written informed consent before the interview process began. We thoroughly explained the study’s objectives, methods, potential risks and benefits, and participants’ rights. Each participant received and signed a written consent form, confirming their voluntary participation. Confidentiality was assured, and participants were informed of their right to withdraw from the study at any time without consequences. To ensure data quality, the lead researcher provided ongoing supervision and support to the research assistants throughout the data collection process.\n\nMeasurement\n\nThe questionnaires were used for data collection as follows: part 1: Individual characteristics, part 2: the Activities of Daily Living (ADLs), and part 3: the World Health Organization Quality of Life – BREF (WHOQOL-BREF).\n\nPart 1, included 12 questions assessing demographic and socioeconomic factors, including age, gender, educational level, monthly income of the elderly person, employment, number of family members, living arrangement, illnesses, caregiver, and ADLs. Additionally, participation in an elderly school program was recorded.\n\nPart 2, The Barthel Index, an ordinal scale with 10 items, was used to measure ADL performance. Each item, encompassing activities like feeding, toileting, bathing, dressing, and mobility, is scored on a 0-2 scale, reflecting the degree of assistance required. The total score, ranging from 0 to 20, indicates functional capability, with lower scores suggesting greater disability.48\n\nPart 3, we used WHOQOL-BREF (Thai version), in which there are 26 questions, ranging from 26 to 130. This questionnaire contains four domains (physical health, psychological health, social relationships, and environment). According to a 5-point Likert scale, each of these domains was scored.49 Following the T-score, raw scores were transformed into a T-score with a range of 20 to 80, with higher scores denoting better QoL in each domain.\n\nThe Elderly School program in Thailand operates on a two-semester basis, with each semester consisting of 50 hours (3 hours per week). This collaborative initiative brings together diverse stakeholders, including the government, Local Administrative Organizations (LAOs), local communities, the private sector, and network partners. Their combined contributions ensure the provision of a wide range of activities and essential facilities for program participants.\n\nThe core curriculum for this learning process adheres to the established standards set by the Ministry of Social Development and Human Security. Quality control of teachers and curriculum implementation falls under the responsibility of LAOs, ensuring adherence to national guidelines. However, recognizing the importance of contextually relevant learning, the program allows for flexibility. Additional activities can be specifically tailored to cater to the unique needs and interests of each participating community. This customization plays a crucial role in enhancing engagement and ensuring the program addresses the specific challenges and opportunities faced by local senior citizens.29 In this study, we operationalize the elderly school program as the treatment variable. Individuals who attend more than 80% of classes throughout the program are as “attending elderly school” while those who do not attend classes regularly are “non-attending elderly school”.\n\nThe elderly school curriculum consists of physical and mental health, social, economic, and environmental domains. The content can be delivered through workshops, seminars and training. LAOs is the main source for providing staff, financial, and material support, as detailed in Table 1.\n\nThis study employed PSM to address potential selection bias. Demographic variables were considered to calculate the predicted probability of covariates (gender, age, educational level, monthly income, employment, number of family members, living arrangement, illnesses, caregiver, and ADLs) for each individual. A balancing score of the propensity score, and distribution of measured baseline covariates between elderly people who attend elderly school and those who do not attend were compared in Table 2 and Figure 1.\n\nCategorical variables were described by frequency and percentage (%). Continuous variables were described by mean and standard deviation (SD). PSM was applied to match between the elderly people who attended the elderly school and those who did not. A regression model based on characteristic variables was used to compute propensity scores for each participant. K-nearest neighbor 1:1 matching model with no replacement and no callipers was employed as the propensity score matching estimator in Python. The standardized difference was used to examine the balance of covariate distribution between groups, which was independent of the unit of measurement. It allows comparison between variables with different units of measurement to calculate the propensity scores with a maximum standardized difference of 10%. Then, the average treatment effects of the population (ATE) were analyzed to investigate the effect size of the elderly schools on QoL, and multiple linear regression was analyzed to investigate the association between elderly school attendance and QoL using Stata 17.0. The level of two-sided statistical significance was set at p < 0.05.\n\n\nResults\n\nThere were 1,508 participants who completed the interview in this study. Following PSM, the sample size remained at 1,374 individuals, with 687 in each group (elderly school non-attending group and attending group).\n\nThere were 687 participants in each group, with 474 (69.00%) elderly women in the non-attending elderly school group and 541 (78.75%) in the attending group. The average age of elderly people in the non-attending group was 67.75 (SD = 5.16) and in the school-attending group was 68.66 (SD = 4.78). Most participants had completed primary school, monthly income of less than 20,000 baht, and were employed in both groups, as over half of the participants lived with their families and had caregivers to take care of them. The results indicate the standardized difference was less than 10% on all covariates, which identified improved balance between the two groups (Table 2).\n\nThe average overall QoL of elderly people in the attending elderly school group was 57.50 (SD = 7.53) and that of those in the non-attending elderly school group was 44.40 (SD = 7.11). The ATE of overall QoL was 10.67 (95% CI: 9.67–11.67, p-value <0.001), indicating a positive effect of attending the elderly school on QoL. Additionally, the ATE between the two groups for QoL domains: physical health, psychological, social relationships, and environmental dimensions were 8.89, 8.17, 6.37, and 8.41, respectively. There was a statistically significant difference in each QoL domain between the two groups (Table 3).\n\nA multiple linear regression was conducted to assess the relationship between factors and QoL. As presented in Table 4, QoL was significantly associated with gender, educational level, monthly income, employment, caregiver, and elderly school attendance (F (8, 1365) = 251.88, p < 0.001 R2= 0.5962 and adjusted R2 = 0.5938). Notably, elderly school attendance showed a strong association with QoL. The unstandardized beta coefficient for elderly school attendance was 10.811. Higher education levels among elderly people were also associated with higher QoL. The unstandardized beta coefficients for primary, secondary, and education higher than vocational certificates are 5.472, 10.090, and 10.157, respectively. This suggests that, for each elderly person with a higher educational level, the QoL score increases by the respective unstandardized beta coefficient (Table 4).\n\n* p < 0.001.\n\n** p < 0.005.\n\n\nDiscussion\n\nThis study investigates the effect of elderly school policy on QoL across its four domains: physical health, psychological, social relations, and environment. Furthermore, the associations between the factors and QoL were identified. Notably, in our study, the QoL of elderly people in the attending elderly school group was higher than that of those in the non-attending elderly school group, and the ATE indicated a positive effect of attending the elderly school on QoL. This finding is comparable with previous research on elderly schools in the northern and eastern regions of Thailand, which similarly found higher QoL among attending elderly school groups compared to non-attending elderly school groups.50–52 Physical health was shown to be the highest domain in ATE, followed by the psychological, environmental, and social relationships domains, all of which had similar values except for social relationships. This result reflects the fact that the elderly people emphasized their health deterioration with increasing age and the burden of diseases.53,54\n\nMoreover, our results resonate with broader international research highlighting the positive impact of interventions based on the concept of lifelong learning. Our finding was consistent with a study in Portugal that investigated the effect of participation in community intervention programs and indicated that QoL was better in the physical domain than others.55 Similarly, a systematic literature review on the effects of later-life formal education on the QoL of elderly people also revealed a positive impact on QoL.56 Additionally, a study in Canada regarding community-based participation in programs for mental health found a positive impact on psychological well-being, particularly in the context of non-formal lifelong learning57 and the elderly individuals attending evening schools for lifelong learning in Korea experienced positive well-being impacts, including in the environmental dimension.58\n\nOur study further strengthens the evidence for a significant positive association between elderly school attendance and QoL after adjusting for other independent variables in a multiple linear regression model. This finding mirrors that of a study in Rayong Province, Thailand, which similarly identified the participation of senior citizens in educational management in elderly schools as a positive predictor of QoL, demonstrating the program’s potential to elevate QoL among attendees.59 Furthermore, our results confirmed that sociodemographic factors, including gender, educational level, monthly income, and employment, were significant factors in QoL. For instance, this result was consistent with a study conducted in a rural area of the northern and northeast region of Thailand that found sociodemographic factors related to the elderly’QoL.60,61 Additionally, male gender, lack of education, and lower economic status are associated with low QOL of elderly people in rural area, India.62 In Korea, higher monthly income of elderly people had a positive effect on QoL.63 Furthermore, the presence of a caregiver was a positively significant factor in the QoL of elderly people. This result was consistent with a study conducted by developing caregivers’ potential to improve the QoL for the elderly in the southern region of Thailand.64 It is important to note that the specific factors associated with QoL vary across these studies. This variability can be attributed to differences in research methodology.\n\nThis study displays several key strengths that contribute to its significance and pave the way for future research. Firstly, the utilization of PSM and estimation of average treatment effects (ATEs) strengthens the study’s internal validity. By creating a setting that mimics real-world conditions, PSM facilitates a comparison between elderly school attendees and non-attendees, minimizing selection bias. Furthermore, it stands as a pioneering analysis of the elderly school policy’s influence on QoL. This comprehensive approach provides a nuanced understanding of the policy’s multifaceted impact, surpassing previous research that primarily focused on program development.\n\nHowever, this study acknowledges several limitations. Firstly, geographical scope: conducted in a single district, the results may not directly generalize to other populations or cultural contexts. Nevertheless, Lomkao district with its significant elderly population serves as a valuable study, offering important insights applicable to similar demographics. Secondly, cross-sectional design: While providing valuable data on QoL and its association with elderly school attendance, the cross-sectional design restricts the ability to establish causal relationships. Longitudinal studies are needed to definitively examine the impact of the policy over time. Future studies may benefit from incorporating additional assessments and corroborative data sources.\n\nThe findings of this study offer profound policy implications and recommendations towards optimizing Thailand’s approach to senior citizens through lifelong learning initiatives like the elderly school program. 1) Integration into broader health promotion strategies: recognizing the significant QoL improvements associated with elderly school attendance underscores the imperative to embed this program within broader health promotion strategies for aging populations. This integration can leverage synergies between lifelong learning and other QoL initiatives. 2) Fostering continuous education policies: our results further advocate for the development of dedicated policies specifically aimed at supporting and promoting continuous education among senior citizens. Such policies could range from targeted funding mechanisms for elderly school expansion to incentivizing the creation of age-friendly learning materials and curricula. 3) Collaborative action for strong support systems: to maximize the impact of elderly schools and similar initiatives, we propose enhanced collaboration and awareness promotion among relevant authorities and stakeholders. This could involve partnerships between government agencies, community organizations, and the private sector to foster robust support systems for aging societies, prioritizing elderly schools, health promotion programs, and QoL initiatives. 4) Rural-specific models for inclusive QoL enhancement: recognizing the unique needs and challenges of rural elderly populations, we strongly recommend the development and promotion of elderly school models specifically tailored for rural communities. These models may require adaptations to curriculum content, delivery methods, and resource allocation to ensure equitable access and maximize QoL improvements for all senior citizens regardless of location. By embracing these policy implications and recommendations, Thailand can leverage the power of lifelong learning to establish a comprehensive and inclusive framework for healthy aging within its growing senior population.\n\n\nConclusion\n\nThe present study underscores the elderly school policy as a potentially impactful health promotion intervention, offering valuable insights into its effectiveness. Notably, the study reveals significantly higher overall QoL, and improvements across specific domains, among senior citizens attending elderly schools compared to their non-attending counterparts. Additionally, attendance at elderly schools emerges as a significant predictor of QoL, highlighting the program’s direct contribution to QoL. While certain sociodemographic factors also exhibit significant associations with QoL, the study’s findings provide compelling evidence that the lifelong learning policy embodied by elderly schools has demonstrably enhanced the QoL of senior citizens in Thailand.\n\nTo maximize the program’s potential, policymakers should prioritize robust support efforts across various domains. Crucial areas include adequate human resources, dedicated financial resources, well-equipped facilities, and effective management structures. Furthermore, encouraging collaboration with LAOs, communities, and the private sector can play a vital role in promoting and expanding the implementation of elderly schools. By prioritizing such strategic investments and collaborative efforts, Thailand can leverage the powerful potential of lifelong learning initiatives to significantly improve the QoL of its aging population.\n\nThis study received ethical approval from the Institutional Review Board (IRB) of Phetchabun Hospital (approval number IEC-20-2565, date: November 9, 2022). The study adhered to the ethical principles outlined in the Declaration of Helsinki, The Belmont Report, CIOMS Guideline, and International Conference on Harmonization in Good Clinical Practice (ICH-GCP). Written informed consent was obtained from all participants before the interview process began. Participants were informed that they could withdraw from the study at any time without providing a reason. The confidentiality of participant data was ensured throughout the entire study.", "appendix": "Data availability\n\nFigshare: Effect of elderly school policy on quality of life among Thailand’s senior citizens, https://doi.org/10.6084/m9.figshare.25894831.v2. 65\n\nThe project contains the following underlying data:\n\n• Data.xlsx\n\n• Ethical considerationsap\n\n• Participant information sheets and consent forms\n\n• Questionnaire\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nQuestionnaire, ethical considerations, participant information sheets and consent forms were provided in data availability https://doi.org/10.6084/m9.figshare.25894831.v2. 65\n\n\nAcknowledgements\n\nWe would like to express our genuine appreciation to all participants in the dissertation seminars at the College of Public Health Sciences, the research assistants involved in this research, the Celebration of Chulalongkorn University 100th Anniversary Scholarship and all the participants in this study. 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Publisher Full Text" }	[ { "id": "310486", "date": "23 Aug 2024", "name": "Aye Sandar Mon", "expertise": [ "Reviewer Expertise My areas of research include maternal health and other public health-related topics", "epidemiological studies in communicable and non-communicable diseases", "and the application of advanced statistical models in various types of research." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nGeneral comment\nThe manuscript is well written and the study findings could contribute to the substantial policy implication.\nSpecific comments\nIn sampling technique, the researchers applied quota and systematic sampling. For systematic sampling, how to calculate the sampling interval was described but I did not find about the random start. Could you please clarify it? In data collection method, was any pre-testing conducted? If so, please mention the procedure and the results including the reliability of the questionnaire and participants’ understanding of the question items. According to previous literature and evidence from international studies, in addition to the factors you considered as covariates in the statistical model, the social support and mental health status such as depression have been recognized as the important predictors for QoL. Although your questionnaire included the items assessing the social support and mental health status (DASS-21), why weren’t these variables considered as covariates in the statistical model? While presenting the results of multiple linear regression in “Table 4”, as the variable “elderly school attendance” is the main factor of interest, this variable should be described first instead of being the second-to-last description. I did not find the statistical procedures for assumption checks for multiple linear regression (regression diagnostics) in the 'Methods' or 'Results' sections. Were these tests performed? If not, please check the necessary assumptions, and if they were, please mention the results 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? 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": "302071", "date": "20 Sep 2024", "name": "Andrew Kweku Conduah", "expertise": [ "Reviewer Expertise § Population Estimates and Projections.§ Population Health and Mortality- Health Emergencies & Preparedness", "Ageing & Intergeneration Relations", "and Non-Communicable Disease & Health Projection (Physical Activity", "Obesity", "Tobacco Control", "etc.)§ Business Demography§ Business Policy and Strategy§ Business Management§ Public Administration", "Entrepreneurial Innovation" ], "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\nEffect of Elderly School Policy on Quality of Life among Thailand’s Senior Citizens: A Propensity Score Matching Approach.\nSummary of the Manuscript: This manuscript evaluates the impact of Thailand’s 'elderly school' initiative on the quality of life (QoL) among senior citizens using a propensity score matching (PSM) approach. The study, conducted in Phetchabun province, found that attending the elderly school significantly improved QoL compared to non-attendees, offering a beacon of hope for the elderly population. The research also identified several factors positively associated with QoL, including gender, income, employment, caregiving, and education. Evaluation of the Introduction Global Context: The introduction effectively situates the research within the global context by highlighting the significant increase in the elderly population worldwide. It references the international trend of an ageing population, emphasizing the impact on healthcare systems. Statistics about the projected growth of the elderly population from 2015 to 2050 and the concentration in middle-income countries provide a strong foundation for understanding the global scale of the issue. The comparison with other regions, such as South India and Myanmar, also enhances the global perspective. Research Problem Articulation and Justification: The research problem is well-articulated and justified. The introduction clearly identifies the urgent need for effective interventions to improve senior citizens' quality of life (QoL) in the face of the ageing population in Thailand. The discussion on the disparities in QoL between urban and rural areas, as well as the specific context of Lomkao district, further justifies the need for the study. The problem is contextualized by noting the lack of comprehensive evaluations of the elderly school initiative’s impact, which underscores the significance of the research. Objectives: The introduction does not explicitly state the research objectives. While the problem is well-defined and justified, and the gap in the literature is highlighted, the study's specific aims should be more clearly articulated. For instance, the introduction could explicitly state that the study aims to evaluate the causal effect of the elderly school initiative on QoL using propensity score matching (PSM) and to investigate the association between various factors and QoL among senior citizens. Opinion: The introduction provides a robust and comprehensive background for the study. It effectively places the research in a global context, identifies the problem, and justifies the need for the study. However, the specific research objectives should be clearly stated to strengthen the introduction. This will provide readers with a clear understanding of the study’s aims and how it intends to address the identified gap in the literature. Additionally, expanding the discussion on similar interventions in other regions could further enhance the global context and relevance of the research. Overall, the introduction sets a solid foundation for the study but would benefit from a more explicit articulation of the research objectives.\nMethodology 1. Research Design Cross-Sectional Study:\nAppropriateness: The cross-sectional design is suitable for simultaneously assessing the prevalence of characteristics or conditions. This study is used to compare the quality of life (QoL) of elderly individuals who attended and did not attend an elderly school. This design effectively examines differences in QoL and determines associations with the elderly school program.\n2. Sample Size Sample Size Calculation:\nAppropriateness: The sample size calculation is based on continuous data and considers effect size, power, predictors, and significance level. The study's sample size of 901 participants is derived from these calculations, ensuring sufficient statistical power for detecting meaningful differences.\n3. Sampling Technique Quota and Systematic Sampling:\nAppropriateness: Combining quota sampling with systematic sampling ensures a representative sample of elderly individuals attending and not attending the elderly school. Quota sampling ensures demographic representation, while systematic sampling introduces randomness into the selection process.\n4. Data Collection Face-to-Face Interviews:\nAppropriateness: Face-to-face interviews effectively collect detailed and accurate data concerning literacy or language barriers. The research team’s training ensures consistency and reliability in data collection.\n5. Measurement Instruments Used:\nDemographic and Socioeconomic Factors: Detailed questionnaires assess various factors relevant to QoL. Activities of Daily Living (ADLs): The Barthel Index is an established tool for measuring ADL performance, suitable for evaluating functional capacity. WHOQOL-BREF: This validated instrument assesses QoL across multiple domains. Using the Thai version ensures cultural and linguistic relevance.\n6. Treatment Variable Elderly School Program:\nAppropriateness: The definition and criteria for attendance in the elderly school program are clear and relevant to the study's objectives. Participants are categorised based on their attendance, which aligns with the study’s aim to evaluate the program’s impact.\n7. Covariates and Propensity Score Matching (PSM) PSM for Addressing Selection Bias:\nAppropriateness: PSM is a robust method for controlling confounding variables and ensuring balanced groups. Demographic and socioeconomic factors are used as covariates, enhancing comparability between attendees and non-attendees of the elderly school.\n8. Statistical Analysis Analysis Methods:\nAppropriateness: The use of PSM, standardised differences, and multiple linear regression is appropriate for analysing the effect of the elderly school program on QoL. These methods effectively control for confounding and assess the treatment's impact.\n\nResults Demographic Characteristics of the Participants A total of 1,508 participants completed the interview. After Propensity Score Matching (PSM), 1,374 individuals remained, with 687 participants in the non-attending and attending elderly school groups. In the non-attending group, 474 (69.00%) were women, and 541 (78.75%) were women in the attending group. The average age in the non-attending group was 67.75 years (SD = 5.16), while in the attending group, it was 68.66 years (SD = 4.78). Most participants in both groups had completed primary school, had a monthly income of less than 20,000 baht, and were employed. More than half of the participants lived with their families and had caregivers. The standardised difference was less than 10% for all covariates, indicating improved balance between the two groups (Table 2). Quality of Life Outcomes The average overall Quality of Life (QoL) score was 57.50 (SD = 7.53) in the attending group and 44.40 (SD = 7.11) in the non-attending group. The Average Treatment Effect (ATE) of attending elderly school on overall QoL was 10.67 (95% CI: 9.67–11.67, p < 0.001). The ATEs for QoL domains were as follows: physical health (8.89), psychological (8.17), social relationships (6.37), and environmental (8.41). Each domain showed a statistically significant difference between the two groups (Table 3). Associations Between Elderly School Attendance and QoL Multiple linear regression analysis revealed that QoL was significantly associated with gender, educational level, monthly income, employment, caregiver presence, and elderly school attendance (F (8, 1365) = 251.88, p < 0.001, R² = 0.5962). Elderly school attendance had a strong positive association with QoL, with an unstandardised beta coefficient of 10.811. Higher education levels were also associated with higher QoL scores (Table 4). Discussion This study examined the impact of attending an elderly school on QoL across four domains: physical health, psychological well-being, social relationships, and environment. The findings revealed that elderly school attendance significantly improved QoL compared to non-attendance. The positive effect of elderly school attendance was consistent with previous research in different regions of Thailand, which also found higher QoL among school attendees. The highest impact was observed in the physical health domain, followed by the psychological, environmental, and social relationships domains. The study's results align with international research, highlighting the benefits of lifelong learning for elderly populations. Studies from Portugal, Canada, and Korea have observed similar positive impacts on QoL, underscoring the global relevance of these findings. Strengths and Limitations The study's strengths include using PSM to enhance internal validity and provide a realistic comparison between groups. It is one of the first to analyze the elderly school policy's impact on QoL comprehensively. However, limitations include the study's geographical scope, as it was conducted in a single district, limiting generalizability. The cross-sectional design also restricts the ability to establish causality, and future longitudinal studies are needed to confirm these findings. Policy Implications and Recommendations The findings suggest important policy implications for optimizing Thailand's approach to ageing populations. The study recommends integrating elderly schools into broader health promotion strategies, developing continuous education policies for seniors, fostering stakeholder collaboration, and creating rural-specific models to enhance QoL for elderly populations in similar contexts.\nThe conclusion is well-structured and effectively summarizes the essential findings and implications of the study. Here’s a brief evaluation:\nClear Summary of Findings: The conclusion restates the primary outcomes, particularly the positive impact of elderly school attendance on Quality of Life (QoL). It effectively highlights the significance of these schools in enhancing overall QoL among senior citizens in Thailand. Implications for Policy: The discussion on policy implications is well-founded. By recommending robust support across various domains (human resources, finances, facilities, and management), the conclusion addresses practical steps that policymakers can take to enhance the program's effectiveness. Encouragement of Collaboration: A strategic recommendation is to emphasise collaboration with local administrative organisations (LAOs), communities, and the private sector. This suggests a comprehensive approach to expanding the program and ensures the reader understands the context needed for success. Forward-looking Perspective: The conclusion reflects on the current findings and looks ahead, suggesting how Thailand can further leverage these initiatives to improve the QoL of its ageing population. This gives the study a forward-looking angle, which is valuable in research conclusions.\nMinor Suggestions for Enhancement:\nReinforce Study Limitations: Depending on what was discussed earlier in the paper, briefly mentioning any limitations or areas for future research here might be helpful. This adds balance and shows a critical engagement with the study’s scope. Broaden the Context: While the focus on Thailand is appropriate, you could briefly mention how these findings might inform similar initiatives in other countries, especially those with ageing populations, to widen the study's impact.\nOverall, the conclusion is appropriate, but adding a sentence or two to address limitations or broader implications could make it even stronger.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] } ]	1	https://f1000research.com/articles/13-735
https://f1000research.com/articles/12-537/v1	23 May 23	{ "type": "Research Article", "title": "The legal and institutional framework for the protection of religious rights in Nigeria and the right to wear Hijab in public institutions.", "authors": [ "CAESAR MANUCHIMSO ELIKWU", "Olusola Joshua Olujobi", "EBENEZER TUNDE YEBISI" ], "abstract": "Background: Religion and its exercise are one of the most sensitive discourses in different parts of the world, especially in Nigeria. The constitution and other laws ensure citizens are afforded basic human rights of which religious rights are included and yet regulated. There are questions of interpretation as the extent to which such rights can be enjoyed and the efficacy of both the legal and institutional frameworks protecting religious rights in Nigeria. Methods: This article utilises a doctrinal legal research approach utilising existing literature, statutes, and laws enacted towards the protection of religious rights in Nigeria with the consideration of primary and secondary sources of laws including the 1999 Constitution of the Federal Republic of Nigeria (as amended), judicial precedents, International Conventions, law textbooks, and peer-reviewed journals. A comparative analysis of Nigeria, Tunisia, Algeria, Turkey and Kazakhstan was done to gain perspectives on balancing conflicting interests in light of Nigeria's heterogeneous status. As part of the contribution to knowledge, a hybrid model for mitigating the socio-legal effect of the usage of hijab in Nigeria’s public institutions is presented to further enrich Nigeria’s jurisprudence. Results: Nigeria, being a multi-ethnic and multi-religious state, demonstrates that the government must protect the public interests as it relates to religious rights regardless of faith or religion. The study reveals that the current legal approach without further legislative intervention on religious issues will be inadequate to address the problem. Therefore, this study presents a hybrid model for mitigating the socio-legal effect of the usage of hijab in Nigeria’s public institutions to avoid harm and further enrich Nigeria’s jurisprudence. Conclusions: This study concludes that Nigeria's legal and institutional frameworks are adequate for their purpose although they must be tweaked to conform with current trends when required to be at par with the widely accepted or world standard.", "keywords": [ "Legal and Institutional Framework", "Protection of Religious Rights", "Nigeria", "Hijab", "Public Institutions." ], "content": "Introduction\n\nThe wearing of hijabs in public institutions in recent times has become a discourse which has called into question the supposed secular compass of the Nigerian state following the decision of the Supreme Court in Lagos State Govt. and Ors v. Asiyat Abdulkareem, (SC/910/16), wherein the court in a split five-two judgement, held that “wearing of the hijab was an Islamic injunction and an act of worship required of Muslims and as such a fundamental right guaranteed to Muslim women” (Premium Times, Lagos, 17 June 2022). By this decision, the Supreme had upheld the Court of Appeal’s judgement wherein it had set aside the decision of the High Court of Lagos State (Honourable Justice Coram Onyeabor) which had earlier held that the prohibition of hijabs within and outside the school premises was not discriminatory and did not go against the provisions of Sections 38 and 42 of the 1999 Constitution of the Federal Republic of Nigeria (as amended), and as such remains the current position of the law in Nigeria on hijab-wearing as a religious right.\n\nThe Supreme Court judgement has without a doubt been met with divergent views by clergymen, legal practitioners, journalists, scholars, and other members of society. For many followers of the Islamic faith, the decision of the Supreme Court upholding that of the Court of Appeal is a victory for democracy as it guarantees their rights (Deji-Folutile, 2021).\n\nOn the other side of the divide, there is the view that the wearing of religious garbs such as the hijab in public institutions is a slippery slope that would usher in chaos as the ardent of other faiths would equally. in the light of the decision, adorn their religious attires in total disregard for the dress codes formulated by public institutions.\n\nNigeria being a multi-ethnic state and consequently, a multi-religious state has by this fact found itself in a peculiar position. It must find a way to protect the interests of the public as it relates to religious rights regardless of whatever faith is obtainable in whatever region in Nigeria. This article provides an exposition on the current legal and institutional framework for the preservation of religious rights as a human right in Nigeria in the context of the right to wear hijabs.\n\nThis study presents a comparative legal analysis of Tunisia, Algeria, Turkey, and Kazakhstan to that of Nigeria. The countries were selected being four advanced countries that have resolved this issue of the right to wear hijabs successfully, whereas the imbroglio of the usage of hijab in public institutions will also be considered to gain useful insight to assist Nigeria to combat this religious problem.\n\nAdekola (2019) in his book contends that in light of the acrimonious nature of litigation proceedings and the strife it would result in, issues bordering on the expression of religious rights should be determined by the less confrontational methods of conciliation and mediation and other alternative disputes resolution (ADR) mechanisms. The author particularly highlights all of the instances across Nigeria where the controversy around wearing hijabs became the subject of litigation and further heated the polity. Adekola further suggests that if such controversies were brought before ADR settings a win-win approach would most likely have been adopted to assuage the concerns of all interest groups.\n\nAdekola’s work is useful to this study as it suggests the utilization of a balanced and all-inclusive approach in addressing the hijab controversy as a human rights issue which is one of the solutions that would be explored by this study.\n\nEzeonu’s (2017) addresses the exasperated issue of the right to wear hijabs as a religious right within constitutional limits and the confines of public policy by appraising the Nigerian Court of Appeal (being the latest decision at the time of writing the article) decision upholding the right to wear hijabs on two major fronts. First, he lauds the judgement of the Court of Appeal in upholding the Constitutional religious rights of the citizenry as it relates to the wearing of hijabs as he notes that the said judgement is accurate in light of the failure of the Respondents (The Lagos State Government) in the instant case to plead any policy or legislation of government that prohibited the wearing of such garbs.\n\nOn the second front, Ezeonu submits that a practical way of addressing the conundrum of balancing various religious interests considering that other religious groups would seek to adorn their religious garbs, is for the government to put in place substantive legislation or at the very least guidelines and circulars stipulating a secular moral code which would prevent a descent into a state of anarchy were every faith would want to demonstrate their religious beliefs in public institutions. This he contends would not be tantamount to trampling on religious rights as such a move would be made under the spirit of the law as contained in Section 45 of the 1999 Constitution of the Federal Republic of Nigeria (as amended) empowering the state to curtail constitutional rights for public safety and order (Ezeonu, 2017).\n\nEzeonu’s work provides a pragmatic approach to balancing religious interests by suggesting legislative intervention. His work is relevant to this study as it suggests legislative intervention in addressing the hijab controversy which constitutes a part of the solution this work would seek to proffer. However, the study fails to carry out a comparative legal analysis of other advanced countries that have resolved successfully the imbroglio of the usage of hijab in public institutions with useful insights Nigeria can gain to combat this religious conundrum. The gap which the current study intends to fill in the existing literature in the field of study.\n\nGarba (2020) makes a case for the propriety of the limitation of religious rights in the country as a failure to do so would occasion anarchy in the light of the tendencies of religious groups to arbitrarily engage in activities likely to jeopardize public safety and order. He draws the instances and the need to regulate religious preaching which is a form of freedom of expression\n\nMyland (2019) in her book review toes a similar path as Terman and Fijabi as she provides an exposition on the fact that the donning of the hijab is not necessarily an expression of the Islamic faith but has become a tool used by terror groups in propagating fundamentalist ideals of what a woman should look like. Like the work of Terman and Fijabi, the work also fails to address the views of persons who see the hijab as a true religious tenet that deserves expression.\n\nYusuf (2018) seeks to balance the Islamic right to wear hijabs with the duty of the government to maintain public peace and order. He submits that by the dictates of the Holy Qur’an and the Hadiths, the wearing of the hijab is a religious obligation, which a woman has to undertake. On the other hand, however, the government in the terrorism-ravaged Northeast have had reasons to place bans on hijab-wearing, in the wake of the insurgency in Northern Nigeria, as hijab-wearing has been identified as a ploy used by female suicide bombers to avoid detection. Yusuf suggests that such measures utilised by the government are truly necessary for maintaining public order and peace. Dagogo (2019), drew attention to the need for the balancing of interests when matters with religious colouration come before the government. According to them, the decision by the government in taking over missionary schools and then trying to enforce certain practices such as permitting the wearing of hijabs contributed largely to the conflicts in Osun and Kwara states as the ardent Christian faiths maintained the belief that this was an attempt by the government to trample on the sanctity of their religions.\n\nThe view expressed by Yusuf is pragmatic and indeed solidifies the claims of this study that it is appropriate to sacrifice religious practices as long as it guarantees the greater good of society.\n\n\nMethods\n\nThis article utilises a doctrinal legal research approach utilising existing literature as well as statutes and laws enacted towards the protection of religious rights in Nigeria with the consideration of primary and secondary sources of laws for instance, the 1999 Constitution of the Federal Republic of Nigeria (as amended), judicial precedents, International Conventions, law textbooks and peer-reviewed journals. Reliance will be on an examination of primary legal sources listed above. Lessons will also be drawn from international legislation and comparative analysis of Nigeria, Tunisia, Algeria, Turkey, and Kazakhstan to gain perspectives on balancing conflicting interests in light of Nigeria’s heterogeneous status. The countries were selected being advanced countries who have resolved successful the imbroglio of usage of hijab in public institutions to gain useful insight to assist Nigeria to combat this religious problem. Information on the topic of hijab restrictions in each country used for comparisons were identified using news articles without a formalised search strategy. As part of the contribution to knowledge, the study designs a hybrid model for mitigating the socio-legal effect of the usage of hijab in Nigeria’s public institutions to further enrich Nigeria’s jurisprudence.\n\nBy drawing the attention of the Nigerian populace, policy-makers, officials of the judiciary, government, and lawmakers on the need to strike an effective balance in preserving the expression of religious rights such as the wearing of hijabs in a polarised state such as Nigeria. The study emphasise the extent to which they can exercise their religious lights and civil liberties within the ambits of the law; for the judiciary it will reemphasize the need for quality judgements that cans stand the test of time in light of the doctrine of judicial precedents and its effects; and for the legislature, it shall emphasize the importance of the need for legislation on religious rights which takes into considerations the concerns of the populace in a bid to ensuring societal stability and lasting peace considering the long history of religious induced violence in Nigeria. The study further creates the necessary awareness on the various fundamental rights guaranteed under the Constitution and the need for an effective legal framework to adequately protect them. In doing so, it critically analyses the role currently played by the judiciary particularly in light of its decision in Lagos State Govt. and Ors v. Asiyat Abdulkareem, as well as the efficacy of the existing legal framework and policies for protecting religious liberties within the constitutional limits. It further appraises the ill of religious intolerance bedevilling the Nigerian society as a consequence of the government failing to manage the religious and ethnic diversity of the Nigerian peoples. Based on the comparative analysis, it makes recommendations to ensure the effective preservation of religious rights within the scope of the Constitution.\n\n\nResults\n\nIn Nigeria, a multi-ethnic and multi-religious state with various uniqueness, the federal government must protect the interests of the citizens as it relates to religious rights regardless of faith or religion. Since the current legal mechanism without further legislative intervention on religious issues is unsatisfactory to combat the scourge. As part of contribution to knowledge, the study designs a hybrid model for mitigating the socio-legal effect of the usage of hijab in Nigeria’s public institutions to further enrich Nigeria’s jurisprudence.\n\nThe article utilises a doctrinal legal research approach by utilising existing literature as well as laws enacted towards the protection of religious rights in Nigeria with the consideration of primary and secondary sources of laws for instance, the 1999 Constitution of the Federal Republic of Nigeria (as amended), judicial precedents, International Conventions, law textbooks and peer-reviewed journals. A comparative analysis of Nigeria, Tunisia, Algeria, Turkey, and Kazakhstan was done to gain perspectives on balancing conflicting religious interests in light of Nigeria’s heterogeneous status, using a utilitarian approach and law to address religious imbroglio in Nigeria.\n\nThe right to freedom of religion is a human right and as such an effective means to evaluate the extent of the guarantee of the right to religion is to examine the broader body of the legal framework for religious rights in Nigeria. The relevant legislations worthy of consideration in this regard include the following: The Constitution of the Federal Republic of Nigeria 1999 (as amended), the Child Rights Act 2003, and the African Charter on Human and Peoples’ Rights (Ratification and Enforcement) Act, the Universal Declaration on Human and Peoples’ Rights, 1948, the Criminal Code, and Penal Code. Others include the Federal Character Commission Act, (Establishment, Etc.) of 1996, Decree 1996 (No. 34 of 1996) and the Public Complaints Commission Act, of 1975 (No. 31) (Chapter 377). Laws of the Federation of Nigeria.\n\nThe Constitution of the Federal Republic of Nigeria 1999 (as amended)\n\nSection 38(1) of the Constitution of the Federal Republic of Nigeria 1999 (as amended), guarantees the right of Nigerian citizens to freedom of thought, conscience, and religion as follows:\n\n“Every person shall be entitled to freedom of thought, conscience and religion, including the freedom to change his religion or belief, and freedom, (either alone or in community with others) and in public or in private, to manifest or propagates his religion or belief in worship, teaching, practice and observance.”\n\nUpon a closer examination of the above provision, there are various aspects of the right to religious freedom beyond the broad sense which include: the right to conscience, the right to independent thought, the right to change religion, and the right to religious propagation. Indeed, in the broad sense of the right to religious freedom. Section 38(1) of the 1999 Constitution guarantees the right to adopt a religion of one’s choice. As such, every Nigerian citizen is guaranteed protection from being coerced to act in any manner adverse to his belief.\n\nIn considering religious freedom in terms of the right to conscience, a viable way the right can be exercised is by permitting a citizen to refuse compulsory military service where the same is inimical to his religious/belief system. However, this religious liberty to opt out of military service attracts a corresponding obligation under Section 34(1) of the 1999 Constitution of the Federal Republic of Nigeria which prescribes undertaking an alternative mode of service instead of military service.\n\nA further sense in which the right to religious freedom is enjoyed under Section 38(1) of the Constitution, is the liberty afforded religious institutions to set up educational institutions which is much more articulated under Section 39(1) of the Constitution which provides that: “every person shall be entitled to freedom of expression, including the freedom to hold opinions and to receive and impart ideas and information without interference” (Section 39(1). In the case of Okogi and Others v. The Attorney General of Lagos State (1981) 2 NCLR 337, the Lagos State Government, via a directive, sought to abolish the operation of private primary and secondary schools to make room for the floating of its policy on education. The Plaintiffs challenged the policy because it infringed on their right to freedom of expression by preventing them from disseminating information to students. The Court declared the policy to be unconstitutional and upheld the right of religious groups to express their religious freedom by the establishment of schools to inculcate knowledge as a religious practice and even as an economic activity (Olujobi et al., 2022b).\n\nThe freedom of religion of persons attending educational institutions is another dimension in which the Constitution affords religious liberty to Nigerian citizens. Specifically, Section 38(2) of the Constitution protects the right of children to not be coerced into observing practices that are alien to their religion/that of their parents or guardians. The section reads:\n\n“No person attending any place of education shall be required to receive religious instruction or to take part in or attend any religious ceremony or observance if such instruction ceremony or observance relates to a religion other than his own, or religion not approved by his parent or guardian” (Section 38: 2).\n\nIt is pertinent that the above section does not delineate any age limit upon which a child/individual would be able to engage in other practices alien to his religion. It is suggested in this regard that a suitable time for an individual to be able to make a such decision should be when he attains the majority age of 18 (Onebunne & Chukwu, 2018).\n\nAnother aspect in which the right to religious freedom is exercised by Nigerian citizens is in their mode of dressing which is a subject that forms the crux of this topic. As in the Supreme Court decision, borne out of citizens approaching the courts to protect the right to wear hijabs, various individuals in other spheres of society have had the cause to do so. The cases of Miss Tulolope Ekundayo who objected to wearing trousers whilst undergoing the National Youth Service Corps (N.Y.S.C.) scheme because it offended her religious beliefs (Afisunlu, 2013) and the continuous agitation by the Muslims Right Concern (M.U.R.I.C.) (Lantana, 2010) are further examples of how Nigerian citizens have demanded their right to express their religious beliefs.\n\nThe Child Rights Act 2003\n\nThe Child Rights Act (CRA) 2003 is another legislative instrument that seeks to protect the right of Nigerian Citizens to religious freedom. The Act has been rightly described as having made more comprehensive provisions to guarantee the religious rights of children in Nigeria (Adamu & Raji, 2020) although the opinion is also held that the CRA only accentuates the existing constitutional provisions (Adetola-Kazeem, 2016). Through an examination of the CRA provisions on religious rights of children, this author believes however, that the act is beyond an accentuation but has provisions that can be described as more far-reaching than those of the 1999 Constitution as amended. Significantly in this regard Section 7(1), (2), (3), and (4) of the CRA read:\n\n“(1) Every child has a right to freedom of thought, conscience and religion.\n\n(2) Parents and, where applicable, legal guardians shall provide guidance and direction in the exercise of these rights having regard to the evolving capacities and best interest of the child.\n\n(3) The duty of parents and, where applicable legal guardians to provide guidance and direction in the enjoyment of the right in subsection (1) of this section by their child or ward shall be respected by all persons, bodies, institutions and authorities.\n\n(4) Whenever the fostering, custody, guardianship or adoption of a child is an issue, the right of the child to be brought up in and to practice his religion shall be a paramount consideration.”\n\nNotably, indeed, subsections (3) and (4) beyond guaranteeing the right to religious freedom like the Constitution, emphasise the need for its respect by all entities and its protection in light of it being integral to a child’s well-being (Intellectual Reserve Inc., 2021).\n\nAfrican Charter on Human and People’s Rights (Ratification and Enforcement) Act CAP A9, LFN, 2004\n\nThe African Charter on Human and People’s Rights (‘The African Charter’) equally contains relevant provisions guaranteeing the rights of Nigerians as it has been domesticated into our laws by the National Assembly. Indeed, under the domestication, courts in Nigeria are now bound to “give effect to it like all laws falling within judicial powers of the courts” (Abacha v Fawehinmi (2001) 1 CHR 20). In Abacha v. Fawehinmi, (2001) 1 CHR 20 the Supreme Court had cause to comment on the status of the African Charter vis-à-vis the Nigerian legal system as it notably stated that regardless of the African Charter, as an Act of the National Assembly being subservient to the Constitution, in light of its international flavour, it is superior to other Acts of the Parliament and by consequence, laws of the various Houses of Assembly.\n\nArticle 8 of the Act, like Section 38(1) of the 1999 Constitution of the Federal Republic of Nigeria (as amended) provides for the right to religious freedom and conscience as follows: “Freedom of conscience, the profession and free exercise of religion shall be guaranteed. No one may, subject to law and order, be submitted to measures restricting the exercise of these freedoms”. According to Adamu and Raji (2020), however, in contrast with the 1999 Constitution, the African Charter has no categorical provision guaranteeing the right to the private and public practice of religion or the right to change one’s religion being aspects of the right to religious freedom which the Constitution provides for. The authors submit regardless that by a holistic appreciation of the Act, these supposedly omitted senses of the right to religious freedom can be deduced.\n\nAnother way in which the African Charter expands the guarantee of the right to freedom of religion contained in the 1999 Constitution is by prohibiting religious intolerance. Article 3 guarantees equality before the law, for all individuals. Indeed, beyond the freedom from discrimination based on religion as provided by Section 42 of the Constitution, Articles 19 and 28 of the Charter prohibits religious tolerance of any form. This is a laudable provision needed in a country as pluralistic as Nigeria where without tolerance, discrimination or domination of one by the other, incidents of mistrust, conflict, and violence would be the order of the day Olujobi et al. (2022a).\n\nThe Universal Declaration of Human Rights 1948\n\nThe Universal Declaration of Human Rights (UNDHR) 1948, like the African Charter and the Constitution, guarantees the right to religious freedom. Section 18 of the Act in this regard reads:\n\n“Everyone has the right to freedom of thought, conscience and religion; this right includes freedom to change one’s religion or belief, and freedom, either alone or in community with others and in public or private, to manifest his religion or belief in teaching, practice, worship and observance.”\n\nThe United Nations encourages member states to adopt relevant human rights provisions like the right to religious freedom and on this basis, regional legislations like the African Charter and the Constitution have been inspired to guarantee the right.\n\nThe Criminal Code Cap.77, Laws of the Federation of Nigeria, 2004 and Penal Code Cap. 89, Laws of Northern Nigeria, 1963\n\nBefore Nigeria gained independence in 1960, the British colonial government had enacted two separate legal regimes to function as the substantive criminal law for northern and southern Nigeria in the form of the Penal Code and the Criminal Code respectively. The Criminal Code was enacted in the year 1916 as the Nigeria Criminal Code Act 1916, while the Penal Code was enacted in the year 1960 as the Nigeria Penal Code Act 1960. Essentially, these laws purported to criminalise criminal acts and provide for the relevant punishment in a bid to discourage crime.\n\nThese legislations also play a role in preserving religious rights by providing against religious intolerance. Both legislations provide against insulting or inciting contempt of a religious creed (blasphemy) and as such Sections 204 and 210 of the Criminal Code Act and Penal Code contain punitive provisions in this regard. Section 204 of the Criminal Code in this regard reads:\n\n“Any person who does an act which any class of persons consider as a public insult to their religion, with the intention that they should consider the act such an insult, and any person who does an unlawful act with the knowledge that any class of persons will consider it such an insult, is guilty of a misdemeanour and is liable to imprisonment for two years.” (Section 204).\n\nSimilarly, Section 210 of the Penal Code also imposes a similar imprisonment term of two years as deterrence for blasphemy. Rather unfortunately, however, the punitive provisions of these legislations have not been effectively stressed by the government as being the punishment for the crime of blasphemy. In Northern Nigeria, several examples abound of how civilians have resorted to killing persons whom they allege to have committed the offence, with the government failing to put a stop to the same as it keeps happening from time to time.\n\nThere exist several institutions/agencies of the government that through their functions serve as mechanisms for safeguarding the constitutional right to freedom of conscience and religion. These institutions include among others: The Judiciary, National Human Rights Commission, Public Complaints Commission, Truth and Reconciliation Commission, and the police.\n\nThe Judiciary\n\nThe Judiciary, as the third arm of government, is composed of all the courts in the country from the lowest courts, such as the Area and Customary courts to the highest Court in the land, the Supreme Court. Section 6 of the Constitution establishes Superior Courts of Record, and these include the High Courts and other courts of coordinate jurisdiction, the Court of Appeal, and the Supreme Court. Various states laws provide for courts below High Courts such as the Magistrate, Area, or Customary Courts. The role of interpreting the various statutes that govern the right to freedom of religion as well as other human rights as enshrined in the Constitution and fundamental human rights procedure rests with the judiciary. The High Court and Federal High Court as the courts of first instance in human rights matters are involved in the enforcement of fundamental human rights as defendants are tried before them with such trials sometimes leading to conviction, fines or damages as the case may be (Ikpeze, 2013).\n\nIndeed, the decision, which forms the crux of this article is one of the several instances in which the Courts have been called upon to address human rights issues. In Esabunor v. Fayewa (2019) LPELR-46961(SC). the Court of Appeal entertained the question of whether a parent could object to life-saving treatment for their child based on the former’s belief. The Court held that a mother could not object to such a lifesaving treatment thus the mother’s freedom of religion was suppressed by the interest of the state in the protection of her child’s right to live. In Medical and Dental Practitioners Tribunal v. Dr Okonkwo 7 NWLR (Pt. 711) 206 at. 237-240 however, the Court upheld the right of a patient to refuse blood transfusion on the clear basis that the decision to do so was being made by an adult of capacity electing to exercise her right to freedom of religion.\n\nThe current author submits that unlike the decision in Esabunor v. Fayewa (Supra) and Medical and Dental Practitioners Tribunal v. Dr Okonkwo (Supra) which took into consideration the overall public interest on the need to safeguard human rights (right to life) and what the consequence of not doing so will have on society, the decision in Lagos State Govt. and Ors v. Asiyat Abdulkareem (Supra), is too legalistic, failing to consider the pluralistic nature of Nigeria with constant suspicions of socio-political and religious domination.\n\nNational Human Rights Commission\n\nThe National Human Rights Commission was established by the National Human Rights Commission Act 1995 under the resolution of the United Nations enjoining her member states to set up Human Rights Institutions to guarantee and promote human rights which are inherent and universal rights to all human beings, regardless of race, sex, nationality, ethnicity, language, religion, or any other status.\n\nThe commission serves as a mechanism to enhance the enjoyment of human rights. Its establishment aims at creating an enabling environment for extra-judicial recognition, promotion and enforcement of human rights, and treaty obligations and providing a forum for public enlightenment and dialogue on human rights issues thereby limiting controversy and confrontation (Nnamani, 2011).\n\nUnder its stipulated functions under Section 5 of the Act, the commission is mandated to receive complaints of human rights violations from any person acting in his or her interest, any person acting on behalf of another person who cannot act in his or her name, any person acting as a member of or in the interest of a group or class of persons or from an association acting in the interest of its members (Gasiokwu, 2003).\n\nQuite commendably, the commission has handled several alleged human rights infringements across the country, including infringements on the right to religious freedom such as the suspected murder of eight people in Zamfara State on the accusation of having committed blasphemy (Chude, 2023) This current author, however, submits that a lot of work is still left undone by the Commission particularly as it relates to the preservation of the right to religious freedom particularly when one considers the spate of killings fuelled by religious intolerance, particularly in Northern Nigeria. In recent memory is the case of Deborah Samuel, a student at a College of Education in Sokoto State, beaten to death and set ablaze by her irate colleagues on the grounds of blasphemy. Considering such gruesome scenarios continue to play out, one is left to wonder how effective the Commission has been in effecting its mandate on human rights protection in Nigeria.\n\nFederal Character Commission\n\nSection 153 of the 1999 Constitution of the Federal Republic of Nigeria obligates the Federal Government to establish a Federal Character Commission. Accordingly, the Federal Character Commission is mandated by its enabling Act “to promote, monitor and enforce compliance with the principles of the proportional sharing of all bureaucratic, economic, media and political posts at all levels of governments” as stated in the preamble to the Federal Character (Establishment) Act, 2004.\n\nOwing to Nigeria’s diverse nature in all aspects, the role of the Commission is particularly important in allaying fears of ethnic and more particularly religious domination. As such by ensuring that economic, social and political opportunities in the country are evenly distributed regardless of an individual’s religious affiliation, the right to express one’s religious beliefs is guaranteed as citizens will do so without the fear of victimization.\n\nThe Commission has however come under severe criticism because it has failed to guarantee an even spread of job opportunities and it sacrifices excellence on the altar of mediocrity by allowing for the employment of persons or admission of students based on filling ‘quota’ systems meant for regions of the country.\n\nPublic Complaints Commission\n\nThe Public Complaint Commission is established by the Public Complaints Commission Act 1975. By Section 5 of the Act, the Commission is given an array of powers to inquire into complaints by members of the public about the administrative action of any public authority and companies or their officials and other related matters.\n\nTo ensure the protection of human rights and prevention of injustice, the Commission is mandated to ensure that public officials or institutions do not carry out any act of injustice against any citizen of Nigeria or any other person resident in Nigeria and for that purpose, the commission shall investigate with special care administrative acts which appear to be contrary to any law or regulation; mistaken in law or arbitrary in the ascertainment of fact; unreasonable, unfair, oppressive or inconsistent with the general functions of administrative organs; improper in motivation or based on irrelevant considerations; unclear or inadequately explained, or otherwise objectionable under Section 5(3) of the Public Complaint Commission Act, 1975.\n\nSection 8(3) imposes a meagre fine of N500 or six months imprisonment on any person who obstructs/induces/interferes with an officer of the Commission in the performance of his duty and Section 8(4) imposes a jail term of one-year imprisonment without the option of a fine on any person who, upon being called upon by the Commission in the course of an investigation, makes any false statement. This writer submits that the punitive mechanism currently put in place by the Commission is insufficient to deter would-be offenders. Worthy of note is that at the time of this research, the current author is unaware of any convictions made under the Act, and this is perhaps suggestive of the lacklustre disposition of the Commission in carrying out its mandate.\n\nTruth and Reconciliation Commission\n\nThe Truth and Reconciliation Commission widely known as the Oputa Panel was an Ad hoc Commission established in the wake of the collapse of decades of military government in Nigeria. Setup by former President Olusegun Obasanjo, the mandate of the Commission was to inquire into human rights abuses between 1984 to 199 (Hayner, 2010). Although the Commission forwarded its findings to the President in 2002, no major action has been implemented regarding the report submitted to date. Commendably, however, the Commission is known to have helped reconcile Nigerian communities in conflict such as several Ogoni communities’ issues.\n\nThe police and other security agencies\n\nThe Police and other law enforcement agencies of the state are established and governed by their specific enabling laws. The Police Act for instance empowers the Police to investigate and arrest persons for offences under any extant law and by implication, certain human rights infringements such as murder for instance, Sections 4 and 23 of Police Act Cap P19, LFN 2020 subject only to the constitutional power of the Attorneys General under the Constitution (This is the power of nolle prosequi granted under Sections 174 and 211 of the Constitution to the Attorney General of the Federation and Attorney General of the State respectively). The National Securities Agencies Act provides for three agencies namely: The Defence Intelligence Agency (DIA); the National Intelligence Agency (NIA); and the State Security Service (SSS). The SSS is the most visible among the trio. Although the statute tried to delineate their functions, they practically dovetail, interrelate or integrate sometimes to assist Nigeria to combat this religious problem (Ikpeze, 2013).\n\nThe results of the comparisons are detailed below with each of the selected countries and sources used for each country in the point-by-point comparative analysis of how each country resolved the imbroglio of wearing of hijabs in public institutions. Information on the topic of hijab restrictions were identified using news articles for each country without a formalised search strategy. The countries banned hijabs in public institutions due to security threats and to combat religious radicalism.\n\nNigeria\n\nThe wearing of the female Islamic dress called hijab is regarded amongst a majority of Muslim faithful as a mandatory religious injunction which has generated complex arguments particularly in the context of human rights to freedom of religion and non-discrimination in education and employment. Respect for individual Muslim women to wear or not wear hijab is fundamental to curtail infringement of their Constitutional rights. This was upheld by the Supreme Court in Lagos State Govt. and Ors v. Asiyat Abdulkareem. However, the Supreme Court decision is now widely regarded as an invitation to chaos in light of the highly pluralistic nature of the Nigeria state and its supposed secular constitution. The case has opened the floodgate of chaotic interpretations which require legislative intervention to address the problem. Nigeria should emulate states like Turkey, regardless of being an Islamic nation, have entrenched secular constitution to allay any internal or concerns from the international community that objective fairness devoid of religious sentiment is not being practiced in the country. Indeed, state resources should be channelled towards the promotion of education, healthcare, industrialisation, the overall wellness of the economy, and not private matters like religion. Nigeria must arrive at a solution in interpreting/managing the decision reached by the Supreme Court in Lagos State Govt. and Ors v. Asiyat Abdulkareem (Supra), in a manner that does not result to carnage.\n\nTunisia\n\nTunisia, with a significantly higher Muslim population than Nigeria, has banned the use of hijabs in public institutions such as universities. Owing to its status as a secular state, the Tunisian government has a ban in force against the wearing of hijabs in public institutions such as schools and workplaces, with the aim of curbing the threats posed by the activities of Islamic fundamentalists (Hawkins, 2011). The view has also been expressed that the ban is also part of the nation’s attempts at gaining global acceptance as a non-extremist state (Simon, 2011). Tunisia, who has resolved successful the imbroglio of usage of hijab in public institutions, will also be considered to gain useful insight to assist Nigeria to combat this religious problem by imbibing global best practices geared towards improving the framework for the preservation of constitutional rights in Nigeria. Tunisia and Turkey are two countries who have decided against its wearing in public places.\n\nAlgeria\n\nBefore the ban on public and civil service institutions, Algeria’s Education Ministry had also imposed a ban on hijabs because it also encouraged cheating and posed a security threat (Middle East Online, 2022). Like Nigeria, where the wearing of hijabs in public schools resulted in clashes between Muslims and Christians, the said ban on hijabs in Algeria resulted in confrontations between the majority Sunni Muslims in support of the ban and the significantly sized Salafist population who is more conservative in their practice of Islam opposed the ban (Rahim, 2022).\n\nTurkey\n\nAlthough Turkey operates as a secular state, it has a majorly Muslim population. Hijabs are not prohibited in the country, rather the country promotes their usage as a symbol of its religious heritage (Reuters, 2022). Between the 1920s and the 2000s, owing to European influence, Turkey had previously placed a ban on hijabs and other headscarves as part of its show of secularism as a European state. With a change of government in the early 2000s, the state lifted the ban on headscarves in various public institutions including judiciary and military (Handy, 2022).\n\nKazakhstan\n\nLike its Algerian counterpart, Kazakhstan banned the use of hijabs in public schools in the year 2016 through a directive issued by the nation’s education Ministry (Urnaliev & Najibullah, 2022). The ban is informed by the concerns of the state that religious extremists who utilize such clothing to occasion harm in this society.\n\n\nDiscussion\n\nThe current legal framework for the protection of human rights in Nigeria inclusive of religious rights is composed of a plethora of laws as well as institutions saddled with the responsibility of guaranteeing various human rights such as the right to wear hijab in public institutions as a religious right. This makes the role of the judiciary very critical as it is invariably responsible for giving effects to the letters of the law upon which persons who seek enforcement of their human rights can bring before it. This study has shown that although Nigeria is not bereft of working institutions like the judiciary, and legislation to address human rights issues such as the wearing of hijabs, the decision of the Supreme Court in Lagos State Govt. and Ors v. Asiyat Abdulkareem (Supra), which has seemingly opened a floodgate of chaotic interpretations, has shown that the current legal approach without further legislative intervention or a hybrid of social and legal solutions will be inadequate to address the problem.\n\nThe study has also found that to effectively address the plausible chaotic aftermath of the decision in Lagos State Govt. and Ors v. Asiyat Abdulkareem (Supra) as it relates to human rights, the government must take steps to promote a balanced and fair state where heterogeneous and pluralistic factors are well considered, by genuinely giving credence to the provisions of the constitution that project Nigeria as a secular state.\n\nThis study also brings to fore the reality that for any guarantee of human rights in the country to be sustained, there must be sincerity of purpose and the right politics should be shown by the government to tackle and deal decisively with impunity, injustice, bias and every action or inaction regardless of status, religion, ethnicity or creed that threatens the human rights of the citizenry on the one hand and the secularity of the Nigerian state on the other (Olujobi & Yebisi, 2023).\n\nLegislative Intervention, owing to the right to wear a hijab in public institutions being permissible as the status quo, the Nigerian government can consider an amendment to Section 45(1) of the 1999 Constitution (as amended) to permit public institutions through administrative policy and enactments to be able to validly limit the right to religious freedom based on the need to promote public order and safety. Such a legislative intervention would be able to adequately make obsolete the decision in Lagos State Govt. and Ors v. Asiyat Abdulkareem (Supra), as the right to religious freedom expressed by the wearing of hijabs would have been limited under the law as prescribed by Section 45 of the Constitution.\n\nNigeria should emulate states like Turkey, regardless of being an Islamic nation, have entrenched secular constitutions to allay any internal concerns from the international community that objective fairness devoid of religious sentiment is not being practised in the country. Indeed, state resources should be channelled towards the promotion of education, healthcare, industrialisation, and the overall wellness of the economy, and not private matters like religion. Accordingly, Nigeria must begin to dismantle the various state apparatus that is paradoxical to our projection as a secular state. For example, the dissolution of the Muslim and Christian Pilgrimage Boards where state resources are expended in sending Nigerians on pilgrimage must be considered as the same only hampers efforts at secularity.\n\n\nConclusion\n\nThe current legal framework for the protection of human rights in Nigeria inclusive of religious rights is composed of a plethora of laws as well as institutions saddled with the responsibility of guaranteeing various human rights such as the right to wear hijab in public institutions as a religious right. This makes the role of the judiciary very critical as it is invariably responsible for giving effects to the letters of the law upon which persons who seek enforcement of their human rights can bring before it.\n\nThis article has shown that although Nigeria is not bereft of working institutions like the judiciary, and legislation to address human rights issues such as the wearing of hijabs the current legal approach without further legislative intervention or a hybrid of social and legal solutions will be inadequate.\n\nThe need for an increased political will to promote secularity in Nigeria, as reiterated in the decision in Lagos State Govt. and Ors v. Asiyat Abdulkareem (Supra), remains the position of the law until overturned despite the problematic consequences it occasions. As such, beyond relying on a purely legalistic approach, the Nigerian government through effecting the right policy must show that it is ready to promote peace by allaying the fears of all religious interests in the country.\n\nThe need to keep up with modern realities by channelling focus and resources towards nation-building and growth, it is submitted that religion is a private matter and should remain as such. The state should not delve into it unnecessarily especially in heterogenous societies where diverse ethnic and religious groups are in constant suspicion of each other.", "appendix": "Data availability\n\nNo data are associated with this article.\n\n\nAcknowledgements\n\nThe financial support of Afe Babalola University Ado–Ekiti, Nigeria, is exceedingly acknowledged and appreciated. Thank you greatly to the Nigeria’s legal icon-Aare Afe Babalola OFR, CON, SAN, D. Litt, the President and Founder of, Afe Babalola University, Ado Ekiti, Nigeria.\n\n\nReferences\n\nAdamu, Raji B: Legal Framework for Freedom of Religion and the Rights of Religious Minorities in Nigeria AJLHR.2020; 4(2). Accessed 29 December 2023. Reference Source\n\nAdekola T: The Wearing of Hijab in Public Educational Institutions in Nigeria: A Call for Alternative Dispute Resolution.Green C, editor. Law, Religion and Human Flourishing in Africa. African Sun Media; 2019; 63.\n\nAdetola-Kazeem A: The Right of Education and Freedom of Religion: Two Constitutional Rights at Odds with each other in a Secular State’, (A Conference Proceedings of the 2016 Annual General Law Conference (AGC) of the Nigerian Bar Association), held at the Civic Centre, Port Harcourt, Rivers State, on the August 24th, 2016.2016.\n\nAfisunlu F: Youth Corp Member Expelled from NYSC Camp for Refusing to Wear Khaki Trousers.2013. Accessed 4 January 2023. Reference Source\n\nAfrican Charter on Human and Peoples’ Rights: (Ratification and Enforcement) Act, Chapter A9. (Chapter 10 LFN 1990). (No 2 of 1983). Accessed March 30, 2023. Reference Source\n\nChude A: The Killing of Deborah Samuel’ (Guardian). Accessed January 2, 2023. Reference Source\n\nDagogo AFD: Education, Ethnicity and Restructuring Debate in Nigeria: The Issues of Schooling System 3(5) RIK-IJPAC).2019. Accessed 11 September 2022. Reference Source\n\nDeji-Folutile O: On Hijab and Controversy in the State of Harmony’ Premium Times (Lagos, 25 March, 2021).2021. Accessed 3 September, 2022. Reference Source\n\nEzeonu O: The School, The Hijab and The Human Rights Question: Abdulkareem V Lagos State Government. African Journal of Law and Human Rights. 2017; 1. Accessed 26 July 2022. Reference Source\n\nGarba A: Permissible Limitations to Freedom of Religion and Belief in Nigeria, 57-76 Religion and Human Rights.2020. Accessed 12 September 2022. Reference Source\n\nGasiokwu M: Human Rights, History, Ideology and Law (Anieh (Nigeria) Limited, 2003).202–203.\n\nHandy N: Why Headscarves Matter So Much to Turkey.2022. Accessed 10 October 2022. Reference Source\n\nHayner P: Unspeakable Truths Transitional Justice and the Challenge of Truth Commissions. 2nd ed.Routledge; 2010.\n\nHawkins S: Who Wears Hijab with the President: Constructing a Modern Islam in Tunisia. J. Relig. Afr. 2011; 41: 35–58. Accessed 6 March, 2023. Publisher Full Text Reference Source\n\nIkpeze N: Fusion of Anti-Corruption Agencies in Nigeria: A Critical Appraisal. Afe Babalola University: Journal of Sustainable Development Law and Policy. 2013; 1(1). Accessed 2 March 2022. Reference Source\n\nIntellectual Reserve Inc: Religious Freedom: A Guide to Your Rights. Nigeria: 2021. Accessed 2 January 2023. Reference Source\n\nInternational Labour Organisation: African Charter on Human and Peoples’ Rights (Ratification and Enforcement) Act.1990. Reference Source\n\nLantana U: Street Hawking and Socio-economic Dynamics of Nomadic Girls of Northern Nigeria. Int. J. Soc. Econ. 2010; 37(9).\n\nMiddle East Online: Algeria Bans Wearing of Full-face Veils in Public Sector.2022. Accessed 10 October 2022. Reference Source\n\nMyland A: Book Review: Veils, Turbans and Islamic Reforms in Northern Nigeria. On Knowing Humanity Journal. 2019; 3(2). Accessed 11 September 2022. Publisher Full Text Reference Source\n\nOkogi and Others v. The Attorney General of Lagos State: 2 NCLR 337.1981.\n\nOlujobi OJ, Olarinde ES, Yebisi TE, et al.: COVID-19 Pandemic: The Impacts of Crude Oil Price Shock on Nigeria’s Economy, Legal and Policy Options. Sustainability. 2022a; 14(18): 11166. Accessed March 23, 2023. Publisher Full Text\n\nOlujobi OJ, Yebisi TE: Combating the Crimes of Money Laundering and Terrorism Financing in Nigeria: A Legal Approach for Combating the Menace. J. Money Laund. Control. 2023; 26(2): 268–289. (March 23, 2023). Publisher Full Text\n\nOlujobi OJ, Olarinde ES, Yebisi TE: The Conundrums of Illicit Crude Oil Refineries in Nigeria and Its Debilitating Effects on Nigeria’s Economy: A Legal Approach. Energies. 2022b; 15(17): 6197. Accessed March 23, 2023. Publisher Full Text Reference Source\n\nOnebunne J, Chukwu I: Shallow Morality and Hollow Religiosity: A Critical Appraisal of 21st Religion-Moral Syncretism. J. Moral Educ. Africa. 2018; 3.\n\nPremium Times: Supreme Court Upholds Students Rights to Wear Hijab to Lagos Schools Premium Times (Lagos, 17 June 2022). Accessed 24 July, 2022. Reference Source\n\nPublic Complaints Commission Act (No. 31) (Chapter 377). 1975. Accessed April 13, 2023. Reference Source\n\nRahim Z: Algeria Bans Women Working in Public Sector from Wearing Full-face Veils.2022. Accessed 10 October 2022. Reference Source\n\nReuters: Turkey Condemns EU Court Ruling on Headscarf Ban as Violation of Freedoms.2022. Accessed 10 October 2022. Reference Source\n\nSimon A: Who Wears Hijab with the President: Constructing a Modern Islam in Tunisia. J. Relig. Afr. 2011; 41. Accessed 6 March, 2023. Reference Source\n\nThe Constitution of the Federal Republic of Nigeria (as amended). 1999. Accessed March 30, 2023. Reference Source\n\nThe Criminal Code Cap.77 Laws of the Federation of Nigeria, 2004. Accessed March 30, 2023. Reference Source\n\nThe Federal Character Commission Act of 1996 the Public Complaints Commission Act, of 1975.\n\nThe Federal Character Commission Act of 1996 (Establishment, Etc.) of 1996, Decree (No. 34 of 1996). Accessed April 13, 2023. Reference Source\n\nUrnaliev S, Najibullah N: Hijab Vs. Education: Kazakh Schoolgirls Face Dilemma Over Head-Scarf Ban.2022. Accessed 11 October 2022. Reference Source\n\nYusuf I: A Study of Perceptions on the Use of Hijab and Its Threats to National Security in Borno State (BA Dissertation Faculty of Social Sciences, Kwara State University, 2018)." }	[ { "id": "238679", "date": "03 Jun 2024", "name": "Dr. Uche Nnawulezi", "expertise": [ "Reviewer Expertise International Humanitarian Law", "International Human Rights Law", "International Migration Law", "International Criminal Law" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe article has been able to address the contentious issues bordering on the protection of religious rights in Nigeria from the perspective of the legal and institutional framework. Drawing from several questions raised and discussed by the authors, issues of religious rights and the right to wear hijab in public institutions was a controversial one given the plurality nature of Nigeria with several cultures and religious background. The authors have been able to resolve these controversies through their reliance to the statutory provisions of the law as contained in the Constitution of the Federal Republic of Nigeria, 1999 as amended. The paper, through a comparative analysis of what obtained in other jurisdictions, contributed to the resolution of the age-long controversies. The paper has contributed to knowledge and should be seen as a scholarly publication of repute. The suggestions made by the authors are really commendable and a panacea for sustainable protection of religious rights in Nigeria and beyond. In terms of relevance, the article is relevant to intellectual discourse on human rights, and has been able to resolve several controversies surrounding religious rights and the right to wear hijab in public institutions. This paper should be indexed in line with its scholarly contributions to knowledge.\n\nIs the work 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": "11848", "date": "27 Jun 2024", "name": "OLUSOLA JOSHUA OLUJOBI", "role": "Author Response", "response": "Dear Distinguished Reviewer, Thank you for the time, effort, and dedication you invested in reviewing our scholarly work. We greatly appreciate your contributions and insights. May you continue to be enriched with wisdom and knowledge. Thank you once again. Regards, Dr Olujobi, Olusola" } ] }, { "id": "280494", "date": "07 Jun 2024", "name": "Olalekan Bello", "expertise": [ "Reviewer Expertise My areas of interests include Environmental Law and theory", "Human Rights", "Legal History", "Legal Theory (Jurisprudence)", "Public International Law", "Resource Conflicts in Frontier Economies", "Third World Approaches to International Law", "Law", "Colonialism", "and Imperialism", "International law and development", "Law", "Security and Development", "Sociolegal Research (Luhmann", "Foucault and Deleuze's theories) and African legal and literary tradition" ], "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\nCLARITY AND SCOPE This has been a refreshing paper to read in the context of the legal and institutional framework for the protection of religious rights in Nigeria and the Right to Wear Hijab in Public Institutions. The introduction provides a clear overview of the topic and its importance. The author’s goals and objectives are clear\nSTRUCTURE, ORGANISATION AND WRITING STYLE The paper is well-organised, with a logical flow of ideas However, the authors need to ensure that the paragraphs and sentences transition smoothly, maintaining a cohesive narrative throughout. The writing is clear and academic in tone. However, the authors are advised to watch their varying sentence structures and to employ more engaging language to enhance readability.\nLITERATURE REVIEW The literature review covers key Nigerian sources but could be expanded to include more recent studies and comparative analyses from other jurisdictions facing similar issues. This would enrich the context and highlight the relevance of the Nigerian situation.\nCRITICAL ANALYSIS: There is a good synthesis of existing literature and thorough engagement with the Nigerian legal frameworks detailing relevant laws and constitutional provisions. Also, case law, particularly landmark cases related to religious rights and the hijab in Nigeria has been used to strengthen the authors’ argument, providing practical insights into how laws are interpreted and enforced. However, the discussion on institutional mechanisms could be more detailed. In the comparative analysis with other jurisdictions, more detail is needed, and we need to see the value of the Algerian, Kazakhstan, and Turkish dynamics and how they can help resolve the current conundrum in Nigeria\nORIGINALITY AND CONTRIBUTION TO KNOWLEDGE The analysis provides a solid examination of the right to wear hijab in public institutions from a balanced perspective. The manuscript provides an original and comprehensive overview of the subject matter, but some sections, indicated in the intext comments, could benefit from more clarity.\nSUMMARY AND IMPLICATIONS: The conclusion effectively summarises the main points but could be more explicit about the broader implications of the findings. Highlighting how these conclusions can influence policy and practice would underscore the paper’s relevance\nFUTURE RESEARCH Suggesting areas for future research would be a valuable addition. Identifying gaps in the current literature and proposing specific questions for further study can guide ongoing scholarly efforts.\n\nIs the work 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": "11892", "date": "03 Jul 2024", "name": "OLUSOLA JOSHUA OLUJOBI", "role": "Author Response", "response": "The authors have ensured that paragraphs and sentences transition smoothly to guarantee a cohesive narrative throughout the paper. The tone is now clear and academic. They have overhauled the varying sentence structures to ensure a more engaging language, enhancing the article's readability. The literature review has been expanded to include key Nigerian sources and recent studies, as well as comparative analyses from other jurisdictions facing similar issues, enriching the work and highlighting the relevance of the Nigerian context. Critical Analysis: The discussion on institutional mechanisms has been detailed, with a comparative analysis involving insights or lessons learned from strategies or dynamics in Algeria, Kazakhstan, and Turkey to address the current challenges in Nigeria regarding the protection of religious rights and the right to wear Hijab in public institutions. Originality and Contribution to Knowledge: Some sections, as indicated in the in-text comments, have been clarified to improve the article's clarity. The conclusion has been revised to effectively summarize the main points and explicitly discuss the broader implications of the research findings. It highlights how the study's conclusions can influence policy and practice regarding the protection of religious rights and the right to wear Hijab in public institutions, underscoring the paper’s relevance in the contemporary world." } ] }, { "id": "280499", "date": "12 Jun 2024", "name": "Oluwatosin Kate Olanrewaju-Elufowoju", "expertise": [ "Reviewer Expertise International Environmental Law", "Environmental Law", "Alternative Dispute Resolution", "Information & Communication Law" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nArticle Summary\n“The legal and institutional framework for the protection of religious rights in Nigeria and the right to wear Hijab in public institutions\" by Caesar Manuchimso Elikwu, Olusola Joshua Olujobi, and Ebenezer Tunde Yebisi examines the intricate nature of religious rights in Nigeria, with a particular emphasis on the right to wear the hijab in public institutions. The report, which was published on May 23, 2023, emphasises the careful balance needed to protect religious freedom in a country with a multi-religious and multi-ethnic nation like Nigeria.\nThe article begins by discussing the constitutional guarantee of religious rights in Nigeria and the legal limitations and interpretations of these rights. It underscores the importance of these rights being protected, while also recognizing the need for regulation to prevent conflicts. The authors review existing literature, statutes, and laws, including the 1999 Constitution of Nigeria, judicial precedents, and international conventions. A comparative analysis is made with countries such as Tunisia, Algeria, Turkey, and Kazakhstan, which have successfully managed similar issues. A key focus of the study is the Supreme Court ruling in Lagos State Govt. and Ors v. Asiyat Abdulkareem, which upheld the right of Muslim women to wear the hijab as a fundamental right. This decision has been met with mixed reactions, highlighting the ongoing debate over the extent of religious expression in public spaces. The study points out that the current legal framework in Nigeria, while adequate, requires further legislative intervention to address these issues effectively. The methodology of the research is a doctrinal legal research approach, relying on primary and secondary legal sources to provide a comprehensive analysis. The authors propose a hybrid model to mitigate the socio-legal impacts of hijab usage in public institutions. They conclude that legislative measures are necessary to align Nigeria’s legal framework with global standards and to promote societal stability.\nIn conclusion, the article provides an insightful legal analysis of religious rights in Nigeria, offering practical recommendations to balance these rights with public interests. By drawing lessons from other countries, the study aims to enrich Nigeria's jurisprudence and foster a more harmonious coexistence of diverse religious practices.\nReviewer’s Report\nThe authors have done their research, thus, contributing their perspective to the body of knowledge relating to the topic of study. Their rigour of research and dexterity with literature is commendable. The literature review is robust and portrays an extensive engagement with literature. However there are some observations which should be addressed by them as follows:\nAbstract Conclusion Page 2\nThe conclusion does not reflect the body of the abstract or the underlined idea of the topic. It should reflect what purpose Nigeria’s legal and institutional frameworks are adequate for? Answering this question, will help to understand what can be tweaked to reflect the topic and body of the abstract.. Perhaps, the conclusion should be reframed in line with the body of the abstract and central idea of the topic.\nMethods Page 4\nThe method should give an insight into what the hybrid model is about. Spelling errors were observed in paragraph 2 of the methods, ‘...religious rights’ not ‘...religious light’; ‘...that can’ not ‘...that cans’.\nContinuation of African Charter on Human and People’s Rights (Ratification and Enforcement) Act CAP A9, LFN, 2004 on Page7\nParagraph 2, line 4 should read ‘...prohibits religious intolerance’ not ‘...religious tolerance’.\nPublic Complaints Commission Page 9\nThe authors have not shown how the public complaints commission relates to the topic. How as the Public Complaints Commission encouraged or discouraged wearing of hijab in public institutions in Nigeria. Perhaps, a relatable example can be given.\nTruth and Reconciliation Commission Page 9\nThere is an omission in Line 3. ‘...between 1984 to what year”? Not 199. The authors have not related this as an institutional framework to the topic.\nThe police and other security agencies Page 9\nThe authors should state an instance where the police and other security agencies have intervened in matters related to the wearing of hijab in public institutions. This will make this institutional framework more robust.\nComparison with other countries - Tunisia Page 10\nThere is an error in line 5 ‘...resolved successfully’ not ‘...resolve successful’. In addition, the last sentence stated that “Tunisia and Turkey are two countries who have decided against its wearing in public places”. This is inconsistent with the current position in Turkey and also as portrayed in the authors’ concluding discuss on Turkey 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? No source data required\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "11899", "date": "03 Jul 2024", "name": "OLUSOLA JOSHUA OLUJOBI", "role": "Author Response", "response": "Author response to Reviewer Comments: 1) Abstract Conclusion Page 2: The conclusion has been revised to align closely with the abstract’s central theme, highlighting the inadequacy of Nigeria’s legal and institutional frameworks concerning the protection of religious rights and the right to wear hijab in public institutions. Therefore, reform is deemed necessary. 2) Methods Page 4: The methodology section has been refined to explain the concept of a hybrid model. Spelling errors identified in paragraph 2 have been corrected: 'religious rights' replaces 'religious light', and 'that can' replaces 'that cans'. 3) Continuation of the African Charter on Human and People’s Rights (Ratification and Enforcement) Act CAP A9, LFN, 2004 on Page 7: Corrections have been made for clarity. Paragraph 2, line 4 now reads: 'prohibits religious intolerance' instead of 'religious tolerance'. 4) Public Complaints Commission Page 9: The authors have clarified the relevance of the Public Complaints Commission to the topic. The Commission receives and addresses complaints in the public interest, providing independent oversight to maintain and enhance public confidence. An example provided is the case of Miss Ufumaka Glory Ukpanken (Corper No. EB/A221514) v. NYSC, where the Federal High Court in Abakaliki ordered the NYSC to allow female corps members to wear skirts if it aligns with their religious beliefs, citing a violation of their fundamental rights under Section 38(1) of the 1999 Constitution. 5) Truth and Reconciliation Commission Page 9: The authors have rectified an omission in line 3, adding 'between 1984 to 1999'. The institutional framework related to the topic has been comprehensively discussed. 6) The police and other security agencies Page 9: The authors have provided an instance where police and other security agencies intervened in matters concerning the wearing of hijab in public institutions to strengthen the institutional framework. In Kwara State in 2019, protests erupted over the hijab policy in public schools in Ilorin, Kwara State. Police were deployed to maintain peace as tensions escalated between opposing groups. This led to heightened security measures around affected schools. In 2020 in Lagos State, tensions and protests also arose over the issue of hijab-wearing in public schools. Police presence was crucial in preventing clashes and ensuring compliance with government directives on hijab-wearing. Similarly, in Osun State, police intervened during disputes and protests regarding the enforcement of hijab policies in public schools. Their presence helped manage tensions and ensure that academic activities were not disrupted. These instances illustrate how police and security agencies play a pivotal role in maintaining peace and enforcing regulations related to the wearing of hijab in public institutions across Nigeria. 7) Comparison with other countries - Tunisia Page 10: An error in line 5 has been corrected to 'resolved successfully'. Additionally, the statement regarding Tunisia and Turkey has been clarified. While Tunisia has resolved issues related to hijab-wearing, Turkey historically had restrictions on hijab in educational and government institutions, which led to protests and legal challenges. Police were involved in enforcing these regulations." } ] }, { "id": "277193", "date": "14 Jun 2024", "name": "Chukwunye Augusta Ojeih", "expertise": [ "Reviewer Expertise Intellectual property law", "Nigerian Legal system", "Criminology", "Law of Tort", "and Equity and Trust." ], "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/Findings: - This article discusses the constitutional and human rights provisions of Nigerians, domiciled in Nigeria, to exercise their freedom of worship/religion. However, this freedom of religion isn’t without challenges in Nigeria because of its special and peculiar kind of political, social, ethnic, and religious entities. The article notes that one of the greatest challenges in Nigeria is freedom of religion – freedom to practice one’s religious beliefs; which has led to fiery litigation in some instances. The wearing of hijab has engendered much debate in public institutions in Nigeria; this in itself has threatened the “supposed secular compass of the Nigerian state following the decision of the Supreme Court” in the much celebrated case of Lagos State & Ors v Asiyat Abdulkareem (SC/910/16) in which case judgment was tilted in favour of the plaintiff cum defendant. The article did justice by presenting the two sides of the divide on the matter; i.e. those for and against the wearing of hijab in public institutions. The comparative analysis between Nigeria and other jurisdictions is quite instructive. Other states (Nations) have placed public interests above religious sentiments/bias. The article points to the fact that although the wearing of hijab by female Muslims is a mandatory religious injunction, it should not affect the secularism of the Nigerian state. For instance in Turkey, which is a predominantly Islamic nation, the wearing of hijab in public institutions is banned. The females are allowed to wear a good head-cover but not hijab. Same goes for Tunisia, which also banned the wearing of hijab in public institutions. Worthy of note is Kazakhstan, an Islamic nation, which banned the wearing of hijab in public institutions partly for public good and because religious “extremists utilized such clothing to occasion harm to the society”. The article notes that reliance should not be placed exclusively on the decisions of the apex court of Nigeria alone; there is the need for legislative intervention. No religion should be promoted over and above the other in Nigeria. Every religion is good as long as it is not repugnant to natural justice, equity, and good conscience. Nigeria being a multi-faceted, multi-ethnic, and a multi-religious nation needs a balance. A healthy balance so that religious groups will not arbitrarily engage in activities which are likely to jeopardies public safety and order. The article recommends that Nigerians, in Nigeria, should exercise their civil liberties and religious freedom within the ambit of the law, bearing in mind overall public interest. Put simply, section 39 (1) CFRN is not absolute but circumscribed in some situations. The authors advocate that Nigeria should align with other nations like Turkey, Kazakhstan, and Tunisia on the issue of wearing of hijab in public institutions and the exercise of religious freedom. This is necessary for the overall wellness of the nations in terms of religious freedom and public safety.\nRelevance: - The article is very significant in the area of the Nigerian constitutional law; it is good for law teachers and policy makers which will in turn affect what the journalists, as gate keepers, report. There is the urgent need for a healthy and balanced legislative intervention in the area of religious freedom in Nigeria, there are many deaths and destructions, especially in the Northern part of Nigeria. Finally, beyond the Constitutional and other statutory provisions, the right of freedom of worship is a God-given right because man is a free-moral agent. So, the issue is really balancing the provisions of section 38 (2) with section 39 (1) CFRN 1999 (as amended). What happens when a child decides to go against the religion of his/her parents/guardians?\nStrong point: The greatest strength of the article is the call for a balanced and beneficial intervention of the legislative arm of the government.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "11900", "date": "27 Jun 2024", "name": "OLUSOLA JOSHUA OLUJOBI", "role": "Author Response", "response": "Dear Distinguished reviewer, Thank you very much for investing your time and effort in reviewing our work. Your insights and feedback are greatly appreciated. May the good Lord bless you and your family abundantly. Warm regards, Dr Olujobi, Olusola" } ] } ]	1	https://f1000research.com/articles/12-537
https://f1000research.com/articles/13-731/v1	02 Jul 24	{ "type": "Brief Report", "title": "Differential physical interactions of wild-type and S59L mutant CHCHD10 with mitochondrial proteases", "authors": [ "Seungjae Oh", "Nam Chul Kim", "Seungjae Oh" ], "abstract": "Background CHCHD10 is a small mitochondrial protein with a C-terminal coiled-coil-helix–coiled-coil-helix domain. The N-terminal region of CHCHD10 is mostly intrinsically disordered. Therefore, CHCHD10 has no catalytic activity other than protein-protein interactions through the CHCH domain or intrinsically disordered region. The S59L mutation in CHCHD10 has been identified as a genetic cause of amyotrophic lateral sclerosis and frontotemporal dementia. However, the disease-causing mechanisms of CHCHD10S59L are not yet fully understood. Our previous study showed that CHCHD10S59L induces PINK1 and Parkin accumulation. PINK1 stabilization in the mitochondria is dependent on proteolytic processing by mitochondrial proteases. It has also been reported that mutant CHCHD10 disrupts protein homeostasis within mitochondria. Therefore, we hypothesized that CHCHD10S59L physically interacts with mitochondrial proteases during the disease pathogenesis.\n\nMethods To test this hypothesis, we performed co-immunoprecipitation using transiently transfected wild-type and mutant S59L CHCHD10 in HeLa cells. We employed a dithiobis (succinimidyl propionate) cross-linker to detect transient physical interactions.\n\nResults We expected that CHCHD10S59L may activate mitochondrial protease processing or expression and that it interacts with more diverse mitochondrial proteases than the wild type. In general, however, there was no difference in the expression and processing levels of mitochondrial proteases and the proteases that interact with wild-type and CHCHD10S59L. LonP1 degrading unfolded proteins in the mitochondrial matrix was the major proteases that can bind to wild-type CHCHD10 and CHCHD10S59L. LonP1 and HtrA2 were significantly less strongly bound to CHCHD10S59L.\n\nConclusions This result can be interpreted in many different ways, including the regulatory role of CHCHD10 in mitochondrial proteases. However, more precise biochemical and cell biological investigations are required to determine the role of CHCHD10 in the activity of mitochondrial proteases, mechanism of PINK1 stabilization, and disruption of mitochondrial proteostasis.", "keywords": [ "CHCHD10", "amyotrophic lateral sclerosis", "frontotemporal dementia", "mitochondrial proteases" ], "content": "Introduction\n\nMutations in the coiled-coil-helix-coiled-coil-helix domain 10 (CHCHD10) gene have been identified as the cause of various neuromuscular degenerative diseases, including amyotrophic lateral sclerosis and frontotemporal dementia (ALS-FTD), mitochondrial myopathy, and congenital cardiomyopathy (Ajroud-Driss et al., 2014; Bannwarth et al., 2014). CHCHD10 is a small mitochondrial protein with a C-terminal coiled-coil-helix–coiled-coil-helix domain. The N-terminus of CHCHD10 is mostly intrinsically disordered and contains a hydrophobic region. CHCHD10 has no catalytic activity other than protein-protein interactions through the CHCH domain or intrinsically disordered region (Baek et al., 2021). Among disease-causing mutations, the S59L mutation in the hydrophobic region associated with ALS-FTD has been relatively well characterized in various models. It shows prominent abnormal phenotypes, even in simple cell models such as HeLa or SH-SY5Y cells. Transiently expressed CHCHD10S59L induces mitochondrial fragmentation, reduces ATP production, and reduces oxygen consumption (Baek et al., 2021). The PINK1/Parkin pathway can be activated by CHCHD10S59L protein in both Drosophila and human cells in vivo. Reducing the PINK1/Parkin pathway ameliorates CHCHD10S59L-mediated degeneration and abnormal mitochondrial phenotypes in Drosophila and human cell models (Baek et al., 2021).\n\nPINK1 and Parkin are critical regulators of mitochondrial quality control. PINK1 acts as a sensor of mitochondrial damage, and Parkin promotes the removal of damaged mitochondria through mitophagy. Upon mitochondrial damage, such as loss of mitochondrial membrane potential, PINK1 accumulates in the mitochondria, and this process is dependent on mitochondrial proteasome-mediated PINK1 processing (Greene et al., 2011). Interestingly, however, we did not observe any significant reduction in membrane potential in CHCHD10S59L-transfected HeLa cells showing PINK1 and Parkin accumulation (Baek et al., 2019, 2021), which implies that there may be another factor causing abnormal PINK1 accumulation in CHCHD10S59L-transfected HeLa cells. In addition, it has been reported that mutations in CHCHD10 induced mitochondrial unfolded protein responses and disrupt protein homeostasis within the mitochondria (Genin et al., 2019; Sayles et al., 2022). Taken together, we hypothesized that the expression or activity of mitochondrial proteases may be affected by mutations in CHCHD10, and this change can be achieved by the direct physical interaction between CHCHD10 and mitochondrial proteases. To test this hypothesis, we performed co-immunoprecipitation experiments with a cross-linker, dithiobis (succinimidyl propionate), to retrieve even weak physical interactions between CHCHD10 and the interacting proteins.\n\n\nMethods\n\nAll complementary DNAs (cDNAs) for human wild-type and CHCHD10S59L were synthesized and inserted into the pcDNA3.1, vector containing a FLAG tag, by GenScript Inc.\n\nThe HeLa cell line was purchased from the American Type Culture Collection (ATCC; CRM-CCL-2). Cells were maintained in Dulbecco’s modified Eagle’s medium (GenClone) supplemented with 10% fetal bovine serum (GenClone), 100 U/mL penicillin and streptomycin (Penicillin-streptomycin, Invitrogen 15140122), and 1 × GlutaMax (Gibco 35050061). Cells were transfected using the jetPRIME (Polyplus) transfection reagent according to the manufacturer’s protocol with an automatic cell counter (NanoEntek, ADAM-MC2 cell counter).\n\nDithiobis (succinimidyl propionate) (DSP, Lomant’s reagent) was purchased from Thermo Fisher Scientific (22586) and used to induce protein cross-linking. HeLa cells transfected with FLAG-tagged CHCHD10 WT or S59L were washed twice with PBS to remove the medium. After adding PBS containing a final concentration of 2 mM DSP, the cells were incubated on ice for 2 h. The reaction was stopped by adding 1M Tris, pH 7.5 (at a final concentration of 20 mM) and incubated for 15 min. Cells were washed twice with PBS and solubilized with NP-40 lysis buffer (20 mM Tris, 137 mM NaCl, 1% NP-40, and 2 mM EDTA with a protein inhibitor cocktail). After sonication on ice, lysates were collected by centrifugation. Equal amounts of protein lysates were incubated with beads conjugated with anti-FLAG antibodies (Sigma, ANTI-FLAG® M2 Affinity Gel, A2220) overnight at 4 °C. After washing thrice with NP-40 lysis buffer, the pellets were resuspended in 1× reduced LDS sample buffer. After heating the samples at 70 °C for 10 min, the samples were subjected to SDS-PAGE and immunoblotting. The following primary antibodies were used for immunoblotting: FLAG (Sigma F1804 mouse monoclonal, and Proteintech 20543-1-AP rabbit polyclonal, 1:1000), AFG3L2 (Proteintech 14631-1-AP rabbit polyclonal, 1:1000), PARL (Proteintech 26679-1-AP rabbit polyclonal, 1:1000), LonP1 (Proteintech 15440-1-AP rabbit polyclonal, 1:1000), PMPCA (Proteintech 26536-1-AP rabbit polyclonal 1:1000), HTRA2 (Proteintech 15775-1-AP rabbit polyclonal, 1:1000), CLPP (Proteintech 15698-1-AP rabbit polyclonal, 1:1000), PITRM1 (Proteintech 26536-1-AP rabbit polyclonal, 1:1000), and actin (Proteintech 20536-1-AP rabbit polyclonal, Santa Cruz Biotechnology SC-47778 Mouse monoclonal, 1:5000). Immunoblots were visualized and analyzed using a fluorescence imaging system (LI-COR, Odyssey® FX Imager).\n\nGraphs for the quantitative analysis of immunoblots (mean difference between groups with 95% confidence interval) were generated using Estimation Stats (Ho et al., 2019) (http://estimationstats.com). We performed an unpaired two-sided permutation t-test to evaluate the data with p-values.\n\n\nResults\n\nWe examined seven mitochondrial proteases for their ability to interact with wild-type CHCHD10 or CHCHD10S59L using transiently transfected HeLa cells and DSP treatment (Figure 1A). The proteases were selected based on information from BioGRID for CHCHD10 and its paralog and binding partner, CHCHD2, as well as the literature on PINK1 processing proteases (Greene et al., 2011). Intact cells were treated with DSP and washed before cell lysis to prevent cross-linking post-lysis. Initially, we examined whether there were any significant changes in protein expression for all seven proteases by wild-type or CHCHD10S59L expression. Although there were some variations among repeated experiments, such as Presenilin-Associated Rhomboid-Like protein (PARL, see supplementary file), we did not observe any significant and consistent changes in the expression level or processing of proteases due to the transient expression of wild-type or CHCHD10 S59L. PARL is involved in the proteolytic cleavage of important substrates, such as OPA1 and PINK1, for maintaining mitochondrial morphology and function (Jin et al., 2010). However, PARL did not interact with CHCHD10, contrary to our hypothesis. Another protease that may be related to PINK1 processing as a component of ClpXp complexes (Greene et al., 2011), CLPP, also did not co-immunoprecipitate with CHCHD10 using an anti-FLAG antibody, although a component of ClpXp, ClpX, was enlisted in BioGRID as an interacting partner of CHCHD10 or CHCHD2. In addition, PITRM1 (Pitrilysin Metallopeptidase 1) degrading cleaved mitochondrial targeting sequences (MTS), and other small peptides (Ståhl et al., 2002) have also been reported to interact with both CHCHD10 and CHCHD2. However, we were unable to detect PITRM1 in our repeated co-immunoprecipitation experiments.\n\n(A) Schematic diagram of in-cell DSP cross-linking and immunoprecipitation with anti-FALG antibody (see methods for a detailed procedure), (B) western blot results with mitochondrial proteases antibodies, 10% of total lysates were used in the left panel, and co-immunoprecipitated proteases were detected in the right panel, (C) quantification of interacting proteases. The raw data are plotted on the right axes. On the left axes, mean differences are plotted. Each 95% confidence interval is indicated by the ends of the vertical error bars. S-W: the difference between S59L and wild-type groups. * <0.05 and *** <0.001.\n\nAFG3L2 is a mitochondrial AAA protease that can process PINK1. It has been reported that siRNA treatment for AFG3L2 causes PINK1 accumulation (Thomas et al., 2014). PMPCA is a subunit of MPP that initially processes PINK1(Greene et al., 2011). Both proteases interact with wild-type CHCHD10 and CHCHD10S59L. However, their interactions were weak, and there were no significant differential interactions, although AFG3L2 tended to bind more to mutant S59L CHCHD10. HTRA2 is a member of the high-temperature requirement A family of proteases that bind to PINK1 (Plun-Favreau et al., 2007). Evidence suggests that HTRA2 is associated with Parkinson’s disease (Plun-Favreau et al., 2007). Notably, the S59L mutation in CHCHD10 resulted in a decreased interaction between HTRA2 and CHCHD10 compared to binding with wild-type CHCHD10. The results were statistically significant. However, their interaction was the weakest among the seven proteases, and the physiological significance of this interaction is uncertain.\n\nThe protease that most significantly interacted with CHCHD10 was LonP1. LonP1 is not listed in BioGRID for CHCHD10 or CHCHD2. Both wild-type and CHCHD10S59L interacted significantly with LonP1. It has been reported that various stress conditions, including reactive oxygen species and unfolded protein stress, can upregulate LonP1 expression. However, we did not observe any significant changes in the expression levels in transiently transfected wild-type CHCHD10 or mutant S59L CHCHD10. LonP1 also degrades PINK1, and silencing LonP1 enhances PINK1 accumulation with subsequent activation of the PINK1-Parkin mitophagy pathway (Jin & Youle, 2013; Thomas et al., 2014). In our co-immunoprecipitation results, the interaction between LonP1 and CHCHD10 was significantly decreased by the S59L mutation.\n\n\nDiscussion\n\nBy co-immunoprecipitation experiments with the cross-linker DSP, we determined that PARL, CLPP, and PITRM1 do not interact with wild-type or mutant S59L CHCHD10. AFG3L2 and PMPCA interacted with both CHCHD10 and mutant S59L CHCHD10. However, no differential interactions were caused by the S59L mutation. Interestingly, two proteases, HTRA2 and LonP1, bind to CHCHD10, and the S59L mutation decreased their interaction. Since we did not observe any consistent expression or processing changes caused by transiently transfected CHCHD10, the changes in the physical interaction between CHCHD10 and mitochondrial proteases may be related to protease activity. The decreased interaction between mutant S59L CHCHD10 and HTRA2 and LonP1 implies that wild-type CHCHD10 somehow maintains the active state of HTRA2 and LonP1, and the mutant S59L protein loses this activity partially due to their decreased interaction. Therefore, less active HTRA2 and LonP1 could not perform their roles in degrading unfolded proteins, preventing protein aggregation, and processing PINK1. However, the role of the physical interaction between CHCHD10 and mitochondrial proteases should be determined by further biochemical analyses, and the effect of the S59L mutation should also be precisely determined.", "appendix": "Data availability\n\nDifferential physical interactions of wild-type and S59L mutant CHCHD10 with mitochondrial proteases.\n\nFigshare: Co-IP with CHCHD10 (https://doi.org/10.6084/m9.figshare.26090764) (Kim and Oh, 2024).\n\nThis project contains the following underlying data:\n\nStatistics data analysis (chchd10 interaction partner).xlsx (raw data for estimation statistics analysis)\n\nSupple.zip (raw image files for all western blots)\n\nSuppl.pptx (individual blots with annotations used in Figure 1)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nAjroud-Driss S, Fecto F, Ajroud K, et al.: Mutation in the novel nuclear-encoded mitochondrial protein CHCHD10 in a family with autosomal dominant mitochondrial myopathy. Neurogenetics. 2014; 16(1): 1–9. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBaek M, Choe YJ, Bannwarth S, et al.: TDP-43 and PINK1 mediate CHCHD10 S59L mutation–induced defects in Drosophila and in vitro. Nat. Commun. 2021; 12(1). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBaek M, Choe Y-J, Dorn GW, et al.: Dominant toxicity of ALS–FTD-associated CHCHD10S59L is mediated by TDP-43 and PINK1. BioRxiv. 2019; 753558. Publisher Full Text\n\nBannwarth S, Ait-El-Mkadem S, Chaussenot A, et al.: A mitochondrial origin for frontotemporal dementia and amyotrophic lateral sclerosis through CHCHD10 involvement. Brain. 2014; 137(8): 2329–2345. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGenin EC, Madji Hounoum B, Bannwarth S, et al.: Mitochondrial defect in muscle precedes neuromuscular junction degeneration and motor neuron death in CHCHD10S59L/+ mouse. Acta Neuropathol. 2019; 138: 123–145. PubMed Abstract \| Publisher Full Text\n\nGreene AW, Grenier K, Aguileta MA, et al.: Mitochondrial Processing Peptidase Regulates PINK1 Processing, Import and Parkin Recruitment. EMBO reports-Peer Review Process File-EMBOR. 2011. Reference Source\n\nHo J, Tumkaya T, Aryal S, et al.: Moving beyond P values: data analysis with estimation graphics. Nat. Methods. 2019; 16(7): 565–566. PubMed Abstract \| Publisher Full Text\n\nJin SM, Lazarou M, Wang C, et al.: Mitochondrial membrane potential regulates PINK1 import and proteolytic destabilization by PARL. J. Cell Biol. 2010; 191(5): 933–942. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJin SM, Youle RJ: The accumulation of misfolded proteins in the mitochondrial matrix is sensed by PINK1 to induce PARK2/Parkin-mediated mitophagy of polarized mitochondria. Autophagy. 2013; 9(11): 1750–1757. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKim NC, Oh S: Co-IP with CHCHD10. Dataset. figshare. 2024. Publisher Full Text\n\nPlun-Favreau H, Klupsch K, Moisoi N, et al.: The mitochondrial protease HtrA2 is regulated by Parkinson’s disease-associated kinase PINK1. Nat. Cell Biol. 2007; 9(11): 1243–1252. PubMed Abstract \| Publisher Full Text\n\nSayles NM, Southwell N, McAvoy K, et al.: Mutant CHCHD10 causes an extensive metabolic rewiring that precedes OXPHOS dysfunction in a murine model of mitochondrial cardiomyopathy. Cell Rep. 2022; 38(10): 110475. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nStåhl A, Moberg P, Ytterberg J, et al.: Isolation and Identification of a Novel Mitochondrial Metalloprotease (PreP) That Degrades Targeting Presequences in Plants. J. Biol. Chem. 2002; 277(44): 41931–41939. PubMed Abstract \| Publisher Full Text\n\nThomas RE, Andrews LA, Burman JL, et al.: PINK1-Parkin Pathway Activity Is Regulated by Degradation of PINK1 in the Mitochondrial Matrix. PLoS Genet. 2014; 10(5): e1004279. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "308062", "date": "07 Aug 2024", "name": "Yuzuru Imai", "expertise": [ "Reviewer Expertise Biochemistry and cell biology on mitochondria." ], "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 a previous study, the authors observed that the CHCHD10 pathogenic mutant S59L results in the PINK1 accumulation independent of changes in mitochondrial membrane potential. In the present study, the authors analyzed the biochemical interaction between CHCHD10 and mitochondrial proteases implicated in the PINK1 processing. Among these proteases, LonP1 and HtrA2 exhibited weaker binding to the CHCHD10 S59L mutant compared to the wild-type CHCHD10. Given that the authors provide only one set of data, they should aim for the results to be robust and of high quality, thus significantly impacting CHCHD10 research. Although the experimental approach involved the overexpression of CHCHD10-FLAG in HeLa cells, it is important to consider that transient overexpression of mitochondrial proteins may induce mitochondrial protein stress. Ideally, endogenous CHCHD10 should be immunoprecipitated with an anti-CHCHD10 antibody in CHCHD10 S59L knock-in or normal cells to verify the interactions. Overexpression could potentially result in the mislocalization of proteins outside their native mitochondrial compartment. Therefore, analyzing the interaction of mitochondrial proteases with endogenous CHCHD10 would provide more physiologically relevant insights.\nTwo additional points merit consideration. One is the question of why not consider OMA1, which is involved in stabilizing PINK1 (PMID: 30733118) and has been reported to bind CHCHD10 (PMID: 35173147). Another question is about the accumulation of PINK1 by CHCHD10 S59L, which is the motivation for this study: has it been verified whether overexpression of CHCHD10 S59L causes mitochondrial misfolded protein stress, resulting in the accumulation of PINK1? Accumulation of misfolded proteins has been reported to be sensed by PINK1 (PMID: 24149988).\nAs additional minor comments, how are the values on the quantitative graphs calculated. Have the values been normalized with precipitated CHCHD10 or other factors?\nThe quality of western blots for PARL and HtrA2 is poor.\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? Yes\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] }, { "id": "308065", "date": "16 Aug 2024", "name": "Gopinath Krishnan", "expertise": [ "Reviewer Expertise Neurodegeneration and biochemical assays" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nMitochondrial defects in ALS/FTD and other neurodegenerative diseases are well documented. In this article, authors explored mitochondrial proteases interaction with CHCHD10 WT and CHCHD10S59L using overexpression system in Hela cell lines. Overall, the work is relevant as it shows a molecular link between CHCHCD10 and PINK1 proteases. I have only two concerns with the current work. 1. Since it’s a overexpression system, can they use reducing agents such as DTT to show that binding between CHCHD10 WT and LonP1 is reversible. 2. Are they colocalizing by any chance? 3. Can the authors measure protease activity of LonP1 to test indeed its activity is affected under the expression of CHCHD10S59L? 4. It would be nice if the authors could validate this cell line overexpression co-IP findings in a disease relevant models such as patient iPSC lines, if any or mouse models of mutant CHCHD10.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate? Yes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] }, { "id": "308064", "date": "22 Aug 2024", "name": "Mórotz Gábor Miklós", "expertise": [ "Reviewer Expertise Neurodegenerative diseases including ALS/FTD and protein-protein interactions." ], "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 manuscript ‘Differential physical interactions of wild-type and S59L mutant CHCHD10 with mitochondrial proteases’ Oh and Kim report some mitochondrial proteases as new interacting partners of CHCHD10 and how their interaction is affected by the ALS-associated S59L mutation of CHCHD10. Understanding details how this disease-causing mutation might damage cellular functions is important and this manuscript adds to this effort. However, the manuscript should be improved by addressing the following observations.\n1. Checking the original blots in almost all empty vector transfected control lanes a band appears in the co-immunoprecipitated protease blots in the position where the tested CHCHD10 binding partners should be. Since these are the negative controls there should be no band there. This raises some concerns about the observed interactions. The authors should address this problem.\n2. To confirm the observed protein-protein interactions without cross-linking which can cause some artefacts protein interaction-wise, authors should use other systems. For example an overexpression system where epitope tagged CHCHD10 and mitochondrial proteases are co-transfected in cells or in vitro binding assay could be used e.g. GST pull-down.\n3. The authors state that CHCHD10 S59L mutation does not affect the expression of the investigated mitochondrial proteases. These quantifications should be shown especially as it seems to me based on the shown representative blots in Figure 1B that CLPP, PMPCA and AFG3L2 express differently.\n4. The quantification of the effect of CHCHD10 S59L on PMPCA interaction is based on two experiments. This should be at least three as in the case of the other investigated interacting partners.\n5. Only Figure 1A but not 1B and 1C is referenced 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? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate? Partly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] } ]	1	https://f1000research.com/articles/13-731
https://f1000research.com/articles/13-730/v1	02 Jul 24	{ "type": "Research Article", "title": "Assessment of COMMUNITY Pharmacists' Knowledge, Attitude, and Practice Towards Oral Health Care in Jordan", "authors": [ "Sabha Mahmoud Alshatrat", "Abedelmalek KalefhTabnjh", "AbdelRahman Murtada Ramadan", "Tamadur Mahmoud Falah", "Reem Saleem Tubaishat", "Abedelmalek KalefhTabnjh", "AbdelRahman Murtada Ramadan", "Tamadur Mahmoud Falah", "Reem Saleem Tubaishat" ], "abstract": "Background Community chemists now provide more professional and public health care, which is beneficial to the community, in addition to traditional medication distribution. While community pharmacists play a vital role in maintaining and promoting health, further research is required to accurately evaluate their knowledge, attitude, and practice toward oral health care among Jordanian pharmacists in northern Jordan.\n\nMethods A prospective cross-sectional study was conducted using an anonymous self-administered questionnaire in Arabic language, targeting 250 community pharmacists in four cities (Irbid, Jerash, Ajloun, and Al-Mafraq) in northern Jordan. The questionnaire comprised four domains: socio-demographic, knowledge, attitudes and practice concerning oral health care. The Statistical Package for the Social Sciences (SPSS) software version 22.0 was used to analyze the collected data, and the significance level was set at P ≤ 0.05.\n\nResults A total of 198 respondents returned the survey form, returning a response rate of 79.2%. Community pharmacists showed a good knowledge score of 58.2%. Only 40.9% said periodontal disease was the most frequent cause of tooth loss. The majority lacked knowledge of the optimal fluoride levels in toothpaste. The average attitude score was 71.05%. The most common oral health issues raised by patients were gingivitis and toothache (43.4% and 38.9%), respectively.\n\nConclusion Community pharmacists have the general knowledge and attitude needed to play a significant role in providing dental care counselling to patients dental care. Nonetheless, community pharmacists stated they needed education and training to improve their practice. Continuing education courses related to oral health are recommended to reduce the risk of oral diseases and improve quality of life.", "keywords": [ "Attitude", "community pharmacists", "Jordan", "knowledge", "oral health care", "practice" ], "content": "Oral health and pharmacy\n\nOral diseases involve a substantial percentage of the world’s population, nearly 3.4 billion globally, and are essential to an individual’s overall health. Furthermore, oral health affects systemic health, especially in patients with diabetes and cardiovascular diseases.1 The World Health Organization (WHO) defined oral health as “the state of the mouth, teeth and orofacial structures that enable individuals to perform essential functions such as eating, breathing and speaking and encompasses psychosocial dimensions such as self-confidence, well-being and the ability to socialize and work without pain, discomfort and embarrassment”.2\n\nTraditionally, the dental profession has provided advice on oral health. Nonetheless, increasing evidence supports directing patients seeking urgent dental advice and offering preventative oral health advice to non-dental health professionals, such as community pharmacists (CPs).3 The (CP’s) responsibilities are not limited to dispensing medication to patients but are broadened to offer the general public dental advice. In addition, (CP’s) are in an advantageous position to recognize patient needs because of their professional understanding and simple accessibility.4\n\nThe most common oral diseases known and widespread among the general population include dental caries, periodontal disease or gingival bleeding, halitosis, and xerostomia. Most often, these conditions are diseases caused by behavior and habits that a person adheres to as a part of their daily duties.5 In addition, oral health issues might herald unfavorable outcomes, so oral health issues, such as mouth ulcers, toothaches, gingival bleeding, and loose dentures are the most prevalent complaints a (CPs) receives.4 Teething troubles, mouth rinse selections, and toothpaste and toothbrush choices are less commonly consulted oral health issues. However, because many oral diseases, such as oral thrush and mouth ulcers, are benign, many people go to their (CPs) instead of the dentist to immediately relieve their symptoms.6–8\n\nIt has been reported that (CPs) receive at least one query per week regarding an oral health issue, with over half of those inquiries being about mouth ulcers. Additional research showed that most individuals with oral health issues may be effectively treated in a pharmacy environment.\n\nStudies have been conducted on pharmacists’ knowledge, attitudes, and self-care practices concerning dental care in England, Australia, India, and Saudi Arabia.3,7,9–11 The general healthcare system considers (CPs) as healthcare advisors, educators, promoters, and preventers. According to a South African study, over 37% of respondents named (CPs) their first option for medical attention in an emergency, and roughly 26.5% said (CPs) were their first choice regarding healthcare providers.12\n\nThe public is prevented from receiving good dental care for several reasons, including expense, fear of dentists, and difficulty accessing dentists due to time and geographical constraints.13 The (CPs) active role in the healthcare system is attributed to several factors, including their strategic location in key areas that facilitate public access to healthcare providers and require little time and effort for symptomatic relief without the need for hospital appointments and associated costs.6 According to a Saudi study, the primary reasons are that people sought care from (CPs) due to the lack of time and difficulties securing a doctor’s or dentist appointment.7\n\nMany people who complain of oral diseases may go to a pharmacy instead of a dentist to relieve the pain as fast as possible. They may suffer from inflammation, bleeding gums or severe toothache, dental hypersensitivity, or even it is possible to get rid of bad breath.6\n\nChoosing the appropriate toothpaste or toothbrush for the patient’s condition is a significant factor in preventing many oral problems, such as tartar, cavities, receding gums, or poor appearance.9 The pharmacies market have the most items needed to maintain or treat oral health issues.9,10 Consequently, (CPs) are qualified to provide appropriate advice about using dental items in the pharmacy, such as toothpaste and mouthwash to prevent tartar buildup and toothdecay, denture hygiene, and gum care.6 Moreover, within their training and experience limits, (CPs) recognize the warning signs and symptoms of the most common oral health issues and know when to recommend a patient to a dentist or physician.14\n\nHajj et al. exemplified that toothaches (84.5%) were the most common oral ailment for which patients asked (CPs) for advice. These were followed by mouthwash, tooth whitening products, and bleeding gums (74.6%, 71.8% and 70.6%) respectively.9 Thirty-six percent of (CPs) reported being approached regarding denture issues.9\n\nIn the literature review, no studies were conducted in Jordan to evaluate the role of (CPs) knowledge, attitude, and practice in oral health care. On this basis, this investigational study assessed the knowledge, attitude, and practice of Jordanian (CPs) in northern Jordan regarding oral health care as a primary objective.\n\n\nMethods\n\nA prospective cross-sectional self-administered study was conducted in community pharmacies in 4 cities, Irbid, Jerash, Ajloun, and Al-Mafraq, in northern Jordan. Full-time (CPs) in northern Jordan employed in pharmacies were invited to participate between September and November. A cover letter in the survey questionnaire contained a brief overview of the study and its importance. The survey was amended to include a disclaimer alerting respondents that their completion and return of the questionnaire would be interpreted as implicit permission.\n\nThe total number of licensed community pharmacies in the four cities is 856: Irbid 591, Al-Mafraq 151, Jerash 86, and Ajloun 27. A minimal sample size was calculated, assuming one community pharmacist worked in each pharmacy. The Sample Size Calculator software22 by Wan Nor Arifin was used according to the method outlined by Aljrais et al.15 Sample size calculations provided with a confidence level of 95%, a margin of error of 5%, and assuming 50% of pharmacists are interested, generated a minimal sample of 250 (CPs).\n\nA probability-stratified random sampling method was used to recruit participants for the study. The pharmacies were divided according to cities, and then a number of pharmacies per city were selected randomly from the districts within the city. The total study population comprised 82 community pharmacies. Participation in this study was voluntary. Participants were allowed to decline or withdraw from participation at any time without any negative consequences.\n\nThe study comprised licenced community pharmacists willing to participate, working in a pharmacy in the cities of study, and holding a minimum diploma degree in pharmacy. The study did not include the CPs outside the study area and those working in hospitals, the pharmaceutical industry, and academia.\n\nAn anonymous self-administered questionnaire in Arabic was developed. The questionnaire’s content and face validity process included item generation, item reduction, question-wording, and the formation of the questionnaire stemming from researchers and a committee of experts. To ensure the validity and reliability of the questionnaire, an expert committee comprising seven members evaluated its content authenticity, and the questionnaire was pre-tested to determine practicability, cogency, and rendition of responses. Moreover, the seven members’ opinions were sought. The questionnaire was pilot-tested twice by the same seven members to test and retest the reliability. The questionnaire was reviewed and modified based on the feedback received from the committee. The Cronbach alpha was examined to test the internal reliability of the questionnaire. Cronbach’s alpha coefficient was equal to 0.85, indicating the items have good internal consistency.\n\nThe questionnaire comprised four sections about the knowledge, attitude, and practice of CPs regarding oral healthcare. Section I (7 questions) described socio-demographic details such as gender, years of qualifying experience in community pharmacy practice, and highest degree attained. Section Two: Knowledge (13 questions) aimed to extract fundamental information about oral health, including gingival bleeding, foul breath, prevalent dental disorders, their causes, symptoms, and treatments, as well as tooth mobility. The (CPs) attitudes about oral health were ascertained using seven questions in Section Three. The respondents’ replies were evaluated using a five-point Likert scale (strongly agree, agree, neutral, disagree, and strongly disagree). The fourth section evaluated practice (12 questions) concerning customer advice on toothbrush kinds, types and frequency of replacement, oral health issues and remedies. The dependent variables in this study were knowledge and practice of herbal medicines; the independent variables were socio-demographic characteristics.\n\nThe data collection was done by the research team, which distributed the questionnaire to the participants as a hard copy. Each research team member was assigned a city to collect the data. A reminder was sent to participants who had not responded. The questionnaire was recollected after three weeks by the researchers. The data was reported in group form and was anonymized and de-identified before the analysis.\n\nFor scoring reasons, a ‘1’ was assigned to each correct response in the knowledge domain, while a ‘0’ was assigned to each incorrect response. The knowledge section’s overall score range was ‘0 – 10’. In the attitude section, a score of ‘5’ was assigned to strongly agree, and a score of’ 1’ was assigned to strongly disagree. In the practice section, a ‘1’ was assigned to the yes choice and a ‘0’ was assigned to the unsure.16 Knowledge, attitude and practice scores were categorized as Poor (0–25%), Moderate (26%–50%), Good (51–75%), and Very Good (76–100%) based on the proportion of total marks received for correct answers.17\n\nDescriptive analysis, such as mean and standard deviation, was used for numerical variables, and frequency with percentage was used for categorical variables. The chi-square test explored the associations between (CPs)’ KAP scores and socio-demographic variables. The software package SPSS [1] Version 22 was used to analyze the data with a 0.05 significance level.\n\nThe current research was conducted per the World Medical Association Declaration of Helsinki. The study protocol was approved by the Institutional Review Board at the Jordan University of Science and Technology (JUST) (Reference: 2022/602).\n\n\nResults\n\nFrom the 250 questionnaires distributed, One hundred ninety-eight (CPs) from different cities in northern Jordan participated in this study, returning a 97.2% response rate. Most respondents were females (54.5%). The mean age of the respondents was 29 (±6.93) years. Most respondents (78.3%) had a B.Sc. of Doctor of Pharmacy qualification (a six-year study curriculum). Forty percent of the respondents had 6–10 years of experience. Approximately 167 (84.8%) of the respondents had a bachelor’s degree in pharmacy, and a small faction held a master’s degree 10 (5.05%) and held a PhD 7 (3.5%) qualification. The vast majority, 104 (52.5%) of the respondents were from Irbid. The lowest number of respondents was from Ajloun 13 (6.6%) (Table 1).\n\nThe (CPs) demonstrated high oral health knowledge, scoring 58.2%. Approximately 53% of respondents knew inadequate dental hygiene was the primary cause of gingival bleeding. Conversely, around 60% of respondents thought bad breath was caused mainly by inadequate dental hygiene. Forty-one percent believed periodontal disease was the most common cause of tooth loss. Most respondents said “yes” to the correct definition of plaque (83%) that tea and coffee beverages caused tooth stains (90%), that dental health was associated with general health (89%), and that they had knowledge of proper tooth brushing techniques (68%). A significant discovery was that only 5.6% knew the ideal fluoride levels in toothpaste for adults and children. At the same time, almost 20% believed children should have less than 1000 parts per million (PPM) fluoride in toothpaste (Table 2).\n\nThe majority of the respondents demonstrated excellent oral health attitudes, scoring (71.05%). Approximately 26% of the respondents agreed that maintaining excellent oral health required cleaning one’s teeth twice daily. Regarding the issue of sweet and sugary meals causing dental caries, 13% of the respondents were impartial. Approximately 6% of the respondents disagreed that sugar-free gum benefits dental health (Table 3).\n\nRegarding (CPs)’ practice to address customer concerns regarding their oral health, 82% of the respondents suggested mouthwashes to their customers as an appropriate oral hygiene tool to eliminate bad breath. Almost 63% of the respondents recommended changing their toothbrushes to their consumers every three months. The majority of respondents (48.5%) suggested fluoridated toothpaste to their customers. At the same time, 61% of respondents suggested drinking water compared to 45.5% who advocated sugar-free gum for treating dry mouth. According to the respondents, gingivitis and toothaches account for 43% and 39% of oral health concerns voiced by patients, respectively. Dental floss as an oral aid between teeth was promoted by 57% of respondents compared to 43% who encouraged dental floss between crowded teeth. However, 41% proposed V-shape brushes as oral hygiene for those wearing orthodontic appliances (Table 4).\n\nThe result of the association between knowledge scores and respondents’ education level showed that there was a strong association (p = 0.00). (CPs) Possessing a master’s degree scored the highest knowledge level (60%) in terms of education level, followed by those with a bachelor’s degree (52.7 %). However, those with a PhD degree scored the highest knowledge level (57.1%) in the “poor” category of knowledge (Table 5). At a 95% confidence level, there was a significant association between knowledge score groups (p < 0.001).\n\nThe result of the association between practice scores and respondents’ city showed that there was an association (p = 0.017). (CPs) from the city of Jerash in the poor category scored the lowest practice level (24.4%), followed by those from the city of Ajloun (23.1%) (Table 6). However, Al Mafraq and Irbid cities have lesser percentages in this group, with 7.5% and 9.6%, respectively. At a 95% confidence level, there was a significant association between practice score groups (p < 0.05).\n\nThe association between knowledge scores and the education level shwed that approximately 53 percent of those with postgraduate certification had good knowledge regarding oral healthcare, closely followed by those with a bachelor’s degree. Those who scored the least score within the good category with a diploma. The association between knowledge scores and the education level demonstrated statistical significance (p < 0.05).\n\nThe results of the association of knowledge in relation to the Cities; the majority of thr CPs (77.5%) from Al Mafraq demonstrated high levels of knowledge, and the lowest score within the same category was scored by those from Ajloun (46%).\n\nRegard to the distribution of gender in relation to scores; the female CPs demonstrated statistically significantly higher mean (7.5 ± 1.9) knowledge levels than their male counterparts (<0.05). However, whilst not statistically significant, the male CPs in the attitude (28 ± 3.4) and practice (4.5 ± 1.9) scores.\n\nThe results showed that the education level in relation to scores, those with a bachelor’s degree demonstrated statistically significantly higher mean (7.4 ± 2.0) knowledge levels than those with a diploma or postgraduate certification (p < 0.05).\n\n\nDiscussion\n\nThe current study was undertaken to study the pharmacists’ oral health knowledge, attitudes, and practices in northern Jordan on the supposition that CPS are effective oral health providers in a community environment., including their knowledge, attitude, and self-care behaviors related to oral health as pharmacies were the first to go to as they provided round-the-clock service to meet people’s healthcare requirements.\n\nSince pharmacies were the first to be relied upon because they offered 24-hour service to meet people’s healthcare needs, the current study was conducted to examine the oral health knowledge, attitudes, and practices of pharmacists in northern Jordan on the assumption that CPS are effective oral health providers in a community setting.\n\nSeveral studies have emphasized that people visited their local pharmacy for several reasons, which included general health and dental hygiene advice. Other reasons included insufficient money for dental or doctor’s fees, trouble getting in to see the local dentist or doctor, lack of nearby hospitals or private clinics, and lack of time.4,6,9–12\n\nThe World Health Organization (WHO) asserts that maintaining good oral health improves people’s quality of life globally and that dental health is essential to overall health and well-being.2 In order to avoid oral health issues, they should be addressed as soon as they arise or send patients to the appropriate healthcare providers when necessary, who should work in concert to establish policies that support oral health based on scientific data.2\n\nThe (CPs) are highly regarded and reliable healthcare providers who may be essential in improving people’s access to and satisfaction with healthcare. Several studies have demonstrated that the general public often talks to their (CPs) on a wide range of issues on their oral health.3,10,18,19 Similar findings have been demonstrated in the current study in that most (CPs) understand their role in promoting oral health care for the community. In Jordanian culture, females are more willing to work the morning shifts while their male counterparts are willing to work the night shifts.\n\nThe findings in the current study demonstrated that the (CPs) in Jordan had a good knowledge score, and the majority of (CPs) knew that poor oral hygiene was the primary cause of bad breath and gingival bleeding. These findings contrast the findings of Baseer et al., which demonstrated only moderate knowledge, a negative attitude, and insufficient self-care habits related to oral health.7 Furthermore, in this study, only 40.9% agreed that periodontal disease is the most frequent reason for tooth loss, and 82.8% claimed to be familiar with dental plaque.\n\nIn addition, the (CPs) in this study further demonstrated an average understanding of oral health for several reasons advocated: a lack of time, the limited encounter with dentists, a lack of possibilities for professional growth, but perhaps the most importantly, a lack of knowledge and training in oral health for the (CPs). Similar findings regarding average oral health have also been reported in Lebanese, Saudi, and Malaysian studies.7,9,20\n\nIn the present study, the CPs have an excellent attitude toward oral health because of their relatively good knowledge, experience, and extensive practical training during their studies. Furthermore, pharmacists are willing to provide customers consultations in oral health care. The average attitude score demonstrated in the current study was high, which could be attributed to their high levels of self-reported knowledge and satisfactory levels of practice. This finding is mirrored by the study of Hajj et al., who demonstrated a positive attitude of pharmacists toward oral health.9 However, this contrasts with a study by Baseer et al., who obtained a negative attitude toward pharmacists’ inadequate self-care practices toward oral health.7 Another study by Badran demonstrated a negative attitude and inadequate self-care practices toward oral health.21\n\nThe current study found a substantial beneficial relationship between the (CPs) knowledge and their actual behavior. The majority of (CPs) suggest that their customers use dental floss, which could be explained by the high level of knowledge and practice of the importance of dental floss in maintaining good oral hygiene.\n\nThe primary oral health problems that cause customers to visit the local pharmacy are bad breath, changing toothbrushes, brushing frequency, dry mouth, dental floss, and oral aids for orthodontic appliances. These individuals’ self-awareness concerning oral self-care activities is positively affected by their general oral health knowledge. The current study’s findings align with the studies of Maunder et al. and Priya et al., who demonstrated that 66% of their customers asked about oral health matters and sought the advice of their (CPs).10,11\n\nThe rewards, as exhibited by this study, are the sizeable sample and the variety of dental health inquiries sought reveal the participants’ knowledge, attitudes, and self-care levels. Since this is the first known Jordanian study to evaluate CPs’ knowledge and attitudes regarding oral health, it is hoped that it will be considered baseline data for future studies. Moreover, the variations of data collection from dispersed geographic locations (4 provinces) make the result more generalized to similar contexts.\n\nThe limitations of the present study were its dependence on a questionnaire, which may sometimes provide inaccurate results due to misconstrued understanding and the phrasing of the questions. Also, due to cultural issues, when the questionnaire was distributed (daytime working hours), it could be an issue covering more females than male pharmacists. Finally, due to the limited “free” time, a CP has to read and comprehend the question correctly to provide a suitable answer.\n\nAccess to a more comprehensive database is needed to devise and develop a practical approach to enhance pharmacists’ oral health. Further research would need to be undertaken nationally, ideally with a sample size typical of Jordanian pharmacists. By addressing the public’s oral health requirements, pharmacists in community pharmacy settings may function as oral health promoters with the help of their expanded knowledge and skills in this area.\n\n\nConclusion\n\nThe (CPs) surveyed in this study displayed good oral health knowledge, a positive attitude, and inadequate university training. This study explicitly demonstrates that despite all obstacles and challenges, Jordanian (CPs) have the general knowledge and attitude needed to play a significant part in dental care.\n\nThe (CPs) surveyed in this study also noted that they desired more active participation in their roles of CPs as well as more education and training to improve their practice. The medical and paramedical colleges at the universities should take on a more active role in implementing various training, educational conferences, and seminars for oral health, which may enhance the pharmacist’s curriculum.\n\nCompetencies in counselling, particularly those relating to smoking cessation, denture cleanliness, the proper use and selection of dental products, and mouthwashes, could improve pharmacists’ basic understanding of oral health and help patients take better care of themselves.\n\n\nEthics and consent\n\nThe study protocol was approved by the Jordan University of Science and Technology (JUST) Institutional Review Board, Jordan, with protocol number (2022/602). The objectives and protocols of the study were explained to the participants and obtained written informed consent from each subject before participation in the study.\n\n\nHuman and animal rights\n\nNo animals were used in this research. All human research procedures followed were in full accordance with the ethical standards of the committee responsible for human experimentation (institutional and national) and with the World Medical Association Declaration of Helsinki of 1975, as revised in 2018.\n\n\nAuthor contributions\n\nSA, AT, TF, AR, and RT concpetulized and designed the study, reviewed the literature, collected data, interpreted data contributed in writing manuscripts. AT analysed, interpreted the data, and contributed in writing the manuscript. SA contribued to study design, interpreted the data, and was a major contributor in writing the manuscript. All authors read and approved the final manuscripts.", "appendix": "Data availability\n\nThis project contains the following underlying data:\n\nFigshare: Pharmacists’ Knowledge, Attitude, and Practice Towards OH Data (participants answers).\n\nfigshare. Dataset. https://doi.org/10.6084/m9.figshare.25992388.v1\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nFigshare: Checklist for Assessment of community pharmacists’ knowledge, attitude, and practice towards oral health care in Jordan, https://doi.org/10.6084/m9.figshare.26075215.v1\n\nSTROBE Statement-Checklist of items that should be included in reports of cross-sectional studies\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgements\n\nWe acknoweledge the Deanship of Research at JUST for support the research.\n\n\nReferences\n\nWorld Health Organization: Global oral health status report. WHO; 2022; vol. 57. ; p. 120.\n\nOral Health: Organization, The World Health.2023. Reference Source\n\nSturrock A, Cussons H, Jones C, et al.: Oral health promotion in the community pharmacy: An evaluation of a pilot oral health promotion intervention. 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PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBawazir OA: Knowledge and Attitudes of Pharmacists Regarding Oral Healthcare and Oral Hygiene Products in Riyadh, Saudi Arabia. J Int Oral Heal. 2014; 6(6): 10–13.\n\nHajj A, Hallit S, Azzo C, et al.: Assessment of knowledge, attitude and practice among community pharmacists towards dental care: A national cross sectional survey. Saudi Pharm J. 2019; 27: 475–483. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMaunder PEV, Landes DP: An evaluation of the role played by community pharmacies in oral healthcare situated in a primary care trust in the north of England. Br Dent J. 2005; 199(4): 219–223. PubMed Abstract \| Publisher Full Text\n\nPriya S, Madan Kumar P, Ramachandran S: Knowledge and attitudes of pharmacists regarding oral health care and oral hygiene products in Chennai city. Indian J Dent Res. 2008; 19(2): 104–108. PubMed Abstract \| Publisher Full Text\n\nSello DA, Serfontein JHP, Lubbe MS, et al.: Factors influencing access to pharmaceutical services in underserviced areas of the West Rand District, Gauteng Province, South Africa. Heal SA Gesondheid. 2012; 17(1): 1–8. Publisher Full Text\n\nBahadori M, Ravangard R, Asghari B: Perceived Barriers Affecting Access to Preventive Dental Services: Application of DEMATEL Method. Iran Red Crescent Med J. 2013; 15(8): 655–662. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBlebil A, Dujaili J, Elkalmi R, et al.: Community Pharmacist’s Role in Providing Oral Healthcare Services: Findings from Malaysia. J Pharm Bioallied Sci. 2020 Jan 1; 12(1): 64–71. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAljrais M, Ingle N, Assery M: Oral-dental health knowledge, attitude and practice among dental and pharmacy students at Riyadh Elm University, KSA. J Int Oral Heal. 2018; 10(4): 198–205. Publisher Full Text\n\nVaidya A, Aryal UR, Krettek A: Cardiovascular health knowledge, attitude and practice/behaviour in an urbanizing community of Nepal: a population-based cross-sectional study from Jhaukhel-Duwakot Health Demographic Surveillance Site. BMJ Open. 2013; 3(10): e002976. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSabouhi F, Babaee S, Naji H, et al.: Knowledge, awareness, attitudes and practice about hypertension in hypertensive patients referring to public health care centers in Khoor & Biabanak. Iran J Nurs Midwifery Res. 2011; 16(1): 34–40. PubMed Abstract\n\nFreeman CR, Abdullah N, Ford PJ, et al.: A national survey exploring oral healthcare service provision across Australian community pharmacies. BMJ Open. 2017; 7(9): e017940–e017911. Publisher Full Text\n\nPreethi M, Suganya C, Ganesh R: Knowledge, attitude, and practice toward oral health among pharmacy students in Chennai. Indian J Multidiscip Dent. 2016 Jan 1; 6(1): 20–20. Publisher Full Text\n\nRajiah K, Jun VC: An assessment of pharmacy students’ knowledge, attitude, and practice toward oral health: An exploratory study. J Int Soc Prev Community Dent. 2014; 4: 56. Publisher Full Text\n\nBadran IG: Knowledge, attitude and practice the three pillars of excellence and wisdom: A place in the medical profession. East. Mediterr Health J. 1995; 1: 8–16. Publisher Full Text\n\nSample Size Calculator software. http\n\n\nFootnotes\n\n1 IBM Corp. Released 2013. IBM SPSS Statistics for Windows, Version 22.0. Armonk, NY: IBM Corp." }	[ { "id": "331487", "date": "28 Oct 2024", "name": "Siddharthan Selvaraj", "expertise": [ "Reviewer Expertise 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\nCoherence and Organization: The article is well-structured and organized effectively, with a clear introduction, methodology, results, and discussion parts. The readability was enhanced by using headings and subheadings and allows for easy navigation through the material. Methodology: The prospective cross-sectional design is appropriate for the study's objectives. However, it would be helpful to provide more information about the sampling method used to select the participants. Using random sampling technique enhances the findings validity. Information about whether the back translation was done for the study questionnaire is needed. Questionnaire Design: The questionnaire appears comprehensive, covering socio-demographic details, knowledge, attitudes, and practices regarding oral health care. Information on how the questionnaire was validated was presented in details, The questionnaire was pilot tested which enhances the reliability and validity of the questions. Data Analysis: The use of the Statistical Package for the Social Sciences (SPSS) for data analysis is appropriate. However, the article should provide more details on the statistical tests used to analyze the data and how they relate to the research questions. This would enhance the transparency of the analysis. Results Presentation: The results are presented clearly. Discussion and Implications: The discussion section successfully put the findings within the context of existing literature. However, more information on the study's practical implications for community pharmacists and public health policymakers in Jordan would be valuable. Suggestions for future research could also be included to address the gaps identified in the study. Limitations: the article mentions the limitations of the study in depth. However, a discussion of potential biases of the study design would provide a more balanced view of the findings. Conclusion: The conclusion summarizes the key findings well, but it could be strengthened by reiterating the significance of the study in improving oral healthcare practices among community pharmacists in Jordan. Overall, this article contributes valuable insights into the role of community pharmacists in oral health care and highlights areas for improvement. With some revisions and additional details, it has the potential to make a significant impact in the field.\n\nIs the work 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": "351771", "date": "25 Jan 2025", "name": "Beverley D Glass", "expertise": [ "Reviewer Expertise Pharmacy practice", "including expanded practice", "delivery of health services to rural", "remote and indigenous communities" ], "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\nOrganization and language: The paper lacks a logical flow of information and there is some repetition. The paper would also benefit from a comprehensive English language edit - use of language, length of sentences etc.\n\nPlease refer to the assessment of the published article here - 152739-Article assessment-Beverley D Glass\nAbstract: The authors present a good summary of the study; however, the final sentence of the conclusion goes beyond the findings of the study and should not be in included. Introduction: See edited paper with comments above ( 152739-Article assessment-Beverley D Glass ) Methods: These are comprehensive and well described Results: The results are comprehensive, however sections related to the description of the statistics are not clear especially that of the associations Discussion. This would benefit from a clear structure and a logical flow of information what a discussion meant to be - statement of findings, comparison to the literature, relevance to practice etc. Conclusion: This conclusion does not really conclude the study's findings and use that to propose future directions for research.\nThis study does however present valuable findings, especially in terms of pharmacists expanding their 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?\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/13-730
https://f1000research.com/articles/12-894/v1	27 Jul 23	{ "type": "Research Article", "title": "Return to work rate of individuals after cardiac rehabilitation and the demographic and impairment factors that influence return to work in the Western Cape, South Africa", "authors": [ "Zakeera Ganie", "Shaheed Soeker", "Anthea Rhoda", "Zakeera Ganie", "Anthea Rhoda" ], "abstract": "Background: Cardiovascular disease commonly affects individuals within the working age group, often resulting in unemployment, particularly in low- to middle-income countries. The purpose of the study was to determine the return-to-work rate of individuals with cardiovascular disease after cardiac rehabilitation (CR) and the impact of impairment and socio-demographics on the individual’s ability to RTW. Methods: A cross-sectional survey, namely the Work Rehabilitation Questionnaire was used to gather the information. The IBM SPSS software (version 25) was used to manage the statistical analysis. Individuals who completed a cardiac rehabilitation program between the ages of 18 and 64 years made up a sample of 63 potential research participants. Results: The return-to-work (RTW) rate reported that only 30 (47.6%) of the participants successfully returned to work after CR and 33 (52.4%) of participants did not RTW. The results also indicated that the older the individual and the higher the degree of impairment experienced, the less likely RTW would occur. Conclusion: The study concluded that only 47.6 % of individuals completing cardiac rehabilitation returned to work. Being older and the degree of impairment impacts on one’s ability to return to work. Factors such as the age and level of functional impairment of the individual with cardiovascular disease must be addressed more aggressively in cardiac rehabilitation programs, particularly if the goal of the individual with cardiovascular disease is to RTW.", "keywords": [ "cardiovascular disease", "cardiac rehabilitation", "vocational rehabilitation", "return to work" ], "content": "Introduction\n\nThe impact that cardiovascular disease (CVD) has on the economy is said to be substantial as it is increasingly affecting individuals in their productive years of life.1 This burden of disease heeds calls to a more comprehensive approach for prevention and management of CVD, particularly in low- to middle-income countries such as South Africa.1 Upon investigating the impact of evidence-based cardiac rehabilitation (CR) programs it was found that participation in such a preventative program does have an impact on decreasing CVD mortality and re-hospitalisation, as well as having an impact on an individual’s ability to return to work (RTW).2 A prospective study conducted with 83 patients of working age during their CR found that job satisfaction and a positively perceived work environment resulted in early RTW after cardiac intervention and may have economic benefits and improve quality of life.3\n\nSlebus et al.4 further explored facilitating factors for RTW and identified the following: no signs and symptoms of the disease, work contentment, positive relationships at work, ability to participate in work activities, information from the doctor that encouraged RTW, medical care was working well, family relationships were positive, financial motivation and intrinsic motivation to work. Similar results from a qualitative study of perpetuating factors for long-term sick leave and promoting factors for RTW, found that illness perceptions and self-efficacy expectations can be promoting factors for RTW.5 Furthermore, financial obligations and culture are also contributing factors of RTW according to a study that reviewed the employment status after myocardial infarction (MI) among men. These men stated that they did not want to take advantage of their wives earning an income and that it was their responsibility as the breadwinner to provide for their families.6\n\nIn a Danish cohort study examining RTW after hospitalisation for heart failure, the authors speculate that a lack of RTW was due to functional limitations as a result of the disease as well as the psychological effects of having the heart failure diagnosis.7 Kearney et al.8 also observed that fatigue was most frequently reported as a barrier to RTW, followed by mild cognitive impairment such as impaired memory and cognitive processing. Similarly, a study with patients who had implantable cardioverter defibrillators (ICDs) estimated that 75% of patients experience mild to severe short-term cognitive impairment, with roughly 33% of these expected to be prolonged at six months.9\n\nPatients suffering from anxiety or emotional distress following the cardiac incident have been found to have increased difficulty in lifestyle modification and less likely to complete CR.10 This could have a negative impact on the individual’s prospects of RTW and successfully maintaining employment. Similarly, in a prospective cohort study examining the associations between depressive episodes and anxiety disorder with RTW after MI at three and six months found that the presence of a depressive episode and anxiety disorder during the first three months after the MI was a significant predictor of not returning to work by 12 months.11\n\nKearney et al.8 also found that patients in occupations such as labourers, tradesman and in the transport industry were less likely to RTW as their jobs were labour-intensive and that their illness had a greater impact on their ability to perform their work tasks. Add the significance of the study- relate the significance to the aim of the study. The significance of the current study was to determine the demographic factors that are associated with return to work (RTW) for individuals with cardiac conditions. The latter information would determine the RTW rate of individuals after they have completed a cardiac rehabilitation program. Furthermore, the study would determine which specific factors influence RTW for individuals with cardiac conditions after the completion of a cardiac rehabilitation program.\n\n\n\n• To determine the RTW rate of individuals with CVD after a cardiac incident\n\n• To determine the impact of impairment and socio-demographic factors on an individual’s ability to RTW after a cardiac incident\n\n\nMethods\n\nAll participants were patients of a district hospital, who were admitted due to a cardiac incident between 2017 and 2018. Each participant was referred to CR as an outpatient. The sampling technique utilised in this study was convenience sampling. A convenient sample was utilised at the data collection site. The advantage of using this sampling technique is that it is inexpensive, and results can be sorted quickly. However, there is a risk of the sample not being representative.12 This study yielded a sample of 63 participants. Cross-sectional surveys in form of the Work Rehabilitation Questionnaire (WORQ) were used to achieve the objective of determining the RTW rate after participation in the CR program. The WORQ is a validated and reliable tool used to measure functioning in the vocational rehabilitation setting.13\n\nFurthermore, the survey provided information regarding gender, age, marital status, education level and an impairment score. After a trial that took place in two months, the researcher collected data over a one-year period. Data was collected through face-to-face interviews and telephonically. The IBM SPSS software was used to conduct measurements of central tendency, frequencies and percentages of variables.\n\nDescription of the study population\n\nThe population for this study comprised individuals attending the CR program at the research site in the Western Cape. The district hospital only accommodates patients residing in the southern suburbs, who have been admitted to the hospital as inpatients. The inclusion criteria for participation was an age of 18-64 years and active employment prior to the cardiac incident. Seventy-seven copies of the questionnaire were administered, however only 63 surveys were accepted for analysis. Fourteen surveys were incomplete and therefore voided.\n\nDemographics and clinical characteristics of the study sample\n\nThe study sample comprised 27 female and 36 male participants, with a mean age of 54 years and a standard deviation of 5.95. Most (60.3%) of the participants in the sample were in the 51-60 year age group. Forty-two of the participants were married, 12 divorced, 7 never married, 1 widowed and 1 was cohabiting. The majority (73%) of participants had a secondary school education. Forty-two participants completed secondary school, with 8 graduates from college/university, 2 had completed post-graduate studies and 7 primary school only. All the participants had experienced a MI between 2016 and 2018 and received medical and therapeutic intervention. Nineteen participants were receiving government support in the form of social grants (Table 1).\n\nDescription of cardiac rehabilitation program\n\nThe individuals diagnosed with a MI were provided with a pamphlet with information on MI, medication, exercise and ADLs that are safe to do. All patients with MI are usually referred for CR at the district hospital. The CR program at the hospital is an education-based program, aimed at lifestyle modification. It consists of weekly education sessions that are arranged in a three-week cycle, that focuses on the use of medication, healthy eating, graded exercise that can be done at home and participation in activities of daily living, as well as psychological aspects that can arise after a cardiac incident. The program is facilitated by the occupational therapist and physiotherapist. Talks by consultant physicians and dieticians are included in the program.\n\nThe pilot study was conducted over a two-month period between October and November 2017. Data collection for the study was conducted over a one-year period from January to December 2018. The researcher liaised with the head of department of internal medicine at the research site to get approval and gain access to contact information of participants in the CR program. Contact information for eligible participants was provided by the records department of the hospital. The pilot study was completed with six participants to determine the practicability of the tool and outcome measure before commencing the study. The participants were contacted telephonically or by face-to-face interviews and it was found that they were able to understand and appropriately complete the questionnaire through both means of communication with the researcher. As some questions required more explanation it was found that interviews were better than self-administration of the questionnaire. No changes to the questionnaire were necessitated. The pilot study also gave the researcher an idea of the time frame required for administration of each questionnaire. It was determined that a maximum of twenty minutes was required per survey. The researcher and the researcher’s supervisor were satisfied with the results of the pilot study and proceeded to commence with the main study.\n\nEligible participants were contacted after the last CR session at the research site. Information sheets describing the study and consent forms were provided for those interested in participating in the study. Once verbal and written consent were obtained, the researcher administered the surveys and interviews. Face-to-face interviews took place either at the district hospital occupational therapy department or at the researcher’s private office. Telephonic interviews were conducted from the researcher’s private office. Questions that some participants chose not to answer were considered as incomplete surveys and were not included in the final sample.\n\nThe WHO14 ethical guidelines help promote ethical conduct of research, through the enhancement and protection of the rights of the research participants and communities. The World Medical Association Helsinki Declaration15 guided this study that involves human participants. Prior to participation in this study, participants gave their informed consent through a signature or verbally for telephonic surveys and interviews. Participants were informed of their right to stop participating in the study at any point, which preserved autonomy. Through safely storing audio interviews and transcription of data on a password-protected computer, confidentiality was guaranteed. Audiotaped recordings will be safeguarded for a period of two years before destroying them. Pseudonyms were used to ensure participants’ anonymity in all documentation related to the study. Counselling was made available to participants who experienced distress during participation in the study. Participation was voluntary and participants were allowed to withdraw from the study at any stage. The researcher commenced with the study only after approval from the University’s Research Ethics Committee and the Department of Health (Western Cape) was obtained.\n\nThe Work Rehabilitation Questionnaire (WORQ) was used to ascertain the information needed to fulfil the first and second objectives. The purpose of the WORQ as an instrument is to assess work functioning in individuals participating in a vocational rehabilitation programme. After permission were obtained from the authors of the WORQ, the researchers used the WORQ in the current study. The WORQ can be administered at any point within the continuum of the RTW process and can be used with any health condition. It is aimed at gaining a fast, yet comprehensive overview of the functional problems experienced during the RTW process. The questionnaire is made up if two parts, part one being the sociodemographic and background information and part two a functional impairment section, comprising various health characteristics.\n\nIn the study conducted by Finger, Escorpizo, Bostan and De Bie,13 to identify the psychometric evidence for the use of the WORQ as a valuable instrument, they concluded that the WORQ showed a high test-retest reliability and good internal consistency. Finger et al.13 reported WORQ to have a high level of internal consistency (Cronbachs alpha=0.88) and interlinker agreement (kappa=0.82). The WORQ also exhibit acceptable levels of test retest reliability (r=0.79) and good face, content and criterion validity.\n\nFor the purpose of this study, the WORQ could be used in its English form as all participants were able to converse adequately in English.\n\nThe IBM SPSS software (version 25) was used to analyse, manage and generate descriptive statistics. The IBM SPSS software package is a well-established program used for batched and non-batched statistical analysis within health sciences research. Measures of central tendency, frequency and percentages for the variables describing rate of RTW were calculated. Binary logistical regression was used to explore the participant’s level of impairment and socio-demographic factors affecting RTW after the cardiac incident. The level of significance accepted in this study was p=0.05.\n\nThe independent variables selected for this study were acquired directly for the WORQ survey. The socio-demographic variables included age, sex, civil status and level of education. Work and health-related variables from part two of the questionnaire were collated to calculate an impairment score. RTW status was captured as the dependent variable. RTW status is described as the resumption of work in the open labour market, including formal employment, informal employment and self-employment. This was captured through a yes or no answer regarding RTW after participating in a CR programme. Furthermore, the capacity of RTW included full-time work, part-time work, changes in work type or adaptation to accommodate cardiac condition.\n\nTo summarise sociodemographic, work and health characteristics in relation to RTW ability, descriptive statistics of central tendency, frequency and percentages were used. Summary statistics of key independent variables were also calculated.\n\nPearson’s Chi-square test\n\nIn order to assess the association between the independent variables (age, gender, civil status, level of education, degree of impairment) and dependent variable (RTW status) Chi-square was conducted. Significance level was set at p≤0.05.\n\nBinary logistical regression\n\nTo determine the variables that influence the ability to RTW for participants with cardiac conditions, binary logistical regression was conducted. For the purpose of this study the probability of RTW after CR was projected based on participants socio-demographics, work- and health-related characteristics. The four socio-demographic variables were age, gender, civil status and level of education. The work, health and activity restriction characteristics that formed the impairment score was derived from part 2 of the WORQ, of which 37 questions from of the following ICF categories: body functions, activities and participation and environmental factors, were used. This study’s sample of n=63 could support the binary logistical regression analysis with a 95% confidence interval.\n\n\nResults\n\nThe results of the study highlights the participants’ responses to the WORQ questionnaire, which helped determine the RTW rate, factors associated with RTW and the work characteristics of the study sample.\n\nResults of the bivariate analysis conducted to determine the RTW rate of individuals with CVD yielded the following results:\n\nOnly 30 (47.6%) of the participants reported, successful RTW after CR and 33 (52.4%) of participants did not RTW, as indicated through answering of questions four and five in the WORQ questionnaire. This was an interesting result in that despite 47.6% of individuals RTW, many of these individuals initially struggled to adapt to their worker roles immediately after completing rehabilitation (Figure 1).\n\nLogistic regression was performed to determine the participant’s ability to RTW and each of their socio-demographic, health and work characteristics were analysed using Pearson Chi-square test, with a significant p-value that is equal to or lower than 0.05.\n\nThe model contained five independent variables. Three of the socio-demographic variables, namely civil status, education level and gender had no significant association with ability to RTW. From the logistic regression it was found that age (p≤0.004) and impairment score (p≤0.034) were significant in influencing RTW (Tables 1 and 2).\n\n* Statistical significance.\n\nFrom the logistic regression it was understood that the older you get the less likely you are to return to work after a cardiac incident. As noted in the figure below, most of the participants in the study sample were in the 57-year-old age group and did not RTW. All participants 44 years and below, returned to work (Figure 2).\n\nA collective score from part two of the WORQ survey was calculated in order to obtain an impairment score. The survey found the impairment score to have a p-value of p=0.034, which informed the researcher that if you experience a higher degree of impairment, the less likely you are to RTW successfully (Table 2).\n\nSixteen categories of body function are represented in the WORQ and Figure 3 below details responses that scored 8-10 on the Likert scale for each category. Problems related to sleep, body aches and pains and endurance rated amongst the highest in the participant responses.\n\nTwenty-one categories of activities and participation are represented in the WORQ and Figure 4 details responses that scored 8-10 on the Likert scale for each category. Lifting items more than 5 kg, walking more than a kilometre and crawling, climbing or running were identified as some of the most difficult activities to participate.\n\nAll of the participants found it challenging (in varying degrees) to participate in work activities, due to affected body functions or activity participation or both.\n\nInformation regarding work characteristics were also obtained from the survey. Participants were either self-employed or employed in the formal private sector or public service. Pre and post classification of work was captured. Changes were noted at most levels of classification pre and post injury, except for the one person doing heavy duty work.\n\n\nDiscussion\n\nResults of the study indicated that 52.4% of the participants did not RTW, despite having had CR (Figure 1). Factors that significantly impacted on the participants’ ability to RTW were age and impairment score as well as work characteristics (Table 1).\n\nSimilar to this study’s low RTW rate, in the study examining factors associated with RTW after acute myocardial infarction (AMI) in China, it was found that almost half of previously employed Chinese patients did not RTW within 12 months of the incident, with the researchers stating that CR availability was low and quality of rehabilitation poor.16 However, contrary, to the Chinese and the current study, a Malaysian study that predicted RTW after a cardiac event, reported that after participating in a CR programme the RTW rate was 66.1% and that a focus on mental health during CR may improve the RTW of these individuals.17 Likewise, in a Danish nationwide register follow-up study, 76.6% of patients RTW by the median time of 4 months post incidence.18 The latter supports the belief that RTW after a cardiac incident can be increased successfully, taking lessons from other programs such as mental health consideration and applying it contextually.\n\nAge\n\nAs reported from the quantitative results, the older you get, the less likely it is for you to RTW after a cardiac incident. Similarly, in an Italian review on the RTW after an acute cardiac incident, it was found that several studies reported that older age was an adverse factor for RTW.19 Jiang et al’s.16 study in China, also indicated that this notion of being older is still a negative factor for RTW. In another Danish study exploring the RTW and subsequent detachment from employment after myocardial infarction, it was also found that the 60-65 year-old age group were at the highest risk of detachment from employment. Second to this age group was the youngest age group of 30-39 years, while their analysis reported that the 40-49-year-old age group had the lowest risk of detachment from employment.20 The current study is similar as all participants under the age of 44 years, RTW and participants between 60 and 65, did not RTW, excluding one 63-year-old participant. Furthermore, the Smedegaard et al.20 study stated that within the 50-59-year-old age group, 51.7% of participants did not RTW and 48.3% of the participants did RTW. This age group’s statistics are very similar to the results of the current study with the mean age being 54 years and the rate of RTW being 47.62% and 52.38 % of participants not returning to work.\n\nGender\n\nAs reported in the results of the current study, gender did not play a significant role in determining RTW after a cardiac event. However, in the review of Fiabane et al.19 it was found that studies reported women to be at greater risk of not returning to work and that married women, in particular, were discouraged. The studies of Kragholm et al.18 and Jiang et al.16 also stated that gender (i.e., males) were significantly associated with successful RTW. Within the context of this study, being located in a suburb where women are often forced to work in order to support or contribute towards the household, could be a possible reason for the insignificance.\n\nMarital status\n\nIn this study 67% of the participants were married; however, marital status was not a significant factor in the RTW of this study population. Similarly, the systematic review of Cancelliere et al.21 on factors affecting RTW after injury or illness, revealed that marital status had no association. Contrary, Dreyer et al.22 postulates that being married, having a professional or clerical job and having no prior coronary problems were seen as more likely to RTW successfully.\n\nEducation level\n\nThis study also reported that educational level was not a significant factor. Contrary to these results the Italian review found that with a higher educational level and higher socio-professional category supported RTW, while blue collar workers were more at risk of not returning to work.19 Similarly, the prospective cohort study on predicting RTW after Acute Mycardial Infarct found that socio-occupational factors such as self-employment, higher educational level and lower levels of depression, were predictors of RTW.23 The study by Smedegaard et al.20 on employment after MI also found that higher education was associated with successful RTW but only for men, not women. In this study, participants’ education level ranged from primary school to post-graduate level, with a majority of the study population having secondary education, however no significance was found. This could be related to the fact that blue collar work is dominant in South Africa due to education levels being lower than developed countries such as the studies mentioned above.\n\nThis study’s calculated impairment score of p=0.034, proved to be a significant contributor to not returning to work. The higher the degree of impairment, the more likely it was for the individual to not RTW. Impaired cardiac functioning was reported to have an impact on various aspects of body functions and activities and participation which collectively affected the participants’ ability and motivation to RTW. In a study that compared young men and women returning to work after AMI, it was found that 63% of those not returning to work could be attributed to deteriorating health from impairments.22 Thus, the degree of impairment must be established at the initial point of assessment and addressed within rehabilitation for it not to have such a negative influence on RTW.24 In another study that compared differences between younger and older adults with multiple conditions, it was found that individuals with comorbidities were more likely to report impairments related to CVD.25\n\nThe type of work the individual is returning to, needs to be addressed early on in the rehabilitation process so that more individuals have the opportunity to prepare for RTW. In this study, work ranged from sedentary to heavy classifications of work. Sedentary work refers to work that involves sitting, some standing and walking with minimal lifting. Light work requires walking, standing, some pushing and pulling objects of about 5 kg. Medium work involved frequent lifting or carrying objects up to 25 kg. Lastly, heavy work is defined as frequent lifting and carrying of objects up to 50 kg.26 Grace et al.27 notes that it is imperative to discuss timing of the return to work of clients and that consideration should be given to the family’s financial situation, as well as the work characteristics (Table 3).\n\nThe study was conducted with a small study sample, however cognisance must be taken of the fact that the district hospital mentioned in the study is the only hospital in the City of Cape Town (South Africa) that provided CR as a service to patients with cardiac conditions. There were therefore no other CR programmes available in the geographical area in the Western Cape. Therefore, due to reasons above caution must be taken in generalising the findings of the current study.\n\n\nConclusion\n\nThe inference of these results suggests that factors associated with age and impairment and its influence on ability to RTW must be addressed more aggressively in CR programs, as well as work characteristics. The significance for an intervention program being developed is that age, degree of impairment and work characteristics can be considered when designing an integrative CR programme which includes RTW preparation and strategies.", "appendix": "Data availability\n\nUniversity of Western Cape: Questionnaire data for ‘Return to work rate of individuals after cardiac rehabilitation and the demographic and impairment factors that influence return to work in the Western Cape, South Africa’, https://doi.org/10.25379/uwc.21750356.v2. 28\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nCappuccio FP, Miller MA: Cardiovascular disease and hypertension in sub-Saharan Africa: Burden, risk and intervention. Intern. Emerg. Med. 2016; 11: 299–305. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBabu AS, Lopez-Jimenez F, Thomas RJ, et al.: Advocacy for out patient rehabilitation globally. BMC Health Ser. Res. 2016; 16: 471. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFiabane E, Argentero P, Calsamiglia G, et al.: Does job satisfaction predict early return to work after coronary angioplasty or cardiac surgery? Int. Arch. Occup. Environ. Health. 2013; 86(5): 561–569. Publisher Full Text\n\nSlebus FG, Jorstad TH, Peters RJG, et al.: Return to work after an acute coronary syndrome: Patients’ perspective. Saf. Health Work. 2012; 3: 117–122. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDekkers-Sanchez PM, Wind H, Sluiter JK, et al.: A qualitative study of perpetuating factors for long-term sick leave and promoting factors for return to work: Chronic work disabled patients in their own words. J. Rehabil. Med. 2010; 42(6): 544–552. PubMed Abstract \| Publisher Full Text\n\nSahan C, Demiral Y, Kilic B, et al.: Changes in employment status after myocardial infarction among men. Balkan Med. J. 2016; 33: 419–425. Publisher Full Text\n\nRorth R, Wong C, Kragholm K, et al.: Return to the workforce after first hospitalisation for heart failure: A Danish nationwide cohort study. Circ. J. 2016; 4(134): 999–1009.\n\nKearney J, Dyson K, Andrew E, et al.: Factors associated with return to work among survivors of out-of-hospital cardiac arrest. Resuscitation. 2020; 146(146): 203–212. Publisher Full Text\n\nKim J, Pressler SJ, Groh WJ: Change in cognitive function over 12 months among patients with an implantable cardioverter-defibrillator. J. Cardiovasc. Nurs. 2013; 28(6): E28–E36. PubMed Abstract \| Publisher Full Text\n\nHuffman JC, Celano CM, Januzzi JL: The relationship between depression, anxiety, and cardiovascular outcomes in patients with acute coronary syndrome. Neuropsychiatr. Dis. Treat. 2010; 6: 123–136. PubMed Abstract\n\nDe Jonge P, Zuidersma M, Buitmann U: The presence of a depressive episode predicts lower return to work rate after myocardial infarction. Gen. Hosp. Psychiatry. 2014; 36(4): 363–367. PubMed Abstract \| Publisher Full Text\n\nMaree K: Qualitative research designs and data gathering techniques in First Steps in Research. 13th ed.Pretoria: Van Schaik Publishers; 2007; 87.\n\nFinger ME, Escorpizo R, Bostan C, et al.: Work rehabilitation questionnaire (WORQ): Development and preliminary psychometric evidence of an ICF-based questionnaire for vocational rehabilitation. J. Occup. Rehabil. 2014; 24(3): 498–510. PubMed Abstract \| Publisher Full Text\n\nWorld Health Organisation: Global statistics report on non-communicable diseases 2010. Geneva: World Health Organisation; 2011.\n\nWorld Medical Association: Declaration of Helsinki 2008.Reference Source\n\nJiang Z, Dreyer RP, Spertus JA, et al.: China Patient-Centred Evaluative Assessment of Cardiac Events (PEACE). Factors associated with return to work after acute myocardial infarction in China. JAMA. 2018; 2; 1(7). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMustafah NM, Kasim S, Isa MR, et al.: Predicting return to work following a cardiac event in Malaysia. Work. 2017; 58(4): 481–488. PubMed Abstract \| Publisher Full Text\n\nKragholm K, Wissenberg M, Mortensen RN, et al.: Return to work in out-of-hospital cardiac arrest survivors: A national register-based follow-up study. Circ. J. 2015; 131: 1682–1690. Publisher Full Text\n\nFiabane E, Omodeo O, Argentero P, et al.: Return to work after an acute cardiac event: The role of psychosocial factors. Prev. Res. 2014; 3(4): 137–141.\n\nSmedegaard L, Nume AK, Charlot M, et al.: Return to work and risk of subsequent detachment from employment after myocardial infarction: Insight form Danish nationwide registries. J. Am. Heart Assoc. 2017; 6(10). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCancelliere C, Donovan J, Stochkendahl MJ, et al.: Factors affecting return to work after injury or illness: Best evidence synthesis of systematic reviews. Chiropr. Man. Ther. 2016; 24(32): 1–23.\n\nDreyer RP, Xu X, Zhang W, et al.: Return to work after acute myocardial infarction: A comparison between young woman and men. Circ. Cardiovasc. Qual. Outcome. 2016; 9(2:1): S45–S52.\n\nStendaro M, Bonci M, Casillo V, et al.: Predicting return to work after acute myocardial infarction: Socio-occupational factors overcome clinical conditions. PLoS One. 2018; 13(12): e0208842. Published 2018 Dec 13. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWorld Health Organization: International classification of functioning disability and health (ICF). Geneva: 2001; 1–303.\n\nAdams ML: Differences between younger and older US adults with multiple chronic conditions. Prev. Chronic Dis. 2017; 14: 1–14.\n\nDictionary of Occupational Titles, Physical Capacity: Tygerberg Hospital, Occupational Therapy Department Vocational Rehabilitation Unit.n.d.\n\nGrace SL, Turk-Adawi K, Contractor A, et al.: Cardiac rehabilitation delivery model for low resource setting. Heart. 2016; 102: 1449–1455. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSoeker M: Return to work rate of individuals after cardiac rehabilitation and the demographic and impairment factors that influence return to work in the Western Cape, South Africa. [Dataset]. University of Western Cape; 2023. Publisher Full Text" }	[ { "id": "206156", "date": "26 Sep 2023", "name": "Thomas Maribo", "expertise": [ "Reviewer Expertise Cardiac rehabiltiation. vocational 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\nHeadings should align with a scientific paper and headings like “description of dependent and independent variable”, “Univariate/descriptive statistics”, and “bivariate analysis” should be removed.\nProcedure starts with \"The pilot study\" – which pilot study? If I understand correct you could start with \"A pilot study\".\nIn the methods section: place the statistical programme at the end, not the beginning.\nDelete redundant sentences like “The IBM SPSS software package is a well-established program used for batched and non-batched statistical analysis within health sciences research.” (this is a scientific paper not a text book).\nIn the methods section, the impairment score is mentioned in 2 or 3 places. Rewrite and describe the outcome measures and then the analyses.\nThe term “the researcher” is used far too much (8 times!). The scientific world does not care what and how the researcher did - it is the study that is important. Rephrase “The researcher liaised with the head of department of internal medicine” - and more like that. And remove \"The researcher and the researcher’s supervisor were satisfied\" we do not care what your supervisor think or do. We want science!\nRewrite and shorten \"Ethics\". This is far too long with redundant sentences like \"The WHO14 ethical guidelines help promote ethical conduct of research, through the enhancement and protection of the rights of the research participants and communities\" – this is a scientific paper! \"Participation was voluntary and participants were allowed to withdraw from the study at any stage.\" is redundant as is it already stated.\nThe results section should start with a description of the population: how many patients were enrolled in CR, how many completed, how many (and who) did not complete CR – and how many did not complete the questionnaire\nThe sentence \"Logistic regression was performed to determine the participant’s ability to RTW and each of their socio-demographic, health and work characteristics were analysed using Pearson Chi-square test, with a significant p-value that is equal to or lower than 0.05.\" is placed in the results section! move to the methods section. If you want other researchers to read your paper it must be rewritten. I urge you to consult an experienced scientist.\nRewrite the discussion and include the following:\nwhy did you use interview and not the questionnaire? What did that mean?\n\nWhy were interviews held at the first authors private place? And could this bias the result?\nMinor: Reread and check for abbreviations. cardiac rehabilitation (CR) is abbreviated in the 1st paragraph, yet cardiac rehabilitation is written out 3 times.\nRewrite \" In the study conducted by Finger, Escorpizo, Bostan and De Bie,13 to identify the psychometric evidence for the use of the WORQ as a valuable instrument, they concluded that the WORQ showed a high test-retest reliability and good internal consistency. Finger et al.13 reported WORQ to have a high level of internal consistency (Cronbachs alpha=0.88) and interlinker agreement (kappa=0.82). The WORQ also exhibit acceptable levels of test retest reliability (r=0.79) and good face, content and criterion validity.\" Use Vancouver style and do not use the names of the authors\nRewrite the results section – report only results here.\n\nIs the work clearly and accurately presented and does it cite the current literature? No\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? No", "responses": [ { "c_id": "10556", "date": "20 Nov 2023", "name": "Shaheed Soeker", "role": "Author Response", "response": "Response to reviewers Dear Professor Thank you so much for the informed comments that you provided. I have provided a detailed response to the comments that you have provided. As a team we have tried to incorporate as many of the suggestions that you provided. Reviewer 2: Thomas Maribo, University of Copenhagen, Aarhus University, Blegdamsvej, Copenhagen, Denmark Comment Headings should align with a scientific paper and headings like “description of dependent and independent variable”, “Univariate/descriptive statistics”, and “bivariate analysis” should be removed. Response Unnecessary headings have been removed Comment Procedure starts with \"The pilot study\" – which pilot study? If I understand correct you could start with \"A pilot study\". Response This has been changed to ‘A’ pilot study Comment In the methods section: place the statistical programme at the end, not the beginning. Response This has been removed from the beginning of the section. Comment Delete redundant sentences like “The IBM SPSS software package is a well-established program used for batched and non-batched statistical analysis within health sciences research.” (this is a scientific paper not a text book). Response Sentence has been removed. Comment In the methods section, the impairment score is mentioned in 2 or 3 places. Rewrite and describe the outcome measures and then the analyses. Response This question has been answered, the outcome measure was described first and then the analysis procedure as it relates to the study was described Comment The term “the researcher” is used far too much (8 times!). The scientific world does not care what and how the researcher did - it is the study that is important. Rephrase “The researcher liaised with the head of department of internal medicine” - and more like that. And remove \"The researcher and the researcher’s supervisor were satisfied\" we do not care what your supervisor think or do. We want science! Response The word ‘researcher’ has been reduced. Suggested removal of sentence done. Comment Rewrite and shorten \"Ethics\". This is far too long with redundant sentences like \"The WHO14 ethical guidelines help promote ethical conduct of research, through the enhancement and protection of the rights of the research participants and communities\" – this is a scientific paper! \"Participation was voluntary and participants were allowed to withdraw from the study at any stage.\" is redundant as is it already stated. Response This section has been shortened and reformatted. Comment The results section should start with a description of the population: how many patients were enrolled in CR, how many completed, how many (and who) did not complete CR – and how many did not complete the questionnaire Response Description of the sample has been moved from methods to results section. As well as information related to the number of participants completing surveys, etc. Comment The sentence \"Logistic regression was performed to determine the participant’s ability to RTW and each of their socio-demographic, health and work characteristics were analysed using Pearson Chi-square test, with a significant p-value that is equal to or lower than 0.05.\" is placed in the results section! move to the methods section. If you want other researchers to read your paper it must be rewritten. I urge you to consult an experienced scientist. Response Methods and result information have been separated into the appropriate sections. Comment Rewrite the discussion and include the following: why did you use interview and not the questionnaire? What did that mean? Why were interviews held at the first authors private place? And could this bias the result? Response Some participants required assistance with reading or comprehension therefore interviews were done. The article describes that educations levels varied which contributed to the level of understanding. Telephonic interviews that were recorded were done from the researchers practice as it was logistically easier. Comment Reread and check for abbreviations. cardiac rehabilitation (CR) is abbreviated in the 1st paragraph, yet cardiac rehabilitation is written out 3 times. Response Abbreviations throughout have been revised. Comment Rewrite \" In the study conducted by Finger, Escorpizo, Bostan and De Bie,13 to identify the psychometric evidence for the use of the WORQ as a valuable instrument, they concluded that the WORQ showed a high test-retest reliability and good internal consistency. Finger et al.13 reported WORQ to have a high level of internal consistency (Cronbachs alpha=0.88) and interlinker agreement (kappa=0.82). The WORQ also exhibit acceptable levels of test retest reliability (r=0.79) and good face, content and criterion validity.\" Use Vancouver style and do not use the names of the authors Response Sentence has been reworded and referenced without the authors name. Comment Rewrite the results section – report only results here. Response Result section has been rewritten as suggested." } ] }, { "id": "200453", "date": "18 Oct 2023", "name": "Barbara Iansã de Lima Barroso", "expertise": [ "Reviewer Expertise I work mainly in the field of Policy", "Planning and Management of the Brazilian Unified Health System", "and its policies for the LGBTQIAP+ population. I have experience and interest in the area of Public Health", "in the following topics: male and female workers' health - contributions on health", "work and society", "precariousness of work", "health work", "management in Occupational Health", "and Systematic Reviews in the field of Work." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe article deals with cardiovascular diseases and the return to work of people after cardiac rehabilitation (CR) in low-to-middle income countries.\nThe article is of great importance for the Return to Work area, however, some adjustments need to be made. Getting started:\nReview the references used, bring more current scientific evidence, systematic reviews and population studies are well evaluated for a more robust introduction and discussion;\n\nThe word return-to-work must be written without a hyphen, although an Entry Terms version with a hyphen appears in MeSH, in current literature we use the word without a hyphen.\n\nAbbreviations throughout the text need to be revised, provide only one complete sentence followed by the abbreviation, then present only the abbreviation.\n\nIn statistical analysis, authors need to scientifically support the choice of method, and not just sampling (this was done to support the convenience sample), please provide more details;\n\nResults can start with a description of the sample;\n\nThe conclusion needs to be redone. Add whether the objectives of the study were achieved, the limits of the study, the strengths and divergent points of the research.\nI hope my contributions can further improve your work. Everything about RTW is very challenging, don't give up, continue to walk your path talking about work and its importance in our lives.\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? No", "responses": [ { "c_id": "10555", "date": "20 Nov 2023", "name": "Shaheed Soeker", "role": "Author Response", "response": "Response to reviewers Dear Professor Thank you so much for the informed comments that you provided. I have provided a detailed response to the comments that you have provided. As a team we have tried to incorporate as many of the suggestions that you provided. Reviewer 1: Barbara Iansã de Lima Barroso, Federal University of São Paulo, São Paulo, Brazil Comment Review the references used, bring more current scientific evidence, systematic reviews and population studies are well evaluated for a more robust introduction and discussion; Response The introduction and discussion was updated with scientific evidence from systematic reviews Comment The word return-to-work must be written without a hyphen, although an Entry Terms version with a hyphen appears in MeSH, in current literature we use the word without a hyphen. Response Hyphen has been removed. Comment Abbreviations throughout the text need to be revised, provide only one complete sentence followed by the abbreviation, then present only the abbreviation. Response Abbreviations have been revised. Comment In statistical analysis, authors need to scientifically support the choice of method, and not just sampling (this was done to support the convenience sample), please provide more details; Response Reference has been added: Kaur P, Stolzfus J, Yellapu V: Descriptive statistics. Int j Acad Med. 2018; 4: 60-63 Comment Results can start with a description of the sample; Response Sample description has been moved from methods to results section. Comment The conclusion needs to be redone. Add whether the objectives of the study were achieved, the limits of the study, the strengths and divergent points of the research. Response Conclusion has been rewritten." } ] } ]	1	https://f1000research.com/articles/12-894
https://f1000research.com/articles/12-1331/v1	16 Oct 23	{ "type": "Case Report", "title": "Case Report: Solid pseudo-papillary tumor of the pancreas", "authors": [ "Olfa Ghanney", "Rim Saad", "soumaya Ben A mor", "Trimech Mayada", "Rim Saad", "soumaya Ben A mor", "Trimech Mayada" ], "abstract": "Solid pseudo-papillary tumors (SPT) of the pancreas are rare neoplasms accounting for less than 2% of all pancreatic tumors and primarily affecting young women. They are generally characterized by a clinical and radiological polymorphism. In most cases, complete surgical resection is curative. We report a case of a young woman presenting with a pancreatic tumor revealed through a vague non-specific abdominal pain. The diagnosis was based on the histological examination of the surgically-removed piece.", "keywords": [ "Pancreas", "Tumor", "surgery", "Solid pseudopapillary neoplasm of the pancreas" ], "content": "Introduction\n\nA solid pseudo-papillary tumor (SPT) of the pancreas is a rare pathological entity accounting for approximately 2% of pancreatic exocrine tumors.1,2\n\nIts pathogenesis is still discussed. Clinical symptomatology is not specific and the discovery may be fortuitous. The diagnosis of this tumor is histological. The treatment is exclusively surgical associated with a good prognosis.3,4\n\n\nObservation\n\nA 19-year-old African woman, a high school student with no history of abdominal trauma, surgery or smoking was hospitalized for the exploration of an abdominal pain in the epigastrium and the left hypochondrium. She also had no specific family medical history. The pain started six months before admission and gradually got worse. It was associated with an alteration of her general state. She reported 11kg weight loss during this period.\n\nThe physical examination was uneventful except for a tenderness at the level of the epigastrium. Laboratory findings were normal. The abdominal Doppler ultrasound showed a round, well limited solid vascular mass. It was actually a large one measuring 42 mm and extending from the retroperitoneum down to the lower pole of the homolateral kidney. It was hyperechogenic and heterogeneous in appearance but mostly cystic in nature. A computed tomography (CT) Scan of the abdomen and the pelvis together with a pancreatic MRI revealed the presence of a 44×42×34 mm solid mass in the pancreatic tail. This mass was spontaneously isodense with a moderate and heterogeneous contrast enhancement and some scattered cysts. This mass presented regular contours with a predominantly lower extension reaching the descending colon without any symptoms of compression. The peritoneal fat was of normal appearance (Figure 1). The biological, hepatic and pancreatic check-up was normal. The patient underwent operation. The surgical operation confirmed the existence of a large exophytic tumor (diameter: 5cm) appended to the lower edge of the pancreatic tail. There was no locoregional invasion or distant metastasis. Surgical resection of the tumor by partially cutting the pancreas was performed. The surgery was without complication. The histological examination revealed a solid pseudopapillary tumor of the pancreas. Indeed, the cyto-architectural aspects confirmed our diagnosis. An immuno-histochemical study showed the existence of CD10 tumor cells. The patient developed well in the postoperative period, with normal US (three, 12 and 24 and 48 months) and CT scans (12, 24 and 48 months) and no evidence of residual disease.\n\n\nDiscussion\n\nSolid pseudo-papillary tumor (SPT) of the pancreas is a rare pathological entity first described by V. K. Frantz in 1959.5 This entity represents 0.7 to 2.7 % of all the exocrine pancreatic tumors and less than 5 % of cystic pancreatic tumors.5 The rarity of this neoplasm makes our case particular.\n\nLess than 1000 cases have been reported in the literature, mostly in isolated cases. It is classically described in young females in more than 95% of cases with an average age of 22 years (from 2 to 85 years)6 as was the case of our patient. Rare cases in males and the elderly have also been reported.7 It was also frequently found in different ethnic groups such as Black and Asian people. Its etiopathogenesis is still unknown. Two diagnostic hypotheses were proposed. The first was based on the role of sex hormones due to the female predominance and the presence of progesterone receptors. The second was more directed towards an embryonic origin with a totipotent stem cell that would be transformed into an exocrine and endocrine pancreatic cell.8\n\nThe tumors were discovered in different circumstances. The revelation pattern was vague abdominal pain in 58% of cases. The discovery may be fortuitous on abdominal imaging performed for another reason. It may also be discovered incidentally on a routine examination.\n\nThe tumor can also be revealed as an abdominal mass or as a complication which can occur in the form of a compression of the digestive, biliary or vascular structures when the tumor becomes voluminous or in the case of an intra-tumor hemorrhage. These complications may be spontaneous or secondary to abdominal trauma (3%).6,9\n\nIn our case, it was the abdominal pain which prompted the need for a follow-up imaging examination. There were no specific biological signs.\n\nThese tumors affect the head, body and tail of the pancreas, but develop preferably in the body and tail region (64% of cases).5,10 Rare cases of extra-pancreatic localizations (retroperitoneum, retro duodenal, meso-colic and hepatic) have been described. These rare extra-pancreatic areas are suggestive of two etiopathogenic hypotheses: a development from ectopic pancreatic tissue, or a development from totipotent stem cells being transformed into pancreatic cells. Macroscopically, the tumor is often voluminous, 10 cm long on average. It can reach 25 cm in diameter. It is often rounded or oval, surrounded by a fibrous capsule.1,11\n\nOn microscopy, the solid zones are composed of tumor cells of small size, monomorphic, cuboid or polygonal. A clear cytoplasm that is sometimes vacuolated and that contains diastase-resistant PAS-positive (periodic acid Schiff) globules can be seen. The nucleus is oval, regular, with peripheral chromatin condensations. The cells are arranged either as solid plaques or as a pseudo-papillary device with a fibrovascular axis bordered by a row of cells. Mitoses and cytotoxic atypia are an uncommon occurrence. Foamy histiocytes and giant cells can be found around cholesterol clefts.11\n\nThe stroma is usually of the endocrine type. It is rich in blood capillaries. The anatomo-pathological criteria for malignancy are found in only 10 to 15% of cases (invasion of adjacent structures, arterial embolism, perineural invasion, and lymph node metastases that are regional or distant). In these cases, the SPTP is classified as solid pseudo-papillary carcinoma. SPTP immunohistochemical profile is variable. Typically, tumor cells are labeled with anti-CD10, alpha-1 antitrypsin, vimentin, NSE, E-caderin and beta-catenin antibodies. Anti-progesterone antibody labeling is also noted. The positive immuno-labeling of tumor cells for some endocrine markers may prove some endocrine differentiation.\n\nMorphological explorations make it possible to study the characteristics of the lesion: its nature (solid, cystic or mixed), to specify the organ of origin, to study its features regarding the neighboring vessels and the organs and to look for metastases at distances.\n\nLocal invasion is reported in 15% of cases. Secondary sites were reported in 5% of the cases mainly affecting the liver.12\n\nAn abdominal ultrasound shows an echogenic and homogeneous mass, or heterogeneous with both cystic and solid zones.\n\nAn abdominal computed tomography (CT) shows a limited heterogeneous lesion that is rather hypodense. It is not very vascularized. It is also of mixed composition associating solid and cystic zones and is little or partially enhanced at the periphery after injection of the contrast agent. Signs of compression of the adjacent organs can be observed. The magnetic resonance imaging (MRI) shows a heterogeneous lesion with a hyper signal in T1 and T2. The capsule is often visible in the form of a hypo-intense border in T1.13,14\n\nAn unequivocal diagnosis remains histological. A preoperative biopsy is not recommended because of the risk of extrapancreatic tumor spread and the transformation of a well-localized tumor with good prognosis into an aggressive tumor with malignant peritoneal scattering.\n\nThe treatment is exclusively surgical involving the complete removal of the tumor with its capsule with preservation of as much pancreatic tissue as possible. Extensive lymph node dissection is not indicated. The choice of the operating method depends on the tumor size, localization and the possible invasion of adjacent organs. It consists of adistal pancreatectomy with possible preservation of the spleen, a pylorous preserving pancreatoduodenectomy.13,15 However, the low degree of malignancy of these tumors and the presence of a dense fibrous capsule have led several surgeons to attempt simple enucleation, especially in the absence of capsular invasion. The excision should be extended in case of invasion of the neighboring organs and possible nodules of peritoneal carcinosis which must be resected. The presence of invasion of the portal or mesenteric veins should not contraindicate a curative treatment, as cases of portal or mesenteric resection have been reported with prolonged survival. Associated metastatic lesions should be resected with a reasonable risk, and tumor recurrences should benefit from a surgical excision.\n\nAdjuvant therapy chemotherapy and radiotherapy has been shown to be effective. in some unresectable cases.12,13\n\nThe prognosis is good even in cases of metastasis.5 Survival, up to 17 years, has been reported for metastatic tumors. Long-term survival after complete resection of a non-metastatic tumor is between 80 and 90%, but associated with a recurrence rate of 10 to 15%.9 No pathological criteria (vascular, perineural and ganglionic invasion or mitotic index) currently predict survival.\n\n\nConclusions\n\nSPTP is a rare tumor with attenuated malignancy. Its diagnosis is based on histology coupled with immune-histochemistry. Surgery remains the treatment of choice even in the presence of metastases.\n\nWe obtained written informed consent from the patient for the use and publication of their data.", "appendix": "Data availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\n\nReferences\n\nKlimstra DS, Wenig BM, Heffess CS: Solid-pseudopapillary tumor of the pancreas: a typically cystic carcinoma of low malignant potential. Semin. Diagn. Pathol. 1 févr 2000; 17(1): 66–80. PubMed Abstract\n\nMaimaijiang A, Wang H, Li W, et al.: Diagnosis and treatment of solid pseudopapillary neoplasm of the pancreas in children: A report of 18 cases. Front. Pediatr. 2022 [cité 12 sept 2023]; 10. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nOmiyale AO: Solid pseudopapillary neoplasm of the pancreas. World J. Hepatol. 27 août 2021; 13(8): 896–903. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChen H, Huang Y, Yang N, et al.: Solid-Pseudopapillary Neoplasm of the Pancreas: A 63-Case Analysis of Clinicopathologic and Immunohistochemical Features and Risk Factors of Malignancy. Cancer Manag. Res. 31 déc 2021; 13: 3335–3343. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAntoniou EA, Damaskos C, Garmpis N, et al.: Solid Pseudopapillary Tumor of the Pancreas: A Single-center Experience and Review of the Literature. In Vivo. 1 juill 2017; 31(4): 501–510. PubMed Abstract\n\nYu PF, Hu ZH, Wang XB, et al.: Solid pseudopapillary tumor of the pancreas: A review of 553 cases in Chinese literature. World J. Gastroenterol: WJG. 14 mars 2010; 16(10): 1209–1214. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHasbi S, Menfaa M, Sakit F, et al.: Tumeur pseudopapillaire et solide du pancréas: une cause rare de masse abdominale. Pan Afr. Med. J. 2015 [cité 12 sept 2023]; 22(1): 361. PubMed Abstract \| Publisher Full Text \| Free Full Text Reference Source\n\nEder F, Schulz HU, Röcken C, et al.: Solid-pseudopapillary tumor of the pancreatic tail. World J. Gastroenterol: WJG. 14 juill 2005; 11(26): 4117–4119. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPapavramidis T, Papavramidis S: Solid Pseudopapillary Tumors of the Pancreas: Review of 718 Patients Reported in English Literature. J. Am. Coll. Surg. juin 2005; 200(6): 965–972. PubMed Abstract \| Publisher Full Text\n\nKlimstra DS, Wenig BM, Heffess CS: Solid-pseudopapillary tumor of the pancreas: a typically cystic carcinoma of low malignant potential. Semin. Diagn. Pathol. 1 févr 2000; 17(1): 66–80. PubMed Abstract\n\nMao C, Guvendi M, Domenico DR, et al.: Papillary cystic and solid tumors of the pancreas: A pancreatic embryonic tumor? Studies of three cases and cumulative review of the world’s literature. Surgery. 1 nov 1995; 118(5): 821–828. PubMed Abstract \| Publisher Full Text\n\nMatsuda Y, Imai Y, Kawata S, et al.: Papillary-cystic neoplasm of the pancreas with multiple hepatic metastases: A case report. Gastroenterol. Jpn. 1 juin 1987; 22(3): 379–384. PubMed Abstract \| Publisher Full Text\n\nGandhi D, Sharma P, Parashar K, et al.: Solid pseudopapillary Tumor of the Pancreas: Radiological and surgical review. Clin. Imaging. 1 nov 2020; 67: 101–107. PubMed Abstract \| Publisher Full Text\n\nDong PR, Lu DSK, Degregario F, et al.: Solid and papillary neoplasm of the pancreas: Radiological-pathological study of five cases and review of the literature. Clin. Radiol. 1 oct 1996; 51(10): 702–705. PubMed Abstract \| Publisher Full Text\n\nZhang H, Liang TB, Wang WL, et al.: Diagnosis and treatment of solid-pseudopapillary tumor of the pancreas. Hepatobiliary Pancreat. Dis. Int. 1 août 2006; 5(3): 454–458. PubMed Abstract" }	[ { "id": "280969", "date": "10 Jun 2024", "name": "Javier Cienfuegos", "expertise": [ "Reviewer Expertise Gaatrintestinal Surgery", "Laparoscopic 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\n1.- The differential diagnosis of cystic lesions of the pancreas is a challenge given that in many cases they are discovered incidentally and due to the heterogeneity they display.\nThe authors present the case of a solid pseudopapillary tumor of the pancreas (SPT) in a 19-year-old patient. In spite of the correct description of the case, two aspects are worthy of comment.\nRegarding the preoperative diagnosis, the authors are not in favor of performing a cytological analysis due to the risk of dissemination. Currently the cytologic characteristics of SPT are well established and the recommendation is to perform endoscopic ultrasound and fine needle aspiration (EUS-FNA).\nSPTs have been reported to have cytoplasmic and nuclear expression of the Wnt pathway (ß-catenin and loss of E-cadherin) in 100% of cases, unlike endocrine tumors whether these be solid or cystic.\nThe other aspect worth mentioning is the surgical technique. Even though most SPTs have a benign behavior, an invasive and metastatic component affecting the lymph nodes has been reported in 10% of cases. As a result, “enucleation” should be avoided and pancreatic resection should be performed using oncologic criteria depending on the size and location of the lesion, using either an open or laparoscopic technique.\nMajor comments:\nThe patient was intervened without a precise diagnosis before surgery. Nowadays, in this type of lesion, the means are available so that the most accurate diagnosis possible can be made before surgery.\nIn this sense, the authors should comment on the case discussion, the opportunity to perform a fine needle puncture and cytological study.\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? Yes", "responses": [ { "c_id": "11755", "date": "14 Jun 2024", "name": "olfa Ghanney", "role": "Author Response", "response": "Dear Reviewer Thank you for taking the time to read our article and for your valuable feedback. Allow me to clarify a few points. Please know that we are open to discussion and look forward to your responses. First Point : It is well known currently that , Echo-endosonography gives the ability of fine-needle aspiration and biopsy and, therefore, setting a correct preoperative pathologic diagnosis of tumor with an accuracy of 97.2%. However, EUS-guided biopsy demands specialized endoscopic skills, and unfortunately, it is not available in our hospital service, That´s why our patient underwent surgery before establishing the diagnosis of solid pseudopapillary tumor of the pancreas . In the discussion section, we mentioned that biopsy is not recommended. We were referring to abdominal CT-guided biopsy, not endoscopic ultrasound-guided biopsy. We did not specify this clearly, leading to confusion. We will rectify this in the manuscript. Here is a paragraph that we will add to the discussion section for correction. An unequivocal diagnosis remains histological. Endoscopic techniques offer ways to diagnose pseudopapillary solid tumor of pancreas(SPTP) before surgery. Like abdominal ultrasound, SPTP can appear as solid, cystic, or a combination of both on endoscopic ultrasound (EUS). EUS-guided fine needle aspiration (EUS-FNA) is now commonly used to diagnose pancreatic tumors, with high accuracy rates of over 80%. This technique not only allows for biopsy but also enables the minimally invasive collection of fluid samples, such as pancreatic juice and cyst fluid.(1) Second Point : Surgical technique Regarding surgical technique, indeed Parenchyma-preserving pancreatectomies, such as enucleation, central pancreatectomy, and duodenum-preserving pancreatic head resection (DPPHR), are being performed more frequently(2) . Studies have shown that these procedures can lower the occurrence of pancreatic endocrine and exocrine insufficiencies while maintaining positive short- and long-term results (3) . Enucleation, duodenum-preserving pancreatic head resection (DPPHR), and pancreaticoduodenectomy are options for SPTP located in the pancreatic(4). Enucleation, central pancreatectomy, and distal pancreatectomy (with or without splenectomy) are available for tumors in the pancreatic body and tail.(5) Minimally invasive techniques, including laparoscopic and robotic surgery, can be suded in both traditional and parenchyma-preserving procedures. To date, no consensus on the best approach for the treatment of SPTP metastasis has been established. Metastasis to lymph nodes is not common, occurring in only 1.0% to 7.9% of cases. Therefore, extended lymphadenectomy may not be needed for most patients (6). References : Antoniou EA, Damaskos C, Garmpis N, Salakos C, Margonis GA, Kontzoglou K, Lahanis S, Spartalis E, Patsouras D, Kykalos S, Garmpi A, Andreatos N, Pawlik TM, Kouraklis G. Solid Pseudopapillary Tumor of the Pancreas: A Single-center Experience and Review of the Literature. In Vivo. 2017 Jul-Aug;31(4):501-510. doi: 10.21873/invivo.11089. PMID: 28652415; PMCID: PMC5566898. Gao Y, Guo F, Lu Z, Xi C, Wei J, Jiang K, Miao Y, Wu J, Chen J. Perioperative safety and prognosis following parenchyma-preserving surgery for solid pseudopapillary neoplasm of the pancreas. World J Surg Oncol. 2023;21:119 Gao Y, Guo F, Lu Z, Xi C, Wei J, Jiang K, Miao Y, Wu J, Chen J. Perioperative safety and prognosis following parenchyma-preserving surgery for solid pseudopapillary neoplasm of the pancreas. World J Surg Oncol. 2023;21:119 headShyr BS, Wang SE, Chen SC, Shyr YM, Shyr BU. Pancreatic head sparing surgery for solid pseudopapillary tumor in patients with agenesis of the dorsal pancreas(4) J Chin Med Assoc. 2022;85:981–986. [PubMed] [Google Scholar] [Ref list . Liu Q, Dai M, Guo J, Wu H, Wang W, Chen G, Hu Y, Han X, Xu Q, Zhang X, Yang S, Zhang Y, Kleeff J, Liao Q, Wu W, Liang Z, Zhang T, Zhao Y. Long-term Survival, Quality of Life, and Molecular Features of the Patients With Solid Pseudopapillary Neoplasm of the Pancreas: A Retrospective Study of 454 Cases. Ann Surg. 2023;278:1009–1017. [PubMed] [Google Scholar] [Ref list] Liu Q, Dai M, Guo J, Wu H, Wang W, Chen G, Hu Y, Han X, Xu Q, Zhang X, Yang S, Zhang Y, Kleeff J, Liao Q, Wu W, Liang Z, Zhang T, Zhao Y. Long-term Survival, Quality of Life, and Molecular Features of the Patients With Solid Pseudopapillary Neoplasm of the Pancreas: A Retrospective Study of 454 Cases. Ann Surg. 2023;278:1009–1017. [PubMed] [Google Scholar] [Ref list]" }, { "c_id": "11891", "date": "02 Jul 2024", "name": "olfa Ghanney", "role": "Author Response", "response": "Cover Letter [Ghannei Olfa] [University of Monastir, Monastir, Tunisia] [Email: gounayolfa@gmail.com] [25 june 2024] [Javier Cienfuegos] [Clínica Universidad de Navarra, Pamplona, Navarra, Spain] Dear Javier Cienfuegos, I hope this letter finds you well. I am writing to express my sincere gratitude for your thorough and insightful review of our manuscript titled \"Solid pseudo-papillary tumor of the pancreas\" Your detailed comments and constructive feedback have been invaluable in enhancing the quality and clarity of our work. We have carefully considered each of your remarks and have made the necessary revisions to address the concerns raised. Below, we provide a point-by-point response to each of your comments Comment 1 : The patient was intervened without a precise diagnosis before surgery. Nowadays, in this type of lesion, the means are available so that the most accurate diagnosis possible can be made before surgery. Response1: it is well known currently that , Echo-endosonography gives the ability of fine-needle aspiration and biopsy and, therefore, setting a correct preoperative pathologic diagnosis of tumor with an accuracy of 97.2%. However, EUS-guided biopsy demands specialized endoscopic skills, and unfortunately, it is not available in our hospital service, That´s why our patient underwent surgery before establishing the diagnosis of solid pseudopapillary tumor of the pancreas . I have included this remark in the manuscript (Line22) Comment 2 : Regarding the preoperative diagnosis, the authors are not in favor of performing a cytological analysis due to the risk of dissemination Response2: In the discussion section, we mentioned that biopsy is not recommended. We were referring to abdominal CT-guided biopsy, not endoscopic ultrasound-guided biopsy. We did not specify this clearly, leading to confusion. Since this message is potentially confusing, we have removed it from the manuscript. Comment 3 : The surgical technique. Response3: We have revised the paragraph discussing the surgical treatment in the manuscript after consulting recent literature Thank you once again for your constructive feedback and your contribution to the improvement of our manuscript. We look forward to your further comments and hope that our revisions meet your expectations. Sincerely, [Ghannei Olfa] [University of Monastir, Monastir, Tunisia] [Gastrology doctor ]" } ] } ]	1	https://f1000research.com/articles/12-1331
https://f1000research.com/articles/11-1238/v1	01 Nov 22	{ "type": "Research Article", "title": "The effects of mouth rinsing and gargling with mouthwash containing povidone-iodine and hydrogen peroxide on the cycle threshold value of Severe Acute Respiratory Syndrome Coronavirus 2: A randomized controlled trial of asymptomatic and mildly symptomatic patients", "authors": [ "Lilies Dwi Sulistyani", "Vera Julia", "Andrianto Soeprapto", "Rumartha Putri Swari", "Febriadi Rosmanato", "Budi Haryanto", "Cahyarini Cahyarini", "Rinaldi Panjaitan", "Diah Ayu Maharani", "Vera Julia", "Andrianto Soeprapto", "Rumartha Putri Swari", "Febriadi Rosmanato", "Budi Haryanto", "Cahyarini Cahyarini", "Rinaldi Panjaitan", "Diah Ayu Maharani" ], "abstract": "Background: Coronavirus disease 2019 can spread rapidly. Surgery in the oral cavity poses a high risk of transmission of severe acute respiratory syndrome coronavirus 2. The American Dental Association and the Centers for Disease Control and Prevention recommend the use of mouthwash containing 1.5% hydrogen peroxide (H2O2) or 0.2% povidone iodine (PI) to reduce the viral load in the upper respiratory tract and decrease the risk of transmission. The aim of the present study was to analyze the effect of mouth rinsing and gargling with mouthwash containing 1% PI, 0.5% PI, 3% H2O2, or 1.5% H2O2 and water on the cycle threshold (CT) value obtained by real-time reverse transcription polymerase chain reaction (RT-PCR). Methods: This study is a randomized single blind controlled clinical trial which has been registered in the International Standard Randomized Controlled Trial Number (ISRCTN) registry on the 3rd February 2022 (Registration number: ISRCTN18356379). In total, 69 subjects recruited from Persahabatan General Hospital who met the inclusion criteria were randomly assigned to one of four treatment groups or the control group. The subjects were instructed to gargle with 15 mL of mouthwash for 30 s in the oral cavity followed by 30 s in the back of the throat, three times per day for 5 days. CT values were collected on postprocedural days 1, 3, and 5. Results: The results of the Friedman test significantly differed among the groups (n=15). The CT values increased from baseline (day 0) to postprocedural days 1, 3, and 5. Conclusions: Mouth rinsing and gargling with mouthwash containing 1% PI, 0.5% PI, 3% H2O2, or 1.5% H2O2 and water increased the CT value.", "keywords": [ "mouthwash", "severe acute respiratory syndrome coronavirus", "povidone iodine" ], "content": "1. Introduction\n\nCoronavirus disease 2019 (COVID-19) spreads quickly and deadly and, thus, has been especially challenging to healthcare workers.1 COVID-19, which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection of the respiratory tract, was first reported in Wuhan, China in December 2019 and declared a pandemic on March 11, 2020.2–4 According to the World Health Organization, SARS-CoV-2 accounted for 262 million infections and 5.2 million deaths globally as of December 1, 2021.5 The average incubation period of SARS-CoV-2 is about 3–9 days.6 Clinical manifestations appear after the incubation period and vary from asymptomatic to severe respiratory disease and life-threatening multiple organ failure.1,7\n\nUp to 80% of cases exhibit mild localized symptoms in the upper respiratory tract (URT) accompanied by non-specific symptoms, especially fever and cough.6,8,9 Virus transmission in about 44% of cases occurs before the onset of symptoms.10 About 18% of cases are asymptomatic but can transmit the virus to others.6 It is difficult to distinguish between truly asymptomatic and pre-symptomatic patients because of the lack of visible symptoms.11 Asymptomatic patients and those with mild symptoms greatly contribute to the transmission of SARS-CoV-2 because of the lack of awareness of an active infection, reluctance to seek medical care, and poor understanding of transmission prevention.12\n\nSARS-CoV-2 is mainly transmitted by inhalation of respiratory droplets or contact with contaminated surfaces.7,13 SARS-CoV-2 rapidly replicates in the URT, producing large numbers of pathogenic progeny at an early stage of disease development that can be transmitted by respiratory droplets.1,14 Further replication in the lower respiratory tract leads to the development of lung disease.15,16 Saliva contains high amounts of SARS-CoV-2 that enters through the lower respiratory tract, URT, or infected salivary glands and acts as a potential source of virus transmission in the oral cavity.17–20\n\nReducing the amount of SARS-CoV-2 in the URT and oral cavity in the early stages of disease is important to prevent virus transmission and reduce the severity and progression of disease.18,21,22 Various active ingredients of mouthwash have virucidal activities that disrupt the lipid envelope of the virus.23 Active ingredients of mouthwash recommended before medical procedures in the oral cavity include 21%–26% ethanol with essential oils, chlorhexidine, povidone iodine (PI), hydrogen peroxide (H2O2), cetylpyridinium chloride, chlorinated water, and hypertonic saline.23–25 The American Dental Association (ADA) and the Centers for Disease Control and Prevention (CDC) recommend gargling with mouthwash containing 0.2% PI or 1.5% H2O2 before medical procedures in the oral cavity because SARS-CoV-2 is susceptible to oxidation.26,27 Current recommendations include mouth rinsing and gargling with mouthwash for 30 s in the oral cavity followed by 30 s in the back of the throat.24\n\nThe objective of this study was to semi-quantitatively evaluate the effect of mouth rinsing and gargling with mouthwash containing various concentrations of PI and H2O2 on the amount of SARS-CoV-2 in the URT using the cycle threshold (CT) value during real-time reverse transcription polymerase chain reaction (RT-PCR) in asymptomatic and mildly symptomatic patients.\n\n\n2. Methods\n\nThe cohort of this single-blind randomized controlled trial included four intervention groups and one control group. The study protocol was approved by the Health Research Ethics Committee of Persahabatan Central General Hospital (CGH) with registration number: 68/KEPK-RSUPP/06/2021. This study has been retrospectively registered in the International Standard Randomized Controlled Trial Number (ISRCTN) registry on the 3rd February 2022 with registered number ISRCTN18356379 (https://doi.org/10.1186/ISRCTN18356379).\n\nIn total, 69 patients infected with SARS-CoV-2 were recruited from Persahabatan CGH, a national COVID-19 referral center hospital, from July to September 2021. SARS-CoV-2 infection was confirmed by RT-PCR. The sample size was calculated using GPower (RRID:SCR_013726) 3.1.9.2 software (https://www.psychologie.hhu.de/arbeitsgruppen/allgemeine-psychologie-und-arbeitspsychologie/gpower). The inclusion criteria were age 19–60 years, CT values ≤ 30, asymptomatic or mild symptoms, and diagnosis of COVID-19 within 3 days prior to recruitment. The exclusion criteria consisted of refusal to participate, comorbid disease, thyroid disease, pregnancy, routine use lithium drugs, radioactive iodine treatment, and allergy to PI and H2O2. All subjects signed an informed consent form after being provided with information regarding the study objective and possible risks and benefits of gargling with mouthwash. The subjects were randomly assigned by one researcher to one of the four treatment groups or the control group using a simple randomization method where each research subject was assigned to a group with specific order: 1% PI, 3% H2O2, control, 0.5% PI, and 1.5% H2O2 consecutively. This study is single blinded where only the research subjects were blinded from their group allocation.\n\nThe subjects were instructed on how to rinse and gargle with mouthwash via video conference and supplied with repackaged mouthwash. The 1% PI group rinsed their mouth with BETADINE® Mouthwash and Gargle solution (Napp Pharmaceuticals Ltd., United Kingdom). The 3% H2O2 group rinsed their mouth with OneMed™ solution (Inti Medicom Retailindo, Indonesia). The group treated with 0.5% iodine peroxide and 1.5% H2O2 rinsed their mouth with a diluted solution of 1% PI BETADINE® Mouthwash and Gargle solution and 3% H2O2 OneMed™ added with sterile distilled water in accordance with the formula Volume1 × Concentration1 = Volume2 × Concentration2. The control group was instructed to rinse their mouth with AQUA™ mineral water (Danone, France). The subjects were instructed to rinse their mouth with 15 mL of mouthwash for 30 s in the oral cavity followed by gargling 30 s in the back of throat three times per day for 5 days. Mouth rinsing and gargling with mouthwash were conducted in a self-isolation room and monitored via video conference.\n\nSamples were collected with oropharyngeal and nasopharyngeal swabs using a disposable virus sampling tube (Baicare Biotechnology Co., Ltd., China) by a trained staff member of Persahabatan CGH on postprocedural days 1, 3, and 5 after gargling with mouthwash. The samples were appropriately packaged, labeled, and sent to the Department of Microbiology for RT-PCR analysis. The specimens were vortexed with an LMS® UZUSIO VTX-3000L vortex mixer (LMS Co., Ltd., Japan) for 20 s and allowed to stand for 15 min. Then, 250 μL of MagNA Pure 96 extraction reagent (Roche Life Science, Germany) were loaded into the cartridge and mixed with 200 μL of the specimen. The cartridge was loaded into the Rosche MagNA Pure 96 instrument for sample extraction. The reaction mix of the mBioCoV-19 RT-PCR Kit (Bio Farma, Indonesia) was used to detect the open reading frame 1b and RNA-dependent RNA polymerase genes. In brief, 15 μL of reaction mix were added to each well and mixed with 5 μL of the extracted specimen. CT values were obtained automatically with an Exicycler™ 96 (Ver.4) (RRID:SCR_022144) Real-Time Quantitative Thermal Block (Bioneer Corporation, South Korea) (https://us.bioneer.com/products/instrument/Exicycler96_V4-overview.aspx) upon detection of SARS-CoV-2 genetic material.\n\nCT values of the open reading frame 1b target gene were analyzed using IBM SPSS Statistics for Windows, version 22.0. (IBM Corporation, USA) (RRID:SCR_016479) (https://www.ibm.com/products/spss-statistics). The data were not normally distributed; thus a nonparametric test was used for analysis. Repeated measurements of each group were analyzed using the Friedman nonparametric test. Comparisons between groups from baseline (day 0) to postprocedural days 1, 3, and 5 were conducted using the Kruskal–Wallis nonparametric test. A probability (p) value of <0.05 was considered statistically significant.\n\n\n3. Results\n\nThe total size estimation was 75 patients with n=15 for each group. However, due to the significant decrease in new COVID-19 cases in Indonesia, only 69 patients were recruited from July to September 2021, as it was difficult to recruit subjects who met the inclusion criteria (Figure 1). Numbers of participants for each group were 1% PI = 15, 0.5% PI = 12, 3% H2O2 = 15, 1.5% H2O2 = 12, and control = 15.\n\nOf the 69 patients, 39 (56.5%) were male and 30 (43.5%) were female. The average age of the subjects was 32.8 (range, 25–44) years. Cough (66.7%) was the most common early symptom of COVID-19 (Table 1). As shown in Table 2, the mean CT values increased in each group from baseline (day 0) to postprocedural days 1, 3, and 5. The results of the Friedman test showed significant differences in CT values among the groups. Post-hoc analysis (Table 3) showed significant differences in most of the CT values with the exceptions of between days 1 and 3 in the 0.5% PI and 3% and 1.5% H2O2 groups and between days 3 and 5 in the 3% H2O2 and control groups. Comparisons of CT values among the groups using the Kruskal–Wallis test showed no significant differences due to the increases in CT values of each group.\n\n p < 0.05.\n\n* p < 0.05.\n\n\n4. Discussion\n\nSARS-CoV-2 infection can spread rapidly and cause severe morbidity and mortality.28 The oral cavity and URT have high viral loads and are potential sources of SARS-CoV-2.29 Kim et al.30 found that viral shedding was high in the URT from the prodromal phase to day 5 after symptom onset. Yoon et al.19 found that the viral load was greater in the saliva than the oropharynx in the early stages of disease. A high viral load in saliva can originate from the respiratory tract or secretions from infected salivary glands.18 Chen et al.20 reported the expression of angiotensin converting enzyme 2, a cell receptor for SARS-CoV-2, in the salivary glands, suggesting possible SARS-CoV-2 infection of the salivary glands.\n\nReducing the amounts of SARS-CoV-2 in the URT and oral cavity is important to prevent virus transmission.21,22 The ADA and the CDC recommend preprocedural mouth rinsing and gargling with mouthwash containing H2O2 or PI because SARS-CoV-2 is susceptible to oxidation.26,27 PI consists of iodine and the water-soluble polymer polyvinylpyrrolidone. Iodine released from polyvinylpyrrolidone penetrates microorganisms and causes oxidation of amino acids and nucleic acids, resulting in disruption of metabolic pathways and cell membranes.17,25 Frank et al.21 claimed that mouthwash containing 2.5% PI is safe to use in the oral cavity for up to 5 months.\n\nAn in vitro study by Eggers et al.31 reported that 0.023% PI exhibited virucidal activities against betacoronaviruses, including SARS-CoV and Middle East respiratory syndrome–related coronavirus (MERS-CoV), after contact for 15 s. The use of mouthwash containing 1% PI to reduce the load of SARS-CoV-2 was also confirmed by an in vitro study conducted by Anderson et al.3 which reported that 1% PI reduced the load of SARS-CoV-2 by more than 99.99% or more than 4log10 after 30 s of contact. An in vitro study by Hassandarvish et al.32 reported that 1% PI reduced of the load of SARS-CoV-2 by more than 5log10 after exposure for 15, 30, and 60 s. An in vitro study by Bidra et al.29 found that PI at 0.5%, 1.25%, and 1.5% fully inactivated SARS-CoV-2 after contact for 15 and 30 s. The results of the present study showed that mouth rinsing and gargling with mouthwash containing 0.5% or 1% PI increased the CT values on postprocedural days 1, 3, and 5.\n\nThe virucidal action of H2O2 involves the release of oxygen free radicals that disrupt lipid membranes.17 O’Donnell et al.23 suggested that the target of H2O2 is the lipid envelope of SARS-CoV-2. The swine flu, rubella, rabies, corona, and influenza viruses are also sensitive to H2O2.24,33 Caruso et al.33 claimed that mouthwash containing 3% H2O2 was safe for mucous membranes after 6 months of use. An in vitro study by Kampf et al.34 reported that H2O2 at a concentration of at least 0.5% effectively inactivated SARS-CoV and MERS-CoV on the surface of inanimate objects in 1 min. The results of the present study showed that mouth rinsing and gargling with mouthwash containing 1.5% and 3% H2O2 increased the CT values on postprocedural days 1, 3, and 5. In contrast with an in vitro study by Bidra et al.,29 which reported that mouthwash containing 1.5% and 3% H2O2 had minimal virucidal activity after contact for 30 s, Gottsauner et al.35 showed that mouth rinsing and gargling with mouthwash containing 1% H2O2 in the mouth and back of the throat for 30 s did not reduce the load of SARS-CoV-2. The difference in the results of the present study and the report by Gottsauner et al.35 was likely due to differences in H2O2 concentrations.\n\nVergara-Buenaventura et al.24 recommended mouth rinsing and gargling with mouthwash for 30 s in the oral cavity and 30 s at the back of the throat. The control group in the present study gargled with water, which surprisingly increased the CT values on postprocedural days 1, 3, and 5. Flushing the URT with fluids can clear excess mucus and mechanically reduce the viral load in the respiratory tract with impaired mucociliary function.36–38 A study by Koparal et al.39 found a delay in mucociliary clearance time in COVID-19 patients as compared to healthy individuals. Robinot et al.40 reported that SARS-CoV-2 infection in ciliated epithelial cells causes loss of ciliary motility, short cilia deformity, and impaired mucociliary clearance, thereby increasing the spread of SARS-CoV-2 in the respiratory tract and increasing the risk of secondary infection in COVID-19 patients. Whirling water can mechanically wash out the virus and virus-infected cells from the oral cavity and pharynx.41 A study by Satomura et al.41 reported that mouth rinsing and gargling with tap water three times per day effectively reduced the incidence of URT infections by 36%.\n\nSeveral current guidelines regarding the management of discharge of COVID-19 patients are based on the timing from onset of symptoms and a CT value > 30.42 CT values are often associated with the risk of SARS-CoV-2 transmission.43 Patients with high CT values are reportedly incapable of transmitting infectious virus particles.44 A study by Hiroi et al.45 reported that a CT value >30 indicates a very low infectious virus titer and a lower risk of infecting others. Scola et al.46 concluded that patients with CT values ≥ 34 are incapable of transmitting SARS-CoV-2 and could be discharged from the infectious disease ward. The entire cohort of the present showed an increase in mean CT score of 34 on day 3 after gargling.\n\nThis study may be limited by its limited and uneven sample number due to the significant decrease in new COVID-19 cases in Indonesia, thus only 69 patients were found to fulfil the inclusion criteria during the recruitment period, with two groups (0.5% PI and 1.5% H2O2) had only 12 samples per group where others had 15 per group.\n\n\n5. Conclusion\n\nMouth rinsing and gargling with mouthwash containing 1% PI, 0.5% PI, 3% H2O2, or 1.5% H2O2 and water increased the CT values. The results of this study suggest that rinsing for 30 s in the oral cavity and 30 s at the back of the throat three times per day for at least 3 days preoperatively as a new preoperative protocol in oral and maxillofacial surgery and other medical procedures in the oral cavity.\n\n\nData availability\n\nZenodo: [Effects of Mouthrinsing and Gargling to CT Values of SARS CoV-2 DATASET]. https://doi.org/10.5281/zenodo.6358988 [Version 1.0].\n\nThe project contains the following underlying data:\n\n‐ [informed-consent-back.jpg] (informed consent form page 2).\n\n‐ [informed-consent-front.jpg] (informed consent form page 1).\n\n‐ [Metadata (Eng).xlsx] (metadata to read the data file)\n\n‐ [Reseach_Data_Revised.pdf] (raw data of each research subject)\n\n‐ [research-information-form.jpg] (information sheet for research participants)\n\n‐ [research-subject-screening-form.jpg] (form filled by the research subject on screening)\n\n‐ [subject-consent-form.jpg] (consent form signed by research participants)\n\n\nReporting guidelines\n\nZenodo: CONSORT checklist for ‘The effects of mouth rinsing and gargling with mouthwash containing povidone-iodine and hydrogen peroxide on the cycle threshold value of Severe Acute Respiratory Syndrome Coronavirus 2: A randomized controlled trial of asymptomatic and mildly symptomatic patients’. https://doi.org/10.5281/zenodo.6409184 [Version 1].\n\nData are available under the terms of the Creative Commons Attribution 4.0 International (CC BY 4.0).\n\n\nAuthor contributions\n\n\n\n• Lilies Dwi Sulistyani conceived and designed the analysis, verified the analytical methods, gaining resources, supervised the study, in charge of overall direction and planning, wrote and revised the paper\n\n• Vera Julia conceived and designed the analysis, verified the analytical methods, supervised the study, wrote and revised the paper\n\n• Andrianto Soeprapto performed the experiment and analysis, drafted and revised the paper\n\n• Rumartha Putri Swari performed the experiment and analysis, drafted the paper\n\n• Febriadi Rosmanato performed the experiment and analysis, drafted the paper\n\n• Budi Haryanto verified the analytical methods, gaining resources, supervised the study\n\n• Cahyarini verified the analytical methods, supervised the study\n\n• Rinaldi Panjaitan verified the analytical methods, supervised the study\n\n• Diah Ayu Maharani designed and verified the statistics", "appendix": "Acknowledgements\n\nThe authors would like to thank Universitas Indonesia, Persahabatan Central General Hospital, and Ministry of Education, Culture, Research, and Technology of the Republic of Indonesia for the support.\n\n\nReferences\n\nAkhter S, Akhtar S: Emerging Coronavirus Diseases and Future Perspectives. 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PubMed Abstract \| Publisher Full Text\n\nTo KK, Tsang OT, Yip CC, et al.: Consistent Detection of 2019 Novel Coronavirus in Saliva. Clin Infect Dis. 2020; 71: 841–843. PubMed Abstract \| Publisher Full Text\n\nYoon JG, Yoon J, Song JY, et al.: Clinical Significance of A High SARS-CoV-2 Viral Load in the Saliva. J Korean Med Sci. 2020; 35: e195. PubMed Abstract \| Publisher Full Text\n\nChen L, Zhao J, Peng J, et al.: Detection of SARS-CoV-2 in Saliva and Characterization of Oral Symptoms in COVID-19 Patients. Cell Prolif. 2020; 53: e12923. Publisher Full Text\n\nFrank S, Capriotti J, Brown SM, et al.: Povidone-Iodine Use in Sinonasal and Oral Cavities: A Review of Safety in the COVID-19 Era. Ear Nose Throat J. 2020; 99: 586–593. PubMed Abstract \| Publisher Full Text\n\nTsai CL, Wu PC: Possible Beneficial Role of Throat Gargling in the Coronavirus Disease Pandemic. Public Health. 2020; 185: 45–46. PubMed Abstract \| Publisher Full Text\n\nDonnell VBO, Thomas D, Stanton R, et al.: Potential Role of Oral Rinses Targeting the Viral Lipid Envelope in SARS-CoV-2 Infection. Function. 2020; 1: 1–12.\n\nVergara-Buenaventura A, Castro-Ruiz C: Use of Mouthwashes Against COVID-19 in Dentistry. Br J Oral Maxillofac Surg. 2020; 58: 924–927. Publisher Full Text\n\nMoosavi M-S, Aminishakib P, Ansari M: Antiviral Mouthwashes: Possible Benefit for COVID-19 With Evidence-Based Approach. J Oral Microbiol. 2020; 12: 1794363. PubMed Abstract \| Publisher Full Text\n\nAmerican Dental Association: ADA Interim Guidance for Minimizing Risk of COVID-19 Transmission.2020. (accessed 21 Dec 2020).\n\nCenters for Disease Control and Prevention: Interim Infection Prevention and Control Guidance for Dental Settings During the COVID- 19 Response.2020. (accessed 21 Dec 2020).\n\nZou L, Ruan F, Huang M, et al.: SARS-CoV-2 Viral Load in Upper Respiratory Specimens of Infected Patients. N Engl J Med. 2020; 382: 1177–1179. Publisher Full Text\n\nBidra AS, Pelletier JS, Westover JB, et al.: Comparison of in vitro Inactivation of SARS CoV-2 With Hydrogen Peroxide and Povidone- Iodine Oral Antiseptic Rinses. J Prosthodont. 2020; 29: 599–603. Publisher Full Text\n\nKim ES, Chin BS, Kang CK, et al.: Clinical Course and Outcomes of Patients With Severe Acute Respiratory Syndrome Coronavirus 2 Infection: A Preliminary Report of the First 28 Patients from the Korean Cohort Study on COVID-19. J Korean Med Sci. 2020; 35: 1–12. Publisher Full Text\n\nEggers M, Koburger-Janssen T, Eickmann M, et al.: In Vitro Bactericidal and Virucidal Efficacy of Povidone-Iodine Gargle/Mouthwash Against Respiratory and Oral Tract Pathogens. Infect Dis Ther. 2018; 7: 249–259. PubMed Abstract \| Publisher Full Text\n\nHassandarvish P, Tiong V, Sazaly AB, et al.: Povidone Iodine Gargle and Mouthwash. Br Dent J. 2020; 228: 900. Publisher Full Text\n\nCaruso AA, Del Prete A, Lazzarino AI: Hydrogen Peroxide and Viral Infections: A Literature Review With Research Hypothesis Definition in Relation to the Current Covid-19 Pandemic. Med Hypo. 2020; 144: 109910. PubMed Abstract \| Publisher Full Text\n\nKampf G, Todt D, Pfaender S, et al.: Persistence of Coronaviruses on Inanimate Surfaces and its Inactivation With Biocidal Agents. J Hosp Infect. 2020; 104: 246–251. Publisher Full Text\n\nGottsauner MJ, Michaelides I, Schmidt B, et al.: A Prospective Clinical Pilot Study on the Effects of a Hydrogen Peroxide Mouthrinse on the Intraoral Viral Load of SARS-CoV-2. Clin Oral Investig. 2020; 24: 3707–3713. PubMed Abstract \| Publisher Full Text\n\nCasale M, Rinaldi V, Sabatino L, et al.: Could Nasal Irrigation and Oral Rinse Reduce the Risk for COVID-19 Infection? Int J Immunopathol Pharmacol. 2020; 34: 205873842094175–205873842094173. Publisher Full Text\n\nYanti B, Maulana I, Sofiana D, et al.: Nasal Rinse and Gargling as an Effort in Preventing COVID-19 Infection With Islamic Approach - A Literature Review. Bali Med J. 2021; 10: 503–506. Publisher Full Text\n\nSingh S, Sharma N, Singh U, et al.: Nasopharyngeal Wash in Preventing and Treating Upper Respiratory Tract Infections: Could It Prevent COVID-19? Lung India. 2020; 37: 246–251. PubMed Abstract \| Publisher Full Text\n\nKoparal M, Kurt E, Altuntas EE, et al.: Assessment of Mucociliary Clearance as an Indicator of Nasal Function in Patients With COVID-19: A Cross-Sectional Study. Eur Arch Otorhinolaryngol. 2021; 278: 1863–1868. PubMed Abstract \| Publisher Full Text\n\nRobinot R, Hubert M, Melo De GD, et al.: SARS-CoV-2 Infection Induces the Dedifferentiation of Multiciliated Cells and Impairs Mucociliary Clearance. Nat Commun. 2021; 12: 4354. PubMed Abstract \| Publisher Full Text\n\nSatomura K, Kitamura T, Kawamura T, et al.: Prevention of Upper Respiratory Tract Infections by Gargling: A Randomized Trial. Am J Prev Med. 2005; 29: 302–307. Publisher Full Text\n\nBuchta C, Görzer I, Chiba P, et al.: Variability of Cycle Threshold Values in an External Quality Assessment Scheme for Detection of the SARS-CoV-2 Virus Genome by RT-PCR. Clin Chem Lab Med. 2021; 59: 987–994. PubMed Abstract \| Publisher Full Text\n\nPlatten M, Hoffmann D, Grosser R, et al.: SARS-CoV-2, CT-Values, and Infectivity - Conclusions to be Drawn From Side Observations. Viruses. 2021; 13: 1459. Publisher Full Text\n\nStang A, Robers J, Schonert B, et al.: The Performance of The SARS-CoV-2 RT-PCR Test as a Tool for Detecting SARS-CoV-2 Infection in the Population. J Infect. 2021; 83: 237–279. PubMed Abstract \| Publisher Full Text\n\nHiroi S, Kubota-Koketsu R, Sasaki T, et al.: Infectivity Assay for Detection of SARS-CoV-2 in Samples from Patients With COVID-19. J Med Virol. 2021; 93: 5917–5923. PubMed Abstract \| Publisher Full Text\n\nLa Scola B, Bideau Le M, Andreani J, et al.: Viral RNA Load as Determined by Cell Culture as a Management Tool for Discharge of SARS-CoV-2 Patients from Infectious Disease Wards. Eur J Clin Microbiol Infect Dis. 2020; 39: 1059–1061. PubMed Abstract \| Publisher Full Text" }	[ { "id": "154813", "date": "06 Dec 2022", "name": "Muhammad Ruslin", "expertise": [ "Reviewer Expertise dentistry", "oral and maxillofacial surgery" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nI appreciate the authors for presenting \"The effects of mouth rinsing and gargling with mouthwash containing povidone-iodine and hydrogen peroxide on the cycle threshold value of Severe Acute Respiratory Syndrome Coronavirus 2: A randomized controlled trial of asymptomatic and mildly symptomatic patients\". This will add more information to the existing literature on COVID-19-related cases.\nHowever, there are some mismatches between the conclusions and the data presented. In the whole manuscript, the authors never mentioned cases specific to oral and maxillofacial surgery; how come they finally recommend this rinsing solution/method for oral and maxillofacial surgery? From my point of view, it would be better to draw a specific conclusion related to the Covid-19 patients, since this is your main issue in the article. Based on the results of your study, what can you recommend for these patients?\n(please see the conclusion part, the second sentence, the sentence does not sound appropriate, please modify)\n\nIs the work 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": "9287", "date": "01 Jul 2024", "name": "Lilies Dwi Sulistyani", "role": "Author Response", "response": "Thank you Prof Muhammad Ruslin. We appreciate your review and suggestions. In the introduction, we mentioned that this study departed from a large number of asymptomatic COVID-19 patients and mild symptoms which made a significant contribution to the spread of SARS-CoV-2 both to medical personnel and the people around the patient because there were no visible signs of active infection. These patients are often difficult to distinguish from healthy people, so there is a lack of awareness from health workers, especially those who perform procedures in the oral cavity, to apply transmission prevention protocols to these patients. We did not use samples for specific cases in the field of oral and maxillofacial surgery but instead used asymptomatic and mildly symptomatic COVID-19 patients. Reducing the amount of virus in the oral cavity and back of the throat before the medical procedure with mouth rinsing and gargling protocol is easy to perform. It can be applied in the field of oral and maxillofacial surgery. Not only oral and maxillofacial surgeons, but colleagues such as anesthesiologists, ENT, and others who perform any medical procedures in the oral cavity can also apply this mouth rinsing and gargling protocol as we stated in the second sentence of the conclusion." }, { "c_id": "11461", "date": "01 Jul 2024", "name": "Lilies Dwi Sulistyani", "role": "Author Response", "response": "Hi Prof Ruslin. Thank you for reviewing the article. I have modified the second sentence in the conclusion as per your suggestion." } ] }, { "id": "257581", "date": "02 Apr 2024", "name": "Rosalina Tjandrawinata", "expertise": [ "Reviewer Expertise Dental materials" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nI learn the authors’ paper \"The effects of mouth rinsing and gargling with mouthwash containing povidone-iodine and hydrogen peroxide on the cycle threshold value of Severe Acute Respiratory Syndrome Coronavirus 2: A randomized controlled trial of asymptomatic and mildly symptomatic patients\" is very interesting and add more information for COVID-19-related cases. However, there are some questions about the effectivity of different concentration, which would be very useful. Statistical analysis should be taken to analyse which mouthwash is the most effective mouthwash for the cases. The conclusion is “that rinsing for 30 s in the oral cavity and 30 s at the back of the throat three times per day for at least 3 days preoperatively as a new preoperative protocol in oral and maxillofacial surgery and other medical procedures in the oral cavity”; while the statistics (Table 3) showed that both concentration of Hydrogen Peroxide and PI 0.5% mouthwash do not have significant difference between 1 day and 3 days and that CT value is already > 30. So, that 1-day rinsing would be effective enough for reducing the virus. It is quite interesting that your data (Table 2) showed PI 0.5% increase CT value similar or more than PI 1%. The most interesting condition is rinsing with mineral water (control group) is also rising the CT value, similar to the treated group. So, should we use mouth rinsing instead of mineral water if we can get similar result? It should be reconfirmed by authors. It will be very useful if the authors compare the difference among the mouth rinses and the control group.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [ { "c_id": "11462", "date": "29 Apr 2024", "name": "Lilies Dwi Sulistyani", "role": "Author Response", "response": "Thank you to Rosalina Tjandrawinata. We appreciate your review and questions. Mouth rinsing and gargling for 1 day shows effectiveness in reducing the number of viruses as seen from the increase in CT values. Based on research by Scola BL et al (Viral RNA load as determined by cell culture as a management tool for discharge of SARS-CoV-2 patients from infectious disease wards) which states that CT values equal or above 34 do not excrete infectious viral particles. Our research data showed an increase in mean CT value equal or above 34 for the five groups after mouth rinsing and gargling for 3 days. Therefore we recommend mouth rinsing and gargling at least 3 days. Surprisingly we found that mouth rinsing and gargling with mineral water could increase the CT values as well. This is due to whirling water can mechanically wash out the virus and virus-infected cells from the oral cavity and pharynx. Mouth rinsing and gargling with mouthwash can disrupt the balance of flora in the oral cavity, therefore mouth rinsing and gargling with mineral water can be an alternative gargling procedure to prevent the attachment of the SARS-CoV-2 virus at an early stage that is safe for long-term use." }, { "c_id": "11652", "date": "30 May 2024", "name": "Rosalina Tjandrawinata", "role": "Reviewer Response", "response": "Dear doctors, Thank you for the explanation. Now it is clear that whirling water can mechanically wash out the virus and virus-infected cells from the oral cavity and pharynx, and it is clearly shown in Table 2 that the content of the liquid does not make any significant difference to the result." } ] } ]	1	https://f1000research.com/articles/11-1238
https://f1000research.com/articles/12-1297/v1	10 Oct 23	{ "type": "Research Article", "title": "How useful is the tuberculin skin test for the detection of active tuberculosis: Assessing diagnostic accuracy metrics and selection of best cut-off value through a large Tunisian multicenter case-control study", "authors": [ "Mariem Nouira", "Hazem Ben Rayana", "Samir Ennigrou", "Hazem Ben Rayana", "Samir Ennigrou" ], "abstract": "Background and aim:\nDuring the past decade, the frequency of extrapulmonary forms of tuberculosis (TB) has increased. These forms are often miss-diagnosed. This statement of the TB epidemiological profile modification, conduct us to reflect about the utility of the Tuberculin Skin Test (TST) in active TB detection. This study aimed to evaluate the diagnostic accuracy performance of the TST for active tuberculosis detection.\nMethods:\nThis was a case-control, multicenter study conducted in 11 anti-TB centers in Tunisia (June-November2014). The cases were adults aged between 18 and 55 years with newly diagnosed and confirmed tuberculosis. Controls were free from tuberculosis. A data collection sheet was filled out and a TST was performed for each participant. Diagnostic accuracy measures of TST were estimated using Receiver Operating Curve (ROC) curve and Area Under Curve (AUC) to estimate sensitivity and specificity of a determined cut-off point.\nResults:\nOverall, 1050 patients were enrolled, composed of 336 cases and 714 controls. The mean age was 38.3±11.8 years for cases and 33.6±11 years for controls. The mean diameter of the TST induration was significantly higher among cases than controls (13.7mm vs.6.2mm; p=10-6). AUC was 0.789 [95% CI: 0.758-0.819; p=0.01], corresponding to a moderate discriminating performance for this test. The most discriminative cut-off value of the TST, which was associated with the best sensitivity (73.7%) and specificity (76.6%) couple was\n\n≥ 11 mm with a Youden index of 0.503. Positive and Negative predictive values were 3.11% and 99.52%, respectively.\nConclusions:\nTST could be a useful tool used for active tuberculosis detection, with a moderate global performance and accepted sensitivity and specificity at the cut-off point of 11 mm. However, it cannot be considered as a gold standard test due to its multiple disadvantages.", "keywords": [ "tuberculosis", "tuberculin skin test", "diagnostic accuracy", "sensitivity", "specificity", "Predictive Value of Tests", "Receiver operating characteristic curve", "case-control study" ], "content": "Introduction\n\nThe tuberculosis (TB) epidemic poses a serious public health problem, with high associated morbidity and mortality rates worldwide.1 It has been estimated that almost a quarter of the total world’s population is infected with latent TB infection and approximately 10 million have developed active TB, with about 1.6 million attributed deaths in 2021, all over the world.2\n\nAccording to the World Health Organization (WHO) estimations, diagnosing and treating TB saved 66 million lives between 2000 and 2020.2 Therefore, there is a need to improve the TB diagnostic procedure. It is a priority requirement to dispose of an accurate diagnostic tool for early detection and appropriate treatment, and set up timely control measures to limit the spread of the infection.3 However, there is no international agreement about a gold-standard test for detection of active nor latent TB.3,4\n\nThe detection of active TB using a simple, rapid, and inexpensive test, like the tuberculin skin test (TST), in diagnosing TB, may help to guide easier clinical diagnosis of disease.\n\nThe TST or Mantoux test is an old, widely used test for TB infection screening and for estimating the delayed hypersensitivity reaction induced by BCG vaccination.5,6\n\nOver the past decade, the frequency of extrapulmonary forms of TB has increased.7,8 These forms, especially lymph node TB type, are often miss-diagnosed, due to unspecific symptoms, and pose a diagnostic challenge for clinicians, requiring the use of invasive methods for diagnostic confirmation.9,10\n\nTunisia is a country of intermediate TB endemicity with an estimated incidence of 29/100,000 inhabitants in 2017. Pulmonary TB constituted 38% of all forms of the disease in 2017, while extra-pulmonary TB represents 62% of cases. The frequency of lymph node forms is relatively high, with a constant increase from 2.3/100,000 in 1993 to 18/100,000 in 2017.11\n\nThese TB epidemiological profile modifications in Tunisia (the increase in the frequency of lymph node forms at the expense of pulmonary forms) and all arguments cited above, leads us to reflect on the utility and the performance of the TST for active TB detection.\n\nThe utility of the TST for the detection of latent TB infection was largely discussed and debated in the literature,12,13 but its utility in diagnosing active TB has not been discussed enough in previous studies.\n\nTherefore, we aimed, through this multicenter case-control study, to evaluate the diagnostic accuracy of the TST for the diagnosis of active TB, and to select its best cut-off value, using the ROC curve and Fagan’s Nomogram methodology.\n\n\nMethods\n\nThis was a case-control, multicenter study for a purpose of a diagnostic test evaluation, conducted in 11 anti-TB centers in Tunisia, during the period from June to November 2014.\n\nInclusion and exclusion criteria\n\nIncluded TB cases were adult patients aged between 18 and 55 years who were newly diagnosed with TB. They had confirmed TB diagnosis (pulmonary and extra-pulmonary forms of tuberculosis) based on a range of anamnestic, clinical, chest X-ray, bacteriological arguments. They were recruited from 11 anti-TB centers from the north, center and south of Tunisia (Ariana, Tunis, Sfax, Gafsa, Ben Arous, Bizerte, Sousse, Kairouan, Sidi Bouzid, Kasserine, Tataouine), at the first-time delivery of their anti-TB treatment.\n\nControls were recruited from basic health centers and from district hospitals, located in the same geographical zone of the anti-TB centers (in which cases were recruited) and during the same study period. The gender distribution frequency was approximately the same as that of TB cases. Overall, the same proportion of men and women in TB cases and in controls was respected. All the included controls had no clinically manifested active TB; they did not present any respiratory or extra-respiratory symptoms that could be of TB origin.\n\nExclusion criteria\n\nWere excluded from the study:\n\n‐ TB cases already treated for pulmonary or extra-pulmonary TB.\n\n‐ TB cases and controls with a pathological condition that may lead to tuberculin anergy: acute viral infections (measles, infectious mononucleosis, influenza), lymphomas, neoplastic pathologies, sarcoidosis, severe bacterial infection, HIV infection, among others.\n\n‐ TB cases and controls having undergone immunosuppressive treatment, corticosteroid therapy for more than one month or vaccination with live attenuated vaccines two months prior to the test.\n\n‐ TB cases and controls with a history of known allergic reaction to one of the components of TST or during a previous administration.\n\nData was collected using a standardized questionnaire for all participants including information regarding demographic variables (age, sex, educational level), as well as medical history of any pathological condition that may lead to tuberculin anergy, the status of participant (case or control) and the type of TB infection for cases (pulmonary or extra-pulmonary), as well as the date of administration and lecture of the TST result.\n\nTuberculin skin testing (TST)\n\nIt should be noted that the TST was performed for all participants, cases, and controls, not as an investigator-mandated intervention, but as part of the normal process of diagnosing the etiology of their disease.\n\nThe test was performed using the Mantoux method, in all participants (cases and controls) by injecting 0.1 mL of tuberculin solution (tuberculin PPD [Purified Protein Derivative RT23 from Copenhagen]), strictly intradermally, on the forearm away from any other scar.6\n\nThe TST results were read 72 hours after administration by the same trained investigator. Diameter of induration was determined by calculating the average of the transverse and longitudinal diameter of induration (in mm).6\n\nContinuous and categorical variables were summarized using the mean (± standard deviation) and relative frequencies (expressed into percentage), respectively. Pearson’s Chi-square test and Student’s T test were used for comparing two percentages or two means for independent samples, respectively. For all statistical tests, the significance level adopted was 0.05. All statistical analyses were performed using SPSS version 23.0 software.\n\nSensitivity and specificity\n\nTo assess the performance of the TST, we first calculated the sensitivity and specificity of the TST induration diameter as well as the Youden index for different possible thresholds (from a diameter of TST ≥ 5 mm to a TST diameter ≥ 15 mm).\n\nThe calculation of the 95% confidence intervals (95% CI) of the sensitivity and specificity was done using an Excel calculator and using the properties of the exact binomial distribution.\n\nSensitivity (Se) was defined as the proportion (ranging from 0 to 1) of tuberculosis cases who tested positive (true positives = TP) with TST. The proportion of cases which were not identified using TST were false negative (FN) results.14\n\nSpecificity (Sp) was defined as the proportion (ranging from 0 to 1) of controls who tested negative for the disease (true negatives = TN) with TST. The proportion of controls which were tested positive using TST were false positive (FP) results.14,15\n\nThe two intrinsic qualities of the test, sensitivity, and specificity, were aggregated into an index, known as the Youden Index noted J such that: J = (Se + Sp) – 1.\n\nYouden index varies between -1 and +1; a value less than or equal to 0 reflects the diagnostic ineffectiveness of the test. The test performance is better when its Youden index is close to 1.16\n\nPositive and negative predictive values (PPV and NPV) (or post-test probabilities) of TST were also determined for different possible TST thresholds by two different methods, using the properties of Bayes’ theorem17 and using Fagan’s nomogram graph.18\n\nThe predictive values were deducted from Fagan’s nomogram graph based on the TB prevalence (or pre-test probability) according to TB patients’ data from three university hospitals in Tunis, Tunisia (The Rabta Hospital, Charles Nicolle Hospital and Abderrahmane Mami hospital). The estimated TB prevalence was around 1% in 2016.\n\nThe positive and negative likelihood ratios (LR) were also determined for different possible thresholds of the TST, and their 95% confidence intervals (95% CI) were calculated using the Excel calculator.\n\nThe positive LR (varies from 1 to +∞) indicates that the TST a test is more discriminating tuberculosis cases from non-cases when it is far from 1 and the specificity approaches 1.\n\nThe negative LR (varies from 0 to 1) indicates that the TST is better able to discriminate TB cases from non-cases when it is closer to 0 and the sensitivity approaches to 1.\n\nROC and area under the curve (AUC)\n\nThe overall discriminative performance of the TST was evaluated using the ROC curve,19 to determine the optimal cut-off value of the best couple (sensitivity, specificity).\n\nWe established a ROC curve, first for all participants (age, sex and site of infection combined), then according to site infection (pulmonary and lymph node tuberculosis) and according to age groups.\n\nThe AUC was calculated for each ROC curve and presented with their 95% confidence intervals (95% CI). The AUC can vary between 0.5 and 1. The closer it is to 1, the better the discriminating ability or overall diagnostic value of the TST.\n\nAll included participants were informed about the purpose of the study and have give their written informed consent to participate to the study and carrying out the TST. They were also informed about their right to refuse participation or drop out at any moment of the study collection. All collected information and data analysis was confidential and anonymous during and after data collection.\n\nIn Tunisia, there was only one national ethics committee at the time of study (2014) which was in charge of requests for clinical trial type studies only. Since no blood samples were taken or procedures performed on the participants for research purposes, and since the normal process of diagnosis and management of all patients was respected without any intervention (the TST was practiced for all participants for a diagnostic purpose and not for a research purpose), we did not submit our study to that committee at the time. The study was retrospectively approved, on August 2023 by the ethics committee of the Faculty of Medicine Of Tunis under the approval number CE-FMT/2023/03/HCN/V1.\n\n\nResults\n\nOverall, 1050 participant were included (336 cases and 714 controls) with a mean age of 35 years. Of the cases, more than half were female (n = 179, 53.3%), sex ratio (M/F) = 0.87, with a mean (± standard deviation) age of 38.3 (±11.8) years. Of the controls, half were female (n = 358, 50.1%), sex-ratio (M/F) = 0.99, with a mean (± standard deviation) age of 33.6 (±11.0) years (see Table 1). The Bacillus Calmette-Guérin vaccination scar was present among all included controls and among most TB cases (83.8%).\n\nThe mean diameter of the TST induration was significantly higher among cases than controls (13.7 mm (SD: 0.7 mm) versus 6.2 mm (SD: 6.4 mm); p = 10-6) (see Figure 1).\n\nThere was no significant difference in the mean diameter of the TST induration between male and female participants (8.5 mm (SD: 6.9 mm) versus 8.7 mm (SD: 7.9 mm); p = 0.6).\n\nThe TST induration diameter disaggregated by sex and by participant status is represented in Table 2 and Figure 2.\n\nFor the global performance of TST among all the 1050 participants, the best discriminant cut-off value of TST was when the induration diameter of TST was ≥11 mm, with a sensitivity and specificity of 73.7% (95% CI: 68.8 % – 78.1 %) and 76.6 % (95% CI: 73.3 % – 79.5 %), respectively, with a Youden Index of 0.503 and an area under the curve (AUC) of 0.789 (95% CI: 0.758 – 0.819; p = 0.01). The sensitivity became >80% from a TST cut-off value ≥9 mm to 5 mm (see Table 3, Figure 3A). Using Fagan’s nomogram for the best selected threshold value of TST (≥11 mm), positive and negative predictive values were determined with values of 3.11% and 99.52%, respectively (see Figure 4).\n\n(A) All 1050 participants. (B) 180 cases of lymph node tuberculosis. (C) 121 cases of pulmonary tuberculosis.\n\nDepending on the sex distribution, the best cut-off value of TST among male participants (sensitivity: 77.2%; specificity: 75.2%; Youden Index: 0.524) and female participants (sensitivity: 70.7%; specificity: 77.9%; Youden Index: 0.486) was also ≥11 mm for both sex groups. The sensitivity became >80% from a TST cut-off value ≥10 mm to 5 mm and a TST cut-off value ≥8 mm to 5 mm, for male participants and female participants, respectively (see Table 4).\n\nHowever, depending on the infection localisation, the best cut-off value for pulmonary TB (121 cases versus 714 controls) and lymph node TB (180 cases versus 714 controls) was also ≥11 mm, with an area under the curve (AUC) of 0.778 (95% CI: 0.733-0.822; p = 0.02) and 0.814 (95% CI: 0.777-0.851; p = 0.01), respectively (see Table 5, Figure 3B and C). The sensitivity became >80% from a TST cut-off value ≥8 mm to 5 mm and a TST cut-off value ≥10 mm to 5 mm, for pulmonary TB and lymph node TB, respectively (see Table 5).\n\nDepending on age groups, the best cut-off value of TST among participants aged <35 years old (n = 148 cases; sensitivity: 79.1%; specificity: 79.8%; Youden Index: 0.589; AUC: 0.822 (95% CI: 0.782 – 0.862; p = 0.02)) and participants aged ≥35 years (n = 188 cases; sensitivity: 70.2%; specificity: 71.3%; Youden Index: 0.415; AUC: 0.750 (95% CI: 0.703 – 0.798; p = 0.02)) was also ≥11 mm for both groups.\n\n\nDiscussion\n\nTB remains a serious public health threat. In this study, we evaluated the performance of TST in a diagnostic situation and we measured its different accuracy metric indicators for different possible cut-off points, among a large size population, with 1050 participants. The best discriminating cut-off value was chosen based on the best couple sensitivity and specificity with the highest Youden Index value.\n\nThe TST is widely used for the detection of a latent TB form and for screening the contacts of a TB patient. This test has the advantage of being easy, rapid and safe to conduct, and low-cost.20\n\nIn view of our results, it may be concluded that the TST can be used for active TB diagnosis with a moderate global performance (AUC = 0.789),19,21 and a good couple of sensitivity and specificity at the cut-off point of 11 mm.\n\nThe results of the positive (3.1) and negative (0.34) LR of the selected cut-off value also indicates a moderate performance and utility of the TST.22\n\nThere is no international agreement about the best cut-off value of the TST which clearly distinguishes between a positive and negative test result. Different suggestions were proposed varying between 5mm and 10mm diameter of induration. But it depends on many epidemiological and immunological patient risk factors.23\n\nConsidering our results, the sensitivity improved (>80%) from a TST cut-off value ≥9 mm to 5 mm. So, the induration diameter threshold of TST can be reduced from 11mm (the best cut-off value) to 9mm to enhance the sensitivity of TST and consequently, reduce the frequency of false negatives and limit the miss-diagnosis of a tuberculosis infection case, regardless of its pulmonary or extra-pulmonary form.\n\nMoreover, the challenging difficulties encountered in diagnosing extrapulmonary TB, which is requiring invasive diagnostic procedures, poses a diagnostic problem for clinicians.24\n\nIn Tunisia, diagnostic confirmation of lymph node TB requires needle aspiration or surgical excision with cytological or pathological and bacteriological study (direct examination, Xpert MTB/RIF test and culture). Generally, the lymph node TB lesions are paucibacillary with a rarely positive direct examination (about 10% of positive rate only).11\n\nSince lymph node tuberculosis is usually more difficult to clinically diagnose than pulmonary tuberculosis, it is thus possible, in case of lymph node tuberculosis suspicion, to use the 10 mm threshold to guarantee a good sensitivity (>80%) of the test.\n\nHowever, the TST has some limitations. the skin induration measurement is operator-dependent and remains subjective; its interpretation depends on many other factors, like the immunological status, co-morbid conditions, and prior Calmette Guerin (BCG) vaccination.20,25\n\nIndeed, the TST is not a specific test that distinguish between TB infection and post-vaccination allergy. The cross-reaction of TST with antigens of other non-tuberculous mycobacteria and with the antigen used for the Calmette Guerin (BCG) vaccine generates false positives, inducing an apparent false increase in sensitivity and a decrease in specificity.3,26\n\nCertainly, progress has been made in developing other rapid tests for TB screening like Xpert MTB/RIF, Xpert MTB/RIF Ultra2 and Interferon-gamma release assay (IGRA) tests. However, they are still often not available and expensive, especially in low- and middle-income countries, which have the highest TB burden.3,27 That is why these novel tests are not an accessible and available option for TB diagnosis in these unfavorable areas.27\n\nThe strengths of our study include the large sample size of included participants (1050), the easy application of the TST and the clear and detailed description of the diagnostic test evaluation methodology, for further repeatability. As any epidemiological study, there were some limitations, essentially including the sample of controls which may not be representative of all non-TB participants the real life, and the non-blinded administration of the test, which may influence the operator interpretation of the test result.\n\nTherefore, for more suitable evaluation of the TST performance for diagnosing active TB, further prospective research studies are needed. We propose to follow-up for a minimum two years, and a sample of closely exposed contacts of TB patients, for prospective detection of incident newly infected cases. At the end of the follow-up period, the contact subjects will be divided into newly diagnosed active cases and controls, which represent a nested case-control study. This method will minimize the selection bias for a good representativeness of included cases and controls. All included participants will receive the TST and the IGRA test, at the same time. It will be therefore possible to compare the performance of the two tests by comparing their corresponding ROC curves.\n\nA progressive diagnostic approach based on a flowchart decision strategy using consecutive tests can also be a good alternative. The TST can be used as the first line test because it is the easiest and cheapest test to apply at a large scale (with good sensitivity); then, considering TST results, the IGRA test can be used in second line for more specific results.28–30\n\nEconomic evaluation of the cost-effectiveness of this diagnostic approach must be conducted to support the usefulness and the rational application of this strategy for public health purposes.\n\nFinally, the ROC curve certainly has an important role in determining the best TST cut-off for the TB diagnosis or screening. However, it is important to consider that the interpretation of the TST characteristics is based on probabilities. Also, its predictive values cannot be properly assessed without considering all other risk factors. So, there is a need to develop a predictive clinical score for TB based on a range of epidemiological (TB prevalence, demographic characteristics, notion of contagion), clinical (individual risk factors, TB symptoms) and paraclinical examinations (chest X-ray, among others) factors. This approach can optimize and guide the use of the various diagnostic methods for TB. Unnecessary invasive examinations and procedures will be, therefore, avoided while reducing TB diagnosis cost.\n\n\nConclusions\n\nThe TST is simple to perform and a low-cost test. It can be used for active TB detection with a moderate global performance and accepted sensitivity and specificity at the cut-off point of 11mm. However, it has some disadvantages, especially its low specificity regarding high rates of false positives in areas with mass BCG vaccination. The association of the TST with another test such as the IGRA test would be a good alternative for early and accurate diagnosis of TB.", "appendix": "Data availability\n\nHarvard Dataverse: Tuberculin Skin Test, https://doi.org/10.7910/DVN/630CJG\n\nThis project contains the following underlying data:\n\n• TST-final.tab (anonymised underlying data collected from 1050 included patient)\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\n\nAcknowledgements\n\nThe authors would like to thank all TB center coordinators involved in this study for their contribution and participation in facilitating the data collection process for the investigators.\n\n\nReferences\n\nGlobal tuberculosis report 2020: [cited 2023 Apr 4]. Reference Source\n\nTuberculosis (TB): [cited 2023 Apr 4]. 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Reference Source\n\nYang D, Kong Y: The bacterial and host factors associated with extrapulmonary dissemination of Mycobacterium tuberculosis. Front. Biol. 2015 Jun 1; 10(3): 252–261. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKetata W, Rekik WK, Ayadi H, et al.: Les tuberculoses extrapulmonaires. Rev. Pneumol. Clin. 2015 Apr 1; 71(2): 83–92. PubMed Abstract \| Publisher Full Text\n\nPopescu MR, Călin G, Strâmbu I, et al.: Lymph node tuberculosis-an attempt of clinico-morphological study and review of the literature. Romanian J. Morphol. Embryol. 2014; 55(2 Suppl): 553–567. PubMed Abstract\n\nDSSB: Le guide national de prise en charge de la tuberculose édition 2018 - Ministère de la santé publique.[cited 2023 Apr 6]. Reference Source\n\nAuguste P, Tsertsvadze A, Pink J, et al.: Comparing interferon-gamma release assays with tuberculin skin test for identifying latent tuberculosis infection that progresses to active tuberculosis: systematic review and meta-analysis. BMC Infect. Dis. 2017 Mar 9; 17(1): 200. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKrutikov M, Faust L, Nikolayevskyy V, et al.: The diagnostic performance of novel skin-based in-vivo tests for tuberculosis infection compared with purified protein derivative tuberculin skin tests and blood-based in vitro interferon-γ release assays: a systematic review and meta-analysis. Lancet Infect. Dis. 2022 Feb; 22(2): 250–264. PubMed Abstract \| Publisher Full Text\n\nEusebi P: Diagnostic Accuracy Measures. CED. 2013; 36(4): 267–272. Publisher Full Text\n\nMancini J, Gaudart J, Giorgi R: Critères d’évaluation des performances et de l’utilité d’un test diagnostique. Méd trop. 2009; 69(1): 78–82.\n\nYouden WJ: Index for rating diagnostic tests. Cancer. 1950; 3(1): 32–35. Publisher Full Text\n\nBayes T: LII. An essay towards solving a problem in the doctrine of chances. By the late Rev. Mr. Bayes, F. R. S. communicated by Mr. Price, in a letter to John Canton, A. M. F. R. S. Philos. Trans. R. Soc. Lond. 1997 Jan; 53: 370–418. Publisher Full Text\n\nFagan TJ: Nomogram for Bayes’s theorem. N. Engl. J. Med. 1975; 293: 257. PubMed Abstract \| Publisher Full Text\n\nNahm FS: Receiver operating characteristic curve: overview and practical use for clinicians. Korean J. Anesthesiol. 2022 Feb; 75(1): 25–36. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNayak S, Acharjya B: Mantoux test and its interpretation. Indian Dermatol. Online J. 2012; 3(1): 2–6. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHajian-Tilaki K: Receiver Operating Characteristic (ROC) Curve Analysis for Medical Diagnostic Test Evaluation. Caspian J. Intern. Med. 2013; 4(2): 627–635. PubMed Abstract\n\nGoeldlina AO, Perrigb M: Examen clinique basé sur l’évidence.\n\nSlogotskaya L, Bogorodskaya E, Ivanova D, et al.: Comparative sensitivity of the test with tuberculosis recombinant allergen, containing ESAT6-CFP10 protein, and Mantoux test with 2 TU PPD-L in newly diagnosed tuberculosis children and adolescents in Moscow. PLoS One. 2018 Dec 21; 13(12): e0208705. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKohli M, Schiller I, Dendukuri N, et al.: Xpert MTB/RIF Ultra and Xpert MTB/RIF assays for extrapulmonary tuberculosis and rifampicin resistance in adults. Cochrane Database Syst. Rev. 2021 [cited 2023 Apr 6]; 2021(1). Publisher Full Text\n\nWang L, Turner MO, Elwood RK, et al.: A meta-analysis of the effect of Bacille Calmette Guérin vaccination on tuberculin skin test measurements. Thorax. 2002 Sep 1; 57(9): 804–809. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDruszczynska M, Seweryn M, Wawrocki S, et al.: The Interferon-Gamma Release Assay versus the Tuberculin Skin Test in the Diagnosis of Mycobacterium tuberculosis Infection in BCG-Vaccinated Children and Adolescents Exposed or Not Exposed to Contagious TB. Vaccines. 2023 Feb; 11(2): 387. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYang Y, Fang Z, Huang W, et al.: Safety of a Novel ESAT6-CFP10 skin test compared with tuberculin skin test in a double-blind, randomized, controlled study. BMC Infect. Dis. 2022 Oct 11; 22(1): 780. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDenkinger CM, Dheda K, Pai M: Guidelines on interferon-γ release assays for tuberculosis infection: concordance, discordance or confusion? Clin. Microbiol. Infect. 2011 Jun 1; 17(6): 806–814. Publisher Full Text\n\nSchaberg T, Bauer T, Brinkmann F, et al.: Tuberculosis Guideline for Adults - Guideline for Diagnosis and Treatment of Tuberculosis including LTBI Testing and Treatment of the German Central Committee (DZK) and the German Respiratory Society (DGP). Pneumologie. 2017 Jun 1; 71(6): 325–397. PubMed Abstract \| Publisher Full Text\n\nJia J, Chen D, Liu L, et al.: Prevalence of Latent Tuberculosis Infection Among Healthy Young Children and Adolescents and a Two-step Approach for the Diagnosis of Tuberculosis Infection in Chengdu, China. Pediatr. Infect. Dis. J. 2022 Jan; 41(1): 6–11. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "257311", "date": "22 Apr 2024", "name": "Oliver Stirrup", "expertise": [ "Reviewer Expertise Medical Statistician", "with limited experience of TB research" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nNouira et al. describe a case-control study evaluating the diagnostic performance of the tuberculin skin test (TST) for active TB. I am a statistician with only limited experience of TB research. As such, I have commented on the statistical methods used and the study design, but not on the scientific novelty and interest of this work.\nThe statistical methods that have been applied are appropriate for the data, and have been described and interpreted correctly. I only have a minor comment regarding the statistical elements: -Methods: “Positive and negative predictive values (PPV and NPV) (or post-test probabilities) of TST were also determined for different possible TST thresholds by two different methods, using the properties of Bayes’ theorem and using Fagan’s nomogram graph”. Fagan’s nomogram is not really a ‘different method’, but rather a graphical application of Baye’s theorem.\nMy main concern in reading this manuscript is the description of the recruitment and selection of the cases and controls, which for me leaves a number of questions unanswered: -Did you approach/include all people who underwent the TST at the participating centers during the time period stated? -No details are given regarding the number of cases and controls excluded due to the exclusion criteria. -Did anyone decline involvement? -Was there any particular reason to evaluate the specific time period chosen? -Why did the cases undergo a TST at the time of their anti-TB treatment? -Why did the controls undergo a TST if they had no signs of TB? -Was the data collection questionnaire filled in by participants? Or was it filled in retrospectively by clinics? -Were participants recruited prospectively at each clinic? This is implied but not explicitly stated.\nFurther minor points: -The English writing throughout can be understood, but would benefit from further review and editing. -I don’t think that there is much value in Figure 2, unless the TST values are divided by both sex and case-control status. -Some of the references cited do not have full details listed (although you can click through the hyperlinks for the intended target documents), e.g. 1 and 2. -Anonymized underlying data have been provided, but the data coding is not clear for all variables. -The data described are 10 years old. Are there likely to have been further changes to TB epidemiology in this time?\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [ { "c_id": "11884", "date": "01 Jul 2024", "name": "Mariem Nouira", "role": "Author Response", "response": "Dear Dr Oliver Stirrup, Thank you very much for your review. We really appreciate your response and time. We have revised our manuscript as you suggested. Here are the responses to your comments: Reviewer Comments: • Fagan’s nomogram is not really a ‘different method’, but rather a graphical application of Baye’s theorem. Author Response: It was corrected Thank you. Reviewer Comments: • Did you approach/include all people who underwent the TST at the participating centers during the time period stated? Author Response: Yes, we included all people who underwent the TST at the participating centers during the time period stated. Reviewer Comments: • No details are given regarding the number of cases and controls excluded due to the exclusion criteria. Author Response: Unfortunately, we do not know their exact number because they were not compatibilized. Reviewer Comments: • Did anyone decline involvement? Author Response: No one declined involvement Reviewer Comments: • Was there any particular reason to evaluate the specific time period chosen? Author Response: No there was not any particular reason for the study period. Reviewer Comments: • Why did the cases undergo a TST at the time of their anti-TB treatment? Author Response: No they did not undergo a TST at the time of their anti-TB treatment. They were recruited at the time of their anti-TB treatment and the TST was done before recruitment. Reviewer Comments: • Why did the controls undergo a TST if they had no signs of TB? Author Response: Controls undergo a TST in the context of contact tracing or to eliminate a TB diagnosis based on a range of anamnestic, radiological and bacteriological arguments. Reviewer Comments: • Was the data collection questionnaire filled in by participants? Or was it filled in retrospectively by clinics? Author Response: It was filled in retrospectively by investigators Reviewer Comments: • Were participants recruited prospectively at each clinic? This is implied but not explicitly stated. Author Response: Yes they were recruited prospectively but the data collection regarding the TST was collected retrospectively Reviewer Comments: • I don’t think that there is much value in Figure 2, unless the TST values are divided by both sex and case-control status. Author Response: Figure 2 was eliminated. Thank you Reviewer Comments: • Some of the references cited do not have full details listed (although you can click through the hyperlinks for the intended target documents), e.g. 1 and 2. Author Response: It was corrected. Thank you Reviewer Comments: • Anonymized underlying data have been provided, but the data coding is not clear for all variables. Author Response: Thank you. It was done. The underlying data have been updated . Reviewer Comments: • The data described are 10 years old. Are there likely to have been further changes to TB epidemiology in this time? Author Response: Yes it is possible that changes have been occured on TB epidemiology. It may be a limit of our study." } ] }, { "id": "266923", "date": "10 May 2024", "name": "Paula Rodríguez-Molino", "expertise": [ "Reviewer Expertise Pediatric Infectious and Tropical Diseases" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors propose a Case-control study to analyze the performance of TST for active TB. I extend my sincere congratulations to them for conducting this study with such a large cohort of patients, which is of great utility. The future study they propose in a nested case-control cohort is interesting, and I encourage them to also include pediatric patients. In general, I recommend reviewing English grammar. - Title: Consider tuberculosis disease instead of active TB, and TB infection instead of latent TB, according to the latest terminology. Also, consider shortening the title length. - Introduction I suggest including a reference in 6th paragraph, referring to Pulmonary and extrapulmonary TB forms in Tunisia. - Methods: Methods section is well explained, easily allowing replication. I just wanted to point out a grammar mistake in the “Sensitivity and specificity”, 10th paragraph: “the TST a test is more discriminating”. Ethical considerations: Another grammar mistake in 1st pg, it should be “have given” Study populations\nThe part that generates the most doubts for me is the definition of cases and controls. I understand that not all cases were microbiologically confirmed. If not, please specify how many had microbiological confirmation. In the case of patients with adenitis, did you rule out the possibility of non-tuberculous mycobacteria that could have cross-reacted with the TST? Regarding the controls, how did you ensure they were free of TB? Did they have chest X-rays, or was it based solely on the absence of symptoms compatible with TB? Since in the controls the TST was performed as part of routine clinical practice and not as part of the study, Was TB infection ruled out in those cases that had a TST >5-10mm? On the other hand, if TST was done as part of contact tracing, Was it repeated after 8-12 weeks? How did you differentiate if the controls were free of TB or latent TB infection?\n\nResults TABLE 1: I recommend that you specify the other sites of extrapulmonary TB Did you analyze the time between the contact risk or the beginning of the symptoms and TST performance? -Did you analyze the reliability of the test according to the severity of the 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": [ { "c_id": "11885", "date": "01 Jul 2024", "name": "Mariem Nouira", "role": "Author Response", "response": "Dear Dr Paula Rodríguez-Molino, Thank you very much for your review. We really appreciate your response and time. We have revised our manuscript as you suggested. Here are the responses to your comments: Reviewer Comment: - Title: Consider tuberculosis disease instead of active TB, and TB infection instead of latent TB, according to the latest terminology. Also, consider shortening the title length. Author Response: It was done. Thank you “how useful is the tuberculin skin test for tuberculosis detection: Assessing diagnostic accuracy metrics through a large Tunisian case-control study” Reviewer Comment: - Introduction I suggest including a reference in 6th paragraph, referring to Pulmonary and extrapulmonary TB forms in Tunisia. Author Response: The ref 11 corresponds to the entire previous paragraph (6th paragraph) Reviewer Comment: - Methods: I just wanted to point out a grammar mistake in the “Sensitivity and specificity”, 10th paragraph: “the TST a test is more discriminating”. Response: it was corrected. Thank you Ethical considerations: Another grammar mistake in 1st pg, it should be “have given” Author Response: it was corrected. Thank you. Reviewer Comment: • I understand that not all cases were microbiologically confirmed. If not, please specify how many had microbiological confirmation. Author Response: Unfortunately, the information regarding microbiological confirmation was not collected. This was a selection criteria that was applicated to include cases and was not noted in the data collection Reviewer Comment: • In the case of patients with adenitis, did you rule out the possibility of non-tuberculous mycobacteria that could have cross-reacted with the TST? Author Response: Yes. The TB diagnosis was not based on a positive result of TST. The TB diagnosis was confirmed based on a range of anamnestic, clinical, chest X-ray and bacteriological arguments. Reviewer Comment: • Regarding the controls, how did you ensure they were free of TB? Did they have chest X-rays, or was it based solely on the absence of symptoms compatible with TB? Author Response: The TB diagnosis was not only based on the absence of TB symptoms. The TB diagnosis was confirmed based on a range of anamnestic, clinical, chest X-ray and bacteriological arguments. Reviewer Comment: • Since in the controls the TST was performed as part of routine clinical practice and not as part of the study, Was TB infection ruled out in those cases that had a TST >5-10mm? Author Response: Yes, the diagnosis was not based on the result of the TST. Many other factors were taken into account to confirm the TB infection Reviewer Comment: • On the other hand, if TST was done as part of contact tracing, Was it repeated after 8-12 weeks? How did you differentiate if the controls were free of TB or latent TB infection? Author Response: No we didn’t collect information regarding the repeat of TST. We only collected information regarding the first TST done. Reviewer Comment: Results TABLE 1: I recommend that you specify the other sites of extrapulmonary TB. Author Response: It was done. Thank you Reviewer Comment: Did you analyze the time between the contact risk or the beginning of the symptoms and TST performance? Author Response: No, unfortunately we did not analyse this information Reviewer Comment: -*Did you analyze the reliability of the test according to the severity of the disease? Author Response: No, unfortunately we did not analyse this information" } ] } ]	1	https://f1000research.com/articles/12-1297
https://f1000research.com/articles/13-327/v1	23 Apr 24	{ "type": "Case Report", "title": "Case Report: AMSAN variant of GBS complicating immediate postpartum period with severe dysautonomia leading to Posterior Reversible Encephalopathy Syndrome", "authors": [ "Koushik Ramachandra", "Hitha Almengada", "Meghana Deepak Madi", "Hitha Almengada", "Meghana Deepak Madi" ], "abstract": "Abstract* A 20’s primiparous woman, following spontaneous expulsion of intrauterine death of the fetus at 30 weeks of gestation, presented on post-partum day 8 with acute onset flaccid quadriparesis and breathing difficulty, which had rapidly progressed to involve the legs on day 3 up to her upper limbs on post-partum day 5. Following examination, Guillain Barre Syndrome (GBS) with ascending diaphragmatic involvement was diagnosed, and plasma exchange was initiated. She developed raised blood pressure, headache, sudden onset visual loss with 2 episodes of generalized seizures on post-partum day 14. Brain MRI and clinical suspicion helped diagnose Posterior Reversible Encephalopathy Syndrome (PRES). The patient was treated with anticonvulsants and antihypertensive agents. She regained her vision over the next two days, completed the treatment for GBS, and made a good recovery with independence for advanced activities of daily living on follow-up.", "keywords": [ "Guillain Barre Syndrome (GBS)", "Acute Motor- Sensory Axonal Neuropathy (AMSAN)", "Posterior Reversible Encephalopathy Syndrome (PRES)", "Plasma Exchange", "Post Partum", "Intrauterine Death" ], "content": "Introduction\n\nThe incidence of Guillian Barre Syndrome (GBS) is relatively low during pregnancy. The risk of developing GBS increases after delivery, particularly during the first two weeks of puerperium.1\n\nHere, we present a case of Acute Motor- Sensory Axonal Neuropathy (AMSAN), he rare and most severe form of GBS, complicating the postpartum period in our patient. Acute Motor Sensory Axonal Neuropathy (AMSAN)-type GBS is characterized by sensory and motor fiber axonal degeneration.2\n\nPrevention of severe axonal damage in the early stages of the disease stays top priority, it being a major impediment to attaining a favourable long-term outcome.3 Preganglionic sympathetic axonal demyelination or postganglionic axonal degeneration causes blood pressure fluctuations in GBS patients.4\n\nOur patient with AMSAN-type GBS developed severe dysautonomia and accelerated hypertension, which ultimately led to Posterior Reversible Encephalopathy Syndrome (PRES). The contribution of a multidisciplinary team towards her care cannot be overstated.\n\n\nCase report\n\nA 20’s postpartum female with antepartum stillbirth, following spontaneous expulsion, with no existing comorbidities or prior neurological disease, presented to the emergency department on post-partum day 8 with chief complaints of inability to move both lower limbs for 5 days, inability to raise her arms for 3 days, and difficulty in breathing since that morning. Her symptoms started immediately post-partum and had rapidly progressed over the last five days. On examination, she was conscious, well-oriented, and afebrile, with stable vitals. Her oxygen saturation was 98% with room air and a single breath count of 13, with the use of accessory respiratory muscles. Neurological examination demonstrated flaccidity in all upper and lower limb muscles with a power of 2/5 for the proximal muscles, 4/5 for the distal muscles of the upper limb, and 1/5 power for both proximal and distal muscles of the lower limb, bilaterally, as per the Medical Research Council scale grading for muscle strength. The patient also demonstrated areflexia with mute plantar reflex. There were features suggestive of bilateral LMN facial and bulbar palsy. The patient had a history of symmetrical glove and stocking-type pin prick sensation in the distal extremities and a loss of temperature sensation but had normal proprioception and vibration senses. No features of autonomic disturbances were observed. At the end of the examination, GBS with ascending diaphragmatic involvement was suspected and confirmed by Nerve Conduction Velocity (NCV) studies. NCV, as shown in Figure 2 and Figure 3, revealed the AMSAN variant of GBS, with reduced amplitudes of CMAPs and SNAPs, and absence of non-anatomical conduction blocks. CSF analysis results were normal.\n\nThe patient was started on emergency therapeutic plasmapheresis and further managed in the intensive care unit. The patient was intubated, and lung-protective ventilation was initiated in view of worsening respiratory distress. Cabergoline was initiated to suppress lactation. On postpartum day 14, she developed sudden onset loss of vision, headache, raised blood pressure of 200/110 mmHg and two episodes of generalized tonic- clonic seizures. Ophthalmic examinations revealed normal extraocular movements, reactive pupils, papilledema, and absent perception of light bilaterally. Brain MRI revealed cortical and subcortical T2/FLAIR hyperintensities with edema in the bilateral high frontal, posterior parietal, occipital regions, and bilateral cerebellar hemispheres, consistent with PRES, as shown in Figure 4. She was treated with anticonvulsants and antihypertensives. The patient regained vision over the next two days. The patient underwent two more cycles of plasmapheresis. Simultaneously, the patient underwent limb and chest physiotherapy. The patient was discharged after one month of hospitalization. The patient was able to walk with support. The timeline of the patient’s course in the hospital is presented in Figure 1.\n\n\nDiscussion\n\nGBS is a set of autoimmune diseases characterized by polyradiculoneuropathy. It is typically preceded by infectious diseases or immunological stimulation that triggers autoimmune reactions in peripheral nerves.5 Our patient did not report infection days or weeks prior to symptom onset. Her symptoms developed post-delivery, and there was no history or records during the antenatal period that were suggestive of GBS prior to delivery. Moreover, there is no evidence to suggest that our patient had GBS prior to delivery, which may have resulted in antepartum stillbirth. A thorough history was taken to rule out the possibility of GBS in the last trimester of her pregnancy, and that her current condition could either be a relapse or a continuation of the disease process post-delivery.\n\nIn the United States, the most prevalent variant of GBS is acute inflammatory demyelinating polyneuropathy (AIDP), while in India, the most prevalent subtype is the axonal variant.2,6,7 Several pathophysiological factors contribute to the development of the various GBS subtypes. In the AMAN variant of GBS, cross-reactivity exists between the antibodies produced against microbial antigenic molecules and peptides in the nerve roots because they share similar epitopes, causing axonal degeneration. In AIDP, antibodies cross-react to specific epitopes in Schwann cells, resulting in demyelination. In AMSAN, the target peptides are located on sensory and motor neuronal axons, comparable to the etiopathogenesis of AMAN.8\n\nGBS can develop in any trimester and postpartum period, but especially in the third trimester and first two weeks after delivery,9 as seen in our patient who developed symptoms 3 days after delivery.\n\nFrom January 2015 to December 2017, a three-year retrospective observational study was conducted at a tertiary care hospital. The medical records of all pregnant and postpartum women diagnosed with GBS based on the clinical, laboratory, and electrodiagnostic criteria were evaluated. Fifty% of the women in this study presented during the postpartum period.10\n\nThroughout the postpartum period, there is an increase in pro-inflammatory cytokines, which may account for the increased incidence of the disease. GBS is frequently reported to deteriorate during the postpartum period because of an increase in delayed-type hypersensitivity, which could also be the reason for our patient’s rapid deterioration of symptoms, in addition to having the AMSAN variant.9\n\nVariants of GBS, as well as the ensuing involvement of respiratory muscles and autonomic dysfunction, contribute to maternal mortality.10 Approximately 20% of GBS patients experience respiratory failure that requires mechanical ventilation.11 By the time our patient reached our care, she had already progressed to respiratory muscle involvement. For patients with deteriorating respiratory and cardiac function, emergency care must include early mechanical ventilation, timely monitoring of vital signs, and cardiac function.12 It is recommended to routinely measure respiratory function, since all individuals with respiratory insufficiency do not have dyspnea. A single breath count of ≤19 indicates the necessity for mechanical ventilation, and other respiratory parameters may include the use of accessory respiratory muscles, vital capacity, and maximal inspiratory and expiratory pressure.11 At the time of presentation, our patient had a single breath count of 13 with accessory respiratory muscles requiring respiratory support. Early intravenous immunoglobulin (IVIG) or plasma exchange therapy has been shown to be effective and is crucial in patients with rapidly worsening weakness,3 and needs to be initiated before irreparable nerve damage develops.5 Most patients must be admitted to a critical care unit because one-fourth of them need respiratory support, and many have dysautonomia.3 In our case, emergency therapeutic plasmapheresis was initiated immediately after admission to the critical care unit on the same day.\n\nAs observed in our patient during the first week, cerebrospinal fluid analysis may be normal for the first seven days.5 Blood pressure variability is a key trait of GBS. The observed variances may be explained by changes in the feedback control caused by preganglionic sympathetic axonal demyelination or postganglionic axonal degeneration.4\n\nPRES is a neurological disorder that typically manifests as visual impairment, seizures, and encephalopathy.13 In neuroimaging, it is characterized by bilateral parietal and occipital cortical/subcortical vasogenic edema, followed by frequent involvement of additional regions.14 Our patient with the AMSAN variant developed severe dysautonomia on post-partum day 14 with accelerated hypertension leading to PRES. Uncertainty surrounds the mechanism of PRES in the setting of GBS. Vasogenic edema may be caused by hypertension due to autonomic dysfunction, which exceeds the limits of cerebrovascular autoregulation.15 Paneyala S, et al. described a similar case of a woman who developed GBS shortly after delivery, but later experienced seizures due to PRES.16\n\nThe fundamentals of GBS care in pregnancy and the postpartum period include timely detection, multidisciplinary input, and swift plasmapheresis or IVIG administration. These measures improve outcomes for the mother and fetus.1 Several potential repercussions of GBS must be addressed and managed prior to patient release.11\n\n\nConsent to participate\n\nWritten informed consent was given by the patient.\n\n\nConsent to publish\n\nWritten consent from the patient was taken for publishing the case after de-identifying and anonymizing all the patient identifiers.", "appendix": "Data availability\n\n“No data are associated with this article.”\n\n\nReferences\n\nMeenakshi-Sundaram S, Swaminathan K, Karthik SN, et al.: Relapsing Guillain-Barre syndrome in pregnancy and postpartum. Ann. Indian Acad. Neurol. 2014 Jul; 17(3): 352–354. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLiu DY, Hollenbach JR, Gregorin JA, et al.: A Case of Acute Motor Sensory Axonal Neuropathy: A Variant of Guillain-Barré Syndrome, with Possible Syndrome of Irreversible Lithium-Effectuated Neurotoxicity. Case Rep. Med. 2020 Apr 20; 2020: 4683504–4683507. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWillison HJ, Jacobs BC, van Doorn PA : Guillain-Barré syndrome. Lancet. 2016 Aug 13; 388(10045): 717–727. PubMed Abstract \| Publisher Full Text\n\nZaeem Z, Siddiqi ZA, Zochodne DW: Autonomic involvement in Guillain-Barré syndrome: an update. Clin. Auton. Res. 2019 Jun; 29(3): 289–299. PubMed Abstract \| Publisher Full Text\n\nAabdi M, Mellagui Y, Bensaid A, et al.: Guillain-Barré Syndrome During the Postpartum Period. Cureus. 2020 Dec 10; 12(12): e12021. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKumar S, Rani P, Sharma J, et al.: Guillain-Barré Syndrome: Clinical Profile and Electrodiagnostic Subtype Spectrum from a Tertiary Care Hospital in Eastern India. Int. J. Nutr. Pharmacol. Neurol. Dis. 2022; 12: 163–169. Publisher Full Text\n\nYadav S, Jain P, Sharma S, et al.: Guillain-Barre syndrome in North Indian children: Clinical and serial electrophysiological features. Neurol. India. 2019 May-Jun; 67(3): 724–727. PubMed Abstract \| Publisher Full Text\n\nHaidary AM, Noor S, Hamed E, et al.: Acute motor-sensory axonal polyneuropathy variant of Guillain-Barre syndrome complicating the recovery phase of coronavirus disease 2019 infection: a case report. J. Med. Case Rep. 2021 Jul 16; 15(1): 379. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPakhale SW, Sehra A, Bhardwaj S: (no date) Guillain-Barre Syndrome in pregnancy- a rare entity. Int. J. Reprod. Contracept. Obstet. Gynecol. (Accessed: 06 March 2024). Publisher Full Text\n\nShetty S, Rupalakshmi V: Guillain–Barre syndrome in pregnancy and its association with maternal and perinatal outcome. Muller J. Med. Sci. Res. 2019; 10: 58. Publisher Full Text\n\nLeonhard SE, Mandarakas MR, Gondim FAA, et al.: Diagnosis and management of Guillain-Barré syndrome in ten steps. Nat. Rev. Neurol. 2019 Nov; 15(11): 671–683. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPritchard J: Guillain-Barré syndrome. Clin. Med. (Lond.). 2010 Aug; 10(4): 399–401. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTriplett JD, Kutlubaev MA, Kermode AG, et al.: Posterior reversible encephalopathy syndrome (PRES): diagnosis and management. Pract. Neurol. 2022 Jun; 22(3): practneurol-2021-003194–practneurol-2021-003189. Epub 2022 Jan 19. PubMed Abstract \| Publisher Full Text\n\nHinduja A: Posterior Reversible Encephalopathy Syndrome: Clinical Features and Outcome. Front. Neurol. 2020 Feb 14; 11: 71. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAlrohimi A, Jassal R: Headache in Guillain-Barré Syndrome: Diagnostic and Management Implications. Can. J. Neurol. Sci. 2018 Mar; 45(2): 240–242. PubMed Abstract \| Publisher Full Text\n\nPaneyala S, Chandrashekaraiah NS, Sundaramurthy H, et al.: “Double” Trouble in Postpartum State. J. South Asian Fed. Obstet. Gynecol. 2021; 13: 138–143. Publisher Full Text" }	[ { "id": "288640", "date": "24 Jun 2024", "name": "Amna Al Futaisi", "expertise": [ "Reviewer Expertise Pediatric 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\nIntroduction and Background The manuscript presents a rare case of Acute Motor-Sensory Axonal Neuropathy (AMSAN), a severe form of Guillain-Barré Syndrome (GBS), occurring in the immediate postpartum period. Novelty and Contribution to Knowledge The case report contributes an unusual and severe presentation of GBS in the postpartum period, complicated by PRES. This dual complication is rare and provides valuable insights into the clinical course, management, and outcomes of such cases. Clinical Data and Discussion The clinical data presented is comprehensive and detailed. The timeline of symptoms, clinical findings, and interventions is well-documented. The inclusion of figures (e.g., Nerve Conduction Studies and MRI findings) adds clarity and supports the diagnostic process. However, the discussion could benefit from a deeper analysis of the pathophysiological mechanisms linking GBS, dysautonomia, and PRES. While the manuscript mentions the possible role of autonomic dysfunction and vasogenic edema in PRES, a more detailed exploration of these mechanisms would strengthen the discussion. Additionally, comparing this case with similar reported cases could provide a broader context and highlight the uniqueness of the presented case. English Language and Writing Quality The manuscript is generally well-written, but there are several areas where the English language could be improved for clarity and readability:\nGrammar and Sentences: Some sentences are complex and could be simplified. For instance, \"Prevention of severe axonal damage in the early stages of the disease stays top priority, it being a major impediment to attaining a favourable long-term outcome\" could be revised for clarity. Consistency: Terms such as \"post-partum\" and \"postpartum\" should be consistently used throughout the manuscript. Technical terms: Anticonvulsants is outdated and should use antiseizure medications\nAdequacy of Clinical Data and Discussion The clinical data provided is adequate and detailed, ensuring a clear understanding of the patient's condition, diagnosis, and treatment. The discussion aptly highlights the clinical management and the importance of timely intervention. However, the discussion would benefit from:\nIncluding more comparisons with existing literature on similar cases to provide context and underscore the significance of the presented case. A more thorough exploration of the mechanisms leading to the complications observed in the patient, supported by relevant literature.\nRecommendations for Improvement\nExpand the Discussion: Enhance the discussion section by including more detailed explanations of the pathophysiological mechanisms involved and comparisons with other reported cases. Language Refinement: Revise the manuscript for grammar, syntax, and consistency to improve readability. Conclusion: Strengthen the conclusion to emphasize the key learning points from the case and the implications for clinical practice.\nConclusion The manuscript presents a valuable case report with significant clinical insights into the rare and severe presentation of AMSAN variant GBS complicated by PRES in the postpartum period. With improvements in the discussion and language, the manuscript could make a contribution to the medical literature. It is suitable for publication pending major revisions that address the identified areas for enhancement and focusing on the link between PRES and GBS and its pathophysiological explanations. May provide a review on the treatment guideline sin such cases. May utilize the following references in the manuscript- (Sorti B. et al., 2020) Ref-1, (Chakraborty T et al., 2020) Ref-2 and (Kobayashi H., 2023) Ref-3.\n\nIs the background of the case’s history and progression described in sufficient detail? Yes\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Yes\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? No\n\nIs the case presented with sufficient detail to be useful for other practitioners? Yes", "responses": [ { "c_id": "11909", "date": "27 Jun 2024", "name": "Koushik Ramachandra", "role": "Author Response", "response": "We thank you for valuable suggestions towards improving our case report. Language and Grammar: As suggested by you, the language and grammar of the entire report has been reworked. Older, outdated terminologies have been replaced. Pathophysiologic understanding: We thank you profusely for sharing 3 articles for us to use. We have tried to incorporate their findings, also comparing them with our case. Conclusions: This section has been reworded to shed light on the importance of dysautonomia in GBS." } ] }, { "id": "288637", "date": "24 Jun 2024", "name": "Ivana Berisavac", "expertise": [ "Reviewer Expertise GBS", "Status epilepticus", "myasthenia gravis crisis" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThere is no previous medical history of patient. We don't know did she have other diseases? The author only says that she was not febrile. It means nothing. What are her laboratory tests? On what basis was the infection ruled out? What is the result of lumbar puncture? Was cerebrospinal neuro panel performed? Where Tu markers, immunological analyzes of blood and cerebrospinal fluid performed? How many PE was done? Is hypertension the only reasons of PRES in this case? The discussion is too extensive.\n\nI see many questions that need to be answered.\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? Yes", "responses": [ { "c_id": "11910", "date": "27 Jun 2024", "name": "Koushik Ramachandra", "role": "Author Response", "response": "We thank you for valuable suggestions towards improving our case report. Previous Medical History: Our patient did not have medical or neurological history contributing to her current presentation. This has been added to the report. Laboratory investigations: Infection was ruled out with the help of blood counts. Immunological and virological etiologies were also ruled. These have been updated in the report. CSF Tumor markers and Neurology panel:As the NCV findings and clinical profile were favoring a diagnosis of GBS, we did not perform tests for tumor markers. Number of plasma exchanges: Our patient underwent 5 cycles of PE. This has been updated in the report." } ] } ]	1	https://f1000research.com/articles/13-327
https://f1000research.com/articles/13-720/v1	01 Jul 24	{ "type": "Research Article", "title": "The impact of sleep hygiene education and lavender essential oil inhalation on the sleep quality and overall well-being of athletes who undergo late-evening training: a randomized controlled trialâ¯â¯", "authors": [ "Atef Salem", "Khaled Trabelsi", "Mohamed Ali Boujelbane", "Ahlem Belgacem", "Mohamed Kerkeni", "Manel kerkeni", "Omar Boukhris", "Haithem Jahrami", "Jordan Glenn", "Achraf Ammar", "Wolfgang Schöllhorn", "Hamdi Chtourou", "Atef Salem", "Khaled Trabelsi", "Mohamed Ali Boujelbane", "Ahlem Belgacem", "Mohamed Kerkeni", "Manel kerkeni", "Omar Boukhris", "Haithem Jahrami", "Jordan Glenn", "Wolfgang Schöllhorn", "Hamdi Chtourou" ], "abstract": "Background Sleep hygiene education (SHE) and lavender essential oil (LEO) inhalation are two effective strategies aimed at enhancing sleep quality and mood states. This study investigated the effects of a single SHE session combined with nightly LEO inhalation for 7 days of late-evening resistance training sessions on sleep quality and mood states in trained athletes.\n\nMethods Forty-two athletes were randomly assigned to four groups: a control group (CG), a SHE group (SHEG), a LEO group (LEOG), and a SHE + LEO group (CSLG). CG and LEOG maintained their sleep habits during the intervention, while SHEG and CSLG followed SHE recommendations. Additionally, LEOG and CSLG inhaled LEO nightly before sleep. Sleep patterns were recorded via actigraphy. The Brunel Mood Scale and the Hooper questionnaires were completed before and after the intervention.\n\nResults Sleep latency was lower in SHEG (p=0.001) and CSLG (p=0.012) compared to the CG. The subjective sleep score improved in SHEG, LEOG, and CSLG (p < 0.001), with greater improvement observed in SHEG (p = 0.002) and CSLG (p < 0.001) compared to CG at post-intervention. Additionally, significant improvements were observed in the Hooper index in the SHEG (p=0.048) and CSLG (p=0.027), with CSLG demonstrating higher scores compared to CG at the post-intervention assessment (p=0.026). Furthermore, the subjective fatigue score significantly decreased in the CSLG (p=0.009).\n\nConclusions Combining SHE and LEO inhalation could be an effective strategy to enhance sleep latency, subjective sleep quality, and overall wellness, and reduce feelings of fatigue in trained athletes following late-evening resistance training sessions.", "keywords": [ "Sleep", "Insomnia", "Hygiene", "Aromatherapy", "Night training" ], "content": "Introduction\n\nThis section should include the aim and objectives of this study in the context of the wider subject area.\n\nAdequate sleep is a crucial component for athletic success, complementing physical and mental training, nutrition, and overall health.1 However, many athletes are prone to experiencing sleep inadequacies,2,3 often characterized by insufficient sleep quantity (<8.2 hrs per night)2 and/or poor sleep quality, such as sleep fragmentation and reduced sleep efficiency.4\n\nAthletes’ sleep is frequently compromised due to various interconnected factors.3,4 These factors include early morning training, increased training load, early departure times for traveling, jet lag, exposure to high altitudes, as well as anxiety and stress, especially on the night before an important competition.3\n\nNight-time training and competition sessions can have detrimental effects on both the quantity and quality of sleep.3,4 Athletes involved in team sports, who have late-evening matches or training, often experience disrupted sleep.5,6 Eagles and Lovell7 found that after a twelve-night period involving training and two competitive matches, athletes reported lower sleep quantity and increased sleep latency. The delay in bedtime on competition nights reduces the overall time available for sleep.8 Therefore, engaging in training and competition sessions during nighttime, especially within one hour before bedtime, can have a detrimental impact on sleep duration and quality.4 This has the potential to negatively affect athletes’ overall performance and recovery.\n\nIdentifying and evaluating effective strategies to mitigate potential sleep disturbances related to late training and/or competition is crucial for optimizing performance and overall well-being. Previous studies highlight the potential of sleep hygiene education (SHE) to improve sleep quality and quantity among athletes.9,10 SHE involves providing a range of recommendations as a simple, accessible, and cost-effective tool to discourage behaviours disrupting normal sleep patterns.11 While initially implemented in clinical populations,12 SHE has evolved to include other behavioural factors such as limiting technological device usage, creating a dark and cool bedroom environment, and avoiding blue light exposure in nonclinical and healthy individuals,13 Educating individuals, including athletes, about sleep and sleep hygiene practices offers strategies to optimize both sleep quantity and quality,14 For example, one session of SHE improved sleep latency and sleep efficiency in elite rugby players during a 4-week intervention.15 Similarly, an enhancement in objective sleep latency has been reported one night following a late-evening small-sided-game session in soccer players who attended one session of SHE.16 SHE also led to improved total sleep time and reduced wake episode duration in elite female netball athletes.9 However, in another study among soccer players, SHE was associated with increased wake episodes compared to the control group,17, Caia, Scott18 observed earlier bedtime and increased sleep duration in rugby league athletes following a SHE session, although sleep indices returned to baseline after one month. Furthermore, previous studies,11,19 examining the effects of SHE on fatigue have consistently shown improvements in fatigue levels following SHE interventions. A more recent study by Biggins, Purtill20 reported that athletes experiencing a sleep problem of clinical importance had a higher tendency to describe poorer sleep habits, increased instances of health-related issues, and disturbances in their mood.\n\nOn the other hand, phytotherapy, which involves the use of herbs, herbal preparations, and phytochemicals for medicinal purposes, has received growing interest in alternative medicine in recent years.21 Aromatherapy, a branch of phytotherapy, utilizes plant-derived essential oils (EOs) for medicinal, cosmetic, and culinary applications.22,23 Aromatherapy has demonstrated effectiveness in reducing stress, improving depression, and enhancing sleep quality in healthy adults by alleviating emotional stress and stabilizing moods.24 Short-term aromatherapy treatments have also shown promising results in improving sleep quality without the need for special equipment.25 These EOs enter the body through the respiratory tract, influencing the limbic system and triggering emotional and physiological responses.25 Various application methods of EOs, such as inhalation, massages, and baths, are reported to have positive effects on sleep quality.24,26,27 Inhalation is the most popular and is often associated with EOs,28 Inhaling essential oils is a quick, easy, and safe method.29,30 Among the EOs, Lavender essential oil (LEO) is highly recommended due to its potential sleep-promoting effects.28 LEO demonstrates positive effects on various clinical issues (e.g., anxiety, depression, fatigue, stress, and pain), and may potentially improve sleep quality and mood.31,32 However, there is a lack of research evaluating the effects of LEO inhalation on sleep quality, mood states, and subjective feelings of recovery, specifically in athletes.\n\nParticularly, there is a paucity of scientific investigations examining the synergistic effects of SHE and LEO inhalation on sleep quality following late-evening resistance training sessions in trained athletes. Evaluating this strategy would not only contribute to the existing literature but also enable coaches to implement effective measures for improving sleep and subsequently enhancing athletes’ performance and recovery. Therefore, the purpose of this study was to examine the effects of combining a single SHE session with LEO inhalation during 7 days of late-evening resistance training sessions on sleep quality and mood states in trained athletes. The hypotheses were as follows: (i) an acute SHE session would enhance both sleep quantity and quality and reduce mood disturbance; (ii) LEO inhalation before bedtime would improve sleep quantity, and quality, and positively impact mood states; and (iii) the combination of an acute SHE session and LEO inhalation before bedtime would result in greater improvements in sleep quality, sleep quantity, and mood states compared to SHE or LEO alone.\n\n\nMethods\n\nThis study adopted a four-arm, parallel-group randomized controlled trial design. Participants were randomly assigned to one of four groups: a control group (CG), a LEO group (LEOG), a SHE group (SHEG), and a combined SHE + LEO group (CSLG). Randomization was performed using a computer-generated list of random numbers. The CG and LEOG were instructed to maintain their usual lifestyle and sleep habits throughout the intervention period (Figure 1). The SHEG and CSLG were provided with sleep hygiene recommendations to follow for the entire 7-day period (Figure 1). The LEOG and CSLG were asked to inhale the LEO every night before going to sleep for the duration of the 7 days (Figure 1). Sleep patterns were accessed using GT3X actigraphy every night for 7 days (Figure 1). The participants completed the Brunel Mood Scale (BRUMS) and Hooper questionnaires before and after the 7-day intervention period (Figure 1). Furthermore, participants in the LEOG and CSLG were asked to report any potential side effects experienced after inhaling LEO before bedtime during the 7-day intervention period. No participants reported any side effects, such as difficulty breathing, headaches, or dizziness.\n\nThe minimum required sample size was calculated using Gpower software (version 3.1.9.6; Kiel University, Kiel, Germany). Based on the effect size estimated from the studies by Lee, Lim24 and Vitale, La Torre,16 a sample size of 32 subjects would be sufficient to detect significant differences (effect size f = 0.8, α = 0.05) with an actual power of 95.66%. In this study, a total of 42 resistance-trained athletes (27 males and 15 females) voluntarily participated. The inclusion criteria required participants to be: (i) aged ≥ 18 years, (ii) engage in nighttime resistance training for at least 1 hour, four times a week, and (iii) females who were in the follicular phase of their menstrual cycle during the experimentation. All training sessions were scheduled between 21:00 and 23:00. Exclusion criteria were being a morning (M-type) or evening (E-type) chronotype, as assessed using the Horne-Ostberg morningness-eveningness Questionnaire (MEQ),33 tobacco use, history of lower extremity injury or surgery within the past 6 months, and previous exposure to SHE or LEO, which would potentially interfere with the validity of the study protocol. Additionally, participants who were anticipated to encounter conditions with the potential to disrupt their sleep patterns, such as traveling and jet lag, were excluded from the study. Finally, participants who experienced any adverse effects as a result of LEO inhalation were excluded from the study. The study was conducted in accordance with the Declaration of Helsinki, and the protocol received full approval from the Ethical Committee for the Protection of Southern Persons (CPP SUD N° 0520/2023) on 31st May 2023 and was registered at the Pan African Clinical Trial Registry (PACTR202306806244897) on 09th June 2023. Participants were allocated to one of four groups: CG (n = 11), SHEG (n = 11), LEOG (n = 10), or CSLG (n = 10). Three participants from the SHEG, one from the LEOG, and one from the CSLG were excluded from the final analysis due to being lost to follow-up for SHE recommendation (n = 4) or incomplete use of LEO (n = 1) during the intervention period. The flowchart of the study according to CONSORT guidelines34 is illustrated in Figure 2 (Checklist: https://zenodo.org/records/11368563).\n\nParticipants in the LEOG and CSLG were provided with lavender (Lavandula angustifolia, of the family Lamiaceae) essential oil (LEO) for inhalation. The LEO was prepared in a laboratory. To use the LEO, as described by Salamati, Mashouf,35 participants were instructed to apply two drops (equivalent to 0.14 mL) of the oil onto a cotton ball. The cotton ball was then placed at a distance of 5 cm from their nose. Participants were asked to inhale the aroma of the LEO for 10 min, engaging in normal breathing, at their convenience prior to bedtime.28\n\nAll participants attended a SHE session led by a specialist in sleep research and athletic recovery. The session took place one day prior to the start of the study and lasted for approximately 40-45 min. The SHE session focused on practical tips that were evidence-based and recommended by Nédélec, Halson.36 These tips included various recommendations such as taking a post-training shower, ensuring a quiet, cool, and dark bedroom environment, removing the bedroom clock, avoiding the use of light-emitting technology devices at least 1 hour before sleep, refraining from consuming caffeine, alcohol, or other stimulants before sleep, drinking high-electrolyte fluids, such as milk instead of only water, between training cessation and bedtime, and eating a light, high-glycaemic index meal with few proteins. All participants were asked to avoid afternoon naps in order to limit the beneficial effects of napping on their sleep patterns at night. Following the educational session, participants were provided with a leaflet summarizing the sleep hygiene recommendations to follow between training cessation and bedtime. All participants slept in their usual beds at home throughout the study.\n\nCircadian typology\n\nCircadian typology was assessed using the Horne-Ostberg Morningness-Eveningness Questionnaire (MEQ).33 MEQ scores were categorized into three groups: morning-type (score ≥ 59), evening-type (score ≤ 41), or neither-type (score 42–58). Based on their MEQ scores, all participants in this study were categorized as neither-type, indicating a lack of strong preference for either morningness or eveningness in their sleep-wake patterns.\n\nWristwatch actigraphy\n\nParticipants were asked to wear the GT3X actigraphy device (Actigraph, FL, USA) on their non-dominant wrist to assess their sleep patterns. The Actilife 6 software was used to analyse the recorded data and calculate various sleep parameters, including in bedtime (IB), out bedtime (OB), sleep latency (SL), sleep efficiency (SE), total time in bed (TTB), total sleep time (TST), wake after sleep onset (WASO), number of awakenings (N° AW), and average awakening (AW). The sleep analysis software categorized each 60-second epoch as either asleep or awake based on the recorded data. By analysing these parameters, the sleep-awake patterns of participants during the night were evaluated.\n\nHooper questionnaire\n\nThe Hooper questionnaire was used to assess signs of pre-fatigue and stress.37 This questionnaire included subjective assessments of sleep quality, fatigue, stress, and muscle soreness. Participants provided their ratings for each of these factors using a seven-point Likert scale, with responses ranging from 1 (very, very good) to 7 (very, very bad) for sleep, and from 1 (very, very low) to 7 (very, very high) for fatigue, stress, and muscle soreness. The responses were then used to calculate the Hooper Index (HI), which represents the total of the four ratings. The HI provides an overall measure of participants’ subjective experiences of sleep quality, fatigue, stress, and muscle soreness. A higher score on the HI indicates better well-being and readiness for training or competition, while a lower score suggests a potential decrease in readiness or the presence of factors that may impact performance.38\n\nThe Brunel Mood Scale (BRUMS)\n\nThe BRUMS39 consists of 32 items assessing mood states. These items are divided into six subscales: anger, tension, depression, vigour, fatigue, confusion, happiness, and calmness. Each item is rated on a 5-point Likert scale, ranging from 0 (not at all) to 4 (extremely). Participants were asked to complete the BRUMS by indicating their current feelings and emotions. The subscale scores are calculated based on four relevant items, with possible scores ranging from 0 to 16. The BRUMS provides a comprehensive assessment of participants’ mood states, including both negative and positive aspects, allowing for a multidimensional evaluation of emotional well-being.\n\nDescriptive statistics were presented as Mean ± standard deviation (SD). The normality of the data was checked using the Shapiro-Wilk test. To assess the statistical significance of differences between groups for participants’ characteristics and actigraphy-based sleep data, the one-way analysis of variance (ANOVA) (when a parametric test was appropriate) or the Kruskal-Wallis test (when a non-parametric test was appropriate) were performed, followed by a post-hoc pairwise comparison or the Dunn’s test, both with the Bonferroni adjustment. To assess the statistical significance of differences between groups and measures times, the two-way ANOVA was performed (when a parametric test was appropriate) or the F1-LD-F1-model was performed (when a non-parametric test was appropriate). This model provides an ANOVA-type statistic for group, time, and the interaction between group and time. When significant main or interaction effects were found, a post-hoc pairwise comparison or the Dunn’s test as post-hoc, both with Bonferroni adjustment, were performed. The effect size statistic (ηp2 and η2H) was calculated to assess the magnitude of the difference between age groups using the following criteria: small = 0.01, moderate = 0.06, and large = 0.14.40 Standardized effect size (Cohen’s d) analysis was used to interpret the magnitude of differences between variables and classified according to Hopkins41 as: trivial (d ≤ 0.20), small (0.20 < d ≤ 0.60), moderate (0.60 < d ≤ 1.20), large (1.20 < d ≤ 2.0), very large (2.0 < d ≤ 4.0), and extremely large (d > 4.0). Upper and lower 95% confidence intervals of the difference (95% CId) were calculated. For all analyses, significance was assumed a priori at p 0.05. Statistical analyses were conducted using the R programming language.42 ANOVAs and post-hoc tests for normally distributed data were conducted with the “afex”43 and “emmeans”44 packages, respectively. The Kruskal-Wallis and Dunn’s tests were conducted with the “rstatix” package.45 The F1-D1-F1 model was performed with “nparLD” package.46\n\n\nResults\n\nParticipants’ characteristics are presented in Table 1. Statistical analysis showed no difference in participant characteristics between the four groups.\n\nOf the initial number of participants in the SHEG and CSLG, four were excluded from the analysis due to not following the sleep hygiene recommendation for more than half of the experimental days. However, the majority of participants in both groups demonstrated a high level of adherence to sleep hygiene recommendations. Specifically, 6 out of 8 participants in the SHEG and 8 out of 9 participants in the CSLG followed all seven sleep hygiene recommendations, achieving a 100% adherence rate (7/7). There were a few participants who did not fully adhere to specific recommendations, such as refraining from consuming caffeine before sleep and avoiding light-emitting technology devices at least 1 hour before sleep. The adherence rate for these participants was 71% (5/7). Overall, total adherence to the sleep hygiene recommendations across both groups was 82%.\n\nObjective sleep indices are presented in Table 2. Statistical analysis reported a significant effect of group for sleep latency, with higher values in CG compared to SHEG (p = 0.001, 95% CId = 0.39 to 2, d = 1.70) and CSLG (p = 0.012, 95% CId = 0.15 to 1.71, d = 1.22). However, there is no significant effect of group for the other indices.\n\n (p = 0.012).\n\n** (p = 0.001): significantly different compared to CG; ANOVA: Analysis of variance; η2 H: eta2 calculated using H-value of Kruskal-Wallis test.\n\nHooper scores are presented in Table 3. There was a significant effect of time and an interaction between group and time for sleep scores. Sleep scores significantly improved from pre- to post- 7-days in SHEG (p < 0.001, 95% CId = 0.93 to 2.57, d = 1.69), LEOG (p < 0.001, 95% CId = 1.45 to 2.99, d = 1.22), and CSLG (p < 0.001, 95% CId = 1.45 to 2.99, d = 2.69). Sleep score in CG post- 7-days was significantly higher compared to SHEG (p = 0.002, 95% CId = 0.61 to 3.74, d = 1.86) and CSLG (p < 0.001, 95% CId = 0.92 to 3.95, d = 2.19), indicating poorer sleep quality in the CG. There was a significant main effect of time and an interaction between group and time for the HI. HI values significantly decreased in SHEG (p = 0.048, 95% CId = -0.3 to 5.8, d = 0.96) and CSLG (p = 0.027, 95% CId = 0.82 to 7.85, d = 1.23) at post-compared to pre-intervention. Additionally, HI in CG post-intervention was significantly higher compared to CSLG (p = 0.026, 95% CId = 1.64 to 8.9, d = 1.4). Additionally, significant main effects of group and time were found for fatigue scores without an interaction between group and time. Subsequent post-hoc test indicated no statistically significant differences. Furthermore, statistical analysis revealed no significant effect of group, time, or interaction between group for stress and muscle soreness scores.\n\n* (p < 0.05).\n\n* (p < 0.001): significantly different compared to pre-intervention.\n\n$$ (p = 0.002): significantly different compared to SHEG.\n\n£ (p = 0.026).\n\n£££ (p < 0.001): significantly different compared to CSLG; CG: Control group; SHEG: Sleep hygiene education group; LEOG: Lavender essential oil group; CSLG: Sleep hygiene education and Lavender essential oil combination group; ANOVA: Analysis of variance.\n\n† ANOVA was performed with the F1-D1-F1 model; ATS: ANOVA-type test statistic; ATSMod: Modified ANOVA-type test statistic with Box approximation.\n\nBRUMS scores are presented in Table 4. There was a significant effect of time and an interaction between group and time for fatigue score. Fatigue score significantly decreased from pre- to post-intervention in CSLG (p = 0.009, 95% CId = 2.18 to 9.6 A.U., d = 1.59). However, statistical analysis showed no significant effect of group, time, or interaction between group and time for the other scores.\n\n (p = 0.009): significantly different compared to pre-intervention. CG: Control group; SHEG: Sleep hygiene education group; LEOG: Lavender essential oil group; CSLG: Sleep hygiene education and Lavender essential oil combination group; ANOVA: Analysis of variance.\n\n† ANOVA was performed with the F1-D1-F1 model; ATS: ANOVA-type test statistic; ATSMod: Modified ANOVA-type test statistic with Box approximation.\n\n\nDiscussion\n\nThis study aimed to investigate the effects of a single session of SHE and LEO inhalation over a 7-day period of late-evening resistance training sessions on actigraphy-based sleep quality, well-being, and mood state indices in trained athletes. The main results revealed (i) the objective measure of SL was significantly better in SHEG and CSLG compared to CG, (ii) the subjective sleep quality score improved in SHEG, LEOG, and CSLG after the intervention period, and (iii) the sleep score was significantly worse in CG compared to the other groups after the intervention. Moreover, HI decreased in the SHEG and CSLG after the 7-day period and was higher in the CG vs. CSLG at the post-intervention assessment. Additionally, subjective fatigue scores improved in the CSLG after the intervention.\n\nThe results of our study highlight the potential benefits of SHE in improving SL among trained athletes practicing resistance training during the night. SL refers to the time it takes for an individual to fall asleep after getting into bed, and a shorter SL indicates an easier and quicker transition into sleep. In the present study, SL values were significantly lower in both SHEG and the CSLG (d = 1.7 and 1.22, respectively) compared to the CG. These findings suggest implementing SHE, even in a single session, can be an effective strategy for reducing SL in athletes. Furthermore, subjective sleep score significantly improved in the SHEG, LEOG, and CSLG (1.22 ≤ d ≤ 2.69) and was significantly better in SHEG and CSLG (d = 1.86 and 2.19, respectively) compared to CG at post-intervention.\n\nThe influence of SHE on sleep quality and quantity has been studied across various populations, although there is limited research specifically focused on athletes.47,48 Recently, two studies investigated the effect of SHE on middle-aged swimmers49 and youth elite rugby union players.15 Dunican, Perry49 revealed no effect of SHE intervention during 16-week training programme on both sleep quality and quantity for the nights after evening training. Contrarywise, Vachon, Sauvet15 demonstrated SHE improved sleep quality (i.e., SL and SE), but not quantity. However, previous studies have shown SHE could have the potential to improve sleep duration and subsequently enhance performance in athletes.5,17,50 Nédélec, Halson36 highlighted several factors, such as cognitive features and sleep environment, that are strongly associated with inadequate SH among elite soccer players. Harada, Wada51 found athletes experienced longer SL and poorer sleep quality during one month of SHE intervention. Conversely, Lastella, Roach14 emphasized the positive effects of implementing SHE on both sleep quantity and quality in athletes. Furthermore, athletes themselves acknowledged the potential influence of improved sleep guidance on their performance.52\n\nIn the context of acute SHE sessions implemented after training or match play, the focus has primarily been on enhancing the quantity of sleep rather than its quality, as observed in various populations and settings.53,54 Fullagar17 conducted a study involving soccer players and investigated the effects of an acute SHE session, which included controlled room temperature, lighting, and restricted use of technological devices before bedtime, following a late-night competition. The study reported a significant improvement in sleep quantity of the players. Similarly, other studies show acute SHE sessions improve TTB and sleep quantity among athletes, with no significant impact on other objective sleep measures such as SL and SE.9,55\n\nThese findings from our study partially align with previous research,16 as we observed significant changes only in SL and not in measures of sleep quality or quantity. The SHE recommendations we used were based on Nédélec, Halson,36 which identified effective strategies for improving sleep in soccer players. We purposely did not enforce a set bedtime to avoid disturbing participants’ usual sleep routines. This may be why we did not observe differences in sleep quality between the groups. However, our SHE strategy did have a positive impact on SL, resulting in a 37% lower SL in the SHEG compared to the CG. This finding is supported by a recent study, reporting an acute SHE session enhanced SL but may have sustained effects on other sleep parameters, emphasizing the need for ongoing support and reinforcement of sleep hygiene strategies in athletes.16 Further, O’Donnell and Driller9 found similar results, indicating that most sleep studies using SHE showed similar sleep quality but varied results in SL. SL improvement may be related to the timing of training, as it could have affected athletes’ core temperatures, thereby delaying the sleep onset time (SOT) and lowering SE percentages. Contradictory to our results, Caia, Scott18 demonstrated SL did not improve in professional rugby players across a two-week intervention period involving SHE. They noted that, even though the SHE session encouraged athletes to have an earlier bedtime, the actual SOT was delayed, resulting in a lower percentage of SE.18\n\nIn the present study, no significant effect was observed regarding the influence of inhaling LEO on sleep quality. Our findings suggest the SL value in the LEOG was slightly higher than in the SHEG and CSLG, although the difference was not statistically significant. However, it was also slightly lower than in the CG, again without statistical significance. This suggests any potential effect on SL in the CSLG was likely due to adherence to the SHE recommendations, rather than the LEO inhalation. Moreover, no significant effects of LEO inhalation were found on any of the actigraphy-based sleep indices. These results are consistent with prior research reporting inconclusive findings regarding the effectiveness of EOs in enhancing sleep. Lin, Lee56 conducted a meta-analysis on non-patient participants and reported overall heterogeneity between studies, indicating the lack of consistent evidence supporting the effectiveness of aromatherapy in improving sleep. The non-significant findings in our study suggest inhaling LEO may not have a substantial impact on objective sleep measures. It is important to consider individual variability in response to aromatherapy and the complexity of factors influencing sleep quality. Further research is needed to better understand the potential benefits and limitations of using EOs for sleep enhancement, considering factors such as dosage, timing, and individual preferences. The effects of EOs inhalation on sleep quality have been studied in different populations. Several studies conducted on different populations report a reduction in SL and an improvement in overall sleep quality with EO inhalation.28,57 Specifically, it has been found that one to three inhalations of EO before bedtime were more effective than continuous indirect inhalation over a 24-hour period.28 Other studies have also explored the positive effects of aromatherapy on sleep quality,31,58 although the exact mechanisms of action are not yet fully understood. Further, LEO is often recommended over other EOs due its potential sleep-inducing effects and safety (i.e., low risk of adverse effects).28,30 LEO has been found to not only improve sleep quality but also have beneficial effects of LEO on many clinical conditions (e.g., anxiety, depression, fatigue, and stress).31,59 In a study examining the effects of LEO inhalation for one night, improvements were observed in sleep quality, TTB, and SE, but not in SL, in healthy participants.58\n\nIn terms of evaluating the wellness index and mood states before and after the 7-day intervention period, the HI decreased in the SHEG (d = 0.96) and CSLG (d = 1.23) and was significantly lower in the CSLG compared to the CG post-intervention (d = 1.4), suggesting the combined effect of SHE and LEO inhalation had a positive impact on the participants’ well-being. Additionally, the fatigue score assessed by the BRUMS questionnaire decreased significantly in the CSLG (d = 1.59). Conversely, the SHEG and LEOG did not show significant decreases in fatigue scores, indicating the observed decrease in the CSLG was primarily influenced by the effects of LEO inhalation rather than the SHE intervention.\n\nA previous review showed varied effects of SHE on athlete fatigue levels.60 Studies found SHE interventions led to fewer awakenings and lower fatigue levels.19 SHE also improves sleep architecture, increasing deep and restorative sleep, leading to rejuvenation and reduced fatigue.61 Moreover, SHE includes strategies for managing stress and anxiety, benefiting both sleep quality and psychological well-being. Irwin, Cole62 demonstrated reduced distress and fatigue with SHE interventions.\n\nMoreover, recent studies showed EO inhalation influenced fatigue scores.63,64 LEO inhalation can lead to a decrease in fatigue through various mechanisms. Firstly, LEO possesses anxiolytic properties (anxiety-reducing). This can contribute to a decrease in fatigue, as anxiety and fatigue often coexist. LEO inhalation may reduce anxiety and improve mood, promoting relaxation and a sense of calmness.65 Additionally, the aromatherapeutic effects of LEO could have a significant impact on fatigue reduction. When inhaled, LEO stimulates the olfactory system, which in turn activates the limbic system in the brain responsible for emotions and mood regulation.66 This activation could induce a sense of calmness, relaxation, and overall well-being, thereby reducing fatigue.67 Neurophysiologically, LEO modulates the activity of neurotransmitters and receptors in the central nervous system. For example, LEO has been shown to interact with gamma-aminobutyric acid (GABA) receptors, which have an inhibitory effect on the nervous system, promoting relaxation and calmness; animal studies demonstrate LEO inhalation increases the expression of GABA receptors, further supporting its potential fatigue-reducing effects.68 Furthermore, the anti-inflammatory properties of LEO may contribute to fatigue reduction. Chronic fatigue is often associated with underlying inflammation, and LEO has been found to possess anti-inflammatory properties.69 Inhalation of LEO decreases the production of inflammatory cytokines in human subjects, suggesting its potential for reducing inflammation associated with fatigue.70\n\nThis study represents a pioneering effort to assess the effectiveness of LEO inhalation on sleep quality in athletes, particularly those who engage in late-evening training sessions. The lack of significant results may be attributed to individual variations in response to EOs. Indeed, it has been previously suggested that the variability in individuals’ sensitivities to aromatherapy treatments could potentially impact the outcomes of the study.71 In this context, a prolonged utilization of aromatherapy has been associated with a potential decrease in olfactory receptor sensitivity, resulting in diminished individual responsiveness and subsequently reducing the therapeutic impact of the aroma.71 To gain a more comprehensive understanding of the contrasting effects, future research should consider stratifying participants based on their response to EO inhalation.\n\nConsiderations when interpreting these results include the study’s duration, which may not have been sufficient to capture long-term changes in sleep quality. Additionally, it is important to explore the impact of different training content on physiological parameters such as blood pressure. For instance, investigating the effects of isometric training, dynamic training, and endurance training on blood pressure changes could provide valuable insights into their potential counter effects. The recommended dose of LEO inhalation in this study was two drops (0.14 mL) for a duration of 10 minutes before sleep. It is worth considering that this dosage may not have been sufficient to significantly improve sleep quality. Further research is necessary to fully understand the effects of EOs on sleep in athletes. Future investigations should focus on optimizing EO selection and accounting for individual variations in response. Conducting larger studies with longer intervention periods could yield more conclusive results on the impact of LEO inhalation on athletes’ sleep quality. Finally, it is important to explore different doses and timings of EOs. For sleep assessment, the use of polysomnography, which is universally identified as the gold standard method for sleep monitoring, is warranted.72\n\n\nConclusion\n\nCombining an acute SHE session with LEO inhalation yielded greater improvements in sleep quality, overall wellness, and fatigue scores compared to using them separately. The findings provided further corroboration for the positive effects of SHE and LEO inhalation on sleep pattern, mood states, and wellness, with the combined intervention showing a greater impact. While the statistical results in this study cannot be generalized, the multiple significant outcomes and their associated effect sizes may have two implications. Firstly, in accordance with Fisher’s original statistics,73 the significant findings warrant further research in this direction. Secondly, the synergistic effects of SHE and LEO could potentially serve as a safe and effective strategy for improving sleep quality and well-being indices in athletes following late-evening resistance training sessions.\n\nThe study was conducted in accordance with the Declaration of Helsinki, and the protocol received full approval from the Ethical Committee for the Protection of Southern Persons (CPP SUD N° 0520/2023) on 31st May 2023 and was registered at the Pan African Clinical Trial Registry (PACTR202306806244897) on 09th June 2023.\n\nPrior to their inclusion in the study, all participants received comprehensive verbal and written instructions that explained the procedures and potential risks involved. They were also informed of their right to withdraw from the trial at any point.", "appendix": "Data availability\n\nZenodo: https://doi.org/10.5281/zenodo.11066092. 74\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nTrial protocol: Zenodo: https://doi.org/10.5281/zenodo.11575185. 75\n\nCONSORT Checklist: Zenodo: https://doi.org/10.5281/zenodo.11368563. 76\n\nCONSORT FlowChart: Zenodo: https://doi.org/10.5281/zenodo.11577279. 77\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgements\n\nThe authors would like to thank the participants for their time and effort.\n\n\nReferences\n\nCook JD, Charest J: Sleep and Performance in Professional Athletes. Curr. Sleep Med. Rep. 2023; 9: 56–81. Publisher Full Text\n\nSargent C, Lastella M, Halson SL, et al.: How much sleep does an elite athlete need? Int. J. Sports Physiol. 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Res. 2018; 49(3): 337–365. Publisher Full Text\n\nFisher RA: On the mathematical foundations of theoretical statistics. Philosophical transactions of the Royal Society of London Series A, containing papers of a mathematical or physical character. 1922; 222(594-604): 309–368. Publisher Full Text\n\nSalem A: The impact of sleep hygiene education and lavender essential oil inhalation on the sleep quality and overall well-being of athletes who undergo late-evening training: a randomized controlled trial. Zenodo. [Dataset]. 2024. Publisher Full Text\n\nSalem A: Experimental protocol. Zenodo.2024. Publisher Full Text\n\nSalem A: Consort checklist. Zenodo.2024. Publisher Full Text\n\nSalem A: CONSORT Flowchart. Zenodo.2024. Publisher Full Text" }	[ { "id": "298909", "date": "25 Jul 2024", "name": "Martha J Greenberg", "expertise": [ "Reviewer Expertise Aromatherapy" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is a very good article on \" the effects of a single Sleep Hygiene Education combined with nightly Lavender Essential Oil inhalation for 7 days of late-evening resistance training sessions on sleep quality and mood states in trained athletes.\"\nMy two criticisms are: -The sample size is the very small n=42 even though the author states that an n of 32 would be adequate. -There is no specific section on limitations-I suggest that one be created and populated with them.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] } ]	1	https://f1000research.com/articles/13-720
https://f1000research.com/articles/13-718/v1	01 Jul 24	{ "type": "Research Article", "title": "Evaluating the Transformation of City Facilities under AMRUT: A Conceptual Model", "authors": [ "Joydeep Biswas", "Koustubh Kanti Ray", "Mohar Banerjee Biswas", "Anupriya Panda", "Koustubh Kanti Ray", "Mohar Banerjee Biswas", "Anupriya Panda" ], "abstract": "Background The objective of this research is to propose a method for evaluating the effectiveness of Atal Mission for Rejuvenation and Urban Transformation (AMRUT) schemes across different parameters and subsequently rank different cities based on the perception of resident citizens. The research contributes to the academic literature of urban management by suggesting a comprehensive evaluation model based on academic literature review, identifying an assessment method to assign criteria to the parameters of the selected evaluation model, and finally proposing an approach to rank select cities covered under AMRUT scheme based on the suggested quantified model.\n\nMethods Conceptual research model is suggested based on review of the past literature. The study further purposes a quantitative method Analytic Hierarchy Process (AHP) to operationalize the identified model by assigning weights to the criteria. Finally, the research demonstrates how the weighted model can be applied to rank cities under AMRUT scheme by using Technique for Order of Preference by Similarity to the Ideal Solution (TOPSIS).\n\nResults Conceptual model to assess the effectiveness of AMRUT scheme has been arrived at by reviewing past literature. The model is found to be exhaustive and applicable for the research problem being investigated. The study further identifies the method for assigning the criteria weights and then eventually how to apply it to rank cities covered under AMRUT scheme on those weights.\n\nConclusion The study contributes to the academic literature in the context of urban management by evaluating AMRUT scheme. The research proposes that impact of AMRUT can be studied by selecting a comprehensive evaluation model based on academic literature review, identifying an assessment method to assign criteria to the parameters of the selected evaluation model, and finally proposing a method to apply the weighted model to rank the cities covered under AMRUT scheme.", "keywords": [ "AMRUT", "Urban Management", "AHP", "TOPSIS" ], "content": "1. Introduction\n\nThe rise of globalization, characterized by the interlinked flow of trade, technology, and information across borders, acted as a powerful facilitator for urbanization. The mitigation of trade barriers and emerging global markets have propelled cities to become pivotal hubs for international businesses, attracting industries, jobs, and investment. Cities, with their diverse talent pools and research institutions, become incubators of innovation, further attracting skilled workers and entrepreneurs, and perpetuating the urbanization cycle. Moreover, globalized economies prioritize efficient transportation and communication networks, often concentrated in urban areas. This enhanced infrastructure attracts businesses and residents, creating a self-reinforcing cycle of investment and growth.\n\nIndia is widely recognized as the fastest-growing economy globally, with the consequential implications for the pace and character of urbanization. The amalgamation of burgeoning aspirations and expanding middle-class demographics, juxtaposed with insufficient planning for the inevitable surge in urbanization, presents a scenario fraught with social, financial, and environmental unsustainability (Gore & Gopakumar, 2015). The imperative confronting India’s planners and policymakers lies in significantly enhancing the urban eminence to accommodate future progress while safeguarding improved living ideals for municipal inhabitants. The Government of India (GOI) has actively embraced urban advance through strategic initiatives, including the establishment of above hundred new towns and metropolises to address demographic, financial, and secretarial necessities (Brown, 1984). Over the ensuing three decades, a considerable number of new urban centers were established, laying the groundwork for essential institutions supporting sustained urban expansion (Shaw, 2009).\n\nThe current phase of urban expansion strategy has witnessed a notable modification towards the privatization of urban strategy in India (Batra, 2009). A pivotal development during this period was the enactment of the 74th Constitutional Amendment Act, aimed at decentralizing decision-making by establishing elected urban local bodies (Batra, 2009). This move also entailed the devolution of essential functions related to city planning and service provision (Nandi & Gamkhar, 2013). Subsequently, new missions concentrating on different aspects of urban expansion have been launched. The notable ones include the Jawaharlal Nehru National Urban Renewal Mission (JNNURM), National Urban Livelihood Mission (NULM), Pradhan Mantri Awas Yojana (PMAY), HRIDAY, and Atal Mission for Rejuvenation and Urban Transformation (AMRUT) mutually covering almost all metropolises across India.\n\n\n2. Atal Mission for Rejuvenation and Urban Transformation (AMRUT) Scheme\n\nAs mentioned earlier, India is experiencing rapid development, accompanied by a significant increase in urbanization rates. The urbanization phenomenon is considered pivotal in the country’s overall development strategy. A primary focus of this urbanization drive is to enhance infrastructure and services, thereby elevating the living standards of the citizens. Launched in 2015 by the Government of India, the Atal Mission for Rejuvenation and Urban Transformation (AMRUT) stands as a comprehensive urban renewal initiative spanning 500 cities across the nation. This initiative incorporates elements akin to smart city development strategies, emphasizing private investments and long-term infrastructure enhancements (Priyadarshi, 2018). Notably, both AMRUT and smart city initiatives aim to stimulate reforms, focusing on infrastructure development that directly addresses the genuine needs of the populace. AMRUT underscores that infrastructure development should have a tangible impact on addressing the essential requirements of the people, leading to improved service delivery, resource mobilization, and greater transparency in municipal office operations. The initiative also places significant emphasis on cooperative partnerships, positioning states as equal stakeholders in the planning and execution of projects (Murugaiah et al., 2018).\n\nThe urbanization trend in India is escalating, and surpassing historical rates according to census data (2011). Given the centrality of urbanization in the city and national development, AMRUT’s objectives are structured around ensuring universal access to tap water with a guaranteed supply and sewerage connections for every household. Additionally, it aims to augment the aesthetic appeal of cities by fostering green spaces such as parks, mitigating pollution through the promotion of public transport, and facilitating non-motorized transport options like walking and cycling. AMRUT, serves as a mechanism to enforce key developmental areas. These initiatives mandate periodic reviews of approved projects to monitor progress, ensuring alignment with the central government’s plan for systematic implementation and sustained development.\n\nThe AMRUT program, inaugurated in 2015 with a visionary mandate to render all cities in India inclusive, sustainable, and citizen-friendly, has significantly influenced the nation’s urban development discourse. This flagship initiative, concentrating on enhancing fundamental infrastructure and living conditions within cities, particularly targeting low-income and marginalized demographics, warrants meticulous scrutiny to assess its accomplishments, impediments, and potential avenues for enhancement. With an allocation exceeding ₹73,000 crores invested in various projects as of January 2023, AMRUT stands distinguished for its commendable outcomes. Notably, the program has positively impacted the lives of over 5 crore individuals by ameliorating water supply and sanitation facilities—crucial components for public health and well-being. While AMRUT confronts inherent challenges, its demonstrable enhancement of the lives of millions of urban denizens, particularly those most susceptible, is evident. The program’s focused attention on core infrastructure, public spaces, and social equity establishes an admirable precedent for forthcoming urban development initiatives. The optimization of AMRUT’s impact hinges on addressing implementation gaps, ensuring an equitable distribution of benefits, and fortifying community engagement. These measures are pivotal in steering India’s urban landscape towards a more inclusive, sustainable, and citizen-friendly future.\n\nThe effective management of rapid urban expansion poses a tough challenge for policymakers in developing nations, such as India (Sanchez and Govindarajulu, 2023). The complexity of this challenge is compounded by the fact that cities in a swiftly growing country like India formulate disparate policies and plans, often crafted by diverse agencies, occasionally with objectives that may be conflicting and contradictory. Therefore, it is critical to assess the progress and success of urban management schemes like AMRUT.\n\nThe diverse nature of cities and their inhabitants significantly complicate the scheme evaluation process. The fact that AMRUT aims to achieve diverse and sometimes conflicting goals, makes it very challenging to evaluate its effectiveness as a single composite indicator. However, it is imperative for the policy makers to comprehensively assess urban management schemes like AMRUT with the objective of ensuring best possible resource management and further improve such transformational schemes. Identifying this research gap, this study outlines a mechanism to quantitatively evaluate AMRUT scheme in a composite manner by combining all its parameters. The study proposes Multiple Criteria Decision Making (MCDM) methods as the basis to evaluate the priority of urban development plan AMRUT, which inherently possess a subjective and often unquantifiable nature and arrive at a composite indicator. The study then further suggests a mechanism to compare various cities under AMRUT scheme based on the composite indicator thus developed.\n\nNumerous studies proposed composite factors as potential tools for evaluating such intricate and holistic plans (Blanke, Chiesa, & Crotti, 2013; Croes & Kubickova, 2013; Zhou, Muambe, Deng & Selin, 2015). However, certain studies have raised significant concerns regarding the utilization of composite factors for urbanization plan evaluations (Mendiola & Volo, 2017). Notable concerns include disparities in definitions (Zhou, Muambe, Deng & Selin, 2015), the absence of a consensus on evaluation parameters (Crouch, 2011), the selection of pertinent and efficacious parameters (Mazanec et al., 2007), the oversight of geographical, economic, and market-related differences among diverse cities (Croes, 2011), and a lack of clarity on the procedural establishment of composite factors (Mazanec & Ring, 2011).\n\nTo fill this research gap, this study contributes to the literature in the context of urban management by evaluating AMRUT scheme and its impact on the applied cities. The research proposes that the impact of AMRUT can be studied by selecting a comprehensive evaluation model based on academic literature review, identifying an assessment method to assign criteria to the parameters of the selected evaluation model, and finally proposing a method to apply the weighted model to rank the cities covered under AMRUT scheme. Therefore, the contribution of this research is three-fold – selecting the evaluation model, identifying the assessment method AHP to operationalize the model by assigning criteria weights scientifically, and finally proposing TOPSIS as a method for ranking AMRUT cities by applying the weighted model.\n\n\n3. Selecting the evaluation Model\n\nRapid urbanization imposes significant strain on infrastructure, systems, services, citizens, and the environment, necessitating innovative and sustainable solutions (Caragliu, Del Bo, and Nijkamp, 2011). Smart Cities, as articulated by the British Standards Institution (BSI, 2014), require a strategic integration of physical, digital, and human elements to ensure a sustainable and prosperous life for their citizens. Critical to the design and implementation of the smart city concept is the evaluation of suggested solutions and actions against a city’s sustainability (Angelakoglou et al., 2020; Barsi, B., 2018; Caird et al., 2019; Shen et al., 2011). This evaluation process necessitates a common and shareable assessment model capable of measuring the effectiveness of interventions for smart city development and sustainable performance progress (Huovila et al., 2019; Antolín et al., 2020). The development of such an evaluation model serves as a valuable tool for decision-makers, aiding in the assessment of smart city interventions and facilitating comparisons of their effectiveness across cities with diverse characteristics. Additionally, a comprehensive model can engage authorities and stakeholders early in the process, crucial for successful smart city solution implementation and raising citizen awareness about proposed changes.\n\nDespite substantial investments and discussions on urbanization, little research has focused on evaluating smart city interventions and measuring outcomes for cities and citizens (Bis, 2013). The absence of a common definition and a standardized measurement approach for evaluating factors influencing city performance has further hindered progress. Without a robust evaluation model, judging the success of projects like AMRUT becomes challenging.\n\nThe first contribution of this study is to identify a robust theoretical model that comprehensively outlines the significance of diverse criteria influencing residents’ decisions in the selection of a city. Through this objective, we construct a conceptual model that provides a methodical understanding of the complex factors pivotal in residents’ city selection processes. This conceptual model is envisioned to serve as a foundational instrument for subsequent phases of the evaluation, ultimately facilitating policymakers and urban planners in the creation of more attractive and livable urban environments.\n\nThe existing researches on evaluating a city can broadly be categorized into three segments based on their focus of study. A group of studies have focused on evaluating specific destinations like, Australia (Dwyer, Mellor & Livaic, 2004), Hong Kong (Li, Song, Cao & Wu, 2013), South Korea (Kim & Dwyer 2003), Spain, Turkey (Kozak, 2003), and Southern Italy.\n\nThe second set of set of studies have explored a few particular aspects of cities. Dwyer, Forsyth & Rao (2002) focused on price component of destinations. Hassan (2000) proposed four determinants of evaluating a destination with sustainability being the major factor. The four determinants included comparative advantage, demand, industry and environment based on sustainability approach. Li, Song, Cao & Wu (2013) examined urban centers in terms of economic returns based on demand elasticity analysis.\n\nThe third group of research effort has been to develop conceptual models that are not restricted to specific cities or parameters thereby being more comprehensive in nature. A review of literature shows that there are three such major models. Dwyer et al. (2004) proposed a model that integrates national and firm resources as shown in Figure 1. The first element of their model is a set of resources comprising of endowed resources (natural as well as heritage), created resources, and supporting resources. Their second core component is Destination Management including government and private industry. The model shows the interaction between resources as well as Destination Management with situational conditions. The result of the interactions influences the destination competitiveness as an intermediary variable and the socioeconomic prosperity of residents as the final output variable.\n\nThe second model by Heath (2002) presents an evaluation model in the form of a house with four components of foundations, cement, building blocks and roof. Foundations, like climate and culture, provide necessary requirements for a city. Cement integrates different aspects and includes communication channels and information management. Building blocks emphasize success drivers like a sustainable development policy and framework. Fourth and final element of the model is roof that comprises ‘people’ part of like community focus and human resource development.\n\nCrouch and Ritchie (1999, 2006) and Ritchie and Crouch (2000, 2003) defined a conceptual model, based on Porter’s model (1990), for evaluating a destination shown in Figure 2, which is one of the most detailed work on the topic (Ayikoru, 2015). The model by Ritchie & Crouch (2003) is based on both Comparative and Competitive advantage concept. Comparative advantage is related to eight ‘Endowment Resource’ which are available to a destination like culture, physical, human, knowledge, capital, infrastructure, tourism superstructure and historical. Competitive advantage, on the other hand, is related to deployment of these resources. These are inventory, growth, effectiveness, efficiency, and maintenance. The model also recognizes two distinct and interrelated environments under which tourism destinations work–micro and macro environment. The micro environment includes “members of the travel trade (i.e. tour packagers, suppliers, retail travel agents, specialty channel partners, and facilitators), tourism markets, competitive destinations, and a destination’s public or stakeholders (residents of the destination, employees of the tourism and hospitality industry, citizen-action groups, the media, financial and investment institutions, relevant government departments, and immediate neighborhoods)” (Crouch & Ritchie, 1999). The macro environment comprises of externalities influencing the microenvironment like greater focus on natural environment, economic restructuring, changing demographics and rising complexity of technology.\n\nThe exhaustive model asserts that a city needs to be evaluated on five main components. The first of these components is core resources and attractors that comprise the primary appeal for staying in a particular destination like the climate of a city. The second component includes the set of supporting factors and resources that support the core resources, like accessibility to the city and the infrastructure. The third attribute focuses on destination policy, planning and development highlighting the importance of common understanding amongst stakeholders. The fourth dimension describes the role of urban management to enhance the appeal of core resources and attractors (e.g. marketing, availability of capital and human resource development). The final element consists of qualifying and amplifying determinants that have the capability to limit the scale or potential of the city. These factors could be its geographical location, safety and security, and the overall cost of living. The model further comprises of 36 sub-categories grouped under these five criteria (Ritchie and Crouch, 2000, 2003).\n\nThis research proposes that the conceptual model of Ritchie and Crouch (2000, 2003) is an appropriate model to evaluate the effectiveness of AMRUT based on the perception of citizens. The first reason for selecting this model is its comprehensiveness and exhaustiveness accounting for almost all the factors (Crouch, 2011; Li, Song, Cao & Wu, 2013). The second reason for selecting this model is that it is one of the most extensively cited model in the literature (Crouch, 2011; Ayikoru, 2015; Botti & Peypoch, 2013). Third, this model has been widely adopted by researchers in the academic literature. Some of the prominent studies that based their study on the model are Cracoli and Nijkamp (2009), Dwyer et al. (2004), Enright and Newton (2004), Botti and Peypoch (2013), and Zhang, Gu, Gu & Zhang (2011). Finally, results of empirical studies like Enright and Newton (2004) have found support for the model. This study proposes to evaluate the effectiveness of AMRUT scheme on the five criteria and thirty-six sub-criteria adopted from the Ritchie and Crouch (2003) model as shown in Figure 3.\n\n\n4. Identifying the method to operationalize the Model\n\nThe previous section discussed the identification of the conceptual models based on a literature review to list the criteria and sub-criteria on which the AMRUT scheme can be evaluated (Ritchie & Crouch, 2003). The review highlights that the evaluation process is characterized by an extensive list of multiple criteria that are mostly subjective and unquantifiable. As noted earlier, the evaluation process of choosing a model must be followed by selecting an assessment method to arrive at a composite indicator to operationalize the model. Having chosen Ritchie and Crouch’s (2000, 2003) conceptual model for evaluation, the study now focuses on identifying the assessment method. The assessment method should thus fulfill the objective of combining all the diverse criteria into one Composite Indicator (CI) with appropriate weights for each indicator. This CI would therefore be a mathematical combination of individual indicators that represent different dimensions of the AMRUT evaluation and provide stakeholders with a holistic picture.\n\nMany recent studies have attempted to arrive at a CI to measure multi-criteria concepts (Blanke, Chiesa, & Crotti, 2013; Croes & Kubickova, 2013; Enright & Newton, 2004; Tseng & Chen, 2013; Cracolici & Nijkamp, 2009). Once the CI is calculated, it can be used to assign different weights to the five criteria and thirty-six sub-criteria and applied for empirically testing the effectiveness of AMRUT schemes in the cities where it is implemented. Since multiple criteria need to be considered while operationalizing the model, the assessment approach should be Multiple Criteria Decision Making (MCDM) methods. MCDM is a general term for a group of quantitative methods to help decision making in problems where multiple criteria and alternatives are involved. As the evaluation of the AMRUT scheme by adopting Ritchie & Crouch’s (2003) model attempts to understand how a citizen perceives different aspects of urban management from a set of possible alternatives based on multiple criteria, the problem of assigning weights to these diverse criteria can be approached as an MCDM problem. In the present study of evaluating the AMRUT scheme’s effectiveness, when extensive criteria have been identified, it is relevant to give weights to these criteria (Dwyer & Kim, 2003; Crouch, 2011). There are multiple ways in which weights can be assigned to these criteria. For instance, all attributes can be considered equally important De Keyser & Vanhove (1994). Some of the methods that can be applied to assign weights through quantitative research include Importance Performance Analysis (Enright & Newton, 2004), simple descriptive analysis (Tseng & Chen, 2013), factor analysis (Gooroochurn & Sugiyarto, 2005), ranking method based on citizen response (Garau-Taberner, 2007), statistical model of PLS_PM (Mazanec & Ring, 2011; Esposito Vinzi, & O’Connor, 2014), and Information Entropy Weights (Zhang, Gu, Gu & Zhang, 2011). The more recent methods to assign weights include Multi Criteria Decision Analysis (MCDA) method ELECTRE I (Botti & Peypoch, 2013), Principal Component Analysis (PCA) (Huang, Li, Zheng, & Li, 2006; Cracolici & Nijkamp, 2009), and cluster analysis (Spencer & Holecek, 2007).\n\nAnalytic Hierarchy Process (AHP), one such MCDM method, first proposed by Saaty (1980), is a mathematical process in which all the factors involved in decision-making are structured in a tree hierarchy and assigned weights. AHP has been used to address decision-making in a number of interdisciplinary contexts where weight assignment to multiple criteria is the goal. However, despite its utility and relevance there seems to be no study that has applied AHP to operationalize multiple criteria in evaluating urban management schemes like AMRUT. Therefore, the present study proposes that AHP an MCDM can be applied for weight assignment of multiple criteria and sub-criteria to evaluate their relative relevance in urban management. This does not seem to have been attempted in urban planning literature until date, thereby filling a literature gap. A detailed description of AHP and how it can be applied to assign weights to the model have been provided in the next section.\n\n\n5. Research methodology\n\nThe proposed study employs an integrated approach combining the Analytic Hierarchy Process (AHP) and the Technique for Order of Preference by Similarity to the Ideal Solution (TOPSIS) to evaluate the effectiveness of the Atal Mission for Rejuvenation and Urban Transformation (AMRUT) scheme in selected cities. The methodology consists of several phases:\n\nPhase 1: Development of Hierarchical Structure using AHP\n\nStep 1: Hierarchical Decomposition\n\n○ Problem Definition: Define the main goal of the evaluation, which is to assess the effectiveness of the AMRUT scheme in various cities.\n\n○ Decomposition into Criteria and Sub-criteria: Decompose the main goal into five primary criteria and thirty-six sub-criteria based on relevant literature and expert consultations. These criteria represent different dimensions of urban transformation and rejuvenation.\n\n○ Hierarchy Construction: Organize these criteria into a hierarchical structure with the main goal at the top, followed by primary criteria and then sub-criteria. The specific courses of action (i.e., the cities under evaluation) are represented at the lowest tier.\n\nStep 2: Measurement Methodology\n\n○ Pairwise Comparisons: Conduct pairwise comparisons among the elements within each level of the hierarchy. Respondents (citizens in this case) will compare each element against every other element at the same level in terms of their relative importance concerning the element in the upper hierarchy.\n\n○ Nine-point Scale: Use the conventional nine-point scale for AHP to facilitate these comparisons, where 1 indicates equal importance, and 9 indicates extreme importance of one element over another (Table 1).\n\nStep 3: Prioritization and Consistency Check\n\n○ Priority Calculation: Calculate the priority weights for each element by normalizing the pairwise comparison matrices and solving the eigenvalue problem.\n\n○ Consistency Ratio: Compute the Consistency Ratio (CR) to ensure the reliability of the comparisons. A CR of 0.1 or less is considered acceptable. If the CR exceeds this threshold, respondents may need to reassess their comparisons to improve consistency.\n\nPhase 2: Evaluation Using TOPSIS\n\nStep 4: Data Collection through Survey\n\n○ Questionnaire Design: Develop a structured questionnaire to collect data on the relative importance of criteria and sub-criteria from citizens. The questionnaire will include definitions of each criterion and sub-criterion to ensure clarity.\n\n○ Likert Scale: Use a Likert scale (1 to 5) for respondents to rank the importance of each criterion and sub-criterion, where 1 signifies “Not Important” and 5 signifies “Very Important”.\n\n○ Sampling Strategy: Implement a robust sampling strategy to ensure a representative sample of the population in each city under the AMRUT scheme. The sampling can be stratified based on demographics, geographical areas, or other relevant factors.\n\nStep 5: Application of the TOPSIS Method\n\n○ Attribute Normalization: Normalize the collected data to ensure all attribute values are on a comparable scale. This step is crucial as TOPSIS requires commensurable units.\n\n○ Weighted Normalization: Multiply the normalized values by the weights obtained from the AHP analysis to get the weighted normalized decision matrix.\n\n○ Ideal Solutions Identification: Determine the positive ideal solution (PIS) and negative ideal solution (NIS). The PIS maximizes benefit criteria and minimizes cost criteria, while the NIS does the opposite.\n\n○ Distance Calculation: Calculate the Euclidean distance of each alternative (city) from the PIS and NIS.\n\n○ Relative Closeness to Ideal Solution: Compute the relative closeness of each city to the ideal solution. Cities closer to the PIS and farther from the NIS are considered more effective under the AMRUT scheme.\n\nStep 6: Ranking and Analysis\n\n○ City Ranking: Rank the cities based on their relative closeness to the ideal solution. The city with the highest score is considered the most effective in implementing the AMRUT scheme.\n\n○ Interpretation and Recommendations: Analyze the results to interpret the effectiveness of the AMRUT scheme in different cities. Provide recommendations for improvement based on the findings.\n\nPhase 3: Integration and Validation\n\nStep 7: Model Integration\n\n○ Framework Integration: Integrate the AHP and TOPSIS methodologies into a coherent framework. Ensure seamless data flow and consistency between the two methods.\n\n○ Validation: Validate the integrated model through expert reviews and pilot testing. Adjust the model based on feedback to enhance its reliability and robustness.\n\nStep 8: Final Application and Reporting\n\n○ Implementation: Apply the validated model to assess the impact of the AMRUT scheme in the selected cities.\n\n○ Reporting: Prepare a comprehensive report detailing the methodology, analysis, results, and recommendations. Include visual aids like charts and graphs to enhance understanding.\n\n○ Dissemination: Share the findings with relevant stakeholders, including urban planners, policymakers, and the general public, to facilitate informed decision-making and policy development.\n\nThe Analytic Hierarchy Process (AHP) stands as a prominent and significant technique for decision-making (Xu, 2012). This approach falls under the classification of Multi-Criteria Decision-Making methods, integrating subjective or objective assessments into a comprehensive model through the utilization of pairwise comparison matrices. The foundational principles of AHP, encompass three pivotal components (Wind and Saaty, 1980):\n\n○ Hierarchical Decomposition: AHP initiates by decomposing a complex problem into a hierarchical structure, wherein each level comprises a manageable set of elements. Successively, each element undergoes further division into sub-elements until reaching the fundamental components of the problem. The specific courses of action are typically represented at the lowest tier of the hierarchy. A distinguishing feature of AHP is its adaptability, allowing decision-makers the flexibility to devise hierarchical structures tailored to the specific context.\n\n○ Measurement Methodology: A systematic measurement methodology is employed to establish priorities among elements within each stratum of the hierarchy. This entails decision-makers conducting pairwise comparisons, evaluating each set of elements in relation to those in a higher stratum. Structurally, the hierarchy is organized into a series of paired comparison matrices, with participants tasked to assess off-diagonal relationships. The nine-point scale, conventionally employed in AHP analysis, facilitates the quantification of these assessments.\n\n○ Measurement Theory for Prioritization and Consistency: The measurement theory serves dual purposes by determining the priorities of the hierarchy and assessing the consistency of judgmental data provided by participants. Prioritization involves pairwise comparisons of elements at the same level concerning an element from the upper hierarchy. Subsequently, a consistency ratio is computed to scrutinize the reliability of judgments. Inconsistencies may arise due to inadvertent errors or exaggerated judgments during pairwise comparisons. A consistency ratio not exceeding 0.1 is deemed an acceptable upper limit, as advocated by Hafeez et al. (2002).\n\nThe result of the Analytic Hierarchy Process (AHP) is the determination of an optimal choice among alternative decisions with quantified weights to the multiple criteria involved. This model incorporates both quantitative and qualitative factors into its analytical model. AHP presents numerous advantages, including its capacity for managing subjective judgment, inherent consistency tests, and appropriate measurement scales (Chen & Huang, 2004). Given these advantages of AHP in various contexts, its application was deemed fitting for evaluating the appropriateness of adopting the Atal Mission for Rejuvenation and Urban Transformation (AMRUT) within the context of the present study. The operationalization of the model would require the citizen respondents to compare the five criteria and thirty-six criteria amongst themselves through an AHP scale that shall measure these relative comparisons. The AHP comparison scale has been provided in Table 1.\n\nThe scale also needs to be accompanied by the definition of these criteria and sub-criteria so that the citizen respondents are clear on what they are comparing. The definition of these criteria and sub-criteria for the evaluation of AMRUT projects is provided in Table 2.\n\n\n6. Applying the weighted evaluation Model to assess the impact\n\nAfter assigning weights to the criteria and sub-criteria of the model, it is proposed that the model can be applied to measure the effectiveness of the AMRUT scheme in the cities where it is implemented. This study proposes to use the weighted attributes for evaluating specific cities covered under the AMRUT scheme through the Technique for Order of Preference by Similarity to the Ideal Solution (TOPSIS) method introduced by Hwang and Yoon (1981), offers a ranking approach in practical applications. Its core principle involves identifying alternatives that exhibit the shortest distance to the positive ideal solution and the greatest distance to the negative ideal solution simultaneously. The positive ideal solution aims to maximize benefit criteria while minimizing cost criteria, whereas the negative ideal solution seeks to maximize cost criteria while minimizing benefit criteria. TOPSIS utilizes attribute information to provide a cardinal ranking of alternatives based on the weighted criteria on which the different criteria are being evaluated without the requirement of preferences to be independent. The only requirement for the application of TOPSIS is attribute values are numeric and possess commensurable units which is fulfilled by the current study.\n\nThe survey designed for implementing the TOPSIS method is proposed to determine the optimal ranking of selected cities under the AMRUT Scheme, considering predefined criteria obtained from the Ritchie & Crouch (2003) model, and associated weights as calculated from the AHP survey. The TOPSIS calculation requires the respondents to rank each of the 5 criteria and 36 sub-criteria for all the cities where the effectiveness of the AMRUT scheme needs to be evaluated. The ranking shall be done on a Likert scale ranging from 1 to 5, where 1 represents “Not Important” and 5 signifies “Very Important”. The data collection process can be conducted through surveys. The seamless integration of Multiple Criteria Decision Making (MCDM) methods, a robust sampling strategy, and a structured questionnaire, informed by a comprehensive literature review, collectively establish a robust model for exploring residents’ perspectives on cities governed by the AMRUT initiative. The proposed integrated methodology of this study has been summarized and shown in Figure 4.\n\n\n6. Conclusion\n\nThe speedy urbanization in India, pushed by initiatives such as the AMRUT, assumes a central and strategic role in the nation’s comprehensive development strategy. Launched in 2014, AMRUT is strategically aligned to enhance living standards through extensive urban renewal initiatives across 500 cities. Bearing a resemblance to smart city development, the initiative places a significant emphasis on private investments, long-term infrastructure improvements, and a genuine responsiveness to the needs of the citizens. Cooperative partnerships, treating states as equal stakeholders, are integral to the planning and execution phases.\n\nIn evaluating the sustainability and effectiveness of AMRUT from the citizens’ perspectives, this study leverages Ritchie & Crouch’s well-regarded conceptual model, recognized for its comprehensive approach to destination competitiveness. The research further proposes application of the Analytic Hierarchy Process (AHP) in decision-making and scientific weight assignment approach for assessing the appropriateness of AMRUT’s strategic criteria. The study suggests that surveys among residents in AMRUT-governed cities, utilizing a questionnaire structured around AHP’s principles shall help the policy makers assign specific weights to the diverse parameters of AMRUT. The analysis of AHP results shall reveal a robust consensus among decision-makers in prioritizing factors within the dimensions of Core Resources, Supporting Resources, City Enhancement Factors, and City Management Factors and the thirty-six sub criteria. Finally, the application of the weighted model to measure the effectiveness of AMRUT scheme in specific cities shall help the policymakers understand which cities are doing better on which all criteria as per the residents.\n\nImplications for policymakers would include identification of critical factors and addressing service gaps to ranking cities based on project outcomes, redesigning projects, and formulating policies that consider the multifaceted influences on urban development success. On a societal level, the study offers profound insights into societal transformation, aids informed decision-making for individuals, identifies social requirements, and evaluates the sustainability of AMRUT projects from a socio-economic perspective. This research contributes to a comprehensive understanding of the impact of the AMRUT initiative on urban development, providing actionable insights for policymakers, fostering informed decision-making, and promoting sustainable and inclusive societal growth. The study underscores the intricate interplay of various factors in shaping urban development and emphasizes the indispensable role of citizen perspectives in accurately evaluating the success of ambitious initiatives like AMRUT.\n\n\nEthics and consent\n\nEthical approval and consent were not required.", "appendix": "Data availability\n\nNo data is associated with this article\n\n\nAcknowledgments\n\nThis research is part of the Short-Term Empirical Research Project of the Indian Council of Social Science Research (ICSSR) with project number ICSSR-CIS-2023-1626.\n\n\nReferences\n\nAngelakoglou K, Batty M, Buckley P, et al.: Smart city policies: A spatial meta-analysis. Urban Stud. 2020; 57(12): 2773–2802.\n\nAntolín J, de Torre C , García-Fuentes MÁ, et al.: Development of an evaluation framework for smartness and sustainability in cities. Sustainability. 2020; 12(12): 5193. 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Manag. 2012; 95(1): 203–210.\n\nZhang H, Gu W, Gu J, et al.: The impact of mega-events on the tourism competitiveness of host cities: A case study of the 2010 Shanghai World Expo. Tour. Manag. 2011; 32(6): 1333–1345.\n\nZhou L, Muambe TD, Deng H, et al.: A review of systems thinking in sustainable urban planning. J. Environ. Plan. Manag. 2015; 58(5): 842–861." }	[ { "id": "310583", "date": "29 Aug 2024", "name": "Prasanth Warrier C B", "expertise": [ "Reviewer Expertise More than 27 years of teaching experience in Applied Mathematics / Statistics / Bio Statistics / Operation Research / Management Science / Operations Management/ Distribution Theory/Urbanization. Published 39 research articles at different Scopus/Web of Science recognized journals. Associated with many International Journals as a Reviewer." ], "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 work is clearly and accurately presented. The article met the objective of this research.It detailed a method for evaluating the effectiveness of Atal Mission for Rejuvenation and Urban Transformation (AMRUT). It well explained a comprehensive evaluation model based on academic literature review, identifying an assessment method to assign criteria to the parameters of the selected evaluation model. The ranking of select cities covered under AMRUT scheme based on the suggested quantified model is also presented. The statistical analysis and its interpretation is nicely narrated. The conclusions drawn adequately supported the objectives. The application of the weighted model to measure the effectiveness of AMRUT scheme in specific cities surely helps the policymakers to understand which cities are doing better on which all criteria as per the residents.\n\nIs the work 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": "12325", "date": "30 Aug 2024", "name": "Joydeep Biswas", "role": "Author Response", "response": "Dear Professor Prasanth, My heartfelt thanks to you for such a positive review of the article. I and my co-authors are grateful to you for reviewing our research paper and sharing feedback with us. Regards, Prof Joydeep KIIT School of Management (KSOM) KIIT University" } ] } ]	1	https://f1000research.com/articles/13-718
https://f1000research.com/articles/13-717/v1	01 Jul 24	{ "type": "Research Article", "title": "‘What seems to be missing is actual reality’ Why don’t postdocs engage with career-focused professional development?", "authors": [ "Mollie Etheridge", "Jessica Hampton", "Becky Ioppolo", "Lara Abel", "Noam Tal-Perry", "Katherine Dawson", "Marie Collier", "Zoe Matthews", "Kate Murray", "Sylvia Osborn", "Liz Simmonds", "Steven Wooding", "Jessica Hampton", "Becky Ioppolo", "Lara Abel", "Noam Tal-Perry", "Katherine Dawson", "Marie Collier", "Zoe Matthews", "Kate Murray", "Sylvia Osborn", "Liz Simmonds", "Steven Wooding" ], "abstract": "Background The relationship dynamics between postdoctoral researchers and their managers – typically Principal Investigators (PIs) - can directly and indirectly impact the professional development activities that postdocs participate in. Although career and development (C&D) conversations can be a platform through which both parties communicate about the postdoc’s development needs and career aspirations, it is unclear how frequently postdocs are having these types of conversations. Evidence from across the UK indicates that this group receive little feedback on their performance.\n\nMethods To explore interventions that could empower postdocs to initiate C&D conversations, we conducted a pilot study at the University of Cambridge where current postdocs were offered workshops utilizing two widely available professional development tools. Both workshops included 360-degree feedback interventions, and we hypothesized that the feedback gathered through these tools could give postdocs both a launching pad for facilitating a conversation with their PI and address the aforementioned feedback shortfall.\n\nResults Although most of the participant sample reported already having C&D conversations, those who did not report as such demonstrated mixed feelings about whether facilitating these types of discussions is even part of the PI role. Insights from participants’ engagement with the 360-degree feedback tools also show that participants were mindful of time constraints when seeking feedback, indicating that the usefulness of such interventions may be inhibited by wider cultural issues in the sector.\n\nConclusions Through the development of what we call ‘the researcher development framework, this study highlights the shortcomings of using professional development interventions to address cultural issues.", "keywords": [ "Mentorship", "careers", "research culture", "postdoctoral researchers", "professional development", "feedback" ], "content": "Introduction\n\nIn Higher Education (HE) settings, the term ‘research culture’ refers to ‘the behaviours, values, expectations, attitudes, and norms of our research communities’ (Royal Society, n.d.). Powell et al. (2024) have put forward a framework for research culture that aims to offer a comprehensive view of the aspects that support open, inclusive, and supportive research cultures and related initiatives. Validated through consultations and interviews with key stakeholders and researcher networks, the framework is organised into four areas:\n\n1. How research is managed and undertaken;\n\n2. How research ensures value;\n\n3. How people are supported;\n\n4. How individuals engage with others;\n\nAlthough Powell et al. (2024) recognise there may be some overlap among the categories, they group effective leadership and management under point four, and professional and career development opportunities within the remit of point three. With an emphasis on the role of career and development (C&D) conversations, in this paper we assume that points three and four are in fact inextricable. In other words, we posit that the professional relationship between postdoctoral researchers (postdocs) and their managers – typically Principal Investigators (PIs) - can directly influence the opportunities for development that postdocs feel willing/able to engage in.\n\nEven in cases where the PI-postdoc relationship is regarded as ‘good’ by the postdoc, there is a tension between the immediate production of research outcomes and the longer-term development needs of junior researchers. PIs are obligated to their funders, and they may sometimes prioritize project-focused tasks over people-focused activities. Conversely, postdocs – who are typically employed on fixed-term, project-based contracts – must explore other research opportunities, secure their own funding, or pursue a different career path should they wish to progress professionally. Whilst developing advanced technical skills may facilitate the research being undertaken in the moment, other forms of professional development, including so-called ‘soft skills’, can help postdocs make deliberate career choices by providing insight on navigating the (academic and non-academic) workplace and on their personal strengths and weaknesses. Both PIs and postdocs may nevertheless be concerned that these forms of development take time away from the projects they are currently employed to complete. In the modern university, academic contribution is assessed through outcome-based metrics, leading to a narrow focus on outputs and publications, things researchers believe will improve their separate and joint academic profiles (Herschberg et al., 2018; Van Der Weijden et al., 2016).\n\nEfforts to enhance research culture need to consider these dynamics in researcher relationships and identify ways of empowering postdocs to navigate these dynamics effectively. In this paper, we contribute to this endeavour by presenting the findings from a pilot study with 14 STEM postdocs at the University of Cambridge. As part of our research efforts, we focused on three interrelated aspects of the postdoc experience: engagement with professional development; C&D conversations; and the barriers faced when requesting and receiving feedback. Our specific objectives were to explore the types of C&D conversations that take place between postdocs and their managers, and to examine the extent to which readily available forms of training could prepare postdocs to facilitate productive conversations. This focus was justified by a common understanding amongst professional services staff (LS) of the difficulties Cambridge postdocs face in initiating productive conversations around their career aspirations and development needs. This experience is not unique to Cambridge, however, and evidence indicates that early career researchers in general do not receive either regular feedback on their performance or guidance in terms of their career aspirations (Gottlieb et al., 2021).\n\nAlthough our research design examined the effectiveness of a variety of professional development tools (including the Myers Briggs Type Indicator), this paper concentrates on the impact of the 360-degree feedback interventions. In the Wellcome Trust Townhalls report (2020a), some members of the research community proposed implementing 360-degree feedback opportunities to address the challenges associated with receiving feedback. We hypothesised that offering 360-degree opportunities to postdocs could both redress the feedback shortfall and provide them with a launching pad for initiating C&D conversations.\n\nIn this paper we explore three insights:\n\n1. PIs have a direct and indirect influence on postdoc engagement with professional development activities. A lack of C&D conversations can lead postdocs to believe that their PI has no interest or support for these activities. While an increase of such conversations could help postdocs understand their PI's perspective, our findings indicate that postdocs do not always view these conversations as a necessary part of the PI's role.\n\n2. The perceived effectiveness of 360-degree feedback tools in facilitating C&D conversations is partially dependent on the type of feedback requested and the postdocs’ level of experience.\n\n3. The potential benefits of professional development activities on PI-postdoc relationship dynamics are undermined by the performance-focussed context of the modern university.\n\nIn what follows we will first discuss the significance of career and development conversations in the workplace generally, after which we will explore the feedback shortfall experienced by early career researchers and the potential ways in which 360-degree feedback interventions may mitigate this shortfall. We will then outline the design of the pilot study we conducted before reviewing our findings and putting forward an original framework of researcher development.\n\n\nCareer and development conversations\n\nC&D conversations are formal and informal discussions which incorporate at least one of the following characteristics (Right Management, 2016; Hirsh, 2018):\n\n• The giving/receiving of feedback about performance.\n\n• Reflection on strengths and weaknesses.\n\n• The identification of development needs and opportunities.\n\n• The giving/receiving of guidance on professional aspirations.\n\n• The management of sensitive workplace matters.\n\nC&D conversations differ from traditional performance evaluations, which are often pre-planned and take place on an annual basis. C&D conversations serve to evaluate and enhance performance in ways that align with the dynamic nature of organisations and the people within them. Frequent C&D conversations can allow employees and their managers to identify and address workplace issues as they arise (Kidd et al., 2004; Winter, 2013).\n\nAn ongoing debate exists in non-academic settings regarding the integration of appraisal discussions focused on past performance with developmental conversations aimed at personal growth and skill enhancement (Evans, 2017). It is also recognised how it can be difficult to ascertain exactly what makes for a ‘good’ career and development conversation. Throughout this paper, there is similarly a recurring theme that explores whether a ‘good’ conversation is necessarily satisfying, and to whom it is so. For instance, is it still a good conversation if an employee is provided with feedback that they may not want to hear? And how can we define a ‘good’ conversation in relationships with an inherent power imbalance, where the person receiving feedback may feel unable to challenge it?\n\nThe Vitae (2019) Concordat to Support the Career Development of Researchers acknowledges the role of institutions, funders, researchers, and their managers in supporting researcher careers. Signatories of this document, including the University of Cambridge, are committed to enhancing their research environment through specific actions. The Concordat states that the managers of researchers must ‘identify opportunities and allow time for their researchers to develop their research identity and broader leadership skills’ (p.7). Similarly, researchers are expected to ‘take ownership of their career, identifying opportunities to work towards career goals’ (p.7). Still, a Wellcome Trust (2020b) survey of over 3,800 members of research staff found that less than half of respondents (44 %) had had career conversations with their manager in the past year. Even fewer respondents reported receiving support such as introductions to relevant individuals within or outside their field (34 %), career advice and guidance (34 %), and training opportunities for skill development (31 %).\n\nThe nature of academic careers leads to uncertainty regarding the significance of career and development discussions, as well as who bears the responsibility for initiating them. Firstly, there is a reluctance amongst researchers to view the PI role as a management one. This may stem from the fact that transitioning from a postdoc to a PI is marked by a tension between ideas around leadership and management. Whilst a postdoc’s primary responsibility is to support the research activities on the PI’s research project, the PI oversees – manages – the people who execute this work (Vitae, 2019; Prosper, 2022). With this shift comes a concern that leadership manifests as a form of top-down control and ‘form-filling’ (Flinders, 2020, 2022), matters which may be perceived to take away from necessary research work and which strip researchers of their autonomy and integrity. Furthermore, and even though we consider the concept of ‘distributed leadership’ relevant to academic work, distributed leadership being a collaborative social process that is dispersed throughout the organization (Grajfoner et al., 2022), popular notions of research ‘excellence’ continue to focus on the singular - that is, the researcher who stands out from the pack (for example, see University of Nottingham, n.d.; University of York, n.d.). This is leads to a disconnect between the management tasks that PIs are expected to undertake with and on behalf of their team, and the sector-wide celebration of ‘leader’ attributes that ultimately separate researchers from the others they work with and above.\n\nSecondly, there is the issue of whether postdoctoral researchers view postdoc work as a stepping stone to academic tenure. The conventional trajectory of academic careers, particularly in STEM, supposes that a PhD candidate graduates into postdoc work, during which they will prepare to secure their own funding and become a group or project leader. Given the fiercely competitive context of early career academic work, postdocs may concentrate on the research activities that they believe will translate into immediate outcomes and outputs. In doing so, they may neglect areas of professional development, such as C&D conversations, that could benefit them in the longer-term. Postdocs may therefore find it challenging to initiate these discussions with their PI. This may be due to concerns regarding taking up the PI’s time on something that may not necessarily further project work, and the optics of looking less focused on core skills and outputs.\n\nGuidance at the postdoc stage is nevertheless paramount. Nowell et al. (2020) report that even though most postdocs have the objective of pursuing an academic career, less than 20 % obtain permanent positions in academia. This underscores the necessity of preparing for a wide range of careers beyond academia. However, partly because of the significant time and effort required to establish an academic career, as well as the perception that successful academics ‘persevere’ when faced with rejection and uncertainty (Afonja et al., 2021), there is an enduring perspective that leaving the profession is akin to, or may feel like personal or professional failure (Gewin, 2023). Postdocs may therefore be reluctant to engage with training associated with non-academic careers (Nowell et al., 2020), as doing so entertains the possibility of this ‘failure’. They may also worry that being seen to engage with such training will be regarded by colleagues and supervisors as a lack of commitment to the ‘vocation’ (Weber, 1989 [1946]) - the calling – of research.\n\n\n360-degree feedback\n\nIn the Wellcome Trust (2020b) report, ‘What Researchers Think about the Culture They Work In’, 360-degree feedback was suggested as a means by which poor academic practice can be identified and deterred. In subsequent Townhall proceedings (Wellcome Trust, 2020a), 360-degree feedback was also put forward as one avenue for ‘improving research culture’, though the report did not elaborate on how these improvements might take place or even who the recipients of 360-degree feedback would be. 360-degree feedback involves collecting performance evaluations from various sources, including supervisors, coworkers, subordinates, and external parties. This feedback process also commonly includes self-evaluation. Anonymised 360-degree feedback is thought to be particularly powerful in improving self-awareness and mitigating the negative effects of biases and power dynamics in the process of giving and receiving feedback (Hensel et al., 2010).\n\nThere are some challenges to implementing 360-degree models. Providing feedback can be time-consuming, which can result in a lack of responses from raters. It can also be difficult to identify appropriate raters. Research indicates that reliability increases with the number of raters, with 10 being considered a desirable number. For a rater to have a strong baseline knowledge of the individual being rated, it is suggested that raters have at least 10 interactions with the individual (Hensel et al., 2010). Furthermore, 360-degree feedback can have negative effects on self-confidence should the employee feel ostracised or judged unfairly by the raters (Karkoulian et al., 2016; Peng & Zeng, 2017). To ensure the effectiveness of the feedback received, it has been proposed that professional support, such as mentoring, is made available to the individual receiving feedback (Vukotich, 2014).\n\nSince 2021, the UK Research and Innovation (UKRI) Future Leader Fellows (FLF) Development Network (n.d.), a UK-wide programme providing leadership and career development opportunities to ‘world-class’ research and innovation leaders in academia and industry, has provided its members with access to a leadership-focused 360-degree feedback model that obtains anonymous feedback and is paired with a 1-2-1 coaching session. Outcomes from the pilot study of this model, which were acquired from Dr Steve Joy, the Deputy Director of the FLF Development Network, observed how 360-degree feedback increased FLF’s awareness around their responsibilities, strengths, and weaknesses. These early insights suggest that 360-degree feedback can support research leaders in identifying and building on good leadership traits.\n\nAt the time of writing, we know of no research on the effectiveness of providing postdocs with 360-degree feedback opportunities. Some potential benefits may be surmised. Advancing 360-degree feedback opportunities to postdocs acknowledges the nexus of relationships in research work. Indeed, PIs may not possess all the information on a postdoc’s performance, especially if they manage a large research group or if the postdoc assumes additional roles such as teaching and mentoring. In enabling postdocs to solicit feedback from various parties, 360-degree feedback may provide postdocs with a more holistic understanding of their skill set and development needs. Furthermore, in conveying the message that performance can be evaluated from multiple perspectives, 360-degree feedback may also encourage postdocs to seek guidance from sources outside of their PI. In this study, we aim to provide empirical evidence to support these speculations.\n\n\nResearch design\n\nOur research design began with the hypothesis that improving the frequency and quality of C&D conversations may help postdocs establish a more informed understanding of their role and their performance within it. Due to the respective obstacles that PIs and postdocs face in broaching such discussions, we sought to identify readily available professional development interventions we believed to be capable of equipping postdocs with the confidence to facilitate C&D conversations. To identify suitable interventions, we consulted with careers professionals at the University of Cambridge and conducted a search for readily available - ‘off the shelf’ - training interventions. We then categorised the identified tools into themes (e.g. self-understanding, feedback from others, conversations with managers, and cross-cutting tools).\n\nOur pilot study was intended to consist of four workshops. Each workshop was designed to include two tools from different themes, each with a different cost associated with delivery. The workshops were advertised to current postdocs at the University of Cambridge. We focussed on this group because of the significant number of postdoc researchers present at the university, which totals just over 4,000 (Postdoc centre n.d.). We hoped this meant we would have a large participant sample from which we would draw reliable insights. However, following practical challenges with recruiting enough participants to carry out all four workshops, only two were carried out. The structures of the workshops we did run are displayed in Table 1. Due to the relevant comparability of the 360-degree feedback tools offered across these workshops, this paper focuses on the effectiveness of these interventions.\n\nWorkshop one delivered one high-cost tool, ‘Challenging Conversations’. The second tool, ‘At My Best’ (AMB) was a low-cost strengths-based 360-degree feedback tool that enables individuals to seek positive feedback from up to 12 ‘raters’, such as colleagues, managers, staff, friends, and family. Workshop two combined an informative session on putting together a narrative CV (low-cost) with access to a customised 360-degree feedback tool and follow up coaching session (high-cost). The 360-degree feedback model was based on a variation offered in the FLF Development Network.\n\n\nMethods\n\nWe evaluated the effectiveness of the workshops through a combination of survey and interview methods. The full experimental protocol is displayed in Figure 1 and was approved by the Cambridge Psychology Research Ethics Committee (approval number: PRE.2023.029) on 20th April 2023. Participants were recruited through flyers, which were distributed over social media, email channels and posted around the university and in postdoc groups. Prospective participants were advised that participating in the research was a condition of attending the workshops.\n\nEach of the blocks and icons within represents a stage in the data collection process, starting from the left-hand side. Our data collection efforts started with the first survey. Then, on the same day as the workshop, we held focus groups with the participants. We then distributed survey two after participants had been given enough time to engage with all the information around the professional development interventions incorporated in the workshops. The orange block indicates a two-month pause in the data collection process, during which participants were expected to undertake a career and development conversation with their manager. After this, as illustrated in the final green block, we distributed one final survey and invited participants to a one-to-one online research interview.\n\nData was collected at three points: before the workshop, immediately after the workshop, and two months after the workshop. As stated in our approved ethics application to the Cambridge Psychology Research Ethics Committee, written consent was obtained at the point when participants registered for the workshop. Consent was verbally reaffirmed at the start of each workshop and prior to the research interviews. Per the Participant Information Sheet (available at Etheridge et al., 2024), participants were aware that they could withdraw from the study at any point during the data collection phase. Prior to attending the workshop, participants were required to answer survey questions on their demographic background, postdoctoral experience, relationship with their PI, and confidence with career conversations. This included responding to a Personal-Growth-Initiative-Scale II (PGIS-II) (Robitschek et al., 2012), which considers the extent to which a person seeks out opportunities to grow and initiate change in oneself. We incorporated the PGIS-II as we believed participant responses would allow us to account for the influence of personality differences in the effectiveness of the workshop interventions.\n\nIn the days following the workshop, participants were invited to complete a second survey. This questionnaire regarded their impressions of the interventions they had been presented with. We also explored these impressions via semi-structured focus groups, which were conducted immediately after the workshops had taken place.\n\nTwo months after the workshops, participants were sent a final survey enquiring about the influence of the development tools on any career and development conversations that had taken place in that time. This survey included a second PGIS-II scale. Our intention was to see if the interventions had a quantifiable effect on participants’ attitudes to personal growth and how, if at all, these changes developed over the course of the study. Participants were also invited to join one-to-one semi-structured interviews. All research instruments, along with collected data and Atlas.ti 23 code manager, is available on the project Open Science Framework repository (see Etheridge et al., 2024).\n\nIn total, we recruited 14 participants. Eight attended the Challenging Conversations/AMB workshop, and six attended the bespoke 360 feedback/Narrative CV workshop. All 14 participants were involved in group interviews and four attended individual interviews. Interview data was analysed using a general inductive approach (Glaser & Strauss, 2017). This is where raw data is compared against raw data before being organized into categories to create a framework capturing key themes and processes. The analysis was undertaken on Atlas.ti 23 Desktop. The exact process is listed below:\n\n1. Researchers BI and ME did an initial read through of all the interview transcripts.\n\n2. Researchers BI and ME then re-read the transcripts and began identifying ‘upper’ and ‘lower’ level themes in the data. Upper-level themes connect with the research aims and focus (e.g. career conversations, PI-postdoc relationships, intervention-specific observations), whereas lower-level themes include things tangential to the research aims or which were unanticipated by the researcher (Thomas, 2006).\n\n3. Researchers BI and ME explored potential relationships between the identified codes.\n\n4. Researchers BI and ME compared their findings and effort was made to merge themes.\n\n5. Researcher LA read the transcripts twice before reviewing the themes identified by researchers BI and ME.\n\n6. Researchers BI, ME and LA met twice to share feedback before coming to an agreement on the final ordering of the themes.\n\n\nFindings\n\nThe main findings from the interview and survey data are as follows:\n\n1. Most participants reported having productive C&D conversations with their PI. In instances where participants felt there was a lack of these conversations, it seemed that they did not regard career development discussions as a crucial aspect of the PI's role.\n\n2. The 360-degree feedback tools tested proved problematic for most postdocs in the study, particularly those who were more junior. This related to either the difficulty the postdocs’ experienced in receiving the requested feedback or concerns around the type of feedback requested.\n\nIn this section we discuss these observations, paying attention to participants’ reported experiences with both career conversations and the 360-degree feedback tools offered as part of the research.\n\nDespite its small size, the participant sample captured reasonable diversity in postdoc experiences and backgrounds. Of the 14 participants, eight participants identified as male, five identified as female, one participant identified as non-binary, and another preferred not to specify their gender identity. The participants belonged to various age groups, as depicted in Figure 2.\n\nParticipant (postdoc) age range. A vertical bar graph depicting the age range of the participants, as determined by the responses given to survey one.\n\nThe participants also reported a diverse range of ethnicities: eight participants identified as White, three of Asian descent, and one participant each as North African/Mediterranean, White Eastern European (Jewish, Greek-Cypriot, Italian), and Mixed or multiple ethnic groups. Regarding confidence when conversing in English, seven participants reported being ‘extremely’ confident, three reported being ‘very’ confident, one person reported feeling ‘reasonably’ confident and another chose not to specify their confidence level.\n\nParticipant characteristics point to a diversity of research experience. The years in which participants were awarded their PhDs ranged from 2000 to a projected graduation date of 2024. Two participants had yet to submit their PhD thesis. Figure 3 shows the gender split regarding the years since PhD submission. The number of postdoc positions held varied from zero to five, with some individuals having had multiple postdoc experiences.\n\nParticipant (postdoc) gender split and years since PhD submission. A horizontal bar graph illustrates the gender split in participants’ professional experience, understood to be the number of years since their PhD submission, as determined by the responses given to survey one.\n\nThe majority of participants worked in a STEM capacity; however, a number of academic disciplines are represented in the data set, including:\n\n• Biological and Medical Science\n\n• Chemistry\n\n• Education\n\n• Engineering and Materials Science\n\n• Geography\n\n• Psychology\n\nOut of the 14 participants, 12 had one primary PI/supervisor and two participants had two supervisors. Two participants were reported to the same PI. Seven of the participants reported to male primary PIs and 7 reported reporting to female primary PIs. For the participants with more than one supervisor, one was supported by a male primary PI and a female secondary PI. The other was supported by two male PIs. PIs had varied levels of experience:\n\n• Half of the participants reported their primary PI/supervisor as having over 20 years of experience\n\n• Four reported their primary PI as having six-ten years of experience\n\n• Three believed their PI had less than three years of experience for their primary PI\n\nAs shown in Figure 4, participants reported that the female primary PIs had relatively less experience. For those with two PIs, one participant worked under two supervisors with over 20 years of experience, and another participant worked under one PI with less than 20 years of experience and a second PI with less than three years of experience.\n\nA horizontal bar graph displays the gender distribution and years of professional experience of the Principal Investigators of postdoctoral researchers involved in our study, as determined by the responses given to survey one.\n\nIn response to the initial survey, most participants (12/14) reported having positive C&D conversations with their PI. Eight responded that their PI is either ‘extremely’ or ‘very’ interested in supporting their development and nine reported how such conversation felt either ‘extremely’ or ‘very’ much like a positive experience. Although we predominantly recruited participants who, on the surface, did not require support facilitating C&D conversations, our findings still point towards some tensions around identifying whether C&D conversations have taken place and whether, or to what extent, these conversations should be satisfying and/or an integral part of the PI role.\n\nOf the 12 participants who had had a C&D conversation with their PI, Participant 8 was the only one who felt negatively about their PI’s ‘genuine openness’ to C&D conversations, selecting ‘rarely’ on the Likert scale. This participant also reported that their PI was only ‘slightly’ interested in their professional development and that their C&D conversations felt only ‘slightly’ like a positive experience. Although participant 8 identified more barriers to holding productive conversations with their PI than any other participant, noting language (‘somewhat of a barrier’), cultural (‘extreme barrier’), class (‘extreme barrier’), age (‘somewhat of a barrier’), career stage (‘somewhat of a barrier’), and care responsibilities (‘somewhat of a barrier’), they also referred to the PI’s generally dismissive attitude to these conversations. During the focus group discussion, this participant outlined how, at the start of their role, they had taken professional development seriously:\n\nIn the beginning I took it very serious. I planned everything, but end of the day there is [no] encouragement to discuss it with the PI, and the PI is only interested to just sign the form. There was no discussion.\n\nDespite the absence of productive C&D conversations with the PI, participant 8 reported being ‘somewhat satisfied’ with the general conversations they have about their career ambitions, disclosing that they speak about these ambitions to mentors, colleagues and ‘postdoc societies’. They also continue to describe the relationship with their PI as a positive one:\n\nIn terms of relation-- relationship, like it was very good in the beginning. First few months or one year … [it then] become kind of stretching, but otherwise it's a business relationship. It’s very good. But it's not there yet where we can discuss career, other things.\n\nParticipant 8’s experience suggests a postdoc and PI can have a positive relationship despite an absence of constructive C&D conversations. Similar sentiments were expressed by Participants 5 and 7, who reported not having any C&D conversations with their PI. Both participants felt lack of time and support were at least ‘moderately important’ factors in preventing them from thinking about their career, and both felt that lack of support from supervisor was a ‘very important’ barrier when looking to access training for wider workplace skills. During a focus group discussion, Participant 5, who had been a postdoc for two years and who reported having progress meetings with their PI between two and six times a year, elaborated on their outcome-driven relationship with the PI:\n\nThey [PIs] need people who can get the idea, develop the idea, make a story if they want to write a paper, and after that, all these things, and they, they just want to the papers. You know, but I thought that this is the general methodology in this university … They just get credit from postdocs and other people … anyway, today [after this workshop] I learned that there, there are some other PIs that, they support, they contribute to scientific discussions.\n\nSimilarly to Participant 8, Participant 5 qualified that they were happy with the relationship to their PI: ‘I like to be independent, so I'm extremely happy with my situation’.\n\nParticipant 7 reported being ‘somewhat satisfied’ with the general conversations they have about their career ambitions and support, claiming to regularly have discussions with mentors, colleagues and friends. In focus groups, Participant 7 shared that they had been a postdoc for six months. Due to this participant’s relative inexperience, it can be surmised that the PI may not yet have initiated routine C&D conversations. Still, Participant 7 was cognizant of their own reluctance to start these discussions. When asked about barriers to thinking about their career, they noted ‘mental capacity’ and ‘lack of time’. Participant 7’s contribution during focus groups also pointed towards a project-focused orientation on their part: ‘you're always thinking of project publications, like funding, like all these things, but career development doesn't necessarily come into that frame line.’\n\nParticipant accounts point to some tension in what it means to have a satisfying conversation. Two participants, 11 and 13, reported feeling ‘extremely’ and ‘somewhat’ dissatisfied with conversations regarding their career ambitions. Despite their dissatisfaction, these participants felt that their PIs were ‘genuinely’ open to supporting their career ambitions, stating they were ‘always’ supportive (Participant 11) or supportive ‘most of the time’ (Participant 13). Both of these participants also mentioned that discussions about career and development would ‘sometimes’ conclude with a clear set of actions and that these conversations were generally positive experiences, rated as ‘very’ and ‘moderately’ positive. Acknowledging how their satisfaction levels may have been affected by their own attitudes, Participant 11 noted that their anxiety sometimes hindered productive discussions, with Participant 13 going on to express: ‘My perception of my supervisor's level of support for my career planning might be more of a challenge than his actual level of support.’\n\nCareer stage may also have influenced these participants’ experience of C&D conversations. Both were in the final stages of their PhD and working under PIs with over 20 years of experience. As they moved towards the end of their PhD work, Participants 11 and 13 may therefore have been looking for more support from their PIs but lacked the capacity to action such advice or request it. In the focus groups, Participant 11 said:\n\nmy supervisor is very supportive if I bring issues to her. If I identify things and bring it to her. But she um {PAUSE}, I feel like she doesn't really provide the options I could then look into … if I want something very specific from her, then she's like, you know, really on it. And she's-- she's emotionally very supportive of my struggles and what I want to do.\n\nParticipant 13 also discussed difference in career stage, and acknowledged the challenges of communicating with someone with a significantly different level of experience:\n\nI think sometimes it can be easier to discuss these things with somebody that's closer to your career path. I think one of the things that's hard about discussing it with the PI or a supervisor is my supervisor is on the verge of retirement. He's a long ways off from where I am now and I think there can be a little bit of a disconnect.\n\nConcerns around seniority recur throughout the findings, though most notably in relation to the perceived usefulness of the 360-degree feedback interventions.\n\nWorkshop one encouraged participants to use the AMB tool to gather feedback from up to 12 raters. Via non-anonymised feedback, AMB aims to give individuals better insight into their strengths and so draws from the understanding that ‘strengths-based’ thinking can improve performance, enhance positive emotions, and minimize negative emotions in employees (Hodges and Asplund, 2010; van Woerkom & Kroon, 2020; Wang et al., 2023)\n\nIn focus groups immediately following Workshop one, seven out of the eight participants in attendance expressed concern around the benefits of strengths-based feedback. Only three used the tool to solicit feedback: participant 7 (5/5), 8 (1/3) and 3 (11/11). The bracketed numbers indicate the number of reviewers contacted and responses received.\n\nSurvey three, which sought to gauge participants’ perspectives on the usefulness of the workshop tools, was completed by six of the workshop participants, four of which reported that AMB was ‘not at all’ useful in improving conversations with PIs or research managers. Participant 7 was the only respondent who selected a somewhat positive response (‘moderately useful’). In survey one, Participant 7 stated that they had not yet had any C&D conversations with their PI. In survey three, they reported having had a one, noting that their PI was ‘very’ interested in their development. As Participant 7 reported being in the first year of their first postdoc, it is difficult to ascertain the extent to which this conversation was facilitated by the AMB tool.\n\nDespite successfully obtaining feedback from eleven raters, Participant 3 was uncertain what to do with the information they had been given:\n\nI don't know if I learned anything … I made sure I sort of contacted everyone afterwards who'd done it for me and most of them in person actually like had a bit of a chat about it … it was just like kind of a happy, uplifting experience, even if it didn't, like, necessarily change anything particularly.\n\nAlthough Participant 3 used AMB to generate multiple conversations with their raters, their perspective returns to the idea that, for some postdocs, time spent on development only feels worthwhile if the development activity can facilitate actions. Concerns around how others would perceive a request to fill in an AMB feedback form were expressed by two participants, who did not choose to engage with the tool. Participant 6, who claimed to work under a PI who was ‘extremely’ interested in his development, stated:\n\nI thought about it quite a lot. But it was then kind of a trade-off between and I had already thought ‘this doesn't seem useful to me’ and then it's always, you know, if you ask this kind of thing from colleagues or PIs that, um, I wondered how they would see such tools and I thought they would rather be a bit annoyed by it.\n\nDespite their critiques, workshop participants still identified an occasion when AMB feedback would be useful. Participant 7 noted: ‘it might be really helpful for someone who's not confident, who's not aware of their strengths’. This sentiment was shared by participant 4: ‘I think if you're someone who has difficulties looking, asking for feedback, um, then sure it might be useful. But I do tend to do that already.’\n\nParticipants in Workshop two were invited to engage with the 360-degree model we had modified from the one offered in the FLF Development Network, which solicits anonymous, qualitative feedback and comes paired with a 1-2-1 coaching session. Four of six workshop participants used the tool, with three reporting that it was ‘very’ or ‘extremely’ useful in improving their conversations with their PI. The remaining participant did not reply to our request for feedback.\n\nExcept for Participant 13, the participants who engaged with this tool were experienced postdocs, having submitted their PhD theses between 2000 and 2015. Whereas two Workshop two participants have since gone on to secure their own funding, Participant 13 was yet to submit their PhD. They spoke of feeling vulnerable about requesting feedback:\n\nI am so early in my path, when I looked at the website and it was asking me to give 9 referees I sort of flinched … reaching out to my supervisor, I don't think that's an unreasonable ask by any stretch of the imagination, but I think, thinking about a couple of other colleagues that are more senior to me and asking them to invest that time, also reaching out to other colleagues, I just was a little hesitant.\n\nParticipant 13’s hesitancies speak to two challenges junior postdocs may face when soliciting this kind of 360-degree feedback. Being so early in their career, this group have had limited opportunity to consolidate a network from which to request feedback. Junior postdocs may therefore struggle to identify appropriate raters who meet the criteria for reliability, such as needing to have had at least ten interactions prior to feedback being requested (Hensel et al., 2010). Participant 13’s concern also speak to the time commitment involved in giving feedback, a sentiment echoed by participant 10, who did not solicit feedback via the 360 tool: ‘9 letters is a lot … and I’m junior and I don’t know … So then asking for them it’s li--it's time consuming’.\n\nParticipant 9, who at the time of the workshop had been a postdoc for 20+ years, reiterated that the anonymous 360-degree tool may not be appropriate for novices researchers:\n\nit could be difficult to have enough confidence to use 360 when you’re just starting and you're not, you know-- you don't need-- you don't want negative feedback which may be forthcoming. You just want to develop and get all those achievements and things in place, but then when you are mid-stage or senior stage there’s more that you want to get out from that [360-degree feedback].\n\nSimilarly, when talking about their decision to undertake the 360 opportunity, participant 12 reflected on their upcoming transition to a leadership role:\n\nThis [anonymous 360-degree feedback] was always something I was looking for because … I’ll be a PI, have a PhD student, et cetera. And I just thought this is a really good moment to think it through … And when you said ‘would I be ready in my kind of junior years?’, I would say, you know, I wasn’t looking for a criticism … and now I just want to actually find out what people think, because I'm now in position to impact other lives in a bit more meaningful way.\n\nIn summary, insights from the different 360-degree tools indicate that postdoc experience may affect which model is deemed appropriate and/or utilised. Postdocs with more experience may be ‘ready’ and have the network necessary for soliciting and working through anonymous 360-degree feedback. In contrast, novice postdocs, who may lack confidence or access to feedback, may benefit from engaging with strengths-based tools, such as AMB.\n\nOne factor that seemed to impact both the participants' engagement with the 360-degree feedback tools and their willingness to participate in broader professional development was the concern for using both theirs and other people’s time effectively. Participants compared the open-ended nature of development activities with the certainties they felt were promised in ‘technical trainings’:\n\n…if I sign up to learn how to use a microscope, I'm going to leave knowing how to use the microscope. Whereas when you sign up to professional development, you, there's more of a hesitation of: Am I gonna get what I thought I was gonna get? (Participant 2).\n\nFor some participants, this uncertainty is exacerbated by activities that are too ‘idealistic’, and which do not sufficiently account for the cultural issues within academic work:\n\noften in workshops it's like, ‘Oh yeah, you should, um, for example, develop your strength and weaknesses and you have to do networking and put yourself out there’, … what seems to be missing is actual reality because whenever you talk to [someone] … involved in choosing applicants, usually it boils down to, ‘Oh, the first thing we look at is: How many publications do you have? Which journals are they in?’ (Participant 6).\n\nTime commitments have been discussed in Nowell et al.’s (2020) research, where the authors concluded that postdocs are likely to attend training that they perceive to be useful. As these perceptions are partially determined by the quality of structure and facilitation, the challenge is that such quality is often determined at or prior to the point of delivery. This means there is a shared issue of getting postdocs in the room in the first place. Although the ability to generalise our research findings is restricted by the small sample size, the difficulty we experienced with participant recruitment indicates a profound limitation with trying to support postdocs’ career development and their access to C&D conversations via training interventions such as those offered in our study. Crucially, although the participants we did recruit appeared to have generally positive relationships with their PIs, participant accounts highlight how a PI can have a direct influence on the usefulness attributed to professional development activities. For participant 8, this was a positive influence: ‘my PI told me to sign up to this, like, “I know we don't have an issue talking about things, but it should be good for you” … I felt like, especially with career development, she's very supportive’. Conversely, Participant 5's perceived ability to engage in professional development was influenced, in part, by what the PI considers to be a valuable use of time.\n\nI wrote to her that I'm sorry, due to attending this workshop I may not be able to attend on time, the group meeting. Then she got back to me, and she said that you have to give us a report just to show us some gain from this workshop.\n\nParticipants were asked to fill out the PGIS-II (Robitschek et al., 2012) on three occasions – prior to the workshop, immediately after the workshop, and two months after the workshop. Only a handful (3/14) of participants filled out the second survey, and therefore the results from that survey were not analysed. Most participants (6/8 and 4/6 from first and second workshops, respectively) filled out surveys one and three. While this sample size is relatively small to conduct inferential statistics, it allowed us to make descriptively assess whether the workshop led to any observable change in their score. The PGIS-II is made up of four subscales – Readiness for change, Planfulness, Using Resources, and Intentional behaviour, each assessed by 3-5 items on a 6-points scale ranging from “Disagree strongly” (0) to “Agree strongly” (5). As in Robitschek et al., the questions for each subscale were averaged, with items not answered given the participant’s scale average. Descriptive findings (see Figure 5) showed an increase in the average score following the workshops for three of the subscales - Readiness for Change (mean difference d¯=0.33±0.30 standard errors (ste) from the mean), Planfulness (d¯=0.36±0.32 ste), and Using Resources (d¯=0.17±0.22 ste), along with a decrease in the average score of the Intentional Behaviour subscale (d¯=−0.13±0.25 ste). None of the results were observed to be significant at an alpha of 5% (t(9) = 0.526-1.127, p = .289-.611), which was not unexpected given the small sample size, as mentioned. The data along with the analysis script in R are available in the study’s online material.\n\nBar graphs depict group-averaged subscale score before attending the workshop and two months after, with error bars depicting 1 standard deviation from the group mean. Scatter plots depict individual participant scores, with the diagonal line depicting the identity line (such that Before score = After score, with participants above the line scoring After > Before, and vice-versa).\n\nThis is a flow chart of the factors informing postdoc engagement with professional development activities. This framework was initially developed as an outcome space of the core themes that emerged from the interviews. These themes, and the number of codes within them, were identified by researchers BI and ME, with the codebooks publicly available at Etheridge et al. (2024).\n\n\nDiscussion\n\nOur study aimed to understand how or, indeed, if, development interventions can improve researcher relationships. Specifically, we tested whether giving postdocs at the University of Cambridge access to 360-degree feedback tools could address the feedback shortfall experienced by postdocs and equip them with the skills to initiate successful C&D conversations. Our ability to comment on this is limited. Only half of the participants made use of the 360-degree feedback tools and most of these participants were already having conversations of this kind with their PI. We did, however, observe that a postdoc’s level of experience can affect their willingness to request feedback from multiple raters. From this we can surmise that future applications of the 360-degree feedback should take into account the diversity of needs amongst postdocs, and effort should be made to inform postdocs of why each model could be appropriate for their career stage. Between AMB and the anonymous 360-degree tool based on the FLF model, participants identified that AMB may be preferable for improving self-efficacy amongst new postdocs whereas the latter model’s emphasis on constructive feedback was better placed for those looking to make the transition to a leadership role. Following the suggestion offered in the Wellcome Trust Townhalls Report (2020a), that 360-degree models may be used to instil positive research culture, further investigation should be conducted into the benefits of implementing different 360-degree opportunities for researchers with varied experience and responsibilities.\n\nOur findings also highlight concerns that postdocs have regarding managing their own time as well as their PIs' time. For some participants, what counted as an ‘effective’ use of time was informed by the needs of the project and the PI, and not by their individual career needs or aspirations. Thus, while research culture initiatives are increasingly concerned with the support obligations PIs have to their postdocs, and, conversely, with empowering postdocs to take ‘ownership’ of their careers (e.g. Vitae, 2019), our findings suggest that project-focused orientations make it unclear to postdocs just how much support they can expect or request from either their PI or the support networks available in their institutions. Furthermore, if, as our study suggests, some postdocs assume that being supported in their career is not a standard practice of PIs, then they may find themselves caught at a support and training deadlock wherein they need and would benefit from support but are neither given it nor do they feel entitled to request it.\n\nThe above themes, alongside other less-commonly mentioned topics from the surveys, focus groups, and interviews have been consolidated into a conceptual framework for postdoctoral engagement, illustrated in Figure 6. This framework, which was developed iteratively by three members of the research team (ME, BI and LA) explores the processes that facilitate postdoc engagement with professional development activities. It consists of six interconnected themes: broader cultural factors (national funding structures and research cultures), institutional influences (institution-specific policies and structures), postdoc and PI characteristics, relationship dynamics, and postdoc engagement levels. These themes interact in a hierarchical manner. Broader cultural and institutional factors serve as a backdrop, shaping postdocs' and PIs' career trajectories and expectations. These, in turn, influence the dynamics of their relationship, impacting the direction and content of any C&D discussions that occur as well as the postdoc’s engagement in professional development activities. Such engagement is also influenced by factors individual to the postdoc, including personality, professional aspirations, and interpretations of broader cultural influences within academia. Indeed, such pressures were observed in participants’ regard for the different 360-degree feedback tools, which were affected by factors such as perceptions around time and applicability of the feedback requested.\n\nWithin the framework, the interplay between PI-postdoc dynamics and postdoc engagement with professional development challenges the division of these matters proposed by Powell et al. (2024). Recognizing the influence PIs can have on postdocs’ engagement with professional development is important to consider when developing interventions to ensure the effective leadership and management of researchers. A number of actors across the sector are already doing this. For example, in 2020, the University of Liverpool’s Prosper programme pioneered a PI network that provides a platform for principal investigators across the UK to meet, share experiences and discuss best practices (McBride, 2023). Moreover, the University of Glasgow have recently piloted a ‘Catalyst Mentoring’ scheme in which collegial conversations between research staff and senior staff were seen to be impactful in supporting self-awareness around relating to others and making conscious career planning decisions (Guccione, 2023). Additionally, during a workshop for PIs around ‘Challenging career assumptions’, Careers Coach, Dr Elizabeth Adams, explored how the assumptions researchers make about careers within and beyond academia can exacerbate barriers to engagement with career development. She encouraged attendees to attempt minimise this influence by asking their postdocs predominantly open-ended questions about their career; by being alert to the postdocs’ inner critique; and by signposting them to support services and networks available at their institutions (Prosper, n.d.).\n\nOn the one hand, interventions such as these are of high importance in seeking to break the silence around the influence of researcher relationships on postdoc careers choices and trajectories. On the other hand, these interventions may suffer from the same issue that we faced with recruiting postdocs to the study – that is, their opt-in nature attracts those who are already thinking about these issues, those who consider them a good use of time, and, crucially, those who feel able to use their time in this way. As the Researcher Development Framework illustrates, these considerations are influenced by wider cultural issues, which speaks to the difficulty of trying to challenge narrow, project-focussed attitudes in a policy landscape that encourages these attitudes at the same time that it endeavours to change them. Participant 6 argued that missing from professional development activities is a sense of ‘reality’, a sentiment we interpret as referring to the lived experience being a researcher in a profession characterized by competition, precariousness and vast racial, gendered and ableist disparities in recruitment (Sarabi & Smith, 2023), research commissioning and funding (Wellcome Trust, 2022), promotion (Lerchenmueller & Sorenson, 2018; Rollock, 2021), attribution, publication and citation practices (Hengel, 2022). While development initiatives may acknowledge these conditions and seek to confront them, this reality still hinders engagement with such initiatives and thus preserves the status quo. It is not necessarily the case, then, that development activities are missing or failing to consider this ‘reality’. Rather, the thing which is missing is the ability to realise conditions in which all researchers across different experience levels can and feel able to effectively engage with and request support and development.\n\n\nConclusion\n\nIn this study, we explored interventions to empower postdocs to initiate C&D conversations with their PI. We offered workshops to current postdocs at the University of Cambridge utilizing widely available professional development tools. However, we found that only a few postdocs made use of the opportunity to engage in this training and many of those who did engage reported already having C&D conversations with their PI. This supports that, with our interventions, we did not manage to reach those postdocs who might need such training, including those with problematic relationships with their PI. Still, our analysis of the survey and interview data produced an overarching framework of the relationship between postdocs and their supervisors within the wider university and academic system. Our analysis reveals that an in-depth exploration of the various factors contributing to the quality of the PI-postdoc relationship is needed to better understand the challenges these parties face in not only prioritizing professional development but in defining professional priorities and expectations. We are currently launching a study, based on the framework we developed, which explores professional expectations of PIs and postdocs on the level of the self, others, the job role, and the wider academic system. We hope that this research will shed further light on possible avenues for supporting postdocs and their PIs to engage in meaningful C&D conversations and to unfold their professional potential.\n\n\nEthical approval and consent\n\nThis research study was approved by the Cambridge Psychology Research Ethics Committee (approval number: PRE.2023.029).) on 20th April 2023.\n\nAs stated in our approved ethics application to the Cambridge Psychology Research Ethics Committee, written consent was obtained at the point when participants registered for the workshop. Consent was verbally reaffirmed at the start of each workshop and prior to the research interviews.", "appendix": "Data availability statement\n\nRepository name: Open Science Foundation, “What Seems to be Missing is Actual Reality”, 10.17605/OSF.IO/CKTH7, Etheridge et al. (2024).\n\nThis project contains the following underlying data:\n\n000 Information on appendices\n\n001 Survey templates\n\n002 Post-workshop focus group protocol\n\n003 post-conversation interview protocol\n\n004 Interview analysis protocol\n\n005 BI - Atlas.ti code manager\n\n006 ME – Atlas.ti code manager\n\n007 Focus group transcript\n\n008 Focus group transcript\n\n009 Focus group transcript\n\n010 Focus group transcript\n\n011 Participant interview transcript\n\n012 Participant interview transcript\n\n013 Participant interview transcript\n\n014 Participant interview transcript\n\n015 survey results\n\n016 PGIS results\n\nStandards for Reporting Qualitative Research\n\nFor the purpose of open access, the authors have applied a Creative Commons Attribution (CC BY) licence to any Author Accepted Manuscript version arising from this submission\n\nThis research study meets the criteria set out by the Standards for Reporting Qualitative Research (SRQR). This is except for the title, which does not describe the methods used in the study but which still captures the range of topics and ideas presented in the paper.\n\n\nAcknowledgements\n\nThe authors acknowledge in-kind support provided by the University of Cambridge. We would like to thank our Project Board: Patrick Maxwell, Chris Young, Jeremy Baumberg, Diane Coyle, Tomas Coates Ulrichsen, Tim Harper, Peter Hedges, Andrea Hudson, Steve Joy, Michael Kenny, Raphael Lyne, and Jon Simons. In addition, we would like to thank our External Advisory Group: Anne Ferguson-Smith, Steph Bales, Stephen Curry, Catherine Davies, Matthias Egger, Steven Hill, Shomari Lewis-Wilson, Molly Morgan Jones, Iben Rørbye, Tom Stafford and Karen Stroobants. Furthermore, we would like to thank our project partners: Sarah de Rijcke, Jacqui Hall, Ulrich Rößler, Sara Shinton and Martine Vernooij.\n\nWe would also like to thank Steve Joy, who contributed by way of providing guidance and support during project development, and Kim Newton-Woof, who provided coaching to participants undertaking the 360-degree feedback opportunity mirroring that offered to Future Leader Fellows. Additionally, we are grateful to the many members of the University of Cambridge community and the Bennett Institute for Public Policy provided feedback throughout the project.\n\n\nReferences\n\nAfonja S, Salmon DG, Quailey SI, et al.: Postdocs’ advice on pursuing a research career in academia: A qualitative analysis of free-text survey responses. PLOS ONE. 2021; 16(5): e0250662. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nATLAS.ti Scientific Software Development GmbH: ATLAS.ti Mac (version 23.2.1) [Qualitative data analysis software].2023. 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Reference Source\n\nVukotich G: 360° Feedback: Ready, Fire, Aim-Issues With Improper Implementation. Perform. Improv. 2014; 53(1): 30–35. Publisher Full Text\n\nWang J, van Woerkom M , Breevaart K, et al.: Strengths-based leadership and employee work engagement: A multi-source study. J. Vocat. Behav. 2023; 142: 103859. Publisher Full Text\n\nWeber M: Max Weber’s ‘science as a vocation’. Lassman P, Velody I, Martins H, editors. Unwin Hyman; 1989.\n\nWellcome Trust: Evaluation of Wellcome Anti-Racism Programme Final Evalution Report—Public.2022a. Reference Source\n\nWellcome Trust: Evaluation of Wellcome Anti-Racism Programme Final Evalution Report—Public.2022b. Reference Source\n\nWellcome Trust: Wellcome Research Culture Townhalls Report.2020a.\n\nWellcome Trust: What researchers think about the culture they work in.2020b. Reference Source\n\nWinter J: Performance and Development Through Conversation. Experience-Driven Leader Development. John Wiley & Sons Ltd; 2013; pp. 347–353. Publisher Full Text" }	[ { "id": "298048", "date": "22 Jul 2024", "name": "Santiago Schnell", "expertise": [ "Reviewer Expertise Dr. Santiago Schnell applies mathematical", "computational", "and statistical methods to address complex biomedical problems. His research focuses on (i) developing standard methods for high-quality measurements in biomedical sciences and scientometrics", "and (ii) developing mathematical models to understand complex biomedical systems. Additionally", "Dr. Schnell has significantly contributed to the development and management of postdoctoral training programs at two academic institutions", "with the outcomes of one program published in The Journal of Physiology (2019", "597(9): 2317-2322)." ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nGeneral Comments\nThe first version of this work presents a timely exploration of the challenges postdoctoral researchers face in engaging with career-focused professional development. The paper's focus on the dynamics between postdocs and their principal investigators (PIs) is important, as is the examination of available feedback tools as a potential intervention. However, as it stands, this version of the paper is an anecdotal study with limited impact on our understanding of career-focused professional development opportunities for postdoctoral fellows. As a result of this, I cannot endorse this paper. Detailed reasons for my decision are stated below.\n\nMajor Points for Consideration\nIncorrect View of the Role of Mentors The first version of the paper incorrectly departs from the principle that principal investigators (PIs) do not view themselves as mentors responsible for the career development of postdoctoral fellows and that there are no incentives from funding agencies or academic institutions to promote mentoring. This view is not supported by my experience as a Principal Investigator, Academic Administrator, and the customs in academia. It indicates a major misunderstanding.\nThe success of faculty members is measured by the successful mentoring and placement of the individuals they mentor in their research groups. Faculty members are very proud to list the achievements and placements of their mentees, whether undergraduate and graduate students or postdoctoral fellows. Moreover, many research funding agencies require the incorporation of postdoctoral mentoring plans in research grants, which support postdoctoral fellows. For example, the US National Science Foundation requires mentoring plans as part of its funding process [1]. In the UK, the Wellcome Early-Career Awards also request mentoring plans for postdoctoral fellows from the mentor [2]. Additionally, the UK Research and Innovation encourages mentors to follow the principles of the Concordat to Support the Career Development of Researchers [3].\nThis reviewer has never been part of an academic institution where a PI is referred to as a manager of a postdoctoral fellow. The PI is generally referred to as a manager of technical staff or administrative staff, but not of trainees: undergraduate and graduate students, or postdoctoral fellows. Perhaps the University of Cambridge is different. However, I doubt that \"The Other Place\" has such a culture.\nThe authors should consult with a group of experienced active academics who are actively training postdoctoral fellows or serve as directors of postdoctoral studies.\nDefinition of Postdoctoral Fellow The first version of the paper lacks a clear definition of what constitutes a postdoctoral fellow. In the large majority of academic institutions, postdoctoral fellowships are advanced training positions with a limit of five to six years. Exceptions to this limit should be permitted only in cases where additional time and training are clearly needed to prepare the postdoctoral fellow for their future career. In the USA, it is exceptional to find an academic institution that will appoint someone who has already served five years as a postdoctoral fellow again in a postdoctoral position. This has been a standard practice for over 20 years, which was promoted by the US National Academies [4].\nIncluding individuals with more than 5 to 6 years of postdoctoral experience would not be considered appropriate. Are those individuals postdoctoral fellows or research technical staff?\nThis aspect is crucial for understanding the context and limitations of postdoctoral training and should be incorporated into the study design.\nSmall Sample Size The small sample size (14 participants out of a population of 4,000 in one institution) further limits the study's generalizability and statistical power. The authors acknowledge this limitation, but it is bold to make broad and concluding statements about PI and postdoc dynamics with such a small sample. As a matter of fact, the sample is probably non-representative of the postdoctoral fellow population. Study participants were not randomly recruited and selected but voluntarily responded through flyers selectively distributed via social media, email, or campus.\nRecruitment Challenges The difficulty in recruiting participants, as noted by the authors, is a significant concern. It suggests that the very postdocs who might benefit most from such interventions are the least likely to engage with them. This could be due to various factors, such as the nature of the evaluation vehicle offered, workshops, time constraints, lack of awareness, or skepticism about the value of professional development.\nFocus on 360-Degree Feedback While the first version of the paper emphasizes 360-degree feedback, it doesn't fully explore other potential interventions or strategies to improve postdoc engagement with professional development. The literature suggests a range of approaches, such as individual development plans (IDPs), mentoring programs, career workshops, and individualized career counseling, that could be considered. The authors seem to be completely unaware of the extensive literature on postdoctoral training programs and resources available. [see, for example, 6, 7, 8, 9 and 10 to cite a few].\n\n360-degree feedback seems to be effective for individuals working in a large corporate, industrial, or government setting. A PI's research group is not the best place to apply such a tool.\nThe title suggests that postdocs do not want to engage on career development. However, it is possible that the 360-degree tool is the problem!\nLack of a Control or Comparison Group The absence of a control or comparison group is a major problem. It makes it difficult to isolate the specific impact of the 360-degree feedback interventions or any other intervention. It's unclear whether any observed changes in career conversations or professional development engagement are attributable to the interventions themselves or other factors.\nFocusing on Postdoc Feelings instead of Career Outcomes Another major problem with the first version of this paper is focusing the results on the feelings of the postdoctoral fellows rather than the career outcomes of the postdoctoral fellows. Is the 360-degree feedback intervention leading to better career outcomes for the postdoctoral fellows than no feedback or other instrument feedbacks? The results of this work are focusing on the wrong objective. I do not want to diminish the value of feelings. However, PIs mentor postdoctoral fellows with the goal of helping them achieve their career objectives and aspirations. It is unclear why the study is not focusing directly on the outcomes of the career development tools.\n\nLimited Generalizability The study's focus on STEM postdocs at a single institution, the University of Cambridge, raises concerns about the generalizability of the findings. The authors are making conclusions about institutional factors when they have only studied one institution. The unique context of Cambridge, with its large number of postdocs and specific institutional culture, may not be representative of other institutions or disciplines.\nMinor points for consideration\n\nClarity of Research Questions The research questions could be more explicitly stated in the introduction. This would help readers better understand the study's specific aims and objectives. Even though this reviewer does not think that the 360-degree feedback tool is the best option, the hypothesis that 360-degree feedback tools can empower postdocs to initiate C&D conversations and address the feedback shortfall is clearly stated. However, the paper would benefit from a more detailed justification of this hypothesis, supported by a broader review of existing literature on feedback mechanisms and their impact on professional development in academic settings.\nTheoretical Framework The paper could benefit from a more robust theoretical framework to guide the analysis and interpretation of the findings. This would help situate the study within the broader literature on postdoctoral training and career development. For example, [6] used a design-based multilevel structural equation model to examine the relationships between IDP use, mentoring support, and career preparedness, demonstrating the potential of such models to inform interventions. In [7], a postdoctoral training program focused on soft skills and IDPs to support postdoctoral fellows and improve long-term career outcomes.\nDiscussion of \"Researcher Development Framework\" The \"Researcher Development Framework\" presented in Figure 6 is a valuable contribution, but its implications could be discussed in more detail. How can this framework be used to inform future interventions or policies aimed at improving postdoc professional development?\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? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] }, { "id": "298045", "date": "27 Jul 2024", "name": "Christine Teelken", "expertise": [ "Reviewer Expertise Academic Careers", "Post-PhD careers", "Higher education" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe paper is well written, clearly structured and concerns an important, but relatively under researched topic (career development of postdocs). The specific focus, the interactions between postdocs and their PIs is specially relevant and intriguing, since the general lack of career perspectives contribute directly to their lack of well being. The presented data are clearly part of a much larger study, this is well explained. I sincerely like the structure and quite practical side of the paper.\nAlso, interestingly, while the paper reports on a comparatively small group of postdocs (STEM, University of Cambridge) their demographics (nationality) and background (disciplinary) are highly diverse. Interesting that you used both individual and group interviews. Given the good quality of the paper I have very few recommendations: 1) the view of the PI, is it possible to interview them as well, or let them join in the group interviews? 2) part of the results are a bit 'add on', quite focussed on the individual respondents, I would like to see a more general focus. 3) the conclusion is interesting but could refer more clearly back to the the theory (specially the C&D conversations part) 4) I have some of my own work in the references, given this open review procedure, that seems quite legitimate.\n\nIs the work 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": "298047", "date": "14 Aug 2024", "name": "Maresi Nerad", "expertise": [ "Reviewer Expertise Higher Education", "doctoral education research", "internationalization of doctoral 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\nSummary of the article The article investigated the relationship between postdoctoral researchers (postdocs) and Principal Investigators (PIs), and how this relationship influenced postdocs' engagement in career-focused professional development. The study was conducted at the University of Cambridge and intended to explore the frequency and quality of Career and Development (C&D) conversations, alongside the barriers faced when requesting and receiving feedback. The study explored the types of C&D conversations between postdocs and their PIs and the extent to which readily available forms of training tools could facilitate effective feedback and career development conversations. The study tested the authors’ hypotheses about using 360-degree feedback as well as the At my Best self-assessment tools. The results found that of the limited number of participating postdocs, most of them had C&D conversations, but those who did often doubted if holding career conversations was part of the PI's role. The findings suggested that the mostly project-focused orientations for new postdocs did not convey to them that they can expect or request career conversations from their PIs. Further, the effectiveness of the 360-degree feedback tool varied by length in the postdoc period, the perception of the role of the PI, and the time constraints, with junior postdocs finding it the least useful. Finally, cultural issues such as the University of Cambridge’s research culture environment, as well as the general academic system of time constraint can limit the effectiveness of professional development interventions.\n\nThe study produced a useful overarching researcher framework between the postdocs and the PI within the context of the university’s values and academic system. It well depicts the postdoc/PI dynamic. Accordingly, the conclusions suggest exploring in-depth the various factors contributing to the quality and the challenges of the PI/postdoc relationship within the context of their universities’ values and academic system and clearly define professional priorities and expectations for postdocs as well as for PIs. Such an exploration may eventually provide possible avenues supporting postdocs and their PIs in conducting useful career and development conversations. The proposed next step by the researchers, to explore the self, others, the job role, and the wider academic system of postdocs and PIs, is highly welcomed and will be useful for many universities, beyond the UK, if the academic context is properly accounted for and described. The provided references are very informative and useful.\nAreas for further improvement It was a bit confusing that some participants were still doctoral candidates, yet the article talks about postdocs. A better description may be early career researchers (ECRs)-- which has been used once--and then list which categories are subsumed under ECR. A disaggregation by UK and international ECRs would be useful, as being from a different country/continent and socialized in a different research cultures may influence the postdoc/PI relationship. For example, in the Asian culture, requesting a C&D conservation from one’s PI, an authority figure, is very unlikely. Also knowing the gender pairing between PIs and ECR would be useful to analyze. U.S. research (e.g., NSF ADVANCE) has shown that it can make a difference whether the PI is a woman or a man in their support of career development vis-à-vis a female or male ECR. Considering that PIs have different roles in various academic contexts across the globe, it may be beneficial to explain the traditional the roles of PIs in the UK and at the particular university. For example, it may be useful to clarify how many PIs were professors and how many were senior researchers. While the authors used the definition of research culture from the Royal Society report, (behaviors, values, expectations, attitudes, and norms of our research communities) the specific research culture of Cambridge university might be described upfront. For Future studies A future study also would benefit from a longer follow-up period to assess the long-term impact of the interventions on postdocs' professional development and career progression. Tracking all participants, 3-6 months after the discussions or/and at the end of their postdoc period, could provide valuable insights into the sustainability of the interventions' effects. As correctly stated, this was a pilot study, given the small sample size (14 STEM participants) and the focus on a single institution. Further a larger and more diverse sample size from multiple institutions naturally allows for greater generalizability, robustness, and applicability of the results. Using statistical methods on a larger sample to analyze the pre- and post-workshop survey data could provide more concrete evidence of the interventions' impact.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] } ]	1	https://f1000research.com/articles/13-717
https://f1000research.com/articles/12-1585/v1	14 Dec 23	{ "type": "Research Article", "title": "The moderating effect of entrepreneurial motivation on the relationship between entrepreneurial intention and behaviour: An extension of the theory of planned behaviour on emerging economy", "authors": [ "Pushparaj M. Nayak", "Harish G. Joshi", "Madhukara Nayak", "Mathew Thomas Gil", "Pushparaj M. Nayak", "Mathew Thomas Gil" ], "abstract": "Background: The study investigates the influence of antecedents of the theory of planned behaviour (TPB) and personality traits on entrepreneurial intention and behaviour among engineering students in an emerging economy. It employs the extension of the TPB model by focusing on the intention-behaviour gap, an under-researched area in research. Furthermore, it investigates the moderating effect of entrepreneurial motivation on the relationship between intention and behaviour to improve conceptual model predictability.\nMethods: A structured questionnaire was used to gather data from 1,564 engineering students, and the data were analyzed using structural equation modelling (SEM) with Amos software.\nResults: The results revealed that subjective norms were the strongest predictor of entrepreneurial intention and behaviour, followed by entrepreneurial alertness, perceived behavioural control, attitude towards entrepreneurship, need for achievement, and risk tolerance. Moreover, the moderation analysis showed that entrepreneurial motivation was crucial in moderating the relationship between intention and behaviour.\nConclusions: The present conceptual model contributes to the existing TPB model by improving predictive power to understand the intention-behaviour relationship. The results of the study will assist policymakers, academicians of higher education institutions, and universities in developing policies, strategies, and curricula to engage more students in entrepreneurial activities.", "keywords": [ "Entrepreneurial intentions", "entrepreneurial behaviour", "theory of planned behaviour", "higher education institution", "structural equation modelling", "engineering students." ], "content": "Introduction\n\nEntrepreneurship has become widely popular due to its ability to promote economic activity and contribute to the overall economic development of a region or country (Veleva, 2020). Entrepreneurs are viewed as individuals who foster economic growth by generating and implementing innovative ideas into successful business enterprises (Turker and SonmezSelcuk, 2009, Voutsina, Papagiannakis and Lioukas, 2022). The growth of entrepreneurship is crucial for generating job opportunities, promoting innovation, and improving the overall efficiency of various economic sectors (Gonçalo Rodrigues Brás, Daniel and Fernandes, 2023; Robert, Frey and Sisodia, 2021).\n\nAccording to Global Entrepreneurship Monitor (GEM) 2021–2022 survey report, the world's largest research organization on entrepreneurship, there was a significant increase in the total entrepreneurial activity (TEA) in India from 5.30% in 2020 to 14.40% in 2021. In addition, India has made remarkable progress in the “ease of doing business” parameter, achieving a fourth rank in 2021, up from its fifth rank in 2020. According to the Times of India 2020 report, 83% of the Indian workforce (aged 25 to 34) expressed a desire to begin their own businesses, notably higher than the global average of 53%. According to Mukesh, Rao and Rajasekharan Pillai K. (2018), a significant disconnect exists between the entrepreneurial potential of students in India and the higher education system. However, Pandit, Joshi and Tiwari (2018) suggest that entrepreneurship education has the potential to cultivate student interest and commitment towards entrepreneurship as a career path. Thus, nurturing the entrepreneurial intention (EI) of young individuals has become an essential requirement for fostering the growth and development of entrepreneurship in any given country.\n\nKrueger and Carsrud (1993) defined EI as the level of determination to engage in the necessary behaviours required to initiate a business venture physically. Baum and Locke (2004) emphasized that entrepreneurship is an intentional process, which is a fundamental aspect of entrepreneurship research. Yar Hamidi, Wennberg and Berglund (2008) conducted empirical studies that concluded that an individual's intention to pursue entrepreneurship is a powerful indicator of his or her future participation in entrepreneurial activities. Two predominant theory-driven models that seek to elucidate the concept of EIs are Shapero and Sokol (1982) Entrepreneurial Event Theory (EET) and Ajzen (1991) Theory of Planned Behavior (TPB).\n\nTPB is a highly influential and frequently employed theoretical model for examining human actions (Ajzen, 2020). Additionally, TPB has been widely employed as a theoretical framework for investigating the EI of students in multiple context and culture (Hosen et al., 2022; Kumar and Shukla, 2023; Zellweger, Sieger and Halter, 2011), selected as the research framework for this study. According to Ajzen (1991), Kolvereid (1996), and Krueger, Reilly and Carsrud (2000), the TPB model highlights three motivational factors, commonly referred to as antecedents that impact the formation of intentions to engage in behaviour that are attitudes towards behaviour (ATB), subjective norms (SN), and perceived behavioural control (PBC). Numerous studies have indicated that ATB, SN, and PBC typically account for 30-50% of the variance in intention, implying that approximately half of the variance in EI remains unexplained (Kolvereid, 1996; Krueger, Reilly and Carsrud, 2000; Liñán and Chen, 2009). Liñán et al. (2010) and other scholars have suggested that incorporating additional variables could help close the gap of unexplained variance. Therefore, researchers have incorporated additional variables, such as the need for achievement (NACH), risk tolerance (RT), and entrepreneurial alertness (EA), into the original TPB model to address its limited explanatory power. NACH, RT and EA are personality characteristics that can drive an individual towards developing an intention to become an entrepreneur. Earlier studies conducted in various countries have established a connection between personality traits such as NACH, RT and EA on EI (Li et al., 2020; Mahmoodi et al., 2023; Marques and Fuinhas, 2012). Although, only a limited number of empirical investigations have explored these factors' impact on students' EI (Ouni and Boujelbene, 2023; Passah and Panda, 2021). A lack of studies has examined the combined impact of personality traits and TPM on students' EI, especially in the Indian context. Thus, the first objective of this study is to examine the influence of personality traits and antecedents of the TPB on the EI and behaviour of engineering students in India.\n\nMany studies on entrepreneurship have used intentions as the dependent variable; however, they have not adequately examined the relationship between intentions and behaviour (Gull et al., 2021). Moreover, evidence suggests that all business intentions are not transformed into actual behaviour or new venture creation. Although research in other fields has found a positive correlation between intention-behaviour, there is a lack of evidence on intention-behaviour linkage, specifically in the context of entrepreneurship (Thomas, 2022). Therefore, the main challenge of entrepreneurship research is to fill the knowledge gap in the intention-behaviour linkage (Gieure, Benavides-Espinosa and Roig-Dobón, 2020). Although a link between intention-behaviour through motivation may exist, the same has not been tested in terms of extension of the TPB (Carsrud and Brännback, 2010). Researchers have recommended a longitudinal study to examine the transformation of intention into behaviour (Farooq et al., 2018). However, applying a longitudinal study to engineering students presents challenges as an engineer's role in the industry evolves with experience and career advancement. Initially, engineers tend to have more technical roles, which transform into managerial positions over time. Therefore, a longitudinal study may not be an immediate solution for investigating the transformation of intention into behaviour. Hence, the study's second objective is to investigate how entrepreneurial motivation moderates the link between intention and behaviour. In this way, our findings are expected to contribute to scholarly debate on the linkage between EI and behaviour. The study proposes practical suggestions for policymakers and academicians on how to advance training content and design the curricula as a result of this research.\n\nThe research has two main goals. Firstly, it examines how antecedents of the theory of planned behaviour (TPB) and personality traits influence entrepreneurial intention and behaviour among engineering students in an emerging economy. Secondly, the study investigates the moderating effects of entrepreneurial motivation on the relationship between entrepreneurial intention and behaviour. The paper begins with a literature review that covers earlier research, followed by hypotheses and a proposed model for the study. The research methodology is then presented to outline the scope of the work, followed by data analysis. The last section includes the conclusion, which discusses the results, implications, further research opportunities, and study limitations.\n\n\nLiterature review\n\nAccording to Ajzen (1991) theory, a person's attitude, whether affective/experiential (feelings of joy or satisfaction) or instrumental/cognitive (beliefs, thoughts, or rational arguments), is the key determinant in initiating any action. Ajzen (1991, 2002) and Kolvereid (1996) research suggests that an individual's ATE reflects their personal evaluation of its desirability, indicating the degree to which they hold a positive or negative view towards being an entrepreneur. An individual's attitude is a predisposition that influences their positive or negative response towards an object, person, institution, or event. This attitude plays a significant role in shaping the individual's behavioural intentions (Ajzen and Driver, 1992; Bell and Cui, 2023; Thoudam et al., 2021). The assessment of an individual's ATE indicates their perception of the positive or negative consequences associated with engaging in entrepreneurial activities (Esfandiar et al., 2019). When considering different career options, an individual considers various potential consequences such as financial gain, risk factors, and level of autonomy (Douglas and Shepherd, 2002; Gibson et al., 2021). According to Lumpkin and Dess (1996), entrepreneurship involves various types of risks such as personal, social, and psychological, while independence pertains to the level of autonomy in decision-making, and income encompasses both material and non-material benefits of entrepreneurship. Although some studies (Gultom et al., 2020; Zahid and Haji Din, 2019; Zainuddin and Mukhtar, 2022) have examined the relationship between ATE and EI, we aim to test this relationship in the Indian context to confirm its validity, as previous research has not extensively examined this relationship in India. Thus, the following hypothesis is proposed:\n\nH1: ATE significantly influences EI.\n\nSubjective norm (SN), a construct associated with TPB, is believed to predict intentions, as it comprises an individual's beliefs such as whether others think they should perform a particular behaviour (Conner and Armitage, 1998). Regarding entrepreneurship, SN measures the perceived social pressure an individual feels to become an entrepreneur, which can come from significant people like family members, friends, teachers, and financiers. The strength of an individual's motivation to comply with these perceptions also plays a role (Krueger et al., 2000; Yasir et al., 2023).\n\nThere needs to be more consensuses among scholars in the existing literature on the impact of SN on EI. While some studies suggest that SN has a weaker influence compared to ATE and PBC (Autio et al., 2001; Echchabi, Ayedh and Omar, 2020; Ruizalba Robledo et al., 2015), other studies have demonstrated a significant relationship between SN and EI (Gultom et al., 2020; Khan et al., 2020; Kolvereid, 1996; Ruiz-Dotras and Lladós-Masllorens, 2022). According to Hofstede (2011) research, the results regarding the relationship between SN and EI are divided into socialistic and individualistic countries. The study found a positive correlation between SN and EI in socialistic countries like Russia, Ghana, and Southeast Asian countries. However, in the context of the USA and EU, a negative correlation or no significant correlation was observed between SN and EI. Considering the communal lifestyle, the limited job opportunities available in the public sector, and the perceived difficulties associated with entrepreneurship in an industrially underdeveloped region with corrupt practices related to setting up a business (Panda, 2000), the investigators are encouraged to reconsider the correlation between SN and EI in the Indian context. Drawing on the literature review results, the investigators have formulated Hypothesis H2 in the following manner.\n\nH2: SN significantly influences EI.\n\nPBC, the third construct of the TPB, plays a critical role in assessing the magnitude of both EI and entrepreneurial behaviours, according to Boyd and Vozikis (1994) research. Ajzen (1991) defines PBC as an individual's perception of the level of difficulty or ease in performing behaviour, taking into account anticipated obstacles and challenges, as well as previous experiences. According to Ajzen (2002), PBC is a more comprehensive construct than self-efficacy, as it considers not only internal factors such as knowledge, skills, and confidence but also external factors like resources, opportunities, and potential barriers. PBC predicts behaviour directly, while self-efficacy only predicts intentions (Armitage and Conner, 2001). Boyd and Vozikis (1994) suggest that self-efficacy, as a control belief, serves as the foundation for an individual's perception of behavioural control. This perception is based on preconceived notions about the availability or unavailability of necessary resources and opportunities (Ajzen, 2001). In addition to differences in conceptualization and operationalization, the construct has become controversial due to the lack of consistent empirical evidence supporting its impact on intention (Yap, Othman and Wee, 2013). Although the positive impact of PBC on EI has been extensively studied in other countries (Giovanni Di Stefano et al., 2023; Krueger and Carsrud, 1993; Ruizalba Robledo et al., 2015), authors here aim to revisit its impact in the specific context of India, where factors such as perceived government support, family support, entrepreneurship development programs, and service quality of entrepreneurship education may affect EI with varying degrees of influence. Drawing on the aforementioned considerations, authors have formulated Hypothesis H3 in the following manner.\n\nH3: PBC significantly influences EI.\n\nEA is an essential trait for an entrepreneur. It refers to the ability of individuals to identify and recognize entrepreneurial opportunities. Several earlier studies have reported a positive relationship between EA and EI (Tang et al., 2012; Hu et al., 2018; Neneh, 2019). EA has garnered significant attention in entrepreneurship, as it facilitates the identification of suitable career paths and enables the exploitation of entrepreneurial opportunities (Tang, 2008; Short et al., 2009; Xin and Ma, 2023). According to Montiel Campos (2017), EA begins with an individual's capability to identify potential opportunities, followed by continuous personal growth necessary to transform those opportunities into actual outcomes. McMullen and Shepherd (2006) suggest that EA should lead to entrepreneurial action. Lu and Wang (2018) found that there is a direct relationship between EA and EI. This is because EA helps individuals recognize business opportunities and make informed judgments, which in turn influences their intent to pursue entrepreneurship. In addition, several scholars have pointed out that alertness is an essential skill for entrepreneurs to anticipate and recognize opportunities (Ardichvili and Cardozo, 2000; Mannino and Schiera, 2017; Shamsudeen, Keat and Hassan, 2017). Thus, it can be inferred that individuals who possess a higher level of alertness are more likely to identify favourable opportunities and embark on an entrepreneurial career. Based on this observation, the study will propose the following hypothesis.\n\nH4: EA significantly influences EI.\n\nMcClelland (1961) proposed the need for achievement, a personality trait characterized by a strong aspiration to establish and sustain elevated performance levels. People with a high need for achievement are highly motivated to succeed, set higher goals, take calculated risks, and select innovative and moderately tricky tasks that are challenging yet achievable. Entrepreneurial careers allow for greater control over outcomes, entail moderate risk-taking, and offer immediate feedback on performance. It is logical to anticipate that individuals with a strong need for achievement would be inclined to pursue entrepreneurship as a profession. McClelland (1965) conducted a longitudinal study, which revealed that a greater number of individuals with a high need for achievement scores were engaged in entrepreneurial occupations compared to those with lower scores on the same trait. Mukesh, Pillai and Mamman (2019) found that NACH was a significant predictor of EI among engineering students in India. Other studies, such as Chaudhary (2017) and Littunen (2000), have also reported that NACH has a stronger link with entrepreneurship than any other trait.\n\nIn contrast, Davidsson and Wiklund (1999) argued that the need for achievement traits has limited significance in predicting entrepreneurial behaviour. The conflicting results highlight the necessity for further investigation into the relationship between the need for achievement traits and entrepreneurial intention. Consequently, the authors propose a hypothesis.\n\nH5: NACH significantly influences EI.\n\nRisk-taking propensity is often considered an important trait for entrepreneurs, as it involves the willingness to take risks in the face of uncertainty. Entrepreneurs face many uncertain situations and must make decisions without complete information, and a high tolerance for risk can help them navigate these challenges. Brockhaus (1980) was one of the first to suggest that risk-taking propensity is an important trait for entrepreneurs. Since then, many studies have reported a positive relationship between risk-taking propensity and entrepreneurial intentions or behaviours (Liñán and Chen, 2009; Rauch and Frese, 2007). However, it's important to note that not all entrepreneurs are high-risk takers, and there is some debate over the extent to which risk-taking propensity is a necessary trait for entrepreneurship (Busenitz and Lau, 1996; Mitchell et al., 2002; Sobaih and Elshaer, 2023). Therefore, authors hypothesize that:\n\nH6: RT significantly influences EI.\n\nThere will be significant differences between intention and behaviour of real start-ups. Although scholars advise longitudinal studies to assess the rate of entrepreneurial intention to actual behaviour (Farooq et al., 2018), the difference cannot be determined using conventional research methods. The objective of research is to transform intentions into action. In the 1980s, Sexton, Donald and Smilor, Raymond (1986) and Smilor and Kuhn (1986) conducted preliminary research on EM from theoretical and practical viewpoints. After that, research on entrepreneurs' characteristics took the lead, and EM research could no longer attract scholars.\n\nBird (1989), and Krueger and Carsrud (1993) stressed the importance of transforming intention into behaviour in realising the complete process of entrepreneurship. The attitude-intention and intention-behaviour links define the relationship between attitude and behaviour. Scholars have not focused on empirical studies on the relationship between entrepreneurial motivation and behaviour (Kuratko et al., 2017); nevertheless, a previous study by Carsrud, Olm and Thomas (1989) addressed motivation and behaviour in the context of business performance. According to Carsrud and Brännback (2010) EM produces the relationship between intention and action. Motivators are impulses that ultimately drive action in pursuit of a goal. Carsrud and Brännback (2010) further found that scholars have researched motivation to explain different reactions of persons to the same stimuli of motivation and choice of diverse personal behaviour.\n\nThe push motivation and pull motivation theories are the two types of motivation theories. The pull factors are the ones that motivate individuals to engage in entrepreneurial endeavours (CantúCavada, Bobek and Maček, 2017; Iqbal et al., 2020). The pull factors include the ability to employ others, social status, the opportunity to use one's education and experience, the support and encouragement of one's family, independence, the potential to learn new skills, market opportunities, financial independence, more negotiating power at home, and more control over household decisions (Chhabra, Raghunathan and Rao, 2020; Lockyer and George, 2012). The push factors are the ones which motivate individuals to engage in entrepreneurial activities (Zgheib, 2018). Push factors include lack of job satisfaction, low household earnings, insufficient pay and necessity (Dawson and Henley, 2012).\n\nThe goal is essential in motivational studies (Lockyer and George, 2012). Goals are intangible, representing future results and motivating people to keep working hard (Chhabra, Raghunathan and Rao, 2020). Also, motivation acts as a link between intention and behaviour. The capacity of individuals to adapt to changing environments originates from their ability to modify their motivations and goals (Chaudhary, 2017).\n\nAccording to Ryan and Deci (2000), motivation is influenced by a combination of an individual's cognitive processes and natural and social factors. Motivational initiatives set the direction with purpose and determination. Therefore, the pursuit of motivation, which is driven by an individual's goals and motives, serves as a crucial factor in bridging the gap between intention and behaviour. Earlier research studies suggest that there is a considerable time lag between the formation of intentions in individuals and their actual manifestation in behaviour (Helmreich et al., 1986). Ajzen (1991) TPB posits that an individual's behavioural intention is influenced by their ATB, SN, and PBC, which in turn leads to the actual manifestation of the behaviour. A link between intention-behaviour through motivation may exist, but the same has not been tested in terms of extension of the TPB (Carsrud and Brännback, 2010). Scholars have highlighted the lack of research on this particular aspect of entrepreneurship, which has been addressed in the present study that aims to elucidate engineering students' intentions, motivations, and behaviours. As a result, the following hypothesis is developed:\n\nH7: EM moderates the relationship between EI and EB.\n\nFigure 1 shows a conceptual framework developed based on the hypotheses discussed above.\n\n\nMethods\n\nCMB needs to be assessed when both independent and dependent variables are assessed using the same survey instrument. CMB was assessed using Harman’s single-factor analysis (Lee et al., 2014). The result of this test shows that a single factor explains 34.99% of the total variance. As this value is significantly less than 50%, it is safe to assume that there does not exist any one dominant factor in the data set. Hence, it is proved that the CMB issue does not exist with the collected samples.\n\nThis study used a survey questionnaire as the research instrument (see Extended data; Nayak, 2023b). All the items used to measure the constructs were adopted from previous studies. The attitude towards entrepreneurship, subjective norms and entrepreneurial intention were measured using a 5-item, 3-item, and 4-item scale adapted from Liñán et al. (2010). Perceived behavioural control and risk tolerances were measured using a 5-item and 7-item scale adapted from Chatterjee, Das and Srivastava (2019). The need for achievement was measured using an 8-item scale developed and adapted by Chatterjee, Das and Srivastava (2019) and Dinis et al. (2013). Entrepreneurial alertness was measured using a 4-item scale developed and adopted by Tang et al. (2012). The entrepreneurial motivation was measured using a 4-item scale developed and adapted by Barba-Sánchez and Atienza-Sahuquillo (2012). Entrepreneurial behaviour was measured using a 4-item scale developed and adopted by Li et al. (2020). All items were measured on a 5-point Likert scale, with 1 indicating “strongly disagree” and 5 indicating “strongly agree”.\n\nA quantitative approach was applied to accomplish the research objectives and test the proposed research model, and a cross-sectional descriptive research design was used in the study. Data were collected from final-year engineering students studying in several colleges across India, using a structured questionnaire which was adapted from earlier studies. The questionnaires were personally distributed to the students, and they were informed that participation in the survey was purely on a volunteer basis. They were also assured that their response would be used only for academic purposes and kept confidential. This study distributed 2000 hard copies of the survey questionnaire; finally, 1564 usable questionnaires were further processed for data analysis, yielding a response rate of 78.2%.\n\nThe proposed research model was analyzed using the SEM supported by AMOS and the SPSS software program. According to Hair et al. (2010), the analysis of moments structures model (AMOS) is one of the latest software. Developed and available in the market, this software is used to assist researchers in performing analysis of the inter-relationships and make models for such inter-relationships within constructs that possess multiple indicators in an efficient, accurate and effective manner. Confirmatory factor analysis was used to evaluate the reliability and validity of each construct in the model. The criteria to consider the model achieve overall fit with actual data when CFI, GFI, TLI, and IFI are all greater than 0.9 and RMSEA is less than 0.08 (Hu and Bentler, 1999). The factor loadings of items within each construct are greater than 0.5, showing that the constructs in the model achieve convergent validity. The constructs achieve reliability when composite reliability (CR) and Cronbach's Alpha are greater than 0.6 and the average variance extracted (AVE) is greater than 50% (Fornell and Larcker 1981; Lee et al., 2013). To test discriminant validity between constructs in the model, we used criteria comparing the square root value of AVE and correlation coefficients in the model or using a 95% confidence interval of correlation coefficients (Fornell and Larcker, 1981). If the square root of AVE values of each construct is greater than the correlation of constructs, or the 95% confidence interval of the correlation coefficient does not contain one value indicating that the constructs reach discriminant validity. We used structural equation modeling to test hypotheses with criteria statistically significant at a level of 5%.\n\n\nResults\n\nAccording to Hair et al. (2010), SEM can be effectively evaluated using a two-step approach that involves first assessing the measurement model and then examining the proposed structural model.\n\nWe used confirmatory factor analysis (CFA) to test the properties of our measures with the saturated model (final model). The results analysis showed that the model achieved overall fits with the actual data: CFI = 0.958; GFI = 0.949; TLI = 0.929; IFI = 0.947, all were larger than 0.9 and RMSEA = 0.041 was less than 0.08 (Nayak, 2023a).\n\nAll the constructs had factor loadings higher than the benchmark level of 0.05, which indicated that the constructs achieved convergent validity. The Cronbach's alpha and composite reliability coefficients of all constructs exceed the 0.7 benchmarks, and all AVEs were larger than 0.5 (Table 1). These tests showed that our measures for constructs have achieved internal consistency and reliability.\n\nThe analysis result indicated that all constructs have the square root of AVE values of all the constructs was greater than the inter-construct correlations (Table 2 and Figure 2). Therefore, based on the Fornell–Larcker criterion, it was proved that adequate levels of discriminant validity exist in the measurement model.\n\nAfter successfully validating the measurement model, researchers proceeded to the next stage of their analysis to evaluate the structural model to test their hypotheses about the relationships between latent variables. To assess the appropriateness of the proposed model, researchers examined the R-squared value of the structural model. The results showed that the constructs of ATE, SN, PBC, NACH, RT and EA explained 81% of the variance in EI. Additionally, the impact of EI on behaviour was also measured and found to be 59%, respectively.\n\nTable 3 shows the results of the hypotheses testing. The results showed that all constructs are significant predictors of EI. Furthermore, SN (Path Coefficients = 0.252, CR = 9.993, P = 0.000) and EA (Path Coefficients = 0.246, CR = 8.044, P = 0.000) show a relatively strong effect on EI, followed by PBC (Path Coefficients = 0.208, CR = 8.020, P = 0.000) and ATE (Path Coefficients = 0.198, CR = 7.482, P = 0.000). However, NACH (Path Coefficients = 0.127, CR = 6.203, P = 0.000) and RT (Path Coefficients = 0.054, CR = 2.073, P = 0.038) show the lowest influence on EI.\n\nAccording to Table 4, the direct influence of entrepreneurial motivation (EM) on entrepreneurial behaviour (EB) is not statistically significant, indicating that EM alone may not significantly impact EB. Nevertheless, the study revealed that the interaction between entrepreneurial intention (EI) and EM (EI x EM) is significant, with a p-value of less than 0.05. This outcome supports the hypothesis that the relationship between EI and EB is moderated by EM, which implies that the influence of EI on EB is reliant on the level of EM. To examine this relationship further, the researchers created a plot illustrating the three variables at three levels of both EI and EM based on their means and standard deviations. These levels include low, medium, and high, providing a better understanding of how the interaction between EI and EM affects EB at varying levels.\n\nThe results obtained from simple slope analyses, as shown in Figure 3, suggest that there is a positive relationship between entrepreneurial intention (EI) and entrepreneurial behaviour (EB) among the engineering students who participated in the study. The plot further reveals that higher levels of entrepreneurial motivation (EM) correspond to higher values of EB for a given level of EI, indicating that motivation amplifies the impact of EI on EB. Moreover, as the level of EI increases, the difference between the plots for various levels of EM also increases, implying that the effect of motivation on EB is more pronounced at higher levels of EI. Thus, the findings suggest that students with high levels of EI and EM are more likely to exhibit entrepreneurial behaviour.\n\n\nDiscussion, implication and conclusion\n\nWhile prior research has extensively investigated the impact of antecedents of the Theory of Planned Behaviour (TPB) on entrepreneurial intention (EI) among higher education students in various contexts (Hassan et al., 2021; Hoang et al., 2020), there is still a gap in understanding the combined effect of personality traits and TPB antecedents on EI among engineering students in South Asian emerging economies. This is particularly significant as entrepreneurship development can vary across different regions of the world. As such, the study aims to explore the influence of both personality traits and TPB antecedents on engineering students' EI and behaviour. The study also examines the moderating effect of entrepreneurial motivation on the relationship between intention and behaviour.\n\nThe study found that Subjective norm (SN) (β= 0.252) was the biggest determinant of EI among engineering students in India, which contrasts with previous research conducted in individualistic societies (Bazkiaei et al., 2021; Boutaky and Sahib Eddine, 2022; Krueger, Reilly and Carsrud, 2000; Liñán and Chen, 2009). These earlier studies have shown that SN is a weak predictor of EI. However, the study suggests that in collectivistic cultures like India, students may be more susceptible to external influences, such as peer pressure, societal expectations, and guidance from relatives and teachers, when it comes to pursuing entrepreneurship (Shrivastava and Acharya, 2020). This is because Indian culture places a significant emphasis on family, friends, and society in shaping an individual's beliefs and behaviours (Marmat, 2021). The findings of the study indicate that interventions aimed at encouraging entrepreneurship among engineering students in India should focus on addressing social barriers and norms that discourage entrepreneurship, and promote a positive attitude towards entrepreneurship among family members and peers. These findings have significant implications for entrepreneurship education and policymaking, as they suggest the importance of creating supportive environments that encourage and facilitate entrepreneurial activity among students.\n\nThe study found that entrepreneurial alertness (EA) (β= 0.246) was the second most important factor impacting the students EI, in line with previous research (Lim, Lee and Mamun, 2021; Minola, Criaco and Obschonka, 2015; Neneh, 2019). This suggests that individuals who are more alert to entrepreneurial opportunities and are better equipped to recognize and act on them are more likely to form EI and behaviours. By improving an individual's ability to search and scan, gather the right information, and identify opportunities, EA can increase their likelihood of starting their own businesses and becoming entrepreneurs (Ugwueze, Ike and Ugwu, 2022). The study's finding that students with higher alertness are better positioned to find and recognize opportunities and are more likely to start their businesses is a valuable insight that can inform efforts to promote entrepreneurship among young people. It highlights the importance of encouraging and developing entrepreneurial skills and mindset in students and suggests that initiatives to promote entrepreneurship should focus not only on technical skills but also on fostering an entrepreneurial mindset.\n\nPerceived behavioural control (PBC) (β= 0.208) was found to be the third most crucial factor impacting engineering students' EI is consistent with prior research studies (Alnemer, 2021; Ambad, 2022; Lopez et al., 2021; Marmat, 2021; Naktiyok, Nur Karabey and CaglarGulluce, 2009). It suggests that engineering students with a higher level of PBC may have a greater intention to pursue entrepreneurship because they believe they have the skills, knowledge, and resources necessary to start and run a successful venture. There could be several reasons why PBC is a significant predictor of EI among engineering students. One potential explanation for this relationship is that engineering students may have a strong sense of self-efficacy, which is a fundamental component of PBC (Nguyen, Nguyen and Ba Le, 2022). Self-efficacy refers to an individual's belief in his or her ability to perform a specific behaviour successfully. As engineering students gain technical and problem-solving skills during their studies, they may develop higher levels of self-efficacy than students from other fields (Nguyen, Nguyen and Ba Le, 2022). Therefore, the finding that PBC is a crucial factor impacting engineering students' EI has significant implications for policymakers and educators interested in promoting entrepreneurship. It highlights the importance of creating an environment that supports self-efficacy and encourages acquiring the skills, knowledge, and resources necessary to pursue entrepreneurial activities.\n\nThe study's results revealed that attitude towards entrepreneurship (ATE) (β= 0.198) was the fourth most significant factor impacting students' EI, indicating a favorable ATE among the students. This finding is consistent with previous studies conducted in diverse cultural and contextual settings, suggesting that the relationship between ATE and EI is likely to hold true across various populations (Al-Mamary et al., 2020; Aloulou, 2016; Maheshwari, 2021). The results suggest that engineering students have a desire to become their own bosses in the future and are more self-reliant. Promoting a positive attitude towards entrepreneurship may be an effective strategy for encouraging more students to consider entrepreneurship, which could have significant economic and social implications in the long run.\n\nNeed for achievement (NACH) (β= 0.127) is the fifth important factor impacting engineering students' EI, suggesting that individuals with a high NACH are more likely to intend to pursue entrepreneurial activities. This could be because individuals with a high NACH desire to set and achieve challenging goals, take calculated risks, and strive for independence and recognition, which are all critical components of entrepreneurial behaviour. Moreover, previous research has consistently shown that NACH significantly predicts EI and behaviour across various contexts and populations (Bağış et al., 2022; Gürol and Atsan, 2006; Hansemark, 2003; Turker and SonmezSelcuk, 2009). This further supports the idea that individuals with a high NACH are more likely to engage in entrepreneurial activities. McClelland (1961) identified NACH as a critical factor in entrepreneurial success. This suggests that students with a higher NACH may be better equipped to handle the challenges and uncertainties of starting a new business and are more likely to succeed.\n\nThe study found that Risk tolerance (RT) (β= 0.054) was the least significant factor impacting engineering students' EI. It suggests that RT may not be a critical predictor for students' interest in pursuing entrepreneurial activities. This result is consistent with prior research conducted by Ibidunni, Mozie and Ayeni (2020), Ilevbare et al. (2022) and Moraes, Iizuka and Pedro (2018). In addition, Lumpkin and Dess (1996) emphasized the importance of risk-taking propensity as a fundamental entrepreneurial trait across all levels. They suggested that individuals more willing to take calculated risks are more likely to become successful entrepreneurs. This view is consistent with the principles of Ajzen's theory of planned behaviour. This study outcome may be attributed to various factors, such as cultural values and norms in India, which tend to prioritize stability and security over risk-taking behaviour (Chaudhary, 2017). Another possibility is that Indian engineering students view entrepreneurship as a low-risk pursuit due to established business networks, government support, and other factors (Dubey, 2022). Nevertheless, it is essential to note that the finding does not imply that RT is not a crucial component of entrepreneurial behaviour. On the contrary, taking calculated risks is often vital for entrepreneurial success. Educators and policymakers can encourage more students to pursue entrepreneurial opportunities and develop successful businesses by promoting a culture of entrepreneurship that highlights the importance of RT in a responsible and strategic manner.\n\nThe study found that the antecedents being hypothesized regarding the TPB accounted for 81% of the variance in students' EI. This percentage of variance explained is higher than the average explained variance reported in previous meta-analyses of TPB studies, indicating that the factors included in the study are highly relevant to predicting students' EI (Mukesh et al., 2020). This finding suggests that the TPB model is a valuable framework for understanding and predicting EI among students.\n\nFinally, the study found that the relationship between entrepreneurial intention (EI) and entrepreneurial behaviour (EB) is influenced by entrepreneurial motivation (EM). The research suggests that highly motivated students are more likely to engage in EB when they have a strong intention to become entrepreneurs. However, for students with low or medium EM, an increase in EI is likely to result in a corresponding increase in EB. These results are consistent with the recommendations of Carsrud and Brännback (2010) and Lechuga Sancho, Ramos-Rodríguez and Frende Vega (2022), who highlighted the importance of investigating the intention-behaviour gap in entrepreneurship, an area that has received limited research attention.\n\nUnemployment is a significant problem in many developing nations, particularly India, where many educated individuals graduate from various academic institutions each year, but employment opportunities are scarce. To tackle this issue effectively, policymakers and educators must put more effort into recognising and cultivating potential entrepreneurs. In this direction, the outcomes of this study have essential practical applications for policymakers and educators in emerging economies.\n\nThe study found that ATE significantly influences students' EI, which supports Hypothesis 1. Policymakers can use this information to develop policies and programs encouraging a positive ATE among engineering students, such as creating an entrepreneurial ecosystem on campuses that fosters innovation and creativity (Dubey, 2022). This can include mentorship and networking programs, competitions, and other experiential learning opportunities that expose students to entrepreneurship. Academicians can incorporate entrepreneurship education into engineering curricula to foster a positive ATE. This can include courses covering topics such as opportunity recognition, business planning, marketing, and financial management, as well as experiential learning such as internships, competitions, and incubation programs (Mukesh et al., 2020).\n\nSN is the most significant determinant of students' EI, which supports Hypothesis 2. This has practical implications for policymakers and academicians. For policymakers, this result suggests that efforts to promote entrepreneurship among engineering students should address the social and cultural norms surrounding entrepreneurship (Boutaky and Sahib Eddine, 2022). This could involve creating awareness campaigns highlighting successful entrepreneurs' impact on society and the benefits of entrepreneurship for individuals and communities. Additionally, policymakers could work towards establishing a supportive environment for entrepreneurs by providing access to financing, infrastructure, and other necessary resources for successful startups. For academicians, the finding emphasizes the importance of developing programs and curricula that address social and cultural norms related to entrepreneurship. Universities and engineering institutes could incorporate case studies and guest lecturers that showcase successful entrepreneurs and their contributions to society (Bazkiaei et al., 2021). Also, establishing mentorship programs that connect students with successful entrepreneurs in their field could be useful. Academics could also work towards identifying and overcoming any cultural or social barriers to entrepreneurship among engineering students by providing resources and support to tackle these challenges.\n\nThe study supports Hypothesis 3, indicating that PBC significantly influences students' EI. Therefore, policymakers and academicians can develop and promote programs that enhance engineering students' PBC towards entrepreneurship. This can include providing opportunities for students to participate in entrepreneurship training and education programs that focus on building their knowledge, skills, and self-efficacy regarding starting and managing a business (Ambad, 2022; Lopez et al., 2021). To increase students' confidence in their ability to start and run a business, policymakers and academicians can collaborate with industry partners to offer hands-on experience and exposure to real-world entrepreneurial settings (Marmat, 2021).\n\nThe study supports Hypothesis 4, indicating that engineering students' EA significantly and positively influences their EI. Policymakers and academicians can take practical steps to develop and enhance students' EA by providing training programs and workshops that expose them to industry experts and successful entrepreneurs. These programs may include case studies and exercises designed to improve students' ability to identify entrepreneurial opportunities and take calculated risks. Additionally, academic institutions can encourage collaboration between students, faculty, and industry to foster an entrepreneurial culture on campus and provide students with more opportunities to hone their entrepreneurial skills (Lim, Lee and Mamun, 2021). Policymakers can also promote innovation and entrepreneurship in the engineering sector by offering funding opportunities for startups and incentivizing businesses to invest in research and development (Neneh, 2019). By creating an environment that values entrepreneurship and innovation, policymakers and academicians can contribute to developing the next generation of successful entrepreneurs in the engineering field.\n\nThe NACH significantly influences students' EI. The result supports hypothesis 5. To encourage more students to pursue entrepreneurship, policymakers can consider creating an environment fostering achievement and success. This can be done by promoting and supporting entrepreneurial events and competitions, offering financial incentives and support to young entrepreneurs, and developing policies encouraging entrepreneurship (Biswas and Verma, 2021). By creating an environment that rewards achievement, policymakers can help increase the number of engineering students who desire to start their own businesses. Academicians can also take note of this finding and use it to design and implement programs that foster a sense of achievement among engineering students. For example, entrepreneurship courses and programs can be developed that emphasize the importance of goal-setting, hard work, and perseverance in achieving success as an entrepreneur. These programs also offer opportunities for students to work on real-world entrepreneurial projects, which can help them to build their confidence and sense of achievement. By providing engineering students with the tools and resources they need to succeed as entrepreneurs, academicians can help increase the number of students pursuing entrepreneurial careers.\n\nThe RT significantly influences students' EI, which supports hypothesis 6. Policymakers can use this information to design policies and programs that encourage and support risk-taking behaviours among engineering students, such as providing access to funding, mentoring, and incubation programs that can help students mitigate and manage risks associated with entrepreneurship (Dubey, 2022). Additionally, policymakers can explore ways to incentivize industry collaborations and startup partnerships that expose engineering students to real-world experiences that can increase their risk tolerance. Academicians can use this finding to design and implement educational and training programs that help students develop and improve their risk-taking abilities (Ilevbare et al., 2022). This can include integrating experiential learning opportunities into the engineering curriculum, such as business plan competitions and hackathons, where students can practice identifying and mitigating risks in a low-stakes environment (Ibidunni, Mozie and Ayeni, 2020). It can also offer courses and workshops on risk management and decision-making to help students develop the skills and knowledge necessary to evaluate and manage risks associated with entrepreneurship.\n\nThe limitations of this study suggest several areas for future research. Researchers could expand the theoretical model used in this study to include environmental and external factors that may influence entrepreneurial intentions and behaviour. Furthermore, researchers could use qualitative or mixed-method approaches to gain a more in-depth understanding of the factors that contribute to entrepreneurial intentions and behaviour. Future studies could also include samples from other countries, such as those in South Asia, to provide cross-country data on the effectiveness of entrepreneurship education. Additionally, future research could explore the generalizability of the findings beyond India by including students from other nationalities. Longitudinal studies could be conducted better to understand the entrepreneurial journey of higher education students as they transition to becoming entrepreneurs. These studies could provide insights into the factors that influence the development and success of entrepreneurs, as well as the challenges they face along the way.\n\n\nEthical approval\n\nEthics approval was obtained on 04 June 2021 from the Kasturba Medical College and Kasturba Hospital Institutional Ethical Committee (Registration number, IEC 235/2021). Completion of the questionnaire also was taken as consent of the students to take part in the study.", "appendix": "Data availability\n\nFigshare: Data set. https://doi.org/10.6084/m9.figshare.24203463 (Nayak, 2023a).\n\nFigshare: Questionnaire. https://doi.org/10.6084/m9.figshare.24217848 (Nayak, 2023b).\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nAjzen I: The Theory of Planned Behavior. Organ. Behav. Hum. Decis. Process. 1991; 50(2): 179–211. Publisher Full Text\n\nAjzen I: Nature and Operation of Attitudes. Annu. Rev. 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Publisher Full Text" }	[ { "id": "233045", "date": "30 Dec 2023", "name": "Pradeep Kumar Mohanty", "expertise": [ "Reviewer Expertise Customer Satisfaction & Loyalty", "Purchase Intention", "Behavior Buyer-Seller relationship", "CSR", "Consumer behaviour" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nDear Editor,\n\nThe article presents a comprehensive and well-structured study on a relevant topic in entrepreneurship research, with clear implications for policy and education in emerging economies.\nPresentation and Literature Citation:\nThe work is clearly presented, with a structured approach to discussing research objectives, methodology, and findings. It cites current literature, particularly emphasizing TPB and its applicability in entrepreneurial studies.\nStudy Design and Soundness:\nThe study design, using a structured questionnaire and SEM analysis, is appropriate for the research objectives. The work is technically sound, with a robust analytical approach.\nMethods and Analysis Details:\nThe article provides sufficient methodological details, including data collection and analysis methods, allowing for potential replication.\nStatistical Analysis:\nThe statistical analysis, primarily SEM, is appropriate and well-interpreted. The authors discuss the significance of various constructs like subjective norms and entrepreneurial motivation in predicting entrepreneurial intention and behaviour.\nSource Data Availability:\nThe article indicates that the underlying data are available, which supports reproducibility.\nSupport for Conclusions:\nThe conclusions drawn are adequately supported by the results, aligning with the established theoretical frameworks and the data analysis presented.\nFeedback:\n\nThe integration of TPB with personality traits and the focus on the intention-behaviour gap is well-justified. The methodology and statistical analysis are robust and clearly articulated. Addressing broader and more diverse contexts in future research would strengthen the external validity of the findings. Overall, the manuscript is commendable.\n\nIs the work 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": "255298", "date": "27 Mar 2024", "name": "Wisuwat Wannamakok", "expertise": [ "Reviewer Expertise Entrepreneurship" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThank you for the opportunity to review this research paper.\nThe introduction provided is well-defined and comprehensive. It starts by contextualizing entrepreneurship's importance in economic development, especially in emerging economies like India, and highlights the increasing interest in entrepreneurship among the Indian youth.\n\nYour literature review provides a detailed exploration of the theoretical constructs related to entrepreneurial intention (EI), including attitude towards entrepreneurship (ATE), subjective norm (SN), perceived behavioral control (PBC), entrepreneurial alertness (EA), need for achievement (NACH), and risk tolerance (RT). To further enrich your literature review, consider the following suggestions:\nInclude Recent Studies: Look for studies published within the last five years to ensure your review incorporates the latest research findings.\nIntegration of Theoretical Perspectives: While you've done a thorough job of summarizing the literature related to each construct, consider integrating different theoretical perspectives that provide a holistic understanding of entrepreneurial intention formation. For example, besides the Theory of Planned Behavior (TPB), you can explore other relevant theories such as Social Cognitive Theory, Theory of Entrepreneurial Event, or Dual Process Theory, which offer complementary insights into entrepreneurial decision-making.\nDiscussion of Empirical Findings: While you've mentioned some empirical studies supporting the relationships between the constructs and entrepreneurial intention, consider providing a more in-depth discussion of the empirical evidence. Highlight the methodologies used, sample characteristics, and key findings of these studies to illustrate the robustness of the relationships in different contexts.\nCritique and Controversies: Discuss any controversies or debates in the literature regarding the relationships between the constructs and entrepreneurial intention. For instance, you briefly mentioned conflicting findings regarding the influence of need for achievement (NACH) on entrepreneurial intention. Expanding on these debates and discussing possible explanations for conflicting results can add depth to your literature review.\nCultural Considerations: Given that your study focuses on engineering students in India, it's important to discuss how cultural factors may shape attitudes, norms, and behaviors related to entrepreneurship in the Indian context. Explore literature that examines cultural dimensions (e.g., collectivism, uncertainty avoidance) and their impact on entrepreneurial intention formation.\nPlease add theoretical implications.\nLastly, the content is grammatically correct overall. However, few minor issues that could be improved for clarity and coherence. Therefore, proofreading is suggested.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [ { "c_id": "11482", "date": "01 Jul 2024", "name": "Madhukara Nayak", "role": "Author Response", "response": "Dear Sir/Madam, I am writing to express my gratitude for the time and effort you have invested in reviewing our manuscript, entitled “The moderating effect of entrepreneurial motivation on the relationship between entrepreneurial intention and behaviour: An extension of the theory of planned behaviour on emerging economy”. Your expertise and thoughtful feedback have been invaluable in helping us to improve the quality and clarity of our work. We appreciate your insightful comments and suggestions, which have helped us to address the issues raised and to strengthen our manuscript. Your efforts have greatly contributed to the further development and refinement of our research. Once again, thank you for your time and expertise in reviewing our manuscript. We are grateful for your input and look forward to the possibility of working with you again in the future. We have given the review response for each questions in Tabular form. Sincerely, Authors Comments & Authors Answers Reviewer 2 Comments & Responses (Dr Wisuwat Wannamakok) Comments: Include Recent Studies: Look for studies published within the last five years to ensure your review incorporates the latest research findings. Responses: We have considered your valuable suggestions and incorporated the necessary changes into the in the revised manuscript. We have added latest relevant literature in the introduction and review of literature section and discussion section. Comments: Integration of Theoretical Perspectives: While you've done a thorough job of summarizing the literature related to each construct, consider integrating different theoretical perspectives that provide a holistic understanding of entrepreneurial intention formation. For example, besides the Theory of Planned Behavior (TPB), you can explore other relevant theories such as Social Cognitive Theory, Theory of Entrepreneurial Event, or Dual Process Theory, which offer complementary insights into entrepreneurial decision-making. Responses: We have considered your valuable suggestions and incorporated the necessary changes into the in the revised manuscript. We have incorporated these changes in the introduction section with the highlights. The current research article has been focused on theory of planned behavior and we have mentioned the usage these theories in other contexts. And also, we have highlighted usage of various other theories in entrepreneurial decision-making. Comments: Discussion of Empirical Findings: While you've mentioned some empirical studies supporting the relationships between the constructs and entrepreneurial intention, consider providing a more in-depth discussion of the empirical evidence. Highlight the methodologies used, sample characteristics, and key findings of these studies to illustrate the robustness of the relationships in different contexts. Responses: We have considered your valuable suggestions and incorporated the necessary changes into the in the revised manuscript. We have added few sentences related to the extensive empirical findings in the discussion section which we had highlighted and also the various methodologies and key findings of these articles and robustness of these theories in other different contexts. Comments: Critique and Controversies: Discuss any controversies or debates in the literature regarding the relationships between the constructs and entrepreneurial intention. For instance, you briefly mentioned conflicting findings regarding the influence of need for achievement (NACH) on entrepreneurial intention. Expanding on these debates and discussing possible explanations for conflicting results can add depth to your literature review. Responses: We have considered your valuable suggestions and incorporated the necessary changes into the in the revised manuscript. We have added few critiques and debates regarding the various constructs in the review of literature section. Comments:Cultural Considerations: Given that your study focuses on engineering students in India, it's important to discuss how cultural factors may shape attitudes, norms, and behaviors related to entrepreneurship in the Indian context. Explore literature that examines cultural dimensions (e.g., collectivism, uncertainty avoidance) and their impact on entrepreneurial intention formation. Responses: We have considered your valuable suggestions and incorporated the necessary changes into the in the revised manuscript. We have added the few sentences regarding the cultural factors effect on entrepreneurial intentions in various cross-cultural contexts. We have added few sentences in review of literature and discussion section which we have highlighted. Comments:Please add theoretical implications. Responses:We have considered your valuable suggestions and incorporated the necessary changes into the in the revised manuscript. We have added the theoretical implications in the discussion section and also have provided various theoretical implications of these research to the existing theory, entrepreneurship education and the academia. Comments: Lastly, the content is grammatically correct overall. However, few minor issues that could be improved for clarity and coherence. Therefore, proofreading is suggested. Responses: We have considered your valuable suggestions and incorporated the necessary changes into the in the revised manuscript. We had done a in depth proof reading of the article and improved the grammatical issues and provided clarity on the paper. It took few times for us in uploading the paper." } ] } ]	1	https://f1000research.com/articles/12-1585
https://f1000research.com/articles/13-301/v1	19 Apr 24	{ "type": "Case Study", "title": "Proposal of a domain model for 3D representation of buildings in Ecuador.", "authors": [ "Luis Alejandro Velastegui Cáceres", "Julia Desirée Velastegui Cáceres", "Pedro A Carretero Poblete", "Manuel Fabian Moyón Gusqui", "María Alejandra Cevallos Díaz", "Luis Alejandro Velastegui Cáceres", "Julia Desirée Velastegui Cáceres", "Manuel Fabian Moyón Gusqui", "María Alejandra Cevallos Díaz" ], "abstract": "The accelerated urban sprawl of cities around the world presents major challenges for urban planning and land resource management. In this context, it is crucial to have a detailed 3D representation of buildings enriched with accurate alphanumeric information. A distinctive aspect of this proposal is its specific focus on the spatial unit corresponding to buildings. In order to propose a domain model for the 3D representation of buildings, the national standard of Ecuador and the international standard (ISO 19152:2012 LADM) were considered. The proposal includes a detailed specification of attributes, both for the general subclass of buildings and for their infrastructure. The application of the domain model proposal was crucial in a study area located in the Riobamba canton, due to the characteristics of the buildings in that area. For this purpose, a geodatabase was created in pgAdmin4 with official information, taking into account the structure of the proposed model and linking it with geospatial data for an adequate management and 3D representation of the buildings in an open-source Geographic Information System. This application improves cadastral management in the study region and has wider implications. This model is intended to serve as a benchmark for other countries facing similar challenges in cadastral management and 3D representation of buildings, promote efficient urban development and contribute to global sustainable development.", "keywords": [ "Building 3D representation", "infrastructure", "urban development", "3D cadastre", "Ecuador." ], "content": "1. Introduction\n\nDue to population growth in urban areas, cities have expanded at an accelerated rate, which in a certain way requires adequate territorial planning, for which it is necessary to have information and representation of buildings with a high level of detail to optimize decision making. The limitation of some developing countries is the lack of updated, standardized and open access cadastral information on parcels and buildings, which makes it difficult to access and integrate the information for different purposes.\n\nIn developing countries, 2D cadastral information is the most demanded, however, due to urban growth, the information provided by traditional 2D models is becoming insufficient in urban areas (Drobež, et al., 2017). It should be noted that the representation of the parcel and buildings must be integrated to the alphanumeric information comprising the cadastre so that it is not considered only as a representation of the cadastral object (parcel/building) but is useful for various purposes in the area. Therefore, the implementation of 3D representation of cadastral objects (buildings) has become a necessity to solve the limitations. With this, cadastral objects are represented both at 2D and 3D level, where the information of both dimensions is integrated and represented in the same territorial management system.\n\nThat is why the 3D representation of buildings is very useful in various areas such as land planning and management, urban development, natural resources and environmental management, risk management, among others, as it provides more accurate, realistic and detailed information, which allows identifying the cadastral object with their respective public open spaces, infrastructure and urban systems in a more realistic way (Ying, et al., 2014; Kumar, Rahman & Buyuksalih, 2017; Toschi, Nocerino & Remondino, 2017a; Toschi, et al., 2017b).\n\nAccording to Koeva and Elberink (2016) 3D physical cadastral objects refer to the buildings located on the parcel, buildings and subway constructions. Although cadastral objects are shaped in this way, it is also necessary to consider that they have a legal component and a physical component. When considered as a legal object it refers to a cadastral data model such as those proposed in ISO 19152:2012 LADM (ISO, 2012) where rights, responsibilities and restrictions are specified. On the other hand, when considered as a physical object, it specifies the building characteristics, such as construction components, dimensions, utility, among others, which allow the representation of the cadastral object in 3D (Aien, 2013). Integrating the two components of cadastral objects makes the 3D cadastre very useful in the multipurpose environment.\n\nThe implementation of a 3D cadastre is not a simple task, as it involves numerous challenges as demonstrated by the researches implemented so far (Ying, et al., 2014; Kumar, Rahman & Buyuksalih, 2017; Toschi, et al., 2017a; Karki, 2013; van Oosterom, 2013; Gruber, Riecken & Seifert, 2014; Bydłosz & Bieda, 2020; Döner & Şirin, 2020; Velastegui, Rodríguez & Padilla, 2020; Ying et al., 2021a, 2021b; Paasch & Paulsson, 2021; Ghawana, Janečka & Zlatanova, 2021). Different factors must be taken into account, such as: existing 2D cadastral information, technological and human resources, costs, among others. Therefore, it is important to have a physical 3D cadastral model that is the basis for implementing the 3D representation of the cadastral object (buildings) with alphanumeric information in which the most essential components are integrated and with this, in the future, the level of detail of the information can be improved to allow a geometric representation of the cadastral objects based on the physical characteristics of the buildings.\n\nEcuador has a 2D level cadastre that still needs to be improved and it can be clearly evidenced by the existence of a small percentage whose development is minimal in view of the lack of georeferenced data, as mentioned by Todorovski et al. (2018). On the other hand, taking into consideration the different levels of cadastral development established in the analysis carried out by Velastegui et al. (2020), it is mentioned that the tendency of most of the cantons presents an intermediate development, which implies an advanced 2D cadastre, since both geospatial and alphanumeric information have a cadastral identifier that allows the linking of both types of information and in turn both are up to the floor level, which is the minimum unit in a building block.\n\nBy having a previous analysis of the cadastral situation in Ecuador, it allows to have a perspective of the strengths and weaknesses of the current information and representation of buildings, which helps to propose the most appropriate domain model for the 3D representation of buildings and thus allows a path towards the 3D cadastre. It should be noted that the physical 3D model considers the limitations of the study area in order to be replicated in areas with similar characteristics to Ecuador.\n\nIt is important to note that municipalities update information, not only at the parcel level, but also with regard to buildings. However, the lack of a 3D presentation domain model of buildings has been identified as a crucial need. A standardized model is therefore essential to achieve a consistent and accurate 3D representation, supported by up-to-date alphanumeric data.\n\nIn order for the Ecuadorian cadastre to be able to initiate a path towards the 3D cadastre, it is desired that the components as such be adapted to the general cadastral model proposed in ISO 19152:2012 LADM (2012). It is worth mentioning that the initial proposal put forward by Velastegui et al. (2020) considers the spatial unit only up to the parcel; however, in the present research emphasis is placed on buildings with their respective subcomponents to propose a 3D physical cadastral model that corresponds to the 3D representation of buildings with alphanumeric information to be useful in various areas.\n\nThe implementation of such a model fills a gap in cadastral management and provides a solid basis for improving urban planning, property rights allocation and decision making in various areas, thus contributing to sustainable development and progress in the Ecuadorian territory.\n\n\n2. Methods\n\nOnce the current cadastral model in Ecuador was reviewed, as stated in Ministerial Agreement 017-20 (2020), we proceeded to propose a domain model for 3D representation of buildings for multipurpose purposes in Ecuador, considering both the current model (national standard) and ISO 19152:2012 LADM (international standard) to ensure the applicability of the proposed model and, thus, achieve the transition from 2D to 3D representation of buildings, which in terms of cadastre are considered as physical cadastral objects.\n\nThe proposed model is largely based on buildings, allowing their representation in a 3D format. It is not simply a visual representation, but a comprehensive approach that includes alphanumeric information and is fully integrated into the framework of the Ecuadorian cadastral model. In this way, the 3D representation becomes official and authentic information, with varied applications in different areas.\n\nThis research develops the domain model for 3D representation of multipurpose buildings in which the initial model proposed by Velastegui et al. (2020) is considered. The main purpose of this consideration is to ensure that the proposal can be successfully replicated in various study areas facing similar challenges and constraints. The adaptability and broad applicability of this domain model for 3D representation of buildings are essential to promote significant improvements not only in the engineering area but also in multidisciplinary areas such as cadastral management at national and regional level, and to support sustainable development.\n\nFor this purpose, the main focus is on the elements of the physical cadastral object, where the parcel and the building are specified as the spatial unit. Therefore, it is assigned as a subclass to the buildings (EC_BuildingUnit) and in it the information of the structural part that is in the subclass EC_StructuralComponent and the information of the non-structural part in the subclass EC_NoStructuralComponent.\n\nWith respect to the coding lists of each of the basic elements, national regulations were considered, as the main guarantor of the standardization of cadastral information throughout the Ecuadorian territory. Specific consideration was given to the category, record number, field, type of data, length/precision and the observations section, in the case of those attributes that had particular characteristics.\n\nIn addition, Table 1 presents a synthesis of these associations, with the objective of adapting the international standard ISO 19152:2012 LADM to the specific cadastral reality of the Ecuadorian territory, following the guidelines established by national regulations. This hierarchical structure of relationships between classes supports a more accurate and complete representation of the physical cadastral object (buildings) and the corresponding alphanumeric information, which promotes efficient management of territorial resources and data-driven decision making based on urban planning and territorial development.\n\nTo implement the proposed domain model for 3D representation of buildings, official cadastral data of the study area were used, which were provided by the Directorate of Appraisal and Cadastre of the Municipality of Riobamba, since they are responsible for preparing and managing urban real estate cadastres within their administrative area.\n\nAn area of 13 blocks was selected, located in two sectors, 04 and 05 of the canton, with a total of 261 properties. The selection of the study area was based on the availability and timeliness of data, as well as on the variety of typologies of uses and buildings present in the area. The Department of Appraisal and Cadastre had access to the thematic layers of properties and buildings, which, in their attribute tables, have a field referring to the cadastral key at the parcel level and at the block level, respectively.\n\nWe also had access to the paper cadastral files stored on the basis of the cantonal zoning in the archive office of the aforementioned department. The information from the cards, referring to the physical, economic, legal and thematic components, was digitized and incorporated into the attribute table of the thematic layers of properties and buildings, thus completing the cadastral information of the study area.\n\nThe usefulness of GIS tools for the generation, updating and management of cadastral information, in general, and of information on certain characteristics of buildings, in particular, is unquestionable. Therefore, Ecuadorian regulations establish that geodatabases must be generated in free software for the storage of this type of data related to parcels and buildings.\n\nIn this research, free software was used for its generation. Therefore, the geodatabase was initially developed in pgAdmin 4 (https://www.pgadmin.org/), which is a graphical interface, developed in Python, essential to manage and administer PostgreSQL (https://www.postgresql.org/). In order to relate alphanumeric and spatial information and the implementation of the 3D model, QGIS (https://qgis.org/en/site/) was used, an open source program that has an extension to connect directly with Postgre databases.\n\n\n3. Results\n\nFigure 1 provides an overview of the integration of the cadastral model previously proposed by Velastegui et al. (2020), with an emphasis on the inclusion of the building unit as an integral part of the spatial unit. This approach allows achieving an accurate 3D representation of the buildings, considering both national regulations and the international standard ISO 19152:2012 LADM.\n\nThis process of unification and adaptation to international standards contributes significantly to the standardization of cadastral information management in Ecuador. In addition, it enables a detailed and accurate representation of buildings, which results in better support for urban planning processes, decision making in property matters and the management of territorial resources. The inclusion of the 3D dimension in the cadastre not only improves the visualization and analysis of buildings, but also promotes greater transparency and efficiency in cadastral management, promoting more sustainable urban development and a better quality of life for inhabitants.\n\nThe cadastral model presented by Aien et al. (2015) offers an innovative approach by integrating legal and physical information in order to achieve more realistic 3D representations in the cadastre. In their model, the physical information is closely related to the legal information and is organized within the PhysicalPropertyObject class.\n\nIt is relevant to note that a part of this model has been adopted to represent the sections of the physical component of the Ecuadorian cadastre, specifically regarding buildings, including their structural and non-structural components. This adoption implies an alignment with international standards and best practices, which contributes to a more accurate and consistent representation of buildings in the Ecuadorian cadastre. The incorporation of these innovative approaches in the 3D representation domain model of buildings not only improves the quality of information, but also supports more informed decision making in urban planning and property rights issues.\n\nIn short, the present model considers, in addition to the legal and physical information of the Ecuadorian regulations, adapting it to ISO 19152:2012 LADM (Figure 2). Thus, the class LA_SpatialUnit is associated to EC_PhysicalPropertyObject, which contains the physical information of the constructions in EC_BuildingUnit; the information of the structural part of the constructions is found in the subclass EC_StructuralComponent and the information of the non-structural part in the subclass EC_NoStructuralComponent.\n\nRegarding EC_BuildingUnit, there are the main attributes of the building block, where the cadastral key is specified at block, floor and/or unit level and, in turn, the block code to identify the buildings. As part of the attributes, descriptive data of the building block are also considered, such as number of floors, height of the building above and below the parcel (in case there are subway sections that are part of the building such as parking lots, warehouses, among others), existence of construction above and below the parcel, physical condition, state of conservation, patrimonial condition (in case there is a patrimonial value in the construction), year of construction, year of restoration, occupancy of the block or floor.\n\nRegarding the constructive elements of the buildings, specific subclasses were defined for a detailed management of the information. The subclass EC_StructuralComponent focuses on the attributes concerning the structural part of the building, including details on foundations, columns, load-bearing walls and other aspects that are essential from an engineering and structural safety perspective.\n\nOn the other hand, the subclass EC_NoStructuralComponent groups and details the attributes related to the non-structural part of the building, which includes elements such as cladding, interior finishes, HVAC systems, windows, doors and other components that do not have a fundamental structural role but are crucial for the functionality and habitability of the building.\n\nThe implementation of these subclasses provides a comprehensive approach to the representation and management of the constructive elements of buildings, ensuring that both structural and non-structural aspects are considered in detail in the cadastre. This supports comprehensive decision making in areas such as architectural design, safety, energy efficiency and occupant comfort, which is essential for the quality and sustainability of buildings in the urban context.\n\nThe subdivision of information into these subclasses provides a detailed and complete management of cadastral building data, ensuring that all structural and non-structural building elements are accurately represented. The integration of these details into a 3D domain model simplifies the management of cadastral information and enhances informed decision making in matters related to urban planning and land development.\n\nThis accurate approach has the potential to optimize the management of urban resources and development policies, while providing decision-makers with a complete and detailed view of the buildings in their environment. The 3D representation of buildings not only contributes to greater efficiency in urban management, but also supports building project planning, structural safety and regulatory compliance, which in turn supports more sustainable and equitable urban development.\n\nFigure 3 shows the compendium of the coding lists corresponding to the attributes of the subclasses EC_BuildingUnit, EC_StructuralComponent and EC_NoStructuralComponent. It should be noted that the coding lists were developed based on national regulations in order to ensure standardization of the information.\n\nThe design process of the domain model for the 3D representation of buildings in Ecuador has followed the structure defined by the ISO 19152:2012 LADM standard. At first, the classes have been established along with their attributes and corresponding list codes, which has provided a solid basis for the 3D representation of the physical cadastral object.\n\nSubsequently, in this specific section, the relationships and associations between the classes proposed in the 3D representation domain model have been addressed. These relationships have been defined considering the order in which the classes are related to each other, which has allowed us to determine the name of the association, the name of the role at end 1 and its multiplicity, as well as the name of the role at end 2 and the corresponding multiplicity.\n\nFinally, the proposal of the domain model for the 3D representation of buildings, which aims to lead to the 3D cadastre in Ecuador, is shown in Figure 4. The classes, subclasses and the relationships between them, which are essential to achieve a detailed and complete representation of buildings in three dimensions, are presented here. It is worth noting that the initial model previously proposed by Velastegui et al. (2020) served as a starting point for the formulation of this research.\n\nAn outstanding feature of this proposal is the inclusion of the building unit component, together with its respective subclasses that address both the structural and non-structural parts of buildings. This approach facilitates the 3D representation of buildings, complemented with alphanumeric information, which is crucial for a variety of multipurpose purposes.\n\nWith respect to the implementation of the proposed domain model in a study area of Ecuador, a geodatabase of seven tables was generated that collected alphanumeric data of the administrative unit, physical cadastral object (properties and buildings), owners, rights, responsibilities and restrictions, as well as those associated with the different shapefiles linked to the geodatabase (parcels and buildings).\n\nThe geodatabase generated and stored in pgAdmin was linked with the parcel and building layers through the PostGIS extension available in the QGIS program; this is a PostgreSQL extension that allows adding geospatial capabilities and functions to ‘conventional’ databases. Once linked, the layers corresponding to the properties and buildings/constructions were added from the QGIS Database Manager. Additionally, the representation of physical cadastral objects at level of detail 1 (LoD1) was obtained based on the information of height and number of floors of the buildings, which allowed an initial 3D modeling (Figure 5).\n\nThis proposed domain model, based on national standards and the international standard ISO 19152:2012 LADM, facilitates a more accurate and complete representation of buildings, which in turn supports urban planning, property rights management and a variety of applications related to territorial development.\n\n\n4. Discussion and conclusions\n\nThe proposal of a domain model for 3D representation of buildings could play a fundamental role as a reference point for those developing nations facing similar challenges in terms of their cadastral systems. This initiative would provide them with the opportunity to assess the feasibility of adapting international standards such as ISO 19152:2012 LADM, which would support the first steps towards the implementation of a 3D cadastre. By taking into account the experience of more advanced countries that have successfully implemented this international standard in their transition towards 3D representation of the physical cadastral object (Zulkifli et al., 2017; Janečka & Souček, 2017; Radulović, Sladić & Govedarica, 2017), valuable lessons and best practices could be established to ensure an efficient and effective process.\n\nAdopting an approach based on the experience of more developed nations, in terms of implementing ISO 19152:2012 LADM, could facilitate planning and decision making in countries with fewer resources and technical capacity. This, in turn, would foster greater global consistency and standardization in cadastral information management, promoting the successful transition to 3D cadastre in various regions globally.\n\nThe proposed domain model for the three-dimensional (3D) representation of buildings presents a versatility that makes it suitable for replication both nationally and internationally. This is due to the fact that the model is designed with an approach based on national standards, incorporating the international standard ISO 19152:2012 LADM as a fundamental basis. This integration of national and international standards ensures that the proposal is adaptable to the different levels of cadastral development that can be found within the study area.\n\nThe ability of this proposal to be implemented in different cadastral contexts, both nationally and internationally, lies in its ability to align with both specific local regulatory requirements and globally supported best practices. This flexibility translates into a powerful tool for the improvement and modernization of cadastral systems in a variety of environments, which, in turn, contributes to the standardization and efficiency of cadastral information management on a global scale.\n\nConsidering the spatial unit in parcels and buildings, both spatially and alphanumerically, allows specifying the attributes of each of them, which would facilitate the transition from 2D to 3D physical cadastre. In the case of the building it is possible to consider the general attributes of the building unit and also of the structural and non-structural components, allowing to specify their respective attributes to project in the future an advanced 3D physical cadastre that facilitates cadastral aspects such as the assignment of rights, responsibilities and restrictions at the level of actors, both municipal and owners.\n\nThe implementation of the domain proposal for the 3D representation of buildings involves an essential process that begins with the acquisition of official data, most of which is provided by municipalities. This step is crucial to ensure that the data meets the minimum requirements stipulated by national regulations. Through the collection of reliable and accurate information, the necessary basis is laid for the creation of a geodatabase that allows proper processing, management and 3D representation of the physical cadastral objects.\n\nThe use of official data and compliance with national regulations are key elements to ensure the integrity and quality of the spatial unit (parcel/building) information in the 3D environment. This, in turn, facilitates more efficient and accurate database management for 3D representation, which is essential for urban planning, property rights allocation, regulatory compliance and informed decision making. Collaboration between municipalities and government entities responsible for cadastral regulation is essential to guarantee the effectiveness of this process and to ensure the availability of reliable and up-to-date data for the benefit of society at large.\n\nIn order to successfully implement the domain model for the 3D representation of buildings, it is essential to have data that meet certain key criteria. Firstly, it is strongly recommended that the data used has been updated within a period of no more than two years. This ensures that the information is as accurate and relevant as possible, which is essential for an accurate 3D representation.\n\nIn addition, it is essential that the data have a unique identifier, such as a cadastral key, at all levels, whether parcel or building. This allows the effective linking of geospatial and alphanumeric data, which facilitates the management and consultation of information related to buildings.\n\nFinally, the data must be presented in formats compatible with the software to be used in the process, ensuring that the data can be easily integrated into the information system and processed efficiently.\n\nThese criteria contribute greatly to the quality and efficiency of the process of implementing the 3D domain model representation of buildings, enabling accurate representation and facilitating the effective management of cadastral information in a unified system. The availability of up-to-date and compatible data is essential for effective decision making in urban planning and cadastral management.\n\nFinally, it can be noted that the implementation of a domain model for the 3D representation of buildings plays a vital role not only in the field of engineering but also in multidisciplinary areas. This revolutionary approach allows for a more accurate and complete representation of structures, which translates into more effective planning and design of construction projects. The ability to visualize and analyze buildings in three-dimensional space provides a deeper understanding of the challenges and opportunities in each project. In addition, detailed 3D building information facilitates more efficient management of resources and time, resulting in significant cost savings and reduced risks associated with construction. Ultimately, the implementation of a 3D domain model has become a fundamental pillar for the execution of more accurate, safe and sustainable projects.", "appendix": "Data availability\n\nNo data are associated with this article.\n\nZenodo: Proposal of a domain model for 3D representation of buildings for the 3D cadastre in Ecuador, https://10.5281/zenodo.10403713 (Velastegui Cáceres et al., 2023).\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nThe cadastral data for this project have been obtained from: https://georiobamba-gadmriobamba.hub.arcgis.com/\n\n\nReferences\n\nAien A: 3D Cadastral Data Modelling. Australia: University of Melbourne; 2013. PhD thesis.\n\nAien A, Rajabifard A, Kalantari M, et al.: Integrating Legal and Physical Dimensions of Urban Environments. ISPRS International Journal of Geo-Information. 2015; 4: 1442–1479. Publisher Full Text\n\nBydłosz J, Bieda A: Developing a UML Model for the 3D Cadastre in Poland. Land. 2020; 9: 466. Publisher Full Text\n\nDöner F, Şirin S: 3D Digital Representation of Cadastral Data in Turkey—Apartments Case. Land. 2020; 9: 179. Publisher Full Text\n\nDrobež P, Fras MK, Ferlan M, et al.: Transition from 2D to 3D real property cadastre: The case of the Slovenian cadastre. Computers, Environment and Urban Systems. 2017; 62: 125–135. Publisher Full Text\n\nGhawana T, Janečka K, Zlatanova S: Development of 3D Spatial Database Enabled IT Framework for Land Agencies: Case Studies of Delhi, India and Prague, Czech Republic. Land. 2021; 10: 248. Publisher Full Text\n\nGruber U, Riecken J, Seifert M: Germany on the Way to 3D-Cadastre. ZFV - Zeitschrift für Geodasie, Geoinformation und Landmanagement. 2014; 4: 223–228. Publisher Full Text\n\nInternational Organization for Standardization (ISO): ISO TC/211—ISO 19152:2012. Geographic Information—Land Administration Domain Model (LADM). 1st ed.Geneva, Switzerland: ISO; 2012.\n\nJanečka K, Souček PA: Country Profile of the Czech Republic Based on an LADM for the Development of a 3D Cadastre. ISPRS International Journal of Geo-Information. 2017; 6: 143. Publisher Full Text\n\nKarki S: 3D Cadastre Implementation Issues in Australia. University of Southern Queensland; 2013.\n\nKoeva M, Elberink SO: Challenges for updating 3D cadastral objects using LiDAR and image-based point clouds. Proceedings of 5th International FIG Workshop on 3D Cadastres 2016, Athens, Greece. 2016 18 October; pp. 169–182.\n\nKumar P, Rahman AA, Buyuksalih G: Automated Extraction of Buildings from Aerial Lidar Point Cloud and Digital Imaging Datasets for 3D Cadastre–Preliminary Results. Cadastre: Geo-Information Innovations in Land Administration. Yomralioglu T, McLaughlin J, editors. Cham: Springer; 2017; pp. 159–165. Publisher Full Text\n\nMinisterio de Desarrollo Urbano y Vivienda: Norma técnica para formación, actualización y mantenimiento del catastro urbano y rural y su valoración. Acuerdo Ministerial 017-20. Vivienda MdDUy, editor. 017-20 ed. Vol. 017-20. . Ecuador: Ministerio de Desarrollo Urbano y Vivienda; 2020.\n\nPaasch JM, Paulsson J: 3D Property Research from a Legal Perspective Revisited. Land. 2021; 10: 494. Publisher Full Text\n\nRadulović A, Sladić D, Govedarica M: Towards 3D Cadastre in Serbia: Development of Serbian Cadastral Domain Model. ISPRS International Journal of Geo-Information. 2017; 6: 312. Publisher Full Text\n\nTodorovski D, Salazar R, Jacome G, et al.: Land administration in Ecuador; Current situation and opportunities with adoption of fit-for-purpose land administration approach. Proceedings of 19th Annual World Bank Conference on Land and Poverty 2018: Land Governance in an Interconnected World, Washington, USA. 2018; pp. 1–11.\n\nToschi I, Nocerino E, Remondino F: Geomatics Makes Smart Cities a Reality: Enriching 3D Building Models with Non-Spatial Data. GIM International-The Worldwide Magazine for Geomatics. 2017a; 31: 25–27.\n\nToschi I, Nocerino E, Remondino F, et al.: Geospatial data processing for 3D city model generation, management and visualization. ISPRS - International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences. 2017b; XLII-1/W1: 527–534. Publisher Full Text\n\nvan Oosterom P : Research and development in 3D cadastres. Computers, Environment and Urban Systems. 2013; 40: 1–6. Publisher Full Text\n\nVelastegui J, Rodríguez V, Padilla O: Urban Cadastral Situation in Ecuador: Analysis to Determine the Degree of Proximity of the Cadastral Systems to the 3D Cadastral Model. Land. 2020; 9: 357. Publisher Full Text\n\nVelastegui Cáceres LA, Velastegui Cáceres JD, Carretero Poblete PA, et al.: Proposal of a domain model for 3D representation of buildings for the 3D cadastre in Ecuador (Versión 1). [Data set]. Zenodo. 2023. Publisher Full Text\n\nYing S, Guo R, Li L, et al.: Construction of 3D Volumetric Objects for a 3D Cadastral System. Transactions in GIS. 2014; 19: 758–779. Publisher Full Text\n\nYing Y, Koeva M, Kuffer M, et al.: Making the Third Dimension (3D) Explicit in Hedonic Price Modelling: A Case Study of Xi’an, China. Land. 2021a; 10: 24. Publisher Full Text\n\nYing S, Li C, Chen N, et al.: Object Analysis and 3D Spatial Modelling for Uniform Natural Resources in China. Land. 2021b; 10: 1154. Publisher Full Text\n\nZulkifli NA, Rahman AA, Hassan MI, et al.: Conceptual Modelling of 3D Cadastre and LADM. Cadastre: Geo-Information Innovations in Land Administration. Yomralioglu T, McLaughlin J, editors. Cham: Springer International Publishing; 2017; pp. 95–111. Publisher Full Text" }	[ { "id": "274274", "date": "29 May 2024", "name": "Uznir Ujang", "expertise": [ "Reviewer Expertise 3D City Modeling", "3D GIS", "Topology", "Geo-BIM", "GIS" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address 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 presents a well-defined problem and rationale for proposing a 3D representation model for buildings in Ecuador. The need for detailed 3D building models for urban planning and resource management is articulated clearly. However, further clarification on the current limitations of the existing 2D cadastre and the specific challenges it poses in the Ecuadorian context would strengthen the introduction.\n1.\n\nPage 3 - How does the proposed model address specific challenges unique to Ecuador that might not be present in other countries with similar urban development issues? 2.\n\nPage 4 - What are the key differences between the national standard of Ecuador and the international standard ISO 19152:2012 LADM that necessitated the specific adaptations you made? 3.\n\nHow do you ensure the proposed model's scalability and applicability to other regions in Ecuador or other countries with different cadastral development stages? 4.\n\nCan you provide more detail on the validation process of the proposed model? How was it tested, and what were the criteria for its success? 5.\n\nHow do you plan to address the potential lack of technological infrastructure and expertise in some regions of Ecuador for implementing the 3D cadastre? 6.\n\nWhat were the specific criteria used to select the 13 blocks in the study area, and how do these criteria ensure the representativeness of the study? 7.\n\nHow does the proposed 3D model integrate with existing cadastral systems and databases currently used by Ecuadorian municipalities? 8.\n\nWhat measures are in place to ensure the continuous updating and accuracy of the data within the proposed 3D cadastral model? 9.\n\nHow does the model handle buildings with complex structures, such as those with multiple sub-levels or mixed-use purposes?\nSuggestions for Improvement: 1.\n\nThe literature review is comprehensive but can benefit from a deeper analysis of case studies where 3D cadastral models have been successfully implemented. Highlighting the outcomes and lessons learned from these implementations can provide more context and justification for your model. 2.\n\nThe methodology section is detailed but can be improved by providing a step-by-step outline of the process used to develop the geodatabase and the tools employed. Including diagrams or flowcharts to illustrate the methodology would enhance clarity and comprehension. 3.\n\nIncorporate more detailed examples of the 13 blocks selected for the study, including before and after comparisons of 2D and 3D representations. This will provide concrete evidence of the model's effectiveness. 4.\n\nDiscuss the potential challenges and limitations encountered during the implementation of the proposed model, such as data quality issues, integration difficulties, and any resistance from local authorities or stakeholders. 5.\n\nOutline the next steps for the broader implementation of the 3D cadastral model in Ecuador. Discuss plans for scaling the model to other regions and how you intend to handle potential scalability issues.\n\nIs the background of the case’s history and progression described in sufficient detail? Partly\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate? Not applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly\n\nIs the case presented with sufficient detail to be useful for teaching or other practitioners? Partly", "responses": [ { "c_id": "11858", "date": "28 Jun 2024", "name": "Pedro Antonio Carretero Poblete", "role": "Author Response", "response": "Dear Dr. Uznir Ujang, Thank you for your valuable comments and suggestions on our manuscript. We appreciate the time and effort you have dedicated to providing feedback that will help improve the quality of our work. In replying to your comments, we took your comments into consideration for the new version of the article to provide a greater understanding of the limitations and challenges in transitioning from a 2D cadastre to a 3D cadastre. In Ecuador, there are regulations for the generation of cartographic inputs, standardization of databases, and catalogs of objects at different scales. Despite this, various procedures for the collection, storage, processing, and visualization of building-related data exist in the country. This diversity limits the adequate representation of buildings, resulting in the predominance of 2D representation of buildings in the country. Proper organization and interoperability of building-related information are fundamental to initiating 3D representations. The proposed domain model considers both national and international standards to more accurately characterize the set of existing buildings. The main difference starts from its general structure. The national standard considers four components: economic, physical, legal, and thematic. On the other hand, the international standard consists of party, basic administrative unit, RRR (rights, restrictions, and responsibilities), and spatial unit. The structure presented by the international standard tends to be more flexible and adaptable to different scenarios. Considering that Velastegui et al. (2020) propose adapting and merging the general structure of the national standard with the international one, this model is used to specifically address the Spatial Unit (parcel and building). The adapted Spatial Unit class essentially considered the minimum elements established by the national standard. While it does not limit these to being the only elements, it leaves room for the incorporation of additional elements. To incorporate necessary elements into the spatial unit (building unit), the international standard was taken into account, thus adapting structural and non-structural components to the Building Unit subclass. To ensure that the proposed model can be applied in different areas of the country, the cadastral development levels of the country were considered. Based on this, a model is proposed that covers the most predominant characteristics of the different areas. For application, a study area representing these characteristics was considered to verify the adaptability of the proposed model. However, as next steps, pilot projects are planned in other cities or regions according to their population density, urban development, and specific needs to validate and adjust the model in different contexts. Based on the pilot projects, performance indicators will be established to monitor the progress and effectiveness of the implementation. Workshops were organized with cadastre technicians, particularly those in charge of geospatial data, to obtain direct feedback on the usability and functionality of the 3D model. As a result of the suggestions and observations from end users, the necessary adjustments and improvements were made to the model. The criteria considered interoperability and usability to ensure that the model can be integrated with various cadastral systems and databases, as well as adopted and used effectively by users. Technological infrastructure challenges are a concern not only for the implementation of the 3D cadastre but for cadastres at all levels. Therefore, the Ministry of Urban Development and Housing, through Agreement 017-20, sets forth transitional provisions indicating that municipalities must standardize and adapt data to a Local Cadastral Geographic Information System (SIGCAL). For this, SIGCAL must meet a series of essential requirements such as being open-source; having an integrated database; allowing implementation on different operating systems and access through various web browsers; and having interoperability capabilities and web-oriented or desktop architecture. The selection criteria for the study area were mainly based on the availability and updating of both geospatial and alphanumeric data. Additionally, the level of cadastral development was considered, as a high percentage of areas in the country have intermediate cadastral development with challenges similar to the selected area. Blocks containing the most representative and diverse characteristics of the study area were defined, such as building types, year of construction, data updates, construction diversity, land use, etc. Therefore, the implementation of the domain model proposal was carried out in 13 blocks that met the mentioned criteria. The integration of the initial 3D model proposal was challenging primarily due to interoperability issues. Databases were used where the geospatial and alphanumeric components were not fully integrated. Therefore, it was necessary to verify the compatibility of both alphanumeric and geospatial data formats. However, with the model proposal, it was feasible to implement free, integrated databases that allowed the storage of both geospatial and alphanumeric components associated through the cadastral key, which is the unique identifier of the cadastral object (parcel/building). The requirement of Ministerial Agreement 017-20 was met by using open-source GIS software that guarantees interconnection with previously implemented platforms and systems. Socializing the process with end users is fundamental to establishing protocols at different levels of cadastral systems. The Ministry of Urban Development and Housing, through the Ministerial Agreement issued in 2020, presents transitional provisions directed at all municipalities in the country to ensure that, regardless of their cadastral development, they adhere to these provisions. Each municipality must update the urban cadastre considering guidelines to ensure data accuracy and quality. These transitional provisions have an established timeframe for compliance, thus ensuring more uniform levels of cadastral development across different areas of the country. The majority of buildings in Ecuador meet the characteristics considered by this domain model. The present model is an initial proposal; however, future research on buildings with complex structures is planned. The authors appreciate your suggestions for improvement, which have been incorporated into the new version of the article as detailed below: An analysis of case studies where 3D cadastral models were successfully implemented has been incorporated into the introduction section. A diagram regarding the development of the geodatabase has been added to the methods section. Additional information regarding the 13 blocks selected for the study, as well as, comparisons of before and after 2D and 3D representations have been included in the results section. Possible challenges and limitations encountered during the implementation of the proposed model have been added to the discussion and conclusions section. Future steps for the broader implementation of the 3D cadastral model in Ecuador and plans to scale the model to other regions have been added to the discussion and conclusions section." } ] }, { "id": "285537", "date": "19 Jun 2024", "name": "John Samuel", "expertise": [ "Reviewer Expertise Data Integration", "Data Warehouses", "Data Analysis", "Big Data", "Web Services", "Knowledge Representation", "Semantic Web", "Multidimensional Data Modeling", "Description Logic", "Geographical Information Systems" ], "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 case study \"Proposal of a Domain Model for 3D Representation of Buildings in Ecuador\" presents a model for 3D representation of buildings, considering the regulations in Ecuador. The study, spanning four sections, is presented in a well-structured manner.\nSection 1 provides the necessary background for the proposed study, presenting some existing works related to the representation of cadastral information, with a particular focus on 3D information. Additionally, this section presents the context of Ecuador, both in terms of the desired functionalities and the current regulations and limitations.\nHowever, I have a significant remark for this section, which I believe can further improve the article. The authors state that \"The implementation of a 3D cadastre is not a simple task, as it involves numerous challenges as demonstrated by the researches implemented so far,\" followed by a list of citations. It is unclear what challenges are presented in this extensive list of articles. I believe the authors could highlight some of the key challenges with references to one (or more, if necessary) articles from this list.\nSection 2 presents the methods, considering the Ministerial Agreement (2020) and basing their proposed method on previous work by Velastegui et al. (2020). They present the selected international standards and explain the open-source tools used in this study.\nIn this section (as well as the previous section), I suggest the authors elaborate more on the study area and its limitations. They state that “The physical 3D model considers the limitations of the study area to be replicated in areas with characteristics similar to Ecuador”. While readers may infer some limitations from the article, these should be clearly presented in Section 1 or 2.\nSection 3 presents the results, especially the proposed extensions to the models and the 3D visualization of a selected area in QGIS with an extension.\nIn this section, my major concern is with Figures 4 and 5. Although the authors have clearly stated that they have extended the previous work of Velastegui et al. (2020), it would be helpful if they highlighted their newly proposed contributions in Figure 4 with different colors or textures. Regarding Figure 5, the authors mention an extension of PostGIS for the 3D visualization, but they need to describe the extension (presumably Mapa 3D, based on the screenshot in Figure 5).\nFinally, Section 4 concludes the article, discussing their proposed models and possible future work. The work is promising, especially because it demonstrates how they consider the local context while remaining global by using international standards.\nOverall, the case study is well-written. However, there is room for improvement. The authors need to consider international standards like CityGML, which already proposes 3D structural information of buildings and some information related to non-structural components. Some proposed attributes could be further improved or justified by comparing them with such city models.\n\nIs the background of the case’s history and progression described in sufficient detail? Yes\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate? Not applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Yes\n\nIs the case presented with sufficient detail to be useful for teaching or other practitioners? Yes", "responses": [ { "c_id": "11857", "date": "28 Jun 2024", "name": "Pedro Antonio Carretero Poblete", "role": "Author Response", "response": "Dear Dr. John Samuel, Thank you very much for your valuable comments and suggestions on our manuscript. We have carefully considered your comments and made the necessary revisions in the new version of the article." } ] } ]	1	https://f1000research.com/articles/13-301
https://f1000research.com/articles/13-222/v1	27 Mar 24	{ "type": "Case Report", "title": "Case Report: Urethral Diverticulum after Distal Hypospadias Repair: An Uncommon Complication.", "authors": [ "Ammar Kheyami", "Abdulla AlMuharraqi", "Mahmood Abbas", "A.K Singhal", "Ammar Kheyami", "Mahmood Abbas", "A.K Singhal" ], "abstract": "Abstract*\nIntroduction A urethral diverticulum can be defined as a pocket that forms from the lining of the urethra and protrudes into the surrounding tissue, a condition which causes voiding dysfunction and may result as a rare complication of hypospadias repair surgery.\n\nCase report We report the case of a 2-year-old child who presented to us in 2019 complaining of a thin forceful stream, ballooning of the ventral aspect of the penis while voiding, and post-void dribbling. He has a history of undergoing a tabularised incised plate urethroplasty for distal penile hypospadias at 18-months-old. Ultrasound showed increased post-void residual volume and cystourethroscopy confirmed a urethral diverticulum extending from the subcorona to the base of the penis. The patient underwent partial excision of diverticulum, urethroplasty, and meatoplasty. He was followed-up 3 months later with complete resolution of his symptoms and a normal urinary stream with no urethral ballooning or dribbling.\n\nConclusion Urethral diverticulum may present as a complication post hypospadias repair. Although it is rare, we believe that it is important for the patient’s parents to understand the possibility and know of the signs and symptoms in addition to attending regular outpatient clinic appointments in order to facilitate early management if needed. Furthermore, it is highly important for physicians to assess newborns for hypospadias before carrying out circumcision as it is a contraindication for the procedure.", "keywords": [ "Urethra", "diverticulum", "hypospadias", "circumcision." ], "content": "Introduction\n\nUrethral diverticulum - an out-pouching of the urethra into surrounding tissues - is an important but uncommon complication of hypospadias repair.1 Studies suggest that it comprises 0.3% of postoperative complications and is mainly associated with proximal hypospadias.2,3 Factors predisposing to its formation include proximal defect, oversized neourethra, poorly supporting tissue covering urethroplasty, and distal urethral stricture.2,3 We present a case of postoperative urethral diverticulum formation after distal hypospadias repair and discuss possible treatment options.\n\n\nCase report\n\nThe child was one-month-old (Figure 1) when referred to our centre in 2019 for review after undergoing Plastibell circumcision. On examination, he was circumcised with a hypospadiac meatus located at distal penile position (Figure 2).\n\nAt 18 months of age, he underwent a tabularised incised plate urethroplasty at an external paediatric urology centre with an excellent outcome (Figure 3).\n\nOne year later, he presented with typical signs and symptoms of a urethral diverticulum and meatal stenosis; thin forceful stream, ballooning of the ventral aspect of the penis during voiding, significant post-void dribbling, and need for manual emptying of the diverticulum (Figure 4).\n\nUltrasound showed diffuse bladder wall thickening with significant post-void residual volume. Ascending urethrogram confirmed the diagnosis of meatal stenosis with proximal diverticulum (Figure 5). Patient underwent cystourethroscopy which confirmed a diverticulum extending from the subcorona to the base of the penis. The diverticulum was opened through a ventral midline incision. A midline strip of 16 mm width of mucosa was preserved, and lateral mucosa was excised preserving the underlying dartos tissue (Figure 6).\n\nThe meatus was opened wider and stitches were taken at the margins.\n\nThe urethroplasty was closed in two layers and was supported by double-breasted Dartos fascia. At the end of the procedure, standard meatoplasty was performed for meatal stenosis. Three months following repair, the child had a normal thick continuous stream with no post-void dribbling or ballooning of the urethra.\n\n\nDiscussion\n\nUrethral diverticulum is an uncommon complication of hypospadias surgery which has several risk factors that could influence its incidence such as a large neourethra, inadequate supporting tissue post-urethroplasty, and a distal urethral stricture.2,3 It can be diagnosed via clinical evaluation and confirmed with cystourethrography and cystoscopy. Partial excision of diverticulum and urethroplasty is an acceptable form of treatment for such cases, as the final aim is to restore a urethra with normal diameter and pressure that is also well supported with enough tissue and no distal obstruction.2,4 In the presented case, the diagnosis of hypospadias was missed at birth and a circumcision was carried out though circumcision is contraindicated in these cases. This certainly requires more awareness since the repair of hypospadias in uncircumcised children is technically easier and has a better outcome. Additionally in this case, excessive circumcision resulted in a very wide meatus along with a severe deficiency in the ventral skin and the underlying supportive tissue which possibly complicated the repair and played an important role in the formation of the diverticulum. Meatal stenosis is another factor that predisposed to diverticulum formation in this child, and it was most likely a post-surgical complication as it can occur after any hypospadias surgery. Therefore, regular follow-up after hypospadias repair is of vital importance for early diagnosis and management of meatal stenosis.\n\n\nConclusion\n\nMeatal stenosis and urethral diverticulum are amongst the possible complications of hypospadias repair. The repair of urethral diverticula is challenging, and the outcome depends on the creation of a well-supported and normal-sized urethra with no distal obstruction. Furthermore, parents should be educated about the signs and symptoms of meatal stenosis and the need for strict and regular follow-up to diagnose and manage any complication as early as possible. It is important to carefully examine the child for hypospadias before circumcision as it is contraindicated.\n\n\nConsent\n\nWe discussed and explained to the patient’s father about the writing and publication of this case report. He had the opportunity to ask questions about everything related to this process, and understood that no identifying information related to the patient will be shared; Written informed consent for the publication of patient details and images was obtained from the patient’s father.", "appendix": "Data availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\n\nReferences\n\nCrescenze IM, Goldman HB: Female Urethral Diverticulum: Current Diagnosis and Management. Curr. Urol. Rep. 2015; 16: 71. PubMed Abstract \| Publisher Full Text\n\nSnodgrass W: Tubularized incised plate hypospadias repair: indications, technique, and complications. Urology. 1999; 54: 6–11. PubMed Abstract \| Publisher Full Text\n\nSnyder CL, Evangelidis A, Snyder RP, et al.: Management of urethral diverticulum complicating hypospadias repair. J. Pediatr. Urol. 2005; 1: 81–83. PubMed Abstract \| Publisher Full Text\n\nBote SM, Gite VA, Siddiqui AK, et al.: Acquired male urethral diverticulum: Report of two cases. Arch. Int. Surg. 2016; 6: 54–56. Publisher Full Text" }	[ { "id": "261654", "date": "05 Apr 2024", "name": "Johannes Wirmer", "expertise": [ "Reviewer Expertise Hypospadiology" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe Report describes a case of urethral diverticulum after tubularized-inzised plate repair (TIP) of a distal Hypospadias. The Hypospadias repair was performed at the age of 18 month, but had a circumcision as a newborn. From the picture taken before the hypospadias repair, he most likely had a MIP-Hypospadias (megameatus intact prepuce).\nThe here described developement of an urethral diverticulum after repair of distal hypospadias is an important complication of the TIP-technique. Even though it has been described before ( Lee H, et al., 2006) [Ref 1], the common assumption is still that it mainly occurs after flap urethroplasty. This article is an important contribution to drawing attention to the complications of tip correction.\nSmall suggestions for corrections would be: Title: Case Report: Urethral Diverticulum after TIP-Repair of distal hypospadias: a not so uncommon complication\nIn addition, tabularized incised plate urethroplasty is mentioned several times throughout the text, where it should correctly be called TUBULARIZED plate urethroplasty.\n\nIs the background of the case’s history and progression described in sufficient detail? Yes\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Yes\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Partly\n\nIs the case presented with sufficient detail to be useful for other practitioners? Yes", "responses": [ { "c_id": "11818", "date": "28 Jun 2024", "name": "Abdulla AlMuharraqi", "role": "Author Response", "response": "Dear Dr. Johannes, Thank you for your review and invaluable comments. Changes have been made as per your suggestions. Kind regards, Dr. Abdulla Al-Muharraqi" } ] }, { "id": "261657", "date": "30 Apr 2024", "name": "Mohamed Zouari", "expertise": [ "Reviewer Expertise Pediatric surgery" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nUrethral diverticula can be congenital or acquired; the most common cause of an acquired diverticulum in children is previous hypospadias repair. The reported incidence of diverticula formation after hypospadias repair is 0–21% [Radojicic ZI, et. al., 2004 (Ref 1)]. Factors increasing the risk of diverticula include a proximal defect, use of poorly supported tissue for interposition grafting (e.g. bladder mucosa or tubularized pedicle grafts), and the presence of a distal stricture resulting in relative obstruction/higher outlet pressures [Horton CE, et. al., 1998 (Ref 2), Snyder CL, et. al., 2005 (Ref 3)].\nIn this article, the authors reported the case of a urethral diverticulum in a 2-year-old child circumcised at the neonatal age. This diverticulum occurred after of distal hypospadias repair as a complication of the TIP-technique. Although the article is interesting and the illustrations attractive, I believe that there are two major problems that need to be corrected.\nThe first problem concerns Figure 1, which clearly shows a mega-meatus with an intact penis. The authors need to clarify whether or not this was an accidental circumcision, and on what grounds this assumption was made. There are no signs of scarring or trauma to the penis. The penile folds are well-defined, showing that the penis has not been damaged.\nMy second problem concerns the English language, which needs revision. For example, I can identify the word \"TUBULARIZED\" which is written in the article \"TABULARISED\" several times. Other sentences use non-technical words such as \"ballooning of the ventral aspect of the penis\". In conclusion, this article is interesting since it highlights an uncommon complication of TIP-uretroplasty in children. This complication could lead to therapeutic challenges, for which there is still no consensus on management.\n\nIs the background of the case’s history and progression described in sufficient detail? Yes\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Yes\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Partly\n\nIs the case presented with sufficient detail to be useful for other practitioners? Yes", "responses": [ { "c_id": "11819", "date": "28 Jun 2024", "name": "Abdulla AlMuharraqi", "role": "Author Response", "response": "Dear Dr. Mohamed, Thank you for your review and invaluable comments. Spelling corrections have been made as per your advice. In regards to your comment concerning Figure 1, when we discussed the case with the General Practitioner who performed the circumcision, they explained that in their opinion it was a mild case of hypospadias and that the foreskin was intact. However, after the procedure the patient presented with the findings described in the manuscript. Kind regards, Dr. Abdulla Al-Muharraqi" } ] } ]	1	https://f1000research.com/articles/13-222
https://f1000research.com/articles/13-243/v1	02 Apr 24	{ "type": "Clinical Practice Article", "title": "Case Series: Pleomorphic adenoma in minor salivary gland", "authors": [ "Meherzi Samia", "Khbou Amin", "Omri Rihab", "Charfi Afifa", "Khbou Amin", "Omri Rihab", "Charfi Afifa" ], "abstract": "Abstract* Pleomorphic adenomas (PA) are the most prevalent benign salivary gland neoplasms. They may occur at any age, with a peak incidence between 40 and 60 years of age. They are more commonly observed in females (60%). These tumors can arise in both the major and minor salivary glands. Approximately 80% of these tumors are diagnosed in the parotid gland, whereas 10% arise in the minor salivary glands, mainly affecting the palates, followed by the lips and cheeks. This report describes two cases of unusual lesions that were diagnosed as (PA) in the minor salivary glands in our department via a review of the relevant literature. The first case involved an 83-year-old man who presented with a slow-growing swelling on the right side of the upper lip, and the second case involved a 45-year-old woman who presented with a slow-growing lesion on the palate. The presence of PA was confirmed histopathologically after surgical resection. Although relatively rare, PA is a benign lesion, the diagnosis of which must be known for appropriate therapeutic management.", "keywords": [ "case report", "salivary gland neoplasms", "minor salivary gland", "pleomorphic adenoma" ], "content": "Introduction\n\nSalivary gland tumors are relatively uncommon, accounting for 1-3% of head and neck cancers. Pleomorphic adenoma (PA) is a benign tumor that is most frequently diagnosed not only in the major salivary glands, namely the parotid gland (85% of cases) and submandibular gland (5% of cases), but also in the minor salivary glands (10% of cases).1 The most common ectopic site of PA in the minor salivary glands is the palate, followed by the upper lip and oral mucosa.2\n\nSalivary gland neoplasms are a heterogeneous group of tumors with variable clinical appearances and histological features.\n\nPA, also known as “Mixed tumor, salivary gland type,” receives its name from its wide pleomorphic architectural appearance and mixed histology that consists mainly of three components: an epithelial and a myoepithelial component within a mesenchymal stroma.3 It is equipped with a fibrous capsule whose integrity must be conserved during surgical treatment to prevent recurrence.4\n\nPA is more common in middle-aged females.\n\nClinically, it is known to be a slow-developing, asymptomatic lesion, typically described as firm, well-delimited, and variable in diameter. Intraoral PAs are normally located in the submucosa with a firm or rubbery consistency. The mucosal lining remains intact, but ulcerations can be observed in some cases.5\n\nAn 83-year-old man with no specific pathological history presented to the ENT Department at our hospital with a 2-year history of painless, slow-growing swelling on the right side of the upper lip.\n\nClinical examination revealed a well-circumscribed, mobile, firm, and non-tender submucosal mass measuring 3×1.5 cm on the right side of the upper lip. The overlying mucosa appeared intact and smooth without bleeding on palpation (Figure 1A). The lymph nodes of the head and neck were not enlarged.\n\nA: Preoperative view: Exposure of the mass in the palate. B: CT scan on axial section showing an oval well-defined lesion of the upper lip with homogeneous post-contrast enhancement. C: Postoperative view showing the site of the sutures. D: Excised specimen.\n\nComputed tomography (CT) showed an oval well-defined lesion of the upper lip measuring 3.2×1.7 cm with homogeneous post-contrast enhancement (Figure 1B).\n\nA total excision of the lesion via the sublabial approach was performed (Figure 1C). The lesion was released from the surrounding tissue, and the mass appeared to be fully encapsulated (Figure 1D). Histopathology of the resected tumor revealed the presence of a PA, a well-encapsulated soft tissue mass consisting of epithelial, myoepithelial, and stromal components (Figure 3). The follow-up 24 months after surgery showed no abnormalities and no evidence of recurrence.\n\nA 45-year-old woman with no medical history presented to our ENT department with a slow-growing painless nodular lesion in the palate that caused difficulty swallowing. Anamnesis revealed that the mass had appeared one year previously and had rapidly increased in size over the last three months.\n\nIntraoral examination revealed a unilocular, mobile, fibrous, endophytic nodule at the junction of the soft and hard palates, measuring approximately 4 cm in diameter. The nodule was well delimited, with a regular contour, smooth surface, and normal overlying mucosa color (Figure 2A). No lymph node involvement was observed during the physical examination.\n\nA: Preoperative view: Exposure of the mass in the palate. B: T2-weighted MRI showing a hyposignal ovoid well-defined mass within the right soft palate. C: Peroperative images: the defect post excision of the mass.\n\nMagnetic resonance imaging (MRI) revealed an ovoid well-circumscribed encapsulated mass measuring 3.7 cm in size, within the midline of the soft palate to its right para-median side. The lesion extended backward to the oropharynx and forward in the left tonsillar pillar (Figure 2B).\n\nThe mass was completely excised with safety margins via an intraoral approach (Figure 2C).\n\nOn final histopathological examination, the report suggested a PA (Figure 3A & B).\n\nA: The tumor consists of three components: epithelial cells (right), myoepithelial cells (left), and myxochondroid tissue stroma (hematoxylin-eosin, 100×). B: Myoepithelial cells with epithelioid and plasmacytoid appearance (hematoxylin-eosin, 400×).\n\nAn 18-month follow-up after surgery showed no abnormalities or evidence of recurrence.\n\n\nDiscussion\n\nAlthough malignant lesions are mostly diagnosed in minor salivary glands, benign lesions have also been reported. PA are the most common benign salivary gland neoplasms, representing approximately 3–10% of all neoplasms of the head and neck region.6\n\nThey represent the most prevalent histopathological benign tumors diagnosed in both the major and minor salivary glands (50% of cases). Additionally, PA mainly affects the major salivary glands, particularly the parotids. The palate is the most prevalent intraoral site (42.8-68.8%), followed by the upper lip (10.1%) and cheek (5.5%).4,6\n\nIt occurs in individuals of all ages but tends to affect more women than men, especially middle-aged individuals.\n\nThe present cases of PA in the minor salivary glands of the palate and the upper lip corroborate literature data showing a relatively low prevalence at these sites.\n\nRegarding the epidemiological features of PA, gender, and age in our present cases, one of our two patients agreed with the literature, which shows that PA in the minor salivary glands may occur in individuals of all ages but most frequently affects women in their fourth to fifth decade of life, with a relevant mean age of 40-60 years.\n\nHowever, in our first case, PA was diagnosed in an 83-year-old man, which does not match the relevant literature as neither the age of occurrence nor the sex of the patient was uncommon.\n\nThe clinicopathological features of our two cases concur with those reported in previous studies. In fact, PA generally presents as a mobile, slowly developing, painless, and firm swelling that does not cause any fixation or ulceration of the overlying mucosa with no lymph node involvement.7\n\nHistopathologically, PA is a complex mixed lesion consisting of both epithelial and myoepithelial components within a mucopolysaccharide stroma, organized predominantly in a duct-like pattern. They tend to have a fibrous capsule that separates the tumor from the surrounding tissues. The proportions of the different components can vary among individuals, parallel to changes in tumor consistency.6,8,9\n\nThe need for complementary investigations into the management of PA in minor salivary glands depends on its localization. Indeed, a biopsy may be performed for additional oral sites.\n\nHowever, if the diagnosis of PA is suspected in intraoral localizations, CT, ultrasonography, and optimal MRI are useful for studying the extent of the tumor and determining eventual bone involvement.3,10\n\nBiopsy is generally avoided because of the fear of the seedling. However, fine-needle aspiration is safe and recommended.11\n\nAccording to recent studies, the treatment of choice is wide local excision of the tumor with adequate margins, followed by histopathological examination to establish the final diagnosis.8\n\nOur therapeutic approach was consistent with the literature, as a total excision of the lesion via a sublabial approach was performed in the case of PA of the upper lip and via an intraoral approach for the patient who presented with PA of the palate.\n\nRegular follow-up is necassary for patients with minor salivary gland neoplasms, not only due to their heightened tendency toward local recurrence but also because of their malignant potential.12,13\n\n\nConclusion\n\nThe diverse presentations of pleomorphic adenomas make diagnosis complicated and challenging. PAs of the minor salivary glands are rare neoplasms. While their occurrence in the minor salivary glands is uncommon, obtaining the correct diagnosis as early as possible is essential because early initiation of appropriate treatment allows for effective management and improves patient prognosis. Complete wide local surgical excision is the treatment of choice. Patients should be followed up for a longer period to detect late recurrences.\n\n\nEthics and consent\n\nWritten informed consent was obtained from both patients for publication and accompanying images.\n\n\nAuthor contribution\n\nSamia Meherzi: writing, review and editing\n\nRihab Omri: conceptualization, writing\n\nAmin Khbou: conceptualization, preparation\n\nAfifa charfi: review", "appendix": "Data availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\n\nReferences\n\nAhmedi J, Ahmedi E, Perjuci F, et al.: Pleomorphic adenoma of minor salivary glands in child. Med Arch. 2017; 71(5): 360–363. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHmidi M, Aatifi H, Boukhari A, et al.: Pleomorphic adenoma of the soft palate: major tumor in a minor gland. Pan Afr. Med. J. 2015; 22: 22. Publisher Full Text\n\nKhan MN, Raza SS, Zaidi SAH, et al.: Pleomorphic adenoma of minor salivary glands. J. Ayub Med. Coll. Abbottabad. 2016 Jul-Sep; 28(3): 620–622. PubMed Abstract\n\nSharma A, Deshmukh S, Shaikh A, et al.: Pleomorphic adenoma of the minor salivary gland of the cheek. Singapore Med. J. 2013 Sep; 54(9): e183–e184. Publisher Full Text\n\nLotufo MA, Júnior CAL, Mattos JPD, et al.: Pleomorphic adenoma of the upper lip in a child. J. Oral Sci. 2008; 50(2): 225–228. PubMed Abstract \| Publisher Full Text\n\nDalati T, Hussein MR: Juvenile pleomorphic adenoma of the cheek: a case report and review of literature. Diagn. Pathol. 2009; 4(1): 32. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJúnior ECF, Dias IJ, Alves PM, et al.: Pleomorphic adenoma of buccal mucosa: a case report and review of the literature. Stomatologija. 2020; 22(3): 92–96. PubMed Abstract\n\nSarma M, Sahoo SR: Pleomorphic adenoma of tongue: a case report. Indian J. Otolaryngol. Head Neck Surg. 2020 Mar; 72(1): 145–147. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNonitha S, Yogesh T, Nandaprasad S, et al.: Histomorphological comparison of pleomorphic adenoma in major and minor salivary glands of oral cavity: A comparative study. J Oral Maxillofac Pathol. 2019; 23(3): 356–362. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYousra Z, Saliha C: Pleomorphic adenoma of hard palate: a case report. Pan Afr. Med. J. 2021 [cited 2023 Dec 16]; 38: 146. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPeriasamy S, Manoharan A, Garg H, et al.: Pleomorphic Adenoma of the Cheek: A Case Report. Cureus. 2019 Aug 3; 11: e5312. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGelidan AG, Arab K: Rare upper lip pleomorphic adenoma presents as cutaneous skin lesion: Case report. Int. J. Surg. Case Rep. 2021 Aug; 85: 106142. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nShah B, Singh A, Sherwani A, et al.: Pleomorphic adenoma of the upper lip: A rare case report. Natl. J. Maxillofac. Surg. 2020; 11(2): 289–291. PubMed Abstract \| Publisher Full Text" }	[ { "id": "262621", "date": "13 Apr 2024", "name": "Atsuto Katano", "expertise": [ "Reviewer Expertise Clinical oncolgy" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nMajor Points:\ni ) In the introduction section, there is no indication of what knowledge gap or research question the study aims to address. A well-defined research objective or question would enhance the significance of the study.\nii) In the introduction section, although the text briefly mentions demographic characteristics, it does not provide a broader epidemiological context. For instance, there is no discussion of incidence trends, geographic variations, or associated risk factors. Providing this information would enhance the reader's understanding of the significance of studying pleomorphic adenoma (PA).\niii) The histopathological description of the pleomorphic adenoma (PA) is brief and lacks detailed information on specific immunohistochemistry, histopathological, and/or genomic features that are characteristic of PA.\niv) In the discussion section, there is no mention of future research directions or unresolved questions arising from the study's findings.\nv) In the conclusion section, the author mentioned the patient prognosis of pleomorphic adenoma (PA). They should discuss the patient prognosis of PA in the discussion section, including overall survival (OS) and/or progression-free survival (PFS).\nMinor Points:\ni) Several statements lack proper citation to support claims made in main text. e.g. - PA is more common in middle-aged females. - It occurs in individuals of all ages but tends to affect more women than men, especially middle-aged individuals. - most frequently affects women in their fourth to fifth decade of life, with a relevant mean age of 40-60 years.\nii) What is \"ENT Department,\" which descrtbed in Case 1.\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? No\n\nIs the conclusion balanced and justified on the basis of the findings? Yes", "responses": [ { "c_id": "11867", "date": "29 Jun 2024", "name": "Meherzi Samia", "role": "Author Response", "response": "We've significantly strengthened the manuscript by incorporating your valuable feedback. The introduction now provides a clear objective and relevant epidemiological context. Additionally, we've enriched the discussion of pleomorphic adenoma (PA) with detailed histological features, immunohistochemistry (IHC) analysis, and a comprehensive exploration of prognosis." } ] }, { "id": "262620", "date": "07 May 2024", "name": "Dorra Chiboub", "expertise": [ "Reviewer Expertise cervical surgery" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe objective of the article must be clarified in the introduction Specify patients' habits (examples: tobacco consumption, alcohol) Physical examination must include, for both cases, the performance of a nasofibroscopy and the result of this examination to look for possible associated lesions, especially malignant Put more recent references\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": [ { "c_id": "11868", "date": "29 Jun 2024", "name": "Meherzi Samia", "role": "Author Response", "response": "In response to your valuable feedback, we've strengthened the introduction by explicitly stating the study objective. Additionally, we've provided clearer details about patient habits and endoscopic findings. Finally, the manuscript now includes recent references to support the research and enhance its credibility." } ] } ]	1	https://f1000research.com/articles/13-243
https://f1000research.com/articles/12-1355/v1	18 Oct 23	{ "type": "Case Report", "title": "Case Report: Bell’s palsy: a neurological manifestation of COVID-19 infection", "authors": [ "Amro Abdelrahman", "Amira Bitar", "Isra Babiker", "Fawaz Elgak", "Mohamed Elgassim", "Amro Abdelrahman", "Amira Bitar", "Isra Babiker", "Fawaz Elgak" ], "abstract": "Background Coronavirus (COVID-19) is the causative agent of the most recent pandemic that hit the globe and has been the cause of a vast range of symptoms, including neurological symptoms. Bell’s palsy is an acute peripheral facial paralysis commonly associated with viral infections.\n\nCase presentation This case report describes a patient with incidental COVID-19 infection that led to acute unilateral peripheral facial paralysis, Bell’s palsy. Our patient is a 35-year-old male with no known comorbidities who was presenting with upper respiratory tract infection symptoms and was found to be positive for COVID-19. Soon after the onset of symptoms, he also developed right-sided facial weakness in association with his symptoms. A thorough examination revealed a peripheral neurological lesion. The diagnosis of Bell’s palsy secondary to COVID-19 virus infection was through the exclusion of other possible causes.\n\nConclusions This case report suggests a potential link between Bell’s palsy and COVID-19, highlighting the importance of a comprehensive understanding of the neurological manifestations of COVID-19. Further research is essential to determine the significance of neuropathies in COVID-19 and enhance treatment strategies.", "keywords": [ "COVID-19", "Coronavirus", "Bell's palsy", "Isolated facial neuropathy", "Acute peripheral neuropathy" ], "content": "Introduction\n\nCoronavirus (COVID-19) infection has affected millions of people worldwide. It’s an infectious disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). People with COVID-19 infection have a wide range of reported symptoms, ranging from a mild cough to acute respiratory syndrome (ARDS).1 Patients with COVID-19 commonly face complications and potential causes of mortality, including conditions such as sepsis, acute kidney injury, ARDS, acute hypoxic encephalopathy, and acute cardiac injury.1\n\nA growing number of COVID-19 cases have been associated with facial nerve paralysis, often presenting as the initial symptom or occurring within the first week after the onset of viral symptoms or a positive COVID-19 test.2 Additionally, individuals may experience other neurological complications such as loss of smell (anosmia), altered taste perception (dysgeusia), encephalopathy, Guillain-Barre syndrome, Miller-Fisher syndrome, and polyneuritis cranialis.3 In this case we’re reporting a case of Bell’s palsy following COVID-19 infection in a previously healthy 35-year-old-male. This case report follows the CARE guidelines.15\n\n\nCase presentation\n\nA 35-year-old South Asian male taxi driver with no past medical history presented to the Emergency Department of Hamad General Hospital complaining of a two day history of sudden right-sided facial weakness associated with fever, cough, and sore throat. Three days before admission the patient had gone to a primary health care center due to upper respiratory tract symptoms, and a diagnosis of COVID-19 was made.\n\nTwo days later, the patient suddenly developed weakness associated with numbness, drooling saliva while eating and difficulty closing the right eye. He had no other neurologic symptoms and denied ear pain, skin rash, or arthralgia. He had no past medical history, a recent history of travel, or a tick bite. The review of other systems was unremarkable.\n\nAt the Emergency Department, his temperature was 37°C, his peripheral pulse rate was 70 bpm, and his respiratory rate was 18 breaths per minute. His oxygen saturation was 98% on room air, blood pressure was 122/74 mmHg. Physical examination revealed the absence of right-sided forehead wrinkles compared to the left, drooping of the right eyelid, and prominent mouth deviation suggestive of right lower motor neuron facial nerve palsy. Careful examination of ears showed dry impacted wax in the right ear with no vesicles. Examination of the parotid gland was unremarkable. Sensation in both upper and lower extremities was intact. No weakness was noted in either the upper or lower limbs. Kernig’s and Brudzinski’s signs were negative. Examination of other systems was unremarkable.\n\nThe patient’s complete blood count and basic metabolic panel were within normal ranges. His COVID-19 rapid antigen test was positive. The chest X-ray was unremarkable. A diagnosis of Bell’s palsy secondary to COVID-19 infection was made, and the patient was discharged and prescribed the following medications:\n\n‐ Prednisolone: 20 mg orally (PO) daily for 10 days.\n\n‐ Levocetirizine: 5 mg PO daily for 5 days.\n\n‐ Gentamicin solution: 0.3% solution, applied twice daily to both eyes for 7 days.\n\n‐ Paracetamol: 1,000 mg PO every 6 hours as needed for 5 days.\n\n‐ Eye drops: Applied twice daily for 14 days.\n\nHe was also referred to a physical therapy clinic. On his four-week follow-up visit, the patient showed no significant improvement. On his 10-week follow up clinic appointment, the patient symptoms showed a significant improvement.\n\n\nDiscussion\n\nBesides the usual and well-known respiratory symptoms, SARS-CoV-2 can affect the peripheral and central nervous systems. Neurological symptoms can be the first manifestation of COVID-19 infection or concurrent respiratory symptoms. A retrospective review reported neurological symptoms in 36.5% of patients.4\n\nTwo different mechanisms could explain the neuropathogenesis of SARS-CoV-2. The first mechanism is due to endothelial damage and the subsequent passing of the virus from the systemic circulation to the cerebral circulation. The alternative mechanism is thought to be due to the direct entering of the virus through the cribriform wall and olfactory bulb, where the olfactory nerve terminates.5 Using the olfactory pathways, the virus can harm the central nervous system (CNS), which may propagate from neuron to neuron by axonal transport.6\n\nWhen glial cells get infected with the virus, the body enters a pro-inflammatory state and releases cytokines. The prolonged exposure to cytokines may lead to nerve damage.7\n\nMoreover, various types of neurological manifestations of COVID-19 infection have been reported. For example, Filatov et al., reported a case of encephalopathy following COVID-19 on the same day of admission.8\n\nAn observational study conducted in Spain documented cases where COVID-19 was associated with cranial nerve manifestations. In one of these cases, polyneuritis cranialis developed on the third day, while in the other case, Miller Fisher syndrome occurred on the fifth day.9 A previous study also described a case of an isolated facial paralysis presented after six days in a patient with COVID-19 infection.2 Our patient experienced a lower motor neuron facial paralysis on the third day of his ongoing COVID-19 infection.\n\nBell’s palsy is a lower motor neuron impairment of the facial cranial nerve, manifesting acutely as a unilateral facial paralysis.10 Although the reason for many cases is unidentifiable, the most common cause of peripheral facial palsy is attributed to infections, mainly Herpes Simplex Virus-1 (HSV-1), Varicella Zoster Virus (VZV), and Lyme disease.11 Our patient denied any recent travel, trauma, insect bite, skin rash, joint pain, itchiness, or tingling sensation in the body. Physical examination was unremarkable, with no skin rash; the outer ear canal was clear, and no signs of meningitis. Causes such as autoimmune and vasculitis were excluded as the patient did not have any systemic findings. Human Immunodeficiency Virus (HIV) infection was also excluded as it is a part of the infectious screening for all people getting their residencies in the country. The patient had a fever, sore throat, and generalized body pain, and his COVID-19 rapid antigen test came positive. Therefore, no other etiologies than COVID-19 infection could be attributed to palsy.\n\nCOVID-19 infection is known to present mainly as respiratory symptoms ranging from mild to severe, such as ARDS and fever.12 In addition, neurological manifestations, including Guillain-Barre syndrome, anosmia/ageusia, encephalopathy, and myelitis, are also encountered.11 Bell’s palsy is one of the manifestations of COVID-19. Poor prognosis is predicted in patients >60 years of age with systemic problems such as diabetes mellitus, severe pain in the ear, and decreased tear production. Bell’s palsy generally has a good prognosis and recovery rate of 90%.13 Regarding the treatment, the most used one in facial paralysis is corticosteroids, with high effectiveness rates.12 Prednisolone’s effect on the facial nerve is by reducing its edema.14 In our case, the patient had no risk factors for poor prognosis; he was prescribed prednisolone (20 mg) for 10 days and referred to a physiotherapy clinic. His four-week follow-up visit showed no significant change in his condition. However, on his 10-week follow-up clinic visit his weakness improved significantly.\n\nThe viral screening wasn’t done to rule out all other viral etiologies.\n\n\nConclusions\n\nThis case report raises the possibility that Bell’s palsy and COVID-19 infection are related. However, to prove the causal association, more cases with epidemiological data are required. For a deeper knowledge of COVID-19 infection, it is crucial to investigate its neurologic symptoms. Therefore, additional research is needed to fully understand the prognostic importance of cranial neuropathies in COVID-19 disease and their natural history and choose the most effective therapy approach.\n\nAny patient with a fever and neurological symptoms should be evaluated for COVID-19.\n\n\nConsent\n\nWritten informed consent for publication of their clinical details was obtained from the patient.", "appendix": "Data availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\nZenodo: CARE checklist for “Case Report: Bell’s palsy: a neurological manifestation of COVID-19 infection”. https://doi.org/10.5281/zenodo.8359632. 15\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgments\n\nWe deeply thank our patient for giving us the chance to share this valuable and scientific information. An earlier version of this article can be found on Authorea (doi: https://doi.org/10.22541/au.166797382.23559879/v1).\n\n\nReferences\n\nChen T, Wu D, Chen H, et al.: Clinical characteristics of 113 deceased patients with coronavirus disease 2019: retrospective study [published correction appears in BMJ. 2020 Mar 31;368:m1295]. BMJ. 2020; 368: m1091. Published 2020 Mar 26. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGoh Y, Beh DLL, Makmur A, et al.: Pearls & Oy-sters: Facial nerve palsy in COVID-19 infection. Neurology. 2020; 95(8): 364–367. Publisher Full Text\n\nZammit M, Markey A, Webb C: A rise in facial nerve palsies during the coronavirus disease 2019 pandemic [published online ahead of print, 2020 Oct 1]. J Laryngol Otol. 2020; 1–4. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMontalvan V, Lee J, Bueso T, et al.: Neurological manifestations of COVID-19 and other coronavirus infections: A systematic review. Clin Neurol Neurosurg. 2020; 194: 105921. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAcharya A, Kevadiya BD, Gendelman HE, et al.: SARS-CoV-2 Infection Leads to Neurological Dysfunction. J Neuroimmune Pharmacol. 2020; 15(2): 167–173. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDubé M, Le Coupanec A, Wong AHM, et al.: Axonal Transport Enables Neuron-to-Neuron Propagation of Human Coronavirus OC43. J Virol. 2018; 92(17): e00404–e00418. Published 2018 Aug 16. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLi Y, Fu L, Gonzales DM, et al.: Coronavirus neurovirulence correlates with the ability of the virus to induce pro-inflammatory cytokine signals from astrocytes and microglia. J Virol. 2004; 78(7): 3398–3406. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFilatov A, Sharma P, Hindi F, et al.: Neurological Complications of Coronavirus Disease (COVID-19): Encephalopathy. Cureus. 2020; 12(3): e7352. Published 2020 Mar 21. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGutiérrez-Ortiz C, Méndez-Guerrero A, Rodrigo-Rey S, et al.: Miller Fisher syndrome and polyneuritis cranialis in COVID-19. Neurology. 2020; 95(5): e601–e605. PubMed Abstract \| Publisher Full Text\n\nEgilmez OK, Gündoğan ME, Yılmaz MS, et al.: Can COVID-19 Cause Peripheral Facial Nerve Palsy? SN Compr Clin Med. 2021; 3(8): 1707–1713. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLima MA, Silva MTT, Soares CN, et al.: Peripheral facial nerve palsy associated with COVID-19. J Neurovirol. 2020; 26(6): 941–944. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nOke IO, Oladunjoye OO, Oladunjoye AO, et al.: Bell’s Palsy as a Late Neurologic Manifestation of COVID-19 Infection. Cureus. 2021; 13(3): e13881. Published 2021 Mar 14. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nÇaytemel B, Kılıç H, Çomoğlu Ş: Approach to otolaryngology emergency in COVID-19 pandemic. Tr-ENT. 2020; 30(1): 24–36. Publisher Full Text\n\nPiercy J: Bell’s Palsy. The BMJ. 2005. Published June 9. Accessed September 30, 2022. PubMed Abstract \| Publisher Full Text \| Free Full Text Reference Source\n\nAbdelrahman A: Case Report: Bell’s palsy: a neurological manifestation of COVID-19 infection. [Dataset]. Zenodo. 2023. Publisher Full Text" }	[ { "id": "274184", "date": "21 May 2024", "name": "Sohyeon Kim", "expertise": [ "Reviewer Expertise neuromuscular 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\nI found it as a quite interesting case, but there are several important issues to be checked over in this case report.\nFirst of all, the diagnostic process seemed somewhat insufficient to me. If someone wants to attribute a certain neurologic symptom to be caused by COVID-19, he/she should explain either a causative mechanism or a temporal relationship together with thorough exclusion of other causes. In the Case presentation section, the author stated as \"A diagnosis of Bell's palsy secondary to COVID-19 infection was made\". I think this sounds too confirmative since the causative mechanism of COVID-19 triggering Bell's palsy in this case is uncertain. Also, regarding the exclusion of other causes, the case is lacking of objective results from the diagnostic evaluations and the diagnosis mostly depended merely on the implications from clinical symptoms. If the authors had performed any laboratory test about autoimmune etiology or auxiliary diagnostic work up such as nerve conduction study, cranial MRI, and etc., I recommend containing the results in the revised manuscript. If the objective data are unavailable, the author should mention this as a limitation and need to tone down about the diagnostic certainty.\n\nSecondly, In the Introduction section, the author mentioned \"A growing number of COVID-19 cases have been associated with facial nerve paralysis, often presenting as the initial symptom or occurring within the first week after the onset of viral symptoms or a positive COVID-19 test\". While I acknowledge that facial paralysis occurred within three days of the COVID-19 diagnosis in the present case and it is close enough to allege their temporal relationship, the above sentence sounds to me as if facial palsy and COVID-19 need to occur within one week from each other to generally define the temporal relationship. As there have been controversy among researchers regarding the definition of the time interval as evidence of a specific temporal relationship between COVID-19 and neurological complications, I suggest that the authors supplements the manuscript with additional references to clarify the definition of the temporal relationship between facial palsy and COVID-19.\nAlso, I am not sure if we could adopt the same prognostic factors of Bell's palsy in COVID-19 related cases as the authors mentioned in Discussion section. I think the clinical characteristics and prognostic factors specifically of COVID-19 related Bell's palsy cases should be investigated and explained with supplementary references.\n\nAdditionally, there are several minor comments for the manuscript as well. - In the Case presentation section, the phrase \"no past medical history\" is repeated in the first and second paragraph, and I recommend omitting one of them to avoid repetition. - In the Discussion section, I think it is out of context to mention the encephalopathy case in the fourth paragraph, or the paragraph can be improved with additional references as there are numerous case reports so far about diverse neurologic manifestations following COVID-19 infection.\n\nThe author presented with an intriguing cases for sure, but I think the manuscript needs a major revision.\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": "11873", "date": "25 Jun 2024", "name": "Amro Abdelrahman", "role": "Author Response", "response": "Dear reviewer Thanks for taking time and review our article. - The diagnosis of Bell's palsy is primarily clinical and typically idiopathic. Our diagnosis was based on the acute presentation of classical symptoms, alongside a recent history of upper respiratory infection. According to local protocols, additional investigations such as nerve conduction studies, MRI, or CT are not routinely indicated unless systemic manifestations, recurrent symptoms, or other nerve involvement are present. Further investigations may be warranted in cases with atypical features. - I agree with you we're not 100% sure about COVID-19 being the etiology in this case. I think changing the sentence to \"A diagnosis of Bell's palsy potenially related to COVID-19 infection was made\" would be suffecient. - The introduction section, a new sentence with a reference will be added for clarification \"The relationship between COVID-19 and neurological complications, including facial palsy, is complex and has been the subject of ongoing research. While some cases report facial nerve paralysis occurring within a week of viral symptom onset, there is variability in the reported timeframes.\" - We just highlighted briefly some of the poor prognostic factors for the healthcare providers to give extra attention and close follow up for those with the mentioned poor prognostic factors. We believe (prognostic factors in bells palsy related to COVID-19) is a big topic to be included in a case report and need a different paper to extensively go through it. - Past medical history will be deleted in the second paragraph - The sentence will be rephrased to \"Various types of neurological manifestations of COVID-19 infection have been reported.\" with a new referance" } ] } ]	1	https://f1000research.com/articles/12-1355
https://f1000research.com/articles/13-21/v1	08 Jan 24	{ "type": "Research Article", "title": "Exploring The Legal Landscape of Islamic Fintech in Indonesia: A Comprehensive Analysis of Policies and Regulations", "authors": [ "Dwi Fidhayanti", "Mohd Shahid Mohd Noh", "Ramadhita Ramadhita", "Syabbul Bachri", "Dwi Fidhayanti", "Mohd Shahid Mohd Noh", "Syabbul Bachri" ], "abstract": "The rapid growth of Islamic fintech in Indonesia necessitates a comprehensive examination of the policy and regulatory framework from a legal perspective. This study explores the legal landscape of Islamic fintech in Indonesia, analyzing the current policies and regulations governing this emerging sector. Using normative legal research with a statutory approach and conceptual approach. The primary and secondary legal materials, including government reports and scholarly articles, this research evaluates recent policy developments and regulatory initiatives supporting Islamic fintech. It identifies gaps and areas for improvement, drawing from best practices and regulatory approaches adopted by other countries with successful Islamic fintech ecosystems. Based on the findings, this research proposes recommendations to enhance the policy and regulatory framework. These include collaboration between regulatory bodies and industry stakeholders, tailored licensing frameworks, enhanced consumer protection mechanisms, and promotion of innovation in Shariah-compliant financial products and services. This study contributes to understanding the legal landscape of Islamic fintech in Indonesia, offering a comprehensive analysis of existing policies and regulations. By addressing challenges and proposing solutions, it aims to facilitate the growth of Islamic fintech and foster an inclusive and sustainable financial ecosystem in Indonesia.", "keywords": [ "Indonesia policies", "Indonesia regulations", "Islamic Fintech" ], "content": "Introduction\n\nIslamic fintech has received significant attention (Alshater et al., 2022; Dawood et al., 2022; Rabbani et al., 2021), especially in the Indonesia context (Ascarya & Sakti, 2022; Hudaefi, 2020; Hudaefi et al., 2023; Muryanto et al., 2021). However, Islamic fintech in Indonesia is still in an early stage of development and is less comprehensive than conventional forms (Aulia et al., 2020). There are many startups that do not comply with the Sharia principles that have been regulated by the Indonesian government (Achsien & Purnamasari, 2016). To be fully sharia-compliant, these platforms must avoid interest-based transactions that are common in the fintech world. This restriction limits Islamic fintech companies’ products and services. There are several reasons for the slow growth of Islamic fintech in Indonesia, including inadequate regulations, complicated licensing procedures, rampant illegal fintech businesses, and consumer disputes in the fintech sector (Muryanto et al., 2021). Nevertheless, Indonesia has huge potential for Islamic fintech. With the right policies and regulations, Islamic fintech could contribute to social funds and finance the agriculture sector, as well as small and micro businesses (Agustina & Faizah, 2023). In addition, the adoption of fintech in Islamic finance assists the government in increasing financial inclusion, conquering financial crises such as COVID-19, and achieving the SDGs for a sustainable country (Alshater et al., 2022). The rise of Islamic fintech in markets such as Indonesia and Malaysia is closely related to the growth of Islamic finance in Southeast Asia. According to the World Bank, Indonesia has the largest number of Islamic fintech companies in the world (Hudaefi, 2020).\n\nThe development of fintech companies over time has been proven to improve banks’ financial stability of banks (Safiullah & Paramati, 2022). A study was conducted to explore the evolving legal landscape surrounding Islamic fintech in Indonesia. Muryanto et al. (2021) found that Indonesia, despite having the largest Muslim population in the world, still lags behind Saudi Arabia, Iran, the United Arab Emirates, and Malaysia in terms of the Islamic fintech market size (Muryanto et al., 2021). The Islamic fintech ecosystem consists of financial consumers, fintech startups, the government, technology developers, traditional financial institutions, and fatwa. Hudaefi examined the growth of the Islamic fintech ecosystem in Indonesia within these core elements and provided valuable insights into the current state of the industry in Indonesia (Hudaefi et al., 2023). In Indonesia, Islamic fintech complies with maqashid sharia (Nafiah & Faih, 2019). One of the points of Sharia compliance in Islamic fintech is the existence of the Sharia supervisory board to ensure compliance with Sharia provisions (Iqbal, n.d.; Muryanto et al., 2021). The implementation of Islamic fintech in protecting the spiritual rights of customers by ensuring that Islamic fintech financing services do not involve interest or usury (riba), uncertainty (gharar), speculation (maysir), hiding damage (tadlis), harming other parties (dharar), or avoiding things (haram) (Sugiarto & Disemadi, 2020). New regulations based on products, policies, and procedures are needed in order to gain more acceptance for the Islamic finance industry (Mazlan et al., 2023). This research aims to examine the gap between the current and desired state of Islamic fintech regulations in Indonesia. By conducting a comprehensive analysis of policies and regulations, this research intends to provide insights to guide the development of a robust legal framework that matches the unique attributes of Islamic fintech. This article makes a significant contribution to the development of Islamic fintech in Indonesia by providing a comprehensive understanding of the legal landscape, addressing regulatory challenges, and providing actionable insights to create a conducive environment for sustainable growth and innovation in the sector.\n\n\nMethod\n\nThe focus of this research is to explore comprehensively analyse the legal landscape of Islamic fintech in Indonesia. The research primarily employs a normative legal approach, aiming to examine and analyse existing policies and regulations related to Islamic fintech. To achieve this, both a statutory approach and a conceptual approach were utilized. The statutory approach involves an examination of government regulations, fatwa, and regulatory policies relevant to both law and fintech. Meanwhile, the conceptual approach is employed to delve into the principles of fintech and sharia that serve as references for ensuring sharia compliance within the Islamic fintech industry.\n\nThe data sources of this research encompass a variety of primary and secondary legal materials. The primary legal materials consist of legislative documents directly related to Islamic fintech in Indonesia. In addition, secondary legal materials such as national and international journal articles, theses, dissertations, and other scholarly works pertaining to the development of Islamic fintech regulations in Indonesia were gathered through a comprehensive literature study.\n\nInterpretative analysis of the gathered data was conducted using both descriptive and comparative methods. The descriptive approach is employed in order to make comparisons with the countries that have a burgeoning Islamic fintech sector. The analysis results are then interpreted with a multifaceted lens, encompassing aspects of Sharia law, practical implications, and potential effects on the growth of the Islamic fintech industry in Indonesia. This interpretative phase adds depth and context to the findings, enabling a more comprehensive understanding of the legal framework surrounding Islamic fintech in the country.\n\n“FinTech” is a rather simple and obvious combination of an application domain (“financial”) and “technology” (Alt et al., 2018). It refers to the integration of digital technologies into financial services, which has the potential to transform the provision of financial services and spur the development of new ones (Feyen et al., 2023). The ongoing digitization of financial services and money creates opportunities to rapidly build a more inclusive and efficient financial sector landscape and blurs the boundaries of both financial firms and the financial sector, which presents a paradigm shift that has various policy implications (World Bank, 2023). Some of these policy implications include fostering beneficial innovation and competition while managing risks, broadening monitoring horizons and reassessing regulatory perimeters, ensuring that public money remains fit for the digital world, and pursuing strong cross-border coordination. Digital transformation has become a disruptor in almost every industry, including fintech, making the sector more customer-centric and technologically relevant. The evolution of digital transformation in the fintech industry has become a business imperative for improving customer experience through the development of new services and products (Alt et al., 2018). The pandemic has accelerated the adoption of fintech and the sector has experienced one of the most drastic changes in its transformation (Abdul-Rahim et al., 2022; Modgil et al., 2022; Nugraha et al., 2022).\n\nIslamic fintech provided a solution during the pandemic for digital financial innovation with the ease of transactions, without physical meetings (Hasan et al., 2023; Karim et al., 2022; Yudhira, 2021). Islamic fintech is a growing sector in Indonesia, which has the largest Muslim population in the world (Muryanto et al., 2021). The Indonesian Sharia Fintech Association (AFSI) noted that from 2020 to 2021, there was a growth of approximately 130% in the Sharia fintech industry. By 2022, it will increase to 180%. Furthermore, The Global Islamic FinTech 2022 Index lists Indonesia as one of the top five conducive ecosystems for Fintech in the rest of the world, including Malaysia, Saudi Arabia, Indonesia, the United Arab Emirates, and the United Kingdom. The potential for Islamic fintech in Indonesia is huge, and the sector is predicted to reach US$179 billion, with a compound annual growth rate (CAGR) of 17.9% by 2026 (Hudaefi et al., 2023). Indonesia’s National Sharia Finance Committee has made the growth of Sharia fintech a top national priority (Potkin, 2020).\n\nThe basic concept of Islamic fintech in Indonesia revolves around combining the principles of Islamic finance with modern technological advancements (Oi, 2023) to provide financial services and solutions that are in line with Islamic teachings (Cherqaoui, 2022). Islamic fintech, also known as “Fintech Syariah,” aims to offer innovative financial products and services that adhere to the ethical and moral guidelines set forth by Islamic law or Shariah. Operating according to Shariah principles, which prohibits interest (riba), uncertainty (gharar), gambling (maysir), and unethical investment (haram) (Sugiarto & Disemadi, 2020). This is the difference between the conventional fintech and Sharia fintech. In Indonesia, Islamic fintech in operation must meet the operational and license requirements set by the regulator. In terms of supervision, the Indonesia Financial Services Authority (OJK) is responsible for supervising and regulating fintech activities in Indonesia, including Islamic Fintech. In order to improve supervision and customer protection, OJK has issued several regulations and policies related to fintech, such as OJK Regulation Number 77/POJK.01/2016 on Information Technology-Based Money Lending and Borrowing Services, and OJK Regulation Number 13/POJK.02/2018 on Digital Financial Innovation in the Financial Services Sector. Islamic fintech also refers to the Fatwa of the National Sharia Council of the Indonesian Ulema Council (DSN MUI), such as Fatwa DSN MUI Number 116/DSN-MUI/IX/2017 on Shariah-compliant electronic money, Fatwa DSN MUI Number 117/2017 on Information Technology-Based Financing Services Based on Shariah Principles, and Fatwa DSN MUI Number 140/DSN-MUI/VIII/2021 on Shariah-Compliant Securities Through Technology-Based Fund Management Services. DSN MUI is part of MUI, which is tasked with developing the application of Sharia values in economic activities in general, and the financial sector in particular, including overseeing Sharia compliance in Islamic fintech. DSN MUI’s fatwas and guidance serve as important references for Islamic fintech providers and users to ensure compliance with Shariah principles. The institution’s role in issuing fatwas and overseeing their implementation contributed to the development and advancement of Islamic fintech in Indonesia (Widyastuti et al., 2020).\n\nCollaboration between DSN-MUI, OJK, and other regulatory bodies is crucial in formulating and implementing these regulations to ensure the proper functioning and oversight of Islamic fintech platforms in Indonesia to maximize the benefits of Islamic fintech. Islamic fintech can bring several benefits to Indonesia, including financial access, compliance with Sharia, and economic empowerment. Islamic fintech can help increase financial inclusion for micro, small, and medium enterprises (MSMEs) by providing easier access to finance (Dwijayanti et al., 2022; Putri & Akbary, 2021; Syarifuddin et al., 2021). Islamic fintech platforms also promote financial inclusion by providing access to Shariah-compliant financial services for underserved populations. Islamic fintech can empower the economy by providing easier access to finance for individuals and businesses, promoting entrepreneurship and increasing financial literacy. Islamic fintech conquers financial crises, such as COVID-19, and achieves SDGs for a sustainable nation (Alshater et al., 2022).\n\nHowever, due to the convenience and benefits of Islamic fintech in Indonesia, Islamic fintech still faces challenges. First, inadequate regulations, it’s because there are no regulations that specifically regulate or contain Islamic fintech lending (Hui et al., 2019; Muryanto et al., 2021; Noor et al., 2022). Second, complicated permit procedures and fintech registration itself are divided into two: for lending-based fintech or peer-to-peer lending is under the management of OJK. Those under Bank Indonesia (BI) supervision are related to the payment system. The Indonesian Bank Indonesia and OJK should walk together to make fintech licensing a single door. In addition, the existence of special requirements for Sharia-based fintech also requires the existence of a Sharia Supervisory Board to ensure Sharia compliance, which also makes regulations through Fatwa DSN-MUI. This complicated licensing has led to the emergence of illegal fintech companies. Third, consumer protection challenges in Islamic fintech in Indonesia encompass issues related to awareness, transparency, data security, dispute resolution, and risk of misuse (Sugiarto & Disemadi, 2020).\n\nThe implication of such cases for legal regulation and industry practice is that they may influence how the Islamic fintech industry is regulated and operated. These cases could be an impetus for regulators to strengthen the rules and regulations related to Islamic fintech to protect consumers and ensure compliance with the Sharia principles. As such, legal cases of Islamic fintech operations in Indonesia have an important impact on the development and regulation of the industry. With a strong role in shaping regulations that support growth and innovation, law plays a key role in shaping the future of Islamic fintech in Indonesia. Thoughtful and progressive laws can help create a conducive environment for Islamic fintech to thrive and contribute to its national ecosystem.\n\nAddressing these consumer protection challenges in Islamic fintech requires a combination of regulatory measures, industry self-regulation, consumer education, and technological protection. Ensuring that consumers are well-informed, have access to dispute resolution mechanisms, and are protected from data breaches and non-compliance with Sharia principles is critical to building trust and confidence in the Islamic fintech sector in Indonesia. Indonesia follows the example of other countries that have fintech industries in terms of regulations and policies. The following table compares the regulations in Indonesia with various countries that have fintech industries, such as Malaysia, Saudi Arabia, the UAE, and the United Kingdom:\n\nIndonesia can emulate the experiences of other countries with the aforementioned Islamic fintech industries. First, Shariah Compliance and Innovation, the regulatory landscape in Indonesia must continue to evolve and remain committed to Shariah compliance so that it can be dynamic to accommodate innovation while upholding Shariah standards. Second, in terms of clarity in regulation, Indonesia can benefit from following the footsteps of the UAE, where clear regulatory guidelines and supportive infrastructure have helped establish the country as a global fintech hub. Clarity in regulation is essential for attracting investment and fostering a conducive environment for startups to thrive. Third, the Market Potential and Challenges, Indonesia, which has the largest Muslim population, face similar challenges to Saudi Arabia, where the growing interest in Shariah-compliant fintech requires clearer guidelines to facilitate adoption across the industry. Fourth, Malaysia’s well-established ecosystem needs to be modelled to benefit from inclusive policies that encourage startups and foster industry expansion. Fifth, regarding Ethical Finance and Diversified Services, The UK’s focus on ethical and faith-based financial services offers an interesting parallel. Indonesia could explore integrating broader ethical finance options alongside Sharia-compliant offerings to serve a diverse customer base.\n\nTo create a solid foundation for the development of Islamic fintech in Indonesia, policies and regulations are needed that can help ensure that the industry grows well in a conducive legal environment in accordance with Sharia principles. In addition, consumer protection in the financial services sector and the Investment Alert Task Force can help consumers from harmful practices but still must be improved in terms of product and service transparency, data security, and consumer rights. Consumers’ right to use services in accordance with Sharia beliefs and values is required to ensure that the product is Sharia-compliant. Other supporters encourage the development of Islamic fintech, namely, the need for a smooth and less complicated licensing process.\n\nThe legal landscape of Islamic fintech in Indonesia is complex and dynamic, and is influenced by broader global trends in financial technology. FinTech, which is an amalgamation of finance and technology, represents a fundamental shift in the provision of financial services. The ongoing digitization of finance has disrupted traditional boundaries within the financial sector, resulting in various policy implications. These implications range from fostering innovation and competition while managing risks to expanding regulatory oversight and ensuring the adaptation of public money to the digital world, while striving for robust cross-border coordination.\n\nThe advent of digital transformation has affected virtually every industry, including fintech. It has not only made the sector more customer-centric but has also positioned digital transformation as a business imperative (Chong, 2021). The COVID-19 pandemic has accelerated the adoption of fintech, resulting in significant changes in the industry’s transformation. In Indonesia, Islamic fintech has emerged as a viable solution during the pandemic, offering digital financial innovation with the convenience of remote transactions. Given Indonesia’s status as the country with the world’s largest Muslim population, the growth in Islamic fintech has been remarkable. The Indonesian Sharia Fintech Association (AFSI) reported a substantial increase in the Sharia fintech industry, with growth rates of 130% from 2020 to 2021, and 180% by 2022. Indonesia is recognized as one of the top five conducive ecosystems for fintech globally, as per The Global Islamic FinTech 2022 Index. Projections indicate that Islamic fintech in Indonesia could reach a market size of US$179 billion with a CAGR of 17.9% by 2026, making it a top national priority for Indonesia’s National Sharia Finance Committee.\n\nThe fundamental concept of Islamic fintech in Indonesia revolves around harmonizing Islamic finance principles with modern technology. Islamic fintech, often referred to as “Fintech Syariah,” aims to provide innovative financial products and services in compliance with the ethical and moral guidelines established by Islamic law Shariah. This adherence to the Shariah principles differentiates Islamic fintech from conventional fintech, particularly in its prohibition of interest (riba), uncertainty (gharar), gambling (maysir), and unethical investments (haram).\n\nRegulation and supervision are integral to Islamic fintech’s functioning in Indonesia. The Indonesian Financial Services Authority (OJK) plays a central role in supervising and regulating fintech activities including Islamic fintech. The OJK has issued several regulations and policies to enhance supervision and customer protection, such as OJK Regulation Number 77/POJK.01/2016 and OJK Regulation Number 13/POJK.02/2018. Additionally, Islamic fintech operates within the framework of fatwas issued by the National Sharia Council of the Indonesian Ulema Council (DSN MUI), addressing matters such as Shariah-compliant electronic money, financing services, and securities through technology-based fund management services. The involvement of DSN MUI’s in ensuring Shariah compliance is a critical aspect of Islamic fintech oversight. Collaboration among regulatory bodies, including DSN-MUI and OJK, is pivotal for formulating and implementing effective regulations to maximize the benefits of Islamic fintech. Islamic fintech offers Indonesia a range of advantages, including enhanced financial access, Sharia compliance, and economic empowerment. By facilitating easier access to finance for micro, small, and medium enterprises (MSMEs), promoting financial inclusion, and encouraging entrepreneurship, Islamic fintech contributes to the country’s economic development and resilience during financial crises such as the COVID-19 pandemic (Muzdalifa and Rahma, 2018).\n\nHowever, Islamic fintech faces several challenges in Indonesia. These include inadequate regulations specific to Islamic fintech lending; complex permit procedures that divide fintech registration between OJK and Bank Indonesia; and consumer protection issues related to awareness, transparency, data security, dispute resolution, and the risk of misuse. Legal cases and challenges within the Islamic fintech industry can influence regulations and operations. These cases may compel regulators to strengthen the rules and regulations to protect consumers and ensure Shariah compliance. The role of law in shaping regulations supporting growth and innovation cannot be understood. A thoughtful and progressive legal framework is essential for creating a conducive environment for Islamic fintech in Indonesia. Addressing consumer protection challenges requires a multifaceted approach that includes regulatory measures, industry self-regulation, consumer education, and technological safeguards. Ensuring that consumers are well informed, have access to dispute resolution mechanisms, and are protected from data breaches and non-compliance with Shariah principles is vital for building trust and confidence in the Islamic fintech sector in Indonesia.\n\nTo develop Islamic fintech in Indonesia further, the country can draw lessons from other nations with established Islamic fintech industries. This includes continually evolving regulatory frameworks that maintain a commitment to Shariah compliance while accommodating innovation. Clear regulatory guidelines, such as those in the UAE, can attract investment and provide a conducive environment for startups. Indonesia can also learn from Malaysia’s inclusive policies, Saudi Arabia’s efforts to strike a balance between innovation and Shariah adherence, and the UAE’s initiatives to establish itself as a global Islamic fintech center. Additionally, exploring ethical finance options alongside Sharia-compliant offerings, as in the United Kingdom, can cater to diverse customer bases. In conclusion, Islamic fintech in Indonesia is a nexus of finance and technology, with tremendous potential for growth and financial inclusion. Effective regulations, collaboration among regulatory bodies, and a focus on consumer protection are critical for harnessing this potential. Learning from global experiences and adopting best practices can help Indonesia create a conducive legal environment for Islamic fintech, while ensuring compliance with Shariah principles and enhancing consumer rights and protection.\n\n\nConclusion\n\nAn examination of Indonesia’s legal landscape for Islamic fintech illuminates a rapidly growing sector that harmonizes digital innovation with Sharia principles. This fusion has yielded a dynamic ecosystem that is responsive to the distinctive requirements of Indonesia’s Muslim population. Collaborative regulatory endeavors involving bodies such as the Indonesian Financial Services Authority (OJK) and the National Sharia Council of the Indonesian Ulema Council (DSN MUI) have fostered an environment conducive to Islamic fintech expansion. This regulatory framework, coupled with the impressive growth rates in the Sharia fintech sector, positions Indonesia as a noteworthy player in the global Islamic fintech stage.\n\nConsidering the study’s limitations, such as its regulatory-centric focus and the limited exploration of individual Islamic fintech platforms, future research directions can enhance our understanding. Delving into consumer behaviour and trust dynamics within these platforms, investigating innovative technological solutions for bolstering Sharia compliance, and scrutinizing cross-border collaboration potential are avenues for deeper exploration. Additionally, researching the socioeconomic impacts of Islamic fintech, aligning Sharia principles with sustainability goals, and continually monitoring the evolution of the regulatory framework will yield a more comprehensive understanding of the Islamic fintech landscape, ensuring that it thrives within Indonesia’s evolving financial ecosystem.", "appendix": "Data availability\n\nNo data are associated with this article.\n\n\nBibliography\n\nAbdul-Rahim R, Bohari SA, Aman A, et al.: Benefit–Risk Perceptions of FinTech Adoption for Sustainability from Bank Consumers’ Perspective: The Moderating Role of Fear of COVID-19. Sustainability. 2022; 14(14): 8357. Publisher Full Text\n\nAchsien I, Purnamasari D: Islamic Crowd-Funding as The Next Financial Innovation in Islamic Finance: Potential and Anticipated Regulation in Indonesia.European Journal of Islamic Finance.1 July 2016. 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Reference Source\n\nYudhira A: ANALISIS PERKEMBANGAN FINANCIAL TECHNOLOGY (FINTECH) SYARIAH PADA MASA PANDEMI COVID-19 DI INDONESIA. VALUE. 2 February 2021; 2(2): 13–28. Publisher Full Text" }	[ { "id": "254340", "date": "20 Mar 2024", "name": "Hazik Mohamed", "expertise": [ "Reviewer Expertise fintech", "Islamic fintech", "innovation", "sustainability", "Shariah applications" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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, I think regulations in the Fintech space has been lagging and can not keep up with the rapid changes of innovation, so this is not new (both in conventional and Islamic Fintech). Due to the lack of a formal Fintech legal framework in Indonesia, this article has tried to put together what is available. The suggestion of measuring impact, aligning with Maqasid Shariah and the UN SDGs is not new but a necessary one. Perhaps, a follow-up paper could be to propose how this can be done. This would be more useful to Islamic regulators and the Fintech ecosystem at large.\nAlso, I wanted to point out that gharar is not accurately \"uncertainty\". It is more closely related to \"ambiguity\", or specifically \"deceptive ambiguity\". That is to be consciously deceiving a counter-party through being vague or deliberately ambiguous. \"Uncertainty\" is the state of not knowing what cannot be ascertained, like the future or unpredictable events. This belongs in God's realm, we can only try to manage it but cannot eliminate it. This is a misconception in many Islamic Finance articles, textbooks and papers.\nThe suggestion to draw lessons from other countries should include the emphasis that these lessons drawn need to be specific to Indonesia's needs and gaps. Also, it is important to import good and relevant lessons while learning from the mistakes of others, and not to repeat them.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? 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": "11338", "date": "13 Apr 2024", "name": "Ramadhita Ramadhita", "role": "Author Response", "response": "Firstly, thank you for your review, the suggestions will be taken into consideration for our next development research. Secondly, for the definition of gharar we have learnt more and we agree that gharar leads to ambiguity rather than uncertainty in the law. Third, for the third review we will make it more specific as the following data: Indonesia can emulate the experience of other countries with Islamic fintech industries mentioned above. In terms of Sharia compliance, Indonesia is very weak because the Sharia Supervisory Board operates under the Indonesia Ulema Council (DSN MUI), which is an independent institution. The DSN is authorized to establish and issue Islamic legal opinions (fatwas) regarding economic and financial activities. However, fatwas are religious opinions, not positive law issued by state institutions. Therefore, fatwas do not have binding legal force in a country, thus there are no sanctions or legal threats for non-compliance. Indonesia should emulate other countries that implement Islamic fintech, such as Malaysia, Saudi Arabia, and the UEA, where these institutions are under state auspices, so fatwas and regulations issued constitute positive law and have legally binding force that must be complied with and enforced. The clear regulatory guidelines and supportive infrastructure can help establish the Indonesia as a global fintech hub and attract investment to foster a conductive environment for startups to thrive." } ] }, { "id": "254337", "date": "11 May 2024", "name": "Adnan Opeyemi Salaudeen", "expertise": [ "Reviewer Expertise Islamic finance", "Islamic Social Financer and Islamic Fintech" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nSummary: The paper conducts a comprehensive examination of the legal landscape of Islamic fintech in Indonesia, aiming to provide insights into the policy and regulatory framework governing this emerging sector. Employing a normative legal research approach with both statutory and conceptual methods, the study analyses existing policies and regulations related to Islamic fintech. The research draws from primary legal materials, such as legislative documents, and secondary legal materials, including scholarly works, to evaluate recent policy developments and regulatory initiatives. Key findings include the rapid growth of Islamic fintech in Indonesia, driven by factors such as the country's sizeable Muslim population, regulatory efforts led by the Indonesian Financial Services Authority (OJK) and the National Sharia Council of the Indonesian Ulema Council (DSN MUI), and the potential for Islamic fintech to contribute to financial inclusion and economic empowerment. However, the study also identifies challenges, including inadequate regulations, complex permit procedures, and consumer protection issues. The paper concludes by emphasising the need for collaborative regulatory efforts, clarity in regulations, and enhanced consumer protection measures to foster the growth of Islamic fintech in Indonesia.\nGeneral Overview: The paper is clearly and accurately presented. It provides a well-structured overview of Islamic fintech's legal landscape in Indonesia, logically discussing key concepts, regulatory frameworks, challenges, and potential solutions. The study design appears appropriate, employing a normative legal research approach to analyse policies and regulations governing Islamic fintech in Indonesia.\n\nStatistical Analysis and Interpretation: Statistical analysis is not applicable since the study primarily involves legal research and analysis of policies and regulations. Interpreting legal frameworks and regulatory policies is appropriate within the context of the study objectives.\nRecommendations for Improvement:\nProvide more in-depth discussions on specific regulatory challenges and potential solutions, supported by empirical evidence or case studies where applicable rather than just one summary paragraph on challenges. Consider incorporating perspectives from industry stakeholders or experts to provide additional insights into the practical implications of the regulatory framework for Islamic fintech in Indonesia.\n\nIs the work 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": "254333", "date": "17 May 2024", "name": "Mohamad Abdun Nasir", "expertise": [ "Reviewer Expertise Islamic law", "Islamic economic", "Islamic studies" ], "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 offers a new perspective on the legal ground for Islamic fintech in Indonesia, showing the dynamic growth of fintech and its harmony with Sharia. This is a very interesting and important finding. It shows how sharia and technology can merge to form economic practices complies with technology and modernity.\n\nThis paper applies appropriate method and data and the analysis is deep and critical. It also uses sufficient bibliographies, both primary and secondary.\n\nThe minor problem is concerned with some sentences which are complete. This grammatical error can be fixed easily.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] } ]	1	https://f1000research.com/articles/13-21
https://f1000research.com/articles/11-1067/v1	20 Sep 22	{ "type": "Study Protocol", "title": "Paravertebral vs. Epidural Analgesia for Liver Surgery (PEALS): Protocol for a randomized controlled pilot study", "authors": [ "Glenio B. Mizubuti", "Anthony M.-H. Ho", "Deborah DuMerton", "Rachel Phelan", "Wilma M. Hopman", "Camilyn Cheng", "Jessica Xiong", "Jessica Shelley", "Elorm Vowotor", "Sulaiman Nanji", "Diederick Jalink", "Lais Helena Navarro e Lima", "Glenio B. Mizubuti", "Deborah DuMerton", "Rachel Phelan", "Wilma M. Hopman", "Camilyn Cheng", "Jessica Xiong", "Jessica Shelley", "Elorm Vowotor", "Sulaiman Nanji", "Diederick Jalink", "Lais Helena Navarro e Lima" ], "abstract": "Background: Perioperative thoracic epidural analgesia (TEA) is commonly used in hepatectomy patients since it is opioid-sparing and reduces cardiorespiratory complications. However, TEA has a high failure rate and is associated with potentially devastating complications (particularly spinal haematoma) and the risk is likely increased with hepatectomy. Thus, some centres favour systemic opioid-based modalities which, in turn, are associated with inferior analgesia and well-known risks/side-effects. Hence, alternative analgesic methods are desirable. Paravertebral block (PVB) has been used in liver resection with advantages including hemodynamic stability, low failure rates, and low risk of spinal haematoma. Our purpose is to conduct a blinded, pilot RCT with hepatectomy patients randomised to receive TEA or PVB for perioperative analgesia. Our hypothesis is that opioid consumption, time to first analgesic request, and pain scores will be comparable between groups, but PVB patients will require fewer perioperative vasopressors/blood products, and have fewer adverse events and a shorter hospital stay. Methods: With ethics approval, this non-inferiority, pilot RCT with a convenience sample of 50 hepatectomy patients will examine whether PVB imparts analgesia comparable to TEA but with fewer adverse effects. Primary outcomes are surrogates of analgesia for 72 h postoperatively (i.e., opioid consumption, time to first analgesic request and pain scores at rest and with coughing); Secondary outcomes are blood products/fluids administered; side effects/complications until 72 h postoperatively; length of hospital stay. The results will be used to plan a large multicentre trial comparing TEA vs. PVB in hepatectomy patients. This study has a high potential to positively impact the quality/safety of patient care. ClinicalTrials.gov registration: NCT02909322 (09-21-2016); Available at URL: https://clinicaltrials.gov/ct2/show/NCT0290932", "keywords": [ "Epidural anaesthesia", "Non-inferiority trial", "Hepatectomy", "Paravertebral block", "Pilot study", "Randomized controlled trial", "Regional anaesthesia" ], "content": "Introduction\n\nContinuous thoracic epidural analgesia (TEA) is commonly used for pain management following hepatectomy1–5 since it is opioid-sparing, reduces cardiovascular/respiratory complications, and improves mobility.6 However, the safety of TEA in this population has been debated.7 TEA is associated with rare complications including epidural haematoma/abscess, and spinal cord injury.5,8 These risks may be higher following hepatectomy compared to other surgeries because of postoperative coagulopathy and thrombocytopaenia.4,9 Additionally, up to 37% of TEAs fail due to an inadequate block, a dislodged/leaking catheter,10–13 or because the catheter has veered to the left (providing analgesia opposite to surgical site). TEA is also associated with hypotension, which may necessitate increased volumes of intravenous (i.v.) fluids perioperatively.11,14,15 The potential effect of increasing central venous pressure (CVP) with this increased fluid load may exacerbate blood loss and haemodilution.1 Finally, TEA can delay mobilisation and prolong the need for a urinary catheter. Given these concerns, some centres prefer patient-controlled opioid analgesia (PCA) post-hepatectomy.16 However, systemic opioids are not as effective for analgesia, and they have serious risk profiles including impaired ventilation, drowsiness, urinary retention, decreased gastrointestinal motility, increased risk of aspiration pneumonia, and postoperative nausea and vomiting (PONV). Thus, there is a continued need for alternative regional analgesic techniques for liver resection patients.\n\nCoagulopathy and/or thrombocytopaenia (not uncommon with liver disease),17,18 worsens in the first two postoperative days following hepatectomy and can remain abnormal for up to five days.4,6,9,19–22 This is a consequence of preoperative liver dysfunction (reflected by the Model for End-Stage Liver Disease (MELD) score),19 the amount of tissue resected, blood loss, and intraoperative liver ischaemia.14,23,24\n\nThoracic paravertebral block (PVB) has been used with several surgical procedures25–36 including ablation of hepatic tumors35 and hepatectomy.36 Previous research suggests that advantages include haemodynamic stability,37,38 low failure rate,39 and a negligible risk of spinal haematoma.40,41 However, there is a small risk of pneumothorax.\n\nA right-sided thoracic PVB is a potential alternative to TEA in hepatectomy patients using a right-subcostal incision, but it appears this has not been compared to TEA over an extended time-period. To our knowledge, the only randomised controlled trial (RCT) currently available compared bilateral thoracic PVB to TEA and concluded that TEA provides a modest analgesic benefit.42 However, patients were only followed for 48 hours which may be insufficient for pain outcomes since hepatectomy patients generally begin to mobilise at 48 hours postoperatively, meaning their pain scores are likely to worsen. Additionally, postoperative coagulopathy and thrombocytopaenia generally peak at 48 hours postoperatively and can persist for extended periods depending upon factors including the capacity of the liver to produce α-1-acid-glycoprotein (AAG), albumin, and coagulation factors, as well as its metabolic capacity (mechanisms which protect against local anaesthetic (LA) systemic toxicity (LAST)). This highlights concerns in the above mentioned study,42 since even patients with normal liver function can develop LAST with a 48-hour infusion of LA via bilateral PVB.43 In addition, pain from a right subcostal incision probably does not justify using a left-sided PVB which may further expose potentially “LAST-vulnerable” patients to additional LA.\n\nAnother study by Richardson et al. (1999) found that thoracotomy patients receiving PVB had less pain and improved pulmonary function than with TEA.44 The TEA cohort also had a higher incidence of PONV, respiratory complications, hypotension, and consumed more morphine.44 In another study, PVB patients had less PONV, hypotension, and/or urinary retention compared to TEA.45 A systematic review of RCTs (comprising 1762 thoracotomy patients) concluded that the most effective analgesic method for preserving spirometric function was PVB.46 A meta-analysis of thoracotomy studies comparing TEA and PVB concluded that PVB is associated with fewer pulmonary complications and less urinary retention, PONV, and hypotension, albeit with comparable analgesia,47 and this was later confirmed.48 Based upon such data, we decided to compare a right-sided PVB with TEA for perioperative analgesia following hepatectomy.\n\n\nHypothesis\n\nOur hypothesis is that surrogates of pain will be comparable between groups but PVB patients will require fewer vasopressors and i.v. fluids/blood products, have fewer side effects/complications, and have a reduced hospital length of stay (LOS).\n\n\nProtocol\n\nNon-inferiority trials typically require larger samples than superiority trials49,50; thus, we anticipate the need to include multiple centres to secure enough participants. Therefore, we propose a single-centre pilot study to generate the data needed to estimate the sample size required for a large, multi-centre trial. Based upon previous studies that compared TEA versus PVB for postoperative analgesia in patients undergoing thoracotomy,45,51 we will aim for a convenience sample of 25 patients per group to generate pilot data upon which to base a larger, multi-centre trial. Our non-inferiority margin will be set at 20% for cumulative opioid consumption at 72 hours postoperatively since we do not consider a difference of <20% to be clinically relevant.\n\nA convenience sample of 50 patients scheduled to undergo a hepatectomy through a right subcostal incision will be recruited from our medium-sized (~407 beds), tertiary care academic centre. Eligible patients will be approached by research personnel at the preoperative screening clinic or, because of COVID concerns, via telephone at least 24-48 hours before surgery and given information about the study. For patients who are eligible and willing, research personnel will obtain signed consent while they are waiting to be taken to the operating room (OR). In all cases, both the anaesthesiologist and the attending surgeon will be made aware at least one to three days before surgery of the potential involvement of the patient, and time will be allowed for discussion and withdrawal at their request. With the volume of liver resection surgical patients at our centre (i.e., ~30/year), we anticipate recruitment/data collection for 50 patients to require two to three years.\n\n\n\n• Patients will be eligible for inclusion to our study if they are:\n\n○ 18-80 years of age\n\n○ American Society of Anesthesiologists (ASA) physical classification I-III\n\n○ Undergoing elective liver resection through right subcostal incision\n\n○ Proficient in English\n\n○ Competent to provide consent\n\n• Patients will not be eligible for our study if they are/have:\n\n○ Pregnant or lactating\n\n○ Do not provide informed consent for participation\n\n○ Body mass index <18 or >40 kg.m-2\n\n○ Dementia or neurological impairment\n\n○ Jaundice (bilirubin >50 μmol/L)\n\n○ Liver resection combined with a secondary surgical procedure\n\n○ Contraindication to neuraxial block (INR ≥1.6, platelet count <100,000/mm3, fever, previous back surgery)\n\n○ Anticipated significant coagulopathy post-liver resection (as indicated by MELD score >8 or predicted liver resection of >500 g)\n\n○ Contraindications to study medications\n\n○ Any type of extended incision that is not restricted to the standard right subcostal incision\n\n○ Remain intubated in the postoperative period\n\n○ Significant heart disease including moderate or severe valvulopathies, left ventricular ejection fraction <35%, moderate or severe cardiomyopathy of any etiology (e.g., ischaemic, dilated, etc.), previous history of malignant arrhythmias (ventricular tachycardia/ventricular fibrillation, prolonged QT syndrome, etc.), or any other cardiac conditions deemed as high surgical risk by anaesthesiologist investigators\n\n○ Pre-existing chronic pain condition requiring chronic opioid intake for >3 months\n\nThis is a randomised, controlled, non-inferiority pilot study. Eligible patients will be randomised using a computer-generated randomisation table prepared by the institutional biostatistician with assignments concealed in envelopes. Participants, surgeons, and dedicated research personnel collecting the data (i.e., study nurses/research assistants) will be blinded to allocation. Anaesthesiologists performing TEA/PVB will not be blinded but will have no involvement in patient assessments/data collection.\n\nTo protect confidentiality, patient data on collection sheets/spreadsheets will be identified only by a study identification number that will be linked to the patient identity only on a master sheet/spreadsheet kept securely and separately from the data. Patient data will then be entered into a password-protected REDCAP file and stored on the institutional server behind a firewall. All study data will be retained for the 15-year storage period required by Health Canada following which, it will be permanently deleted and/or destroyed. Only study personnel will have access to identifiable study data and it will not be shared with a third party. Final data may be placed in a public depository but no publicly accessible information will be identifiable.\n\nDescriptive demographic data including patient height, weight, age, sex, ASA physical classification, MELD score, comorbidities, type and length of surgical procedure, number of resected liver segments, estimated blood loss, intraoperative complications, surgeon, the main surgical indication, and preoperative functional liver status will be recorded.\n\nEthical approval was provided by the Queen’s University Health Sciences and Affiliated Teaching Hospitals Research Ethics Board (ANAE-270-15) and the study registered on Clinicaltrials.gov (NCT02909322 09-21-2016) available at URL: https://clinicaltrials.gov/ct2/show/NCT02909322. This non-inferiority pilot RCT in which hepatectomy patients will be randomly assigned to receive either TEA or PVB for postoperative analgesia, is also in compliance with the Standard Protocol Items: Recommendations for Interventional Trials (SPIRIT) guidelines. As clearly stated in the informed consent, in the unlikely event that participants are injured due to participation in the current study, medical care will be provided to them free of charge until resolution of the problem. By providing consent to participate, they are not waiving their legal rights or releasing the investigator(s) and sponsors from their legal and professional responsibilities.\n\n\nProtocol-version 1.4, 03-23-2022\n\nThe standard of care for elective hepatectomy will be followed. Apart from intraoperative management of the regional block and postoperative analgesia, perioperative management will be identical in both groups. After general anaesthesia (GA) induction, invasive monitoring will be with an arterial line with or without a central venous line. Arterial blood gases will be monitored every hour. Fluid management will be at the discretion of the anaesthesiologist. Intraoperative haemodynamics will be managed by adjustment of the depth of GA and vasoactive drugs, and with fluid administration, all at the discretion of the anaesthesiologist. The quantities of crystalloids, colloids and blood products, and the intraoperative fentanyl dosage (up to 5 μg/kg allowed) will be recorded. No long-acting opioid (hydromorphone, morphine) or ketamine will be administered intraoperatively. Prophylactic ondansetron (4 mg) will be administered upon surgical completion. With the exception of unstable patients, tracheal extubation will be carried out in the OR before transfer to the post-anesthetic care unit (PACU). After PACU discharge, patients will be managed in a high dependency unit (step down bed) or the intensive care unit at the discretion of the anaesthesiologist.\n\nControl group: TEA\n\nTEA procedures will follow the standard of care at our centre. The TEA catheter will be sited preoperatively at T7-T9 using the landmark technique, and a lignocaine test dose (4-6 mL of 2% lignocaine with epinephrine 1:200,000) will be given. After GA induction, bupivacaine 0.1% with hydromorphone 10 μg/mL will be infused at 6-10 mL/h and five mL boluses will be allowed at 30 min intervals at the discretion of the anaesthesiologist. Upon admission to the PACU, patient-controlled epidural analgesia (PCEA) will be initiated. The PCEA bolus of the same solution will be set at three mL with a lockout period of 30 min, and the epidural infusion of the same solution will be set at six mL/h and adjusted in two mL/h increments (or decrements) up to 10 mL/h depending upon pain scores and sensory block tested with ice in the PACU.\n\nIf at any time point during the first 72 hours post-surgery patients complain of moderate-severe pain (i.e., >4/10 on a numeric rating scale (NRS) where 0 = no pain, 10 = worst pain imaginable) despite maximal epidural infusion (10 mL/h), a bolus of five mL bupivacaine 0.25% will be given, provided the patient is haemodynamically stable, and the block height will then be re-tested. If two boluses of five mL bupivacaine 0.25% over 60 min (30 min. apart) fail to control pain and there is no demonstrable sensory block upon testing with ice, the catheter will be removed (if coagulation profile allows). The decision to remove the epidural catheter will be made by the clinical management team. Therapeutic failure is defined as catheter removal and/or discontinuation of infusion prior to completion of the study (72 hours postoperative). In this case, patients will be started on a standard i.v. PCA (hydromorphone 0.2 mg/mL, 0.2 mg demand dose, 8 min lockout interval).\n\nIntervention group: PVB\n\nPVB will be performed following our standard of care protocol. In the institutional block room, a preoperative paravertebral catheter will be sited on the right side at T7-T9 using the landmark technique or under ultrasound guidance, and a bolus of 20 mL ropivacaine 0.25% will be administered. An infusion of ropivacaine 0.25% at a rate of 0.1 mL/kg/h will be started shortly after induction of GA. In addition, five mL boluses of ropivacaine 0.25% will be allowed at 30 min intervals intraoperatively at the discretion of the anaesthesiologist. Upon transfer to the PACU, patient-controlled paravertebral analgesia (PCPA) will be started. The PCPA bolus will be five mL ropivacaine 0.25% with a lockout period of two hours, and an infusion of ropivacaine 0.25% will be continued at 0.1 mL/kg/h and increased in two mL/h increments up to 10 mL/h, depending on the pain scores and sensory block to ice tested in the PACU. This initial infusion will be continued for the first 24 h after surgery, and then reduced by 25% on postoperative day (POD) two, and further reduced another 25% on POD3 to reduce the risk of LAST.\n\nIf at any time point during the first 72 hours post-surgery, patients complain of moderate to severe pain (NRS >4/10) despite maximal PVB infusion (10 mL/h) and if there are no signs of LAST, a bolus of five mL ropivacaine 0.25% will be given, and the sensory block distribution will be re-tested with ice. If two boluses of 5 mL ropivacaine 0.25% over 60 min are unsuccessful in maintaining pain scores <4/10, and there is no demonstrable block on sensory testing with ice, the PVB infusion will be discontinued and the catheter removed (if coagulation profile allows), and the case will be counted as a PVB failure. The decision to remove the PVB catheter will be made by the clinical management team. Therapeutic failure in the PVB group is defined as PVB catheter removal prior to completion of the study at 72 h postoperative. In this case, patients will be started on a standard i.v. PCA (hydromorphone 0.2 mg/mL, 0.2 mg demand dose, eight min lockout interval).\n\nAll patients will receive i.v. hydromorphone (0.5-1.0 mg every hour) until they are able to tolerate oral fluids/medications, at which point they will be given oral hydromorphone (1-2 mg every 4 h) as required starting on the morning of POD2. A member of the research team (blinded to randomisation) will assess the presence/severity of pain and PONV. The assessment will be performed 30 min after arrival to the PACU, and at 4, 8, 24, 48, and 72 h postoperatively. We will ask all patients to rate their pain (NRS scale) at rest and with coughing and their PONV at each of the above listed time points. An antiemetic will be offered to any patients with a PONV score ≥ 2 (where 0 = none, 1 = mild, 2 = moderate, 3 = severe (retching/vomiting)). At 72 hours postoperatively, patient satisfaction with analgesia will be assessed.\n\nNotably, our protocol follows the standard institutional practice for TEA and PVB, including specific LAs used and infusion regimens. Any changes to the study protocol will be amended to the approved ethics application and communicated to all involved in study execution.\n\nSerious adverse events (SAEs) such as epidural haematoma or abscess, pneumothorax, LAST, serious respiratory depression, massive transfusion, refractory hypotension, myocardial infarction, will be reported as per standard of care for our centre and also to the institutional research ethics board as required. All SAEs will be documented and discussed by investigators. If deemed to have potentially resulted from the study protocol, the study will be halted pending further independent investigation.\n\n\nOutcomes\n\nThe primary outcomes will be pain surrogates during the first 72 hours postoperatively: cumulative opioid consumption, time between the end of surgery and first analgesic request, pain scores (NRS) at rest and with coughing 30 min following arrival to the PACU and then at 4, 8, 24, 48 and 72 hours postoperatively (Figure 1).\n\nSecondary outcomes will be PONV scores, patient satisfaction with analgesia (where 1 = very poor, 2 = poor, 3 = satisfactory, 4 = good, 5 = excellent) at 72 hours, and success/failure of TEA/PVB (Figure 1). Haemodynamic parameters will also be recorded (i.e., mean arterial pressure (MAP), CVP (if applicable), urine output, acid-base data, total volume i.v. fluids (crystalloids, colloids, and blood products) and vasopressors given perioperatively up to 72 hours postoperatively), the number of days to resume a full oral diet, hospital LOS, and any complications/side effects. Additionally, postoperative adverse events will be recorded, including hypotension (MAP<50 mmHg) requiring intervention, respiratory depression, sedation (Ramsay score), urinary retention, and pruritus.\n\nData will be entered into REDCAP and then imported to SPSS (ver. 28.0 for Windows, Armonk, NY, 2020) for data analysis. Data will be analysed using an intent-to-treat strategy, regardless of whether the catheter is removed early. Since intent-to-treat strategies are often “anti-conservative” when used in non-inferiority trials,52 we will also analyse our data using the per-protocol strategy, excluding those participants who were excluded, lost, or deviated from the protocol. All continuous data will be checked for normality using the Shapiro-Wilk test. The two groups will be compared using Student’s t-tests for normally distributed data, and the Mann-Whitney U for non-normally distributed data. Continuous data collected at several points in time, such as pain, PONV, patient satisfaction, and sedation scores, will be compared using the repeated measures ANOVA (Tukey’s post hoc test for comparisons between individual time points), or the Friedman test (Wilcoxon signed rank test with Bonferroni adjustment for comparison between individual time points) for non-normally distributed data. Categorical data will be compared using Pearson’s Chi Square test, or the Fisher’s Exact test, as appropriate. No adjustments will be made for multiple comparisons, no adjustment or imputation will be made for missing data, and a p-value of <0.05 will be used as the criteria for statistical significance.\n\n\nDiscussion\n\nAfter major surgery such as hepatectomy and other upper abdominal surgery, inadequate analgesia can lead to hypertension, tachycardia, pulmonary splinting, and inability to breathe deeply and cough. The result could be myocardial ischaemia, pneumonia, and/or the need for prolonged respiratory support. Over-reliance on opioids can lead to excessive sedation, poor pulmonary toilet, constipation, delayed mobilisation, and can lead to long-term opioid dependence. Use of regional analgesia can mitigate the risks associated with systemic opioids. Although TEA does provide satisfactory postoperative analgesia and remains our current standard of care for liver resection patients, it still has a significant failure rate, and disadvantages (outlined above) with respect to haemodynamic instability, pruritus, urinary retention and lower limb weakness. It is also associated with other rare but potentially devastating complications (i.e., haematoma, abscess and/or spinal cord injury). A right thoracic PVB has a much lower risk of spinal cord injury, and less (or even a negligible) chance of causing hypotension, lower rates of limb weakness, pruritus, urinary retention, and a zero chance of ‘veering to the left’. However, it does carry small risks of pneumothorax and LAST. Because PVB is used less frequently than epidurals, some anaesthesiologists may find a PVB technically more challenging.\n\nStudy status: Currently recruiting.\n\nThis study will be used to design a powered, multi-centre RCT comparing TEA to PVB in hepatectomy patients. This work has a high potential to positively impact the quality and safety of care in the liver resection patient population with a reduction in associated costs. Upon completion, study results will be disseminated through international conferences and peer reviewed publication(s). Results will also be communicated to anaesthesiologists and hepatic surgeons at other centres.\n\n\nData availability\n\nNo data are associated with this article.\n\n\nReporting guidelines\n\nQueen’s University Dataverse. SPIRIT checklist. DOI: https://doi.org/10.5683/SP3/M0VO8N53\n\nThis dataset is available under the Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) license.\n\n\nAuthor contributions\n\nGlenio B. Mizubuti: Conceptualization, Data curation, Funding acquisition, Investigation, Methodology, Writing – Original Draft Preparation; Writing – Review and Editing\n\nAnthony M-H. Ho: Conceptualization, Data curation, Funding acquisition, Investigation, Methodology, Writing – Original Draft Preparation; Writing – Review and Editing\n\nDeborah DuMerton: Methodology, Investigation, Project administration, Supervision, Data curation, Writing – Review and Editing\n\nRachel Phelan: Data curation, Project administration, Writing – Review and Editing\n\nWilma M. Hopman: Methodology, Writing – Review and Editing\n\nCamilyn Cheng: Data curation, Investigation, Writing – Review and Editing\n\nJessica Xiong: Data curation, Investigation, Writing – Review and Editing\n\nJessica Shelley: Data curation, Investigation, Writing – Review and Editing\n\nElorm Vowotor: Data curation, Investigation, Writing – Review and Editing\n\nSulaiman Nanji: Data curation, Investigation, Writing – Review and Editing\n\nDiederick Jalink: Data curation, Investigation, Writing – Review and Editing\n\nLais Helena Navarro e Lima: Writing – Review and Editing\n\nAll authors reviewed and approved the final manuscript for submission and can attest to the originality of this work. In addition, all authors made important intellectual contributions.", "appendix": "References\n\nPage A, Rostad B, Staley CA, et al.: Epidural analgesia in hepatic resection. J. Am. Coll. Surg. 2008; 206: 1184–1192. 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Publisher Full Text\n\nKomatsu T, Kino A, Inoue M, et al.: Paravertebral block for video-assisted thoracoscopic surgery: Analgesic effectiveness and role in fast-track surgery. Int. J. Surg. 2014; 12: 936–939. Publisher Full Text\n\nKomatsu T, Sowa T, Takahashi K, et al.: Paravertebral block as a promising analgesic modality for managing post-thoracotomy pain. Ann. Thorac. Cardiovasc. Surg. 2014; 20: 113–116. Publisher Full Text\n\nKarmakar MK, Booker PD, Franks R: Bilateral continuous paravertebral block used for postoperative analgesia in an infant having bilateral thoracotomy. Paediatr. Anaesth. 1997; 7: 469–471. PubMed Abstract \| Publisher Full Text\n\nWassef MR, Randazzo T, Ward W: The paravertebral nerve root block for inguinal herniorrhaphy--a comparison with the field block approach. Reg. Anesth. Pain Med. 1998; 23: 451–456. PubMed Abstract\n\nWeltz CR, Klein SM, Arbo JE, et al.: Paravertebral block anesthesia for inguinal hernia repair. World J. Surg. 2003; 27: 425–429. Publisher Full Text\n\nFahy AS, Jakub JW, Dy BM, et al.: Paravertebral Blocks in Patients Undergoing Mastectomy with or without Immediate Reconstruction Provides Improved Pain Control and Decreased Postoperative Nausea and Vomiting. Ann. Surg. Oncol. 2014; 21: 3284–3289. Publisher Full Text\n\nKlein SM, Bergh A, Steele SM, et al.: Thoracic paravertebral block for breast surgery. Anesth. Analg. 2000; 90: 1402–1405. Publisher Full Text\n\nCanto M, Sanchez MJ, Casas MA, et al.: Bilateral paravertebral blockade for conventional cardiac surgery. Anaesthesia 2003; 58: 365–370. PubMed Abstract \| Publisher Full Text\n\nSato N, Sugiura T, Takahashi K, et al.: Analgesia with paravertebral block for postoperative pain after thoracic or thoracoabdominal aortic aneurysm repair. Masui 2014; 63: 640–643.\n\nRichardson J, Vowden P, Sabanathan S: Bilateral paravertebral analgesia for major abdominal vascular surgery: a preliminary report. Anaesthesia 1995; 50: 995–998. PubMed Abstract \| Publisher Full Text\n\nPiccioni F, Fumagalli L, Garbagnati F, et al.: Thoracic paravertebral anesthesia for percutaneous radiofrequency ablation of hepatic tumors. J. Clin. Anesth. 2014; 26: 271–275. Publisher Full Text\n\nMoussa AA: Opioid saving strategy: bilateral single-site thoracic paravertebral block in right lobe donor hepatectomy. Middle East J. Anesthesiol. 2008; 19: 789–801. PubMed Abstract\n\nCheema SPS, Ilsley D, Richardson J, et al.: A thermographic study of paravertebral analgesia. Anaesthesia 1995; 50: 118–121. PubMed Abstract \| Publisher Full Text\n\nRichardson J, Lönnqvist PA, Naja Z: Bilateral thoracic paravertebral block: potential and practice. Br. J. Anaesth. 2011; 106: 164–171. PubMed Abstract \| Publisher Full Text\n\nNaja Z, Lönnqvist P-A: Somatic paravertebral nerve blockade: incidence of failed block and complications. Anaesthesia 2001; 56: 1184–1188. PubMed Abstract\n\nRichardson J, Lönnqvist PA: Thoracic paravertebral block. Br. J. Anaesth. 1998; 81: 230–238. Publisher Full Text\n\nKarmakar MK: Thoracic paravertebral block. Anesthesiology 2001; 95: 771–780. Publisher Full Text\n\nSchreiber KL, Chelly JE, Lang RS, et al.: Epidural Versus Paravertebral Nerve Block for Postoperative Analgesia in Patients Undergoing Open Liver Resection: A Randomized Clinical Trial. Reg. Anesth. Pain Med. 2016; 41(4): 460–468. PubMed Abstract \| Publisher Full Text\n\nHo AM-H, Karmakar MK, Ng SK, et al.: Local anaesthetic toxicity after bilateral thoracic paravertebral block in patients undergoing coronary artery bypass surgery. Anaesth. Intensive Care 2016; 44(5): 615–619. PubMed Abstract \| Publisher Full Text\n\nRichardson J, Sabanathan S, Jones J, et al.: A prospective, randomized comparison of preoperative and continuous balanced epidural or paravertebral bupivacaine on post-thoracotomy pain, pulmonary function and stress responses. Br. J. Anaesth. 1999; 83: 387–392. PubMed Abstract \| Publisher Full Text\n\nRaveglia F, Rizzi A, Leporati A, et al.: Analgesia in patients undergoing thoracotomy: epidural versus paravertebral technique. A randomized, double-blind, prospective study. J. Thorac. Cardiovasc. Surg. 2014; 147: 469–474. PubMed Abstract \| Publisher Full Text\n\nRichardson J, Sabanathan S, Shah R: Post-thoracotomy spirometric lung function: the effect of analgesia. A review. J. Cardiovasc. Surg. 1999; 40: 445–456. PubMed Abstract\n\nDavies RG, Myles PS, Graham JM: A comparison of the analgesic efficacy and side-effects of paravertebral vs epidural blockade for thoracotomy--a systematic review and meta-analysis of randomized trials. Br. J. Anaesth. 2006; 96: 418–426. PubMed Abstract \| Publisher Full Text\n\nDing X, Jin S, Niu X, et al.: A comparison of the analgesia efficacy and side effects of paravertebral compared with epidural blockade for thoracotomy: an updated meta-analysis. PLoS One. 2014; 9: e96233. PubMed Abstract \| Publisher Full Text\n\nJones B, Jarvis P, Lewis A, et al.: Trials to assess equivalence: The importance of rigorous methods. BMJ. 1996; 313: 36–39. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPiaggio G, Elbourne DR, Altman DG, et al.: Reporting of noninferiority and equivalence randomized trials: An extension of the CONSORT statement. JAMA 2006; 295: 1152–1160. PubMed Abstract \| Publisher Full Text\n\nGrider JS, Mullet TW, Saha SP, et al.: A randomized, double-blind trial comparing continuous thoracic epidural bupivacaine with and without opioid in contrast to a continuous paravertebral infusion of bupivacaine for post-thoracotomy pain. J. Cardiothorac. Vasc. Anesth. 2012; 26: 83–89. PubMed Abstract \| Publisher Full Text\n\nBrittain E, Lin D: A comparison of intent-to-treat and per-protocol results in antibiotic non-inferiority trials. Stat. Med. 2005; 24: 1–10. PubMed Abstract \| Publisher Full Text\n\nMizubuti GB, Ho AM-H, DuMerton D, et al.: Paravertebral vs. Epidural Analgesia for Liver Surgery (PEALS): protocol for a randomized controlled pilot study. Borealis 2022; V1. Publisher Full Text" }	[ { "id": "235498", "date": "13 Feb 2024", "name": "Jacques Chelly", "expertise": [ "Reviewer Expertise Regioaal Anesthesia and Pain" ], "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 are proposing to compare thoracic epidural analgesia (TEA) to a right continuous Paravertebral block (PVB) in 50 patients undergoing hepatectomy using a subcostal approach. The hypothesis being that PVB may represent a safer alternative because it is established that PVB provides hemodynamic stability, low failure rates, and low risk of spinal hematoma compared to TEA. This study will be conducted in 50 patients. This study will be a proof of concept and will allow to propose a multicentric study to include 450 patients, The authors are listing postoperative opioid consumption over 72 hours as the primary end point is. Secondary end points include opioid related side effects, hemodynamic stability, respiratory depression, complications (particularly spinal haematoma). In this study patients will be randomized to either TEA or PVB. The authors hypothesis is that opioid consumption, time to first analgesic request, and pain scores will be comparable between groups, but PVB patients will require fewer perioperative vasopressors/blood products, and have fewer adverse events and a shorter hospital stay.\nCritics The comparison of TEA and PVB is certainly interesting and clinically relevant especially in the context of a subcostal approach. However, if the authors want to conduct the study because they expect that the use of PVB would be safer than TEA, Why is opioid consumption used as the primary end point, There are a number of design questions? 1-If the authors interested is to compare TEA to PVB which make sense for this reviewer why is the local anesthetics protocol different for TEA or PVB. Patients in the TEA group are schedule to receive bupivacaine 0.1% with hydromorphone 10 μg/mL will be infused at 6-10 mL/h and five mL boluses will be allowed at 30 min intervals at the discretion of the anaesthesiologist. Upon admission to the PACU, patient-controlled epidural analgesia (PCEA) will be initiated. The PCEA bolus of the same solution will be set at three mL with a lockout period of 30 min, and the epidural infusion of the same solution will be set at six mL/h and adjusted in two mL/h increments (or decrements) up to 10 mL/h depending upon pain scores and sensory block tested with ice in the PACU. Whereas patients in the PVB group will be scheduled to receive An infusion of ropivacaine 0.25% at a rate of 0.1 mL/kg/h will be started shortly after induction of GA. In addition, five mL boluses of ropivacaine 0.25% will be allowed at 30 min intervals intraoperatively at the discretion of the anesthesiologist. Upon transfer to the PACU, patient-controlled paravertebral analgesia (PCPA) will be started. The PCPA bolus will be five mL ropivacaine 0.25% with a lockout period of two hours, and an infusion of ropivacaine 0.25% will be continued at 0.1 mL/kg/h and increased in two mL/h increments up to 10 mL/h, depending on the pain scores and sensory block to ice tested in the PACU. This initial infusion will be continued for the first 24 h after surgery, and then reduced by 25% on postoperative day (POD) two, and further reduced another 25% on POD3. This means that the authors are not comparing TEA vs PVB but rather TEA + specific infusion solution vs PVB + a different infusion solution. Why not use the same solution for both TEA and PVB? Also please consider eliminating opioid in the TEA solution. This is adding 1.2 to 2,4 or more mg of hydromorphone in the TEA group 2- Why are the authors administrating IV hydromorphone at a dose of 0.5 to 1 mg every hour without any reference to the pain of the patient? Can these administration be q 2 or 3 hrs and the among establish according to the pain level of the patient? 3-The authors provide a long list of variables that they are going to monitor, but do not provide any details on they intend to qualify these variables? Example hypotensive episode define as MPA < 50 mh requiring intervention ? urinary retention? At the very least they need to refer to articles if they don’t want to include a definition in their protocol. 4- Including both a blind or US approach to perform PVB is a design problem. Please chose one or the other It is important that the technique used for the placement of a catheter in the PVB space is consistent and reliable. In contrast of what is stated by the authors, placing a catheter in the PVB space is difficult and required both expertise and the use of an ultrasound. Without the use of ultrasound, it is really possible to establish is what is being performed is a true PVB or an ESP block. In this reviewer experience, in most cases a blind technique doesn’t result in the catheter being placed in PVB space. However, in the past a blind approach has being used. Therefore, the recommendation of this reviewer would be for the authors to use either a blind or an ultrasound approach but not both.\nOther requests. a-Please provide details of the PVB technique either blind or with US. b- the authors use 20% as their inferiority margin for cumulative opioid consumption at 72 hours postoperatively, because they consider that 20% is not clinically significant ? Although, this reviewer would prefer 10% instead of 20%, the confounding variable is the excessive among of opioid expected to be administered. Please consider eliminating opioid from the TEA solution and consider a PRN administration according to the pain level instead of a systematic administration of 0.5-1 mg of hydromorphone q1hr. In addition this is incredibly time. Please consider, q 2 or 3 hr interval.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? No\n\nAre sufficient details of the methods provided to allow replication by others? No\n\nAre the datasets clearly presented in a useable and accessible format? Yes", "responses": [ { "c_id": "11529", "date": "21 Jun 2024", "name": "Anthony Ho", "role": "Author Response", "response": "Dear Drs. Chelly and Goel, Thank you for taking the time to review our protocol. Please see our responses to your comments below and the revised version of the manuscript uploaded to F1000. Dr Chelly’s summary: The authors are proposing to compare thoracic epidural analgesia (TEA) to a right continuous paravertebral block (PVB) in 50 patients undergoing hepatectomy using a subcostal approach. The hypothesis being that PVB may represent a safer alternative because it is established that PVB provides hemodynamic stability, low failure rates, and low risk of spinal hematoma compared to TEA. This study will be conducted in 50 patients. This study will be a proof of concept and will allow to propose a multicentric study to include 450 patients. The authors are listing postoperative opioid consumption over 72 hours as the primary end point is. Secondary end points include opioid related side effects, hemodynamic stability, respiratory depression, complications (particularly spinal haematoma). In this study patients will be randomized to either TEA or PVB. The author’s hypothesis is that opioid consumption, time to first analgesic request, and pain scores will be comparable between groups, but PVB patients will require fewer perioperative vasopressors/blood products, and have fewer adverse events and a shorter hospital stay. Critics The comparison of TEA and PVB is certainly interesting and clinically relevant especially in the context of a subcostal approach. However, if the authors want to conduct the study because they expect that the use of PVB would be safer than TEA, why is opioid consumption used as the primary end point, There are a number of design questions?1 - If the authors interest is to compare TEA to PVB which make sense for this reviewer why is the local anesthetics protocol different for TEA or PVB. Patients in the TEA group are schedule to receive bupivacaine 0.1% with hydromorphone 10 μg/mL will be infused at 6-10 mL/h and five mL boluses will be allowed at 30 min intervals at the discretion of the anaesthesiologist. Upon admission to the PACU, patient-controlled epidural analgesia (PCEA) will be initiated. The PCEA bolus of the same solution will be set at three mL with a lockout period of 30 min, and the epidural infusion of the same solution will be set at six mL/h and adjusted in two mL/h increments (or decrements) up to 10 mL/h depending upon pain scores and sensory block tested with ice in the PACU. Whereas patients in the PVB group will be scheduled to receive an infusion of ropivacaine 0.25% at a rate of 0.1 mL/kg/h will be started shortly after induction of GA. In addition, five mL boluses of ropivacaine 0.25% will be allowed at 30 min intervals intraoperatively at the discretion of the anesthesiologist. Upon transfer to the PACU, patient-controlled paravertebral analgesia (PCPA) will be started. The PCPA bolus will be five mL ropivacaine 0.25% with a lockout period of two hours, and an infusion of ropivacaine 0.25% will be continued at 0.1 mL/kg/h and increased in two mL/h increments up to 10 mL/h, depending on the pain scores and sensory block to ice tested in the PACU. This initial infusion will be continued for the first 24 h after surgery, and then reduced by 25% on postoperative day (POD) two, and further reduced another 25% on POD3. This means that the authors are not comparing TEA vs PVB but rather TEA + specific infusion solution vs PVB + a different infusion solution. Why not use the same solution for both TEA and PVB? RESPONSE: The reason for setting opioid consumption as a primary end point is that the major complications (neuraxial hematoma, pneumothorax, total spinal) associated with TEA and PVB are rare. Furthermore, opioid consumption comparison is almost universal when comparing any 2 or more analgesic regimens. As for why the differences in the blocking solutions, (a very valid question), we are trying to adhere to industry (as well as local) standards of using a motor-sparing LA concentration supplemented by a very small amount of opioids in epidural infusions, and a higher LA concentration without opioids in thoracic PVB. Hence, to answer the reviewer’s question (“Why not use the same solution for both TEA and PVB?”), using a similar solution for both groups would completely deviate from industry (and local) standard practice and render our study irrelevant. We have added the following to clarify this point (see bottom of page 8): “Notably, the difference in LA solutions between the TEA (bupivacaine 0.1% with hydromorphone 10 mcg/mL) and the PVB (ropivacaine 0.25%) groups aligns with industry as well as our institutional standard practice and accounts for the fact that the paravertebral space, being anatomically larger than the epidural space, requires higher volume and concentration of LA to achieve similar analgesia. In addition, PVB has traditionally only involved the use of LA without opioids.” Also please consider eliminating opioid in the TEA solution. This adds 1.2 to 2.4 more mg of hydromorphone in the TEA group. RESPONSE: We acknowledge the systemic and some central analgesic effect of the opioid in the epidural group. The amount of epidural opioid, however, is small. For an infusion of 7 mL/h, for example, the hydromorphone infused is 0.07 mg/h, or 1.68 mg/24 h. Adding opioid to PVB, as stated earlier, is not standard practice. 2. Why are the authors administrating IV hydromorphone at a dose of 0.5 to 1 mg every hour without any reference to the pain of the patient? Can the administration be a q2 or 3 hrs and the amount established according to the pain level of the patient? RESPONSE: Thank you for pointing this out. In fact, this sentence is indeed inconsistent with our practice as we routinely offer subcutaneous hydromorphone 0.5-1 mg every 1-2 hours and upon patient request as we expected some breakthrough pain from the epidural (which has a diluted motor-sparing LA concentration), and from the PVB (which may not cover the medial/midline portion of the surgical incision of ~5 cm). This has now been corrected (page 9, 2nd paragraph). We apologize for not picking up this inconsistency prior to the initial publication of our protocol, and sincerely thank the reviewer for pointing out this inconsistency. 3 -The authors provide a long list of variables that they are going to monitor, but do not provide any details on they intend to qualify these variables? Example hypotensive episode define as MPA < 50 mh requiring intervention? urinary retention? At the very least they need to refer to articles if they don’t want to include a definition in their protocol. RESPONSE: The authors are not totally certain about what the reviewer means by this comment; however, our intention in collecting these variables is simply descriptive, i.e., to determine whether their incidence would be similar/vary according to the treatment (i.e., TEA vs. PVB) modality. The differences between TEA and PVB need to be highlighted. Among these differences, TEA almost always cause a drop in blood pressure and thoracic PVB almost never. Likewise, TEA commonly causes urinary retention whereas PVB simply does not. We use MAP<50 mmHg as qualifying for hypotension and the need for urinary bladder catheterization as a surrogate for retention. These are rather well-defined markers. Similarly, the Ramsay score is a validated metric for sedation. The other outcomes such as vasopressor use, fluid requirement, urine output, and length of stay are all well defined endpoints that we quantify. 4 - Including both a blind or US approach to perform PVB is a design problem. Please chose one or the other It is important that the technique used for the placement of a catheter in the PVB space is consistent and reliable. In contrast of what is stated by the authors, placing a catheter in the PVB space is difficult and required both expertise and the use of an ultrasound. Without the use of ultrasound, it is really possible to establish is what is being performed is a true PVB or an ESP block. In this reviewer experience, in most cases a blind technique doesn’t result in the catheter being placed in PVB space. However, in the past a blind approach has being used. Therefore, the recommendation of this reviewer would be for the authors to use either a blind or an ultrasound approach but not both. RESPONSE: US-guided paravertebral block was not commonplace at our institution when the protocol was written, and some experienced anesthesiologists were actually more comfortable with the landmark “blind” technique. In the end, we decided to let anesthesiologists choose the technique with which they were most comfortable. We usually aim for a “true” PVB by seeking a loss of resistance upon piercing the superior costotransverse ligament. This loss of resistance is more subtle than that in an epidural block. Therefore, we agree that sometimes a block akin to an erector spinae plane (ESP) block may be the result if a loss of resistance is not discerned after walking off the transverse process and advancing the needle by ~1 cm or slightly more (depending on the needle angle). In the end, this represents reality as ultrasound guided thoracic PVB can be challenging, and resorting to blindly advancing the needle beyond the transverse process is still practiced by some. Whether the resulting block is an ESP block or a true PVB, while important, is simply a reflection of actual clinical practice. Other requests. a-Please provide details of the PVB technique either blind or with US. RESPONSE: The blind technique is now well described as follows: “In the landmark technique, once the appropriate thoracic level is identified, the needle is inserted at 2.5-3 cm lateral to the most cephalad aspect of the spinous process and advanced perpendicular to the skin in all planes to contact the transverse process of the vertebra below. The needle is then walked above the transverse process and gradually advanced until a loss of resistance to saline is felt as the needle tip traverses the thin superior costotransverse ligament.52” (page 8, 3rd paragraph, Ref: Karmakar MK, Ho AMH. Thoracic and lumbar paravertebral block. In: Modern Regional Anesthesia. Ed. Hadzic A, McGraw-Hill 2007, New York: Chapter 43: pp. 583-97.) The US-guided technique is as follows: a high-frequency linear US transducer is placed 2.5-3 cm lateral to the most cephalad aspect of the spinous process and oriented vertically at the target thoracic level. Once the transverse process is identified as a “squared” bony structure (note, the identification of a “round” bony structure is usually consistent with the rib, indicating that the probe should be slowly moved medially), the superior/cephalad aspect of the probe is maintained static, while its inferior/caudal aspect is slightly (~30o) rotated counterclockwise until the costotransverse ligament (usually ~0.5 cm superficial to the pleura) is brought into view. The block needle is carefully advanced in plane with the probe in a cephalad direction until it pierces the costotransverse ligament. Correct LA deposition is evidenced by the inferior displacement of the pleura under direct US visualization. b- the authors use 20% as their inferiority margin for cumulative opioid consumption at 72 hours postoperatively, because they consider that 20% is not clinically significant? Although this reviewer would prefer 10% instead of 20%, the confounding variable is the excessive among of opioid expected to be administered. Please consider eliminating opioid from the TEA solution RESPONSE: We respectfully disagree as adding a small amount of opioid in the epidural solution is a common practice - and an industry-wide and our institutional standard of care - since it allows the use of a diluted local anesthetic solution thereby decreasing the incidence of motor block while still providing adequate, or even enhanced, analgesia) and consider a PRN administration according to the pain level instead of a systematic administration of 0.5-1 mg of hydromorphone q1hr. In addition, this is incredibly time. Please consider, q 2 or 3 hr interval. RESPONSE: Please refer to our response question #2 above where we indicate that the sentence pertaining to postoperative hydromorphone administration is indeed inconsistent with our practice as we routinely offered subcutaneous hydromorphone 0.5-1 mg every 1-2 hours and upon patient request (i.e., on a PRN basis) as we expected some breakthrough pain from the epidural (which has a diluted LA concentration), and from the PVB (which may not cover the medial/midline portion of the surgical incision), page 9, 2nd paragraph)." } ] }, { "id": "235497", "date": "04 Mar 2024", "name": "Andrea De Gasperi", "expertise": [ "Reviewer Expertise anesthesia", "intensive care", "abdominal organ transplants", "infections" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\n1) Postoperative hemostatic profile is not by default pro-hemorrhagic particularly in case of neoplastic diseases or in HCC in patients included in CHILD A / MELD < 11. 2) Viscoelastic tests should be strongly considered (TEG/ROTEM) to describe the pre/intra/post hemostatic profile.: to be considered the \"rebalanced hemostasis \" in cirrhotic patiens (Tripodi et al Am J Gastroenterol, 2017; 112: 274-81 1 3) for the periop hemostatic profile in liver resection please consider also a) Cerutti et al Liver transplantation 2004; 10: 289-94 2 ---b) DePietri et al, World J Gastroenterol, 2018; 24: 2931-48 3 4) 50 pts to be randomized : please provide the statistical justification of this number (enough power ??) 5) First lines of the \"Discussion\" seem to be to too dramatic\" \"Inadequate analgesia can lead to hypertension, tachycardia, pulmonary splinting, and inability to breathe deeply and cough. The result could be myocardial ischaemia, pneumonia, and/or the need for prolonged respiratory support.\". I would be much more concerned for these complications (particularly for MACEs, respiratory complications ) for the intraop anesthetic management 6) CFR to be provided\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Partly\n\nAre sufficient details of the methods provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a useable and accessible format? Partly", "responses": [ { "c_id": "11530", "date": "21 Jun 2024", "name": "Anthony Ho", "role": "Author Response", "response": "Dear Dr. De Gasperi, Thank you for taking the time to review our protocol. Please see our responses to your comments below and the revised version of the manuscript uploaded to F1000. Postoperative hemostatic profile is not by default pro-hemorrhagic particularly in case of neoplastic diseases or in HCC in patients included in CHILD A / MELD < 11. RESPONSE: We acknowledge that preoperative liver functional status is one of several major factors influencing postoperative hemostatic function (please see 2nd paragraph of Introduction). Viscoelastic tests should be strongly considered (TEG/ROTEM) to describe the pre/intra/post hemostatic profile.: to be considered the \"rebalanced hemostasis \" in cirrhotic patients (Tripodi et al Am J Gastroenterol, 2017; 112: 274-81 1 3) for the periop hemostatic profile in liver resection please consider also a) Cerutti et al Liver transplantation 2004; 10: 289-94 2 ---b) DePietri et al, World J Gastroenterol, 2018; 24: 2931-48 RESPONSE: Thank you for emphasizing the potentially crucial role of thromboelastometry/graphy in discerning hemostatic status. We acknowledge the complex nature of coagulation in many clinical situations, including liver resection with or without cancer and/or cirrhosis. However, TEG/ROTEM’s role in liver resection and neuraxial block is still not well established. This area is indeed ripe for more research endeavors but is not the goal of our project. Future research may very well show that TEG/ROTEM results can be important indicators as to whether neuraxial blocks should be contraindicated but at the present time, platelet count and INR remain the standard tests (however imperfect). As we are only using the platelet count and INR to exclude patients preoperatively as per industry standard and are not studying hemostatic changes associated with liver resection, we respectfully decline to include the Tripodi, Cerutti, and De Pietri references thoughtfully suggested. 3) 50 pts to be randomized: please provide the statistical justification of this number (enough power ??) RESPONSE: Please see the Protocol section (under Sample size, page 5) where it reads: “Non-inferiority trials typically require larger samples than superiority trials;49,50 thus, we anticipate the need to include multiple centres to secure enough participants. Therefore, we propose a single-centre pilot study to generate the data needed to estimate the sample size required for a large, multi-centre trial. Based upon previous studies that compared TEA versus PVB for postoperative analgesia in patients undergoing thoracotomy,45,51 we will aim for a convenience sample of 25 patients per group to generate pilot data upon which to base a larger, multi-centre trial.” 4) First lines of the \"Discussion\" seem to be to too dramatic\" \"Inadequate analgesia can lead to hypertension, tachycardia, pulmonary splinting, and inability to breathe deeply and cough. The result could be myocardial ischaemia, pneumonia, and/or the need for prolonged respiratory support.\". I would be much more concerned for these complications (particularly for MACEs, respiratory complications) for the intraop anesthetic management CFR to be provided RESPONSE: We have shortened and softened the argument on the importance of good postoperative pain management without excessive reliance on opioids in the Discussion section (bottom page 10). We agree that intraoperative stable management is vital to avoid cardiorespiratory complications. We did not think it was necessary to explicitly mention that as such is the universal goal of all anesthetic management." } ] }, { "id": "249114", "date": "23 May 2024", "name": "Heitor J S Medeiros", "expertise": [ "Reviewer Expertise Anesthesiology", "regional anesthesia" ], "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 study's purpose and goals are clearly explained. It addresses the risks and downsides of TEA and explores if PVB can provide the same pain relief with fewer complications.\nDesign flaws: Different drugs are used for TEA and PVB, which could affect the results - Is the result coming from technique or simply by drug differences? This needs to be well adressed in discussion. Using the same anesthetic for both groups would provide a clearer comparison. The study uses both blind and ultrasound-guided PVB, which adds variability. Sticking to one method (eg ultrasound) would have improved consistency. The protocol for intravenous hydromorphone administration is not ideal as it doesn’t consider patient pain levels - why is this done this way? institutional protocol? please clarify and adress accordingly . Adjusting doses based on pain levels would be more effective?\n\nAre the datasets clearly presented in a usable and accessible format? Partly: While data storage and recording are described, the format isn't clear. This could impact external validity. Providing examples as supplementary material or templates of the datasets would improve clarity.\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? Partly", "responses": [ { "c_id": "11685", "date": "05 Jun 2024", "name": "Anthony Ho", "role": "Author Response", "response": "Dear Dr. Medeiros, Thank you for taking the time to review our protocol. Please see our responses to your comments below and the revisions made to the second version of the manuscript uploaded to F1000. Best Regards, Anthony Ho Dr. Medeiros’ comments and the authors responses: NOT APPROVED The study's purpose and goals are clearly explained. It addresses the risks and downsides of TEA and explores if PVB can provide the same pain relief with fewer complications. Response: Thank you. Design flaws: Different drugs are used for TEA and PVB, which could affect the results - Is the result coming from technique or simply by drug differences? This needs to be well adressed in discussion. Using the same anesthetic for both groups would provide a clearer comparison. Response: Your comment is very similar to one asked by Chelly and Goel in the first review to which we responded: “As for why the differences in the blocking solutions, (a very valid question), we are trying to adhere to industry (as well as local) standards of using a motor-sparing LA concentration supplemented by a very small amount of opioids in epidural infusions, and a higher LA concentration without opioids in thoracic PVB. Hence, to answer the reviewer’s question (“Why not use the same solution for both TEA and PVB?”), using a similar solution for both groups would completely deviate from industry (and local) standard practice and render our study irrelevant. We have added the following to clarify this point (see bottom of page 8): “Notably, the difference in LA solutions between the TEA (bupivacaine 0.1% with hydromorphone 10 mcg/mL) and the PVB (ropivacaine 0.25%) groups aligns with industry as well as our institutional standard practice and accounts for the fact that the paravertebral space, being anatomically larger than the epidural space, requires higher volume and concentration of LA to achieve similar analgesia. In addition, PVB has traditionally only involved the use of LA without opioids.” The study uses both blind and ultrasound-guided PVB, which adds variability. Sticking to one method (eg ultrasound) would have improved consistency. RESPONSE: Once again your concern is virtually the same as one noted by previous reviewers to which we responded: “US-guided paravertebral block was not commonplace at our institution when the protocol was written, and some experienced anesthesiologists were actually more comfortable with the landmark “blind” technique. In the end, we decided to let anesthesiologists choose the technique with which they were most comfortable. We usually aim for a “true” PVB by seeking a loss of resistance upon piercing the superior costotransverse ligament. This loss of resistance is more subtle than that in an epidural block. Therefore, we agree that sometimes a block akin to an erector spinae plane (ESP) block may be the result if a loss of resistance is not discerned after walking off the transverse process and advancing the needle by ~1 cm or slightly more (depending on the needle angle). In the end, this represents reality as ultrasound guided thoracic PVB can be challenging, and resorting to blindly advancing the needle beyond the transverse process is still practiced by some. Whether the resulting block is an ESP block or a true PVB, while important, is simply a reflection of actual clinical practice.” We have now described both the blind and US-guided methods within the text (page 8). The protocol for intravenous hydromorphone administration is not ideal as it doesn’t consider patient pain levels - why is this done this way? institutional protocol? please clarify and adress accordingly . Adjusting doses based on pain levels would be more effective? Response: Once again, your comment is very similar to one made by Drs. Chelly and Goel to which we responded: “Thank you for pointing this out. In fact, this sentence is indeed inconsistent with our practice as we routinely offer subcutaneous hydromorphone 0.5-1 mg every 1-2 hours and upon patient request as we expected some breakthrough pain from the epidural (which has a diluted motor-sparing LA concentration), and from the PVB (which may not cover the medial/midline portion of the surgical incision of ~5 cm). This has now been corrected (page 9, 2nd paragraph). We apologize for not picking up this inconsistency prior to the initial publication of our protocol, and sincerely thank the reviewer for pointing out this inconsistency.” Are the datasets clearly presented in a usable and accessible format? Partly: While data storage and recording are described, the format isn't clear. This could impact external validity. Providing examples as supplementary material or templates of the datasets would improve clarity. Response: Given that this is a protocol manuscript and not a final manuscript with results, the authors believe the data collection processes are adequately described. As stated previously, final data may be placed into a public depository although no identifiable information will be used. Is the rationale for, and objectives of, the study clearly described? Yes Is the study design appropriate for the research question? Partly Are sufficient details of the methods provided to allow replication by others? Partly Competing Interests No competing interests were disclosed. Reviewer Expertise Anesthesiology, Regional anesthesia I confirm that I have read this submission and believe that I have an appropriate level of expertise to state that I do not consider it to be of an acceptable scientific standard, for reasons outlined above." } ] } ]	1	https://f1000research.com/articles/11-1067
https://f1000research.com/articles/13-708/v1	27 Jun 24	{ "type": "Software Tool Article", "title": "The fifth international hackathon for developing computational cloud-based tools and resources for pan-structural variation and genomics", "authors": [ "Sontosh K Deb", "Divya Kalra", "Jędrzej Kubica", "Erik Stricker", "Van Q. Truong", "Qiandong Zeng", "Christopher J. Fiscus", "Daniel Paiva Agustinho", "Adam Alexander", "Marlon Arciniega-Sanchez", "Lorianne Bosseau", "Christian Brueffer", "Astrid Canal", "Joyjit Daw", "David Enoma", "Alison Diaz-Cuevas", "Colin Diesh", "Janet M. Doolittle-Hall", "Luis Fernandez-Luna", "Tina Han", "Wolfram Höps", "Peiming Peter Huang", "Tony Huang", "Michal Bogumil Izydorczyk", "Farhang Jaryani", "Rupesh K. Kesharwani", "Shaheerah Khan", "Sina Majidian", "Ayan Malakar", "Tania Girão Mangolini", "Sejal Modha", "Mauricio Moldes", "Rajarshi Mondal", "Abdullah Al Nahid", "Chi-Lam Poon", "Sagayamary Sagayaradj", "Philippe Sanio", "Tania Sepulveda-Morales", "Muhammad Shahzaib", "Muhammad Sohail Raza", "Trinh Tat", "Ishaan Thota", "Umran Yaman", "Jason Yeung", "Qiyi Yu", "Xinchang Zheng", "Medhat Mahmoud", "Fritz J. Sedlazeck", "Ben Busby", "Christopher J. Fiscus", "Daniel Paiva Agustinho", "Adam Alexander", "Marlon Arciniega-Sanchez", "Lorianne Bosseau", "Christian Brueffer", "Astrid Canal", "Joyjit Daw", "David Enoma", "Alison Diaz-Cuevas", "Colin Diesh", "Janet M. Doolittle-Hall", "Luis Fernandez-Luna", "Tina Han", "Wolfram Höps", "Peiming Peter Huang", "Tony Huang", "Michal Bogumil Izydorczyk", "Farhang Jaryani", "Rupesh K. Kesharwani", "Shaheerah Khan", "Sina Majidian", "Ayan Malakar", "Tania Girão Mangolini", "Sejal Modha", "Mauricio Moldes", "Rajarshi Mondal", "Abdullah Al Nahid", "Chi-Lam Poon", "Sagayamary Sagayaradj", "Philippe Sanio", "Tania Sepulveda-Morales", "Muhammad Shahzaib", "Muhammad Sohail Raza", "Trinh Tat", "Ishaan Thota", "Umran Yaman", "Jason Yeung", "Qiyi Yu", "Xinchang Zheng", "Medhat Mahmoud", "Fritz J. Sedlazeck", "Ben Busby" ], "abstract": "Background The goal of the Fifth Annual Baylor College of Medicine & DNAnexus Structural Variation Hackathon was to push forward the research on structural variants (SVs) by rapidly developing and deploying open-source software. The event took place in-person and virtually in August 2023, when 49 scientists from 14 countries and 8 U.S. states collaboratively worked on projects to address critical gaps in the field of genomics. The hackathon projects concentrated on developing bioinformatic workflows for the following challenges: RNA transcriptome comparison, simulation of mosaic variations, metagenomics, Mendelian variation, SVs in plant genomics, and assembly vs. mapping SV calling comparisons.\n\nMethods As a starting point we used publicly available data from state-of-the-art long- and short-read sequencing technologies. The workflows developed during the hackathon incorporated open-source software, as well as scripts written using Bash and Python. Moreover, we leveraged the advantages of Docker and Snakemake for workflow automation.\n\nResults The results of the hackathon consists of six prototype bioinformatic workflows that use open-source software for SV research. We made the workflows scalable and modular for usability and reproducibility. Furthermore, we tested the workflows on example public data to show that the workflows can work. The code and the data produced during the event have been made publicly available on GitHub (https://github.com/collaborativebioinformatics) to reproduce and built upon in the future.\n\nConclusions The following sections describe the motivation, lessons learned, and software produced by teams during the hackathon. Here, we describe in detail the objectives, value propositions, implementation, and use cases for our workflows. In summary, the article reports the advancements in the development of software for SV detection made during the hackathon.", "keywords": [ "SVs", "k-mers", "RNASeq", "Metagenomics", "Mosaic", "Long-reads", "Hackathon", "NGS" ], "content": "Introduction\n\nStructural variants (SVs) are large genomic variations with sizes of at least 50 bps occurring in form of insertions (INS), deletions (DELs), inversions (INVs), duplications (DUPs), and inter-chromosomal translocations.1–3 Recent discoveries have shown SVs to exhibit clinical relevance for multiple diseases beyond classical mendelian diseases, such as multiple types of cancer,4 neurodevelopmental,5 and cardiovascular disorders.6 Nevertheless, detection and evaluation of SVs is still plagued by high false positive and negative rates along with the inaccuracies of breakpoint predictions due to the complex nature of mutations and inherent sample heterogeneities despite the advances in next-generation sequencing technologies.7,8 Third generation sequencing technologies provided by Pacific BioSciences,9 Oxford Nanopore Technologies,10 optical mapping,11 and NanoString,12 as well as new short read technologies provide exciting new tools to enhance SV detection. However, these advancements require new bioinformatic methods for implementation to consequently offer potential for understanding the relationship between these variants and various phenotypes. Accordingly, the objective of the Fifth Baylor College of Medicine & DNAnexus hackathon was to propose and develop novel bioinformatic tools and workflows to improve the use of SV data in disease modeling.\n\nAt the Fifth Baylor College of Medicine & DNAnexus hackathon, in August 2023, 49 scientists from 14 nations (see Figure 1) participated in-person and remotely - focusing on different topics on SV related research.\n\nParticipants from around the world for the Fifth Annual Baylor College of Medicine & DNAnexus Structural Variation hackathon.\n\nOverall, this manuscript details our tools’ objectives, value-add, implementations, and applications to set the foundation for further concept development. In this article we present six software workflows that were the result of this hackathon.\n\nAlternative splicing is one of the most complicated cellular processes. The joining or skipping of exons from the same gene in various combinations leads to different, but related, mRNA transcripts (isoforms). These mRNA isoforms can be translated to produce diverse proteins with distinct structures and functions. It has been shown that changes in isoform diversity might affect the phenotype, potentially leading to diseases, such as cancer or neurodegenerative disorders. These novel isoforms have been associated with cancer, including novel variants of oncogenes. For instance, novel isoforms and the usage of alternate promoters were found in cell lines in subtypes of gastric cancer.13 Moreover, a positive correlation was found between the presence of particular isoforms of Alzheimer’s disease-associated proteins and pathological severity.14 These findings might help with the development of specific diagnostic biomarkers.\n\nNext Generation Sequencing (NGS), especially transcriptome sequencing (RNA-seq), including short- and long-read sequencing, characterizes gene expression at the isoform level and sheds light on biological processes inside the cell, as well as on how the cell responds to changes in the environment. Short-read sequencing is limited and provides low confidence when predicting alternative splicing, novel exons and junction sites, as well as the characterization of complete isoforms.15,16 Long-read sequencing, however, is expected to overcome the inherent limitations of short-read sequencing. Analysis of long-read sequencing data, that uses multiple variant calling algorithms to detect insertions, deletions, inversions and duplications, found nearly 2.5 times more SVs than short-read data, with ~83% of insertions missing.17 Long-read sequencing technologies, e.g., PacBio High-Fidelity (HiFi) and Oxford Nanopore, have been shown to lower the error rates and to provide high-quality full-length reads that cover the entire length of all isoforms, removing any uncertainty in determining exon composition.\n\nThere exist tools that compare sets of short-read transcript annotations, including GffRead (RRID:SCR_018965) and GffCompare,18 AGAT,19 and bedtools20 (RRID:SCR_006646). However, to our knowledge, no tool currently exists which takes advantage of the long-read sequencing data to compare inferred isoforms.\n\nHere we present IsoComp, a bioinformatics pipeline to identify differences in isoform expression between individuals using long-read RNA-seq data. IsoComp can be used to make comprehensive comparisons of isoform profiles between multiple samples, with application in e.g. trio-sequencing or subtyping of cancer cell lines. We have tested IsoComp on HG002 samples (NA27730, NA24385, NA26105, NA24385, NA26105, NA27730) from GIAB (Genome in a Bottle)21 to demonstrate its potential use for distinct isoform detection and comparison.\n\nIn the context of individual genome comparison, mutations that appear with very low minor allele frequencies are referred to as rare variants.22 Similarly, mosaicism is observed when unique genetic differences arise at low frequencies within the population of cells in a tissue of an individual giving rise to mosaic variants (MVs).23 Recent studies have shown potential disease implications for certain MVs.23 Since MVs can have low allele frequencies and are mixed in with data from the non-mutated cells in the same sequencing output file, they can be challenging to detect as they may appear as noise in the NGS data. Therefore, several pipelines have been developed or adjusted to extract mosaic single nucleotide, structural or indel variants from whole-genome sequencing data, including Sniffles11 (RRID:SCR_017619), DeepMosaic,24 Mutect2,25 DeepVariant.26 To benchmark and validate the efficiency and accuracy of these methods, we developed two workflows called SpikeVar (Spike in Known Exogenous Variants) and TykeVar (Track in Your Key Endogenous Variants). As input SpikeVar takes data from two different sample sets, and mixes them in a user defined ratio. In contrast, TykeVar generates random mutations in the reference genome that are then introduced into existing sample data at a user defined ratio. Both these methods generate potentially low allele frequency, sporadic events in the resulting dataset.\n\nSpecies evolve continuously, which causes a drastic shift in the architecture of their genome over time. To consider a single genome as a reference for different studies could produce biases. Bacterial evolution in particular involves different mechanisms like homologous recombinations, horizontal gene transfer (HGT) and mutations.27 Conventional comparative genomic analyses that solely rely on linear reference sequences can introduce biases rooted in reference sequences and potentially disregard the spectrum of population or strain diversity. To mitigate these limitations, pangenomes using a graph genome approach have been proposed, encompassing entire genomes of different strains of species lying under one clade. This approach increases the accuracy of analyses by considering innately the concept that the existence of different haplotypes can cause drastic change in the overall study involving that species.28\n\nPseudomonas aeruginosa (P. aeruginosa) is a Gram-negative bacterium and an opportunistic pathogen that has been deeply studied due to its significant role in causing serious health concerns in humans. P. aeruginosa presents high genome plasticity, possessing a significant assortment of genes acquired by HGT. These genes are frequently localized within integrons and mobile genetic elements, such as transposons, insertion sequences, genomic islands, phages and plasmids. This genomic diversity results in a non-clonal population structure, and consequently in highly variable strain phenotypes concerning virulence, drug resistance and morbidity. Consequently, this makes P. aeruginosa a prime candidate for a pan-genome graph approach.29,30\n\nHere, we made an amalgamation of several in-silico processes used to create a graph genome of P. aeruginosa, intended for open access within the scientific community. We also compared read alignments methods between a graph-genome and a standard linear genome approach.\n\nMendelian inconsistencies are identified when a child has a genotype that is not possible given the genotypes of the parents, for example, when a child is homozygous for an allele that does not exist in either parent. Mendelian inconsistency in SV calls can indicate two possibilities: challenges in SV calling leading to false positive or negative calls across the trio, or a genuine de novo SV. De novo SVs are rare, with an estimated rate of 0.16 de novo SVs per genome in healthy individuals.31 Despite their rarity, de novo SVs have been associated with human disease, including Autism Spectrum Disorder, Pulmonary Alveolar Proteinosis and Alzheimer’s disease.32–35 In addition, benchmarking studies have used the rarity of de novo SVs to support the validity of their SV calls under the assumption that calls inconsistent with Mendelian inheritance are likely incorrect.36–38\n\nWe present SalsaValentina, a pipeline which identifies putative de novo SVs based on Mendelian inconsistency, and subsequently validates them using a local genome assembly of the region in question. SalsaValentina could assist in diagnosis variants underlying rare diseases, and inform other strategies for more accurate SV calling.\n\nCopy number variation (CNV) is a common form of SV polymorphism where segments of DNA are either duplicated or deleted when compared to a reference genome.39 CNV plays a pivotal role in genome evolution40 and has been associated with phenotypic diversity41 including human diseases.42 To date, the predominant strategies to detect CNVs using whole-genome sequencing data have relied upon analyzing the distribution of mapping coverage across the genome and identifying regions with outlying coverage compared to the background.43 However, these coverage-based approaches are susceptible to ascertainment bias because they can only detect CNV of sequences present in the reference assembly, failing to capture the complete spectrum of CNV within a population. Furthermore, coverage-based CNV detection methods to detect CNV are dependent on high-quality genome assemblies, which are not available for many non-model systems.\n\nAs an alternative approach, we here present PhytoKmerCNV, a tool for estimating copy number of specific sequences using k-mer frequencies derived from whole-genome sequencing reads. Our approach involves comparing the k-mer frequency distributions between reads originating from the sequences of interest to the distribution of frequencies calculated from all sample reads.\n\nRecent studies have shown that SVs are widely present in human genomes. They shape the genome evolution and play important roles in human health and diseases by changing the protein-coding regions, cis-regulatory elements and gene expression profiles.44 While a number of NGS-based SV detection tools have been developed in the past few years, it remains unclear how well these tools perform for the detection of SVs.45\n\nCurrently available SV-calling tools roughly fall into three groups depending on the different types of input data used in the SV detection step: mapping-based, assembly-based and mapping-free methods. The mapping-based approaches use SV-related alignment features such as soft-clipped read ends, alignment breakpoints and discordant mates to detect SVs.46 For the assembly-based methods, reads can be assembled directly into contigs (“global assembly”), e.g., in DISCOVAR47 (RRID:SCR_016755) or reads could be aligned to a reference genome first and then reads aligning to each region could be assembled into contigs (“local assembly”), and the contigs (and the corresponding reads) are then aligned to the reference genome for SV calling.48 The mapping-free approach works by checking the genomic signatures (e.g. k-mers) of known SVs directly in the raw NGS reads, as is done in Nebula.49 The alignment-based approach has a number of advantages, including low computing resource requirement and shorter run-time in most cases. By contrast, the assembly-based approach generally requires substantially more computing resources and input sequencing data, but could take advantage of the longer input sequences from the assembled contigs and theoretically, could perform better for SV detection. The mapping-free approach is computationally efficient, but is limited to the genotyping of known SVs and will not be discussed further.\n\nThe performance of SV calling tools also depends on the targeted regions and read lengths. While it is generally believed that long read based SV calling tools have better sensitivity, a recent study shows that most large SVs in cancer can be detected without using long reads.50 The targeted regions for SV calling can range from small gene panels to whole exome sequencing to whole-genome sequencing. Targeted panel sequencing and whole exome sequencing are currently dominating in clinical NGS testing due to cost advantages by focusing on protein-coding regions. However, genetic diagnosis by whole exome sequencing can only be made in 25-50% of cases.51 On the other hand, the whole-genome shot-gun sequencing (WGS) data has more uniform coverage and provides a comprehensive view across the coding regions, non-coding regions and intergenic regions. As the sequencing cost continues to drop, whole-genome sequencing is becoming increasingly cost-effective and can serve as a great starting point for detecting SVs and other genetic changes.\n\nThe goal of the SV-genie project was to develop a generalized framework to evaluate the performance of SV calling tools for WGS short-read dataset. Specifically, we use the Illumina short-reads data set for GIAB HG002 (ASJ son) as the input, run a number of alignment-based and assembly-based SV calling tools and compare the results with the GIAB HG002 SV dataset to gain insights into the performance difference between mapping-based and assembly-based approaches for the detection of SVs.\n\n\nMethods\n\nIsoComp: Comparing Isoform composition between cohorts using high-quality long-read RNA-seq\n\nThe IsoComp pipeline identifies and compares distinct isoforms across multiple samples. Before running the IsoComp pipeline, GTF files need to be created and pre-processed to serve as input to IsoComp. The IsoComp algorithm is outlined in Extended data.\n\nIso-Seq analysis\n\nThe first step is to create GTF files to subsequently serve as input to IsoComp. First, demultiplexed HiFi reads (Q20, single-molecule resolution) from lima (https://github.com/pacificbiosciences/barcoding/) were processed using IsoSeq3 v3.2.2 (https://github.com/PacificBiosciences/IsoSeq). Next, the transcripts were mapped against the GRCh38 (v33 p13) reference genome using Minimap252 (RRID:SCR_018550) (v2.24-r1122; command: minimap2 -t 8 -ax splice:hq -uf --secondary=no -C5 -O6,24 -B4 GRCh38.v33p13.primary_assembly.fa sample.polished.hq.fastq.gz). Then, cDNA_cupcake (v28.0.0) (https://github.com/Magdoll/cDNA_Cupcake) was used to filter away redundant isoforms from the BAM file, followed by filtering low-count isoforms by 10 and discarding 5’-degraded isoforms as they are not biologically significant. Afterwards, SQANTI3 v5.053 was used to generate the final FASTA transcripts and GFF files, as well as the isoform classification reports. The external databases including reference data set of transcription start sites (refTSS), list of polyA motif, tappAS-annotation and Genecode GRCh38 annotation were utilized during the isoform classification by SQUANTI3.53 Finally, IsoAnnotLite (v2.7.3) (https://isoannot.tappas.org/isoannot-lite/) was used to annotate the GTF files obtained from SQUANTI3.53 The workflow, shown in Extended data, outlines each step to generate the GFF files from individual samples of HG002, a necessary pre-processing step for subsequent comparisons using IsoComp.\n\nIsoform clustering and comparison\n\nIn each GTF file created in the Iso-Seq analysis step, the ‘source’ column is replaced with the base filename (no extension) of the file. Next the GTF files are converted into PyRange objects, which are filtered on the ‘transcript’ feature. Then, overlapping ranges (the start to end coordinates of the transcripts) of clusters are determined. Clusters are sequentially numbered, so that each cluster comprises a discrete group of transcripts with overlapping ranges of coordinates.\n\nIn the next step, in each cluster, all isoforms are filtered by the coordinate overlap and compared against one another. If there is only one isoform in the cluster, it is reported as unique. Isoforms with unique or partial overlap of coordinate ranges within clusters are reported as unique, whereas isoforms with an identical overlap undergo a pairwise sequence comparison. The sequence comparison step allows for the detection of variability among isoforms within each cluster.\n\nThe workflow of the Isoform clustering and comparison step is presented in Figure 2.\n\nSpikeVar\n\nThe SpikeVar workflow outputs a mixed sequencing read dataset in the BAM format, containing reads from one dominant sample and reads from another sample spiked in at a user defined ratio corresponding to the simulated mosaic variant allele frequency (VAF), plus a VCF file annotating the confirmed mosaic variant locations within the mixed dataset (Figure 3(i)). The SpikeVarDatasetCreator takes aligned sequencing reads from sample A and sample B as input. In this step, a spike-in methodology is applied to strategically introduce x% of mutations from one sample to another using samtools54(RRID:SCR_002105) view -s option. Accordingly, sample A is first down-sampled to retain (100-x)% of its original reads, then sample B is down-sampled to x% considering the coverage differences between the samples. Using samtools merge command, both down-sampled datasets are then merged to create a mixed dataset that represents a sequence read dataset with mosaic variants, including SVs, single nucleotide variations (SNVs), and insertions/deletions (indels).\n\ni) SpikeVar workflow and ii) TykeVar workflow, with major steps to assess the sensitivity and accuracy of the mosaic variant callers. (A, B: individual samples, A/B: merged samples, .bam and .vcf: input and output file formats in different steps, Black header boxes: tool or file names, Green header boxes: simulated files or final files used for validation comparisons.)\n\nThe SpikeVarReporter then determines VAFs for each variant in the mixed dataset depending on the variant type and sequencing technology SNVs (samtools mpileup command), Sniffles211 (SV and long-reads) (RRID:SCR_017619), and Paragraph55 (SV and short-reads), based on the mixed variant locations derived by merging the VCF files from sample A and sample B using samtools.54 Variants with VAFs exceeding or equal to the introduced mutations (i.e., x%) are then selected to create a truth set for benchmarking using bcftools54 (RRID:SCR_005227).\n\nTo assess a mosaic variant caller sensitivity and accuracy, the same mixed dataset is used to call mosaic variants. The output mosaic variant locations and VAFs are then compared to the truth set for validation.\n\nTykeVar\n\nThe TykeVar workflow produces a modified aligned sequence file in the BAM format (Figure 3(ii)). This file contains modified reads simulating randomly positioned mosaic variants with user-defined VAF in random locations and is accompanied by a VCF file containing the locations of the simulated mosaic variants with user-defined VAF.\n\nThe TykeVar workflow can be broadly split into 3 parts:\n\n1) The TykeVarSimulator takes an aligned BAM file, a reference and several parameters (such as range of VAF, variant sizes). to generate a set of simulated mosaic SVs and SNVs. It does so by choosing a random location and VAF from the given range and then evaluating whether that location has sufficient coverage for the desired VAF. If that condition is met, that variant is added to the output VCF file.\n\n2) The TykeVarEditor is responsible for inserting the simulated variants into the query sequences from the original dataset to generate modified reads with the mosaic variants built-in. The TykeVarEditor accepts a BAM file, reference and the simulated VCF file as input. Then, for each variant, it fetches the overlapping reads from the BAM file, subsamples the reads to get the coverage that satisfies the desired VAF, and traverses the cigar string, query and reference sequences for each alignment to find the exact location to insert the variant. Once a modified read is created, it is written out into a FASTQ file. Note that for all new bases (SNVs or inserts), the q-score of 60 is chosen.\n\n3) The TykeVarMerger re-introduces the modified reads into the original dataset. It does so by first removing the modified read IDs from the input BAM file to create a filtered BAM file. Then, the modified reads are aligned against the reference, and merged with the filtered BAM file. The end result is a BAM file with the same set of read IDs as the original dataset, except for some reads modified to contain the mosaic variants.\n\nThe output of this pipeline is thus a modified BAM file and a VCF file which provides the truth set for the mosaic variants.\n\nThe PGGP process involves two main simultaneous steps (Figure 4). For the pangenome approach, we initially constructed a graph genome by utilizing the accessible assemblies of Pseudomonas aeruginosa. This was accomplished using the pggb tool.56 Then we performed graph alignments with GraphAligner57 to align a dataset of short-read clinical isolates from Sequence Read Archive (SRA)58 (RRID:SCR_004891) to our graph genome. Concomitantly, we downloaded a standard linear reference genome and performed read alignments with the same dataset used for the graph genome using BWA-MEM59 (RRID:SCR_010910). Finally, we compared alignment efficiency between the two approaches. The details of the implementation of PGGP can be found in our Github repository (https://github.com/collaborativebioinformatics/SVHack_metagenomics). They consists of:\n\n1. Graph Approach\n\na. The graph genome construction: Out of 773 available assemblies, 499 complete P. aeruginosa genomes were downloaded from NCBI. Metadata for the included sequences is included in the linked GitHub repository - https://github.com/collaborativebioinformatics/SVHack_metagenomics/tree/2797b9eec54665258a67ef0277fbd4d06d4e26c7/assemblies_info. Pangenome graphs of varying sizes (5, 10, 20, 50, 100, 500 genomes) were created using the reference NC_002516.2 and complete genome assemblies such that all genomes in the smaller pangenome graphs are contained in the larger graphs. All pangenome graphs were created using the pggb tool (command: pggb -i assembly.fasta.gz -o. -t 16 -n 5 -p 90 -s 5000).56\n\nb. Read mapping to pangenome: Read mapping to single reference Genome: 59 Illumina sequencing datasets including P. aeruginosa (NCBI Taxonomy ID 287) reads were downloaded from the Sequence Read Archive58 (metadata for these samples is included in the linked GitHub repository - https://github.com/collaborativebioinformatics/SVHack_metagenomics/tree/2797b9eec54665258a67ef0277fbd4d06d4e26c7/reads_info). The reference sequence NC_002516.2 (Genome assembly ASM676v1) derived from the PA01 strain was also downloaded. Similar to the single reference genome, reads were mapped to pangenome graphs using GraphAligner (v1.0.10)57 from the Docker image jmonlong/job-graphaligner:latest. Default values related to seeding and extension were used (options: -seeds-minimizer-count 5 --seeds-minimizer-length 19 --seeds-minimizer-windowsize 30 --seeds-minimizer-chunksize 100 -b 5 -B 10 -C 10000).\n\nc. Statistics related to alignment were extracted from the resulting GAM files using vg (1.23.0)60 (RRID:SCR_024369) from the Docker image biocontainers/vg.\n\n2. Linear Genome Approach\n\na. Reference genome: The reference sequence NC_002516.2 (Genome assembly ASM676v1) derived from the PA01 strain was downloaded and indexed using bwa index ref.fa.\n\nb. Linear read alignment: An array of different genome assemblies of Pseudomonas aeruginosa were downloaded from the NCBI repository. This included the full-length genome of diverse strains isolated from different environments. A total of 59 Illumina sequencing datasets for P. aeruginosa (NCBI Taxonomy ID 287) that were retrieved from the Sequence Read Archive (metadata for these samples is included in the linked GitHub repository - https://github.com/collaborativebioinformatics/SVHack_metagenomics/tree/2797b9eec54665258a67ef0277fbd4d06d4e26c7/reads_info). BWA-MEM (BWA-0.7.17 [r1188])59 was used for short-read alignment to the reference genome for all 59 datasets (command: bwa mem ref.fa read1.fq read2.fq > aln-pe.sam). Quality control statistics were obtained from output files using Picard (2.26.11) (http://broadinstitute.github.io/picard) (RRID:SCR_006525).\n\nTrue de novo SVs are expected to be rare, however, in practice, a high rate of inconsistent SVs will be identified, indicating false positives or negatives due to noise inherent in SV calling and merging. SalsaValentina creates a ‘naive’ de novo SV candidate list, and develops a QC-framework tool that enables users to visualize the alignments in inconsistent SV regions across the trio and create a local assembly of every de novo SV candidate locus to aid in confirmation of the variant as either a de novo SV or an incorrect call.\n\nSalsaValentina is an integrated pipeline for Mendelian inconsistency of SVs. We demonstrate the pipeline using the Genome in a Bottle (GIAB) Ashkenazim trio (HG002 son, HG003 father & HG004 mother) sequenced on Sequel II System with 2.0 chemistry and aligned to the GRCh38 genome reference. SVs are called using the Sniffles2 variant caller.11\n\nTo merge the SV calls into a single VCF file, two methods are compared: multi-sample SV calling using Sniffles211 and variant merging with SURVIVOR61 (RRID:SCR_022995) using default parameters (https://github.com/fritzsedlazeck/SURVIVOR). Each of the resulting merged VCFs is annotated for Mendelian inconsistencies using the mendelian plugin to bcftools62 ( https://samtools.github.io/bcftools/howtos/plugin.mendelian.html). The positions of each SV inconsistent with Mendelian inheritance is extracted from the merged VCFs and samplot63 is used to visualize the region of each variant in each member of the trio.\n\nTo further investigate the validity of the candidate variants, Mendelian inconsistent SVs were filtered to remove breakends (BNDs) and variants involving alternate contigs in GRCh38. The candidates from Sniffles11 multi-sample calling were ranked by coverage. The candidates from SURVIVOR61 merging were filtered for variants with a ratio of variant reads to total read coverage between 0.3 and 0.7, resulting in 48 top candidates. For top ranking candidates, local assembly was performed by extracting reads aligned 50 kb upstream and downstream of the region of interest and assembling with Hifiasm64 (command: --primary; to generate primary and alternate assembly) (RRID:SCR_021069). The YASS65 Genomic Similarity Search Tool web server was used to create dotplots visualizing pairwise alignments of the resulting contigs to GRCh37 to verify the deletion in HG002. SalsaValentina workflow is shown in Figure 5.\n\nPhytoKmerCNV takes raw whole-genome sequencing reads in the FASTQ format as input and produces k-mer distributions for both the total sample, as well as a captured subsample of sequencing reads. The captured reads correspond to sequences of interest in the genome that are captured based on alignment to a protein database. From the k-mer distributions, copy number estimates for the sequences of interest can then be derived from the captured subsample by comparing summary statistics calculated from the respective k-mer distributions for captured versus total reads.\n\nPrior to the pipeline execution, the sequences of interest must be identified, converted to a protein FASTA file, and used to make a BLAST84 protein database. The pipeline then begins with raw sequencing reads in the FASTQ format as input, which can be either uncompressed or compressed with gzip. The sequencing reads are adapter- and quality-trimmed using fastp (0.23.4)66 with the default parameters. The processed FASTQ file is then converted to the FASTA format using seqtk (1.4).67 The sequences are then queried against the protein database using blastx to identify reads putatively originating from the sequences of interest. The BLAST results are filtered to retain hits with a match length≥20 and the E-value<1. Reads with hits to the database are then extracted using samtools faidx. Canonical 21-mers are then counted in the matching reads, as well as the full sample of reads. The sum of k-mer frequencies found in the matching reads, as well as the total sample were then calculated using awk before being fed into an R script that derives copy number estimates from the calculated sums, as well as plotted the k-mer distributions.\n\nAs a practical example, we have developed this tool with the goal of estimating the copy number of resistance genes (R genes) for pathogen recognition in a collection of 32 resequenced tomato genomes.68 R genes encode for proteins which recognize pathogen effectors in plants and are classified according to their domain organization, with nucleotide binding site (NBS) and extracellular leucine-rich repeat (LRR) domains.69,70 We selected R genes to test our tool since they evolve rapidly, with copy number variation observed both between and within plant species.71,72 PhytoKmerCNV workflow is shown in Figure 6.\n\nTo evaluate the performance of the mapping-based and the assembly-based SV calling methods, we select a number of SV calling tools and analyze Illumina short reads of whole-genome sequencing data to generate SV calls. Once the SV calls are available, the performance of the SV calling protocols are evaluated by comparison with an independently developed high-confidence truth (Figure 7). For this purpose, we used the GIAB HG002 (ASJ son) SV dataset36 as the truth (https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/analysis/NIST_SVs_Integration_v0.6/). The findings could help us to assess the pros and cons for each method and to recommend an optimized SV calling protocol for NGS short reads.\n\nWe selected 2x250bp and 300X BAM files (70X coverage) from HG002 (Ashkenazim Trio Son, NA24385, ftp://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/AshkenazimTrio/HG002_NA24385_son/NIST_Illumina_2x250bps/novoalign_bams/HG002.GRCh38.2x250.bam69ff2c644140bcf2396afed00907e24f; ftp://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/AshkenazimTrio/HG002_NA24385_son/NIST_Illumina_2x250bps/novoalign_bams/HG002.GRCh38.2x250.bam; ftp://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/AshkenazimTrio/HG002_NA24385_son/NIST_HiSeq_HG002_Homogeneity-10953946/NHGRI_Illumina300X_AJtrio_novoalign_bams/HG002.GRCh38.300x.bam as input for the mapping-based SV calling with Lumpy73 (RRID:SCR_003253), Delly74 (RRID:SCR_004603), Manta75 (RRID:SCR_022997), Breakdancer76 (RRID:SCR_001799), BreakSeq2,77 CNVnator78 (RRID:SCR_010821), Parliament279 (RRID:SCR_019187) and SURVIVOR.61 We also ran dysgu,46 cue80 separately for SV calling. For assembly-based SV calling, the BAM files were converted to FASTQ files and used as input for SVABA48 (RRID:SCR_022998). The individual SV calls and the consolidated SV calls were then compared with the HG002 SV truth dataset to assess the performance by Truvari.81\n\nThe recently available Telomere-to-Telomere (T2T) genomes gave us the starting point for developing an alternative ‘self-alignment’ method for evaluating artifacts and false positives from variant callers including small variant detection and SV callers. Since this is a collinear synteny test, we designated this as the Colins Test. Briefly, read alignment was generated by aligning the T2T genome reads back to the corresponding finished T2T reference genome, and the alignment was then used as input for SV calling (see Extended data). SV calls from the SV callers are by definition artifacts and false positives. This alternative performance metric for SV callers serves as an independent complementary approach to the stats generated by Truvari.81 This self-alignment method is also different from SalsaValentina (discussed above), since the self-alignment method does not require trio info to work.\n\nIn the Colins Test for GIAB HG002, we mapped GIAB HG002 reads back to the HG002 T2T phased genome assembly (both maternal and paternal haplotypes included) to assess how the Colins Test would perform. We also aligned the HG002 T2T phased genome assembly to the HG19/GRCh37 chr22, and aligned the HG002 T2T maternal to the paternal genome assembly, so then we could inspect the NGS alignments at the matched locations, with the intent of finding the source of errors in the reference based SV calls.\n\n\nOperation\n\nThe IsoComp pipeline is written in python and it can be implemented in any Linux-based environment with Python>3.9. After installing IsoComp from PyPI with pip (command: pip install isocomp), the program is ready to use in the command-line terminal. The IsoComp pipeline consists of two steps, run one after the other. The first step (Creating windows) takes GTF files of multiple samples as input and produces a GTF file with clustered isoforms. The second step (Finding unique isoforms) takes the clustered GTF file created in Step 1 as input, as well as a CSV file with information about sources and the FASTA files of particular samples. This step produces a CSV file with unique isoforms. Dependencies include SQANTI3,53 minimap2 (v2.24-r1122),52 samtools (v1.15.1),54 Isoseq3 (v3.2.2) (https://github.com/pacificbiosciences/isoseq/), poetry (v1.6.1), pandas (v1.5.1), biopython (v1.80), pysam (v0.20.0), edlib (v1.3.9), numpy (v1.16), matplotlib (v3.7.1), tqdm (v4.66.1). The code is available inn our GitHub repository: https://github.com/collaborativebioinformatics/isocomp.\n\nThe SpikeVar workflow requires Python>3.6.8. The SpikeVar workflow includes two major steps. First, the SpikeVarDatasetCreator takes aligned sequencing reads from two samples to strategically introduce x% of mutations from one sample to another using mosdepth (0.3.2)82 (RRID:SCR_018929) and the two down-sampled datasets are then merged using samtools (1.15.1)54 to create a mixed dataset that represents a sequence read dataset with mosaic variants. In the second step, the SpikeVarReporter determines VAFs for each variant in the mixed dataset using bcftools (1.18)54 based on the mixed variant locations derived by merging the VCF files from sample A and sample B. Variants with VAFs exceeding or equal to the introduced mutations (i.e., x%) are then selected to create a truth set for benchmarking.\n\nThe TykeVar package has been tested using Python>3.10. The TykeVar workflow can be broadly split into 3 parts. The TykeVarSimulator takes an aligned BAM file, a reference, and several parameters (such as range of VAF, variant sizes) to generate a set of simulated mosaic SV and SNVs. It does so by choosing a random location and VAF from the given range and then evaluating whether that location has sufficient coverage for the desired VAF. If that condition is met, that variant is added to the output VCF file. The TykeVarEditor is responsible for inserting the simulated variants into the query sequences from the original dataset to generate modified reads with the mosaic variants built-in. For each variant, it fetches the overlapping reads from the BAM file, subsamples the reads to get the coverage that satisfies the desired VAF, and traverses the cigar string, query and reference sequences for each alignment to find the exact location to insert the variant using pysam (0.21.0). Once a modified read is created, it is written out into a FASTQ file. Note that for all new bases (SNVs or inserts), the q-score of 60 is chosen. The parsing and traversing of the VCF, BAM and reference files are performed using APIs from pysam, biopython. SeqIO and NumPy. Lastly, the TykeVarMerger re-introduces the modified reads into the original dataset using minimap2 (v2.24-r1122)52 and bwa-mem2 (v2.2.1).59 Additional non-standard dependencies include NumPy (1.25.2), and BioPython (1.81), all of which are available through the pip package management system.\n\nPGGP is not a workflow that can be run, but an analysis pipeline for a graph genome approach applied to P. aeruginosa. The P. aeruginosa graph genome obtained can also be downloaded from that page, and it is available to the scientific community. This pipeline can be replicated following the instructions in our Github repository (https://github.com/collaborativebioinformatics/SVHack_metagenomics). To re-run this pipeline, we suggest using pggb56 inside a Docker container. Instructions on how to run pggb56 in these conditions can be found in the pggb Github repository (https://github.com/pangenome/pggb). If the user wants to replicate read alignments with GraphAligner,57 even though it was not adequate for short reads (see Results), we recommend running it from inside a Docker container (https://github.com/maickrau/GraphAligner). Other aligners, such as vg Giraffe60 might be more adequate for short reads, however. For a linear genome alignment, we used the reference sequence NC_002516.2 (Genome assembly ASM676v1) as a reference genome, and performed alignment with BWA-MEM (BWA-0.7.17 [r1188]).59 Lastly, vg60 was used to obtain statistics from the graph alignments, while Picard tools (2.26.11) (http://broadinstitute.github.io/picard) was employed to assess the quality and the statistics of the aligned reads aligned to the graph or linear genomes respectively. For more details, see the Github repository (https://github.com/collaborativebioinformatics/SVHack_metagenomics).\n\nSalsaValentina is implemented as a Snakemake pipeline, requiring the sample names and BAM files of the mother, the father, and the child (trio) and a reference genome. The pipeline calls SVs using Sniffles (v2.0.7),11 then merges the variant calls across the trio using both Sniffles11 multi-sample calling and SURVIVOR (v.1.0.7).61 Mendelian inconsistencies are identified with bcftools mendelian plugin (v1.17)62 and automatically visualized with samplot (v1.3.0).63 The pipeline outputs merged VCF files, a text file of Mendelian inconsistencies, and a PDF file with visualizations from samplot.63 Additional scripts, dependent on the Python version (v3.9) and the Pandas module (v2.1.3), enable filtering of the de novo SVs identified by either Sniffles11 or SURVIVOR61 and local assembly of selected regions of interest using samtools to extract regions from the BAM file and hifiasm (v0.19.6).64\n\nThe main PhytoKmerCNV pipeline is provided as a Bash script that can be deployed on any Unix system, although the pipeline was initially built and executed on AWS via DNAnexus. Software dependencies can be installed via conda/bioconda using the provided YAML file and include Python≥3.10.12, R≥4.3.2, jellyfish (2.3.0)83 (RRID:SCR_005491), ncbi-blast+ (2.14.1),84 seqtk (1.4),67 sra-tools (3.0.7) (https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software), samtools (1.17),54 fastp (0.23.4),66 and awk. Further dependencies include the following R libraries: pacman, ggplot2, cowplot, and ggpubr.\n\nThe SV-Genie pipeline has two major branches executed via shell scripts. The first branch is for the mapping-based SV calling, which uses BAM files as input for SV calling with Parliament2 (v0.1.11),79 executing SV callers such as Lumpy (v0.2.13),73 Delly (v0.7.2),74 Manta (v1.4.0),75 Breakdancer (v1.4.3),76 CNVnator (v0.3.3),78 and followed by SURVIVOR (v.1.0.7).61 This branch also runs dysgu (v1.6.0)46 and cue (v0.2.2)80 for SV-calling. The second branch is for the assembly-based SV calling, where the BAM files are converted to FASTQ files and used as input for the assembly-based SV calling via SVABA (v1.1.3).48 The individual SV calls and the consolidated SV calls are then compared with the SV truth dataset to assess the performance by Truvari (4.1.0).81 To evaluate the impact of different read coverage on SV calling, we used seqtk (1.4)67 or samtools (1.17)54 to generate decimated bam files as input for SV calling.\n\n\nResults and use cases\n\nIn our approach, we aim to compare transcripts based on their composition rather than solely relying on coordinates, distinguishing our method from others. We have developed a tool called Isocomp, publicly available on GitHub at “https://github.com/collaborativebioinformatics/isocomp” under the MIT License. IsoComp can be installed using pip (command: pip install isocomp==0.3.0) and comprises two main steps. The initial step involves creating comparison windows (command: isocomp create_windows), which takes a GTF file for the samples to be compared and a transcript file as input, producing a cluster file for all samples that serves as a seed for the subsequent step. The next step utilizes the IsoComp algorithm (command: isocomp find_unique_isoforms) and the output from the previous step to compare shared transcripts between samples based on the composition. This step outputs unique transcripts that may overlap with other transcripts in the compared samples but differ in sequence composition.\n\nWe applied our tool to two publicly available samples, namely NA24385 and NA26105, and successfully differentiated isoforms between those two samples. However, further development is required.\n\nThe refinement and clustering steps generated in the Iso-Seq analysis step full-length HQ transcripts of high quality (i.e., predicted accuracy≥Q20) are shown in Table 1, Table 2 and Table 3\n\nTable 2 shows the basic statistics of the alignment of each sample (HG002: NA27730, NA24385, NA26105) to the reference genome.\n\nTable 3 shows the isoform classification report generated by SQUANTI3.\n\nThe output results (supplementary table 4) were performed by running IsoComp on DNAnexus (total running time: 15 mins, with 16 CPU and 8 GB RAM). Our tool can find and compare intervals, multithreading, easy to install and generate a convenient TSV output file.\n\nIn Figure 8, we represent the cluster sizes, which indicate the number of transcripts whose intervals overlap and how many clusters contain such transcripts. We obtained this data by comparing three replicates of the HG002 sample, which is publicly available in GIAB (ftp://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/AshkenazimTrio/HG002_NA24385_son/Ultralong_OxfordNanopore/guppy-V3.2.4_2020-01-22/HG002_hs37d5_ONT-UL_GIAB_20200122.phased.bam).\n\nUsing the SpikeVar workflow, we successfully spiked in the Genome in a Bottle (GIAB) sample HG002 (ASJ son)36 (https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/analysis/NIST_SVs_Integration_v0.6/) at a 5% concentration into sample HG0733 (Puerto Rican female) (ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR398/ERR3988823/HG00733.final.cram), to result in a 5% mosaic variant allele frequency (VAF). Figure 9(i) displays the successful detection of a deletion of 287 bp on chromosome 5 at a 5% rate. This deletion originated from the HG002 sample and was not present in the original HG00733. Similarly, Figure 9(ii) shows a 341 bp long insertion at a 5% VAF originating from HG002.\n\nScreenshot for SVs (i) deletion and (ii) insertion from HG002 and was successfully spiked in the HG00733 BAM.\n\nWe successfully used the TykeVar workflow to modify reads of HG002 directly at their reference position by including artificial mutations. To demonstrate the wide application of our tool, we generated a random distribution of allele frequencies between 1% and 40%, which can be seen in Figures 10(i) and (ii). Figure 10(i) shows the simulation of a 5952-bp long insertion which was simulated at 22% VAF, while Figure 10(ii) shows the simulation of a A>T mutation on chromosome 22 at 8% VAF.\n\n(i). A mosaic insertion introduced into the reads by modifying a subset of the reads. ii). A mosaic SNP introduced into the reads by modifying a subset of the reads.\n\nThe simulated data generated by both SpikeVar and TykeVar workflows include simulated SNVs, SV, and indels and is therefore optimal for the comparison and benchmarking of different mosaic variant callers. Mosaic variant caller sensitivity and accuracy can be determined for variable VAFs and read coverages to determine minimum requirements for detection. To validate long SVs and indels detection, SpikeVar is a more suitable workflow for the creation of a validation dataset as it uses naturally occurring variants for spike-in and is not restricted by the read length. Moreover, in simulated datasets created by the TykeVar workflow, haplotypes remain unchanged and therefore TykeVar datasets are more suitable for phasing dependent callers. Both SpikeVar and TykeVar can be applied to long- and short-read whol-genome sequencing files. Hence, different technologies (ONT, Pacbio, Illumina) can be assessed for their suitability of mosaic variant detection.\n\nFor the graph genome construction, we built graph representations for Pseudomonas aeruginosa using 5, 10, 20, 50, 100, and 500 genomes (see Extended data). As more assemblies are used, the graph grows in complexity and more regions of the genome are accessory regions and not core. Observing the sequenced alignments of the 20 assemblies used to create that graph, one can see big chunks of the sequences being absent from most of the different isolates, while others are present in all. The assembly accession numbers with additional details can be found in the metadata table in our GitHub repository: https://github.com/collaborativebioinformatics/SVHack_metagenomics.\n\nLinear Read Alignment\n\nAs part of the PGGP project, we wanted to compare our graph approach to the regular linear genome alignment approach. We obtained 59 Illumina read datasets from SRA and aligned them to the ASM676v1 reference genome (see Methods). We can observe the alignment efficiency for this approach (see Extended data). To gauge graph alignment accuracy, we also developed a method for graph based MAPQ sampling accuracy check. The quality scores provided in the GAM files are tricky to interpret as we have few details about the calculation method used here and it might be different from linear alignments MAPQ scores calculation methods.57 To count the number of aligned reads on the graph, a criteria for a valid aligned read needs to be defined. Here we look at the distribution of the quality scores found for one of our GAM files to get an idea of its range and have a better overall insight of the threshold. This helps to choose an appropriate threshold to filter the aligned reads and count the one that passes (see Extended data). Based on the distribution of the score, we plotted the selectivity of the filter based on the value of the chosen threshold (see Extended data).\n\nFinally, a comparative analysis between the aligned reads between the pangenome and a single reference genome for different assemblies was done, which shows a better view of the difference in the analysis using a single reference genome and a pangenome (Figure 11).\n\nA comparison between the aligned reads between the pangenome and a single reference genome for different assemblies.\n\nOur pipeline offers a valuable resource for the scientific community: a collection of graph genomes using different numbers of isolates, representing different iterations of the Pseudomonas aeruginosa pangenome. These graphs were constructed using a carefully curated list of publicly available genome assemblies from bacterial isolates. The list is also provided alongside the graph genomes, allowing for transparency and reproducibility. Additionally, the pipeline provides a flexible framework for generating various iterations of these graph genomes. This enables users to experiment with different parameters and isolate selections, further tailoring the resource to their specific research needs.\n\nSalsaValentina compares two different methods of merging SV calls within the trio: multi-sample calling using Sniffles11 and merging using SURVIVOR.61 The two methods give different numbers of overall SV calls within the trio, as well as percentages of SVs that are inconsistent with Medelian inheritance. We found a total of approximately 32,000 SV calls in our merged call set using either the Sniffles11 multi-sample calling or SURVIVOR.61 For the Sniffles11 multi-sample calling, 5.2% of these were Mendelian inconsistent, while for SURVIVOR61 2.4% were inconsistent (Extended data). The different number of inconsistent SV calls between the two methods is due to differences in genotype assignment between the tools, with SURVIVOR61 treating some variants as missing, whereas Sniffles11 reports them as reference.\n\nA Mendelian inconsistent deletion was identified in HG002 at chr7:142,786,222-142,796,849 by the Sniffles11 multi-sample calling method (Figure 12(A)). This is in the T-cell receptor beta locus and thus, likely the result of somatic recombination rather than a de novo germline variant. However, it can still be used to demonstrate the usability of our method. This deletion was called heterozygous with 12 reads supporting the reference and 13 supporting the variant in HG002, while it was homozygous reference supported by 45 and 44 reads respectively in HG003 and HG004. In addition, GIAB previously reported a de novo deletion in HG002 at chr17:51,417,826–51,417,932 using GRCH37 reference as part of their v0.6 SV benchmark set, which was derived from high confidence calls supported by multiple methods.36 This deletion was also identified in this study, at chr17:53,340,465-53,340,571 when using GRCH38 as reference (Figure 12(B)). This heterozygous deletion was supported by 30 reads and the reference at this location by 27 reads, while the parents had only reads supporting the reference allele (65 in HG003 and 72 in HG004).\n\nCandidate de novo deletions at (A) chr7:142,757,892-142,824,789 and (B) chr17:51,417,826–51,417,932. The top panel shows a deletion in HG002, which is absent in the parents (father HG003 middle panel, and mother HG004 bottom panel).\n\nSalsaValentina can aid users in identifying and confirming SVs that demonstrate Mendelian inconsistency. We envision two primary use cases. First, genuine de novo SVs may be candidates for rare disease diagnosis. Second, candidate SVs that are mendelian inconsistent due to coverage issues or variant calling inconsistencies help to inform the error modes of sequencing and software for SV calling, to refine methods for accurate SV calling.\n\nWe executed the PhytoKmerCNV pipeline on a dataset of 32 resequenced tomato genomes and compared the CNV estimates produced by the pipeline with empirical NBS-LRR genes parsed from genome annotations. Briefly, we counted the number of genes with the NBS-LRR domains among annotated peptides for each genome and used the resulting value as a relative ground truth value, upon which the k-mer estimates were compared to determine the accuracy of our gene copy number predictions. The corresponding results are shown in Figure 13. Our approach did not yield a significant result, thus we were unable to confidently infer the copy numbers for each NBS-LRR gene in the resequenced tomato genome. There is much room for further refinement of PhytoKmerCNV.\n\nThe regression analysis shows the relationship between the number of NBS-LRR genes estimated from the gene annotations compared to the 21-mer based abundance estimates derived from captured reads. The R2 value is 0.011 indicating a very low correlation between the above variables, while the p-value of 0.58 suggests that the results are not statistically significant.\n\nThere are three potential use cases of PhytoKmerCNV. First, it would be interesting to compare CNV patterns of the NBS-LRR genes within a species and/or across multiple plant species, highlighting variations and conserved patterns. Second, it would be informative to be able to estimate CNV in a non-model plant genome lacking extensive resequencing data, especially including gene identifiers and inferred copy numbers. Third, extending this approach to assess CNV using low-pass sequencing data would reduce associated costs. These practical use cases illustrate the versatility of PhytoKmerCNV for CNV analysis in plant genomes. Researchers can adapt the tool to address a wide range of research questions, from investigating genetic diversity to understanding the functional implications of CNVs in plant biology.\n\nWe ran the SV-Genie pipeline on the GIAB HG002 2x250bp WGS Illumina short-reads as a use case. Specifically, we executed the mapping-based SV-calling including Parliament2,79 dysgu46 and cue,80 as well as the assembly-based SV-calling SVABA.48 We then compared the SV calls with the GIAB HG002 SV reference data set v0.636 via Truvari.81 The performance stats are summarized in Extended data.\n\nThis use case gave us a number of insights:\n\n1. SV callers have false negative rate of 50-60% or higher and false positive rate is also high, consistent with previous observations.46,79\n\n2. SV callers have much better performance for deletions than for duplications/insertions, suggesting more challenges for duplication/insertion SV calling.\n\n3. Parliament279 is designed to launch all six included SV callers, but two of these SV callers (breakdancer76 and lumpy73) failed to run, even though all these SV callers were included as part of the Docker image.\n\n4. Parliament279 generated final SV calls from the four successful SV caller runs (breakseq2,77 cnvnator,78 delly2,74 and manta75) even when two of the included SV caller failed to generate any results.\n\n5. The dysgu46 SV caller alone out-performed Parliament279 with better recall and F1-score, even though Parliament279 integrated the results from multiple SV callers.\n\n6. The SV calling performance has a strong dependency on the coverage, where the 70X coverage for 2×250bp data has the best performance. However, the 300X coverage dataset has significantly worse performance, suggesting the possibility of an optimal coverage for SV calling, or the read length difference between the 300X data and the 2×250bp data.\n\n7. SVABA48 is the only assembly-based SV caller evaluated, but its performance with default settings is far worse than the mapping-based SV callers. SVABA48 for 2×250bp data (70X) completed in a few hours by just assembling clipped/discordant/unmapped/gapped reads (default). When the -r all option is turned on to generate assembly for the whole genome, the job ran for seven days without completion on a large DNAnexus instance (mem2_ssd1_v2_x96: 375 GB total memory, 3348 GB total storage, 96 cores).\n\nTo complement the performance metrics generated by Truvari,81 we created a genome browser instance containing the read alignment with T2T reference genome to demonstrate manual review and confirmation. The screenshots shown in Figure 14 and Extended data were created with an automated script that prepared the alignments and the genome browser setup.\n\nNotably, the maternal chromosome is 4 Mbp longer than the paternal chromosome.\n\n\nConclusion and next steps\n\nWhile various tools exist for comparing transcripts, they often overlook the significance of the transcript sequence order. To address this gap, we have devised a prototype algorithm capable of comparing transcripts by considering both their coordinates and sequence compositions. Our ongoing objective is to optimize the algorithm for scalability, with a specific focus on employing memory-efficient techniques suitable for extensive projects, such as the 1000 Genome Project. This optimization will involve refining cluster algorithms and adopting an alignment-free methodology to facilitate transcript comparisons across diverse samples. Presently, our algorithm generates a basic table indicating shared and unique transcripts. However, our ultimate future goal is to exploit this table to provide more comprehensive insights, including information on the spatial relationships between transcripts within each sample. This advancement aims to enhance the depth of analysis and contribute to a more nuanced understanding of transcriptomic data.\n\nSpikeVar and TykeVar successfully enabled creation of simulated genomic data containing known mosaic variants with VAFs between 5% and 20%. To our knowledge, these are the first workflows that simulate mosaic variants for the benchmarking and quality control of mosaic variant callers. The strengths of our workflows include a rapid and reproducible creation of simulated genomic truth datasets with accompanying index VCF files with mosaic variant location and VAF. In addition, both files are widely compatible with mosaic variant callers and provide a variety of different types of variants including SNVs, SVs, and indels and both workflows require only basic packages and are therefore easily installed and implemented.\n\nBenchmarking mosaic variant callers is essential in order to generate reliable data for evaluation of disease associations of mosaic variants. Therefore, we plan to convert both TykeVar and SpikeVar into a one-step tool for the generation of simulated data. We also want to enable the user to have the option to define a global VAF as well as variant specific VAF. In a final step, we will compare our simulated data with data of physically mixed and sequenced samples.\n\nPangenomes have been used in the past to elucidate the core genomes of pathogens, to improve detection of horizontal gene transfer events, and to study their evolutionary trajectories in different environments. These applications greatly expand our understanding of bacterial and host-pathogen dynamics with practical applications to both medicine and agriculture.\n\nMetagenomics and sequencing of clinical isolates are gaining traction for identification of antimicrobial resistance profiles and diagnosis. Pan-genomics can greatly benefit these clinical applications. Creating pangenomes provides additional insight into pathogen evolution and transmission. For example, including local isolates in pangenomes could inform outbreak investigation efforts and lead to improved infection prevention within hospital systems. Mapping reads directly to pangenomes is a recent advance that may improve detection of polymorphisms related to antimicrobial resistance or virulence. Examining practical considerations and comparison with standard practices demonstrates the promise of alignment to pangenomes and drawbacks.\n\nSalsaValentina enabled identification of putative de novo SVs, two of which were investigated in further detail. One was determined to occur in the T-cell receptor locus, and thus is a likely somatic event that may not be interesting for the use cases of de novo disease associated SVs or variant calling refinement. However, we were able to verify the deletion in HG002 using a local assembly, demonstrating the capability of the pipeline. In future, results could be restricted to certain regions of interest in the genome, excluding known recombination regions. Furthermore, visualization of the candidate de novo SVs could aid in screening candidates in problematic regions or regions of interest. In addition, we observed and confirmed a previously reported de novo SV in HG002, at chr17:51417826–51417932. This variant was identified as part of a comprehensive benchmarking effort for HG002 and thus demonstrates the ability of SalsaValentina to identify genuine events.36 One potential limitation of our local assembly to verify the SV calls is that we used only reads that mapped near the putative SV. In the future, we recommend including unmapped reads in the assembly to ensure reads that failed to map may be incorporated into the contigs.\n\nWe set out to fill a critical niche within plant genomics by building a pipeline for analyzing genomes that have not been extensively resequenced, particularly non-model plant systems with limited genomic resources. Our method, PhytoKmerCNV, demonstrates great promise as a reference-free approach for genotyping copy number variation using whole-genome sequencing reads. Moreover, its ploidy-agnostic nature would make it adaptable to genomes with varying levels of ploidy. Such k-mer-based approaches, known for their sensitivity, offer the intriguing possibility of low-pass sequencing, potentially opening up new avenues for exploring CNV dynamics albeit being rather risky. The proposed tool is dependent on the ability to identify reads which match a specific protein domain. Therefore, one of the major risks of this approach is the potential to miss reads originating from sequences of interest but missing the captured protein domain.\n\nMoving forward, several promising improvements can be made. Currently, the existing pipeline generates a k-mer based estimate from the ratio of the sum of k-mers in the NBS-LRR genes captured reads over the sum of k-mers in the total sample. One challenge this approach must overcome is the incredibly high sum of k-mers which return a count of 1. In future hackathons, the sum could be substituted with other summary statistics such as mean, median, and/or statistical methods which account for the inflated counts. Additionally, several other types of gene families could be studied (e.g., transcription factors with specific DNA binding domains, cytochrome P450s, kinase families, heat shock proteins, pathogenesis-related proteins, MADS-box genes, ABC transporters, RNA-binding proteins, and/or late embryogenesis abundant proteins). Each of these have their own pros and cons and must be considered with respect to the type of biological data.\n\nUpon further modification and refinement, we expect the pipeline to generate accurate CNV estimations and help researchers observe the range of variability of CNV across plant genomes. Some genomes may have higher copy numbers of specific NBS-LRR genes, while others may have fewer copies, reflecting the natural genetic diversity within the tomato species. Additionally, an optimized method would allow for further validation of the previously annotated NBS-LRR genes in genome assemblies, and potentially highlight novel gene copies or variants which were not initially annotated. Extending the application of PhytoKmerCNV to a broader range of plant species, especially those with unique genomic characteristics, will enhance its utility in diverse research contexts. Incorporating phenotypic data alongside the CNV analysis can uncover genotype-phenotype relationships, shedding light on the functional significance of CNVs, particularly in the context of disease resistance and other traits.\n\nIn the future, we believe that it would be valuable to develop a user-friendly interface and detailed documentation to make the tool more accessible to researchers with varying levels of computational expertise. And finally, we encourage collaboration and feedback from the research community on this particular approach with hopes of fostering improvements and adaptations of PhytoKmerCNV to meet evolving research needs.\n\nSV-Genie provides a generalized framework for evaluating the performance of SV-calling tools. Our analysis shows that SV-calling tools still have a long way to go, since even the best performing SV caller (dysgu46) has a modest recall rate and a high false positive rate, confirming previous reports.46,79 Another issue is that some SV callers (cue80 and SVABA48) have far worse performance with default settings, compared with what was stated in the original publications. In addition, SVABA48 assigns BND as the SVTYPE for all SV calls, but does not provide a script for converting the SV caller output to the standardized VCF format with the standard ‘SVTYPE (e.g., DEL, DUP, INS), while Parliament279 has different chromosome naming conventions. Looking forward, it is strongly recommended that all SV callers should have a minimum set of standardized fields such as SVTYPE, END, SVLEN to make it more straightforward for the end user to use and for SV caller performance evaluation.\n\n\nEthics and consent\n\nAll data and software used in this study is open-source.", "appendix": "Data and software availability\n\nIn this study we used the following data:\n\nGenome in a Bottle: Genomic data. Accession numbers HG002 samples (NA27730, NA24385, NA26105, NA24385, NA26105, NA27730), HG002 son, HG003 father, HG004 mother, HG0733 Puerto Rican female; Data available from: https://www.nist.gov/programs-projects/genome-bottle 21\n\nTelomere-to-telomere consortium HG002 “Q100” project: Genomic data; Data available from: https://github.com/marbl/HG002 under the [CC0] license.\n\nGenome assembly GRCh37: Reference genome; Data available from: https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000001405.13\n\nIsoComp: All code is provided at the following Github repository: https://github.com/collaborativebioinformatics/isocomp. The code is available under the [MIT] license.\n\nSpikeVar/TykeVar: All code is provided at the following Github repository: https://github.com/collaborativebioinformatics/SpikeVarTykeVar. The code is available under the [MIT] license.\n\nPseudomonas Graph Genome Project (PGGP): All code is provided at the following Github repository: https://github.com/collaborativebioinformatics/SVHack_metagenomics. The code is available under the [MIT] license.\n\nSalsaValentina: All code is provided at the following Github repository: https://github.com/collaborativebioinformatics/SVHack_Mendelian. The code is available under the [MIT] license.\n\nPhyoKmerCNV: All code is provided at the following Github repository: https://github.com/collaborativebioinformatics/PhytoKmerCNV. The code is available under the [MIT] license.\n\nSV-Genie: All code is provided at the following Github repository: https://github.com/collaborativebioinformatics/SVHack_assemblyvmapping. The code is available under the [MIT] license.\n\nZenodo:\n\nIsoComp (https://github.com/collaborativebioinformatics/isocomp): 10.5281/zenodo.11111370\n\nSpikeVar/TykeVar (https://github.com/collaborativebioinformatics/SpikeVarTykeVar): 10.5281/zenodo.11111360\n\nPseudomonas Graph Genome Project (PGGP) (https://github.com/collaborativebioinformatics/SVHack_metagenomics): 10.5281/zenodo.11111368\n\nSalsaValentina (https://github.com/collaborativebioinformatics/SVHack_Mendelian): 10.5281/zenodo.11111363\n\nPhyoKmerCNV (https://github.com/collaborativebioinformatics/PhytoKmerCNV): 10.5281/zenodo.1111357\n\nSV-Genie (https://github.com/collaborativebioinformatics/SVHack_assemblyvmapping): 10.5281/zenodo.11111365\n\n\nAcknowledgements\n\nThe authors would like to thank Baylor College of Medicine (BCM), BCM administrators and administrative staff, DNAnexus (for compute and the time of BB), PacBio, Oxford Nanopore Technologies and Todd Treangen. 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PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "297030", "date": "13 Jul 2024", "name": "German Demidov", "expertise": [ "Reviewer Expertise Bioinformatics" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn the paper by Deb, Kalra, Kubica, Strickler, Truong, Zeng et al., the authors describe the outcomes of the 5th International Hackathon on the Development of Computational Tools for Pan-Structural Variants and Genomics. While publishing papers that cover educational events is important, there are several critical points that should be addressed.\nThe target audience of this paper is unclear. If it is intended for scientists working in these fields, the five prototypes developed during the hackathon may hold limited interest for them. If the paper is aimed at educators, the selection of participants and the organizational aspects of the hackathon are not covered in sufficient detail.\nBased on the GitHub repositories of the five prototypes, it appears that only one continued development beyond the initial hackathon, and even that one did not last long. The chapter titled \"Conclusion and Next Steps\" is particularly puzzling, given that almost a year has passed since the hackathon. There is no evidence that the \"future work\" mentioned was pursued further.\nSome of the criticisms mentioned seem to have been raised in reviews of previous hackathons as well. It appears that the authors have not addressed these issues in the current paper.\nIn summary, while the paper could serve as an engaging blog post, it lacks substantial scientific or educational value in its current form.\nI do not doubt the value of the hackathon itself, the personal connections that arise during such events, mutual learning between the participants and potential future impact of such collaborations, all my notes are only about the current research paper (“software tool article”) itself.\n\nIs the rationale for developing the new software tool clearly explained? Yes\n\nIs the description of the software tool technically sound? Yes\n\nAre sufficient details of the code, methods and analysis (if applicable) provided to allow replication of the software development and its use by others? Yes\n\nIs sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool? Yes\n\nAre the conclusions about the tool and its performance adequately supported by the findings presented in the article? Yes", "responses": [] }, { "id": "301963", "date": "23 Jul 2024", "name": "Istvan Albert", "expertise": [ "Reviewer Expertise bioinformatics", "data analysis", "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\nFirst, let me state that I think the authors are making many valuable contributions and that each tool may be of notable value. That being said, each software appears to be in various states of completeness and usability.\n\nOverall, however, having seven distinct and disjoint tools in a single paper results in a challenging reader experience. The paper, as written, feels like someone would select seven publications from the Journal of Open Science (JOSS), cut each into pieces, and then stitch them all together: all the first sections, then all the second sections, and so on.\nThat's the feeling I get when I attempt to read this paper. It is extraordinarily jarring and does not look like typical bioinformatics software paper. The reader is asked to context switch or jump around in the paper.\nIn my opinion, the coincidence of space and time that led to the development of all these tools simultaneously does not warrant presenting them under a single unifying umbrella with forty-three authors.\nIf it were up to me I would recommend that the authors submit each software separately to a journal like JOSS that focuses on software alone and presents each result as a single, coherent piece of information, where a reader deals with one specific tool they might be interested in.\nBut then I will admit that I was not knowledgeable about how hackathon results are disseminated, and now that I have looked into it, this type of structure and presentation seems to have quite an expansive precedent.\n\nIn that light, this paper clearly matches and even exceeds those prior papers, and as much as I rather avoid this type of structure, it would feel unfair for me to argue against indexing of this paper.\nI will just note my reservations here, stating that bioinformatics software would be of much higher quality if we created fewer and higher quality applications.\n\nIs the rationale for developing the new software tool clearly explained? Yes\n\nIs the description of the software tool technically sound? Yes\n\nAre sufficient details of the code, methods and analysis (if applicable) provided to allow replication of the software development and its use by others? Partly\n\nIs sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool? Partly\n\nAre the conclusions about the tool and its performance adequately supported by the findings presented in the article? Partly", "responses": [] } ]	1	https://f1000research.com/articles/13-708
https://f1000research.com/articles/13-707/v1	27 Jun 24	{ "type": "Research Article", "title": "Roles and Current Challenges of Peer Educators in delivering HIV/AIDS-related services: a case study in VietNam", "authors": [ "Thuy Thanh Hua", "Ha Thu Nguyen", "Huyen Thu Nguyen", "Chi Thi Hue Cao", "Huong Thanh Nguyen", "Thuy Thanh Hua", "Huyen Thu Nguyen", "Chi Thi Hue Cao", "Huong Thanh Nguyen" ], "abstract": "Background Increasing the participation of peer educators (PEs) to deliver HIV/AIDS services in a limited income context remains challenging, despite their profound effectiveness, and this has become more evident since the COVID-19 outbreak. This study examines the roles of PEs and the current challenges in delivering HIV/AIDS services in Vietnam.\n\nMethods A mixed-method approach was employed. The study was conducted in seven large provinces in Vietnam from December 2021 to March 2022. An online cross-sectional survey was administered to 63 health staff and 147 PEs to collect quantitative data on PEs’ roles. Qualitative interviews included seven focus-group discussions with 39 PEs and in-depth interviews with 25 key informants, including seven leaders and 14 health staff from district health centers and provincial centers for disease control (CDCs), one national-level HIV/AIDS program manager, one non-government organization representative, and two senior experts.\n\nResults Results show the diversified roles of PEs in delivering HIV/AIDS activities in Vietnam. The roles could be categorized into two main groups, including community-based activities and facilities-based activities. Prominent roles are identifying and referring customers to HIV testing services, conducting communication and education activities, and referring patients to treatment services. The study shows a decrease in the roles of PEs in delivering HIV/AIDS services in Vietnam despite the high demand for their participation from healthcare providers. Critical challenges in employing PEs in HIV/AIDS services are related to lack of funding, inadequate training, lack of recognition, and stigma.\n\nConclusion To keep the right path to the goal of ending the HIV pandemic by 2030, it is important to maintain and increase the roles of PEs in delivering HIV/AIDS services. Raising better acknowledgment from stakeholders of PEs’ roles could help overcome the remaining challenges and expand their participation toward this goal.", "keywords": [ "HIV/AIDS", "peer educators", "roles", "Vietnam", "community-based organization", "health promotion", "health education", "community-based activities", "facility based-activities" ], "content": "Introduction\n\nVietnam has made significant progress in the fight against HIV/AIDS over the last three decades. In 2015, Vietnam was the first country in Asia to adopt the 90-90-90 target, i.e., 90% of people living with HIV (PLWH) knowing their HIV status, 90% of whom know their HIV-positive status accessing treatment, and 90% of patients having suppressed viral loads. In 2020, the target was expanded to 95-95-95, aiming to end the HIV epidemic by 2030 (Prime Minister, 2020). To achieve the target, the National HIV/AIDS Prevention and Control program must overcome several challenges. Notably, the AIDS epidemic is still concentrated in key populations, including men who have sex with men (MSMs), female sex workers (FSWs), and people who inject drugs (PWID). These groups not only have a higher chance of contracting HIV/AIDS but also face considerable stigma and discrimination and have limited healthcare access. Thus, achieving universal coverage of sufficient HIV prevention and treatment services among key populations would become more challenging than ever.\n\nVietnam has employed peer educators (PEs) for HIV/AIDS prevention and control activities among key populations since the early-1990s (Vu, Chung, Hoang, & Dondero, 2000). A large body of international (Berg, Page, & Øgård-Repål, 2021; He et al., 2020) and domestic literature (Cuong et al., 2016; Go et al., 2013; Sabin et al., 2019) has proven the effectiveness of peer-driven HIV/AIDs interventions. However, PEs have not been granted official positions within the health system. PEs have been recruited by the local health authorities (Khoat, West, Valdiserri, & Phan, 2003) or community-based organizations (CBOs) (Pham, Pham, & Le, 2022) to participate in project-based activities. In the former case, PEs work closely with the health staff from the commune health centers (CHCs) and district health centers (DHCs). In the latter case, CBOs work under the management of Non-Governmental Organizations (NGOs) or CDCs. It is worth noting that, a network of more than 11,000 CHCs forms the foundation of Vietnam’s primary healthcare. CHCs are responsible for implementing priority public health programs, organizing community-level preventive health services, examining and treating common diseases, etc. In addition to CHCs, DHCs provide more complex services and supervise their subordinate CHCs in service delivery. At the provincial level, the Department of HIV/AIDS Prevention and Control, a unit under the Provincial Centers for Disease Control (CDC) is responsible for implementing HIV/AIDS program.\n\nPeer-driven activities were mainly supported by external funding, with minimal state budget payment channelled through the National HIV/AIDS Program (Ministry of Finance & Ministry of Health, 2012). However, since the National HIV/AIDS Program was the national target program in 2016 (Prime Minister, 2017), the former provincial HIV/AIDS Administration Center was incorporated into the CDC, currently operating as a department under the CDC, as explained above. This organizational structure alteration introduces additional challenges in retaining the PEs in HIV/AIDS control and prevention initiatives since advocating for state funding has become more competitive.\n\nConsequently, the inevitable decreased donor funding together with the organizational structure change has caused a significant reduction in the PEs workforce, from about 8,000 PEs in 2013 to 1,000 PEs in 2018 (VAAC, 2018). The COVID-19 pandemic also struggled barriers to PEs in delivering HIV/AIDS services and, more severely, caused the dispersal of many CBOs (Nguyen, Nguyen, Khuat, Le, & Nguyen, 2022). To maintain and further expand the peer educator workforce to effectively reach the key populations, PEs’ roles must be well recognized. However, evidence of their current roles has still been limited. This study is the first nationwide study in Vietnam that aims to examine the roles and current challenges of PEs in the field of HIV/AIDS. Understanding the roles and challenges of PEs in delivering HIV/AIDS services will help local authorities and stakeholders recognize the roles of PEs appropriately and create a favorable environment for utilizing this workforce effectively.\n\n\nMethods\n\nStudy Sites: Hanoi, Son La, Thai Nguyen, Thua Thien Hue, Lam Dong, Khanh Hoa, and Kien Giang were selected based on their ecological characteristics and representation of the HIV epidemic.\n\nStudy Design: Employing a mixed-method approach, including quantitative survey and qualitative interviews. The quantitative survey was conducted first; then qualitative interviews were conducted later to provide detailed information on PEs’ roles and challenges. The data collection period lasted from December 2021 to March 2022.\n\nAn online survey platform was administered to 147 PEs (including 73 PWIDs, 60 MSM, and 14 FSWs) and 63 health staff (See Table 1 for more characteristics of respondents). The selected PEs were required to be leaders of their respective PE groups, while health staff participants were chosen from the project districts and were responsible for overseeing the activities of the PEs. We approached PEs based on the introduction of the corresponding health staff. Once the PEs agreed to participate in the survey, we contacted them via mobile phone to introduce the purpose of the study and administer the online survey. Each respondent answered whether the PEs were performing the specific roles and rated the importance of these roles based on the 5-point Likert scale, with one corresponding to “totally disagree” and five corresponding to “totally agree” with a specific role. Health staff also rated the demand and regularity of PEs in performing their roles. The list of key PEs’ roles (Table 2) was developed based on a literature review and consulted with a group of PEs in the same study sites.\n\nThe FGDs and IDIs aimed to further describe the specific PEs’ roles and focus on identifying the challenges that PEs face in fulfilling their roles. We conducted seven FGDs (with a total of 39 PEs) and 25 in-depth interviews (IDIs) with 14 health staff from DHCs and CDCs, seven CDCs managers, one senior manager from Vietnam Administration for AIDS Control (VAAC), and three senior experts. Key informants in the PEs group were selected based on the snowball sampling method, where initial participants identified other potential informants, creating a chain referral process to recruit individuals with relevant experience and insights into the study topic. The initial participants of the PE group were chosen for their extensive background in HIV/AIDS prevention and control services, specifically those with a minimum of five years of experience and who are actively working as peer educators in the HIV/AIDS field. In terms of key informants in the health staff group, we selected key informants who have at least three years of experience working with peer educators in the field of HIV/AIDS at both the provincial and district levels using the purposive sampling approach. Senior experts must have at least seven years of prior experience. The selected key informants were invited to participate in the study via email or mobile phone.\n\nSince the data collection period took place during the COVID-19 pandemic, the FDGs and IDIs were conducted through in-person sessions or virtual meetings, depending on the circumstances and the availability of the key individuals. When it was feasible and convenient, the interviews took place in person. However, in cases where in-person meetings were not possible or practical, the interviews were conducted virtually, ensuring that the research process remained adaptable to and accommodating the needs and constraints of the participants. The IDIs were recorded after receiving the agreement of the key informants.\n\nWe applied descriptive statistics to analyze quantitative data. FGDs and IDIs records were transcribed, and the data were analyzed thematically. The qualitative analysis was illustrated by direct quotations from the interviews, which were translated from Vietnamese. The dataset, survey questionnaire, and qualitative interview instructions are available for online access (Hua Thanh Thuy, 2024a, 2024b).\n\n\nResults\n\nThe survey shows the dynamic roles of PEs in HIV/AIDS prevention and control. Generally, there was a consensus reporting the PEs’ roles from both health staff and PEs (See Table 3).\n\nHealth staff highlighted that the distinct roles of PEs arise from their ability to effectively engage with the “hard-to-reach” population, while the health staff encounter numerous barriers in reaching these individuals.\n\n“peers can effectively locate and easily access their customers. They are much better than us (health staff) in answering where and when to approach and whom to provide the services” (IDI, health staff 2)\n\n“The advantage of PE is that they have the same living situation, interests, and habits, making reaching the hard-to-pick group easier … they can communicate and provide services such as referring customers to health facilities and HIV-self testing … They do not directly treat the patients, but they guide them and bring them to the health facilities … without customers, the healthcare system could do nothing …” (IDI, expert 1)\n\nQualitative interviews revealed additional roles not captured by the quantitative survey. Firstly, regarding health education and promotion, all HIV-specific topics, such as HIV prevention, stigma, ART literacy, co-infection control, etc., were mentioned in terms of “approach and education” in general. Non-HIV topics (i.e., healthy lifestyle, nutrition, and other common diseases) were recorded in several IDIs and FDGs:\n\n“we teach them (PLWH) all kinds of subjects, HIV/AIDS and general health issues, like how to exercise, what is a healthy diet, what to do with back pain …” (FGD, PE, Thua Thien Hue)\n\n“They have crucial roles in educating people, both PLWH and people with high-risk behaviors. The topics are diverse, from prevention of HIV and other STDs, how to disclose the HIV status, HIV stigma and discrimination, ART treatment, and treatment of other co-infections … sometimes and some topics, the target population only listens to their peers” (IDI, CDC 2)\n\nSecondly, regarding HIV-specific care, key informants identified additional PEs’ roles in “identifying co-infections and side effects” (i.e., screening for co-infections and screening for treatment-related side effects) and “tracing patients who have missed their appointments.” Thirdly, regarding treatment support, key informants reported the roles of PEs in supporting PLWHs with treatment for other chronic conditions (e.g., tuberculosis) or methadone maintenance treatment (MMT) through motivating and reminding patients to collect their medication, and acting as “role models.” Fourthly, regarding service organization and delivery, key informants extrapolated the PEs’ roles in “accompanying patients to health facilities,” “supporting patients in administrative procedures,” and “delivering HIV self-test kits.” Last but not least, “collecting data on HIV epidemiological situation” was reported as one of the roles in the health system-oriented category.\n\nFigure 1 presents the importance of PEs’ roles and their current practice. We presented the means of respondents’ answers. Although there were differing perspectives between health staff and PEs, they both agreed on the seven roles that were considered the most important and frequently performed: (1) Identifying and persuading at-risk populations to HIV testing services; (2) Referring at-risk groups to HIV testing services; (3) Counseling HIV pre-test; (4) Dispensing condom/lubricant; (5) Giving instructions for using condom/lubricants; (6) Educating PLHW about ART treatment; and (7) Referring PLWH to ART services.\n\nHealth staff generally placed a higher value on the importance of PEs’ roles compared to the value placed by PEs themselves. Only in the case of “providing HIV pre-test counseling” and “providing support for ART, PEP, and PrEP treatment,” PEs reported the importance of those roles higher than the health staff did. IDIs revealed that those roles might be under-recognized by healthcare providers since it is often believed that PEs are unable to be involved in treatment processes:\n\n“peers could only do a good job in educating their peers, they can not provide treatment-related services” (IDI, health staff 5)\n\nQualitative interviews revealed the decreasing PEs’roles in HIV/AIDS interventions despite healthcare providers’ high demand. This decline is attributed to several challenges faced by PEs in HIV/AIDS services delivery.\n\nLack of funding\n\nThe qualitative interviews identified the challenges of “inadequate incentives” for PEs due to decreasing external funding:\n\n“We couldn’t retain enough PEs due to inadequate incentives for payment. Funding has decreased, and the situation worsened during the COVID-19 pandemic, making it challenging to provide the necessary support for them.” (IDI, health staff 3)\n\nFGDs further emphasized the inadequate resources (e.g., personal protection equipment, communication materials, and other harm-reduction products) for PEs in delivering services due to lack of funding:\n\n“We lack personal protection equipment like masks, medical gloves, and hand sanitizer, especially during the COVID-19 pandemic … we must equip ourselves and share with each other” (FGD, PE, Son La)\n\n“We can not deliver services without adequate products. If we want to educate them, we need more communication materials that are updated and meet their needs, and we need more quality HIV self-test kits, more products like condoms and lubricants. Even now, it is easy to buy condoms and lubricants, but some of our customers cannot afford them” (FGD, PE, Ha Noi)\n\nKey informants expressed concerns about inadequate and delayed funding for PEs, leading to a loss of trust from the key population. Consequently, PEs’ roles are diminishing.\n\n“In the COVID-19 outbreak, lockdown and stay-at-home order led to the interruption in ARV supply … PEs struggled in their personal lives … without livelihood support, they cannot continue their job, they cannot timely support their customers, and their roles gradually faded away …” (IDI, VAAC)\n\nInadequate training\n\nIn the quantitative survey, PEs reported low confidence levels in performing specific roles, e.g., only 23% and 47% of PEs felt confident and very confident in providing HIV pre-test counseling and home-based care for PLWH, respectively. IDIs also reported “the limited capacity among PEs” due to the lack of intensive training and the “changing needs of the target population”:\n\n“The number of PE is decreasing due to less financial support and a lack of intensive training compared to the past … they (CBOs) have new members all the time, and it is difficult to train them as well as before …” (IDI, Expert 1)\n\n“Interventions have changed significantly compared to the past. PEs should be familiar with updated services, including virtual counseling techniques, instead of relying solely on traditional face-to-face interactions.\" (IDI, CDC1)\n\nFGDs also revealed PEs’ low confidence in performing treatment support and home-based care activities, and even in conductinging health promotion for unfamiliar subjects due to a lack of training:\n\n“We are willing to take care of the patients. However, we can only easily do domestic work like cooking, and washing clothes, feeding them, helping them take a bath … when it comes to other things that require some knowledge or experience, we are afraid that we may do it wrong and it can harm the patients, such as replacing the bandage on a wound, taking care of very ill patients in the hospital …” (FGD, PE, Kien Giang)\n\n“PWIDs are getting younger, as young as 12-15 years old. We fear supporting them as we did not experience similar situations at such a young age. Due to our limited knowledge about this young generation, we struggle to educate them effectively” (FGD, PE, Thai Nguyen)\n\n“there was only a workshop in which the health staff showed us how to do with the test (HIV-self testing) … We lack of knowledge, but no workshop, no training … we need to share with other peer educator groups in Sai Gon, Dong Thap, Ben Tre …” (FGD, PE, Lam Dong)\n\nLack of recognition from healthcare providers and stakeholders\n\nBoth PEs and health staff reported that healthcare workers and other stakeholders might lack recognition of PEs’ work and even discriminate against them, thus, creating many challenges for PEs in delivering HIV/AIDS services.\n\n“Sometimes, health staff do not know who we are and why we do so. They even give us a strange look. It may lessen the clients’ belief in us” (FDG, PE, Lam Dong)\n\n\"CDC does not acknowledge them; when encountering the police, they are easy to be misunderstood as engaging in a vice or be told it is not their job …” (IDI, Expert 2).\n\nDue to insufficient recognition from stakeholders, PEs lack a formal status in the healthcare system, resulting in a lack of appropriate payment methods for this workforce:\n\n“They are not health staff so there are no personnel policies and insurance. We do not have appropriate methods for paying for their activities because these activities are not like those of health staff” (IDI, Health Staff 4)\n\nStigma\n\nFGDs showed that remaining stigma paired with a “very thin workforce” was currently the major challenge for PEs in approaching their target population.\n\n“patients, especially FSWs, PWIDs, MSM … are fear of disclosing their status due to severe stigma. They are hiding from us; finding them in a vast and complex area is tough. There are not enough PEs to approach them” (FGD, PE3)\n\n\nDiscussion\n\nTo our best knowledge, this is the first study to collect data on a nationwide scale to synthesize the PEs’ roles in Vietnam. Their roles could be categorized into community-based and facilities-based activities. The prominent roles of PEs are identifying and referring customers to HIV testing services, communication, and education, and referring patients to treatment services. It is understandable since the word “educator” often relates to advocacy, counselling, distributing materials, making referrals to services, and support (Kerrigan, 1999).\n\nThe diverse roles of PEs in the HIV/AIDS program in Vietnam resemble those identified in a previous systematic review (Mwai et al., 2013; Ngcobo, Scheepers, Mbatha, Grobler, & Rossouw, 2022). However, this study acknowledges different roles of PEs reported in existing literature, such as linking and referring PLWH to specific services such as PreP or MMT, end-of-life care and funeral arrangement for PLWH, and conducting screening tests for drug abuse. This difference may originate from the characteristics of the healthcare system of different countries, the specific design of interventions involving PEs, characteristics of the HIV/AIDS epidemic, and cultural context.\n\nWhile there is a general consensus among PEs and healthcare providers about PEs’ roles, there are still divergent viewpoints. For instance, some variations exist in the reported percentages of PEs providing HIV pre-test counseling and supporting ART, PEP, and PrEP treatment. Qualitative interviews suggest that these differences could be attributed to healthcare providers’ beliefs that PEs should not be involved in treatment processes. At the same time, PEs showed low confidence in performing these roles due to inadequate training. Thus, in the near future, to promote PEs’ roles in general and in delivering those HIV/AIDS treatment-related services, PEs’ roles need to be widely acknowledged among healthcare providers, and intensive training needs to be provided to help PEs effectively fulfil their roles.\n\nDespite its profound effectiveness, the study shows that PEs’ roles in HIV/AIDS program in Vietnam seem to decrease. This observation is further supported by comparing the PEs’ roles reported in this study to those reported in the domestic literature published between 2003 and 2021. Indeed, some roles, including providing ART medication to patients who cannot go to health facilities; caring for women and children with HIV during hospitalization (Pham, 2009); referring patients with hepatitis B/C to relevant health facilities (Vu et al., 2019); referring patients to reproductive health services (Ngo, Ha, Rule, & Dang, 2013; Vu et al., 2019); and providing training and livelihood support (Nguyen et al., 2022; Pham, 2009), were no longer mentioned in this study. The remaining high demand for PEs in HIV/AIDS program is concerning as no replacement workforce is currently available.\n\nThe reduction in PEs’ roles could be explained in two ways. Firstly, there are many activities that PEs are still performing but have not been fully acknowledged, particularly in official reports. As explained by key informants, the current reporting requirements primarily emphasize quantitative indicators, including the number of people reached, at-risk cases tested, people tested, and those treated with ART rather than considering other activities that PEs performed. Secondly and more importantly, it is due to increasing challenges related to insufficient funding, inadequate training, lack of recognition, and stigma, as described in this study and other research (Khoat et al., 2003; Nguyen et al., 2022).\n\nThe lack of recognition was a profound challenge that linked to other difficulties. PEs’ roles and cost norms for peer-driven activities were only mentioned in Circular 163/2012/TTLT-BTC-BYT (2012-2015 period) (Ministry of Finance & Ministry of Health, 2012) and Circular 26/2018/TT-BTC (2016-2020 period) (Ministry of Finance, 2018). Since the national HIV/AIDS program was no longer the national target health program (Prime Minister, 2017), no updated guidance for peer-driven activities was promulgated, creating difficulties in allocating the state budget for those activities. Insufficient funding, coupled with decreasing international funding, created tremendous challenges in recruiting enough PEs to serve the increasingly hard-to-reach population, providing proper training for PEs to work effectively in the changing environment, and equipping them with adequate resources for their work. To address the challenges, some provincial CDCs have piloted signing social contracts with CBOs in selected peer-driven interventions (e.g., referral to HIV testing services, ART/PrEP treatment, and treatment support). By signing contracts with CBOs, provincial health authorities could grant PEs higher recognition. This study helps to provide local authorities with evidence of PEs’ roles to tailor the specific roles and responsibilities of PEs in those contracts. However, further investigation should be done to investigate the piloting results, the methods to measure PEs’ performance, and the payment mechanism to effectively and sustainably engage this workforce in HIV/AIDS interventions.\n\nThe study limitation lies in the study setting. We could only include seven provinces; thus, some activities of PEs, such as “training and livelihood support,” may not be vigorously carried out in these provinces. Besides, the cross-sectional survey only included a very small group of female-sex-worker- PEs. This may lead to underestimating some specific PEs’ roles related to FSW.\n\nIn conclusion, PEs have performed dynamic roles in HIV/AIDS prevention and control in Vietnam. Prominent roles are primarily related to identifying and referring customers to HIV testing services, performing communication and education activities, and referring patients to treatment. Despite its effectiveness, the decreasing roles of PEs seem not to meet the healthcare providers’ high demand. To maintain their roles, addressing the challenges of inadequate funding and training, lack of recognition, and remaining stigma issues is essential.\n\nApproval for this specific study, which constitutes a subset of a broader project, was obtained from the Ethical Review Board for Biomedical Research at Hanoi University of Public Health, Vietnam, under reference No. 148/2020/YTCC-HD3 dated April 13, 2020. This approval extends to all studies conducted within the encompassing project. Written consent was obtained from all participants.", "appendix": "Data availability statement\n\nZenodo: Roles and current challenges of peer educators in delivering HIV/AIDS-related services in Vietnam: a dataset. https://doi.org/10.5281/zenodo.12168661 (Hua Thanh Thuy, 2024b).\n\nThis project contains the following underlying data: A raw dataset of the present study that contains answers from all respondents.\n\nRequests to access these data should be directed to the corresponding author, who will need to obtain approval from the funding organization prior to sharing any data.\n\nZodeno: Roles and current challenges of peer educators in delivering HIV/AIDS-related services in Vietnam: a supplementary file. https://doi.org/10.5281/zenodo.12176131 (Hua Thanh Thuy, 2024a).\n\nThis project contains the following extended data: A supplementary file that contains the survey questionnaires and the instruction for qualitative interviews.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgments\n\nWe would like to thank and acknowledge the participation of health staff and peer educators in Hanoi, Son La, Thai Nguyen, Thua Thien Hue, Lam Dong, Khanh Hoa, and Kien Giang.\n\n\nReferences\n\nBerg RC, Page S, Øgård-Repål A: The effectiveness of peer-support for people living with HIV: A systematic review and meta-analysis. PLoS One. 2021; 16(6): e0252623. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCuong DD, Sönnerborg A, Van Tam V, et al.: Impact of peer support on virologic failure in HIV-infected patients on antiretroviral therapy - a cluster randomized controlled trial in Vietnam. BMC Infect. Dis. 2016; 16(1): 759. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGo VF, Frangakis C, Le Minh N, et al.: Effects of an HIV peer prevention intervention on sexual and injecting risk behaviors among injecting drug users and their risk partners in Thai Nguyen, Vietnam: A randomized controlled trial. Soc. Sci. Med. 2013; 96: 154–164. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHe J, Wang Y, Du Z, et al.: Peer education for HIV prevention among high-risk groups: a systematic review and meta-analysis. BMC Infect. Dis. 2020; 20(1): 338. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHua Thanh Thuy: Roles and Current Challenges of Peer Educators in delivering HIV/AIDS-related services in Vietnam: a supplementary file.2024a.\n\nHua Thanh Thuy: Roles and Current Challenges of Peer Educators in delivering HIV/AIDS-related services: a case study in Viet Nam [Data set]. 2024b.\n\nKerrigan DJ: Peer education and HIV/AIDS: Concepts, uses and challenges. Geneva: UNAIDS; 1999.\n\nKhoat DV, West GR, Valdiserri RO, et al.: Peer education for HIV prevention in the Socialist Republic of Vietnam: a national assessment. J. Community Health. 2003; 28(1): 1–17. PubMed Abstract \| Publisher Full Text\n\nMinistry of Finance: Circular 26/2018/TT-BYT dated 21/03/2018 Prescribing management and use of state expenditure on implementation of health population target program in the 2016-2020 period.2018.\n\nMinistry of Finance, & Ministry of Health: Circular 163/2012/TTLT-BTC-BYT dated 8/10/2012 approved the regulations for management and use of fund for implementation of the national target program for HIV/AIDS prevention and control period 2012-2015. Vietnam; 2012.\n\nMwai GW, Mburu G, Torpey K, et al.: Role and outcomes of community health workers in HIV care in sub-Saharan Africa: a systematic review. J. Int. AIDS Soc. 2013; 16(1): 18586. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNgcobo S, Scheepers S, Mbatha N, et al.: Roles, Barriers, and Recommendations for Community Health Workers Providing Community-Based HIV Care in Sub-Saharan Africa: A Review. AIDS Patient Care STDs. 2022; 36(4): 130–144. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNgo AD, Ha TH, Rule J, et al.: Peer-based Education and the Integration of HIV and Sexual and Reproductive Health Services for Young People in Vietnam: Evidence from a Project Evaluation. PLoS One. 2013; 8(11): e80951. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNguyen HT, Nguyen AQ, Khuat OH, et al.: Impact of the COVID-19 pandemic on provision of HIV/AIDS services for key populations. Int. J. Health Plann. Manag. 2022; 37(5): 2852–2868. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPham PM: The Emergence of Peer Groups in Vietnam. ScholarBank@NUS Repository; 2009. Reference Source\n\nPham PM, Pham QL, Le MG: Diversity of activities: The operation of community-based organizations in HIV/AIDS in contemporary Vietnam. Int. J. Prev. Med. 2022; 32(4): 64–73. Publisher Full Text\n\nPrime Minister: Decision 1125/QD-TTg dated 31/07/2017 approved the national target program on health and population period 2016-2020. Vietnam; 2017.\n\nPrime Minister: Decision 1246/QD-TTg dated 14/08/2020 promulgated National Strategy to end the AIDS epidemic by 2030. Vietnam; 2020.\n\nSabin LL, Semrau K, DeSilva M, et al.: Effectiveness of community outreach HIV prevention programs in Vietnam: a mixed methods evaluation. BMC Public Health. 2019; 19(1): 1130. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nVAAC: A study report: Towards the sustainability of civil society organizations.2018. Reference Source\n\nVu BN, Green KE, Thi Thu Phan H, et al.: Lay provider HIV testing: A promising strategy to reach the undiagnosed key populations in Vietnam. PLoS One. 2019; 13(12): e0210063. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nVu MQ, Chung A, Hoang TL, et al.: HIV in Vietnam: the evolving epidemic and the prevention response, 1996 through 1999. J. Acquir. Immune Defic. Syndr. 2000; 25(4): 360–369. PubMed Abstract \| Publisher Full Text" }	[ { "id": "301784", "date": "16 Aug 2024", "name": "Ann-Margaret Dunn Navarra", "expertise": [ "Reviewer Expertise HIV", "peer-led community level interventions", "Health equity", "paediatric/adolescent health" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThank you for the opportunity to review this highly significant research and scholarship. This work is of high significance for reaching target goals to end the HIV epidemic. I made a number of comments below to provide support in further development and refinement of this important research.\nBackground and Significance: Robust evidence is provided to demonstrate the disparities in HIV acquisition among high-risk groups and the relevance of peer educators in Vietnam. I would suggest adding some more data/evidence on current prevalence/incidence of HIV and a brief description of the health system (as part of providing context on barriers – i.e. economic burdens). Two citations provided below. I also suggest operationalizing the role of a peer educator for the purposes of this study. Given the heterogeneity in the role and function, I do believe that this definition is key for this study.\n\n[1],[2].\n\nMethods: This study is described as a mixed-methods design with quantitative surveys conducted first. I recommend being more specific – i.e. explanatory sequential design. I also recommend providing a rationale on the mixed-methods design and describe how the data was triangulated. This NIH resource is quite helpful – and may serve as a resource. https://obssr.od.nih.gov/research-resources/mixed-methods-research\nConceptual underpinnings: Was there a framework or model applied in the development of this research?\nData collection: please provide some more details on how virtual qualitative interviews were conducted (phone, zoom). Who conducted these interviews, was an interview guide used? I suggest providing more specifics on the qualitative data analysis including method (i.e. content analysis), transcription, coding, software (if any used), sample size (was saturation reached), etc.\nAlso suggest adding content related to the quantitative survey including the number of survey items, psychometric data (if available), time to administration. Is there a copy of the quantitative survey that could be added as an appendix?\nResults: Table 3 presents themes. However, it seems that these themes are extracted from the quantitative survey. Were there any common themes that emerged from the qualitative data? If so, how does the qualitative and quantitative data compare or contrast? Please address triangulation if a mixed-methods approach will be used.\nDiscussion: Given that financial resources and funding is a major challenge to increasing the peer educator role for people living with HIV, what are some potential strategies to help mitigate these barriers. For example, would mobilization using technology (smartphone with videoconferencing, text messaging) increase patient access and reach without increasing cost? Technology could also be used to help train peer educators. Other considerations for the discussion include targeted strategies to reach female sex workers – given the low survey response of 9.5%.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? No\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] } ]	1	https://f1000research.com/articles/13-707
https://f1000research.com/articles/12-1183/v1	21 Sep 23	{ "type": "Research Article", "title": "Technology integration during teaching and learning: the COVID-19 context", "authors": [ "Awelani V. Mudau", "Lettah Sikhosana", "Lettah Sikhosana" ], "abstract": "Background: The aim of this paper was to explore how the Fourth Industrial Revolution shapes teaching and learning during COVID-19 in some of the schools located in the Gauteng and Mpumalanga provinces, South Africa. This paper employed qualitative interpretative multiple case study design. Purposive sampling was used to sample our participants. Methods: We selected four teachers who separately taught at the early childhood development stage, intermediate phase, senior phase, and further education and training phases. Data was collected telephonically through semi-structured interviews with teachers from Limpopo, Gauteng and Mpumalanga provinces of South Africa. Data was collected from their experiences of COVID-19 from 2019 to 2021. Collected data was analysed using a typology approach whereby themes that derived from the literature reviewed and research questions were used. Results: We inferred from the results of the paper that teachers had challenges with teaching and availability of learning resources, such as limited access to internet and socio-economic backgrounds, which hindered the integration of the Fourth Industrial Revolution in the teaching and learning process. There were also challenges related to teachers’ background on the usage of the Fourth Industrial Revolution and the lack of school management teams support. The paper revealed that the integration of the Fourth Industrial Revolution in teaching and learning was affected negatively by the existence of the above-mentioned challenges, which needs to be addressed. Conclusions: Therefore, we recommended that the government and stakeholders within the education sector provide resources such as smart-boards, computers, and network access in schools lacking such facilities, as well as providing professional development interventions and training teachers to have an in-depth understanding of the Fourth Industrial Revolution within the teaching and learning context.", "keywords": [ "Fourth Industrial Revolution", "School Management Teams", "Integration", "Blended learning." ], "content": "Introduction\n\nThe effect on the COVID-19 pandemic has exposed a number of imbalances in the South African education system. COVID-19 also showed the impediment of teacher and learner knowledge in digital learning and teaching in this Fourth Industrial Revolution (4IR) era as most of the learners were unable to use these technological devices. Whereas teachers also were afraid to explore the possibilities of teaching using the technology just like some of their learners. Davis (2016) defines 4IR as “the fusion of technologies that is blurring the lines between the physical, digital, and biological worlds”. The pedagogical knowledge during teaching practice becomes the contested phenomenon in the era of the 4IR.\n\nInadequate technological or digital knowledge negatively affects the existing South African Curriculum and Assessment Policy Statement (CAPS) subjects, despite the attempt at introducing the evolution of 4IR as part of the school curriculums. The stakes of knowledge possession in education during the 4IR era is high and is the prevailing phenomenon for an effective digital teaching during Education and Information Technologies (Grossman, 2018). Moreover, Mpungose (2016) agrees with Nkambule and Mukeredzi (2017) that having adequate technological teaching knowledge in the field of education leads to advanced ways of knowing the subject content, pedagogical strategies, and digital resources that are appropriate and needed.\n\nOne of the key rules of the COVID-19 pandemic, which is the social distancing, has compelled the teaching process to take a form of a virtual classroom or online interactive forum, or digital ways that includes; Microsoft teams teaching, google classroom teaching, telegram teaching, WhatsApp teaching, zoom teaching, and hub teaching (Mpungose, 2019). The hub digital system is when one of the classroom at school is used as a center to connect digitally, the other classrooms where learners are seated in view of observing all the covid-19 rules to combat the spread of the corona virus.\n\nCurrently, there is no available model or empirically based report that shows positive correlation between closure of schools and curbing of the spread of COVID-19 (Viner et al., 2020). However, the recent developments in technology 4IR demand more intimate technological knowledge about more advanced digital technologies, such as the internet and digital video (Schäfer, 2018). Schwab (2016) resists that 4IR is influenced by a much more advanced knowledge on a universal and internet, by smaller and more powerful sensors that have become cheaper, and by artificial intelligence and machine learning. As a result, this paper explored how the 4IR shaped teaching and learning during the COVID-19 pandemic in some of the schools located in Gauteng and Mpumalanga province, South Africa.\n\nCOVID-19 is a contagious disease caused by a new virus known as SARS-CoV-2 (World Health Organisation [WHO], 2020). This novel disease was originally known in China in Wuhan city in 2019. Mahaye (2020) indicates that South Africa has its first confirmed case of COVID-19 on 5 March 2020 and, within a month, the total of infected cases increased to 1,585. As of 23 April 2020, the number of confirmed cases in South Africa increased to 3,953 with 75 related deaths. COVID-19 is spread from one person to another through respiratory droplets that are expelled when an individual with the disease sneezes, coughs, or talks (Centers for Disease Control and Prevention [CDC], 2020).\n\nThus, medical specialists suggested social distancing as a means of containing the transmission of the dreaded virus (CDC, 2020). Mahaye (2020) states that the rapid spread of the pandemic in several countries of the world led to the temporary closure of schools at all levels of learning. The global statistics has it that above1.6 billion of youngsters have been out of school due to the abrupt and short-term closure of institutions (World Bank, 2020). The aftermath of the school closure propelled governments across the world to embrace distance learning to curtail the spread of the virus and enable home learning despite the virulent pandemic.\n\nThus, the World Bank (2020) is working relentlessly to support Ministries of Education to offer online learning to various institutions of learning during the ravaging pandemic. All schools in South Africa were temporarily closed down on 27 July 2020 during the pandemic rise and alternative methods of teaching such as blended learning was effectively introduced to the school systems to allow learners’ access to education during the lockdown period (Mahaye, 2020).\n\nThe World Economy Forum (2018) indicates that 4IR connotes technological innovation that shapes the boundaries between physical, biological, and digital worlds. Kayembe and Nel (2019) also state that 4IR is based on the present digital revolution that leads to the creation of fresh opportunities and possibilities for society. Erboz (2017:2) contends that the components of 4IR include the Internet of Things (IoT), Cyber-Physical Systems, Internet of Services, and Smart Factory. Other components are artificial intelligence, three-dimensional (3D) printing, robotics, block chain technology, cryptocurrency, quantum computing, nanotechnology, and bioengineering. Universally, cloud-based platforms like Zoom, Google Hangouts, and WebEx, are useful for teachers and learners to complete their tasks from home during the pandemic. Beetham and Sharpe (2013) indicate that digital technology promotes interactions between teachers and learners thereby transforming the teaching and learning activities. However, Rashid and Asghar (2016) found that there is insignificant impact of digital technologies on learners’ academic performance.\n\nKayembe and Nel (2019) found that the education system in South Arica is facing some challenges during 4IR implementation. The challenges are inadequate funding, infrastructure, and adequate skills needed for 4IR implementation. The teachers’ challenges are in the areas of pedagogical adaptation, teacher development and infrastructure for technological innovation (Kayembe and Nel, 2019). The 4IR provides the following opportunities such as:\n\n• Provision of an environment of creativity and innovations (Kayembe and Nel, 2019).\n\n• The application tends to solve social exclusion issues (Chetty and Pather, 2015:5) on how the gaps between the rich and poor can be closed as well as among the racial differences.\n\n• The 4IR provides opportunities for the education systems to collaborate with government and private establishments (Kayembe and Nel, 2019). Thus, based on the opportunities, the 4IR therefore, requires schools to prepare learners effectively with the necessary tools for innovation to solve immediate and future challenges in society.\n\nThe COVID-19 pandemic led to temporary school closure that drastically affects the academic calendar (Mhlanga and Moloi, 2020). In order to minimise the rate of academic disruptions by the nationwide lockdown, several institutions of learning embark on online programmes (Mhlanga and Moloi, 2020). Before the pandemic, not all teachers in South Africa had the required training in line with the new technology to support blended or online learning (The Conversion, 2020). The temporary closure of schools by the Ministry of Basic Education compelled teachers to adjust to the new technology to forestall any impediment to learning activities (Jantjies, 2020). The teachers in South African schools had to provide adequate support to learners using online resources and face-to-face discussions on platforms like Zoom, WhatsApp, and Google apps for video calls (Jantjies, 2020). The teachers had to supplement learning by the use of educative programmes on Radio and television (Kuwonu, 2020). Before the pandemic, the focus of South Africa was on the digital revolution in the 4IR, thus, teachers play a leading role in digital skills progress and sustainability (Jantjies, 2020).\n\nFor some years now, teachers and studies have suggested blended learning for future learning (Best, 2020). The school closure caused by the pandemic enabled the concept of blended learning to be placed into practice (Best, 2020). Mahaye (2020) defines blended learning as a technology-based teaching system that integrate a traditional teaching method with an online learning method. Also, Best (2020) defines blended teaching as an instructional strategy that uses digital approaches in combination with conventional practice in the classroom. In this concept, digital and conventional face-face teaching may support depending on the timetable. In this case, learners might take one class in the classroom and another class entirely online.\n\nThe blended learning normally occurs in tertiary institutions. This concept can be defined as the combination of the traditional and online learning methods (Dziuban et al., 2018; Hrastinski, 2019). Its use involves learners and teachers within the classroom where face-to-face instruction is carried out. Besides, blended learning is described as the total means of teaching and learning that involve traditional face-to-face classroom methods of instruction with online learning (Siemens, Gasevic, and Dawson, 2015). The recent lockdown has propelled teachers to implement online, blended learning teaching practices. Oliver (2020) reports that almost 10% of homes in South Africa have access to an internet connection. Limited schools implemented blended learning before lockdown and few schools adopted it in the lockdown period. Thus, schools with inadequate resources as well as required skills are redundant.\n\nThis paper was guided by the need to explore how the 4IR shaped teaching and learning during the COVID-19 pandemic in some of the schools located in Gauteng and Mpumalanga province, South Africa.\n\nThe following are the research questions that guided this paper:\n\n1. How does the teacher understanding of 4IR and COVID-19 shape the integration of 4IR in teaching and learning?\n\n2. What was the role of school management teams in the integration of 4IR in teaching and learning during COVID-19 pandemic?\n\n3. What are the challenges and opportunities provided by the 4IR during the COVID-19 within the context of education?\n\n\nMethods\n\nThe Unisa College of Education ethics review committee approved this study (Ref: 2021/06/09/51994186/17/AM). Written informed consent was obtained from participants prior to data collection. The records are available from the authors.\n\nThe theoretical framework for this paper was based on constructivism theory. According to Vygotsky, social constructivism propounds that people play an active role in creating their knowledge (Schreiber and Valle, 2013). Vygotsky’s theory is based on the social construct that learning takes place in social groups (Schreiber and Valle, 2013). He established a learning model that enables the teachers to be very active so that they will lead the learners to develop their understanding in the way they think. Vygotsky discovered the Zone of Proximal Development concept (ZPD) that explains what learners can do, build, understand, and learn when they get help.\n\nConstructivism theory is a vital theory that is used in the education system. This theory utilised technology to serve constructivism principles theory. Constructivism theory was used to guide this paper as it involved the integration of 4IR in the teaching and learning. Constructivism theory has assisted the researchers in exploring teachers’ understanding of 4IR, role of SMT in the integration of 4IR as well as the challenges and opportunities in the integration of 4IR in the teaching and learning. Constructivism believes that learners should be actively involved in learning while the teachers’ role is to assist the learners in their learning activities (Williams, 2018).\n\nIn this paper, the constructivist approach was utilised in online teaching and learning activities during the COVID-19 pandemic since access to face-to-face traditional teaching methods was not possible. These teaching and learning activities involved using mobile phones and laptops to access Google classrooms, Zoom, Microsoft Teams, and WhatsApp applications. These applications enable teachers and learners to engage themselves in knowledge construction. By using constructivism theory, the researchers were able to evaluate whether the teachers do have appropriate understanding in support of the teaching and learning through 4IR. Hence, teachers with appropriate knowledge supporting integration of 4IR understood that 4IR comprises of technology, internet and electronic devices.\n\nIn this context, teachers and learners were actively involved in the teaching and learning, as it will require the use of technology. According to Kaur (2017) in constructivist perspectives, teachers play the role of a facilitator by guiding and motivating the learners. As a result, for teachers to be able to facilitate their role in the teaching and learning through integration of 4IR, support from district officials and SMT will be required in order for learners to receive quality education. Kaur (2017) reported that teachers ensure a conducive learning environment that will enable the learners to become effective thinkers. Nevertheless, effective teaching and learning through integration of 4IR requires adequate teaching and learning resources such as smartboards, computers as well as internet access.\n\nThis paper followed a qualitative interpretative multiple case studies design. We employed a case study design in order to provide rich descriptions of how 4IR shaped the teaching practices of teachers during the COVID-19 pandemic. We considered a case study design to be appropriate for this paper as it enabled us to gain concrete, contextual, in-depth knowledge about the phenomenon under exploration (McCombes, 2019). In addition, the paper also focused on the teachers’ knowledge about 4IR and the challenges that teachers’ experienced when teaching during the COVID-19 pandemic in their school setting. Multiple case studies design was used, as the target group was four teachers from Gauteng and Mpumalanga provinces.\n\nThe sample of this paper consisted of four teachers; two teachers taught in schools located in the Gauteng province, one teacher taught in a school located in Limpopo province and one teacher taught in the school located in Mpumalanga province. The participants were identified purposefully as they taught in different school context, in an essence such that their contexts ranged from technical, independent, and government schools which we used as our selection criteria. The participants were contacted telephonically as they are our acquaintances to participate in this paper. By using a purposeful sampling, the researchers managed to include four cases according to relevant criteria, such as teachers offering teaching in any phase of school located in Gauteng, Limpopo and Mpumalanga province. Although the sample size is small, in qualitative research it is not foreign. The advantage is that it allows the in-depth analysis of the case studies. According to Crossman and Nicki (2020), purposive sampling in qualitative research is a non-probability sampling method, which researchers selected, based on the population characteristics and the aim of this paper. The selected participants had assisted the researchers in answering the proposed research questions and achieving the aim of this paper. Consequently, it was not necessary for researchers to collect data from each teacher from selected provinces in order to acquire valid findings.\n\nThe four teachers that participated in this paper were three females and one male. We used keywords and symbols for each participant. The four participants were referred to as P1/F/46/TS, P2/M/40/TS, P3/F/26/PS, and P4/F/25/GS. These symbols represent participant number, gender, age, and the nature of the school. The first two participants who were referred to as P1/F/46/TS and P2/M/40/TS were based in Limpopo province but they are currently working in Gauteng province. Three participants were teaching at the Senior and FET phase whereas one participant was teaching foundation phase and all participants were qualified to teach the subjects they were currently teaching. Moreover, the participants have different teaching experience. Table 1, below, summarises participants’ demographic details:\n\nData of this paper was collected telephonically using a semi-structured interviews tool. The entire interview with each participant was in English and was audio-recorded. The rationale for this data collection method was for convenience purposes as the telephonic interviews offered an opportunity to probe. The interviews were conducted in October to November 2021. Participants’ permission was requested by researchers prior to interview in order to ensure reliability and to avoid a mix-up of data collected during the process of analysing data. The semi-structured interview is a qualitative data collection technique where researchers prepared questions to ask the participants in advance. Additionally, in a semi-structured interview, interviewers do not necessarily follow a formalised list of questions but ask open-ended questions which allow for discussions with the interviewee (Doyle, 2017).\n\nThe interview tool was used to collect data based on teachers’ knowledge about the 4IR in education, teacher understanding of COVID-19 pandemic, teaching and learning experience during pandemic, challenges and opportunities in integrating 4IR in teaching and learning. The recording device, i.e., audio recorder was used to capture the data of the entire interview process and researchers ensured that the participants were asked the same open questions. We developed the tool based on our research questions and the context of the study. The questions were validated by the authors. We piloted them with one of the teachers who was not part of the research.\n\nValidity in qualitative research rest on the accuracy of instrument suggested for data collection, processes and data collected from participants (Leung, 2015). To ensure validity in this paper, a pilot study was conducted with one teacher who was not part of the main paper where semi-structured interview tool was tested to ensure it was valid. What we found from this pilot study was that some of the questions were not clear in terms of the language and content and we had to change them. Again the interview was too long and as we were using telephone interviews we had to reduce the questions to avoid being cut off. This participant was identified purposefully for the pilot study and was contacted telephonically as he was our acquaintance. By using a purposeful sampling, the researchers managed to include four cases according to relevant criteria, such as teaching in different school contexts in schools located in Gauteng, Limpopo and Mpumalanga province. Although the sample size is small, in qualitative research it is not foreign. Additionally, the pilot study assisted researchers to develop and implement data analysis scheme (DAS). The researchers enhanced the validity of the data by ensuring that the statements said by participants are not changed.\n\nThe data attained from four cases were analysed and interpreted separately. Researchers transcribed audio-recorded semi-structure interviews verbatim, to a word document. After transcribing data from the audio-recordings to word documents, the researchers replayed the audio in order to check if the words transcribed corresponded with what was on the audio thereafter they were destroyed. Moreover, researchers did not correct any grammatical errors of the participants. This was done to ensure that data collected was presented accordingly and did not lose its original meaning. Hence, the data that the researchers transcribed was communicated to relevant participants before being considered as final product.\n\nThe data collected was presented in the form of case studies i.e., case 1, case 2, case 3, and case 4. The data of this paper was analysed using Data Analysis Scheme (DAS), which was confirmed during piloting. McMillan and Schumacher (2010) report that inductive analysis is a process in which qualitative researchers synthesise and extract meaning from the data by deriving categories and patterns from specific data. The data was analysed using a typology approach whereby themes that derived from the literature reviewed and research questions were used. The following are the themes derived from the literature reviewed and research questions.\n\n➢ Understanding of 4IR and coronavirus pandemic (COVID-19) by teachers (it was necessary to understand the teachers’ perspectives of what 4IR is as well as the coronavirus pandemic as it was not going to do justice to the study to simple found out how technology was integrated without comprehending their perspectives)\n\n➢ The role of the School Management Team (SMT) during the COVID-19 pandemic within 4IR context (in integrating technology it was important for the researchers to find out the nature of the role of the school management teams during the coronavirus pandemic)\n\n➢ The challenges provided by the COVID-19 within the 4IR context of education (this focus on what is it that was hindering them when using or wanting to use technology)\n\n➢ The opportunities provided by the COVID-19 within the 4IR context of education ( this focused on what opportunities were there for the teachers to integrate the 4IR)\n\nAdditionally, only data related to themes suggested for this paper were considered and assisted researchers in responding to the research questions and fulfilling the aim of this paper.\n\n\nResults\n\nThe results of each case were presented separately as a single case as our intention was not to conduct comparative research but to have an in-depth understanding of each case within their own context (Mudau, 2023a, 2023d). We used the following keywords and symbols to present cases of each participant:\n\nParticipant 1/Female/46/technical school= P1/F/46/TS\n\nParticipant 2/Male/40/technical school= P2/M/40/TS\n\nParticipant 3/Female/26/Private school= P3/F/26/PS\n\nParticipant 4/Female/25/Government school= P4/F/25/GS\n\nThe following became our themes:\n\n• Understanding of the 4IR and coronavirus pandemic (COVID-19) by teachers.\n\n• The role of School Management Team (SMT) during the COVID-19 pandemic in the 4IR within the context of education.\n\n• The challenges provided by COVID-19 within the 4IR context of education and the opportunities provided by the COVID-19 pandemic within the 4IR context of education.\n\nTheme 1: Understanding of 4IR and coronavirus pandemic (COVID-19) by teachers\n\nFor the purpose of this paper, we had to ask the teacher about her understanding of 4IR and COVID-19 within the context of the teaching and learning process. During the interview process, we noted that the teacher had an idea of what 4IR entails, as she was able to highlight some of the aspects that enables the integration of 4IR. She indicated that 4IR entails technology, internet, and electronic devices. This was evident in the statement from the interview below:\n\n“Eh according to my understanding Fourth industrial revolution concerning teaching and learning. Is when the learners are learning through eh technology or internet or electronic devices that’s my opinion.” P1/F/46/TS.\n\nWe had to ask further as to what she understands about the ‘4IR’ abbreviation. She indicated that 4IR stands for “Industrial Revolution” which was incorrect in this context. This led us to probe about her understanding of COVID-19 as this shaped how 4IR is integrated in teaching and learning. However, the teacher could not explain what COVID-19 is but she was able to describe some of the COVID-19 regulations that she had to adhere too, such as using hand sanitisers and maintaining social distancing in her classroom. She indicated that:\n\n“When I entered the classroom I had to sanitise I had to do anything that can be done eh following the protocol that they have given us and the learners were coming in twenties eh they were only 20 in the classroom.” P1/F/46/TS.\n\nTheme 2: The role of the School Management Team (SMT) during the COVID-19 pandemic within 4IR context\n\nThe SMT plays an important role in ensuring that there is quality of teaching and learning in school. As a result, we had to find out the role that was played by the SMT during the COVID-19 pandemic within the 4IR context. The teacher revealed that the SMT was not fully involved in incorporating 4IR during COVID-19 pandemic. However, the district officials introduced the 4IR initiatives at the school with the aim of teaching teachers how to use 4IR tools such as “Zoom”. Nonetheless, they failed to complete the training task. This was evident in the statement from the interview below:\n\n“Eh those people who were from the district they came and they said that they are going to train us for teams those zoom teams and what what but they failed because they only let us eh login only but they didn’t train us how to invite learners how to teach learners through those zoom teachings.” P1/F/46/TS.\n\nIt was apparent that the lack of consistency and commitment from the district officials was one of the barriers that hindered the integration of 4IR, as they did not train the teachers on how to use “Zoom” as one of the 4IR tools.\n\nTheme 3: The challenges provided by the COVID-19 within the 4IR context of education\n\nWe had to probe further on other challenges that the teacher encountered when she had to integrate 4IR during the COVID-19 pandemic. Based on our findings, the teacher encountered numerous challenges to an extent that she ended up classifying herself as a “Born before Technology (BBT)” teacher. This was a challenge because she created a negative viewpoint that older teachers are not interested in integrating 4IR, as they do not have a background of using technology or adequate knowledge and skills of 4IR. She also indicated that she did not integrate 4IR during the COVID-19 pandemic as she is teaching senior phase. She asserted that:\n\n“Eh no unfortunately no I was using chalkboard and the my chalk just because I am teaching GET or eh GET (General Education and Training phase) then which is eh senior phase which is grade 8 and 9.” P1/F/46/TS.\n\nThe teacher pointed out that the COVID-19 pandemic brought more challenges in the classroom, in relation to the matters of social distancing because learners were coming to school in groups and rotating. As a result, some groups would participate actively while other groups would not do that during her lessons. This was evident in the statement from the interview below:\n\n“So eh the problem was the learners were coming in twenties eh they were only 20 in the classroom while back then before COVID-19 in the classroom they were eh 40 or 30 something. So those 20 groups of people they were concentrating and the other group were not concentrating just because eh they were rotating according to the days that they were given too yah.” P1/F/46/TS.\n\nFurthermore, inadequate teaching and learning resources were a contributing factor to some of these challenges. The teacher indicated that they do have access to internet, but the computer laboratories are no longer useful since the COVID-19 pandemic. When asked if they all have their own personal laptops, she indicated that the Department of Basic Education (DBE) only offered the departmental laptops to Further Education and Training (FET) teachersin the school. This was evident in the statement below:\n\n“Not all of us, those who are teaching eh senior phase they didn’t get them from the department but they are having their own personal laptops. Those who are teaching FET phase each and everyone have departmental laptops.” P1/F/46/TS.\n\nSocio economic background was also a challenge that hindered the incorporation of some 4IR tools such as the creation of a WhatsApp group for the purposes of teaching and learning during the COVID-19 pandemic. We had to ask the teacher if her learners had access to smart phones. She indicated that not all of them have smart phones. As a result, it makes it difficult for her to have a WhatsApp group. This was evident in the statement below:\n\n“No. I don’t have any WhatsApp group for my learners. Eh I think learners with WhatsApp groups are grade 12s only but not grade 11, 10, 9, 8 No they do not have but only Grade 12.” P1/F/46/TS.\n\nAs the teacher had already mentioned that she did not integrate 4IR during the COVID-19 pandemic, we had to probe further whether there were other teachers that did or did not integrate 4IR in teaching and learning during the COVID-19 pandemic. We were also interested in finding out if other teachers used tools that are aligned to 4IR such as “Zoom or Microsoft Teams” or not. The teacher asserted that:\n\n“Eh in my school there are those subjects whereby the learners were taught through smartboards eh physical science, technical science, math’s and technical math’s the other subjects they were using chalkboards but even the mechanicals technology were using the smartboards but others were using eh chalkboard only I don’t think they were incorporating industrial revolution in it.” P1/F/46/TS.\n\nBased on the above statement, it was evident that the incorporation of 4IR during COVID-19 was a personal choice as there were teachers that incorporated it while others did not.\n\nTheme 4: The opportunities provided by COVID-19 within the 4IR context of education\n\nThe teacher has hope that 4IR can bring about opportunities that can make teaching and learning more effective. This was evident in the statement below:\n\n“Eh I think in order to make this teaching and learning effective eh I think we can involve learner through 4IR but because it is because this learners are interactive between their cell phones mostly they are interacted in electronic devices. But, if I can put them inside the classroom, teach them with chalkboard, and chalk ah they don’t even care they are not interested anymore but if we can eh get this eh training and involve learners through electronic devices. I think it can be effective enough just because they are interested in electronic devices and their cell phones, that’s my opinion.” P1/F/46/TS.\n\nTheme 1: Understanding of 4IR and coronavirus pandemic (COVID-19) by teachers.\n\nDuring the interview process, we asked the teacher what he comprehends about 4IR within the context of education. He described 4IR as:\n\n“Eh I’m likely to be short in terms of Fourth Industrial Revolution is when we look into the system that is used for teaching and learning. Of which you will find out that there’s no longer a direct contact of the teacher and the learner. So the system that is used is part of the Forth Industrial Revolution.”\n\nP2/M/40/TS.\n\nThe teacher displayed inadequate knowledge of what 4IR is, as he was of the impression that 4IR focuses on the system that limits direct contact between the teacher and the learner which, in this context, was a misconception. Furthermore, he explained that COVID-19 is a virus that spreads and affects the whole world. His understanding of COVID-19 was limited. This is evident in the statement from the interview below:\n\n“Eh the COVID-19 pandemic is when we talk about the spreading of the virus that affects the eh the whole country or the whole world.” P2/M/40/TS.\n\nTheme 2: The role of the School Management Team (SMT) during COVID-19 pandemic within 4IR context\n\nWe had to find out more on the roles that the SMT played during the COVID-19 pandemic towards the integration of 4IR in teaching and learning. The teacher revealed that the SMT was disorganised when it comes to the incorporation of 4IR in teaching and learning. He asserted that:\n\n“When it comes in, we had to be on lockdown for a longer period and we couldn’t set things into place. We didn’t have contacts or the devices, we didn’t train the learners how to use the devices, we didn’t have any preparations. So during that time teaching and learning was stopped in term 1. We were focusing on direct contact. So, when learners were coming back in July, a lot was wasted. Time was no longer there we had to train the learners. That process which was supposed to be prepared before so that during from March to July we were going to be able to use that teaching and learning process, but we didn’t manage to do it because we didn’t prepare on time. So the teaching and learning was very affected.” P2/M/40/TS.\n\nIt was evident that the SMT played a minimal role in ensuring that the teaching and learning was not affected. There was nothing planned or prepared to continue with the lessons and this affected the process of teaching as time was also wasted.\n\nTheme 3: The challenges provided by the COVID-19 within the 4IR context of education\n\nThere were also challenges when he had to integrate 4IR in teaching and learning. The teacher indicated those challenges in the statements from the interviews below:\n\n“The challenge that we had was that majority of learners do not have access to internet. Especially on our high school learners, they do not have data. Eh not all the learners have cell phones. In terms of integrating the learners that I was working with, the majority of them, they were able to do it on their own. But with other I had to make a phone call to them explaining what they need to do. Because if I can send them a text via WhatsApp and say press this and this they are failing to follow.” P2/M/40/TS.\n\nThe teacher revealed that not all learners have smart phones, some do not have access to internet and, even if he can incorporate 4IR in teaching and learning, it was not effective. This is so because other learners were unable to do the work given to them. As a result, the teacher will have to spend more time in using 4IR tools such as WhatsApp and phone calls to try and explain the work given to learners individually on what needs to be done and this time consuming. When using 4IR tools such as Zoom and WhatsApp, he experienced the following challenges:\n\n“So the challenge I was only having was the internet connection because if was using the zoom some were not going to be able to access zoom the time I’m presenting it. In terms of the WhatsApp, issue even if it’s the WhatsApp for the parent the parent will be at work after work.” P2/M/40/TS.\n\nAnother challenge he encountered was that some of his colleagues were reluctant in teaching online as it was based on personal interest, which led them to be resistant to change. This was evident in the statement below:\n\n“Some of the people are afraid they got this fear of attempting things that they never done before so they prefer to do the old teaching. So what I think is better is to integrate bit by bit through the training.” P2/M/40/TS.\n\nTheme 4: The opportunities provided by the COVID-19 within the 4IR context of education\n\nThe school itself had enough resources that can be used to incorporate 4IR during the pandemic but those resources were not used effectively. For instance, he revealed that the school has access to the following resources that were provided by the DBE which learners had an opportunity to access them:\n\n“The school it got eh tablets, the school also have the computer lab, the school also have the internet, and the whole school has Wi-Fi. So once learners are at school, they have access to internet.” P2/M/40/TS.\n\nWe had to find out about the opportunities that led to the incorporation of 4IR during the COVID-19 pandemic. The teacher indicated that he did incorporate 4IR in teaching and learning during this pandemic. He incorporated 4IR by the doing the following:\n\n“I implemented it by the means of using internet, there is other website where I log in as a teacher then I send in the question paper. The Grade 12 were doing online and other grades (8-9) were using WhatsApp.” P2/M/40/TS.\n\nFurthermore, he also used 4IR tools such as Zoom, YouTube, and Microsoft Teams but his preference was WhatsApp as it was conducive for his lessons and consumes less data. This was evident in the statement below:\n\n“Eh the platform that I prefer which is much quicker is WhatsApp because this one for zoom can only assist if there is something I want to introduce to them that they can’t be able to understand through WhatsApp. But the medium that I prefer is WhatsApp it’s the one that I was using the most and in terms of them to complete the task.” P2/M/40/TS.\n\nTheme 1: Understanding of 4IR and coronavirus pandemic (COVID-19) by teachers\n\nThe teacher’s understanding of what 4IR was in teaching and learning context was limited as she indicated that 4IR was introduced with a motive of making life, teaching and learning easier. However, she did not elaborate further about those aspects that are capable of making teaching and learning accessible. This was evident in the statement from the interview below:\n\n“What I understand about 4IR in teaching and learning is that it’s not reflecting the teacher but for me is making life more easier and making a teacher and the learner to teach in a new way because we are in a globalised world. So it makes it easier to make information accessible for teacher and learner in terms of teaching, as they really don’t have to be face to face in order for teaching and learning to take place. So it makes teaching easy and accessible.” P3/F/26/PS.\n\nThe teacher showed that she had an in-depth understanding of the COVID-19 pandemic. She was able to explain the origin of this virus, how it spreads, and how one can protect themselves from contracting it. She asserted that:\n\n“So the COVID-19 pandemic I’d say is a virus that uh that originates from China, like that’s the information that we have. Umm it spreads through the droplets from the surfaces, it’s a virus that has uh shows for instances that you have a flue like symptoms and then it’s respiratory if I may say so yah. In order to contain the whole virus you need to uh taking necessary precaution in place by making sure you clean up the bacteria that’s in surfaces, social distancing etc.”\n\nP3/F/26/PS.\n\nTheme 2: The role of the School Management Team (SMT) during COVID-19 pandemic within 4IR context\n\nThe SMT played an important role in ensuring that teaching and learning of the school continues uninterrupted. The teacher indicated that the SMT did not have lot of strategies at hand for introducing online lessons however with time; they were able to come up with strategies that they implemented to continue with the lessons. This was evident in the statement from the interview below:\n\n“We were working so we had to send our lesson plans on the platform called google classroom not sure if you know it. During the lockdown, we were sending lesson plans and videos to the parents. I think the school wasn’t really sure on how they would go about the online learning so I think they took two weeks to plan so during that period we would take a video with your phone and send to parents via email or phone or via the google drive so yah.”\n\nP3/F/26/PS.\n\nTheme 3: The challenges provided by the COVID-19 within the 4IR context of education\n\nShe also indicated that she faced certain challenges during the COVID-19 pandemic, which hindered her from incorporating 4IR in teaching and learning. Load shedding and poor network connection were some of the challenges she encountered. This was evident in the statement from the interview below:\n\n“Okay the bigger challenge I encounter is uh load shedding uh because in our school we obviously have to use Wi-Fi because if there’s electricity we can use Wi-Fi. There was a time where we have to cancel the lessons for the day because we didn’t have electricity so load shedding is the biggest challenge and poor network connection. So with poor network connection you can’t have a lesson.” P3/F/26/PS.\n\nTheme 4: The opportunities provided by COVID-19 within the 4IR context of education\n\nCOVID-19 pandemic brought lot of opportunities in teaching and learning. The teacher was able to incorporate 4IR in her lessons. Numerous platforms for 4IR were implemented as indicated in the statement below:\n\n“Uh I am definitely umm for me teaching in a private school we have to use technology to teach I’d say uh maybe 90% of the time. From the time, umm the pandemic started uh before we even got back to work uh we starting teaching uh our online lessons to the learners uh. How we integrated 4IR uh we had what we call zoom calls or zoom lessons sorry or lessons via google meet so that when the child logs in each learner has email address to login into our lessons, we have codes and my code for example would be math’s. I’d create slides for my lessons and then my slides would appear on the screen so I’d teach along with my slides. Uh another example is sending uh google meet not google meet uh google forms so I found out that was a very alight part coz I get immediate responses as to how learners are grasping the objective.” P3/F/26/PS.\n\nIt was evident that the COVID-19 pandemic provided the teacher with opportunities to use 4IR platforms such as technology frequently, teach online lessons, zoom lessons, google meet and google forms. This enabled the teacher to have effective lessons, as she was able to assess work given to learners using these 4IR platforms. Furthermore, she indicated that 4IR and the COVID-19 pandemic enabled teachers to bridge the gap between traditional teaching methods and online learning.\n\nTheme 1: Understanding of 4IR and coronavirus pandemic (COVID-19) by teachers\n\nDuring the interviews that were conducted with the teacher, she demonstrated that she has an idea as to what 4IR was all about. She asserted that 4IR is:\n\n“Uh for me is using Technology to make learning and teaching easier. Bringing the outside world into a classroom environment.” P4/F/25/GS.\n\nWe had to probe further to understand what she means by using 4IR to bring outside world in the classroom environment. She indicated that:\n\n“Okay for example, during the lesson. Uh let’s take for example in Mathematical Literacy we teach about budgets so there are pupils who have never seen uh for an example an ATM or a bank. So allowing them to see those pictures in a classroom makes it easier for them to relate to the outside world with what they are learning.” P4/F/25/GS.\n\nHer explanations led us to enquire what she comprehends about COVID-19. She asserted that:\n\n“Uh COVID-19 is abbreviated from Corona Virus 2019” P4/F/25/GS.\n\nTheme 2: The role of the School Management Team (SMT) during COVID-19 pandemic within 4IR context\n\nFor teaching and learning to be effective, SMT’s need to support teachers in order to achieve that goal. However, that was not the case with this teacher as her SMT was not supportive towards the incorporation of 4IR during COVID-19. In fact, based on our findings it was evident that there was no unity amongst staff members as seen in the statement below:\n\n“Eish what I observed is that school management team do not take you seriously. You don’t have a say so they just look at you like hmmm. They judge you because of our age. Hey from what I have experienced with my staffroom. Number 1 there is no teamwork or communication, everyone was doing what they thought was right for themselves and their subject. So there was no form of communication as to what can we use to better the education of all the learners in all subjects, none of them.” P4/F/25/GS.\n\nTheme 3: The challenges provided by COVID-19 within the 4IR context of education\n\nLack of support from the SMT was not the only challenge that the teacher experienced especially when she had to incorporate 4IR during the COVID-19 pandemic. We had to find out about her actual teaching experience during COVID-19. She indicated that:\n\n“Ey as a first time teacher I must say that it was the worse the worse experience. I was teaching for the first time last year and there was COVID-19. So I did not enjoy it. Plus we using the environment where we cannot use technology in our classrooms because of lack of resources. There is no electricity in our classes. There are no smart boards so it was a bit difficult.” P4/F/25/GS.\n\nShe mentioned that lack of resources and lack of electricity in the classroom were major challenges as it hindered the incorporation of 4IR, as the classrooms did not have electrical plugs. She indicated that she did not integrate 4IR during COVID-19. We further probe to find out if she did or did not use some of the 4IR tools such as WhatsApp or Facebook. She asserted that:\n\n“It did not cater for all learners. Not all of them had access to all those things. So even if some of them had access to that, when you reopen you were supposed to repeat what you said so that everyone could be catered for.” P4/F/25/GS.\n\nFurthermore, the socio-economic background of the learners served as a challenge as a majority of them came from poor backgrounds. This led us to find out the percentage of learners who have smart phones. She indicated that less than 60% of learners have access to smart phones. We had to find out about the opportunities that 4IR could bring in teaching and learning. She indicated that:\n\n“Hmm okay for teachers it will make our jobs very easier because we will stop using papers and use technology. For learners will mean that when they leave high school they will be computer literate they would have been exposed to technology more than using physical books because the world is moving towards eLearning now. It saves time as well. I believe that if our schools were well resourced it would save us time especially with photocopying and all of that.” P4/F/25/GS.\n\nTheme 4: The opportunities provided by COVID-19 within the 4IR context of education\n\nIn order for the incorporation of 4IR to be success, the teacher suggested that:\n\n“Uh okay so firstly I feel like it’s going to be important for teachers to sit down and communicate properly. Come up with strategy or method that will make it easier for us to teach and be able to finish the content in time. With regards to 4IR, hmm I feel like it’s going to be easier if examples that learners can relate too are used rather than the old way of teaching, because what I picked up is that the textbook is using old examples. So technology makes it easier for us to use new things but it’s going to be difficult because number 1 not all parents can afford to buy cell phones or laptops and I don’t think the school could resource or fund us with electricity so that we can bring laptops in our classrooms. Because at our school there’s only one classroom that has, that can be used with a projector and those learners cannot fit in that classroom.” P4/F/25/GS.\n\n\nDiscussion\n\nRamukumba (2019) described 4IR as a third revolution, which combines multiple technologies from the digital, biological and physical worlds. This is so because it provides opportunities for various countries to advance themselves through innovative technology that is driven by growth. It is the advanced technology based on communication and information (Min et al., 2019). This is similar to P1/F/46/TS who indicated that 4IR consist of technology, internet and the use of electronic devices to make teaching and learning easier. A similar perspective was given by P4/F/25/GS when she mentioned that 4IR has to do with technology used to enhance teaching and learning.\n\nThe Minister of Basic Education emphasised on the need to enhance the quality of teaching and learning in schools in order to prepare for 4IR adequately (Motshekga, 2018). Hence, it is important for teachers to have access to internet and technology in schools in order to prepare the next generation for the 4IR (Doucet et al., 2018). By doing so, teachers will be able to share skills such as innovation, critical thinking, and the ability to solve problems and collaboration rather than only focusing on technology and internet access.\n\nThe 4IR has brought numerous changes on how learners are taught and how they must learn (Ilori and Ajagunna, 2020). Hence, P3/F/26/PS had a different view regarding her understanding of 4IR where she asserted that 4IR does not reflect the teacher but it is there to make teaching and learning easier. Similar perspectives where also evident when P2/M/40/TS described 4IR as a system that is used for teaching and learning to reduce a direct contact between the teacher and a learner. This is similar to Scepanovič (2019) who revealed that 4IR has altered the way we do things.\n\nThese assertions reveals that there is still more work that needs to be done in order for teachers to have an in-depth understanding of 4IR. Hence, the President of South Africa said; “the country and teachers needed to change the direction of secondary school education to develop relevant skills to match the fourth industrial revolution” (Ramaphosa, 2019). This is so because most teachers that taught in the old system are not fully equipped on the use of computers.\n\nFor the purpose of this paper, we had to tap into what the teachers understands about the COVID-19 pandemic. A study by Cennimo (2021) defined COVID-19 as an illness that is caused by a novel coronavirus which is now referred to as acute respiratory syndrome coronavirus 2 which was first identified in Wuhan City, Hubei Province, China. This is similar to P3/F/26/PS, P4/F/25/GS, and P2/M/40/TS who indicated that COVID-19 is a virus that originates from China, which spreads through droplets from the surfaces.\n\nThis relates to who revealed that COVID-19 is transmitted through respiratory droplets (Kord, et al., 2020). There are measures such as disinfecting surfaces, wearing of personal protective equipment, lockdown, and social distancing that can be implement to assist in preventing and controlling the COVID-19 pandemic (Xiao and Torok, 2020). This is similar to P1/F/46/TS who indicated that she adheres to COVID-19 regulations such as using hand sanitisers and maintaining social distancing in class.\n\nFor the purpose of this paper, we had to understand the leadership role that is played by SMT especially during this pandemic. SMT plays an important role in giving leadership guidance, assistance and direction in teaching and learning situation (Mathipa et al., 2014). This is similar to P3/F/26/PS who indicated that the SMT did manage to provide teachers with support needed for teaching and learning even though they encountered challenges. This showed that the SMT managed to improve the quality of teaching and learning as they were able to assist teachers to continue with teaching and learning during the pandemic (Kgothe, 2013).\n\nHowever, that was not the case with P1/F/46/TS, P2/M/40/TS, and P4/F/25/GS as there was no support or guidance from the SMT. This is similar to who revealed that most SMT members have a challenge when they have to work as a team and some members do not know their roles in the SMT (Maja, 2016). As a result, this affects the management effectiveness, impacts negatively on the leadership and affect teaching and teaching.\n\nTeachers encountered numerous challenges during COVID-19 pandemic when they had to integrate 4IR during teaching and learning process. A study conducted by Kayembe and Nel (2019) revealed that lack of funding, resources and skills are major challenges that hinders the incorporation of 4IR. Connectivity is an important aspect towards successful integration of 4IR in teaching and learning but most of public schools do not have access to internet (Moyo, 2019).\n\nThis is similar to P1/F/46/TS, P3/F/26/PS, P2/ F/46/TS, and P4/F/25/GS as they mentioned that lack of teaching and learning resources, access to internet, and socio-economic background are some of the challenges that hindered the incorporation of 4IR effectively. Furthermore, Oke and Fernandes (2020) revealed that there is insufficient knowledge regarding the acceptability and consequences of the 4IR in the education sector. This is similar to P1/F/46/TS who indicated that inadequate knowledge and skills of using technology were some of the factors that hindered 4IR incorporation. Hence, Feza (2019) indicated that the incorporation of 4IR and advanced technology in teaching and learning would be a challenge on teachers who are already been overworked.\n\nThe incorporation of 4IR in teaching and learning process has developed many opportunities for teachers, such as the use of google in classroom situation, which has replaced the teacher as the oracle of knowledge (Naude, 2019). This is similar to P3/F/26/PS who indicated that Google meet were one of the tools that contributed successfully in the integration of 4IR during the COVID-19 pandemic. This clearly indicates that 4IR has opened up new opportunities that allows new and innovative solutions to problems (Munasi and Madikizela-Madiya, 2020). This is so because P1/F/46/TS, P2/M/40/TS, P3/F/26/PS, and P4/F/25/GS indicated that 4IR tools such as smartboards, Google meets, WhatsApp, Zoom, YouTube, Microsoft Teams and Zoom were used to integrate 4IR during the COVID-19 pandemic. Hence, it is important for schools to be equipped for teaching with and 4IR (Musgrave, 2019).\n\nTherefore, it is recommended that the government should develop interventions in training of the teachers for professional development in the usage of 4IR for teaching and learning activities. These will enable the teachers to be more skillful and competent in the implementation of 4IR technology. Furthermore, adequate support is also required from the government and stakeholders in the education sector concerning the supply of resources such as smartboards, computers, and network access in schools lacking such facilities. The limitations of this paper is that the sample was small but the advantage is that the findings can be inferred to similar cases. Only one data collection technique was used.\n\n\nConclusion\n\nThese findings of this paper ranged from lack of teaching and learning resources, access to internet and socio-economic background, which were some of the challenges, hindered the integration of 4IR in the teaching and learning process. There were also challenges related to teachers’ background on the usage of 4IR and lack of SMT support during COVID-19. This paper diagnosed that integration of 4IR in the teaching and learning was negatively affected by the existence of the above-mentioned challenges, which need to be addressed.", "appendix": "Data availability\n\nFigshare: CASE 1 4IR TRANSCRIBED DATA.docx. https://doi.org/10.6084/m9.figshare.22664680.v2 (Mudau, 2023a).\n\nThe project contains the following underlying data:\n\n• CASE 1 4IR TRANSCRIBED DATA.docx. (Anonymised transcription of interview with participant 1 - P1/F/46/TS).\n\n• CASE 2 4IR TRANSCRIBED DATA.docx. (Anonymised transcription of interview with participant 2 - P2/M/40/TS).\n\n• CASE 3 4IR TRANSCRIBED DATA.docx. (Anonymised transcription of interview with participant 3 - P3/F/26/PS).\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nFigshare: Case 4. https://doi.org/10.6084/m9.figshare.22775678.v1. (Mudau, 2023d).\n\n• CASE 4 4IR TRANSCRIBED DATA.docx. (Anonymised transcription of interview with participant 3 - P4/F/25/GS)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nFigshare: interview schedule. https://doi.org/10.6084/m9.figshare.22664740.v1 (Mudau, 2023b).\n\nThis project contains the following extended data:\n\n• Interview schedule.pdf. (Interview questions used in this study).\n\nFigshare: SRQR checklist for ‘Technology integration during teaching and learning: the COVID-19’. https://doi.org/10.6084/m9.figshare.22664818.v1 (Mudau, 2023c).\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nBeetham H, Sharpe R: Rethinking Pedagogy for Digital Age: Designing for 21st century Learning. Appollon, UK: Routledge; 2013.\n\nBest J: How to use Blended Teaching in Your classroom.2020. Reference Source\n\nCenters for Disease Control and Prevention: COVID-19 & IPC overview.2020.\n\nCennimo DJ: What is COVID-19?2021. Reference Source\n\nChetty R, Pather S: Challenges in higher education in South Africa.Condy J, editor. Telling Stories Differently: Engaging 21st century students through digital story telling. Stellenbosch: SUN MeDIA; 2015.\n\nCrossman A, Nicki LC: Understanding Purposive Sampling. ThoughtCo;2020. pp. 1–2. 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PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "226456", "date": "14 Feb 2024", "name": "Layane Thomas Mabasa", "expertise": [ "Reviewer Expertise My areas of expertise are in research methodology", "Educational leadership and governance" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nReviewer Report F1000 Research Journal Title: Technology integration during teaching and learning: the COVID-19 context\nIntroduction\nThis report is composed of the different aspects that are necessary for decision-making regarding the readiness of the manuscript to be considered for approval by the F1000 Research Journal. It outlines the introduction, the strong points, the weaknesses, and the approval status.\nStrong points of the manuscript\nEven though the manuscript has several weaknesses which will be outlined later, it has strong points. The strong points are that: The abstract is in line with the journal's expectations. There is consistency in terms of how sources have been referenced. There is an attempt by the authors to use current literature. Verbatim quotations of the responses from the participants have been used to give voice to the participants. The manuscript is within the scope as it focuses on technology integration during teaching and learning in the context of the COVID-19 pandemic.\n\nWeak points of the manuscript\nSome weaknesses need to be addressed to improve its quality and by the F1000 Research Journal. Weaknesses are that: The title seems to suggest that the study is about technology integration during teaching and learning, whereas in the text, the focus is on the Fourth Industrial Revolution (4IR). The question that arises will be “Is technology integration during teaching and learning the same as the Fourth Industrial Revolution (4IR)?” The authors need to explain and align the title accordingly. The claim made in par.2, sentence no.1 under Introduction needs to be supported by a source. The manuscript can benefit from another editing phase. For example, the spelling of “South Arica” in par.2, sentence no.1 under Fourth Industrial Revolution (4IR) needs to be written as “South Africa”. There is a need to use past tense in sentence no.1, par.1 under Effects of COVID-19 pandemic in the teaching and learning process. The word “affects”, needs to be written as “affected”. The last but one sentence under the Blended learning approach during the COVID-19 pandemic needs to be edited. Sentence no.2 in par.2, under Theoretical framework, is not clear. It needs to be rephrased. Sentence no.1 in par.4 under Theoretical framework is not clear. It needs to be rephrased. There is a need to edit sentence no.2 in par.2 under The role of the School Management Team during the COVID-19 pandemic with 4IR context. The authors under Research Design and Methodology, indicate that the manuscript is based adopted a multiple case study design for use in the study. However, there is no indication of how the study is a multiple-case study. The four teachers' participation does not mean that this is a multiple-case study. The question that arises is what is the case in this study? The participants in this context are not cases. The case seems to be the integration of technology during teaching and learning and not the teachers. The authors may also improve this section by indicating how the constructivism theory guided them to adopt the semi-structured interviewing tool for use to generate data. They can also indicate settings where interviews were held, challenges, and how they dealt with the challenges. There is a need to explain ethical issues in detail. The authors may add respect, dignity and care, benefits, risks, and harm, privacy and anonymity, and how data were managed and protected. There is a need to anonymise the university that issued the ethics certificate under the Ethical statement.\nDue to the nature of the study, which is qualitative, there is a need for authors to use concepts that are in line with qualitative studies. For example, instead of using the concept “validity”, authors may use “trustworthiness” which can be enhanced through credibility, confirmability, transferability, and dependability.\nThere is a need for a detailed explanation of the way in which data were analysed and themes developed. The themes listed above the sub-heading on results are four but those listed under Results are three. Is there any justification for the omission of the fourth theme Results? Authors are also advised to avoid using gender related designations like “he” or “she”. This can be done by using codes developed in line with anonymity. Furthermore, instead of discussing the responses of the participants separately, all their responses can be discussed under one theme. For example, the theme on Understanding of 4IR and coronavirus pandemic (COVID-19) by teachers, authors may indicate the responses by P1/F/46/TS, P2/M/40/TS, P3/F/26/PS and P4/F/25/GS. Where their understanding is the same, the authors may indicate that, and where their understanding is different the authors may indicate that and give an interpretation of their similarities and or differences. In its current form, the manuscript is difficult to read and makes it a bit too long.\nThere is a need to rewrite the Conclusion section of the manuscript. This can be done by indicating how research questions were answered and the aim and objectives of the study were achieved through the results and the findings of the study. There is also a need to highlight the contribution of the study to the knowledge base. On the list of references, a source by Moyo (2019) may be removed where it is currently placed, and be placed in an appropriate slot following the alphabetical order as it has been done with the other sources.\nThe approval status\nNoting that the manuscript has some strong points, it can be considered after major issues and concerns have been addressed. This is because some of the concerns raised under the weaknesses section, do affect the conceptualisation of the study. I therefore recommend Approved with reservations. More significant revisions need to be done.\n\nIs the work clearly and accurately presented and does it cite the current literature? No\n\nIs the study design appropriate and is the work technically sound? No\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? No source data required\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [ { "c_id": "11834", "date": "27 Jun 2024", "name": "Awelani Mudau", "role": "Author Response", "response": "We are grateful for the comments. They were plausible indeed and they should make our paper better." } ] }, { "id": "237897", "date": "28 Feb 2024", "name": "Samuel Ouma Oyoo", "expertise": [ "Reviewer Expertise Science and pedagogy: Current focui are in (1) School science teachers classroom practice including use of technology in the transformation of science content (2) Language use icluding teacher talk for and in teaching 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 study reported here is a worthy contribution to the field of science education, especially with regard to curriculum delivery in the context of the study. This included issues on the role of the school management teams and at different levels of schooling in the context of the study. The place of use of technology in teaching as may have been made more urgent by the prevalence of covid-19 came out clearly. These are issues that will now be applicable to continued delivery of science content in the schools in the context of the study.\n\nReading through the work however, the authors needed to give closer attention to the grammar issues including the tenses. There are instances where the work should have been in the past tense - covid-19 is no longer a challenge in the context of the study and the writing should be to address that fact.\n\nWhile the design including the data analysis approach is appropriate, the results are reported with the apparent assumption that all the readers will be well versed in the education system in the context of the study. The authors need to brief up on the system of education in the context of the study including issues on the types of schools and how they are relatively endowed. The participants were drawn from the respective types/categories and levels of schooling in the context of the study.\n\nThe results will thereafter relate better to the study context.\n\nThe authors need to represent the participants and their respective locations more accurately. Two of the participants are reported to have moved to Gauteng from Limpopo province yet there is still mention of them as having been in Limpopo at the time of the study. This will make it clear that the study was conducted in two provinces (Gauteng and Mpumalanga), not three (Gauteng, Limpopo and Mpumalanga).\n\nThe conclusion is well presented. However, the paragraph on recommendations that comes immediately above the conclusion can be moved to become the very last paragraph of the work.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "11833", "date": "27 Jun 2024", "name": "Awelani Mudau", "role": "Author Response", "response": "We are grateful for your comments. They have been addressed" } ] } ]	1	https://f1000research.com/articles/12-1183
https://f1000research.com/articles/10-1064/v1	19 Oct 21	{ "type": "Method Article", "title": "Skin swabbing protocol to collect DNA samples from small-bodied fish species", "authors": [ "Ceinwen Tilley", "Iain Barber", "William Norton", "Ceinwen Tilley", "Iain Barber" ], "abstract": "Fish species are commonly used as experimental models in the laboratory. DNA is routinely collected from these animals to permit identification of their genotype. The current standard procedure to sample DNA is fin clipping, which involves anaesthetising individuals and removing a portion of the caudal fin. While fin clipping reliably generates good quality DNA samples for downstream applications, there is evidence that it can alter health and welfare, leading to infection and impacting on the fish’s behaviour. This in turn can result in greater variation in the data collected. In a recent study we adapted a skin swabbing protocol to collect DNA from small-bodied fish, including sticklebacks and zebrafish, without the use of anaesthetics or sharp instruments. A rayon-tipped swab was used to collect mucus from the flank of the fish, which was then used for DNA extraction. We subsequently demonstrated that compared to fin clipping, skin swabbing triggered fewer changes in stress axis activation and behaviour. We also found that data collected from fish that had been swabbed were less variable than data from fish that had been fin clipped, potentially allowing smaller sample sizes in experimental groups after using this technique, and thereby reducing animal use. Here we provide a detailed protocol explaining how to collect DNA samples from small laboratory fish using skin swabs.", "keywords": [ "Zebrafish", "stickleback", "skin swabbing", "fin clipping", "DNA extraction", "refinement", "reduction" ], "content": "\n\nScientific benefits\n\nSkin swabbing causes less variation in subsequent data collection compared to fin clipping. This can improve the quality of data collection with the potential to aid comparison of results across laboratories.\n\n3Rs benefits\n\nDNA collection by skin swabbing causes fewer changes to stress axis activation and behaviour than fin clipping, the current standard technique. Skin swabbing also removes the need to use anaesthetic, and decreases the potential for fish to experience pain or infection compared to removal of tissue by fin clipping. In addition, the smaller variation in data collection caused by skin swabbing compared to fin clipping means that fewer animals need to be included in experiments.\n\nPractical benefits\n\nSkin swabbing is quick to perform, relatively non-invasive for the fish and collects DNA of suitable quality for PCR amplification. In addition, skin swabbing does not require sharp scalpels, reducing the possibility of harm to researchers.\n\nCurrent applications\n\nSkin swabbing can be used to collect DNA samples from fish species with a body size that is greater than 20 mm, the smallest body size that we could swab without risk harm to the animal. It is particularly useful when genotype information is needed from fish, such as identifying transgenic or mutant carriers in a group of animals.\n\nPotential applications\n\nSkin swabbing should be suitable to collect DNA from any species with a mucus layer on the body, including fish, frogs and toads. The technique may also be suitable for automation in the future.\n\n\nIntroduction\n\nModel fish species including zebrafish and sticklebacks are used frequently for experiments in the laboratory. Some of the advantages of these species include their small size, short life cycle and ease of maintenance, making it easy to keep many fish within laboratory aquaria. Fish also tend to be easy to manipulate genetically, and display similarities to other vertebrates permitting data to be translated across species (Bert et al., 2016; Schaeck et al., 2013; NC3Rs, 2014; Flecknell, 2002). Fish are used to study a range of disciplines including developmental biology, ecology, neuroscience and behaviour. They are also used as models for aspects of human disease including cancer (Hason and Bartunek, 2019), visual impairments (Richardson et al., 2017) and neurological disorders (Kalueff et al., 2014; Norton, 2013). The recent development of techniques to manipulate the genome, including transgenesis (Higashijima, 2008), optogenetics (Wyart and Del Bene, 2011) and CRISPR-Cas9 mutagenesis (Cornet et al., 2018; Albadri et al., 2017) means that DNA needs to be collected from many of these animals to facilitate identification of their genotype. In addition, the number of fish used in experiments is increasing each year. For example, in 2015, 14% of all regulated animal procedures in Britain were undertaken on fish (Home Office, 2014) and this rose to 30% in 2019, which represents more than one million procedures in the UK alone (Home Office, 2019). Accordingly, the number of fish undergoing DNA sampling is also likely to rise over time.\n\nThe current standard procedure to sample DNA is fin clipping under non-terminal anaesthesia (Xing et al., 2014). Typically, animals are immersed in anaesthetic until they become unresponsive to touch. A small part of the caudal fin is removed using a sterile scalpel before fish are allowed to recover in fresh system water. In some cases, pre-operative analgesia is applied by immersing the fish in water containing lidocaine (Schroeder and Sneddon, 2017). A recent survey indicated that 85% of zebrafish labs use fin clipping to collect DNA (Lidster et al., 2017). However, despite its popularity, there is evidence that fin clipping can alter health and welfare, leading to infection and altering growth and survival (Taslima et al., 2015). Fish display signs of pain after fin clipping (Deakin et al., 2019), as well as alterations to anxiety-like behaviour, including increased ventilation (Schroeder and Sneddon, 2017), reduced activity (Deakin et al., 2019; Schroeder and Sneddon, 2017), increased time at the bottom of a tank (Deakin et al., 2019; De Lombaert et al., 2017; Schroeder and Sneddon, 2017; White et al., 2017) and decreased feeding (De Lombaert et al., 2017). Fin clipping can also trigger the release of the primary stress hormone cortisol (White et al., 2017). This suggests that there is a need for alternative, more refined techniques to collect DNA from model fish species.\n\nOur recent research has shown that skin swabbing – collecting mucus from the flank of a fish and extracting DNA from it (Breacker et al., 2017) – provides a suitable alternative to fin clipping in small laboratory fish. The skin swabbing protocol had already been used to collect DNA from many fish species (Sebire et al., 2015; Taslima et al., 2015; Mirimin et al., 2011; Le Vin et al., 2011; Campanella and Smalley, 2006) including sticklebacks (Sebire et al., 2017), and we adapted it for use in zebrafish (Tilley et al., 2020; Breacker et al., 2017). In this methods paper, we describe how to swab and extract DNA from fish mucus in a step-by-step manner. We also present data from our recent research (Breacker et al., 2017; Tilley et al., 2020) showing that skin swabbing is a refinement compared to fin clipping, with the added potential to reduce the number of animals used in experiments.\n\n\nMethods\n\nAll work was conducted under a UK Home Office licence to Dr Norton (licence no. P8F9CCE8B), and was approved by a local Animal Welfare and Ethical Review Body (AWERB) committee at the University of Leicester.\n\nThreespined sticklebacks\n\nStocks of F2 generation lab-bred three-spined sticklebacks (Gasterosteus aculeatus) were generated by in vitro fertilisation in July 2017 (Barber and Arnott, 2000). The parental background was a wild freshwater population originally collected from the River Welland (Market Harborough, Leicestershire, UK) in 2015. Adult sticklebacks were fed an ad libitum diet of defrosted bloodworm (Chironomus sp. larvae). Groups of fish were pooled into large stock tanks (27 L) in a dedicated fish facility at the University of Leicester. The choice of which groups to mix was haphazard, matching fish of similar size and age. We did not expect this to cause changes in behaviour such as aggression, based upon our previous research into adult fish behaviour (Norton et al., 2011). The tanks housed 40 fish on a re-circulating system (Xenoplus systems, Techniplast) with a flow rate of two tank changes per hour. The system water was made from reverse osmosis water with Instant Ocean marine salts added (Aquarium Systems, UK). The water parameters were pH ~7.1, 0 ppm ammonia, 0 ppm nitrate, ~4 ppm nitrite and ~4000 DKH conductivity. Temperature and light–dark conditions were adjusted periodically to simulate natural seasonal variation until March 2018. Fish were then kept at 12±1°C on a 12:12 h light:dark cycle (i.e. March conditions) to maintain non-breeding conditions for the duration of the experiments, which were conducted from May 2018 onwards. 567 adult sticklebacks were used to develop this protocol, with a mean (± standard deviation) length of 36.74 mm (±2.98 mm) and a mean weight of 0.67 g (±0.2 g). All experimental studies were carried out using non-reproductive individuals, avoiding confounding factors associated with territorial and courtship behaviours. This means that although the sticklebacks were about one year old and adult size and weight, they had not developed sexually because they had not been exposed to spring light conditions and temperatures.\n\nZebrafish\n\nAdult AB wild-type zebrafish (Danio rerio) were generated from stock maintained at the University of Leicester. Fish were fed ad libitum each afternoon at the end of the experiments (Zebrafeed (Sparos)). The animals used in this study were arbitrarily netted from a group of 40 fish in 8 L tanks on a re-circulating system (ZebTEC multi-link water treatment unit, Techniplast) with a flow rate of 7.6 L per tank per hour (ca. one tank change per hour). The system water was made from reverse osmosis water with Instant Ocean salts (Aquarium Systems, UK) added. The water parameters were pH ~7.1, 0 ppm ammonia, 0 ppm nitrate, ~4 ppm nitrite and ~525 DKH conductivity. The fish were maintained at 28±1°C and in a 14:10 h light:dark cycle, standard lighting conditions for laboratory-housed zebrafish. The following zebrafish strains were used; AB wild-type and Tg (Vmat2:GFP) (Wen et al., 2008). The zebrafish used to develop this protocol (n = 630) had a mean (± s.d.) length of 34.99 mm (±1.66 mm) and a mean weight of 0.38g (±0.08 g) and included a mix of sexually mature males and females (approximate ratio 1.5:1 males:females) between three and six months old.\n\nNo enrichment was provided, as is standard procedure in our fish facility. No fish of either species died during these experiments, and all animals were killed by a Schedule 1 procedure at the end of this study.\n\nThis experiment was first reported in Breacker et al. (2017). To collect DNA by fin clipping, a single fish was removed from its home tank using a small hand net. The fish was pre-treated with an anaesthetic by placing it in a tank containing 168 mg/L ethyl 3-aminobenzoatemethanesulfonate (MS-222) buffered to pH 7.2 with sodium bicarbonate dissolved in fresh system water. Once the fish was no longer responsive to touch, it was gently caught in a net and placed into a Petri dish containing a small amount of water. Fins were clipped using a sterile razor blade taking care to only remove about one third of the caudal fin. The excised fin tissue was placed into a sterile labelled Eppendorf tube, and the fish was moved to a recovery tank containing system water. The fish’s behaviour was monitored until it had recovered consciousness, so that it swam around in the tank freely. Fish were placed into individual holding tanks until DNA extraction and identification was complete. Fin clip DNA was extracted using the same DNA extraction buffer as for skin swabbing (see section 4.1.2. below), but with the addition of 15 μl of 20 mg/ml Proteinase K. This was incubated at 57°C for 30 minutes, followed by addition of 400 μl chilled isopropanol. The solutions were mixed and the DNA solution was then chilled at −80°C for 30 minutes. The solution was centrifuged for 10 minutes at 10,625 g, the supernatant decanted, and the remaining pellet washed with 190 μl 70% EtOH. After a further centrifugation step (two minutes at 10,625 g) the DNA pellet was air dried and resuspended in 30 μl ddH2O.\n\nTo collect DNA by skin swabbing, a single fish was removed from its home tank using a small hand net. The fish was pre-treated with an analgesic by placing it in a tank containing 2 mg/L lidocaine dissolved in fresh system water. The fish was immersed in this solution for 45 minutes immediately before skin swabbing was carried out. The fish was then re-caught in the net, and gently restrained on top of a wetted sponge. The uppermost surface of the fish was exposed to the air to permit DNA collection. A sterile swab was gently stroked along the flank of the fish, from head to tail, five to ten times. The swab was placed into a clean labelled Eppendorf tube, and the fish was placed into a holding tank until DNA extraction and identification was complete. The DNA was extracted from the swab by adding DNA extraction buffer warmed to 55°C and letting it incubate for two minutes. The swab was then removed, taking care to squeeze out as much liquid as possible. The DNA was precipitated by addition of 400 μl chilled isopropanol. The solutions were mixed and the DNA solution was chilled at -80°C for 30 minutes. The solution was centrifuged for 10 minutes at maximum speed (10,625 g), the supernatant decanted, and the remaining pellet washed with 190 μl 70% EtOH. After a further centrifugation step (two minutes at 10,625 g) the DNA pellet was air dried and resuspended in 30 μl ddH2O.\n\nFor experiments comparing skin swabbing to fin clipping in the same animal, fish were first swabbed and then fin clipped immediately afterwards. No lidocaine was used in these experiments, which were performed before we investigated whether pain relief could improve the skin swabbing protocol. Their recovery and welfare was monitored by looking for changes in balance, locomotion or respiration in the hour after the procedure was completed.\n\nAdult sticklebacks and zebrafish were tested for changes in locomotion and anxiety-like behaviour in the open field test, novel tank diving test and black and white test as described in Norton and Carreño Gutiérrez (2019). Fish were filmed for five minutes the side (novel tank diving test) or above (open filed and black and white tests). In the novel tank test, we compared distance swum, and the time spent in the top or bottom half of a novel trapezoid-shaped tank. An anxious fish should prefer to remain close to the bottom of the tank. In the open field test we measured distance swum, and time spent at the side or in the centre of a novel tank. An anxious fish should prefer to swim close to the side of the tank. In the black and white test, we analysed the preference to spend time on the black or white side of the tank. A more anxious fish should prefer to stay on the black side of the tank. Behaviour was then analysed using videotracking software from ViewPoint Lifesciences.\n\nThe DNA samples obtained from three-spined sticklebacks were amplify the sex-linked molecular marker Isocitrate dehydrogenase (IDH) using the following primers: STKSEX forward primer 5′ GGGACGAGCAAGATTTATTGG 3′; STKSEX reverse primer 5′ TATAGTTAGCCAGGAGATGG 3′. Females produce a single band of approximately 300 bp, whilst males produce two products of 270 bp and 300 bp. 10 μl PCR reactions were set up using 5 μl Red Taq master mix (Sigma-Aldrich, UK), 0.5 μl of the forward and reverse primer, 3 μl of DNA template and 1 μl ddH2O). The PCR conditions were 94°C for 5 min, followed by 40 cycles of: 95°C for 30 sec, 56°C for 30 sec, 72°C for 30 sec, with a final extension of 72°C for 10 min. PCR products were visualised on a 5% agarose gel. PCR reactions were run on a Veriti 96 well thermal cycler.\n\nFor zebrafish, PCR was used to identify AB WT and transgenic Tg (Vmat2:GFP) fish. This used primers designed against the genes microphthalmia-associated transcription factor a (for WT) and green fluorescent protein for Tg (Vmat2:eGFP). The primers used were: mitfa forward primer 5′ GCCAACTAAATTTCATGAACC 3′; reverse primer 5′ AAATCAACTAATTGTTTACACG 3′as described by Lister et al. (1999) and GFP forward 5′ TCGAGCTGGACGGCGACGT 3′; reverse 5′ GGTGCTCAGGTAGTGGTTGTC 3′. 10 μl reactions were set up (5 μl Red Taq master mix (Sigma-Aldrich, UK), 0.5 μl of the forward and reverse primer 3 μl of DNA template and 1μl ddH2O). The PCR conditions were 94°C for 2 min, followed by 35 cycles of: 94°C for 30 sec, 60°C for 30 sec, 72°C for 1 min, with a final extension of 72°C for 10 min. Products were visualised on a 2% agarose gel. PCR reactions were run on a Veriti 96 well thermal cycler.\n\nCortisol was extracted from the water samples by pumping it through Sep-pak Plus C18 solid phase extraction cartridges (Waters Ltd., UK) following the protocol developed by the Cefas Weymouth Laboratory (Ellis et al., 2004). Cartridges were primed with 5 ml of methanol followed by 5 ml of distilled water (dH20) and water samples were pumped through the cartridges at 5 ml/min. Each cartridge was washed with 5 ml of dH20, then air-dried, wrapped in Parafilm® and stored at −80 °C until elution with 5 ml ethyl acetate. For the quantification by radioimmunoassay the eluted extracts were evaporated at 45°C under nitrogen and each residue was reconstituted in 500 μl of RIA buffer until assayed. The elution and the quantification were carried out in a blind manner to reduce bias when analysing the data.\n\nStatistical analyses were carried out using GraphPad Prism7. Data were tested for normality using the using the Shapiro–Wilk test. Since the majority of data were not distributed normally, we analysed all data using the non-parametric Kruskal–Wallis test followed by a Dunn's multiple comparisons test comparing each treatment to the control group.\n\n\nDetailed skin swabbing protocol\n\nPlease refer to Videos 1 and 2 to see how the DNA collection part of this protocol can be carried out.\n\n• Fish for DNA sampling, for example available from ZIRC or similar organisations.\n\n• Two aquariums large enough to hold a single fish, e.g. Techniplast ZebTEC 1.1 L tank or similar, e.g. Techniplast ZB300BF.\n\n• Access to fresh water from the main aquarium system.\n\n• A small sponge to rest fish on during swabbing, e.g. Vitrex 10 2904 square sponge or similar, available online. We use a sponge measuring approximately 10 cm length × 5 cm width × 3 cm depth. We cut a small 0.5 cm groove into the upper surface of the sponge to make it easier to restrain the fish.\n\n• A clean net large enough to comfortably catch and restrain a single fish, e.g. Marina Fine Soft Mesh Fish Net with Plastic Coated Handle or similar, available online. The net can be rinsed with aquarium water in between use.\n\n• A sterile rayon-tipped swab such as a cotton bud or a similar commercially available product/. Cotton buds should be autoclaved and dried before use to sterilise them.\n\n• A sterile 1.5 ml Eppendorf tube, labelled with a name or number to identify the fish e.g. Sigma Aldrich Ref. EP0030120086. RRID:SCR_000786.\n\n• Clean scissors, suitable to cut the stem of a sterile swab e.g. Brabantia 121746 Tasty+ Kitchen Scissors, or similar, available online.\n\n• Lidocaine hydrochloride e.g. Sigma Aldrich Ref. PHT1257.\n\n• DNA extraction solution (see preparation of reagents below).\n\n• Isopropanol (also known as 2-Propanol) e.g. Sigma Aldrich Ref. I9516.\n\n• Absolute ethanol e.g. Sigma Aldrich Ref. 51976.\n\n• Trizma Base (TRIS) e.g. Sigma Aldrich Ref. 648310-M.\n\n• Ethylenediaminetetraacetic acid (EDTA) e.g. Sigma Aldrich Ref. EDS-100G.\n\n• Sodium chloride (NaCl) e.g. Sigma Aldrich Ref. S7563.\n\n• Sodium dodecyl sulphate (SDS) e.g. Sigma Aldrich Ref. L3771.\n\nPrepare stock solutions to make the DNA extraction solution:\n\n• 1 M TRIS pH 7.5\n\n• 0.5 M EDTA\n\n• 2 M NaCl\n\n• 10% SDS\n\nMake 100 ml DNA extraction buffer from the stock solutions.\n\nMix:\n\n• 20 ml 1 M TRIS pH 7.5\n\n• 5 ml 0.5 M EDTA\n\n• 12.5 ml 2 M NaCl\n\n• 57.5 ml dH2O\n\nAutoclave the individual stock solutions before use. Once autoclaved, add 5 ml 10% SDS (do not autoclave once SDS has been added). This solution can be stored at room temperature for several weeks until signs of precipitation or contamination become evident.\n\nMake a 70% ethanol solution by adding 3 ml ultrapure water, distilled water or similar to 7 ml absolute ethanol.\n\nMake a solution of 2 mg/L Lidocaine to use for pre-swabbing analgesia. Make a stock by dissolving 2 g lidocaine in 1 ml ultrapure water. Add 1 ml stock solution to 1 L system water to generate a final concentration of 2 mg/L.\n\nSet up equipment in the laboratory\n\nLabel one 1.5 ml Eppendorf tube with a name or number to identify the fish to be swabbed.\n\nMake sure that you have one sterile swab for each animal.\n\nLabel enough holding tanks to maintain each fish separately until identification is complete. These tanks should be placed onto the main aquarium system so that fish have access to flowing oxygenated water.\n\nFill a small tank with system water up to depth of 1 cm or 2 cm (the swabbing tank). Place the grooved sponge into this water, groove side up, making sure that it is completely wet. The top of the sponge should not be covered in water, so that the exposed flank of the fish can be swabbed easily without getting the swab too wet.\n\nPlace the group of fish that you wish to identify into a holding tank close to the swabbing tank.\n\nSet up a tank containing 2 mg/L lidocaine for pre-operative analgesia/pain relief.\n\nApply pain relief before DNA collection\n\nAdminister lidocaine prior to swabbing to provide pain relief. Immerse the group of fish in a solution of 2 mg/L lidocaine for 45 minutes prior to swabbing. The fish require 45 minutes for the lidocaine to take effect, and swabbing should be carried out immediately afterwards.\n\nSwab the fish to collect DNA\n\nPre-warm an aliquot of DNA extraction solution to 55°C; chill the isopropanol to −20°C.\n\nGently catch a single fish from the analgesia tank in a net and transfer it to the swabbing tank containing the sponge. Use the net to restrain the fish on top of the wetted sponge, positioning the body into the groove. Using thumb and forefinger hold the net so that the side of the fish against the sponge rests on the net, whereas the uppermost side of the fish is exposed for swabbing. The underside of the fish rests on the net, not the sponge, thereby minimising contamination for the sponge between different fish (Video 1).\n\nUsing a sterile rayon-tipped swab (such as a cotton bud or similar), gently stroke the fish five to ten times from the operculum to the base of the caudal fin. Very little pressure is required to collect enough mucus for DNA extraction. Be as gentle as possible to avoid damaging the animal. The whole procedure – netting, swabbing and returning the animal to the tank should only take around 30 seconds (Video 2).\n\nPlace the swab into a labelled 1.5 ml Eppendorf tube. The handle of the swab can be cut off using scissors, and the tip stored at room temperature (either dry or in DNA extraction solution) with the lid of the tube closed.1\n\nPlace each fish into a labelled holding tank on the aquarium system. Monitor its health and welfare, including locomotion, balance and respiration, in the immediate recovery period afterwards. The fish will remain in this tank until identification is complete.2 Typically it takes half a day to extract DNA, run a PCR and identify the fish. Therefore, fish may be held in single tanks for a few hours up to overnight.\n\nDNA extraction from swabs3\n\n• Check that the DNA extraction buffer has been pre-warmed to 55°C.\n\n• Add 400 μl DNA extraction buffer into a 1.5 ml Eppendorf tube containing the swab.\n\n• Incubate the swab at room temperature for at least two minutes.\n\n• Remove the swab using fingers or forceps, and squeeze it against the side of the tube to retain as much extraction solution as possible.\n\n• Add 400 μl of pre-chilled isopropanol to the extraction solution.\n\n• Mix the tube three to five times using a vortex mixer.\n\n• Place the tube into a −80°C freezer for at least five minutes4.\n\n• Remove the tube from the −80°C freezer and allow it to defrost.\n\n• Centrifuge the tube for 10 minutes at full speed (ca. 10,625 g using a desktop centrifuge).\n\n• Dry the pellet by gently pouring the supernatant away onto a tissue.\n\n• Add 190 μl 70% EtOH and gently flick tube to mix the contents.\n\n• Centrifuge the tube for two minutes at full speed (ca. 10,625 g using a desktop centrifuge).\n\n• Dry the resulting pellet by removing the excess liquid using a P200 pipette set to 200 μl. Incubate the tube in a heat block set at 55°C for 5-10 minutes until it is fully dry.\n\n• Pipette 30 μl dH2O into the tube to resuspend the DNA. This can be achieved by aspirating the liquid into a pipette tip and releasing is again several times until the pellet is no longer visible. Incubate the tube in a dry heat block for five to ten minutes at 65°C. The DNA can now be stored at 4°C (for long term use in applications other than genotyping), or immediately used in a PCR reaction.\n\n\nResults\n\nIn previous studies from our lab we compared the concentration of DNA collected by skin swabbing and fin clipping, and the ability to amplify genes when using both techniques in stickleback and zebrafish. We also investigated the possibility for cross contamination of mucus samples, and changes to stress axis activity and behaviour following DNA collection. The data presented have all be published previously in Breacker et al. (2017) and Tilley et al. (2020).\n\nConcentration of DNA collected by fin clipping vs skin swabbing\n\nSkin swabbing may be expected to be less invasive than fin clipping since it does not require removal of a portion of tissue from the animal. However, it was not clear whether both techniques are equally useful to genotype animals. We first investigated whether skin swabbing led to similar levels of DNA collection as fin clipping, the current standard procedure (Xing et al., 2014). Comparing swabs and fin clips taken from the same fish revealed that fin clips produced higher yields of DNA, suggesting that it is a more efficient method (Table 1). However, the DNA samples collected using both methods had similar levels of purity, measured by calculating the 260/280 and 260/230 ratios using a spectrophotometer (Table 1 and Figure 1). Pure DNA samples should have a 260/280 ratio of ~1.8 and a 260/230 ratio of between 2.0 and 2.2. However, slight deviations from this ratio may not affect amplification of genes by PCR.\n\nSkin swabbing led to a lower concentration of DNA extraction than fin clipping in both species. The quality of the DNA collected was similar when using both techniques. DNA concentration was measured using a spectrophotometer following extraction as described above. The purity of the DNA was measured using the 260/280 and 260/230 ratios. Pure DNA samples should have a 260/280 ratio of ~1.8 and a 260/230 ratio of between 2.0 and 2.2. We compared n = 10 sticklebacks and n = 10 zebrafish. Modified with permission from Breacker et al. (2017). Detailed methods for fin clipping, and a description of the experimental design can be found in Breacker et al. (2017) as well.\n\nThis data is taken from Breacker et al. (2017). Fin clipping led to more DNA being collected in both species compared to skin swabbing. The same fish were used in both procedures. n = 10 zebrafish and n = 10 sticklebacks. One-way ANOVA followed by Tukey’s post hoc test. ** = p < 0.001. SB = stickleback and ZF = zebrafish.\n\nPCR results comparing skin swabbing and fin clipping\n\nDNA extracted from fin clipping is commonly used to identify animals via PCR amplification of marker genes. We investigated whether skin swabbing collected enough DNA to allow PCR amplification of genes in stickleback and zebrafish, despite the lower yield recovered compared to fin clipping. In this experiment we used a different group of zebrafish and sticklebacks from those presented in Table 1. In stickleback, we amplified the gene coding for the sex-linked marker Isocitrate dehydrogenase (IDH). In zebrafish, we compared amplification of the microphthalmia-associated transcription factor a (mitfa) gene using both sampling techniques. We also compared fish of different sizes, to show that swabbing can be used in animals that have not yet reach adulthood. In both zebrafish and stickleback, skin swabbing and fin clipping led to amplification of genes by PCR, suggesting that both techniques can be used for genetic identification. In addition, we were able to collect mucus from fish with a body size greater than 20 mm without damaging the animals (Figure 2).\n\n(a) Amplification of mitfa from zebrafish fin clips, swabs and size range; 1-3 = fin clips, standard length (measured from nose to beginning of tail fin) adults, at 6 months old; 4-6 = swabs standard length adults, at 6 months old; 7-9 = swabs from 20 mm standard length adults; 10-12 = swabs from 35 mm standard length adults; 13-15 = swabs from 50 mm standard length adults; 16 = blank. n = 15 zebrafish, one fish per band. The amplified band has a size of around 1,500 bp. (b) Amplification of Isocitrate dehydrogenase from stickleback swabs and size; 1-2 = 50 mm standard length adult male swabs; 3-4 = 50 mm standard length adult female swabs; 5-6 = 20 mm standard length adult male swabs; 7-8 = 20 mm standard length adult female swabs. n = 8 sticklebacks, one fish per band. Females produce a single 300 bp band, whereas male fish produce two bands that are 270 bp and 300 bp. L marks the position of the 1 Kb DNA ladders, and the numbers on the right-hand side show ladder band sizes in Kb. Reproduced with permission from Breacker et al. (2017).\n\nSkin swabbing and fin clipping appear to be equally useful when amplifying genes to identify fish. We next examined whether mucus cross contamination occurs in fish held at high density, and whether either technique alters stress axis activation and behaviour following DNA collection.\n\nNo cross contamination of mucus samples when fish are held at high density\n\nSkin swabbing appears to be a suitable technique to collect DNA from small laboratory fish without the need to excise fin tissue (Tilley et al., 2020; Breacker et al., 2017). We investigated the potential for cross contamination of mucus samples when housing zebrafish in close proximity in a small aquarium. We created a group by mixing 10 AB wild-type and 10 Tg (vmat2:GFP) zebrafish and maintained them in a small 3 L tank overnight. Tg (vmat2: GFP) carry a green fluorescent protein (GFP) transgene that can be amplified by PCR (Wen et al., 2008) and have long ornamental fins allowing them to be distinguished visually from the AB wild-type animals. We first swabbed the AB wild-types and then the Tg (vmat2: GFP) fish, and we did not assess whether this order of collecting DNA might influence the results. We amplified both mitfa (a control gene that should be present in all animals) and the gene coding for GFP, which should be present in the transgenic carriers but not wild-type. Figure 3 shows a subset of four of these fish for clarity. As hypothesised, mitfa was present in both genotypes (Figure 3; lanes 1-4 AB and 13-16 Tg (vmat2: GFP)), whereas gfp was only present in the transgenic fish (Figure 3; lanes 5-8 AB and 9-12 Tg (vmat2: GFP)). This suggests that cross-contamination of mucus had not occurred when keeping fish at high density.\n\nWe used n = 15 zebrafish in this experiment, and show n = 4 WT and n = 4 Tg (vmat2: GFP) zebrafish here for clarity. The mitfa bands are approximately 1,500 bp long, and the vmat band is approximately 2,500 bp long. L marks the position of the 25 bp DNA ladders. Reproduced with permission from Breacker et al. (2017). Refer to Breacker et al. (2017) for detailed methods.\n\nNo changes in cortisol release after skin swabbing\n\nRelease of cortisol – the primary stress hormone in vertebrates – can be used as a read-out of stress axis activity following experimental manipulation (Sebire et al., 2007). We compared cortisol release in separate groups of sticklebacks and zebrafish that were either non-manipulated, fin clipped or swabbed. We then collected the cortisol they had excreted into their tank water one hour later as described previously (Sebire et al., 2007, 2009; Ellis et al., 2004). The cortisol was extracted from the fish’s holding water and quantified by radioimmunoassay. Collecting mucus by skin swabbing did not trigger an increase in cortisol release compared to control, non-manipulated fish that had not been handled at all, whereas fin clipping led to heightened release of this hormone (Figure 4). This suggests that fin clipping is more stressful for fish than skin swabbing when used to sample DNA. This likely occurs because the fin clipping procedure involves application of the anaesthetic MS-222, whereas skin swabbing does not.\n\nWe measured the concentration of cortisol release (in ng) per fish body weight (grams body weight) in an hour. n = 27 fish in each group. Kruskal-Wallis test followed by Dunn’s multiple comparisons test. indicates a significant difference compared to control, p < 0.001. NS indicates a non-significant difference compared to control. Reproduced with permission from Tilley et al. (2020). Detailed methods are available in Tilley et al. (2020), and the groups shown here have been taken from a larger experiment.\n\nGreater variability in results after clipping compared to swabbing\n\nWe next examined the effect of skin swabbing and fin clipping on subsequent experimental data. We recorded the opercular beat rate (OBR, a read out of ventilation response to stress in fish (Bell et al., 2010; Brown et al., 2005), and behaviour in the open field (Norton and Carreno Gutierrez, 2019), novel tank and black and white tests (for anxiety-like behaviour: Norton and Carreno Gutierrez, 2019; Blaser and Rosemberg, 2012; Egan et al., 2009). Both skin swabbing and fin clipping caused complex changes to behaviour that varied over time (Tilley et al., 2020). Fin clipping caused a decrease in opercular beat rate in sticklebacks and an increase in zebrafish, whereas skin swabbing did not affect this behaviour. In the novel tank test, skin swabbing decreased the distance swum and increased time spent at the bottom of the tank by zebrafish, an index of anxiety-like behaviour on days 2 and 7. Conversely, fin clipping increased the distance swum in a novel tank by sticklebacks on day 1, and decreased zebrafish swimming on day 1 in both the novel tank and open field tests (see figure 7 in Tilley et al., 2020). Fin clipping also led to greater variation in the data collected following DNA sampling compared to skin swabbing. Behavioural data collected subsequent to fin clipping showed more variable data compared to skin swabbed animals, meaning that more individuals need to be measured to test hypotheses with sufficient statistical power (Tilley et al., 2020). This means that collecting DNA by skin swabbing may lead to a reduction of total number of animals needed in experiments.\n\n\nDiscussion\n\nThis protocol describes in detail the steps needed to collect DNA from small-bodied fish species using skin swabbing. We have also included findings from our previous research, comparing PCR amplification of genes in zebrafish and stickleback, and investigating the potential for cross-contamination of mucus samples during husbandry (Tilley et al., 2020; Breacker et al., 2017). We also show that skin swabbing does not activate release of the stress hormone cortisol, suggesting that it may be less stressful than fin clipping (Tilley et al., 2020). In summary, both skin swabbing and fin clipping can alter stress axis activation and behaviour. However, skin swabbing appeared to have less impact upon zebrafish and stickleback than fin clipping, since fewer of the read-outs that we measured were altered by this technique.\n\nSeveral previous studies have shown that fin clipping can have side effects that may alter the outcome of experimental studies. For example, it can lead to secondary infections and elevate the non-specific immune response (Dash et al., 2018). In addition, fin clipping is painful for fish (Deakin et al., 2019), and therefore requires them to be anaesthetised, raising the potential for further disruption of the stress response or behaviour. As a result of these observations, concerns have been raised about the welfare implications of collecting DNA by fin clipping.\n\nSkin swabbing appears to be a less invasive method for obtaining DNA samples since it only requires a small amount of mucus to be removed from the fish’s flank. In a recent set of experiments, we demonstrated that skin swabbing can be performed in the absence of anaesthetic without exacerbating changes in cortisol release (Tilley et al., 2020). However, our previous comparison of both techniques uncovered complex changes in gene expression and behaviour that varied over time following DNA collection. Importantly, we observed a greater variation in behaviour in groups of fish that had been fin clipped compared to those that had been swabbed (Tilley et al., 2020), meaning that fewer animals need to be measured in order to generate sufficiently powered data when DNA is collected with a swab. This can improve the quality of data collection and reduce the number of animals used, thereby decreasing the cost of experiments.\n\nRemoval of tissue during fin clipping led to an acute increase in water-borne cortisol release in both fish species whereas skin swabbing did not (Tilley et al., 2020). Most changes to experimental data due to fin clipping appeared on the first day after DNA collection. In contrast, the changes in gene expression and behaviour caused by skin swabbing tended to appear between two and seven days after manipulation, perhaps due to the activation of an immune response, or changes in ionic or osmotic regulation (Dash et al., 2018). However, we also observed changes in the behaviour of control non-manipulated fish over time, demonstrating the difficulty of comparing repeat measures of behaviour and accounting for the influence of routine maintenance on animals (Tilley et al., 2020). Some differences between species were observed as well. Zebrafish displayed more changes in behaviour than sticklebacks after manipulation; and both fin clipping and skin swabbing had a greater effect on gene expression in stickleback than zebrafish (Tilley et al., 2020).\n\nWe also confirmed that cross-contamination of mucus samples did not occur when fish were held at high densities overnight. We maintained a group of wild-type and transgenic zebrafish at densities greater than those recommended for normal housing conditions (Le Vin et al., 2011). Nevertheless, we were still unable to amplify the gene coding for Green fluorescent protein in wild-type fish, despite crowding them together with transgenic Tg (vmat2:GFP) carriers (Figure 2). This suggests that skin swabbing is an appropriate technique to collect DNA even when fish have been in close contact with each other.\n\nIn summary, our previous research has shown that skin swabbing can yield DNA concentrations and purities that are comparable to fin clipping when combined with a low-cost recovery method (Table 1, adapted from Breacker et al., 2017). Swabbing is a suitable technique for small laboratory fish that are as small as 20 mm – when used on smaller animals there is the potential for harm when swabbing (Breacker et al., 2017). Skin swabbing triggers fewer changes in stress axis activation, behaviour and gene expression than fin clipping. In addition, no sharp scalpels are needed when collecting DNA by skin swabbing, therefore reducing the possibility of harm to researchers. Skin swabbing is simple to perform once researchers have been trained in the technique, although care must be taken to swab the fish from anterior to posterior using very light pressure. In the future, the use of skin swabbing might be expanded to other species that have a mucus layer on their body such as fish, frogs and toads.\n\n\nData availability\n\nOpen Science Framework: Skin swabbing protocol to collect DNA samples from small-bodied fish species, https://doi.org/10.17605/OSF.IO/HS83T/.\n\nThis project contains the following underlying data:\n\n- Breacker et al. (2017) raw data.xlsx\n\n- Skin swabbing protocol to collect DNA samples from small-bodied fish species file 2.csv\n\n- Tilley et al. (2020) raw data.xlsx\n\nFigshare: Swabbing videos 1 and 2, https://doi.org/10.6084/m9.figshare.17049590 (Norton et al., 2021).\n\nThis project contains the following extended data:\n\n- Swabbing video 1.mp4\n\n- Swabbing video 2.mp4\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReporting guidelines\n\nOpen Science Framework: ARRIVE checklist for Tilley et al., Skin swabbing protocol to collect DNA samples from small-bodied fish species, https://doi.org/10.17605/OSF.IO/HS83T/.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).", "appendix": "Acknowledgements\n\nWe are grateful to Carl Breacker, Kieran Dewing, Aimee Mason, Dave White and members of the Preclinical Research Facility (University of Leicester) for fish care, and to Volko Straub for insightful discussions about this data. 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Trends Pharmacol. Sci. 2014; 35: 63–75. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLe Vin AL, et al.: Validation of swabs as a non-destructive and relatively non-invasive DNA sampling method in fish. Mol. Ecol. Resour. 2011; 11: 107–109. PubMed Abstract \| Publisher Full Text\n\nLidster K, et al.: International survey on the use and welfare of zebrafish Danio rerio in research. J. Fish Biol. 2017; 90: 1891–1905. PubMed Abstract \| Publisher Full Text\n\nMirimin L, et al.: A quick, least-invasive, inexpensive and reliable method for sampling Gadus morhua postlarvae for genetic analysis. J. Fish Biol. 2011; 79: 801–805. PubMed Abstract \| Publisher Full Text\n\nNC3Rs: Five Reasons Why Zebrafish Make Excellent Research Models.2014.Reference Source\n\nNorton WHJ: Toward developmental models of psychiatric disorders in zebrafish. Front Neural Circuits. 2013 Apr 26; 7: 79. eCollection.Publisher Full Text\n\nNorton WHJ, Stumpenhorst K, Faus-Kesler T, et al.: Modulation of Fgfr1a signaling in zebrafish reveals a genetic basis for the aggression-boldness syndrome. J. Neurosci. 2011 Sep 28; 31(39): 13796–807. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNorton WHJ, Gutierrez HC: The three-spined stickleback as a model for behavioural neuroscience. PLoS One. 2019; 14: e0213320. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNorton W, Tilley CA, Barber I: Swabbing videos 1 and 2. f1000research.com. Media. 2021. Publisher Full Text\n\nPercie du Sert N, et al.: The experimental design assistant. PLoS Biol. 2017; 15: e2003779. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRichardson R, Tracey-White D, Webster A, Moosajee M: The zebrafish eye-a paradigm for investigating human ocular genetics. Eye. 2017 Jan; 31(1): 68–86. Epub 2016 Sep 9.Publisher Full Text\n\nScott A, Sheldrick E, Flint A: Measurement of 17α, 20β-dihydroxy-4-pregnen-3-one in plasma of trout (Salmo gairdneri Richardson): seasonal changes and response to salmon pituitary extract. Gen. Comp. Endocrinol. 1982; 46: 444–451. PubMed Abstract \| Publisher Full Text\n\nSchaeck M, et al.: Fish as research tools: alternatives to in vivo experiments. Altern. Lab. Anim. 2013; 41: 219–229. PubMed Abstract \| Publisher Full Text\n\nSchroeder PG, Sneddon LU: Exploring the efficacy of immersion analgesics in zebrafish using an integrative approach. Appl. Anim. Behav. Sci. 2017; 187: 93–102. Publisher Full Text\n\nSebire M, et al.: Prozac affects stickleback nest quality without altering androgen, spiggin or aggression levels during a 21-day breeding test. Aquat. Toxicol. 2015; 168: 78–89. PubMed Abstract \| Publisher Full Text\n\nSebire M, Katsiadaki I, Scott AP: Non-invasive measurement of 11-ketotestosterone, cortisol and androstenedione in male three-spined stickleback (Gasterosteus aculeatus). Gen. Comp. Endocrinol. 2007; 152: 30–38. PubMed Abstract \| Publisher Full Text\n\nSebire M, Katsiadaki I, Scott AP: Further refinement of the non-invasive procedure for measuring steroid production in the male three-spined stickleback Gasterosteus aculeatus. J. Fish Biol. 2009; 75: 2082–2094. PubMed Abstract \| Publisher Full Text\n\nSpence R, et al.: The behaviour and ecology of the zebrafish, Danio rerio. Biol. Rev. Camb. Philos. Soc. 2008; 83: 13–34. PubMed Abstract \| Publisher Full Text\n\nTaslima K, et al.: DNA sampling from mucus in the Nile tilapia, Oreochromis niloticus: minimally invasive sampling for aquaculture-related genetics research. Aquac. Res. 2015; 47(12): 4032–4037.\n\nTilley CA, et al.: Skin swabbing is a refined technique to collect DNA from model fish species. Sci. Rep. 2020; 10: 18212. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nVenta PJ, et al.: A 13-plex of tetra- and penta-STRs to identify zebrafish. Sci. Rep. 2020; 10: 3851. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWhite LJ, et al.: The impact of social context on behaviour and the recovery from welfare challenges in zebrafish, Danio rerio. Anim. Behav. 2017; 132: 189–199. Publisher Full Text\n\nWyart C, Del Bene F: Let there be light: zebrafish neurobiology and the optogenetic revolution. Rev. Neurosci. 2011; 22: 121–130. PubMed Abstract \| Publisher Full Text\n\nXing L, et al.: Rapid and efficient zebrafish genotyping using PCR with high-resolution melt analysis. J. Vis. Exp. 2014; e51138. Publisher Full Text\n\n\nFootnotes\n\n1 We have posted a swab in DNA extraction solution to ourselves using the normal postal service. DNA was recovered successfully from the swab one week later.\n\n2 This protocol can be completed in around four hours – one hour to extract DNA, two hours to run a PCR and one hour to visualise the product on an electrophoresis gel. We routinely identify around twenty animals at a time.\n\n3 Other research groups have reported DNA extraction by the hot-shot method following skin swabbing: e.g. Venta et al. (2020).\n\n4 The tubes can be stored at -80°C overnight if required." }	[ { "id": "117243", "date": "27 Jan 2022", "name": "Luigi Margiotta-Casaluci", "expertise": [ "Reviewer Expertise Fish physiology", "endocrinology", "behaviour", "3Rs", "toxicology. Referee suggested by the NC3Rs for their scientific expertise and experience in assessing 3Rs impact." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nGeneral comments\n\nIn this article, the authors describe a skin swabbing protocol for DNA collection from small laboratory fish species that could provide a suitable alternative to the commonly used fin clipping procedure. The latter is an increasingly common procedure used in most zebrafish laboratories at global level. As mentioned by the authors, 85% of zebrafish laboratories use fin clipping to collect DNA. This procedure requires anaesthesia and involve surgical removal of tissue; therefore, the development of alternative minimally invasive methods in this area may have significant implications for the welfare of laboratory fish. The alternative skin swabbing protocol presented in this article is well described, and the work provides a valuable contribution to the advancement of laboratory fish welfare. However - although the potential welfare benefits of skin swabbing vs fin clipping may sound obvious - I believe that the specific datasets presented in the article do not allow a robust cost-benefit assessment of the protocol from a 3Rs perspective and the evaluation of its superiority compared to the commonly used fin clipping procedure. Hence, I suggest that that aspect of the article should be improved, expanded, and integrated with other data (if available). Specific comments and suggestions are provided below.\n\nSkin swabbing protocol\n\nThe methodology described in the article appears to be sound, and I believe that the details provided allow to reliably replicate the simple method in other laboratories. The supplemental video clips are clear and very informative.\nDespite a lower DNA yield obtained with skin swabs, the DNA samples collected using both methods had similar levels of purity. The authors demonstrated that DNA extracted from skin mucus allows a reliable amplification of target genes, and that no mucus cross contamination occurs in fish held at high density.\nThe supplemental videos are very good and clearly demonstrate the key practical steps. In the video the operator apparently restrains the fish on the sponge by gently covering the eyes with a gloved finger. I suppose this procedure calms the fish and reduces potential harm. Do the authors suggest that this should be a key step of the protocol? If yes, I suggest to add more details about this step in the main text.\nIn the published protocol the authors reported that fish were immersed in lidocaine for 45 minutes before performing the procedure. Can the authors explain why this duration was selected? Does water temperature affect uptake and pharmacokinetics of lidocaine in different species, and in turn the incubation time? Considering the time needed to perform the skin swab, how many fish should be added to the lidocaine solution to ensure that no fish experiences an excessive exposure? Considering the use of static water conditions for the exposure to lidocaine, I foresee that the temperature may change very rapidly unless the room temperature is controlled. Can the authors recommend a specific strategy to ensure the maintenance of optimal water temperature (and hence the reduction of stress) throughout the lidocaine exposure phase? E.g. using an incubator or a dedicated genotyping rack.\nTable 1 shows the comparison of DNA concentration from fin clips and skin swabs of the same sticklebacks and zebrafish. I believe the top row displaying the column titles is missing.\nCross-contamination\n\nTo evaluate the potential cross contamination of mucus samples when fish are held at high density, the authors kept 10 AB wild-type and 10 transgenic zebrafish in a small 3 L tank overnight. The analysis show that, in these conditions, there is no contamination. However, it appears that the authors reached this conclusion after a non-random sampling where all ABs were swabbed first, followed by all transgenic fish (displaying a longer tail). Although one may conclude that there is no cross contamination in the fish tank, the experimental design does not allow to evaluate whether the full procedure itself (i.e. including the transfer onto the sponge) may be a source of contamination. Although the probability is low, do the authors think that the sponge may represent a contamination source? If yes, do they recommend to replace the sponge after sampling a certain number of fish (e.g. how many?).\nSimilar considerations are valid for gloves and nets. How often should these elements be replaced/washed?\nClaims of adversity of fin clipping – Introduction and discussion\n\nThe Introduction reports the following statement: “However, despite its popularity, there is evidence that fin clipping can alter health and welfare, leading to infection and altering growth and survival (Taslima et al., 2015)”. However, Taslima et al. (2015)1 appears to be an aquaculture-related paper focused on Nile tilapia and, as far as I can see, that paper does not provide any evidence of fin clipping-induced damage. Taslima et al. (2015) provided the following generic statement “tissue biopsy may have negative impacts on fish, potentially including infection and effects on survival, growth or behaviour”, and to support this statement they cited Le Vin et al. (2011) (this paper is also cited in the present manuscript).[red-2] The latter concerns the validation of swabs methods for DNA sampling in fish. Again, the study did not investigate the adverse effects of fin clipping. On the other hand, Le Vin et al. (2011) also stated that fin clipping can be detrimental. This time, to support that statement, they cited several papers from the 60s, 70s, and 80s. However, those papers appear to be referred mainly to aquaculture and field ecology studies where fish are reintroduced in the environment after fin-clipping. Going back to the introduction of the present paper, I believe that whereas the potential adverse effects of fin clipping on behaviour are evidenced with appropriate supporting citations, the other potential adverse effects on infection, growth. and survival are not.\nIs there any evidence that fin clipping can adversely affect growth, survival, and infection susceptibility in a laboratory setting? If not, the authors should specific that it is not the case, and discuss potential effects observed in aquaculture studies providing an accurate citation and reporting of the primary papers. If yes, it would be useful to have specific data on this important aspect.\nSimilarly, in the Discussion, the authors wrote that “Several previous studies have shown that fin clipping can have side effects that may alter the outcome of experimental studies. For example, it can lead to secondary infections and elevate the non-specific immune response (Dash et al., 2018)”. However, Dash et al. (2018) do not seem to mention fin clipping at all, as it is a study focused on the role played by fish mucus in health maintenance.3 Please, revise this reference and replace with primary papers, if possible.\nBehavioural studies and variability of behavioural and stress endpoints\nIn the present paper, the negative effects of fin clipping of fish behaviour was used as key argument to justify the potential superiority of skin swabbing over fin clipping. However, I believe that this argument is only weakly supported by the data presented here. I suggest to add more data, if available, to strengthen this argument.\n\nThe methodological description of the behavioural tests is too basic and requires more details. For example, in the novel tank diving test, fish were observed/recorded for the first five minutes. Is this observation time justified by other studies for both stickleback and zebrafish? If yes, what are the supporting references? Were multiple fish/tanks filmed simultaneously using multiple tanks? If yes, did the operator add the fish using a specific sequence or removed the first seconds of the video where the operator was still in the room? (The operator in the room is a source of stress). The results section indicates that multiple time points were tested. However, the different timepoints and the rationale behind their selection are not described in the methods section. The importance of providing an accurate description of the methods is clearly demonstrated by the following, and more important, point.\nThe results section indicates that there is “Greater variability in results after clipping compared to swabbing”. I found that statement confusing as, by itself, it leads one to believe that there is a variability in genotyping results whereas the authors refer to behavioural and stress endpoints (which are not the focus of the paper). Later, the article provides the following statement: “Behavioural data collected subsequent to fin clipping showed more variable data compared to skin swabbed animals, meaning that more individuals need to be measured to test hypotheses with sufficient statistical power (Tilley et al., 2020).4 This means that collecting DNA by skin swabbing may lead to a reduction of total number of animals needed in experiments”. In my opinion, it is unclear why skin swabbing could allow to use fewer animals. Do the authors refer to a specific context? I suggest to clarify this point or to remove it.\nOverall, this specific aspect of the work (i.e. data variability) has been highlighted very strongly in the manuscript; however, my main concern is the data does not appear to support the hypothesis of a treatment-dependent effect. The present manuscript does not provide any figure or table of the behavioural data; however, this data can be retrieved from Tilley et al. (2020). Reading the latter, it is possible to note that the observed behavioural effects appeared to be (almost always) driven by fish handing procedures and not by fin clipping or skin swabbing themselves. The same consideration is valid for the assessment of opercular beats. The fact that control fish display behavioural responses more often (or as often) as fish that underwent DNA collection weakens the argument of treatment-specific effects, and hence treatment-specific benefits, including 3Rs benefits. Can the authors provide more data concerning this aspect?\nEffects on cortisol release\n\nTo measure the effects of the different procedures on the stress axis, the authors measured cortisol excretion in the tanks of fish that underwent 1) no manipulation, 2) skin swabbing, 3) fin clipping. I believe that the experimental design described in the article is not suitable to provide an answer to the specific research question considered here. Although measuring the cortisol released by a non-manipulated group provided a useful reference value, I believe that there are multiple factors to consider for a more rigorous comparison. 1) Fish handing – it is known that fish netting and air contact are major stress factors that induce an increase of cortisol release in the surrounding water (Ellis, James, Scott 2004).5 Measuring cortisol concentrations in tanks of non-manipulated fish will very likely indicate lower values, independently from skin swabbing or fin clipping. Hence, a more appropriate control would be represented by fish that underwent the same handling (i.e. netting and transfer to a new tank) without DNA sampling procedure. 2) The pre-procedure treatment of fish that underwent skin swabbing or fin clipping were very different (i.e. 45 minutes exposure to lidocaine in a confined space versus rapid treatment with MS-222). From the results presented here, it is not possible to evaluate whether the 45 minutes pre-treatment with lidocaine did or did not affect cortisol release. In conclusion, this suggests that an experiment aimed at evaluating the stress response to different DNA sampling procedures should include specific negative controls for each treatment type and fish handling procedure.\nOther comments\n\nIn the discussion, the authors reported that “changes in gene expression and behaviour caused by skin swabbing tended to appear between two and seven days after manipulation, perhaps due to the activation of an immune response, or changes in ionic or osmotic regulation (Dash et al., 2018)’. In my opinion, this possibility is concerning and should be explored in further studies, as it may hamper any 3Rs benefit of skin swabs. For example, are swabbed fish in the laboratory more susceptible to infection and disease in the longer term compared to fin clipped fish?\n\nThe reference de Lombaert et al. (2017) is not present in the reference list.\n\nAre a suitable application and appropriate end-users identified? Yes\n\nAre the 3Rs implications of the work described accurately? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate? Partly\n\nIs the rationale for developing the new method (or application) clearly explained? Partly\n\nIs the description of the method technically sound? Yes\n\nAre sufficient details provided to allow replication of the method development and its use by others? Yes\n\nIf any results are presented, are all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions about the method and its performance adequately supported by the findings presented in the article? Partly", "responses": [ { "c_id": "11491", "date": "27 Jun 2024", "name": "Will Norton", "role": "Author Response", "response": "Author Response: The reviewer has provided us with excellent feedback upon the first version of this study. We have answered these comments in full, and our responses to the comments are included below. We are very sorry that it has taken us so long to respond to these suggestions, and we hope that you still accept to re-review this paper. A change in person circumstances prevented us from addressing your suggestions sooner. Thank you for reading this study so thoroughly, and for helping us to improve this manuscript. Reviewer Comment: Although the potential welfare benefits of skin swabbing vs fin clipping may sound obvious, I believe that the specific datasets presented in the article do not allow a robust cost-benefit assessment of the protocol from a 3Rs perspective and the evaluation of its superiority compared to the commonly used fin clipping procedure. Hence, I suggest that that aspect of the article should be improved, expanded, and integrated with other data (if available). Specific comments and suggestions are provided below. 1. The methodology described in the article appears to be sound, and I believe that the details provided allow to reliably replicate the simple method in other laboratories. The supplemental video clips are clear and very informative. Author Response: We thank the reviewer for this positive comment about our article. The video forms a core part of this protocol, and bearing this in mind we have now made a new, more professional, film demonstrating the swabbing technique. This video has been incorporated into the updated version of this paper. Reviewer Comment: 2. Despite a lower DNA yield obtained with skin swabs, the DNA samples collected using both methods had similar levels of purity. The authors demonstrated that DNA extracted from skin mucus allows a reliable amplification of target genes, and that no mucus cross contamination occurs in fish held at high density. Author Response: Thank you for highlighting this aspect of our research. Reviewer Comment: 3. The supplemental videos are very good and clearly demonstrate the key practical steps. In the video the operator apparently restrains the fish on the sponge by gently covering the eyes with a gloved finger. I suppose this procedure calms the fish and reduces potential harm. Do the authors suggest that this should be a key step of the protocol? If yes, I suggest to add more details about this step in the main text. Author Response: The reviewer is correct that gently covering the eyes of the fish can help stop them from moving. We routinely carry this out using a hand net. Our new video shows this step of the protocol in more detail. We have also added this information to the main text describing the technique as suggested. Reviewer Comment: 4. In the published protocol the authors reported that fish were immersed in lidocaine for 45 minutes before performing the procedure. Can the authors explain why this duration was selected? Does water temperature affect uptake and pharmacokinetics of lidocaine in different species, and in turn the incubation time? Considering the time needed to perform the skin swab, how many fish should be added to the lidocaine solution to ensure that no fish experiences an excessive exposure? Considering the use of static water conditions for the exposure to lidocaine, I foresee that the temperature may change very rapidly unless the room temperature is controlled. Can the authors recommend a specific strategy to ensure the maintenance of optimal water temperature (and hence the reduction of stress) throughout the lidocaine exposure phase? E.g. using an incubator or a dedicated genotyping rack. Author Response: Since submitting the first version of this protocol, we have published a follow up study that shows that lidocaine treatment is not needed for DNA collection by skin swabbing (Tilley et al., 2023, Validating skin swabbing as a refined technique to collect DNA from small-bodied fish species). We have therefore removed all mentions of lidocaine pre-treatment from the protocol steps included here. Reviewer Comment: 5. Table 1 shows the comparison of DNA concentration from fin clips and skin swabs of the same sticklebacks and zebrafish. I believe the top row displaying the column titles is missing. Author Response: Thank you for spotting this error. Table 1 does miss the top column indicating whether the samples came from swabbed or fin clipped fish. We have now replaced this table with a new version that contains this information. Reviewer Comment: 6. To evaluate the potential cross contamination of mucus samples when fish are held at high density, the authors kept 10 AB wild-type and 10 transgenic zebrafish in a small 3 L tank overnight. The analysis show that, in these conditions, there is no contamination. However, it appears that the authors reached this conclusion after a non-random sampling where all ABs were swabbed first, followed by all transgenic fish (displaying a longer tail). Although one may conclude that there is no cross contamination in the fish tank, the experimental design does not allow to evaluate whether the full procedure itself (i.e. including the transfer onto the sponge) may be a source of contamination. Although the probability is low, do the authors think that the sponge may represent a contamination source? If yes, do they recommend to replace the sponge after sampling a certain number of fish (e.g. how many?). Author Response: The reviewer makes a good point about the possible transfer of mucus on the sponge leading to cross-contamination. We routinely rinse the sponge between sample collection, an important detail that was not described in our protocol. We have now added this information to the updated version of the protocol as suggested. Reviewer Comment: 7. Similar considerations are valid for gloves and nets. How often should these elements be replaced/washed? Author Response: We routinely wash the net that is used to restrain the fish between sampling. This detail has been added to the protocol as per the reviewer’s suggestion. However, we do not change gloves, because we have not noticed any issues with cross-contamination, and this is our standard practice when handling animals and genotyping. Reviewer Comment: 8. The Introduction reports the following statement: “However, despite its popularity, there is evidence that fin clipping can alter health and welfare, leading to infection and altering growth and survival (Taslima et al., 2015)”. However, Taslima et al. (2015) appears to be an aquaculture-related paper focused on Nile tilapia and, as far as I can see, that paper does not provide any evidence of fin clipping-induced damage. Taslima et al. (2015) provided the following generic statement “tissue biopsy may have negative impacts on fish, potentially including infection and effects on survival, growth or behaviour”, and to support this statement they cited Le Vin et al. (2011) (this paper is also cited in the present manuscript). The latter concerns the validation of swabs methods for DNA sampling in fish. Again, the study did not investigate the adverse effects of fin clipping. On the other hand, Le Vin et al. (2011) also stated that fin clipping can be detrimental. This time, to support that statement, they cited several papers from the 60s, 70s, and 80s. However, those papers appear to be referred mainly to aquaculture and field ecology studies where fish are reintroduced in the environment after fin-clipping. Going back to the introduction of the present paper, I believe that whereas the potential adverse effects of fin clipping on behaviour are evidenced with appropriate supporting citations, the other potential adverse effects on infection, growth. and survival are not. Is there any evidence that fin clipping can adversely affect growth, survival, and infection susceptibility in a laboratory setting? If not, the authors should specific that it is not the case, and discuss potential effects observed in aquaculture studies providing an accurate citation and reporting of the primary papers. If yes, it would be useful to have specific data on this important aspect. Author Response: The reviewer makes an important point here. Our statement about effects on growth, infection and survival are not sufficiently supported by the references that we have provided. This has occurred because we over-interpreted the Taslima et al. study, which in turn mis-cited earlier papers including Le Vin et al. 2011. We have now modified the introduction section to reflect this, deleting the suggestion that fin clipping can alter growth, survival and infection. We apologise for this mistake, and hope that the new version of the introduction is acceptable in its current format. Reviewer Comment: 9. Similarly, in the Discussion, the authors wrote that “Several previous studies have shown that fin clipping can have side effects that may alter the outcome of experimental studies. For example, it can lead to secondary infections and elevate the non-specific immune response (Dash et al., 2018)”. However, Dash et al. (2018) do not seem to mention fin clipping at all, as it is a study focused on the role played by fish mucus in health maintenance. Please, revise this reference and replace with primary papers, if possible. Author Response: I am afraid that this is also a mistake on our part. The Dash et al. paper does indeed focus on mucus sampling and not fin clipping, making our statement incorrect. We have removed this sentence in the discussion as suggested by the reviewer. Although skin swabbing is a refined technique compared to fin clipping, it is important not to overstate its benefits. We thank the reviewer for spotting these errors and pointing them out to us. Reviewer Comment: 10. In the present paper, the negative effects of fin clipping of fish behaviour was used as key argument to justify the potential superiority of skin swabbing over fin clipping. However, I believe that this argument is only weakly supported by the data presented here. I suggest to add more data, if available, to strengthen this argument. Author Response: The main aim of this paper is to provide an easy-to-follow protocol for researchers who wish to adopt skin swabbing for DNA collection. The experimental data that is shown aims to provide a background for the technique, and to convince researchers to give it a go. All of the data shown here is modified from previous publications (e.g., Tilley et al., 2020; Breacker et al., 2017). However, the reviewer is correct that this issue could be presented more clearly. To address this issue, we have now added a second data table, modified from Tilley et al., 2020, that shows the greater variability in gene expression and behavioural data following fin clipping compared to skin swabbing. Reviewer Comment: 11. The methodological description of the behavioural tests is too basic and requires more details. For example, in the novel tank diving test, fish were observed/recorded for the first five minutes. Is this observation time justified by other studies for both stickleback and zebrafish? If yes, what are the supporting references? Were multiple fish/tanks filmed simultaneously using multiple tanks? If yes, did the operator add the fish using a specific sequence or removed the first seconds of the video where the operator was still in the room? (The operator in the room is a source of stress). The results section indicates that multiple time points were tested. However, the different timepoints and the rationale behind their selection are not described in the methods section. The importance of providing an accurate description of the methods is clearly demonstrated by the following, and more important, point. Author Response: As per the responses above, the behavioural information mentioned here is not the main focus of this paper. Rather, we have used data from Tilley et al., 2020 to demonstrate the variability in experimental results seen after fin clipping. The behaviour methods that we have used here are standard for the field of zebrafish research. The novel tank diving test protocol mentioned here is based upon the published work of Egan and colleagues in zebrafish, (Egan et al., 2009 – now included in the reference list), and modified for sticklebacks by Gutierrez and colleagues (Norton and Gutierrez, 2019). In brief, we recorded a single fish at a time for 5 minutes, and analysed the entirety of the behavioural response. Each timepoint that we looked at was recorded separately, using the same setup in the same room. The experimenter was present in the room throughout recording. Reviewer Comment: 12. The results section indicates that there is “Greater variability in results after clipping compared to swabbing”. I found that statement confusing as, by itself, it leads one to believe that there is a variability in genotyping results whereas the authors refer to behavioural and stress endpoints (which are not the focus of the paper). Later, the article provides the following statement: “Behavioural data collected subsequent to fin clipping showed more variable data compared to skin swabbed animals, meaning that more individuals need to be measured to test hypotheses with sufficient statistical power (Tilley et al., 2020). This means that collecting DNA by skin swabbing may lead to a reduction of total number of animals needed in experiments”. In my opinion, it is unclear why skin swabbing could allow to use fewer animals. Do the authors refer to a specific context? I suggest to clarify this point or to remove it. Author Response: We published data showing that compared to skin swabbing, fin clipping led to a greater variation in gene expression and behavioural data in Tilley et al., 2020. This data used an asymptotic test for the equality of coefficients of variation from k populations to contrast physiological and behavioural data after skin swabbing or fin clipping. When compared to control undisturbed fish, fin clipping led a large variation in data whereas skin swabbing did not. This means that fewer animals would need to be included in each experimental group in order to collect statistically significant data, if skin swabbing is used for DNA collection rather fin clipping. We have included table 2 in this manuscript, and re-written the results and discussion section to make this clearer. Reviewer Comment: 13. Overall, this specific aspect of the work (i.e. data variability) has been highlighted very strongly in the manuscript; however, my main concern is the data does not appear to support the hypothesis of a treatment-dependent effect. The present manuscript does not provide any figure or table of the behavioural data; however, this data can be retrieved from Tilley et al. (2020). Reading the latter, it is possible to note that the observed behavioural effects appeared to be (almost always) driven by fish handing procedures and not by fin clipping or skin swabbing themselves. The same consideration is valid for the assessment of opercular beats. The fact that control fish display behavioural responses more often (or as often) as fish that underwent DNA collection weakens the argument of treatment-specific effects, and hence treatment-specific benefits, including 3Rs benefits. Can the authors provide more data concerning this aspect? Author Response: The data shown here is modified from Tilley et al., 2020, where we investigate which components of the fin clipping and swabbing procedures trigger a stress response in fish. While handling fish does trigger stress, we were able to show that the fin clipping procedure in its entirety is more stressful than the swabbing or handling alone. We have included a new table 2 in this version of the manuscript that shows some of this information, as suggested by the reviewer. Reviewer Comment: 14. To measure the effects of the different procedures on the stress axis, the authors measured cortisol excretion in the tanks of fish that underwent 1) no manipulation, 2) skin swabbing, 3) fin clipping. I believe that the experimental design described in the article is not suitable to provide an answer to the specific research question considered here. Although measuring the cortisol released by a non-manipulated group provided a useful reference value, I believe that there are multiple factors to consider for a more rigorous comparison. 1) Fish handing – it is known that fish netting and air contact are major stress factors that induce an increase of cortisol release in the surrounding water (Ellis, James, Scott 2004). Measuring cortisol concentrations in tanks of non-manipulated fish will very likely indicate lower values, independently from skin swabbing or fin clipping. Hence, a more appropriate control would be represented by fish that underwent the same handling (i.e. netting and transfer to a new tank) without DNA sampling procedure. 2) The pre-procedure treatment of fish that underwent skin swabbing or fin clipping were very different (i.e. 45 minutes exposure to lidocaine in a confined space versus rapid treatment with MS-222). From the results presented here, it is not possible to evaluate whether the 45 minutes pre-treatment with lidocaine did or did not affect cortisol release. In conclusion, this suggests that an experiment aimed at evaluating the stress response to different DNA sampling procedures should include specific negative controls for each treatment type and fish handling procedure. Author Response: The author is right to note that handling fish, and removing them from their tank could affect cortisol release. We have already investigated the constituent steps that make up the swabbing and fin clipping procedures, and these results have been published in two separate papers (Tilley et al., 2020; Tilley et al., 2023). Since the focus of this paper is the step-by-step protocol that to aid uptake of the swabbing technique, we have chosen not to include all of this data here. We have made this point clearer, by modifying the legend to figure 4 (showing the cortisol results) to read “Please refer to Tilley et al., 2020 for further control treatment groups and data points”. Reviewer Comment: 15. In the discussion, the authors reported that “changes in gene expression and behaviour caused by skin swabbing tended to appear between two and seven days after manipulation, perhaps due to the activation of an immune response, or changes in ionic or osmotic regulation (Dash et al., 2018)’. In my opinion, this possibility is concerning and should be explored in further studies, as it may hamper any 3Rs benefit of skin swabs. For example, are swabbed fish in the laboratory more susceptible to infection and disease in the longer term compared to fin clipped fish? Author Response: Thank you for this suggestion. We don’t know why we see such as delayed impact of swabbing upon gene expression and behaviour, but we are currently investigating this. We hope to be able to report the effect of swabbing upon the mucus layer in more detail in a future publication. Reviewer Comment: 16. The reference de Lombaert et al. (2017) is not present in the reference list. Author Response: Thank you for spotting this error. We have now added de Lombaert et al., 2017 to the reference list." } ] }, { "id": "144865", "date": "17 Aug 2022", "name": "Errol Cason", "expertise": [ "Reviewer Expertise Genetics", "Genomics", "Microbiomes" ], "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 provides detailed steps to collect DNA from small-bodied fish species using skin swabbing. This is offered as a alternative, easier, less invasive and more ethical methods of acquiring DNA from fish during trials when compared to the standard method of fin clipping.\nEvidence is provided that enough DNA an be obtained for downstream application with less stress, discomfort and pain to the fish.\nIn essence this paper is a \"manual\" for methods already put out in Breaker et al. (2017) and Tilley et al. (2020).1,2 It appears to only exist as a easily accessible and referenceable recipe. It will save scientists time and effort to go and dig through the other papers if all they really want is A) to know if the method works and B) how to do it.\nWhile this is not a novel study, and is just a bullet point + video version of previously published methods, I do however feel that this is not a bad thing. I can see how the other two papers might not be getting the traction they deserve for a method that mostly works just as well but you don't need to mutilate an animal to get DNA. I therefore see no reason not to index this.\n\nAre a suitable application and appropriate end-users identified? Yes\n\nAre the 3Rs implications of the work described accurately? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate? Yes\n\nIs the rationale for developing the new method (or application) clearly explained? Yes\n\nIs the description of the method technically sound? Yes\n\nAre sufficient details provided to allow replication of the method development and its use by others? Yes\n\nIf any results are presented, are all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions about the method and its performance adequately supported by the findings presented in the article? Yes", "responses": [] } ]	1	https://f1000research.com/articles/10-1064
https://f1000research.com/articles/11-1578/v1	23 Dec 22	{ "type": "Research Article", "title": "Expression of Fascin and SALL4 in odontogenic cysts and tumors: an immunohistochemical appraisal.", "authors": [ "Spoorti Kulkarni", "Harishanker Alampally", "Vasudev Guddattu", "Gabriel Rodrigues", "Sunitha Carnelio", "Spoorti Kulkarni", "Harishanker Alampally", "Vasudev Guddattu", "Gabriel Rodrigues" ], "abstract": "Background: Various stemness markers (SOX2, OCT4, and NANOG) have been studied in odontogenic cysts and tumors. However, studies on SALL4 having similar properties of stemness has not been documented. Additionally, insight into fascin as a migratory molecule is less explored. In this study, the expression of SALL4 and fascin were evaluated in ameloblastoma, adenomatoid odontogenic tumor (AOT), odontogenic keratocyst (OKC), dentigerous cyst (DC), radicular cyst (RC), and calcifying odontogenic cyst (COC). Methods: Semi-quantitative analysis of fascin and SALL4 immuno-positive cells was done in a total of 40 cases of ameloblastoma (11 plexiform, 12 follicular, 12 unicystic, and 5 desmoplastic) variants, 6 cases of AOT, 15 each of OKC, DC, RC and 5 of COC. Chi-square test was applied to evaluate the association between SALL4 and fascin expression in odontogenic cysts and tumors. Results: Fascin immunopositivity was observed in peripheral ameloblast-like cells, and weak or absent in stellate reticulum-like cells. A moderate to weak immune-reactivity to SALL4 was observed in the cytoplasm of ameloblastoma, epithelial cells of dentigerous and radicular cysts, having a marked inflammatory infiltrate, which is an interesting observation. COC and AOT had negative to weak expressions. No recurrence has been reported. Conclusions: Expression of fascin in ameloblastomas elucidate their role in motility and localized invasion. Its expression in less aggressive lesions like DC, COC, AOT will incite to explore the other functional properties of fascin. SALL4 expression in the cytoplasm of odontogenic cysts and tumors may represent inactive or mutant forms which requires further validation.", "keywords": [ "Fascin", "SALL4", "ameloblastoma", "immunohistochemistry", "cyst", "odontogenic tumor" ], "content": "Introduction\n\nOdontogenic cysts and tumors are said to originate from odontogenic apparatus or oral epithelium. Ameloblastoma, the most common odontogenic tumor is known for its local but aggressive biological behaviour.1 The 2017 World Health Organisation (WHO) classification on ameloblastomas have reclassified them into ameloblastoma, unicystic and extraosseous/peripheral types.2 Adenomatoid odontogenic tumors (AOT) are benign with less recurrence.2,3 Among the odontogenic cysts, keratocysts arising from the dental lamina are said to have aggressive behavior, appearing as multilocular radiolucencies with cortical thinning, tooth displacement and root resorption radiographically and a postoperative recurrence rate ranging from 2.5 to 62%.4,5\n\nResearch to identify new markers to determine the biological behavior of odontogenic cysts and tumors is ongoing. Literature review reveals many preliminary observations with no concrete evidence of a single marker being specific to these tumors and hence there is a need to determine new markers.6 In this study, we have employed two markers: fascin and SALL4. Fascin, a 55-kDa is a cytoskeleton binding proteins that bundle actin filaments, assists the cell in forming stress fibres (or ruffled borders or micro spikes) and assists cell motility and migration hence it fascin can be used for predicting the aggressive clinical course of a tumor.7–10 Usually, in normal adult epithelial cells its fascin expression is low or absent.11 The gene encoding fascin-1 in humans is located on chromosome 7q22.12 SALL4 is a stem cell marker and a master zinc-finger transcriptional factor, as well as being a member of the spalt-like (SALL) gene family. SALL4 is mapped to chromosome 20q13.2 and plays its part in maintaining pluripotency and self-renewal of embryonic and hematopoietic stem cells by interacting with other molecules such as OCT4, SOX2 and NANOG.13–15 SALL4 incorporated along with OCT4, SOX2 and KLF4 (OSK) helps in forming stable induction of pluripotent cells (iPS) cells with a higher efficiency.16 Several studies noted the aberrant SALL4 expression in different types of malignant neoplasms and various autosomal dominant diseases such as Okihiro/Duane-radial ray syndrome, acro-renal-ocular syndrome, Instituto Venezolano de Investigaciones Cientificas syndrome (IVIC) and are suspected to cause thalidomide embryopathy.17–20 Literature review has no reports of combination of fascin and SALL4 in odontogenic cysts and tumors to address their biological behavior and thus taking into consideration the local aggressive behavior of ameloblastoma, we hypothesise that fascin might contribute for the local migratory behavior of these odontogenic cells and SALL4 may exhibit the stemness on odontogenic cells. Thus, the aim of the present study was to evaluate the expression of fascin and SALL4 in histopathological variants of ameloblastoma, AOT and various odontogenic cysts.\n\n\nMethods\n\nThis study was approved (IEC approval number 360/2019, 14-05-2019; IEC 156/2014, 12-03-2014) by the Institutional Ethical Committee, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India. Participant consent was waived by the committee.\n\nFormalin fixed paraffin embedded tissue (FFPE) was used for the study. Materials included a total of 40 cases of ameloblastoma (11 plexiform, 12 follicular, 12 unicystic, 5 desmoplastic) variants, 6 cases of AOT, 15 each of OKC, DC, RC and 5 of COC. Before the start of the study, statistician was consulted and based on the literature review, availability of the material in the archives of the department and the availability of the budget the sample was decided.\n\nSamples were retrieved from the Department of Oral and Maxillofacial Pathology, Manipal College of Dental Sciences, Manipal, India after the approval from the Institutional Ethical Committee. This study used previously diagnosed samples of odontogenic cysts and tumors that were granted to us after obtaining written approval from the Head of the Department to use for this study. The samples were stored in the biobank of our department.\n\nThe diagnosis of the above said odontogenic cysts and tumors were done based on clinical and histological features (using H&E staining) according to WHO guidelines.2 Sample selection was done based on inclusion and exclusion criteria: only histopathologically diagnosed cases of odontogenic cysts and tumors from 2012-2017 were considered, all the samples taken for the current study were prior to the patient receiving any treatment, cases with recurrence were excluded.\n\nImmunohistochemical staining of the tissue sections from each of the cases selected was done using the streptavidin-biotin method. In brief, 4 𝜇m sections were mounted on 3-aminopropyltriethoxysilane (APES) coated slides (Novolink Polymer Detection System, Novocastra). Sections were then deparaffinized in xylene, which is done in three grades for 10 minutes each as per standard immunohistochemical protocol. The document of the protocol has been uploaded in the repository (Open Science Framework protocol.io)26 and hydrated in different grades of alcohol (ranging from absolute alcohol (10 minutes), 95 % alcohol (10 minutes), 70% (10 minutes), 50% (10 minutes) each).26 Slides were then incubated with primary antibodies (rabbit monoclonal IgG for SALL4 and mouse monoclonal IgG1 for fascin)26 against fascin (clone SC-21743, Santa Cruz Biotechnology USA, Inc) diluted 1:200, SALL4 (clone EP-299, PathnSitu, Livermore, USA) at a dilution of 1:100 for one hour. The sections were subsequently washed in tris-buffered saline and incubated with secondary biotinylated antibody and streptavidin-biotin peroxidase complex (Novolink Polymer Detection System, Novocastra) for 30 minutes each. Diaminobenzidine (DAB) was used as the chromogen and the sections were counterstained with Mayer’s hematoxylin. Buccal mucosa tissue was used as positive control and endothelial cells were internal controls for fascin antibody (Figure 1), while dysgerminoma was taken as a positive control, bud and bell stage of tooth development were also included for the expression of SALL4 (Figure 2). The primary antibody was omitted during IHC staining for the negative control.\n\nHistopathological variants of ameloblastoma: (A) Follicular (IHC, 10×), (B) Plexiform (IHC, 10×), (C) Unicystic (IHC, 10×), (D) Desmoplastic (IHC, 4×), (E) Focal immune-positivity for fascin in AOT (IHC, 10×), (F) COC (IHC, 10×), (G) OKC (IHC, 4×), (H) Dentigerous cyst (IHC, 10×), (I) Radicular cyst, (IHC, 10×), (J) Immuno-positivity for fascin in basal cells of the oral epithelium (IHC, 4×), (K) Oral squamous cell carcinoma used as positive control stained with fascin (IHC, 10×). IHC-Immunohistochemistry. The software used record images is Olympus-DP2BSW (ver 2.1).\n\nVariants of ameloblastoma (A) Follicular (IHC, 10×), (B) Combination of follicular & plexiform (IHC,10×), (C) Unicystic (IHC, 4×), D) Immuno-negative in AOT (IHC, 10×), (E) OKC (IHC, 20×), (F) Dentigerous cyst (IHC, 10×), (G) Radicular cyst (IHC, 20×), (H) Immuno-negative COC (IHC, 10×), (I) Epithelial cells & ectomesenchyme surrounding the bud stage (IHC, 10×), (J) Bell stage: Focal positive to SALL4 in inner enamel epithelium (IEE) and sporadic expression in dental papilla (DP) (IHC, 10×), (K) Strong expression of SALL4 in dysgerminoma (positive control 20×). IHC-Immunohistochemistry.\n\nPresence of brown color at the end of staining was considered as positive reactivity. The slides were evaluated with a light microscope (Olympus BX41) attached with Olympus DP20 microscope camera (Olympus Singapore Pvt Ltd, Singapore) at 20× & 40× magnification. The distribution of antibodies were assessed in the cytoplasm and cell membrane of ameloblastic lining of the lesions for fascin while SALL4 staining was evaluated in nuclear and cytoplasmic areas. In each case, three fields were randomly selected and evaluated.\n\nA semi-quantitative method was used to score the fascin and SALL4 expression in the epithelial odontogenic cells.\n\nBased on intensity: (a) of the immunostaining in the epithelial odontogenic cells (0-1 = absent/weak, 2 = moderate, 3 = strong).\n\nDegree of staining: (b) the percentage of positive odontogenic cells (1 ≤ 25% positive cells, 2 = 25-50% positive, 3 = 51-75% positive and 4 ≥ 75% positive cells).\n\nTotal staining: The final immunostaining score was determined by the sum of (a) + (b). Final scores ranged from 0 to 7 (0 = absent, 1-4 = weak and 5-7 = strong).\n\nThe data obtained was statistically analyzed with the statistical software program SPSS (version 17.0). The statistical significance of fascin and SALL4 in histopathological types of ameloblastoma was analysed using the chi-square test. P values less than 0.05 were considered to indicate statistical significance.\n\n\nResults\n\nImmunohistochemically stained sections of various odontogenic cysts and tumor tissue were evaluated for expression of SALL4 in the cytoplasm as well as nuclei of peripheral ameloblastic cells and stellate reticulum like cells while expression of fascin was observed in the cell membrane, between cell boundaries and cytoplasm of peripheral ameloblastic cells, stellate reticulum like cells and stromal cells of 40 cases of ameloblastoma variants from the year 2012 to 2017. The expression of fascin and SALL4 varied from case to case as well as in the same tissue section. Most of the variants of ameloblastoma were strongly positive for fascin but cases of desmoplastic ameloblastoma (5/5) were negative for fascin (Table 1A, Figure 1D). To eliminate bias, two observers independently evaluated the expression of these, selecting the most representative site separately under a light microscope at 200× and 400× magnification. The SALL4 positivity was heterogeneous with varied intensity and staining pattern with absence of expression in few follicles (Figure 2) but in most of the follicular, plexiform and unicystic ameloblastoma, the immunopositivity was observed diffuse in the cytoplasm and less localised to the nucleus (Figure 2A–C) but the stromal cells were devoid of its expression except in the endothelial cells. Fascin expression was found to be weak or absent in stellate reticulum like cells (Figure 1). In cases of unicystic ameloblastoma, positivity for fascin was observed in the basal as well as in the upper layers (Figure 1C). However intra-group comparison did not show any significant difference. The final scoring was obtained after combining the intensity and percentage scoring and was found to be strong in most of the cases (Table 1A).\n\nAOT was immune-positive to fascin in few areas (< 25%) with mild to moderate intensity (Figure 1E), while immune-negative for SALL4 expression (Figure 2D). Fascin expression in odontogenic cysts (OKC, RC, DC) (Figure 1G–I) was strongly positive with greater than 75% cells, while intensity ranged from moderate to strong along the cystic lining. COC revealed immune-positivity ranging from 25-50% (Figure 1F). SALL4 expression in odontogenic cysts was strongly positive with greater than 75% cells stained, while intensity ranged from mild to moderate with a diffuse cytoplasmic staining, at places nuclear staining was evident (Table 1B), Figure 2E–G). COC was immune-negative (Figure 2H).\n\n\nDiscussion\n\nResearchers have worked on the molecular mechanism to understand the nature of local invasion of ameloblastomas into the surrounding tissues which include molecules degrading the extracellular matrix, those involved in bone remodelling, molecules associated with angiogenesis and molecules related to proliferation. Though the results are partially promising, the exact molecular mechanism of invasion in ameloblastomas is not completely understood.6 Cell motility is essential for tumor invasion and subsequent dissemination or metastases. This increase in motility occurs via the modulation of actin filaments to form finger-like plasma membrane protrusions termed invadopodia. Numerous actin-binding proteins, including fascin, regulate such dynamic rearrangement of the actin cytoskeleton. Fascin, being one of the actin cross-linking proteins, localizes to filopodia at the leading edge of migratory cells by organising f-actin into well-ordered, tightly packed parallel bundles observed in vitro studies.21\n\nFascin overexpression is observed in various precancerous lesions and oral squamous cell carcinoma (OSCC).9,12 In our study, we observed that a majority of our cases were strongly positive for fascin in the various subtypes of ameloblastoma. Various in vitro and in vivo studies have observed that fascin has a functional role in cell invasion and motility.13 This could account to the local aggressiveness of ameloblastoma clinically. Few of the ameloblastic follicles did not exhibit fascin, we speculate this could be attributed to loss of antigen during processing or reduced motility in these cells.\n\nIn various histopathological grades of ameloblastoma, SALL4 was expressed in the majority of cases. Studies have documented transcription activity of SALL4, which could be reflected by its positivity in the nucleus.15,22 We observed that the odontogenic epithelial cells were positive for SALL4 in the cytoplasm, stained diffusely, which we speculate could be in an inactive/dormant or mutant form which requires further investigation. Majority of OKC were devoid of SALL4 except in the basal cells. Radicular and dentigerous cysts, having marked infiltration of inflammatory cells had strong immune-positivity for SALL4 in the cytoplasm, an interesting finding of this study. Hence the role of cytokines in stimulating SALL4 needs to be ruled out. Odontogenic tumors, AOT and developmental odontogenic cysts, COC (simple type) were negative for SALL4. Studies have shown that OKCs expressed higher amount of PCNA and Ki-67 when compared to other jaw cysts, indicating its inherently increased proliferative potential of OKC.23 This speculates that various other molecular pathways could play an important role in the disease process. Further studies are required to explore this possibility, since this is a preliminary study.\n\nNormal connective tissue cells such as fibroblasts, vascular endothelial cells, neural and glial cells, brain and splenic tissue expressed fascin, which relates to its function, required to maintain normal homeostasis.9 In embryogenesis, various migratory cells express fascin, except in terminally differentiated squamous cells where its expression is low or absent.9,24 Our previous study on tooth buds showed fascin expression in various stages of tooth development was site and time specific, thus confirming its role in cell remodulation.3 SALL4 expression was not detected in tooth bud stage, however focal positivity was observed in the cytoplasm of the epithelial cells of bell stage, this could attribute to the cells to undergo more differentiated state of the cells.25 The papillary cells in various stages of tooth germ were positive (Figure 2J) and this could relate to stemness due to the pluripotency nature of dental papilla. Further studies are required to understand the crosstalk with other stem cell markers in maintaining the stemness or pluripotency state of the cells.\n\nIn conclusion, the findings of the present study on the expression of fascin elucidate their role in motility and localized invasion or in maintaining the cellular homeostasis, while the expression of SALL4 remains elusive.\n\n\nData availability\n\nOpen Science Framework: Expression of fascin and SALL4 in odontogenic cysts and tumors: an immunohistochemical appraisal. https://doi.org/10.17605/OSF.IO/9ZFRS.26\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\nEffiom OA, Ogundana OM, Akinshipo AO, et al.: Ameloblastoma: current etiopathological concepts and management. Oral Dis. 2018; 24: 307–316. PubMed Abstract \| Publisher Full Text\n\nReichart P, Sciubba JJ, Philipsen HP: Splitters or lumpers: The 2017 WHO Classification of Head and Neck Tumors. J. Am. Dent. Assoc. 2018; 149: 567–571. Publisher Full Text\n\nAlampally H, Chandrashekar C, Rodrigues G, et al.: Fascin in tooth germs: an immunohistochemical analysis. J. Histotechnol. 2018; 41: 24–28. Publisher Full Text\n\nRajendra Santosh AB: Odontogenic cysts. Dent. Clin. N. Am. 2020; 64: 105–119. Publisher Full Text\n\nBilodeau EA, Collins BM: Odontogenic cysts and neoplasms. Surg. Pathol. Clin. 2017; 10: 177–222. Publisher Full Text\n\nJúnior JF, de França GM , da Silva Barros CC , et al.: Biomarkers involved in the proliferation of the odontogenic keratocyst, glandular odontogenic cyst and botryoid odontogenic cyst. Oral Maxillofac. Surg. 2022 Jan 21; PubMed Abstract \| Publisher Full Text\n\nLamb MC, Tootle TL: Fascin in cell migration: more than an actin bundling protein. Biology (Basel). 2020; 9: 403.\n\nYamashiro S: Functions of fascin in dendritic cells. Crit. Rev. Immunol. 2012; 32: 11–22. PubMed Abstract \| Publisher Full Text\n\nLamptey J, Czika A, Aremu JO, et al.: The role of fascin in carcinogenesis and embryo implantation. Exp. Cell Res. 2021; 409: 112885. PubMed Abstract \| Publisher Full Text\n\nAdams JC: Fascin protrusions in cell interactions. Trends Cardiovasc. Med. 2004; 14: 221–226. PubMed Abstract \| Publisher Full Text\n\nZhang X, Cho IH, Park JH, et al.: Fascin is involved in cancer cell invasion and is regulated by stromal factors. Oncol. Rep. 2019; 41: 465–474. PubMed Abstract \| Publisher Full Text\n\nLiu H, Zhang Y, Li L, et al.: Fascin actin-bundling protein 1 in human cancer: promising biomarker or therapeutic target? Mol. Ther. Oncolytics. 2021; 20: 240–264. PubMed Abstract \| Publisher Full Text\n\nXiong J: SALL4: engine of cell stemness. Curr. Gene Ther. 2014; 14: 400–411. PubMed Abstract \| Publisher Full Text\n\nZhang X, Yuan X, Zhu W, et al.: SALL4: an emerging cancer biomarker and target. Cancer Lett. 2015; 357: 55–62. PubMed Abstract \| Publisher Full Text\n\nTatetsu H, Kong NR, Chong G, et al.: SALL4, the missing link between stem cells, development and cancer. Gene. 2016; 584: 111–119. PubMed Abstract \| Publisher Full Text\n\nParchem RJ, Ye J, Judson RL, et al.: Two miRNA clusters reveal alternative paths in late-stage reprogramming. Cell Stem Cell. 2014; 14: 617–631. PubMed Abstract \| Publisher Full Text\n\nKohlhase J, Chitayat D, Kotzot D, et al.: SALL4 mutations in Okihiro syndrome (Duane-radial ray syndrome), acro-renal-ocular syndrome, and related disorders. Hum. Mutat. 2005; 26: 176–183. PubMed Abstract \| Publisher Full Text\n\nBorozdin W, Boehm D, Leipoldt M, et al.: SALL4 deletions are a common cause of Okihiro and acro-renal-ocular syndromes and confirm haploinsufficiency as the pathogenic mechanism. J. Med. Genet. 2004; 41: e113. PubMed Abstract \| Publisher Full Text\n\nParadisi I, Arias S: IVIC syndrome is caused by a c.2607delA mutation in the SALL4 locus. Am. J. Med. Genet. A. 2007; 143: 326–332. PubMed Abstract\n\nGao S, Wang S, Fan R, et al.: Recent advances in the molecular mechanism of thalidomide teratogenicity. Biomed. Pharmacother. 2020; 127: 110114. Publisher Full Text\n\nPfisterer K, Levitt J, Lawson CD, et al.: FMNL2 regulates dynamics of fascin in filopodia. J. Cell Biol. 2020; 219: e201906111. PubMed Abstract \| Publisher Full Text\n\nYang J, Corsello TR, Ma Y: Stem cell gene SALL4 suppresses transcription through recruitment of DNA methyltransferases. J. Biol. Chem. 2012; 287: 1996–2005. PubMed Abstract \| Publisher Full Text\n\nKaplan I, Hirshberg A: The correlation between epithelial cell proliferation and inflammation in odontogenic keratocyst. Oral Oncol. 2004; 40: 985–991. PubMed Abstract \| Publisher Full Text\n\nDe Arcangelis A, Georges-Labouesse E, Adams JC: Expression of fascin-1, the gene encoding the actin-bundling protein fascin-1, during mouse embryogenesis. Gene Expr. Patterns. 2004; 4: 637–643. PubMed Abstract \| Publisher Full Text\n\nRodas-Junco BA, Villicaña C: Dental pulp stem cells: current advances in isolation, expansion and preservation. Tissue Eng. Regen. Med. 2017; 14: 333–347. Publisher Full Text\n\nKulkarni S, Alampally H, Guddattu V, et al.: Expression of fascin and SALL4 in odontogenic cysts and tumors: An immunohistochemical appraisal. OSF. 12 Sept. 2022. Publisher Full Text https://osf.io/9zfrs/" }	[ { "id": "171400", "date": "16 May 2023", "name": "Pentti Nieminen", "expertise": [ "Reviewer Expertise Statistical reporting and data presentation" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 expression of SALL4 and fascin were evaluated in odontogenic tumours and cysts. The findings of the study on fascin expression clarify their role in motility and localized invasion or maintenance of cellular homeostasis. However, the expression of SALL4 remains unclear.\nThe focus of this review is mainly on data reporting. My comments to the authors are as follows:\nOne positive aspect of your manuscript was that it was a short report, which kept the focus on the main objective.\n\nI enjoyed reading the introduction section of this manuscript. The research question related to was well described.\n\nIntroduction, last sentence: Please consider specifying the aims of your study. It would help your readers if you stated that the aim was to estimate the prevalence of two biomarkers, SALL4 and fascin, in histopathological variants of ameloblastoma, AOT and various odontogenic cysts. In addition, your aim was to compare the prevalence of biomarkers between different tumours and cysts.\n\nAs a short report, the statistical intensity of the manuscript was lower than the average of articles published in visible general medical journals. However, the quality of statistical reporting and data presentation was weak: I gave it a score of 3 on a scale of 0 (poor) to 10 (very high). In particular, the quality of data presentation in tables should be improved.\n\nConsider including a table describing the distributions of the basic characteristics of the cases, their clinical history, and the main outcome variables. If many characteristics of human cases are described, the details of the cases and the number of cases contributing to the analysis are best included in a tabular presentation.\n\nTables 1A and 1B are not well prepared. Tables with proper titles, clear labelling and optimally presented data will enable readers to scrutinise the data. The tables did not have clear titles. The current formatting of these tables resembled a spreadsheet, and the lines of the same size between each row and column did not help to clarify the different data presented in the tables. Not all abbreviations were defined. What differences do the statistical significance tests evaluate?\n\nStatistical analysis section should help a knowledgeable reader to judge the appropriateness of the methods for the study and to verify the methods reported. You should improve the description of statistical methods. State clearly that total staining scores of SALL4 and fascin are your main outcome measures. Then describe that the prevalence of these response variables was estimated in different tumour and cyst groups. Clarify the variables and methods for each significance test performed in the study.\n\nThe small number of cases in several subgroups of tumours and cysts is a limitation of your study. Please address this in the discussion section.\n\nIs the work clearly and accurately presented and does it cite the current literature? No\n\nIs the study design appropriate and is the work technically sound? No\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNo\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [ { "c_id": "10172", "date": "06 Sep 2023", "name": "Dr. Spoorti Kulkarni", "role": "Author Response", "response": "We thank Pentti Nieminen for reviewing our article and giving us valuable comments. I appreciate the time and efforts spent to make our work better. I have carefully reviewed the comments and revised the manuscript accordingly. All comments pointed out by the reviewer have been corrected. I have responded question wise. 3. Introduction, last sentence: Please consider specifying the aims of your study. It would help your readers if you stated that the aim was to estimate the prevalence of two biomarkers, SALL4 and fascin, in histopathological variants of ameloblastoma, AOT and various odontogenic cysts. In addition, your aim was to compare the prevalence of biomarkers between different tumours and cysts. Response: We have explained the same in the abstract and didn’t want to repeat the same in the introduction. However as advised we have modified the same in the introduction. Also from the oral pathologist view prevalence is synonym to expression and estimate is synonym to evaluate, we have incorporated the same in introduction. Thus, the aim of the present study was to evaluate the expression of these two biomarkers fascin and SALL4 in histopathological variants of ameloblastoma, AOT and various odontogenic cysts namely Odontogenic keratocyst, Dentigerous cyst and Radicular cyst. Since the biological behaviour of cyst and tumors differs, we didn’t do the comparison between them. 4. As a short report, the statistical intensity of the manuscript was lower than the average of articles published in visible general medical journals. However, the quality of statistical reporting and data presentation was weak: I gave it a score of 3 on a scale of 0 (poor) to 10 (very high). In particular, the quality of data presentation in tables should be improved. Response: We have revised the data presentation in the Tables 1 and Table 2 (other tables have been added as supplementary files S1, S2,S3,S4). 5. Consider including a table describing the distributions of the basic characteristics of the cases, their clinical history, and the main outcome variables. If many characteristics of human cases are described, the details of the cases and the number of cases contributing to the analysis are best included in a tabular presentation. Response: The excel sheet with the clinical details of the patients has been attached as a supplementary file in the OSF repository. 6.Tables 1A and 1B are not well prepared. Tables with proper titles, clear labelling and optimally presented data will enable readers to scrutinise the data. The tables did not have clear titles. The current formatting of these tables resembled a spreadsheet, and the lines of the same size between each row and column did not help to clarify the different data presented in the tables. Not all abbreviations were defined. What differences do the statistical significance tests evaluate? Response: The tables have been modified as per reviewers comments and have been uploaded in the OSF repository. Regarding the evaluation of the statistical significance test, in all the odontogenic tumors, the staining intensity of fascin is similar compared to SALL4. With regard to the stained cell count, higher counts are observed with fascin as compared to SALL4. In relation to odontogenic cysts viz odontogenic keratocyst and dentigerous cyst, the intensity of fascin staining is more than SALL4.Also the higher cell counts were observed in fascin as compared to SALL4 in odontogenic keratocyst. 7. Statistical analysis section should help a knowledgeable reader to judge the appropriateness of the methods for the study and to verify the methods reported. You should improve the description of statistical methods. State clearly that total staining scores of SALL4 and fascin are your main outcome measures. Then describe that the prevalence of these response variables was estimated in different tumour and cyst groups. Clarify the variables and methods for each significance test performed in the study. Response: We have uploaded the modified tables and these tables are self-explanatory, as per the advice of the reviewer. Fischers exact test was used to compare the distribution of staining intensity and cell count across SALL4 and Fascin. 8. The small number of cases in several subgroups of tumours and cysts is a limitation of your study. Please address this in the discussion section. Response: The small number of cases in the present study with regard to odontogenic tumors and its subgroup as well as in odontogenic cysts were limitation of this study. Further studies with large sample size is required for the better understanding of these biomarkers in these lesions." } ] }, { "id": "179066", "date": "13 Jul 2023", "name": "Konstantinos I Tosios", "expertise": [ "Reviewer Expertise Oral pathology" ], "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 immunohistochemical study on the expression of Fascin and SALL4 in ameloblastoma, adenomatoid tumor and odontogenic cysts. The manuscript could be considered for indexing, as it presents some new information, following full reconsideration of every sentence, as it is not properly written. The authors should carefully document the aim through the Introduction and state the aim clearly and concisely. In its present form the manuscript gives the impression that the authors applied two non-related antibodies in a convenient sample of odontogenic cysts and tumors, without having a working hypothesis to test. They should avoid the M&M critical mistakes, i.e., differences in positive controls among legends and texts - that alone could lead to a rejection. The Results and Discussion are not well structured, prohibiting their comprehension. All the above, coupled with the many grammatical errors, do not allow the (possible) significance of the findings to surface and make this manuscript, in its present form, not suitable for indexing.\n\nMajor concerns\nThe Title refers to odontogenic cysts and tumors, but as it turns out the study includes two tumors and many different cysts. Why did the authors choose to examine those lesions?\n\nIn the Introduction there is some information on three of the lesions investigated (what about DC, RC or COC?) and this is inconsistent, i.e., they present recurrence rate for OKC, but not for ameloblastoma or AOT. The authors should consistently present the same data for each lesion.\n\nFascin and SALL4 seem to be two unrelated. Is there any association between them? Why did they choose to examine them? The authors use some references about the role in malignant neoplasms, however the lesions under consideration are not malignant neoplasms, while most of the references do not include studies on their expression in malignant neoplasms. Please carefully check your references.\n\nThe aim of the study should be concise and clear. It should be reconsidered.\n\nM&M: “Before the start of the study, statistician was consulted and based on the literature review, availability of the material in the archives of the department and the availability of the budget the sample was decided”. Are 6 AOTs or 5 COC’s an adequate sample size?\n\nThe Patients and Tissues samples section needs restructuring. Origin of material, inclusion/exclusion criteria, IRB etc.\n\nWhat was the positive control for Fascin, the basal cells of the oral epithelium (Figure) or the endothelial cells of the buccal mucosa (text)? Any supporting reference of any of them?\n\nIn general, please present the findings in a more orderly manner, i.e., what did you see in the positive controls (membranous and cytoplasmic expression in the basal cells of the epithelium, etc.).\n\nFollow the same order of the antibodies, i.e., if you choose Fascin/SALL4 then present the results first for fascin and then for SALL4.\n\n“40 cases of ameloblastoma variants from the year 2012 to 2017”. This information is not proper here.\n\nResults should be rewritten in a more orderly manner.\n\nDiscussion: “Researchers have worked on…”. There are no references to support this.\n\nDiscussion: “the odontogenic epithelial cells were positive for SALL4 in the cytoplasm, stained diffusely, which we speculate could be in an inactive/dormant or mutant form which requires further investigation”. Is there any literature supporting that cytoplasmic expression in not a cross reaction with another protein?\n\nThe last paragraph of the Discussion is interesting but lacks connections with the rest of the Discussion.\nMinor considerations:\n“Are said to”: this is not an “mouth to ear” information, it is well established in the literature.\n\n“for its local but aggressive biological behavior”: What do they mean by “local” behavior?\n\n“are benign with less recurrence”. What is “less” recurrence?\n\nPlease check the classification of ameloblastomas, it is not correct. Furthermore, in the M&M, ameloblastomas are subclassified based on their histopathological features, but there in no mention to them in the Intro.\n\n“fascin might contribute for the local migratory behavior of these odontogenic cells”. Which cells?\n\n“The document of the protocol has been uploaded in the repository (Open Science Framework protocol.io)26 and hydrated”. Was the protocol hydrated? Please carefully check the text throughout the manuscript.\n\n“incubated with primary antibodies (rabbit monoclonal IgG for SALL4 and mouse monoclonal IgG1 for fascin)26 against fascin (clone SC-21743, Santa Cruz Biotechnology USA, Inc) diluted 1:200”. Please correct.\n\n“To eliminate bias, two observers independently evaluated the expression of these, selecting the most representative site separately under a light microscope...” This information should not be presented here.\n\n“Odontogenic tumors, AOT and developmental odontogenic cysts, COC”. Isn’t OKC a developmental cyst?\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?\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": "10173", "date": "06 Sep 2023", "name": "Dr. Spoorti Kulkarni", "role": "Author Response", "response": "We thank Konstantinos I. Tosios for reviewing our article and giving us your valuable comments. To the best of my ability I have tried to answer the queries and revised the manuscript accordingly. I have responded question wise. Q: The Title refers to odontogenic cysts and tumors, but as it turns out the study includes two tumors and many different cysts. Why did the authors choose to examine those lesion? Response: Literature review states among the odontogenic lesions Ameloblastoma and Odontogenic keratocyst are locally aggressive and recurrent lesions, also the commonest and prevalent odontogenic tumor in Indian population is ameloblastoma which ranges from 14.02% to 71.4% when compared to other odontogenic tumors3,4,while globally, pooled estimate of the incidence rate of ameloblastoma is 0.92 per million population per year.5The archives of the department did have other odontogenic lesions which were taken up for study References: Ahire MS, Tupkari JV, Chettiankandy TJ, Thakur A, Agrawal RR. Odontogenic tumors: A 35-year retrospective study of 250 cases in an Indian (Maharashtra) teaching institute. Indian journal of cancer. 2018 Jul 1;55(3):265-72 Pandiar D, Shameena PM, Sudha S, Varma S, Manjusha P, Banyal VS, Vijayan P. Odontogenic Tumors: A 13-year Retrospective Study of 395 Cases in a South Indian Teaching Institute of Kerala. Oral & Maxillofacial Pathology Journal. 2015 Jul 1;6(2) Hendra, F. N., Van Cann, E. M., Helder, M. N., Ruslin, M., de Visscher, J. G., Forouzanfar, T., & de Vet, H. C. W. Global incidence and profile of ameloblastoma: a systematic review and meta‐analysis. Oral Diseases. 2020 Jan;26(1):12-21 Q: In the Introduction there is some information on three of the lesions investigated (what about DC, RC or COC?) and this is inconsistent, i.e., they present recurrence rate for OKC, but not for ameloblastoma or AOT. The authors should consistently present the same data for each lesion. Response: Among the odontogenic cyst we have highlighted only Odontogenic keratocyst, since these lesions are aggressive and recurrent compared to other cysts such as DC, RC or COC, we have incorporated the same in introduction. We have also modified the same for Ameloblastoma as well, in ‘Introduction’: ‘The recurrence varies among various populations, 9.8% according to a Chinese study,6while in European multicenter study it is reported to be 19.3%,7 also tumors larger than 6 cm and involving the soft tissues or adjacent anatomical structures are associated with early recurrence irrespective of method of surgery. Also, conservatively (marsupialization, enucleation, curettage) treated cases have a high recurrence rate compared to radical treatment.1 however there is no concrete data pertaining recurrence on AOT References: Yang R, Liu Z, Gokavarapu S, Peng C, Ji T, Cao W. Recurrence and cancerization of ameloblastoma: multivariate analysis of 87 recurrent craniofacial ameloblastoma to assess risk factors associated with early recurrence and secondary ameloblastic carcinoma. Chinese Journal of Cancer Research. 2017 Jun;29(3):189. Boffano P, Cavarra F, Tricarico G, Masu L, Brucoli M, Ruslin M, Forouzanfar T, Ridwan-Pramana A, Rodríguez-Santamarta T, Ranz MR, de Vicente JC. The epidemiology and management of ameloblastomas: A European multicenter study. Journal of Cranio-Maxillofacial Surgery. 2021 Dec 1;49(12):1107-12.]. Q: Fascin and SALL4 seem to be two unrelated. Is there any association between them? Why did they choose to examine them? The authors use some references about the role in malignant neoplasms, however the lesions under consideration are not malignant neoplasms, while most of the references do not include studies on their expression in malignant neoplasms. Please carefully check your references Response: Literature review confirms fascin contributes for cell motility and migration in many studies (Pubmed 376 articles), SALL4 contributes to stemness along with other stem cell markers (SOX2, OCT4, and NANOG).8-13 Studies have shown the expression of these stem cell markers in Ameloblastoma & OKC except SALL4.14 Most of the studies in SALL4 are related to malignant soft tissue tumors,15,16 no reports are available of SALL4 expression in odontogenic lesions. Hence the present study aimed to evaluate the expression of fascin and SALL4 in odontogenic cysts & tumors. References: Matoba R, Niwa H, Masui S, Ohtsuka S, Carter MG, Sharov AA, Ko MS. Dissecting Oct3/4-regulated gene networks in embryonic stem cells by expression profiling. PloS one. 2006 Dec 20;1(1):e26. Nishimoto M, Fukushima A, Okuda A, Muramatsu M. The gene for the embryonic stem cell coactivator UTF1 carries a regulatory element which selectively interacts with a complex composed of Oct-3/4 and Sox-2. Molecular and cellular biology. 1999 Aug 1;19(8):5453-65. Wang J, Rao S, Chu J, Shen X, Levasseur DN, Theunissen TW, Orkin SH. A protein interaction network for pluripotency of embryonic stem cells. Nature. 2006 Nov 16;444(7117):364-8. Wu Q, Chen X, Zhang J, Loh YH, Low TY, Zhang W, Zhang W, Sze SK, Lim B, Ng HH. Sall4 interacts with Nanog and co-occupies Nanog genomic sites in embryonic stem cells. Journal of Biological Chemistry. 2006 Aug 25;281(34):24090-4. Zhang J, Tam WL, Tong GQ, Wu Q, Chan HY, Soh BS, Lou Y, Yang J, Ma Y, Chai L, Ng HH. Sall4 modulates embryonic stem cell pluripotency and early embryonic development by the transcriptional regulation of Pou5f1. Nature cell biology. 2006 Oct 1;8(10):1114-23. Zhou Q, Chipperfield H, Melton DA, Wong WH. A gene regulatory network in mouse embryonic stem cells. Proceedings of the National Academy of Sciences. 2007 Oct 16;104(42):16438-43. Phattarataratip E, Panitkul T, Khodkaew W, Anupuntanun P, Jaroonvechatam J, Pitarangsikul S. Expression of SOX2 and OCT4 in odontogenic cysts and tumors. Head & Face Medicine. 2021 Dec;17:1-7. Zhang X, Zhong N, Li X, Chen MB. TRIB3 promotes lung cancer progression by activating β-catenin signaling. European Journal of Pharmacology. 2019 Nov 15;863:172697 Jiang G, Liu CT. Knockdown of SALL4 overcomes cisplatin-resistance through AKT/mTOR signaling in lung cancer cells. International Journal of Clinical and Experimental Pathology. 2018;11(2):634. We agree on the fact that Fascin and SALL4 seems to be two unrelated molecules. SALL4 is activated by various pathways such as Wnt/β-catenin,15 PI3K/AKT, signalling pathway through targeting PTEN16or Notch signalling pathway17, thus facilitating migration, invasion and proliferation, while Fascin is activated via PI3K/ Akt pathway.18Also, literature reports cross talk between Wnt/β-catenin and PI3K/ Akt pathways or simultaneous activation of these pathways contributing for proliferation and cell migration.19-21 Hence we have made an attempt to study the expression of these two markers. References: Zhang X, Zhong N, Li X, Chen MB. TRIB3 promotes lung cancer progression by activating β-catenin signaling. European Journal of Pharmacology. 2019 Nov 15;863:172697 Jiang G, Liu CT. Knockdown of SALL4 overcomes cisplatin-resistance through AKT/mTOR signaling in lung cancer cells. International Journal of Clinical and Experimental Pathology. 2018;11(2):634. Park JT, Chen X, Tropè CG, Davidson B, Shih IM, Wang TL. Notch3 overexpression is related to the recurrence of ovarian cancer and confers resistance to carboplatin. The American journal of pathology. 2010 Sep 1;177(3):1087-94. Fleming-de-Moraes CD, Rocha MR, Tessmann JW, de Araujo WM, Morgado-Diaz JA. Crosstalk between PI3K/Akt and Wnt/β-catenin pathways promote colorectal cancer progression regardless of mutational status. Cancer biology & therapy. 2022 Dec 31;23(1):1-3. Laguë MN, Paquet M, Fan HY, Kaartinen MJ, Chu S, Jamin SP, Behringer RR, Fuller PJ, Mitchell A, Doré M, Huneault LM. Synergistic effects of Pten loss and WNT/CTNNB1 signaling pathway activation in ovarian granulosa cell tumor development and progression. Carcinogenesis. 2008 Nov 1;29(11):2062-72. Deming DA, Leystra AA, Nettekoven L, Sievers C, Miller D, Middlebrooks M, Clipson L, Albrecht D, Bacher J, Washington MK, Weichert J. PIK3CA and APC mutations are synergistic in the development of intestinal cancers. Oncogene. 2014 Apr;33(17):2245-54. Pearson HB, Phesse TJ, Clarke AR. K-ras and Wnt signaling synergize to accelerate prostate tumorigenesis in the mouse. Cancer research. 2009 Jan 1;69(1):94-101. Q: The aim of the study should be concise and clear. It should be reconsidered. Response: The aim of the present study was to evaluate the expression of fascin and SALL4 in histopathological variants of ameloblastoma, AOT and various odontogenic cysts namely OKC, Dentigerous cyst and radicular cyst. Following a thorough literature search we hypothesise that fascin might contribute for the local migratory behaviour of the odontogenic tumors and cysts while SALL4 may contribute to stemness property. M&M: “Before the start of the study, statistician was consulted and based on the literature review, availability of the material in the archives of the department and the availability of the budget the sample was decided”. Are 6 AOTs or 5 COC’s an adequate sample size? Response: The small number of cases in the present study regarding odontogenic tumors and its subgroup as well as in odontogenic cysts were limitation of this study. Further studies with large sample size is required for the better understanding of these biomarkers in these lesions. Q: The Patients and Tissues samples section needs restructuring. Origin of material, inclusion/exclusion criteria, IRB etc. Response: Samples were retrieved from the Department of Oral and Maxillofacial Pathology, Manipal College of Dental Sciences, Manipal, India after the approval from the Institutional Ethical Committee. This study was approved (IEC approval number 360/2019, 14-05-2019; IEC 156/2014, 12-03-2014) by the Institutional Ethical Committee, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, India. Participant consent was waived by the committee. The samples taken up for the study did comply to inclusion and exclusion criteria which included histologically diagnosed cases of odontogenic cysts and tumors from 2012-2017. All the samples taken for the current study were prior to the patient receiving any treatment, cases with recurrence were excluded. The diagnosis of the above said odontogenic cysts and tumors were done based on clinical and histological features (using H&E staining) according to WHO guidelines. Q:What was the positive control for Fascin, the basal cells of the oral epithelium (Figure) or the endothelial cells of the buccal mucosa (text)? Any supporting reference of any of them Response: Buccal mucosa tissue22 (Figure 1), was considered as external positive control while endothelial cells with in the samples to be tested was considered for internal positive control for Fascin expression. The reference article is as below. Rodrigues PC, Sawazaki-Calone I, Ervolino de Oliveira C, et al. Fascin promotes migration and invasion and is a prognostic marker for oral squamous cell carcinoma. Oncotarget. 2017;8(43):74736-74754. Q:In general, please present the findings in a more orderly manner, i.e., what did you see in the positive controls (membranous and cytoplasmic expression in the basal cells of the epithelium, etc.) Response: For fascin, the positive control used was buccal mucosa, the cytoplasm of the basal cells of the epithelium were stained positive. In case of SALL4 dysgerminoma was taken as positive control where in nuclear expression in the cells is seen. Q:Follow the same order of the antibodies, i.e., if you choose Fascin/SALL4 then present the results first for fascin and then for SALL4. Response: Correction is done as follows: Immunohistochemically stained sections of various odontogenic cysts and tumor tissue were evaluated for expression of fascin in the cell membrane, between cell boundaries and cytoplasm of peripheral ameloblastic cells, stellate reticulum like cells and stromal cells of 40 cases of ameloblastoma variants while expression of SALL4 was observed in the cytoplasm as well as nuclei of peripheral ameloblastic cells and stellate reticulum like cells. The total IRS score was the main outcome (Table 1, Table 2). The expression of fascin and SALL4 varied from case to case as well as in the same tissue section. Most of the variants of ameloblastoma were strongly positive for fascin but cases of desmoplastic ameloblastoma (5/5) were negative for fascin (Figure 1D). Fascin expression was found to be weak or absent in stellate reticulum like cells (Figure 1). In cases of unicystic ameloblastoma, positivity for fascin was observed in the basal as well as in the suprabasal layers (Figure 1C). However intra-group comparison did not show any significant difference. AOT was immune-positive to fascin in few areas (< 25%) with mild to moderate intensity (Figure 1E). Fascin expression in odontogenic cysts (OKC, RC, DC) (Figure 1G–I) was strongly positive with greater than 75% cells, while intensity ranged from moderate to strong along the cystic lining. COC revealed immune positivity ranging from 25-50% (Figure 1F). The SALL4 positivity was heterogeneous with varied intensity and staining pattern. In most of the histopathological variant of ameloblastoma, the immunopositivity observed, was diffuse in the cytoplasm and less localised to the nucleus (Figure 2A–C). The stromal cells were devoid of its expression except in the endothelial cells. SALL4 expression in odontogenic cysts was strongly positive with greater than 75% cells exhibiting diffuse cytoplasmic staining. Nuclear staining was evident in few cells (Figure 2E–G). COC was immune-negative (Figure 2H). Regarding the evaluation of the statistical significance test, in all the odontogenic tumors, the staining intensity of fascin is similar compared to SALL4. With regard to the stained cell count, higher counts are observed with fascin as compared to SALL4. In relation to odontogenic cysts, odontogenic keratocyst and dentigerous cyst,the intensity of fascin is more than SALL4.Also the higher cell counts were observed in fascin as compared to SALL4 in odontogenic keratocyst. (S1,S2,S3,S4,Table1,Table2) Q:Results should be rewritten in a more orderly manner. Response: Correction has been made Q:40 cases of ameloblastoma variants from the year 2012 to 2017”. This information is not proper here. Response: The above sentence has been removed as instructed. Q:Discussion: “Researchers have worked on…”. There are no references to support this Response: The reference article for support, Ref no 23: Fuchigami T, Ono Y, Kishida S, Nakamura N.Jpn Dent Sci Rev. 2021 Nov;57:27-32. : Molecular biological findings of ameloblastoma. Q:Discussion: “the odontogenic epithelial cells were positive for SALL4 in the cytoplasm, stained diffusely, which we speculate could be in an inactive/dormant or mutant form which requires further investigation”. Is there any literature supporting that cytoplasmic expression in not a cross reaction with another protein? Response: Studies pertaining to immunogenicity of SALL4 oncogenic protein-derived peptides, especially A18 K and R18 A peptides have been reported, however this needs to be validated in odontogenic tumors. Kroemer, M., Spehner, L., Mercier-Letondal, P., Boullerot, L., Kim, S., Jary, M., Galaine, J., Picard, E., Ferrand, C., Nguyen, T., Larosa, F., Adotévi, O., Godet, Y., & Borg, C.SALL4 oncogene is an immunogenic antigen presented in various HLA-DR contexts. Oncoimmunology.2018: 7(4);e1412030. Q: The last paragraph of the Discussion is interesting but lacks connections with the rest of the Discussion. Response: The origin of odontogenic cysts and tumors are from the odontogenic apparatus. Hence an attempt was made to study the expression of these biomarkers in pre and post stages of tooth germ. Minor considerations: Q:Are said to”: this is not an “mouth to ear” information, it is well established in the literature Response: The sentence has been corrected as, ‘ Odontogenic cysts and tumors originates from odontogenic apparatus or oral epithelium’ Q: “for its local but aggressive biological behavior”: What do they mean by “local” behavior? Response: The term ‘local’ refers to localized region of the Jaws Q:are benign with less recurrence”. What is “less” recurrence Response: The sentence has been modified to ‘ Adenomatoid odontogenic tumors (AOT) are benign with rare recurrence. Q:Please check the classification of ameloblastomas, it is not correct. Furthermore, in the M&M, ameloblastomas are subclassified based on their histopathological features, but there in no mention to them in the Intro Response: Due to word limitations in introduction we have incorporated the histopathological variants in M&M. Q:fascin might contribute for the local migratory behavior of these odontogenic cells”. Which cells? Response: Fascin might contribute for the local migratory behavior of the odontogenic epithelial cells of Ameloblastoma, AOT, OKC,RC,DC,COC. Q:The document of the protocol has been uploaded in the repository (Open Science Framework protocol.io)26 and hydrated”. Was the protocol hydrated? Please carefully check the text throughout the manuscript. Response: This has been an oversight, we have corrected as follows Immunohistochemical staining of the tissue sections from each of the cases selected was done using the streptavidin-biotin method. In brief, 4 ��m sections were mounted on 3-aminopropyltriethoxysilane (APES) coated slides (Novolink Polymer Detection System, Novocastra). Sections were then deparaffinized in xylene, which is done in three grades for 10 minutes and hydrated in different grades of alcohol (ranging from absolute alcohol (10 minutes), 95 % alcohol (10 minutes), 70% (10 minutes), 50% (10 minutes) each). Sections were then incubated with primary antibodies,rabbit antihuman SALL4 monoclonal antibody at a dilution of 1:100(IgG, clone EP-299, PathnSitu, Livermore, USA ),mouse antihuman fascin monoclonal antibody ( IgG1,clone55K-2, SC-21743, Santa Cruz Biotechnology USA, Inc) diluted at 1:200. The sections were subsequently washed in tris-buffered saline and incubated with secondary biotinylated antibody and streptavidin-biotin peroxidase complex (Novolink Polymer Detection System, Novocastra) for 30 minutes each. Diaminobenzidine (DAB) was used as the chromogen and the sections were counterstained with Mayer’s hematoxylin. Buccal mucosa tissue was used as positive control and endothelial cells were internal controls for fascin antibody (Figure 1), while dysgerminoma was taken as a positive control, bud and bell stage of tooth development were also included for the expression of SALL4 (Figure 2). The primary antibody was replaced during IHC staining for the negative control as per standard immunohistochemical protocol. The document of the protocol has been uploaded in the repository (Open Science Framework protocol.io)48 Q:“incubated with primary antibodies (rabbit monoclonal IgG for SALL4 and mouse monoclonal IgG1 for fascin)26 against fascin (clone SC-21743, Santa Cruz Biotechnology USA, Inc) diluted 1:200”. Please correct. Response: We corrected the same as follows: Sections were then incubated with primary antibodies,rabbit antihuman SALL4 monoclonal antibody at a dilution of 1:100(IgG, clone EP-299, PathnSitu, Livermore, USA ),mouse antihuman fascin monoclonal antibody ( IgG1,clone55K-2, SC-21743, Santa Cruz Biotechnology USA, Inc) diluted to 1:200 Q:“To eliminate bias, two observers independently evaluated the expression of these, selecting the most representative site separately under a light microscope...” This information should not be presented here Response: We have removed the sentence from results and incorporated in ‘Immuno staining evaluation’. Immunostaining evaluation Presence of brown color at the end of staining was considered as positive reactivity. The slides were evaluated with a light microscope (Olympus BX41) attached with Olympus DP20 microscope camera (Olympus Singapore Pvt Ltd, Singapore) at 20× & 40× magnification. The distribution of antibodies was assessed in the cytoplasm and cell membrane of ameloblastic lining of the lesions for fascin while SALL4 staining was evaluated in nuclear and cytoplasmic areas. In each case, three fields were randomly selected, and two observers independently evaluated the expression of these, selecting the most representative site separately under a light microscope at 200× and 400× magnification. Q:Odontogenic tumors, AOT and developmental odontogenic cysts, COC”. Isn’t OKC a developmental cyst? Response: Yes, OKC, dentigerous are developmental while radicular cyst is inflammatory in origin" } ] }, { "id": "186991", "date": "16 Aug 2023", "name": "Qi-Wen Man", "expertise": [ "Reviewer Expertise Immunohistochemistry", "RNA sequencing", "Odontogenic tumors" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 carefully reviewed your research on the immunohistochemical expression of Fascin and SALL4 in ameloblastoma, adenomatoid tumor, and odontogenic cysts. The study aims to provide insights into these lesions by examining the expression of specific biomarkers. While the research direction is promising, there are several areas that require further attention to enhance the overall quality of the study:\nThe inclusion of multiple diseases as research subjects is commendable for its comprehensiveness. However, a critical concern lies in the lack of detailed characterization of each disease and their potential interrelationships. Providing a comprehensive description of their specific characteristics and how they relate to each other would enrich the study and offer a more robust foundation for future research.\n\nThe research would benefit from a more in-depth discussion of the developmental prospects of the selected biomarkers, Fascin, and SALL4. Additionally, it is essential to highlight the advantages of these biomarkers compared to other potential candidates.\n\nWhile you have highlighted Fascin's involvement in the invasiveness of ameloblastoma, further elucidation is necessary regarding the reasons for its overexpression in Dentigerous cysts, Odontogenic Keratocyst, and Radicular cysts, or put forward corresponding conjectures. Similarly, the role of SALL4 in these dental pathologies requires more thorough exploration and explanation.\n\nThe absence of normal tissue as a control for IHC staining results is a notable concern. To strengthen the study's validity, it is crucial to include normal tissue controls or appropriate references for comparison.\n\nThe statistical tables used to present the IHC results require improvement. Employing more robust statistical methods, such as significance testing, to analyze the differences between lesions would enhance the analysis and provide more reliable conclusions.\n\nRegarding the speculation on the functional roles of the two biological markers, it is suggested to conduct further experimental validation to elucidate their functional significance in the corresponding pathologies.\n\nThe background of the IHC staining was not the same which might influence the scores and analysis.\n\nIs the work clearly and accurately presented and does it cite the current literature? No\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [ { "c_id": "10174", "date": "06 Sep 2023", "name": "Dr. Spoorti Kulkarni", "role": "Author Response", "response": "We thank Qi-Wen Man for reviewing our article and giving us valuable comments. I appreciate the time and efforts spent to make our work better. I have carefully reviewed the comments and revised the manuscript accordingly. All comments pointed out by the reviewer have been corrected. I have responded question wise. 1: The inclusion of multiple diseases as research subjects is commendable for its comprehensiveness. However, a critical concern lies in the lack of detailed characterization of each disease and their potential interrelationships. Providing a comprehensive description of their specific characteristics and how they relate to each other would enrich the study and offer a more robust foundation for future research. Response: In current study we have included Odontogenic tumors and cyst, which are pathology or disease arises from the odontogenic epithelium. Among the odontogenic tumors we have included, Ameloblastoma with its various histopathological variants (No:40),Adenomatiod odontogenic tumors (AOT) ( No:15),while odontogenic cyst includes 15 cases of each of Odontogenic cyst (OKC), Dentigerous cyst (DC), Radicular cyst (RC) and Calcifying odontogenic cyst( COC)(No:5). Literature review states among the odontogenic lesions Ameloblastoma and Odontogenic keratocyst are locally aggressive and recurrent lesions, also Ameloblastoma are the commonest and prevalent odontogenic tumor in Indian population is ameloblastoma which ranges from 14.02% to 71.4% when compared to other odontogenic tumors 3,4, while globally, pooled estimate of the incidence rate of ameloblastoma is 0.92 per million population per year5. Among the odontogenic cyst we have highlighted only Odontogenic keratocyst, since these lesions are aggressive and recurrent compared to other cysts such as DC, a cyst associated with impacted tooth, RC, a cyst associated with caried or non-vital tooth, COC, a developmental cyst associated with calcification and ghost epithelial cells. We have incorporated the same in introduction. References: Ahire MS, Tupkari JV, Chettiankandy TJ, Thakur A, Agrawal RR. Odontogenic tumors: A 35-year retrospective study of 250 cases in an Indian (Maharashtra) teaching institute. Indian journal of cancer. 2018 Jul 1;55(3):265-72 Pandiar D, Shameena PM, Sudha S, Varma S, Manjusha P, Banyal VS, Vijayan P. Odontogenic Tumors: A 13-year Retrospective Study of 395 Cases in a South Indian Teaching Institute of Kerala. Oral & Maxillofacial Pathology Journal. 2015 Jul 1;6(2) Hendra, F. N., Van Cann, E. M., Helder, M. N., Ruslin, M., de Visscher, J. G., Forouzanfar, T., & de Vet, H. C. W. Global incidence and profile of ameloblastoma: a systematic review and meta‐analysis. Oral Diseases. 2020 Jan;26(1):12-21 Reichart P, Sciubba JJ, Philipsen HP. Splitters or lumpers: The 2017 WHO Classification of Head and Neck Tumors. J Am Dent Assoc. 2018;149:567-571. 2: The research would benefit from a more in-depth discussion of the developmental prospects of the selected biomarkers, Fascin, and SALL4. Additionally, it is essential to highlight the advantages of these biomarkers compared to other potential candidates. Response: Literature review confirms fascin contributes for cell motility and migration in many studies (Pubmed 376 articles), SALL4 contributes to stemness along with other stem cell markers 8-13 SOX2, OCT4, and NANOG. Studies have shown the expression of these stem cell markers in Ameloblastoma & OKC except SALL4.14 Most of the studies in SALL4 are related to malignant soft tissue tumors ,15-16 no reports are available of SALL4 expression in odontogenic lesions. Hence the present study aimed to evaluate the expression of fascin and SALL4 in odontogenic cysts & tumors. References: Matoba R, Niwa H, Masui S, Ohtsuka S, Carter MG, Sharov AA, Ko MS. Dissecting Oct3/4-regulated gene networks in embryonic stem cells by expression profiling. PloS one. 2006 Dec 20;1(1):e26. Nishimoto M, Fukushima A, Okuda A, Muramatsu M. The gene for the embryonic stem cell coactivator UTF1 carries a regulatory element which selectively interacts with a complex composed of Oct-3/4 and Sox-2. Molecular and cellular biology. 1999 Aug 1;19(8):5453-65. Wang J, Rao S, Chu J, Shen X, Levasseur DN, Theunissen TW, Orkin SH. A protein interaction network for pluripotency of embryonic stem cells. Nature. 2006 Nov 16;444(7117):364-8. Wu Q, Chen X, Zhang J, Loh YH, Low TY, Zhang W, Zhang W, Sze SK, Lim B, Ng HH. Sall4 interacts with Nanog and co-occupies Nanog genomic sites in embryonic stem cells. Journal of Biological Chemistry. 2006 Aug 25;281(34):24090-4. Zhang J, Tam WL, Tong GQ, Wu Q, Chan HY, Soh BS, Lou Y, Yang J, Ma Y, Chai L, Ng HH. Sall4 modulates embryonic stem cell pluripotency and early embryonic development by the transcriptional regulation of Pou5f1. Nature cell biology. 2006 Oct 1;8(10):1114-23. Zhou Q, Chipperfield H, Melton DA, Wong WH. A gene regulatory network in mouse embryonic stem cells. Proceedings of the National Academy of Sciences. 2007 Oct 16;104(42):16438-43. Phattarataratip E, Panitkul T, Khodkaew W, Anupuntanun P, Jaroonvechatam J, Pitarangsikul S. Expression of SOX2 and OCT4 in odontogenic cysts and tumors. Head & Face Medicine. 2021 Dec;17:1-7. Zhang X, Zhong N, Li X, Chen MB. TRIB3 promotes lung cancer progression by activating β-catenin signaling. European Journal of Pharmacology. 2019 Nov 15;863:172697 Jiang G, Liu CT. Knockdown of SALL4 overcomes cisplatin-resistance through AKT/mTOR signaling in lung cancer cells. International Journal of Clinical and Experimental Pathology. 2018;11(2):634. 3. While you have highlighted Fascin's involvement in the invasiveness of ameloblastoma, further elucidation is necessary regarding the reasons for its overexpression in Dentigerous cysts, Odontogenic Keratocyst, and Radicular cysts, or put forward corresponding conjectures. Similarly, the role of SALL4 in these dental pathologies requires more thorough exploration and explanation. Response: We speculate the expression Fascin in cysts[(Dentigerous cysts(DC),Odontogenic keratocyst(OKC) and radicular cyst(RC)] could influence cell dynamics and focal adhesions.35 We observed that the odontogenic epithelial cells were positive for SALL4 in the cytoplasm, stained diffusely, which we speculate could be in an inactive/dormant or mutant form which requires further investigation. Majority of OKC were devoid of SALL4 except in the basal cells. RC and DC, having marked infiltration of inflammatory cells had strong immune positivity for SALL4 in the cytoplasm, an interesting finding of this study. Hence the role of cytokines in stimulating SALL4 needs to be ruled out. Reference: Villari G, Jayo A, Zanet J, et al. A direct interaction between fascin and microtubules contributes to adhesion dynamics and cell migration. J Cell Sci. 2015;128(24):4601-4614. 4:The absence of normal tissue as a control for IHC staining results is a notable concern. To strengthen the study's validity, it is crucial to include normal tissue controls or appropriate. references for comparison Response: We have included the following under: Immunohistochemistry (IHC) Buccal mucosa tissue was used as positive control, the basal cells of the epithelium were stained positive and endothelial cells with in the lesional tissue were internal controls for fascin antibody (Figure 1), while dysgerminoma was taken as a positive control for SALL4, bud and bell stage of tooth development was also included for the study(Figure 2). 5.The statistical tables used to present the IHC results require improvement. Employing more robust statistical methods, such as significance testing, to analyze the differences between lesions would enhance the analysis and provide more reliable conclusions. Response: Statistician was consulted for statistical analysis. The tables have been modified and have been uploaded in the OSF repository (S1, S2,S3,S4). In the main manuscript the tables are Table1, Table2.Regarding the evaluation of the statistical significance test, in all the odontogenic tumors, the staining intensity of fascin is similar compared to SALL4. Regarding the stained cell count, higher counts are observed with fascin as compared to SALL4. In relation to odontogenic cysts, viz odontogenic keratocyst and dentigerous cyst,the intensity of fascin staining was more than SALL4.Also the higher cell counts were observed in fascin as compared to SALL4 in odontogenic keratocyst. Fischer’s exact test was used to compare the distribution of staining intensity and cell count across SALL4 and fascin 6. Regarding the speculation on the functional roles of the two biological markers, it is suggested to conduct further experimental validation to elucidate their functional significance in the corresponding pathologies. Response: Thank you for your valuable advice. We will continue the experiments as an when we receive grants for further study. 7.The background of the IHC staining was not the same which might influence the scores and analysis Response: To eliminate the bias, two observers independently evaluated the expression of these biomarkers, selecting the most representative site separately under a light microscope at 200X and 400X magnification." } ] } ]	1	https://f1000research.com/articles/11-1578
https://f1000research.com/articles/13-702/v1	27 Jun 24	{ "type": "Clinical Practice Article", "title": "Management of Strangulated Richter’s Hernia in a Resource-Limited Setting: Report of Two Cases and Literature Review", "authors": [ "Yahouza Boka Tounga", "Ousmane Issoufou Hamma", "Aliou Zabeirou", "Kadi Ide", "Rachid Sani", "Yahouza Boka Tounga", "Aliou Zabeirou", "Kadi Ide", "Rachid Sani" ], "abstract": "Richter’s hernia is a rare type of abdominal wall hernia characterized by high morbidity and mortality. It occurs when the anti-mesenteric border of the bowel is partially trapped in a tight hernial ring. The femoral ring is the most common site, with the ileum being the most frequently involved intestinal segment. However, the advent of laparoscopic surgery has introduced another potential site for Richter’s hernia formation. In our region, this pathological entity is exceptionally diagnosed due to limited access to abdominal imaging and delayed management. Additionally, the wide variety of clinical manifestations resulting from incomplete intestinal obstruction makes it particularly difficult to diagnose. Consequently, it is usually identified during surgery. We present here the case of two adult patients (a 33-yeairs-old woman and a 59-year-old man), the first with a history of surgical procedures and the second with a spontaneously reducible painless inguinal swelling. They were transferred to the surgical emergency department for an acute abdomen with abdominal distension and cessation of matter and gas. Clinical and paraclinical examinations (including hydroaeric level on abdominal X-ray) indicated mechanical intestinal obstruction. Emergency laparotomy, necessitated by the unavailability of abdominal computed tomography due to financial constraints, confirmed the diagnosis of Richter's hernia, with the first case located in the right inguinal region and the second in the linea alba. Surgical management involved reduction of the hernia contents and suture repair in both cases. Despite requiring bowel resection in the second patient, the postoperative course was straightforward. These two rare cases highlight that emergency exploratory laparotomy is the cornerstone of Richter hernia management in resource-limited conditions.", "keywords": [ "Abdominal hernia", "inguinal hernia", "Richter’s hernia", "emergency surgery performed", "developing countries", "case report" ], "content": "Introduction\n\nRichter’s hernia is a rarely encountered surgical entity. It is defined as the protrusion and/or strangulation of only part of the circumference of the intestine’s anti-mesenteric border through the hernia orifice, leading to a risk of ischemia, gangrenous bowel, and perforation.1–4 The most common location of this pathology is the femoral canal (36-88%), followed by the inguinal canal (12-36%) and incisional hernia of the abdominal wall (4-25%).3–5 The increase in laparoscopic and robotic surgery has contributed to the rise in Richter-type hernias at trocar sites.6 Diagnosis of this pathology is challenging in our region due to long admission times, limited availability of abdominal imaging, and varied clinical presentations. The management of Richter's hernia depends on the viability of the incarcerated intestine, which must be assessed; intestinal resection is indicated in the event of necrosis.5,7 We report two rare cases of Richter's hernia found during emergency exploratory laparotomy; with the first case located in the right inguinal region and the second in the linea alba. Post-operative management was straightforward in both patients, although bowel resection was necessary in the second. These cases highlight the important role of emergency exploratory laparotomy.\n\nThis case report has been reported in line with the SCARE Criteria.8\n\n\nCase report\n\nA 33-year-old married woman with an obstetrical history of three births, two parities, one abortion, and two cesarean sections (the most recent about four weeks prior) was transferred to the surgical emergency department for rapidly progressive diffuse abdominal pain associated with vomiting and cessation of matter and gas lasting four days. Clinical examination revealed an overweight, afebrile patient with a core temperature of 36.5-37°C. The patient was hemodynamically and respiratory stable with a blood pressure of 130/67 mmHg, pulse rate of 108 beats/min, and respiratory rate of 24 breaths/min, and blood oxygen saturation was 96% on ambient air. Abdominal examination revealed a distended abdomen, and tympany on the percussion, with an old Pfannenstiel-type surgical scar. The examinations of cardiovascular, gynecology, neurology, and pelvic touch were without peculiarities. Following this clinical examination, mechanical intestinal obstruction was suspected. Abdominal X-ray showed signs of small bowel obstruction in the form of distension and hydroaeric levels with a large dilated loop image (Figure 1). Abdominal computed tomography (CT) scan was not performed due to financial constraints; however, other biological tests were normal. The patient was resuscitated with intravenous crystalloid fluids and received intravenous analgesia (Paracetamol 5g/24h, tramadol hydrochloride 300mg/24h) and antibiotic prophylaxis (ceftriaxone 2g/24h). The patient was admitted to the operating room for emergency median laparotomy under general anesthesia in the supine position. Surgical exploration revealed a strangulated loop at the linea alba, located on the anti-mesenteric face of the ileum, 80 cm from the ileocecal valve (Figure 2). The diagnosis of Richter's hernia of the linea alba was confirmed. The incarcerated loop was viable. We proceeded with disincarceration and reintegration of the contents of the hernia, followed by resection of the hernia sac and suture repair of the hernia. The postoperative course was straightforward; antibiotic prophylaxis was discontinued after 96 hours, and early ambulation was recommended. The patient was discharged after seven days of hospitalization and was advised to avoid heavy lifting for 3 months. After six months of follow-up, there was no sign of recurrence, and the patient resumed her daily activities.\n\nDamaged loop on its antimesenteric edge (blue arrow), distension of its proximal part (yellow arrow), and distal flattening (purplish arrow).\n\nA 59-year-old married man with a history of painless, spontaneously reducible right inguinal swelling, cough impulse, and chronic constipation for two years; was transferred to the emergency department with a right inguinal swelling that had become very painful, firm, non-reducible, and without cough impulse, which had been evolving for around 72-96 hours. The clinical picture worsened approximately 8-9 hours before admission, with the onset of abdominal distension, vomiting, and cessation of matter and gas. Clinical examination showed the patient to be agitated but without any alteration in consciousness. He was hemodynamically and respiratory stable with a blood pressure of 110/65 mmHg, pulse rate of 120 beats/min, and respiratory rate of 23 breaths/min, and his blood oxygen saturation 98% on ambient air. His core temperature was 37-37.5°C, and his body mass index (BMI) was normal at 23 kg/m2. The right inguinal swelling remained painful, non-reducible, and without cough impulse (Figure 3), but the rest of the abdomen was soft and painless to palpation. Biological examination revealed an inflammatory process characterized by neutrophilic leukocytosis of 14,900 cells/μL (reference range: 4,000 – 10,000 cells/μL) and 78.12% neutrophils (reference range: 50-70%), along with an increase in C-reactive protein (CRP) levels to 78 mg/L (reference range: < 6 mg/L). However, renal function tests were normal, and there were no ionic or coagulation disorders. A diagnosis of strangulated right inguinal hernia was suspected, but the patient did not undergo abdominal imaging due to financial constraints. The patient was resuscitated with intravenous crystalloid fluids and received in intravenous, an analgesia (paracetamol 5g/24h, tramadol hydrochloride 300mg/24h) and antibiotic prophylaxis (ceftriaxone 2g/24h, metronidazole 1500mg/24h). The patient was then taken to the operating room for an emergency exploratory laparotomy. An elective oblique right kelotomy was performed under general anesthesia in supine position. Intra-operatively, the loop of the ileum was partially incarcerated on its anti-mesenteric border, 35 and 45 cm from the ileocecal junction, resulting in necrosis of the bowel (Figure 4). The diagnosis of Richter's hernia was confirmed, and elective oblique kelotomy was converted to median laparotomy. The necrotic segment of the ileum was segmentally resected, followed by an end-to-end ileo-ileal anastomosis. Finally, primary repair of the hernia was performed. The postoperative course was favorable; antibiotic prophylaxis and intravenous crystalloids were discontinued after 96 hours, and early ambulation was recommended. Digestive transit resumed 72 hours after surgery, and the patient was discharged on the ninth day. He was advised to avoid heavy lifting for 3 months. After six months of ambulatory follow-up, the patient showed no signs of hernia recurrence, despite resuming normal activities.\n\n\nDiscussion\n\nRichter’s hernia is defined as a rare hernia of the abdominal wall in which a portion of the circumference of the intestinal tract is trapped and strangulated at the hernial orifice.2,3,5 In 1558, Fabricius Hildanus was the first to report a case of Richter's hernia. However, it was not until 1778 that the German surgeon August Gottlieb Richter provided a scientific description of this surgical entity, which would later take the name “Richter’s hernia”.4,7,9,10 These two cases of Richter hernia are the first to be documented and reported in our region. In the scientific literature, this hernia is most often diagnosed in patients aged between 60 and 80 years and accounts for up to 10% of all strangulated hernias.2,3,7,11 The average age of our patients was 46 years (33 and 59 years). The clinical picture depends on the location of the hernia. However, it remains exceptional in our region due to difficult access to abdominal imaging and long admission times to the operating theatre. In our cases, abdominal CT scans were not performed due to financial constraints, so an exploratory laparotomy was performed. We confirmed the diagnoses intraoperatively, consistent with the findings reported by most authors. It is important to note that these hernias can occur on anterior incisions but are more frequently observed in small hernial rings large enough to entrap a small portion of the bowel wall. Both our patients developed a hernia at the natural orifice. The most frequent locations were femoral hernias (72-88%), followed by the inguinal canal (12-24%) and umbilical and linea alba hernias (4-25%).1,2,4 The clinical presentation of Richter's hernia is highly varied; one of our patients presented with a typical occlusive syndrome, whereas the other had an atypical clinical picture. Because patients rarely present with obstructive symptoms, they tend to progress more rapidly to gangrene than other types of strangulated hernia. Repair is usually approached via the preperitoneal route, with mandatory laparotomy and bowel resection in cases of gangrene or perforation. The silent nature of this hernia presentation and the fact that the patient continues to emit flatulence and stools make it particularly dangerous. At the time of presentation, there is usually ischemia of the affected bowel, and bowel resection is mandatory.1,3,4,5,11,13 The necrotic bowel is not the only worrying aspect of these hernias. Other complications described in the literature include spontaneous fistulas from the affected bowel and skin necrosis. Atypical presentations of Richter's hernias have also been reported, such as complications from colonoscopy.3,5 There have also been cases of Richter's hernia simulating a groin abscess, with the diagnosis only being made during laparotomy or the drainage of inguinal abscesses revealing amylaceous material.14 These examples highlight the diverse clinical presentation of this pathology. Despite the small size of our study population, we recommend rapid surgical intervention (emergency exploratory laparotomy) in patients presenting suspicious clinical signs in resource-limited environments. This approach can lead to an uneventful recovery. However, more studies are needed to establish a guideline for this pathology in resource-limited settings.\n\n\nConclusion\n\nRichter hernia is a rare surgical entity with very high mortality and morbidity. However, this condition has rarely been reported in our region due to limited access to abdominal imaging, long management delays, and varied clinical manifestations. Despite these challenges, our patients achieved favorable operative outcomes, contrary to what is often reported in the literature. Therefore, the management of this pathology in resource-limited settings must be centered on emergency exploratory laparotomy in patients presenting with suspicious clinical signs.\n\n\nConsent\n\nWritten informed consent for publication of the clinical details and clinical images was obtained from the patient.\n\n\nChecklists and flow charts\n\nFigshare: CARE checklist for ‘Scare 2020 Checklist Article Richter Hernia HNN’.15\n\nhttps://doi.org/10.6084/m9.figshare.26027293.v1\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC PAR 4.0 Public domain dedication).\n\n\nAuthors’ contributions\n\nConceptualization: YBT, OIH, AZ, KI, RS; Data Curation: YBT, OIH, KI, RS; Project Administration: RS; Resources: YBT, RS; Supervision: RS; Validation: YBT, OIH, AZ, KI, RS; Visualization: YBT, OIH, AZ, KI, RS; Writing – Original Draft Preparation: YBT, OIH, AZ, KI, RS; Writing – Review & Editing: YBT, OIH, AZ, KI, RS", "appendix": "Data availability statement\n\nNo data are associated with this article.\n\n\nAcknowledgements\n\nThe authors are grateful to the following teacher-researchers: Pr. ABARCHI Habibou, the late Pr. SANOUSSI Samuila, Pr. CHAIBOU Mamane Sani, Pr. YOUNSA Hama Dr. GARBA Ide, and Dr. SAIDOU Adama for their unconditional support.\n\n\nReferences\n\nBayeh A, Limenh S: Richter’s Type Recurrent Indirect Inguinal Hernia, an Extremely Rare Occurrence: A Case Report. Open Access Emerg Med OAEM. 2022; 14: 323–326. Publisher Full Text\n\nBirhanu AM, Mohammed SH, Mohammed SM, et al.: Incarcerated Richter’s congenital umbilical hernia in a young male: A case report. Int. J. Surg. Case Rep. 2023; 109: 108576. Publisher Full Text\n\nFoster D, Nagarajan S, Panait L: Richter-type Spigelian hernia: A case report and review of the literature. Int. J. Surg. Case Rep. 2015; 6: 160–162. Publisher Full Text\n\nKhuroo S, Wani AA, Kaur I, et al.: Unusual Richter’s Hernia: Impacted foreign body leading to incarceration and perforation - A rare clinical entity. Int. J. Surg. Case Rep. 2021; 79: 492–495. Publisher Full Text\n\nYonekura S, Kodama M, Murano S, et al.: Richter’s Type of Incarcerated Obturator Hernia that Presented with a Deep Femoral Abscess: An Autopsy Case Report. Am. J. Case Rep. 2016; 17: 830–833. Publisher Full Text\n\nTobe T, Yuen K, Yasufuku T, et al.: Laparoscopic port site Richter’s hernia after robot-assisted radical prostatectomy. IJU Case Rep. 2022; 5: 501–504. Publisher Full Text\n\nAhi KS, Moudgil A, Aggarwal K, et al.: A rare case of spontaneous inguinal faecal fistula as a complication of incarcerated Richter’s hernia with brief review of literature. BMC Surg. 2015; 15: 67. 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; 84: 226–230. Publisher Full Text\n\nParmar VS, Vaghasiya GN, Dave JP: A Rare Case of Richter’s Variety of Obstructed Femoral Hernia in a Male. Indian J. Surg. 2015; 77: 79–80. Publisher Full Text\n\nSkandalakis PN, Zoras O, Skandalakis JE, et al.: Richter Hernia: Surgical Anatomy and Technique of Repair. Am. Surg. 2006; 72: 180–184. Publisher Full Text\n\nChen W, Liu L, Huang H, et al.: A case report of spontaneous umbilical enterocutaneous fistula resulting from an incarcerated Richter’s hernia, with a brief literature review. BMC Surg. 2017; 17: 15. Publisher Full Text\n\nRammohan A, Naidu RM: Laparoscopic port site Richter’s hernia – An important lesson learnt. Int. J. Surg. Case Rep. 2011; 2: 9–11. Publisher Full Text\n\nSahsamanis G, Samaras S, Gkouzis K, et al.: Strangulated Richter’s incisional hernia presenting as an abdominal mass with necrosis of the overlapping skin. A case report and review of the literature. Clin. Case Rep. 2017; 5: 253–256. Publisher Full Text\n\nHartin CW, Caty MG, Bass KD: Laparoscopy for perforated Richter hernia with incarcerated foreign body. J. Pediatr. Surg. 2011; 46: 1449–1451. Publisher Full Text\n\nIssoufou Hamma O, Boka Tounga Y, Zabeirou A, et al.: Scare 2020 Checklist Article Richter Hernia HNN. figshare. 2024. Publisher Full Text" }	[ { "id": "301504", "date": "23 Jul 2024", "name": "Enrique Salazar-Rios", "expertise": [ "Reviewer Expertise General Surgery" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis article is a case report that describes the workup and successful surgical management of two cases of Richter's hernia, with one requiring intestinal resection. This condition is rarely reported in the authors' country of origin due to limited access to imaging studies, often necessitating emergency laparotomy for diagnosis. The authors conclude that in resource-limited settings, the management of this pathology must focus on prompt surgical intervention.\n\nIs the background of the cases’ history and progression described in sufficient detail?\nThe authors do a great job of detailing the patients’ progression and outcomes, as well as the medical history of case 1. However, case 2 lacks any previous medical history. If there is no relevant medical history for case 2, this should be specified.\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes?\nOverall, the authors do a good job of providing the details of the physical examination and other diagnostic tests. Specifically, in case 1, the authors state that the patient had a history of two cesarean sections. However, they do not specify whether the hernia identified was at the site of the previous scar or another location in the aponeurosis. This information is relevant in the discussion section where the authors state, \"Both our patients developed a hernia at the natural orifice.\" Please clarify whether the patient presented with a hernia at the previous scar (incisional Richter’s hernia) or at a location with previously healthy aponeurosis.\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment?\nThe discussion centers on the need to undergo prompt surgical treatment because of the lack of access to imaging studies. The authors state that the \"clinical presentation of Richter's hernia is highly varied,\" but they do not explain why. Richter's hernias often present with nonspecific symptoms, frequently due to spontaneous reduction. Including this explanation in the article would be beneficial, as the nonspecific nature of the symptoms can lead to delays in diagnosis and treatment. A large portion of the article’s discussion is previously described in the article A Case of Richter Hernia: A Rare Entity (Katragadda K, DeStefano LM, Khan MF. A Case of Richter Hernia: A Rare Entity. ACS Case Reviews in Surgery. 2019;2(3):5-7.). The authors should rewrite this section describing the experiences obtained from addressing their own cases to reduce the possibility of it being classified as plagiarism.\n\nIs the conclusion balanced and justified on the basis of the findings?\nThe conclusion accurately addresses the importance of prompt surgical intervention, especially in the setting of resource-limited countries.\n\nIs the background of the cases’ 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 conclusion balanced and justified on the basis of the findings? Yes", "responses": [] }, { "id": "313967", "date": "04 Sep 2024", "name": "Harsh Sheth", "expertise": [ "Reviewer Expertise Inguinal hernia", "ventral hernia", "surgical gastroenterology" ], "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 limited in its scope, yet, it's very well written and explained in detail. That Richter's hernia's are an uncommon entity is evident and its treatment is usually straight forward, a laparotomy in a resource limited setting or a diagnostic laparoscopy otherwise.\n\nThis article summarises everything well and is written with a clear flow, which is why I am accepting it.\n\nIs the background of the cases’ history and progression described in sufficient detail? Yes\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Yes\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Yes\n\nIs the conclusion balanced and justified on the basis of the findings? Yes", "responses": [] } ]	1	https://f1000research.com/articles/13-702
https://f1000research.com/articles/13-701/v1	27 Jun 24	{ "type": "Systematic Review", "title": "A systematic review on Artificial Intelligence applied to predictive cardiovascular risk analysis in liver transplantation", "authors": [ "Netra Hirani", "Parag Chatterjee", "Netra Hirani" ], "abstract": "Liver transplantation is the ultimate therapeutic option for patients with end-stage liver disease. The clinical management of transplant patients significantly impacts their prognosis, with outcomes influenced by multiple interacting variables. Cardiovascular complications count as a leading cause of both short-term and long-term morbidity and mortality in liver transplant recipients. In this respect, accurate risk assessment and stratification are crucial for optimizing clinical outcomes. Modern artificial intelligence (AI) techniques have significant potential for early risk prediction, providing comprehensive risk assessments in both diagnosed cohorts and early clinical phase patients. This systematic review examines the state of the art in AI applications for predicting cardiovascular risks in liver transplantation, identifying current issues, challenges, and future research directions. We reviewed articles from digital repositories such as PubMed, IEEE Xplore, and ScienceDirect published between 2000 and 2023, using keywords including artificial intelligence, machine learning, cardiovascular, and liver transplantation. Our analysis revealed a diverse range of machine learning algorithms used in this domain. Despite the potential, only 12 papers met the criteria for adequate topic coverage, highlighting a scarcity of research at this intersection. Key challenges include integrating diverse datasets, isolating cardiovascular effects amid multifaceted influences, ensuring data quality and quantity, and the issues to extrapolate machine learning models to day-to-day clinical practice. Nevertheless, leveraging AI for risk prediction in liver transplantation could significantly enhance patient management and resource optimization, indicating a shift towards more personalized and effective medical practices.", "keywords": [ "Artificial Intelligence", "machine learning", "liver transplantation", "cardiovascular", "risk", "prediction" ], "content": "1. Introduction\n\nThe domain of healthcare has seen a significant rise in the implementation of artificial intelligence, and liver transplantation is no exception, especially from the perspective of data analytics. Liver transplantation is the last therapeutic option for patients with end-stage liver disease,1 and is the second most common organ transplantation. Several countries across the world have seen a sharp rise in the number of liver transplants, owing to the population growth, public educational campaigns to enhance awareness of transplantations, and an expansion of organ procurement organizations, among other reasons.2 For example, just in the USA, 9236 liver transplants were performed in 2021.3 The requirements and outcomes of liver transplantations involve complex multidimensional relationships of different variables concerning the donor, recipient, surgical procedure, and post-transplantation medical management,4 in addition to the clinical indicators. With respect to analysis of candidates for liver transplantation, it is often observed that factors like age, cardiovascular comorbidities such as, coronary heart disease, and other medical conditions such as cirrhosis, acute alcohol hepatitis and nonalcoholic fatty liver disease, significantly impact the risk evaluation of the patients destinated for the transplant. To determine the priority and urgency in the waiting list for liver transplantation, most countries adopted the Model for End-Stage Liver Disease (MELD/MELD-Na) scores for evaluation and subsequent risk profiling of the candidates. The MELD score and its modified versions have provided reasonably robust predictions of short-term mortality among patients with end-stage liver disease, making it a widely used tool for clinical prognosis.5 Nevertheless, liver transplantation is a continuously evolving field, and while further studies suggest the presence of several complex variables and new biomarkers and risk predictors, advanced techniques of artificial intelligence are now being developed for improvements in predictive risk analysis in liver transplantation.\n\nArtificial Intelligence is being used in the organ transplant settings in a formalized manner increasingly. Most of the machine learning algorithms are data-adaptive and help producing predictive models that self-learn from clinical data with reasonable accuracy. Liver transplantation involves complex interactions and often nonlinear relationships between demographic, clinical, laboratory, imaging, lifestyle data and several other parameters. Machine learning algorithms are particularly attractive in this context to take advantage of this wide gamut of features and to develop predictive models on that. On one hand, supervised models work on labeled datasets and can help with predictive outcomes. Especially in risk or disease predictions, supervised learning encompasses classification, where the predicted outcome could be a labeled class (disease prediction) and regression, where the predicted outcome could be a continuous range or number (for example, treatment outcome prediction). On the other hand, unsupervised learning uses unlabeled data, examines hidden patterns and relationships between data, for example, performing data clustering.\n\nMachine learning can be a supportive tool in liver transplantation to resolve pre-transplantation predicaments like graft allocation, hepatic steatosis assessment, and the effectiveness of liver segmentation. The Donor Risk Index (DRI) and Model for End-Stage Liver Disease (MELD) are clinical tools widely used for graft allocation. However, since conventional models often fail to consider the complex nonlinear relationships between donor, recipient, and surgical procedure, machine learning tools are used to overcome these limitations. Furthermore, MELD score often fails to reflect the liver disease severity of some patients, which can create a discrepancy in the 90-day waitlist mortality risk. However, well-trained decision-tree-based models can help to create a different waitlist by incorporating all necessary variables, resulting in higher accuracy. Machine Learning also assists in solving post-liver transplantation challenges such as graft rejection, graft failure, patient survival, and post-operative morbidity. Patient survival prediction is one of the most explored research areas for the intersection of liver transplantation and artificial intelligence since predictive models based on machine learning can handle large volumes of uncorrelated data and can assess short-term and long-term post-liver transplantation mortality.\n\nWith respect to risk assessment in liver transplantation, cardiovascular diseases hold an important impact. Specific cardiovascular responses and symptoms in cirrhosis can be deleterious for patients’ health and suggest an increased risk in liver transplantation. Patients with cirrhosis requiring liver transplant often exhibit conditions like cirrhotic cardiomyopathy, which is present in up to 30% of patients with cirrhosis6 and is characterized by increased cardiac output and inept ventricular response to stress. Patients with underlying cardiovascular conditions are prone to complications in the post-liver transplantation tenure, highlighting the need for the analysis of underlying cardiovascular status during the assessment of the waiting list for transplantation to determine whether the patients are suitable for the procedure. While there exists empirical data and research looking into the various aspects of cardiovascular implications on liver transplants, there is a paucity of a systematic framework that can be incorporated into clinical practice for improved risk analysis and perioperative management of transplant candidates. With the introduction of artificial intelligence, especially with the techniques of machine learning, the domain of identification of risk predictors and biomarkers has been amplified largely.\n\nConsidering the importance of assessing cardiovascular risks in liver transplantation setup, in this work, we present a systematic review on the aspect of using artificial intelligence applied to cardiovascular risk assessment in liver transplantation, aiming at identifying the principal lines of development, key issues, and challenges, as well as the future direction.\n\n\n2. Methods\n\nThis systematic review has been performed focusing on the implementation of artificial intelligence (AI) for the assessment and predictive analysis of cardiovascular risks in liver transplantation. Digital repositories- IEEE Xplore, PubMed, ScienceDirect, Springer Link, and Wiley Online have been explored for a qualitative analysis of publications. For the review, we used a systematic structure,7 consisting of definition of the key research questions, precise definition of the research scope, search and screening of relevant publications, analysis in terms of the research questions, and finally, a general perception of the current and future lines of the field. To perform a specific selection of the studies to be included in this review, we have established the definition of inclusion criteria. At first, only journal articles, conference papers, and book chapters written in English were considered from the digital repositories. Secondly, the year of publication was set from 2000 to 2023. Regarding the scope of the studies, the incorporation of artificial intelligence was set, followed by the consideration of the specific domain of predictive analysis of cardiovascular risks in liver transplantation.\n\nThe following sets of search keywords have been used in different combinations: artificial intelligence, machine learning, liver transplant, liver transplantation, and cardiovascular. Following the search, a careful analysis of the publications has been made with respect to the inclusion-exclusion criteria (Figure 1). During this research, 119 papers were identified which were deemed pertinent to the study. Subsequently, 10 duplicate papers and an additional 33 papers were excluded due to irrelevance to the systematic study, subject to the inclusion-exclusion criteria. Furthermore, 64 papers were eliminated from consideration due to inadequate coverage of the designated research topics.\n\nWith respect to the analysis of the relevant literature, research questions have been established (Table 1).\n\n\n3. Results\n\nAfter an exhaustive search, from a total of 119 papers subsequently passing through preliminary filtering and application of the inclusion-exclusion criteria and subject relevance i.e. the use of artificial intelligence in liver transplantation with respect to cardiovascular risks, 12 papers were obtained and considered as the core of this systematic review. Each publication has been critically analyzed in terms of the research questions modeled before, and finally, a general perspective of the outcome of the review is presented.\n\nFigure 2 depicts the outcomes of the search methodology. A notable observation is the insufficient coverage of all three research topics in several papers, which focused solely on singular or dual aspects. This underscores the underexplored intersection of artificial intelligence with liver transplantation and cardiovascular risks, suggesting a potential domain with limited prior investigation or scholarly studies.\n\nAs a background of this study, several reviews related to the application of artificial intelligence in liver transplantation were analyzed (Table 2). These reviews provide a general approach to the state of the art of artificial intelligence in this field.\n\nReviews,8,9,13 and17 focus on the various applications of artificial intelligence and machine learning on liver transplantation and hepatology, highlighting the strengths, downfalls, and future perspectives. In,8 21 papers were broadly reviewed between a period of 1997 to 2019; 4 papers focusing on the pre-liver transplantation period i.e., prediction of 3-months Waitlist mortality, outcomes after hospitalization; 7 papers on prediction of short-term mortality post-liver transplantation; 3 papers on prediction of long-term survival post liver transplantation and 7 papers focusing on post-liver transplantation complications. The potential fields of interest for future development of machine learning suggested by8 were resolution of bacterial infections, allocation of extended criteria donors and donors after circulatory death, and immunosuppression management. Paper9 focused on the use of machine learning in liver transplantation for both pre-transplant and post-transplant applications, by analyzing 29 articles out of a total 216 articles, identified from various databases, between a period of 2015-2021. Various machine learning algorithms were assessed for different applications, however XGBoost deemed to be most suitable for liver transplantation-clinical decisions given its rapid processing and high accuracy.13 analyzed 40 papers from MEDLINE (PubMed) and Embase (Elsevier), suggesting the efficient replacement of machine learning in place of biostatistics.17 discusses aspects of AI in liver transplantation, with a focus on applications which require accurate decisions such as organ allocation and survival prediction. The paper highlights classifiers such as ANNs, decision tree classifiers, random forest, and Naïve Bayes models.10 is a systematic review assessing 9 articles and 18,771 Liver transplants with a focus to predict survival of grafts using Artificial Intelligence. A maximum AUROC of 0.84 was achieved using the ANN models, compared to linear regression and standard predictive modeling.11,12 are systematic reviews about the applications of AI for predicting NAFLD and NASH. NAFLD is one of the leading causes of liver failure and it has been found that cardiovascular and renal risks are highly prevalent in NAFLD patients as well.11 analyzes summarized diagnostic/assessment models which perform diagnostic tasks on medicinal data and optimize their function for better accurate diagnostic effects.12 has summarized various domains concerning NAFLD by analyzing 4 papers from Electronic Medical Records (EMR), 1 paper from Imaging, 1 from Microbiome and 5 papers from Histology.14 is a systematic review of studies that predict patient survival after liver transplantation using AI techniques and compares the proposed models with existing models such as SOFT score, MELD score, DRI score and BAR score. Among all the models of all the studies analyzed, a highest AUROC of 0.9 was achieved by ANN model on different datasets.15 is a review that highlights the application of ML methods in assessing and predicting various diseases. The studies primarily investigate the prognosis of NAFLD and acute liver failure, using decision tree models. The studies demonstrate the growing application of data mining techniques to analyze medical data and provide insights for clinical diagnosis and risk assessment in common diseases.16 discusses the increasing use of AI in organ transplantation, with an emphasis on donor-recipient matching. Deep Learning models (ANN, Random Forest) handle a multitude of variables and hold potential to improve organ allocation by enhancing predictability. Both ANN and RF outperform the metrics such as MELD and post-LT survival outcome scores.\n\nThe selected reviews collectively illustrate the significant strides made in applying artificial intelligence and machine learning to liver transplantation. Particularly supervised learning models like decision trees, random forests, and artificial neural networks have shown superior accuracy in predicting short-term and long-term survival, complications, and graft rejection compared to traditional clinical models. The reviews also highlight the emerging role of artificial intelligence in addressing complex challenges such as optimizing organ allocation and managing immunosuppression. Furthermore, the ability of machine learning to process and learn from vast and multidimensional datasets makes it a valuable tool in this domain, offering potential improvements in both the precision and efficiency of clinical decision-making in liver transplantation.\n\nNarrowing down the analysis to the specific area of cardiovascular risks in liver transplantation (Figure 2), Table 3 highlights the studies that used artificial intelligence for the same.\n\n1has analyzed the cardiometabolic risks during pre-liver transplantation and post-liver transplantation of patients registered in the National Liver Transplantation Program (NLTP) program in Uruguay. A size of 165 patients of the 2014-2019 cohort was considered, considering vascular age as the significant factor. A maximum AUC score of 0.74 and AIC score of 0.8125 was obtained using Logistic Regression. Similarly,18 aimed to perform a risk-group analysis by dividing the NLTP patients into clusters based on their health parameters, with a specific focus on Cardiovascular risk.29,28 are studies which focus on the analysis of ECGs to predict and evaluate cardiovascular complications after liver transplantation, with the help of AI algorithms.16 included 2 cohorts of adult patients with end-stage liver disease either undergoing LT evaluation or receiving transplant between 2017 and 2019 for their retrospective study. The study analyzed the performance of an AI based algorithm (AI-ECG) which reflected an AUROC of 0.69 for prediction of subsequent low left ventricular ejection fraction. Similarly,28 developed a deep learning model to provide an AI-Cirrhosis-ECG (ACE) score to correlate cirrhosis with cardiovascular dysfunction. The model resulted in an AUC of 0.908 with consistency. Similarly,26 utilized CT scans to assess cardiovascular risk. The study used automated ML algorithms focused to evaluate biomarkers on non-contrast chest CT (Emphy-Alg, LD-Alg, CCS-Alg) which was followed by multivariate logistic regression and statistical analysis. The algorithms demonstrated their potential to predict CVD incidence and mortality. The studies suggest that AI can be a potential tool for identifying cardiovascular complications in transplant evaluations.20 aimed to predict the post liver transplantation cardiovascular events and mortality, wherein 1459 patients undergoing liver transplantation between January 2008 and December 2019 were studied. Various machine learning algorithms were analyzed, however the GBM model XGBoost achieved the best results, with an AUC=0.71 for overall survival and AUC=0.72 for cardiovascular mortality. Similarly,23 aims to predict risks and early signs of chronic diseases by analyzing the health data. A cohort of 104 patients from the NLTP, Uruguay program between 2014-2017 was considered and k-means was applied on the data for clustering. The study related the risk groups before liver transplantation with cardiometabolic risks using vascular age.\n\nNon-alcoholic Fatty Liver Disease (NAFLD) can lead to enhanced cardiovascular risks which may lead to the need for a liver transplant.28,22 aim to study the correlation of Cardiovascular risks with NAFLD28; studies 2239 hypertensive patients to analyze the most relevant features of NAFLD using adverse machine learning algorithms, resulting in a maximum AUC=0.79.22 aimed to develop a machine learning model that integrates various risk factors to identify cardiovascular disease in liver transplant patients. Seven various Supervised Learning methods were analyzed, with Random Forest giving the highest AUC of 0.849, in the UK Biobank cohort. Similarly.30 demonstrated the use of Random Forests in predicting the patients with a high risk for developing NASH. Data of patients who attended the Cardiovascular Risk Unit of Mostoles University Hospital (Madrid, Spain) from 2005 to 2021 was used. E-health records were analyzed using 6 models entailing different pre-processing strategies. Random Forest models provided impressive results (best model accuracy- 0.87, worst model accuracy- 0.79), highlighting the power of ML to provide insightful results in disease prediction.24 aimed to assess the use of CT-derived fractional flow reserve (CT-FFR) in differentiating coronary stenosis in patients being evaluated for LT. The patients were preliminary tested to rule out coronary artery disease (CAD), and CT-FFR was computed using a ML algorithm. The diagnosis reflected an accuracy of 0.85, suggesting a promising noninvasive tool to exclude hemodynamically significant coronary stenosis, thereby reducing the need for invasive measures to achieve the same.25 focused on the correlation between metabolic-associated fatty liver disease (MAFLD) and cardiovascular disease (CVD) risk. The study divided the 191 patients into two groups: 144 without CVD and 47 with CVD. The best model operating on 5 most discriminative features correctly identified 114/144 low-risk and 40/47 high-risk patients, highlighting the potential of ML in predicting identifying MAFLD in patients with a CVD risk.27 aimed to investigate the correlation between hepatosteatosis (HS) and cardiovascular disease (CVD) risk in HIV-positive individuals. CT images of 1306 subjects (HIV-positive and HIV-negative individuals) were analyzed to determine the presence of HS and CVD using Logistic regression and Random Forest models. The results suggested that metabolic dysfunction may contribute to the increased CVD risk in this population.\n\nThese studies (Table 3) provide an in-depth idea of how artificial intelligence is being applied to assess cardiovascular risks in liver transplantation, highlighting the diversity in the algorithms used, cohort sizes, and specific cardiovascular outcomes examined. The use of logistic regression, deep learning, and various supervised and unsupervised learning methods across different studies demonstrates the versatility of applying artificial intelligence in this domain. Several studies focused on pre-liver transplantation cardiovascular risk assessment, employing models like logistic regression and k-means clustering to predict cardiometabolic risks based on health parameters and vascular age. Others utilized AI-enabled electrocardiograms (AI-ECG) and deep learning models to predict cardiovascular complications and dysfunction in liver transplant candidates, achieving promising AUC scores that underscore the predictive power of AI. Additionally, machine learning algorithms, including Random Forest, Support Vector Machines (SVMs), and Gradient Boosting Models (GBM), were applied to predict major adverse cardiovascular events post-transplantation, often potentially outperforming traditional clinical models in terms of accuracy and predictive capability. In the context of non-alcoholic fatty liver disease (NAFLD) and metabolic-associated fatty liver disease (MAFLD), which are linked to heightened cardiovascular risks, AI models have been used to identify relevant features and predict cardiovascular diseases with high accuracy. These studies also employed various imaging techniques, such as computed tomography (CT) scans, coupled with AI algorithms to noninvasively assess coronary artery disease risk and evaluate cardiovascular biomarkers, further illustrating AI's potential in improving pre-transplant evaluation and post-transplant outcomes.\n\nWith respect to RQ1, the studies reveal a variety of AI algorithms employed to predict cardiovascular risks in liver transplantation, reflecting diverse methodological approaches. Logistic regression is commonly used for its simplicity and interpretability, particularly effective in smaller cohorts and for binary classification tasks. Unsupervised learning techniques like k-means are applied to cluster patients based on health parameters, useful for identifying underlying patterns without labeled data. Convolutional Neural Networks (CNNs) are utilized in AI-enabled electrocardiograms (AI-ECG) to extract features from ECG data for risk prediction. Other methods such as Random Forests, SVMs, LASSO, and Gradient Boosting Models (GBM) are preferred for their ability to handle complex, high-dimensional data and their robustness in various predictive tasks. Deep learning models, employed for ECG analysis and CT-derived fractional flow reserve (CT-FFR), are effective in capturing intricate relationships within large datasets. The choice of algorithms often correlates with the nature of the dataset, the type of prediction needed, and the existing knowledge of intra-data relationships.\n\nIn terms of RQ2, the results across different studies highlight AI's potential in risk prediction. AI models have often shown improved accuracy and reliability over traditional models, as they can better manage complex datasets and uncover hidden patterns. The use of AI-enabled ECGs and CT-FFR models showed significant promise in noninvasive risk assessment, highlighting the effectiveness of AI methods in providing accurate and reliable predictions, which are crucial for improving clinical outcomes in liver transplantation.\n\nRegarding RQ3, validation of AI models stands as a critical point due to several factors. The absence of one-size-fits-all structure in AI models often limit the functionality of a predictive model to a specific cohort or dataset and is not directly transferable to other cohorts, unlike several traditional clinical models. Limited information has been obtained on the validation and clinical reproducibility of the AI-based predictive models. In addition to validating through clinical trials or retrospective analysis of large patient cohorts, it is crucial to ensure that the models are robust and applicable in real-world settings.\n\nFor RQ4, several design and implementation challenges were identified from a general perspective. Ensuring the availability of high-quality, comprehensive datasets is crucial for training robust AI models. Balancing model complexity with interpretability remains a challenge, especially in clinical settings where transparency is essential. Integrating AI models seamlessly into existing clinical workflows requires careful consideration of usability and acceptance by healthcare professionals. Moreover, addressing ethical and legal considerations related to patient privacy, data security, and the ethical use of AI in healthcare is paramount.\n\nWith respect to RQ5, future research directions in the field of artificial intelligence for cardiovascular risk assessment in liver transplantation are expected to prioritize the enhancement of model interpretability and transparency. This focus aims to bolster clinical trust and facilitate the broader integration of AI technologies into healthcare settings. The development of hybrid AI models that amalgamate the predictive capabilities of various algorithms could potentially elevate both the accuracy and robustness of risk assessments. Moreover, future studies are anticipated to extend the validation of these AI models across more diverse and larger cohorts, which is essential for confirming their applicability and generalizability across different patient demographics. The integration of AI with innovative technologies such as wearable health devices and telehealth services of day-to-day clinical settings promises to revolutionize patient monitoring by enabling continuous and proactive management of individuals at elevated risk. Additionally, future research will need to rigorously address the ethical, legal, and social challenges posed by the deployment of AI in medical contexts, ensuring that these technologies are used responsibly and equitably.\n\nNevertheless, the studies reviewed in this work suggest that AI provides valuable tools for enhancing cardiovascular risk assessment in liver transplantation, offering more precise and efficient predictive models compared to traditional methods. This can significantly impact clinical decision-making, leading to better management and outcomes for liver transplant patients.\n\n\n4. Discussion\n\nThe disruptive development of artificial intelligence has seen the domain of healthcare being reengineered to incorporate predictive modeling in different areas. In both domains of liver transplantation and cardiovascular diseases, machine learning is being used profusely, but quite independently. From an implementational perspective, the application of artificial intelligence, especially machine learning algorithms to predict cardiovascular risk in patients suffering from liver diseases, undergoing liver transplantation, or recovering post-surgery. Liver transplantation patients in several the intersection between the fields of liver transplantation and cardiovascular diseases, given the high impact of cardiovascular risks in affecting the patients undergoing liver transplantation. For example, cardiovascular disease is the leading cause of mortality among patients with nonalcoholic fatty liver disease, which in turn, is the most prevalent liver disease worldwide.22 Through this work, the research questions presented at the beginning are answered. Primarily, the review identified the key methods used in this domain, and their subsequent results and validation parameters. Discussions on the key challenges and future scope follow.\n\nMachine learning stands as a highly potential tool in the intersection of cardiovascular diseases and liver transplantation, not only from the predictive point of view, but also from the perspective of discovering new patterns and relationships between the hepatic and cardiometabolic features, useful for eventual prediction of risks. The lack of studies in this joint area of artificial intelligence applied to cardiovascular diseases in liver transplantation is the evidence highlighting the need of transdisciplinary interactions. It involves challenges at different levels. At the first place, the integration of the data sets is a crucial challenge, considering the difficulties in developing and handling a unified database shared between the cardiovascular and hepatic profiles despite the focus being on liver transplantations. Secondly, in the domain of mortality in liver transplantation, the interference of multifarious factors makes it difficult to isolate cardiovascular impact. Cardiovascular complications in orthotopic liver transplantation are quite seldom; however, since they compromise the blood flow of the transplant, they are the most feared complications with a high incidence of both graft loss and mortality. In this respect, diagnosis and therapeutic management of vascular complications constitute a major challenge in terms of enhancing the success rate of liver transplantations.31 Especially from the implementational perspective of artificial intelligence, data quality as well as quantity are significant challenges. The diversity among hepatic and cardiometabolic data from different countries makes it difficult to develop unified models to avoid one-size-fits-all approach for risk predictions. Also, the lack of prospective studies poses a significant challenge on the confidence of the machine learning algorithms, besides its sensitivity and reliability when applied to different cohorts with differed attributes. However, despite the current challenges, the need of integrating cardiometabolic and hepatic aspects while applying artificial intelligence to predict cardiovascular risks in liver transplantation is the call of the hour. By incorporating AI methodologies into routine risk assessment protocols and throughout the Electronic Health Records (EHR)-creation procedure, healthcare practitioners can harness the power of advanced algorithms to refine patient stratification, optimize resource allocation, and facilitate timely intervention strategies. As we navigate toward an era of personalized medicine, the convergence of artificial intelligence and cardiovascular risk prediction in liver transplantation emerges as a pivotal avenue for transformative advancements, fostering a paradigm shift towards more effective and patient-centric healthcare practices.", "appendix": "Data availability\n\nNo data are associated with this article.\n\nMendeley Data: Systematic Review: AI applied to predictive cardiovascular risk analysis in liver transplantation. https://doi.org/10.17632/p5m2hg5zt4. 32\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nChatterjee P, et al.: Predictive Cardiometabolic Risk Profiling of Patients Using Vascular Age in Liver Transplantation. 2021 43rd Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC). Mexico: IEEE; Nov. 2021; 1715–1718. 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Publisher Full Text\n\nDrożdż K, et al.: Risk factors for cardiovascular disease in patients with metabolic-associated fatty liver disease: a machine learning approach. Cardiovasc. Diabetol. Nov. 2022; 21(1): 240. Publisher Full Text\n\nStemmer A, et al.: Using machine learning algorithms to review computed tomography scans and assess risk for cardiovascular disease: Retrospective analysis from the National Lung Screening Trial (NLST). PLoS One. Aug. 2020; 15(8): e0236021. Publisher Full Text\n\nHeseltine T, Murray S, Ortega-Martorell S, et al.: Associations of Hepatosteatosis With Cardiovascular Disease in HIV-Positive and HIV-Negative Patients: The Liverpool HIV–Heart Project. JAIDS J. Acquir. Immune Defic. Syndr. Aug. 2021; 87(5): 1221–1227. Publisher Full Text\n\nGarcia-Carretero R, Vigil-Medina L, Barquero-Perez O, et al.: Relevant Features in Nonalcoholic Steatohepatitis Determined Using Machine Learning for Feature Selection. Metab. Syndr. Relat. Disord. Nov. 2019; 17(9): 444–451. Publisher Full Text\n\nAlexander S, Teshome M, Patel H, et al.: The diagnostic and prognostic utility of risk factors defined by the AHA/ACCF on the evaluation of cardiac disease in liver transplantation candidates. BMC Cardiovasc. Disord. Dec. 2019; 19(1): 102. Publisher Full Text\n\nGarcía-Carretero R, Holgado-Cuadrado R, Barquero-Pérez Ó: Assessment of Classification Models and Relevant Features on Nonalcoholic Steatohepatitis Using Random Forest. Entropy. Jun. 2021; 23(6): 763. Publisher Full Text\n\nPiardi T: Vascular complications following liver transplantation: A literature review of advances in 2015. World J. Hepatol. 2016; 8(1): 36. Publisher Full Text\n\nChatterjee P, Hirani N: Systematic Review: AI applied to predictive cardiovascular risk analysis in liver transplantation. [Dataset]. Mendeley Data. 2024; V2. Publisher Full Text" }	[ { "id": "297060", "date": "05 Jul 2024", "name": "Jonathan Soldera", "expertise": [ "Reviewer Expertise AI for Hepatology", "IBD" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis systematic review explores the application of artificial intelligence (AI) in predicting cardiovascular risks in liver transplant patients. By examining articles from various digital repositories published between 2000 and 2023, the authors identified a range of machine learning algorithms used in this domain but noted a scarcity of research meeting their criteria. The review highlights the potential benefits and current challenges of integrating AI into clinical practice for liver transplantation. This study is particularly relevant as it adds valuable insights to the existing literature on the use of AI in medical prognostication, specifically in the context of liver transplantation, and underscores the potential of AI to enhance patient management and resource optimization, moving towards more personalized medical practices. Major Points\nComprehensive Overview: The authors provide a thorough overview of the various AI algorithms employed for predicting cardiovascular risks in liver transplant patients. The review is well-structured, and the methodology for selecting articles is clearly explained. Potential Benefits of AI: The review effectively highlights the potential benefits of AI in improving patient outcomes and optimizing resource allocation. The discussion on the impact of AI on personalized medicine is particularly compelling. Challenges in Implementation: The review identifies significant challenges in integrating AI into clinical practice, including data quality issues, the need for large datasets, and the lack of standardized protocols. However, it would benefit from more detailed exploration of these challenges and possible solutions.\nMinor Points\nLimited Research: The authors note the limited number of studies meeting their criteria. It would be helpful to discuss why this might be the case and suggest areas for future research to fill these gaps. Additional References: To enhance the depth and context of the discussion, I suggest adding references to additional publications on the use of AI for prognosticating liver disease. This could provide a broader perspective on the current state of research and its potential clinical applications. For example, the following articles could be included:[1],[2] Practical Implementation: While the study provides a comprehensive overview, it does not fully resolve the broader questions surrounding the practical implementation and clinical integration of these AI techniques. A discussion on how current AI models could be practically implemented in clinical settings would be beneficial.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Yes\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? Yes\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes\n\nIf this is a Living Systematic Review, is the ‘living’ method appropriate and is the search schedule clearly defined and justified? (‘Living Systematic Review’ or a variation of this term should be included in the title.) No", "responses": [] } ]	1	https://f1000research.com/articles/13-701
https://f1000research.com/articles/13-700/v1	27 Jun 24	{ "type": "Research Article", "title": "Computational Evaluation For The Survival Times Of Patients Under Truncated Life Tests: Simulation And Application", "authors": [ "Azam Zaka", "Riffat Jabeen", "Azam Zaka" ], "abstract": "Background Statistical process control (SPC) is utiled in manufacturing and service applications. It is used to monitor the behavior of the process, also to discover and solve the issues in internal systems. SPC allows immediate corrective actions to prevent defects and maintain process stability. There are two types of control charts are available in the literature: variable control charts and attribute control charts.\n\nMethods The use of attribute control charts for two positively skewed distributions such as power function distribution and weighted power function distribution is discussed in this research paper. We compared the behavior of both types of control charts and presented the results in form of tables.\n\nResults We conclude that control charts under a weighted power function distribution perform better than control charts using a power function distribution. Furthermore, these results will help in the early detection of errors that enhance the process reliability of the telecommunications and financing industries.", "keywords": [ "power function distribution", "weighted power function distribution", "attribute control chart", "truncated life test", "average run length", "simulation" ], "content": "1. Introduction\n\nStatistical process control is used as an effective tool to monitor the manufacturing process and prevent products from being out of the given provisions. Two different types of control charts are available in the literature: variable control charts and attribute control charts. When numerical measurements of the variable of interest from any process are available, the use of a variable control chart is preferred. However, there are many processes that have a variable of interest in the form of attributes and are not measurable. In such situations, it is preferable to use attribute control charts instead of variable control charts.\n\nAttribute control charts are used to monitor a process with two possible outcomes: conforming and nonconforming. The basic condition for using these charts was the assumption of normality. However, in real-life situations, whenever a process is working, the outcome may not follow a normal distribution.\n\nIt is possible that the shape of the distribution is skewed. For such cases, many studies, such as Chang and Bai,1 Lin and Chou,2 and Rao and Subbaiah,3 have been conducted. Work on attribute control charts considering different skewed distributions has also been done by Aslam et al.,4 Karagöz,5 and Noiplab and Mayureesawan.6 We can also refer to Zaka et al.,7 who modified the attribute control chart for the shape of the process using the power function and survival-weighted power function distribution.\n\nThe shape of any distribution can be studied by estimating its shape parameter. Several estimators have been developed to estimate the shape parameters of any distribution. Zaka et al.7 introduced and studied an attribute control chart for the shape of the process using the power function and survival-weighted power function distribution. Dallas8 introduced the power function distribution (PFD) as a powerful tool to study many processes in reliability and health sciences, which was further assumed and modified to increase its applicability in unequal probability theory by Zaka et al.9 as the weighted power function distribution (WPFD). Jabeen and Zaka10 proposed modified control charts based on shape parameters.\n\nWe introduce the PFD and WPFD in Section 2. In Section 3, we propose an attribute control chart for PFD and WPFD. A discussion of the use of the proposed control chart is presented in Section 4.\n\n\n2. Methods\n\nThe weighted power function distribution (WPFD) was used by Zaka et al9 by modifying the existing Power function distribution (PFD). The cumulative distribution function and probability density fuction for PFDand WPFD is given asintroduced\n\nThe mean of PFD and WPFD are respectively\n\nThe control limits for attribute control charts to monitor the shape parameter of weighted Power fuction distribution is illustrated in from Zaka et al.7 and similarly the control limits for attribute control charts is given by Aslam et al.11 , the proposed control limits are given as:\n\nwhere p0 is the failure probability, n is the sample size, and L is the control coefficient. Thus, it is obtained from (1) and (2) as follows:\n\nThe control limits are presented as\n\nWe can find the ARL using the following formulae\n\n2.1.1. The probabilities of failure for PDF in out of control process are\n\n→ When the shape parameter varies → P11=(aβo1γ11γ11+1βo1)γ11\n\n→ When the scale parameter varies → P21=(aβ11γo1γo1+1β11)γo1\n\n→ All the parameters vary → P31=(aβ11γ11γ11+1β11)γ11\n\n2.1.2. The probabilities of failure for WPFD in out of control process are\n\n→ When the shape parameter varies → P12=(a2βo2γ122γ12+1βo2)2γ12\n\n→ When the scale parameter varies → P22=(a2β12γ022γ02+1β12)2γ02\n\n→ All the parameters vary → P32=(a2β12γ122γ12+1β12)2γ12\n\nWe used γ11,γ12 when the shape parameters varied fromγo1,γ02 for the first and second distributions, respectively. We also used β11,β12 when the shape parameters varied from βo1,βo2 for the first and second distributions, respectively.\n\nWhen the parameter is shifted from β1=Cβ0, the probability in the control process is\n\nThe ARL for the shifted process is given as\n\nWe adopt γ1=Cγ0. The probability of in-control for the shifted process is\n\nThe ARL to compare the efficiency of the process after the shift is\n\nWhen the scale and shape parameters are shifted as β1=Cβ0 and γ1=Cγ0we get the probability\n\nThe ARL for the shifted process is\n\nZaka et al.7 provided the simulation steps to conduct the monitoring of the shape parameter of weighted power function distribution. By considering these steps we assumed different observations of the ARL, shape parameter, and a. For these observations of ARL, we took the values of the shape and scale parameters of the control chart and sample size (n) in such a way that the ARL from equation (ARL0) was close to R0. Using equation (ARL1) and the values fixed in equation (2), we found ARL1 using different values of c,γ0, R0, a, and n, which are in Tables 1-4.\n\n\n3. Results and Discussion\n\nTo study the proposed control charts (Section 3), we assume the shape parameter as γo1=0.5andγo2=1. We also assumed a target ARL value of 300 and simultaneously for the in-control process. We assume a shift of 0.1 in the shape parameter for PFD and WPFD, and n = 5, 10, and 20. The results are presented in Tables 1-3 and Figures 1-2. We observed a rapid decrease in ARL for WPFD compared to PFD, with a decrease in C and an increase in n. We see that for γo1=0.5 to γo1=1, there is an early detection in out of control ARLs for both the PFD and WPFD control chart. We also observed that with an increase in the size of the sample and the value of the shape parameter, the WPFD proved to be more reliable for use instead of PFD.\n\nIn this section, we generated data from the PFD and WPFD. Let n=10 and R0=300,γoi=0.5and βoi=1, where i=1, 2. We generated the first 10 observations from the process under control and the next 20 observations from the shifted process using shift = 0.85, as presented in Table 4. We used the life test termination times t01=0.31259μo1and t02=0.2235101μo2. Figures 3 and 4 show the 30th observation (10th observation after the shift) using the WPFD control chart. We conclude that WPFD is more efficient than the PFD control chart.\n\nWe used survival time data for a group of patients given by Bekker et al.12 The data consisting of survival times (in years) for 46 patients were: .0470, .1150, .1210, .1320, .1640, .1970, .2030, .2600, .2820, .2960, .3340, .3950, .4580, .4660, .5010, .5070, .5290, .5340, .5400, .6410, .6440, .6960, .8410, .8630, 1.0990, 1.2190, 1.2710, 1.3260, 1.4470, 1.4850, 1.5530, 1.5810, 1.5890, 2.1780, 2.3430, 2.4160, 2.4440, 2.8250, 2.8300, 3.5780, 3.6580, 3.7430, 3.9780, 4.0030, 4.0330.\n\nWe used the maximum likelihood estimator (MLE) to estimate the PFD and WPFD parameters. The statistics used to show the application of the control charts are shown in Figures 5 and 6. Zaka et al.9 showed that the above data follow the WPFD with the shape parameterγo1=0.3087394. We also assumed that ao1=0.35548. We obtained the control coefficient of the proposed chart as ko1=2.978, n=15, and p01 = 0.465220. From Figure 5, we observe that the control chart based on the PFD shows an in-control situation. All the points lie between the control limits.\n\nFrom Figure 6, the WPFD control chart is presented with shape parameter γo2=0.3087394. The plotting statistics are shown in Figure 6, which are used to apply the proposed control chart. The data are known to follow the WPFD with shape parameterγo2=0.308739,ao2=0.262064 and control coefficients ko2=2.869, n=15, and p02 = 0.423427. From Figure 6, we see that all points are in the control area, but the 30th observation shows an out-of-control situation.\n\nWe see that it is better to use the WPFD-based control chart to control the process than the PFD control chart.\n\n\n4. Conclusion\n\nIn this paper, we proposed attribute control charts assuming that the lifespan of the products under study follows the PFD and WPFD simultaneously when the shape parameter is unknown. We used the average run length (ARL) as the performance criterion to assess the competence of the proposed idea. The results of the ARLs are presented in the form of tables using different parameter values and sample sizes. The paper is concluded as follows.\n\n• We observed that the WPFD is a more applicable control chart because of its narrower control limits than the PFD control chart.\n\n• We also observed that the detection ability of the proposed control charts increased with increasing sample size.\n\n• A real-life application and simulation study were conducted to demonstrate the applicability of the proposed control charts, which showed the outstanding execution of the suggested idea.\n\n• The proposed control charts can be extended using other sampling schemes, such as repetitive sampling and multiple dependent state sampling, in future work.\n\n• The proposed chart under WPFD efficiently detected the shift in the process.\n\n• We suggest further applications of the proposed work in Engineering and Medical Sciences. In addition, more probability distributions could be used to construct the ACC under TTLT.", "appendix": "Data Availability\n\nAll underlying data are available as part of the article and no additional source data are required.\n\n\nReferences\n\nChang YS, Bai DS: Control charts for positively-skewed populations with weighted standard deviations. Qual. Reliab. Eng. Int. 2001; 17(5): 397–406. Publisher Full Text\n\nLin YC, Chou CY: Non-normality and the variable parameters X control charts. Eur. J. Oper. Res. 2007; 176(1): 361–373. Publisher Full Text\n\nRao KS, Subbaiah KV: Optimal operating policies of X-bar control chart for non-normal variables with generalised Pareto in-control times. International Journal of Productivity and Quality Management. 2010; 6(1): 91–111. Publisher Full Text\n\nAslam M, Arif OH, Jun CH: A control chart for gamma distribution using multiple dependent state sampling. Industrial Engineering and Management Systems. 2017; 16(1): 109–117. Publisher Full Text\n\nDaragöz K: Asymmetric control limits for range chart with simple robust estimator under the non-normal distributed process. Math. Sci. 2018; 12(4): 249–262. Publisher Full Text\n\nNoiplab T, Mayureesawan T: Modified EWMA control chart for skewed distributions and contaminated processes. Thailand Statistician. 2019; 17(1): 16–29.\n\nZaka A, Naveed M, Jabeen R: Performance of attribute control charts for monitoring the shape parameter of modified power function distribution in the presence of measurement error. Qual. Reliab. Eng. Int. 2022; 38: 1060–1073. Publisher Full Text\n\nDallas C: Characterization of Pareto and power function distribution. Ann. Inst. Stat. Math. 1976; 28: 491–497. Publisher Full Text\n\nZaka A, Akhter AS, Jabeen R: Asymmetry approach to study for chemotherapy treatment and devices failure times data using modified power function distribution with some modified estimators. Int. J. Comput. Sci. Math. 2022; 15(2): 99–116. Publisher Full Text\n\nJabeen R, Zaka A: Error detection through modified phase II process monitoringunder different classical estimators. Journal of the National Science Foundation Sirilanka. 2023; 51(3): 465–477. Publisher Full Text\n\nAslam M, Jun CH: Attribute control charts for the Weibull distribution under truncated life tests. Qual. Eng. 2015; 27(3): 283–288. Publisher Full Text\n\nBekker A, Roux J, Mostert P: A generalization of the compound Rayleigh distribution: using Bayesian methods on cancer survival times. Communication in Statistics Theory and Methods. 2000; 29: 1419–1433. Publisher Full Text" }	[ { "id": "297242", "date": "27 Jul 2024", "name": "Ahmed Z. Afify", "expertise": [ "Reviewer Expertise Statistics", "Probability theory", "Inference", "Data 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\nI have some comments to improve the current version of the paper. The author should addressed the following comments carefully.\n1.\n\nIn the introduction section, the authors have already done a good job on the literature review. Based on that, it is suggested to link the motivation of this work to the existing gaps of the existing works 2.\n\nThe reason(s) for considering the shape parameter for monitoring purposes should be clearly stated. 3.\n\nReferences to the related conclusions in section 1 are needed. All the formulas/equations should be indexed 4.\n\nPlease check the spaces between words and symbols; more places no space between them, 5.\n\nWhy ARL0=300? 6.\n\nWhat could the possible areas for future studies? 7. Many of the references are fairly old. The authors should check the last 2 years or so of this journal and ones that publish related papers to see if there are any more recent papers that should be cited.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] }, { "id": "309911", "date": "29 Aug 2024", "name": "Alaa El-Alosey", "expertise": [ "Reviewer Expertise Statistics", "Probability theory", "Inference", "Data 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\nI have some comments to improve the current version of the paper. The author should addressed the following comments carefully.\n1.\n\nIn the introduction section, the authors have already done a good job on the literature review. Based on that, it is suggested to link the motivation of this work to the existing gaps of the existing works. 2. In Page 3 lines 14 and 17, Zaka et al. repeated with same meaning. Provide space between words for example Page 3 lines 28 (asintroduced). 2.\n\nThe reason(s) for considering the shape parameter for monitoring purposes should be clearly stated. 3.\n\nReferences to the related conclusions in section 1 are needed. All the formulas/equations should be indexed 4.\n\nWhy ARL0=300? 5.\n\nWhat could the possible areas for future studies? 6. Many of the references are fairly old. The authors should check the last 2 years or so of this journal and ones that publish related papers to see if there are any more recent papers that should be cited.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] }, { "id": "297249", "date": "29 Aug 2024", "name": "Shakila Bashir", "expertise": [ "Reviewer Expertise Mathematical Statistics", "Distribution Theory", "Probability Theory", "reliability 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\nThe authors utilized attribute control charts for two positively skewed distributions—the power function distribution (PFD) and the weighted power function distribution (PWFD). They compared the performance of both types of control charts, presenting their findings in the form of tables. Their conclusion indicates that control charts based on the weighted power function distribution outperform those using the power function distribution. Additionally, the authors suggest that their proposed results can aid in the early detection of errors, thereby enhancing process reliability in the telecommunications and finance industries. While the proposed PWFD model appears to be superior to the PFD in attribute control charts and in detecting early shifts, I have some reservations about the findings, such as:\nGrammatical errors are present throughout the article, and the first sentence of the abstract's methods section needs correction. The PWFD model shows better performance, but there should be a valid discussion explaining why the weighted model produces superior results. The assignment of weights to models in specific situations could be explored here, with reference to applications or real-life examples. The distinction between cases 2.3 and 2.5 needs to be made clearer. Currently, they appear similar, especially in the titles and text. Although a formula is provided, further clarification is required. Figures 1 and 2 need to be clearer. Comparisons should be made separately for 'n' and model types. If presented on the same graph, the lines should be more distinct. The current color scheme makes it difficult to differentiate between PFD under n = 5 and WPFD under n = 10. The title of the article, \"Computational Evaluation for The Survival Times Of Patients Under Truncated Life Tests: Simulation And Application,\" is not fully aligned with the content. The introduction and findings focus on SPC to monitor manufacturing processes and prevent products from failing, which are terms typically used in reliability engineering or quality inspection. These concepts should be related to the survival times of patients, which is the subject of the paper, not products. Additionally, the concept of truncated life tests is not clearly described, leading to a title that contradicts the findings of the paper and does not match the real-life example discussed. The introduction section and body of the article too need to be revised according to the finding of the paper and also provide the motivation of proposing this work. The conclusion is not comprehensive and needs to be refined to align more closely with the findings.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? 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/13-700
https://f1000research.com/articles/13-699/v1	27 Jun 24	{ "type": "Research Article", "title": "Correlation of therapeutic pressure between home automatic positive airway pressure and in laboratory polysomnography manual titration in patients with obstructive sleep apnea", "authors": [ "Apiwat Pugongchai", "Kanyada Leelasittikul", "Narongkorn Saiphoklang", "Apiwat Pugongchai", "Kanyada Leelasittikul" ], "abstract": "Background Continuous positive airway pressure (CPAP) is an effective treatment for obstructive sleep apnea (OSA). Automatic positive airway pressure (APAP) at home might be an alternative choice to identify optimal treatment pressure for OSA patients requiring CPAP treatment. Data on the association of effective treatment pressure between laboratory polysomnography (in-lab PSG) and home APAP has been limited. The aim of this study was to determine the correlation of effective CPAP pressure between in-lab PSG and home APAP.\n\nMethods A prospective cohort study was conducted. OSA participants aged 18 years or older who required CPAP therapy were included. Patients underwent in-lab PSG with manual CPAP titration to identify an effective treatment pressure. Patients also underwent APAP at home for 2 weeks to identify 95 percentile treatment pressure as an effective pressure.\n\nResults Fifty OSA patients (82% male) were included. Mean age was 48.9±14.6 years. Body mass index was 28.7±6.1 kg/m2. Polysomnographic data showed the effective treatment pressure of 10.4±2.9 cmH2O and the apnea-hypopnea index was 55.1±29.0 events/hour. Severe OSA was 76%. Home APAP data showed effective treatment pressure of 10.8±1.8 cmH2O. There was positive correlation of effective pressure between home APAP and in-lab PSG (r=0.472, P=0.001). The equation for predicting an in-lab effective pressure was: predicted pressure (cmH2O) = 2 + (home APAP ⁎ 0.78). Bland-Altman analysis showed good agreement between them, with a low mean difference of -0.428 cmH2O and 96% within the limit of agreement.\n\nConclusions Home APAP pressure is moderately positively correlated with in-lab PSG effective pressure. The accuracy of home APAP is in agreement with in-lab PSG with manual CPAP titration. This APAP might be able to determine an effective therapeutic pressure in the sleep laboratory for OSA treatment.", "keywords": [ "APAP", "automatic positive airway pressure", "continuous positive airway pressure", "CPAP", "obstructive sleep apnea", "OSA" ], "content": "Introduction\n\nObstructive sleep apnea (OSA) is a condition caused by obstruction of the upper airway during sleep and can occur at any age, but the incidence is highest in middle-aged individuals. This disease is more prevalent in males than females.1,2 The main risk factor is obesity, which has been found in 70% of OSA patients.2 Symptoms of OSA usually include snoring, gasping during sleep, excessive daytime sleepiness, and lack of concentration while working. Diagnosis of OSA relies on the patient's medical history, symptoms, and risk assessment from a sleep questionnaire. Polysomnography (PSG), also known as a sleep test, is the standardized tool for diagnosing OSA.3\n\nContinuous positive airway pressure (CPAP) is a standard effective treatment for moderate to severe OSA.2,4,5 CPAP delivers air pressure through a mask into the airway to keep the airway open during sleep to prevent apnea.4,5 There are two CPAP systems; 1) fixed-pressure or manual CPAP, and 2) automatic positive airway pressure (APAP). Fixed-pressure CPAP provides the optimal constant pressure determined by a full night CPAP titration in-laboratory PSG (in-lab PSG) or a split-night in-lab PSG. APAP provides multiple pressure levels, which can be adjusted automatically according to the patient's condition, detected by airflow resistance, body position, and nasal congestion. APAP can improve compliance and reduce daytime sleepiness better than fixed CPAP.4 Some previous studies have found no significant difference in treatment pressure between APAP and fixed-pressure CPAP,6–12 while other studies have reported significant differences in pressure.13–20 CPAP pressure titrated in-lab by an automatic device is usually higher than that titrated in-lab manually.16,18–20 There are conflicting data and unclear results. Advantageously, home APAP titration is more cost-effective than manual laboratory titration to determine optimal CPAP pressure for long-term use.9 Therefore, the aim of this study was to evaluate the correlation of the effective CPAP pressure between in-lab PSG and home APAP in Thai patients with OSA.\n\n\nMethods\n\nThis study, entitled “Correlation of therapeutic pressure between home automatic positive airway pressure and in laboratory polysomnography manual titration in patients with obstructive sleep apnea”, was prospectively registered with Thaiclinicaltrials.org with number TCTR20210331002 on 31 March 2021. https://www.thaiclinicaltrials.org/export/xml/TCTR20210331002\n\nA prospective cohort study was conducted in Thammasat University Hospital, Thailand from April 2021 to January 2022. Subjects with suspected OSA aged 18 years or older and undergoing split-night PSG were included. Exclusion criteria were congestive heart failure, myocardial infarction, obesity hypoventilation syndrome, chronic obstructive pulmonary disease, stroke, claustrophobia, tracheostomy, uncontrolled psychiatric disorders, and residual apnea-hypopnea index (AHI) of 5 events per hour or more during in-lab CPAP titration.\n\nDemographic data including age, sex, height, weight, body mass index, neck circumference, Epworth sleepiness scale (ESS), comorbidity, and in-lab PSG data including AHI, lowest pulse oxygen saturation, 3%oxygen desaturation index, optimal CPAP pressure and residual AHI after optimal CPAP trial were recorded. Moreover, home auto-CPAP data including 95th percentile pressure, residual AHI after optimal CPAP use, and duration of CPAP use were also recorded.\n\nEthic approval was obtained from the Human Research Ethics Committee of Thammasat University (Medicine), Thailand (IRB No. MTU-EC-OO-6-087/63, the approval number: 142/2020, the date of approval on July 2, 2022), in full compliance with international guidelines such as the Declaration of Helsinki, the Belmont Report, CIOMS Guidelines, and the International Conference on Harmonisation-Good Clinical Practice (ICH-GCP). All methods were performed in accordance with these guidelines and regulations. All participants provided written informed consent. This study was registered with thaiclinicaltrials.org with number TCTR20210331002 on 31 March, 2021.\n\nAll subjects underwent split-night PSG using Compumedics Profusion® Sleep Software (Compumedics, Ltd, Victoria, Australia, Available from: https://www.compumedics.com.au/en/products/profusion-sleep-software/). Titration and scoring procedures followed the American Academy of Sleep Medicine guideline version 2.6.21,22 PSG data were manually scored by a certified sleep technician and were reviewed and verified by a certified a sleep specialist. CPAP titration was performed to determine a pressure to reduce the AHI to less than 5 events per hour and achieve a supine REM sleep duration of at least 15 minutes. CPAP was manually titrated with Resmed Lumis® 150 VPAP ST-A (Resmed, Sydney, Australia) in our sleep lab under full PSG monitoring that included electroencephalogram, electrooculogram, submental electromyogram, airflow from a thermistor, snoring, body position, thoracic and abdominal movements, and oxygen saturation. CPAP began at 4 cmH2O and gradually increased by 1 cmH2O steps every 10 min until apnea-hypopnea events disappeared. Optimal pressure, residual AHI, and all PSG data were also recorded.\n\nAll subjects used Resmed AirStart®10 APAP model (Resmed, Sydney, Australia) for a period of 2 weeks within 3 months after split-night PSG. APAP data were downloaded using ResScan® software version 5.9.0.9629 (Resmed, Sydney, Australia, Available from: https://support.resmed.com/en-gb/software-and-data-management/resscan/). An effective APAP pressure was the 95th percentile of the pressure results. An effective pressure, residual AHI, and all APAP data were also recorded. Good APAP compliance was defined as usage ≥4 hours per night for ≥70% of nights.23\n\nBased on a previous study,16 the optimal CPAP pressure determined by in-lab APAP titration in OSA patients was 9.8± 2.2 cmH2O, whereas the optimal CPAP pressure determined by in-lab manual CPAP titration was 7.3 ± 1.5 cmH2O. We hypothesized that the two titration methods in our study would provide optimal pressures like this previous study. Thus, we needed to study 34 participants with 90% power and 5% type I error.\n\nData is presented as number (%) and mean ± standard deviation (SD). Student’s t-test was used to compare continuous variables between in-lab PSG and home APAP groups. Pearson’s correlation was used to determine the relationship of optimal pressure between two groups and to develop a predictive equation of the optimal CPAP pressure of in-lab PSG. Bland-Altman plots were used to determine agreement between the optimal pressures obtained from in-lab PSG and home APAP. The 95% limits of agreement, which represent where 95% of the future differences between the two methods would be expected, were calculated. The proportional bias was also assessed by performing a linear regression between the difference between the two measures and mean pressure for paired measurement. Two-tailed P-values of less than 0.05 were considered statistically significant. All data analyses were done on SPSS version 26.0 software (IBM Corp., Armonk, NY, USA).\n\n\nResults\n\nA total of 55 subjects with suspected OSA were screened, and 5 subjects were excluded (Figure 1). Fifty OSA subjects were included. Mean age was 48.9±14.6 years. 82% of subjects were male. Body mass index was 28.7±6.1 kg/m2. ESS score was 8.7±4.7. Common comorbidities were hypertension (40%), hyperlipidemia (44%), and allergic rhinitis (36%). PSG data showed AHI of 55.1±29.0 events/hour, optimal CPAP pressure of 10.4±2.9 cmH2O, and residual AHI was 1.6±1.5 events/hour. 76% of patients had severe OSA. The effective pressure of home APAP was 10.8±1.8 cmH2O, residual AHI was 1.5±1.0 events/hour and good APAP compliance was 58% (Table 1). There are no significant differences in the optimal pressure and the residual AHI between in-lab PSG and home APAP groups (Table 2).\n\nAPAP=automatic positive airway pressure, CPAP=continuous positive airway pressure.\n\nIn all patients, including severe OSA patients, the optimal pressure obtained by in-lab PSG had significant moderately positive correlation with the effective pressure obtained by the home APAP (Table 3). Overall, an equation for predicting in-lab PSG derived optimal pressure is predicted pressure (cmH2O) = 2 + (0.78 ⁎ home APAP derived effective pressure) (Figure 2). The Bland-Altman comparison of the pressure obtained from in-lab PSG and the home APAP in all patients showed that there was very good agreement between them, with a low mean difference of -0.428 cmH2O (95% CI: -5.548 to 4.692 cmH2O) and only 2 of 50 measurements (4%) were outliers; 96% were within the limit of agreement (Figure 3). However, a proportional bias was detected (B = 0.648, P <0.001).\n\nThe equation for predicting an in-lab effective pressure is predicted pressure (cmH2O) = 2 + (0.78* home APAP derived effective pressure).\n\nThe continuous line indicates the mean difference of optimal pressure between CPAP titration in the lab and home APAP titration (-0.428 cmH2O), while the dotted lines indicate 95% confidence intervals (-5.548 to 4.692 cmH2O). SD=standard deviation.\n\nFurthermore, all patients and severe OSA patients with good APAP compliance had higher significant positive correlation than those without good compliance (Table 3). In patients with severe OSA, a predictive equation for the optimal pressure is in-lab PSG (cmH2O) = 4.28 + (0.64 ⁎ home APAP derived effective pressure) (Figure 4). In OSA patients with good compliance, a predictive equation for the optimal pressure is in-lab PSG (cmH2O) = 1.49 + (0.83* home APAP derived effective pressure) (Figure 5).\n\nThe equation for predicting an in-lab effective pressure is predicted pressure (cmH2O) = 4.28 + (0.64* home APAP pressure).\n\nThe equation for predicting an in-lab effective pressure is predicted pressure (cmH2O) = 1.49 + (0.83* home APAP pressure).\n\n\nDiscussion\n\nThis is the first study to determine the relationship of optimal CPAP pressure between in-lab pressure titration and home APAP in Thai patients with OSA. Our results showed that there was moderately positive correlation between the two titration methods with acceptable agreement, particularly for severe OSA patients with good APAP compliance. Also, the difference of mean optimal pressure between two methods was 0.4 cmH2O in our study.\n\nCPAP is a standard, effective treatment for OSA patients.2,4 Conventionally, the optimal pressure for treating OSA is determined by a standard PSG with manual CPAP titration in a laboratory, whether split-night PSG or full-night PSG. The latter is often performed as a follow-up to the first PSG if the optimal pressure hasn't been successfully determined.3 However, this method is time consuming and expensive. Alternatively, automatic titration is recommended instead of manual titration to identify the proper pressure for CPAP treatment in clinical practice, providing the same outcome in less time for less expense.24 Automatic titration is as effective as standard manual titration in improving AHI and somnolence. In addition, automatic titration has the same effect on acceptance and compliance of CPAP treatment as manual titration.24 Therefore, home APAP is an alternative choice for determining the optimal pressure.\n\nIn our study, we hypothesized that the difference of optimal pressure between home APAP and in-lab PSG study would not be more than 2 cmH2O. Our results showed an average pressure difference of 0.4 cmH2O between the two methods and a moderately positive correlation (correlation coefficient of 0.47). These findings are consistent with a study by Elshahaat HA, et al6 and Wongsritrang K, et al,18 which found weakly to strongly positive correlations of optimal pressure between in-lab PSG and home APAP with pressure difference ranging from 0.25 to 3.5 cmH2O. It can be observed that as the difference in the optimal pressure increases, the positive correlation between two titrating methods decreases. However, there might be a few limitations of the titrating study for optimal pressure due to differences in sleep position and sleep stages between home APAP and in-lab PSG settings. The optimal pressure obtained by in-lab PSG needs to maintain an AHI less than 5 events per hour and at least 15 minutes of REM sleep in the supine position,22 which might differ from the pressure requirements of home APAP machines due to differences in sleep posture and sleep stage.\n\nOur results showed that the majority of patients had severe OSA (approximately 76%) while moderate and mild OSA accounted for 20% and 4%, respectively. Among patients with severe OSA, there was significant moderately positive correlation (correlation coefficient of 0.45) between the pressure from home APAP and in-lab PSG study. However, there was no significant correlation in patients with mild to moderate OSA. These findings may be explained by the small sample size of this population.\n\nIn OSA patients using home APAP with good compliance (approximately 58% of all patients), there was significant moderately positive correlation between the home APAP pressure and the pressure adjusted during the in-lab PSG study (correlation coefficient of 0.586), whereas there was no significant correlation in patients without good compliance. Moreover, there was greater moderately positive correlation in severe OSA patients with good compliance for home APAP, (correlation coefficient of 0.615). These findings indicate that regular home APAP use for OSA patients, especially severe OSA, leads to closer optimal pressure obtained from both titrating methods.\n\nAccording to some previous studies, the effective pressure obtained by APAP and by in-lab PSG manual titration did not usually differ significantly.4,6–12,18,19,25 However, some studies did show differences in optimal pressures between them,14–17 with the pressure obtained from an APAP being about 2.5 cmH2O higher than that obtained from in-lab PSG manual titration.16 In contrast, some studies found that the pressure obtained from in-lab PSG manual titration was higher than that obtained from APAP.14,17\n\nWhen focusing on the compliance of CPAP use, some studies found that APAP had better compliance than manual CPAP,4,12,25 with APAP used 11 statistically significant minutes longer than manual CPAP.4,12 However, several studies found no difference in compliance between APAP and manual CPAP.10,12,14,15,26 Fietze I, et al found that APAP was used approximately 48 minutes longer than manual CPAP.10\n\nClinical outcomes after following APAP or CPAP uses did not differ in quality of life for OSA patients.10,12,17,18 There was also no difference in Epworth sleepiness scale.11,12,14 Moreover, the initial use of APAP improved the quality of sleep.10 Because APAP machines are more expensive than manual CPAP machines, cost should be considered before starting of positive airway pressure treatment.11 Nevertheless, APAP is cost-effective because it saves time and reduces the expense of undergoing pressure analysis.6,8,9,27,28\n\nThere are a few limitations in our study. Firstly, the sample size was small, however study results could detect the correlation of the two titrating methods for optimal pressure. Secondly, only one commercial CPAP machine was investigated, therefore study results might not apply to another type of CPAP machine. A larger study with other types of CPAP machine is needed for comparison. Furthermore, the equation for predicting in-lab PSG effective pressure is required to verify the accuracy of the optimal pressure obtained by home APAP.\n\n\nConclusions\n\nHome APAP pressure is moderately positively correlated with in-lab PSG effective pressure. The optimum pressures of home APAP agree with in-lab PSG with manual CPAP titration. APAP might be able to determine effective therapeutic pressure for OSA treatment in the sleep laboratory. A large prospective study is needed to verify the accuracy of home APAP effective pressure for OSA patients and to determine the predictive equation for detecting in-lab PSG effective pressure.\n\n\nRegistration\n\nthaiclinicaltrials.org with number TCTR20210331002", "appendix": "Data availability statement\n\nFigshare: Correlation of therapeutic pressure between home automatic positive airway pressure and in laboratory polysomnography manual titration in patients with obstructive sleep apnea. https://doi.org/10.6084/m9.figshare.24503671.v3. 29\n\nThe project contains the following underlying data: OSA_TUH.xlsx\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nFigshare: CONSORT checklist for ‘Correlation of therapeutic pressure between home automatic positive airway pressure and in laboratory polysomnography manual titration in patients with obstructive sleep apnea’. https://doi.org/10.6084/m9.figshare.26010529.v1. 30\n\nData are available under the terms of the Creative Commons Zero license (CC0).\n\n\nAcknowledgements\n\nThe authors would like to thank Michael Jan Everts, Faculty of Medicine, Thammasat University, for proofreading this manuscript. This work was supported by Thammasat University Research Unit in Allergy and Respiratory Medicine, and Medical Diagnostics Unit, Thammasat University Hospital, Thailand.\n\n\nReferences\n\nJordan AS, McSharry DG, Malhotra A: Adult obstructive sleep apnoea. Lancet. 2014; 383(9918): 736–747. Publisher Full Text\n\nSpicuzza L, Caruso D, Di Maria G: Obstructive sleep apnoea syndrome and its management. Ther Adv Chronic Dis. 2015; 6(5): 273–285. Publisher Full Text\n\nKapur VK, Auckley DH, Chowdhuri S, et al.: Clinical practice guideline for diagnostic testing for adult obstructive sleep apnea: An American Academy of Sleep Medicine clinical practice guideline. J. Clin. Sleep Med. 2017; 13(3): 479–504. Publisher Full Text\n\nIp S, D'Ambrosio C, Patel K, et al.: Auto-titrating versus fixed continuous positive airway pressure for the treatment of obstructive sleep apnea: a systematic review with meta-analyses. Syst. Rev. 2012; 1: 20. Publisher Full Text\n\nDonovan LM, Boeder S, Malhotra A, et al.: New developments in the use of positive airway pressure for obstructive sleep apnea. J. Thorac. Dis. 2015; 7(8): 1323–1342.\n\nElshahaat HA, Mahfouz TAE, Elshora AE, et al.: Different continuous positive airway pressure titration modalities in obstructive sleep apnea syndrome patients. Int J Gen Med. 2021; 14: 10103–10115. Publisher Full Text\n\nKim H, Lee M, Hwangbo Y, et al.: Automatic derivation of continuous positive airway pressure settings: comparison with in-laboratory titration. J. Clin. Neurol. 2020; 16(2): 314–320. Publisher Full Text\n\nShaarawy H, Gharraf HS: Comparison between the use of APAP and manual titration during split night polysomnography for diagnosis and treatment of OSA. The Egyptian Journal of Chest Diseases and Tuberculosis. 2018; 67(2): 181–194. Publisher Full Text\n\nMcArdle N, Singh B, Murphy M, et al.: Continuous positive airway pressure titration for obstructive sleep apnoea: automatic versus manual titration. Thorax. 2010; 65(7): 606–611. Publisher Full Text\n\nFietze I, Glos M, Moebus I, et al.: Automatic pressure titration with APAP is as effective as manual titration with CPAP in patients with obstructive sleep apnea. Respiration. 2007; 74(3): 279–286. Publisher Full Text\n\nResta O, Carratu P, Depalo A, et al.: Effects of fixed compared to automatic CPAP on sleep in Obstructive Sleep Apnoea Syndrome. Monaldi Arch. Chest Dis. 2004; 61(3): 153–156.\n\nHukins C: Comparative study of autotitrating and fixed-pressure CPAP in the home: a randomized, single-blind crossover trial. Sleep. 2004; 27(8): 1512–1517. Publisher Full Text\n\nSharma S, Wali S, Pouliot Z, et al.: Treatment of obstructive sleep apnea with a self-titrating continuous positive airway pressure (CPAP) system. Sleep. 1996; 19(6): 497–501. Publisher Full Text\n\nAyas NT, Patel SR, Malhotra A, et al.: Auto-titrating versus standard continuous positive airway pressure for the treatment of obstructive sleep apnea: results of a meta-analysis. Sleep. 2004; 27(2): 249–253. Publisher Full Text\n\nHussain SF, Love L, Burt H, et al.: A randomized trial of auto-titrating CPAP and fixed CPAP in the treatment of obstructive sleep apnea-hypopnea. Respir. Med. 2004; 98(4): 330–333. Publisher Full Text\n\nLuo J, Xiao S, Qiu Z, et al.: Comparison of manual versus automatic continuous positive airway pressure titration and the development of a predictive equation for therapeutic continuous positive airway pressure in Chinese patients with obstructive sleep apnoea. Respirology. 2013; 18(3): 528–533. Publisher Full Text\n\nChang ET, Shen YC, Wang HM: Comparison of improvement in quality of life between continuous positive airway pressure and autotitrating positive airway pressure treatment for obstructive sleep apnea: A randomized crossover study. Tzu Chi Medical Journal. 2015; 27(3): 110–112. Publisher Full Text\n\nWongsritrang K, Fueangkamloon S: Comparison of the clinical outcomes between unattended home APAP and polysomnography manual titration in obstructive sleep apnea patients. J. Med. Assoc. Thail. 2013; 96(9): 1159–1163.\n\nGan WL, Ban AYL, Mohamed Faisal AH: Comparing fixed and auto adjusting continuous positive airway pressure (CPAP) amongst symptomatic Obstructive Sleep Apnoea patients - A randomised controlled trial. Med J Malaysia. 2021; 76(5): 611–616.\n\nLu DX, Wu HG, Luo JY, et al.: Comparison of manual versus automatic titration in pressure determination for long-term therapy of continuous positive airway pressure in patients with obstructive sleep apnea hypopnea syndrome. Zhonghua Yi Xue Za Zhi. 2013; 93(36): 2898–2900.\n\nBerry R, Quan S, Abreu A, et al.: The AASM manual for the scoring of sleep and associated events: Rules, terminology and technical specifications, Version 2.6. Darien, IL: American Academy of Sleep Medicine; 2020.\n\nKushida CA, Chediak A, Berry RB, et al.: Clinical guidelines for the manual titration of positive airway pressure in patients with obstructive sleep apnea. J. Clin. Sleep Med. 2008; 4(2): 157–171.\n\nKribbs NB, Pack AI, Kline LR, et al.: Objective measurement of patterns of nasal CPAP use by patients with obstructive sleep apnea. Am. Rev. Respir. Dis. 1993; 147(4): 887–895. Publisher Full Text\n\nGao W, Jin Y, Wang Y, et al.: Is automatic CPAP titration as effective as manual CPAP titration in OSAHS patients? A meta-analysis. Sleep Breath. 2012; 16(2): 329–340. Publisher Full Text\n\nTingting X, Danming Y, Xin C: Non-surgical treatment of obstructive sleep apnea syndrome. Eur. Arch. Otorrinolaringol. 2018; 275(2): 335–346. Publisher Full Text\n\nTovichien P, Kulbun A, Udomittipong K: Comparing adherence of continuous and automatic positive airway pressure (CPAP and APAP) in obstructive sleep apnea (OSA) children. Front. Pediatr. 2022; 10: 841705. Publisher Full Text\n\nBraghiroli A, Insalaco G, Esquinas AM: Auto-CPAP: saving money as a single tool for OSA. Sleep Breath. 2016; 20(1): 249–250. Publisher Full Text\n\nKrieger J: Therapeutic use of auto-CPAP. Sleep Med. Rev. 1999; 3(2): 159–174. Publisher Full Text\n\nSaiphoklang N: Correlation of therapeutic pressure between home automatic positive airway pressure and in laboratory polysomnography manual titration in patients with obstructive sleep apnea. [Dataset]. figshare. 2023. Publisher Full Text\n\nSaiphoklang N: Correlation of therapeutic pressure between home automatic positive airway pressure and in laboratory polysomnography manual titration in patients with obstructive sleep apnea. figshare. 2024. Publisher Full Text" }	[ { "id": "313793", "date": "23 Aug 2024", "name": "Matthew Rahimi", "expertise": [ "Reviewer Expertise Sleep medicine", "Clinical trials", "Digital health", "OSA physiology" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nTitle: Correlation of therapeutic pressure between home automatic positive airway pressure and in laboratory polysomnography manual titration in patients with obstructive sleep apnea\nThank you for the opportunity to review the above journal article.\nThis prospective cohort study investigates the correlation between optimal CPAP pressures determined through home Automatic Positive Airway Pressure (APAP) and those obtained through in-laboratory Polysomnography (PSG) with manual CPAP titration. The authors aim to assess the agreement between these two methods and explore the potential of home APAP as a reliable tool for identifying effective treatment pressure for obstructive sleep apnea (OSA). The study included 50 OSA patients who underwent both in-lab PSG with manual CPAP titration and home APAP therapy for two weeks. The authors analysed data on demographics, clinical characteristics, PSG findings (AHI, optimal CPAP pressure), and home APAP effectiveness (effective pressure, residual AHI, compliance). Bland-Altman plots and linear regression analysis were used to assess the agreement between the two methods.\nI commend the authors in writing a concise and easy-to-read manuscript. The strength of the study was its relevant research question and clear methodology.\nThe Paper would perhaps benefit from providing a clearer rationale in terms why the comparison between PSG and APAP is clinically relevant and how it could impact patient care. Although the objective has been mentioned clearly, the authors could consider a brief mention of their hypothesis in the introduction.\nThe authors have calculated the study’s sample size based on a previous study which then determined a sample size of 34 was needed to complete the study. Although the study finished with 50 participants. Was there a reason data collection did not stop at 34 participants? Perhaps a brief explanation of why the study over-recruited would improve the paper.\nThe trial registration lists the timepoint of the home APAP pressure as ‘at 1 week’. This does not seem to match the description of the methods for this outcome in the paper. Could this be elaborated on?\nDid the analysis account for any potential confounding factors (e.g. sleep position or body mass index (BMI))?\nThe authors have provided the correlation of optimal pressure between in-lab PSG and home APAP in table 3. Could the authors perhaps consider discussing what level of correlation would be considered strong enough to justify using the at home APAP rather than in-lab PSG titration studies?\nTable 1 shows data for n=50 patients. However, it includes data on comorbidities that have been listed as exclusion criteria (e.g. stroke, COPD). Please clarify this data.\nIn the discussion the authors have done an excellent job of interpreting the data. However, they could briefly discuss whether the study's findings are generalisable to all patients with OSA or if they are specific to the demographic and clinical characteristics of the study sample.\nThe discussion of clinical significance of the findings are somewhat broad. The author could provide more specific recommendations for how APAP devices could be integrated into clinical practice; for example, they could suggest criteria for selecting patients who might be good candidates for APAP titration based on the observed correlations. The finding of 11 minutes difference in compliance may be statistically significant, but is it clinically significant?\nCompliance is the main drawback of CPAP therapy. How does the APAP compliance data in this study compare with the literature? Do the authors think that this may impact their findings?\nOverall, the study provides an important clinical question and valuable data. The paper could be strengthened by providing more detailed explanations in the methods and results sections, particularly regarding the increase in sample size and the potential impact on the study's validity. I would suggest performing a post-hoc power analysis given the increased sample size or conduct additional analyses to confirm that the larger sample did not introduce biases.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] }, { "id": "356153", "date": "06 Feb 2025", "name": "Krishna Sundar", "expertise": [ "Reviewer Expertise Intermittent hypoxia" ], "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 looked at effective CPAP pressures for managing OSA in 55 patients seen at Thammasat University Hospital, Thailand that underwent split night PSG and then were placed on AutoPAP Resmed S10 for 2 weeks. The PAP pressure obtained from the split night study was compared with 95th percentile pressures obtained from APAP downloads. Following are the major and minor concerns with this study. Major concerns\nMethodology needs considerable clarification. This study is mentioned as a prospective cohort study although there is only one set of patients. It is not clear how patients were screened or selected for enrolment into this study except that the study was done between April 2021 and January 2022. There were 50 patients selected and out of this, majority had moderate or severe OSA (48/50) but 2/50 had mild OSA, so it is not clear what criteria was used to split these patients. There is mention of at least 15 minutes of supine REM sleep required during titration and it is not clarified whether this was met in all patients. There needs to be mention of the quality of titration based on AASM’s manual titration clinical guidelines. Good compliance was defined as usage of CPAP for more than 70% of nights for 4 hours or more and while this definition has been widely used within clinical care, there are studies that have shown improvements with higher durations of PAP use. Whether this degree of CPAP usage for a period of 2 weeks is sufficient to determine optimal PAP pressures on an APAP machine is also not clear. Table 3 outlines the proportion of patients that did not meet the optimal defined compliance criteria – approximately 42% of patients had poor compliance. Additionally, in table 1, the leak values are close to the threshold for the degree of leak that is considered significant (24L/min for Resmed devices) being at 22.7±13.3L/min. The accuracy of assessing optimal pressures can significantly decrease with total leak and it is not mentioned what the individual leak values were and how they affected the AHIflow obtained from autoPAP machines. The power calculation used for determining the number of subjects for assessing significant differences are based on a prior similar study of 51 subjects where a similar protocol was followed. However, in this reference provided, the APAP pressures were higher than the manual titration pressures but details of how data from this study was used to generate the number of 34 patients (to determine differences at 90% power and 5% type I error) is not provided. This study compared 95th percentile APAP pressures and CPAP pressures determined using manual titration 2 weeks prior to initiating CPAP but how much time elapsed between the manual titration and initiation of autoPAP is not provided. Authors have used multiple ways to compared pressure values between two groups – the t test that did not show any significant differences and Pearson correlation coefficients and Bland-Altman plots. In terms of the values of correlation coefficients, authors have used terms such as “moderately positive” to describe correlation coefficients of 0.58-0.61 in the good compliance group whereas these correlation coefficients should be much higher. In terms of Bland-Altman’s degrees of agreement, while the mean differences are small, the 95% confidence intervals result in values being in much bigger pressure ranges of up to -5.4 to 4.9cm. From an individual patient standpoint, for almost 20 patients, the pressure values between manual titration and autoPAP 95th percentile pressures differ by 2cm or more. This has been observed in other studies and discussed in the meta-analysis (Iftikhar et al. Sleep and Breathing 2023;27:1759). The authors need to discuss the implications of such individual differences in pressures seen with autoPAP downloads as compared to the pressures determined by manual titration. Depending on the degree of compliance with AutoPAP, authors have created different groups of patients to assess how correlation coefficients differ, and the poor compliance group had much lower correlation coefficients as compared to those with compliance. Were these the patients that had greater differences between APAP and manual titration pressures? This needs to be discussed. Also had this poor compliance been accounted for (which is significant in ALL patients starting PAP therapy), the initial power calculations would have indicated a need for enrolling twice the number of patients. Other details need to be provided. Was EPR used during therapy? Were all patients initiated on same autoPAP pressure range for 2 weeks? How severe was the COPD in the one patient that was included? Were obese patients put on higher autoPAP range of pressures?\nMinor criteria Language and grammar need to improve significantly. Some of suggested changes include the following Abstract – in Methods, last line 95th instead of 95 percentile. In results, instead of “Severe OSA was 75%”, it should be that “75% of patients had severe OSA”. Bland-Altman plot showed good agreement between “them” (what is them?). Conclusions regarding “home APAP is in agreement with manual CPAP titration and that home APAP might be able to determine effective pressure” needs to reworded. Manuscript – In introduction, OSA is caused by “dynamic obstruction” during sleep rather than just obstruction. Polysomnography “also known as sleep test” can be omitted.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] } ]	1	https://f1000research.com/articles/13-699
https://f1000research.com/articles/12-1351/v1	17 Oct 23	{ "type": "Data Note", "title": "Intention for internal whistleblowing to report sexual violence in higher education institutions: a Nigerian national study", "authors": [ "Adesola A. Ogunfowokan", "Saleh N. Garba", "Monica A. Orisadare", "Ayobami G. Adeleke", "Patience E. Samson-Akpan", "Mathew O. Olatubi", "Omowumi R. Salau", "Ayotunde Titilayo", "Saleh N. Garba", "Monica A. Orisadare", "Ayobami G. Adeleke", "Patience E. Samson-Akpan", "Mathew O. Olatubi", "Omowumi R. Salau", "Ayotunde Titilayo" ], "abstract": "Background\n\nSexual violence is prevalent in higher education institutions in Nigeria and stakeholders have encouraged staff and students to blow the whistle whenever they fall victim to or are aware of any sexual violence case. However, there is lack of data about whether the staff and students of these institutions have the intention to blow the whistle internally (within the institution) or not. There is also a lack of data on the existing reporting mechanisms or preferred whistleblowing mechanisms in these institutions. These have hindered the analysis of stakeholders’ opinions on this topic.\n\nMethods\n\nThis data note presents a comprehensive quantitative and qualitative data set collected from staff and students of three categories of government owned higher education institutions (Universities, Polytechnics, Colleges of Education) in Nigeria. Data collection was between February and December, 2021, during which quantitative data were collected from 21,937 students and 3,108 staff. Qualitatively, 138 students and 111 staff participated in a total of 35 focus group discussion sessions. The study provides unique information on respondents’ attitude, self-efficacy, and subjective norm to sexual violence whistleblowing. It also provides information on self-reported sexual violence experiences, whistleblowing intention, reporting systems in higher institutions and the preferred sexual violence whistleblowing mechanisms.\n\nConclusions\n\nIn this data note, we provide a detailed account of the variables in the dataset and then highlight the potential of this study to contribute to improved sexual violence reporting in higher education institutions, thereby reducing the occurrence of the social menace.", "keywords": [ "Higher education", "Sexual violence", "Rape", "Sexual Harassment", "Attempted rape", "Dataset", "Whistleblowing." ], "content": "Introduction\n\nSexual violence has been a global issue for many years, most especially in the 21st century among the young population. Students of higher education have been reported to fall victim to and have also been documented to be perpetrators of this social menace. In Nigeria, there are reports of increased prevalence of sexual violence among higher education students (Egbegi et al., 2019; Yesufu & Adimula, 2018, April, 23; Onoyase, 2019; British Broadcasting Corporation - BBC, 2019). Due to the magnanimity of sexual violence in educational institutions in Nigeria, the Independent Corrupt Practices and other Related Offences Commission (ICPC) (an agency established to prosecute perpetrators of corrupt practices in Nigeria) instructed students to report cases of sexual harassment to the commission (ICPC, 2019) and that such cases will be handled under anti-corruption laws. Anecdotal evidences have shown that, the reporting systems for sexual violating acts have not been very effective in many of these institutions as many cases still go unreported, thereby perpetuating the menace. As far back as 2004, Lee and others have documented that whistleblowing can be used to report sexual harassment just like any other organizational wrongdoings (Lee et al., 2004). There has been a call for the use of internal whistleblowing for reporting sexual violence in higher education institutions in Nigeria by many stakeholders. Less than two years ago, the Shehu Musa Yar’Adua Foundation, in partnership with the Gender and Development Policy Centre, University of Nigeria Nsukka, launched the ’Gender Justice Whistleblowing Portal’ for reporting sexual violence at the university (Odu, 2021; Nov. 19).\n\nNonetheless, we are of the opinion that an individual must have intention to blow the whistle to report sexual violence before carrying out the task. An enabling environment or recognized laid down mechanism must be put in place to ensure effective whistleblowing. As of today, we are not aware of any dataset that provides information on all of these variables which may subsequently be analysed and used for policy formulation for sexual violence prevention in higher educational institutions in Nigeria. Therefore, this data note provides information on the variables included in the study dataset which are: respondents’ attitude, self-efficacy, subjective norm; self-reported sexual violence experiences; whistleblowing intention, reporting systems in higher institutions and the preferred sexual violence whistleblowing mechanisms. In this data note, we provide detailed account of the variables in the dataset and then highlight the potential of this study to contribute to improved sexual violence reporting in higher education institutions thereby reducing the occurrence of the menace.\n\nThe six specific objectives of the study were to\n\n1. describe the sexual violence experiences of students in tertiary educational institutions;\n\n2. determine the influence of attitude, subjective norm and perceived behavioural control on intentions of students and staff to internally blow the whistle for reporting sexual violence cases;\n\n3. identify socio-demographic factors (academic level, course of study, gender, age, sexual violence experiences, tribe and religion) that predict students’ intention to internally blow the whistle for reporting sexual violence cases;\n\n4. identify socio-demographic factors (gender, age, tribe, religion, designation and length of service) that predict staff intention to internally blow the whistle for reporting sexual violence cases;\n\n5. explore possible internal whistleblowing strategies for reporting sexual violence cases; and\n\n6. explore strategies for protecting sexual violence whistleblowers.\n\nThis study was hinged on the Theory of Planned Behaviour (TPB). The theory describes that behavioural intention of an individual to engage in a particular behaviour is a product of three determinants: the individual’s attitude (opinions of oneself towards the behaviour); the subjective norms (opinions of others towards the behaviour); and perceived behavioural control (self-efficacy towards the behaviour) (Ajzen, 2012). For an individual to have intention to blow the whistle for reporting sexual violence act, he/she must have a positive attitude towards whistleblowing as an effective mechanism. Such individual must also consider that, his/her action will be acceptable by significant others and that he/she has the capacity and the wherewithal to blow the whistle. However, aside from the three determinants, background variables such as demographic factors have been identified to indirectly influence behavioural intention through the three determinants and consequently the behaviour (Menozzi et al., 2015). It is expected in this study that the socio-demographic factors of the students and staff such as academic level, course of study, gender, age, sexual violence experiences, tribe, religion, designation and length of service will influence their intention to internally blow the whistle for reporting sexual violence cases. In cases of sexual violence, being a culturally sensitive issue, a reprisal attack on the whistleblower is inevitable. Therefore, it is essential that protection mechanisms are established to protect the whistleblower (Figure 1).\n\n\nMethods\n\nA concurrent mixed method design using quantitative and qualitative data collection methods was adopted for the study. The study was carried out in 18 institutions comprising Federal Colleges of Education, Polytechnics and Universities in all the six geo-political zones of Nigeria. The target population of the students in the selected schools was 246,216 students while that of staff was 31,982 (National University Commission - NUC, 2017; Federal Ministry of Education, 2019; National Bureau of Statistics, 2019). The sample size calculation was in two modes; qualitative and quantitative methods.\n\nInstitutions where the study was conducted were those owned and controlled by the Federal Government of Nigeria and must either be a polytechnic, college of education or university. The students were those undergoing full-time traditional face-to-face programmes and were undergraduates. Staff participants were those who work full-time mode in the selected institutions. Contract or part-time staff were excluded from the study.\n\nUsing Cochran’s survey sample size formula: n = z2pq/e2 where n = sample size; z = standard normal deviate set at 1.95 which corresponds to 95% confidence level; p = 0.5 (set at 50% for unknown prevalence of whistleblowing intention); q = 1-p = 0.5; e = permitted error of margin set at 2.5% (in order to get a large representative sample), a sample size of 1,521 students was obtained per institution. Adding non-response rate of 10%, a final sample size of 1,673 was obtained per institution giving a total of 30,114 students’ respondents for the 18 institutions. Using the same Cochran’s formula: n = z2pq/e2 and same parameters for the staff except for the permitted error of margin set at 5%, a sample size of 418 was obtained per institution after adding 10% non-response rate. Therefore, a total of 7,524 staff (academic & non-academic) was selected and distributed proportionately in all the 18 institutions and into equal proportion of male and female staff.\n\nThe number of participants in non-commercial focus groups is recommended to be between six and 10 in order to be able to control the group (Kabir, 2016). Therefore, we proposed to have eight members (four males and four females) of the Student Union Government in each of the institutions to participate in the study making a total of 144 students for the 18 institutions. Also, two representatives (a male and a female) from each of the Staff Unions in each institution were selected to participate in the FGD. The Unions represented are listed according to the type of school:\n\n• University: Academic Staff Union of Universities (ASUU); Senior Staff Association of Nigerian Universities (SSANU); National Association of Academic Technologies (NAAT); and the Non-Academic Staff Union of Universities (NASUU).\n\n• Colleges of Education: Colleges of Education Academic Staff Union (COEASU); Senior Staff Union of Colleges of Education in Nigeria (SSUCOEN); and Non-Academic Staff Union of Colleges of Education (NASUCED).\n\n• Polytechnics: Academic Staff Union of Polytechnics (ASUP); Senior Staff Association of Nigerian Polytechnics (SSANIP); and Non-Academic Staff Union of Polytechnics (NASUP).\n\nTherefore, for Universities, there were eight Executive Officers (four males, four females) from each institution giving a total of 48 participants for the six Universities. For Colleges of Education and Polytechnics, there were six officers (three males and three females) from each institution giving a total of 72 participants for the 12 institutions. Overall, a total of 120 staff formed the sample size for the staff FGD participants.\n\nMultistage stratified sampling technique was adopted in this study. Nigeria is already stratified into six geo-political zones and in each zone, government-owned higher institutions were stratified by University, Polytechnic and College of Education. In each of the stratum, one institution was selected using simple random sampling technique (balloting) thereby giving a total of three schools from each zone (Figure 2 - produced by the authors). A random selection of departments from each of the schools were done followed by the students’ and staff stratification into male and female gender and also stratification into academic and non-academic staff. A random selection was finally used to select the respondents by proportion as shown in Table 1. For the qualitative strand, the Presidents of each of the unions were contacted to nominate members of their cabinet to participate in the FGD putting into consideration equal gender in the nomination. However, it was observed that there were more males in many of the cabinets than females hence, more male officers participated in the FGD than females.\n\nSource: the authors.\n\nTwo instruments were used for data collection: Sexual Violence Whistleblowing Intentions Questionnaire (SeVWIQ) and a Focus Group Discussion Guide. The SeVWIQ was in two forms. The first was administered to students and it elicited information on their attitude to whistleblowing, subjective norm, self-efficacy, whistleblowing intentions, sexual violence experiences and demographics. The second was for the staff and it elicited information on their attitude to whistleblowing, subjective norm, self-efficacy, whistleblowing intentions, and demographics. The questionnaire had 10 attitudinal questions on a 3-point Likert scale of Not True (1), Moderately True (2) and Very True (3). The subjective norm questions were nine on a 3-point Likert scale of Not Proud (1), Slightly Proud (2) and Very Proud (3). The self-efficacy questions were six on 3 point-Likert scale of Not Likely (1), Moderately Likely (2) and Very Likely (3). The questions on the attitude, subjective norm and self-efficacy were adapted from the work of Zakaria et al. (2016). The sexual violence experiences component was adapted from the Sexual Experiences Short Form Victimization (SES-SFV) scale developed by Koss et al. (2006). The SES-SFV scale assessed sexual violence victimization in the past 12 months and the number of occurrence. The whistleblowing intention component of the questionnaire were formulated using three vignettes which were adapted from the work of Ahmad (2011). The vignettes represented cases of rape, attempted rape and sexual harassment and were rated on a scale of 1 to 5. The Focus Group Discussion Guide (FGDG) which was developed from the review of literature, explored information on sexual violence cases on the school campuses, institutional laid down strategies for reporting sexual violence, factors that may predict the staff and students’ intention to blow the whistle, strategies for reporting and protecting whistleblowers, and the effectiveness of internal whistleblowing strategies.\n\nThe pilot study was carried out in a University of Technology in South West Nigeria. Using the recommendation of Connelly, (2008) that 10% of main sample size can be used for pilot study, therefore, 167 students (10% of 1,673) and 42 staff (10% of 418) were selected to participate in the pilot study. Eight members of the Student Union Government and eight members of the leadership of the four Staff Unions of the school participated in the two separate FGD sessions (one for the students and the other for staff). During the pilot study, the questionnaire was subjected to face and content validity and internal consistency, while trustworthiness of the FGD data was ensured. Part of the findings from the pilot study has been published in Ogunfowokan et al. (2023a). Also, the questionnaire’s internal consistency was further assessed during the main study to further evaluate its reliability. The Cronbach alpha results for both the pilot and the main studies are stated in Table 2.\n\nA field supervisor was identified in each of the schools except the three Northern regions where only one field supervisor was identified and he worked with the investigator from the North to collect the data. The supervisors were responsible for the logistics of sampling and the data collection process. They were trained twice using the virtual mode between December 2020 and January, 2021. The principal investigator was the chief trainer supported by other investigators. The field supervisors then appointed field workers in their respective schools and were trained in the administration of the questionnaires. Also, the two mentees who were postgraduate students as required in the funding call served as the research assistants for the study. The mentees have been part of the writing process for the grant proposal and they were further trained alongside the supervisors.\n\nInstitutional board approval for the study was obtained on 11th December, 2019 from the Institute of Public Health, Health Research and Ethics Committee (IPH HREC) of the Obafemi Awolowo University with approval number IPH/OAU/12/1460. An extension of the approval was obtained on 5th May, 2021 at the expiration of the initial approval when data collection has not been completed. Informed consent of the students and staff was obtained using the informed consent form formatted after the IPH HREC form. The informed consent was obtained by the field staff after the purpose of the study has been explained to participants and concerns clarified. However, due to the sensitivity of the questions, many participants declined appending their signatures on the consent form but preferred verbal consent without recording, which was granted them. In addition, written permission to collect data was also obtained from the administrators of the respective study institutions.\n\nDue to the sensitivity of the study and the non-appealing nature of electronic data collection to many Nigerians as previously observed (Tella, 2015), we decided to use the paper-based questionnaire administration methods. The selected students were contacted by the field workers in their various lecture rooms and questionnaires were administered to them and same were retrieved immediately after completion. Some of them requested to return the questionnaire the following day. Also, some class representatives assisted in retrieving the questionnaires from those who made such request. The questionnaires for the staff were administered to them in their various offices. Some of them returned the questionnaires immediately after completion while others requested to return them after some days. Some staff also dropped the questionnaires in their pigeon holes for pick up. In addition, two FGD sessions (one for students and the other for staff) were conducted in each of the schools giving a total of 35 FGD sessions (the staff in a particular school refused to participate in the FGD). For the students’ FGD, they were carried out at the Student Union Government building except for one of the schools in which the school management insisted it should be conducted at the Students’ Affairs building. The staff FGD were conducted at a designated venue agreed-on between the field supervisors and the participants. The principal investigator facilitated the sessions in support of other team members for the Southern regions. For the Northern regions, the field supervisor and the investigator from the North facilitated the FGD sessions. Recordings of the sessions were taken using Android phones while field notes were taken by other support staff.\n\nOut of the 30,114 students’ questionnaires and 7,524 staff questionnaires administered, a total of 21,937 students’ questionnaires and 3,108 staff questionnaires were completely and properly filled and were adequate for data analysis giving a response rate of 72.8% for students and 41.3% for staff. There were eight data entry clerks who were recruited and trained in June, 2021. Two data analysts were also employed for the quantitative strand and these analysts trained the data entry clerks on how to enter the coded data from the questionnaires into Epi Info software version 3.1. Hands-on training was done using pre-coded demo-questionnaires. All the questionnaires were numbered and coded for data entry. The clerks received different quantities of questionnaires on different days for entry into Epi info software. A standby research office assistant was also employed to assign the questionnaires to the clerks and also ensured that correct quantities of the questionnaires were returned after data entry. Data entry was done within a period of seven months. Following the entry of the data and the merging of the data files from the clerks by the analysts, the data were then exported to SPSS version 27 (IBM Corp. Released, 2020).\n\nThe quantitative dataset (Ogunfowokan et al., 2023b) consists of 44 variables for the students and 42 variables for the staff that are grouped into six: (i) attitude to whistleblowing; (ii) subjective norm; (iii) self-efficacy; (iv) whistleblowing intention; (v) sexual violence experience; and (vi) socio-demographic characteristics. However, the staff dataset does not contain the sexual violence experience data. The list of all the variables and their corresponding response options are found in Tables 3 and 4. The qualitative dataset contains transcripts on responses to the six probing questions used for the FGD which are: (i) sexual violence cases in the school; (ii) institutional reporting systems; (iii) factors influencing intention; (iv) preferred whistleblowing strategies; vi) protection of whistleblower; and (vii) effectiveness of internal whistleblowing.\n\nDuring sampling of the schools, some areas in the Northeast and Northwest regions were avoided because of insurgency. After sampling, two schools were dropped because the field workers could not gain access to the schools due to ongoing insurgency in the areas. Also the study was conducted in government owned schools thereby excluding higher institutions owned by private individuals, organizations and State Governments. Other higher institutions like diploma schools of nursing, technical and specialized higher education schools among others were also not captured in the study. Hence, generalization of the findings from this study should only be for Universities, Polytechnics and Colleges of Education that are Federal government-owned. Also, FGD for staff could not be conducted in a particular university because the executive officers for the staff unions did not give their consent to participate despite all pleas and provision of information about the study.\n\nQuantitative dataset\n\nThe questionnaires that were brought from the field were assessed for completeness by the research office assistants and two other young people employed for the job. All incompletely filled questionnaires were discarded. Consistency checks were done by ensuring that the data on each of questionnaires were consistent. For example, on the staff questionnaire, an academic staff who reported to be a Senior Lecturer later ticked the non-academic status had the non-academic status corrected. Duplicate and outliers on the dataset were also observed and compared with the original raw data on the corresponding questionnaires and corrections were made where necessary. Missing data were attended to by using mean substitution as documented by Kang (2013). However, we were aware of the bias related to self-reported data collection most especially on a sensitive issue as sexual violence and this may impact on the quality of the dataset. Also, we could not do external validation of the data set as we could not lay our hands on a similar dataset on any of the variables.\n\nQualitative dataset\n\nA most profound validation for the qualitative dataset that we carried out is the data member checking. During and after the interview, participants were regularly instructed to confirm their statements as true reflections of their opinions by listening to the recordings. Facilitators were also encouraged to clarify participants’ opinions from the statements that they made to avoid biases. Peer debriding was also done among the investigators, supervisor and the research assistants immediately after concluding an FDG session to discuss the findings in proper perspective and to also avoid biases. All these efforts were to ensure the trustworthiness of the qualitative data (Stahl and King, 2020).\n\nThere are six investigators and two research mentees in the research team. The team consists of individuals who are academics from four universities spread across three regions in Nigeria. The research mentees were Ph.D. students (a male and female) in community health nursing, of whom one of them focused on adolescent boys’ sexual violence perpetration in her Ph.D. project while the other focused on work-related stress among nurses. Both mentees were trained in the use of qualitative and quantitative data collection methods for their M.Sc. and Ph.D. projects. The six investigators (three males and three females) had Ph.D. certificates in diverse specialised areas, which include health promotion, civic education, gender and policy studies, demography and population studies, medical sociology, and community health. Some of the investigators were trained in phenomenology studies, while others were trained in quantitative data collection. The strengths of the investigators were identified and made use of during data collection. The principal investigator, who is a community health nurse expert, facilitated the FGD sessions in the southern regions. The assigned field supervisor for the Northern region, who is a sociologist and a demographer, facilitated the FGD for the Northern region in conjunction with the investigator from the North, who is a medial sociologist. In order to eliminate any form of bias, information about the researchers was also given alongside the research information at the point of obtaining informed consent from the participants.\n\nSome schools in the northern part of the country were intentionally avoided as a result of the insurgency going on in those areas at the time of conducting the study. Also, two schools that were sampled initially were replaced at the point of data collection when the field workers could not gain access to the schools due to insurgency. Other higher institutions, like diploma schools of nursing technical schools and specialised higher education schools, among others, were not captured in the study. Hence, generalisation of the findings from this study should only be made for students in universities polytechnics, and colleges of education. The staff in one of the institutions refused to participate in the FGD despite all efforts to convince them that the study is solely for research purposes with no implication for any individual.", "appendix": "Data availability\n\nQualitative data\n\nThe underlying qualitative data (transcripts) are not made publicly available due to the sensitivity of the information as a sexual violence issue. Any request for the data should be made to the corresponding author at solafowokan@oauife.edu.ng or adesolaogunfowokan@gmail.com. The applicant for the dataset must be affiliated with a research or academic institution and must explicitly indicate the purpose of the dataset request. The qualitative dataset will be made available following de-identification of the set.\n\nQuantitative data\n\nZenodo: Sexual Violence Whistleblowing Intention by Higher Education Students and Staff. https://doi.org/10.5281/zenodo.8234061 (Ogunfowokan et al., 2023a).\n\nThis project contains the quantitative data for staff and students.\n\nZenodo: Sexual Violence Whistleblowing Intention by Higher Education Students and Staff. https://doi.org/10.5281/zenodo.8234061 (Ogunfowokan et al., 2023a).\n\nThis project contains the blank questionnaires and focus group discussion guide.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgements\n\nThe authors acknowledge the support of the participants, field supervisors, field workers, research office assistants, the data entry clerks and the data analysts for their tremendous contributions to this study.\n\nAuthors’ ORCID details\n\n1. Adesola Adenike Ogunfowokan\n\nhttps://orchid.org/0000-0002-7814-2928\n\n2. Saleh Ngaski Garba\n\nhttps://orchid.org/0000-0001-9160-6275\n\n3. Monica Adele Orisadare\n\nhttps://orchid.org/0000-0003-3286-0067\n\n4. Ayobami Gideon Adeleke\n\nhttps://orchid.org/0000-0002-7635-9381\n\n5. Patience Edoho Samson-Akpan\n\nhttps://orchid.org/0000-0001-6947-6953\n\n6. Mathew Idowu Olatubi\n\nhttps://orcid.org/0000-0001-6527-5257\n\n7. Omowumi Romoke Salau\n\nhttps://orchid.org/0000-0002-1579-585X\n\n8. Ayotunde Titilayo\n\nhttps://orchid.org/0000-0002-0496-8639\n\n\nReferences\n\nAhmad SA: Internal Auditor and Internal Whistleblowing Intentions: a Study of Organisational, Individual, Situational and Demographic Factors.2011. Reference Source\n\nAjzen I: The Theory of Planned behavior.Lange PAM, Kruglanski AW, Higgins ET, editors. Handbook of Theories of Social Psychology. Vol. 1. . London, UK: Sage; 2012; pp. 438–459. Publisher Full Text\n\nBritish Broadcasting Corporation – BBC: Sex for grades’: Undercover in West African universities.2019. Reference Source\n\nEgbegi FR, Benjamin OA, Onyejebu DC: Eradicating Sexual Assault in Nigerian University System: The Role of Investigative Journalism. Annals of Journalism and Mass Communication. 2019; 1(1): 1–6.\n\nFederal Ministry of Education: Nigeria Digest of Education Statistics.2019. Reference Source\n\nIBM Corp. Released: IBM SPSS Statistics for Windows, Version 27.0. Armonk, NY: IBM Corp; 2020.\n\nIndependent Corrupt Practices and other Related Offences Commission (ICPC): Report Sexual Harassment extortion: ICPC tells students.2019. https://icpc.gov.ng/2018/07/05/report-sexual-harassment-extortion-icpc-tells-students/\n\nKabir SMS: Methods of Data Collection. Basic Guidelines for Research: An Introductory Approach for All Disciplines. 1st Ed.Chittagong-4203, Bangladesh: Book Zone Publication; 2016.\n\nKang H: The prevention and handling of the missing data. Korean Journal of Anesthesiology. 2013; 64(5): 402–406. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKoss MP, Abbey A, Campbell R, et al.: The Sexual Experiences Short Form Victimization (SES-SFV). Tucson, AZ: University of Arizona; 2006. Version V 8/28/2012 V:\\Dr Koss--SHARE\\SES\\06 11 08 SES-SFV.doc.\n\nLee J, Heilmann SG, Near JP: Blowing the Whistle on Sexual Harassment: Test of a Model of Predictors and Outcomes. Hum. Relat. 2004; 57(3): 297–322. Publisher Full Text\n\nMenozzi D, Sogari G, Mora C: Explaining Vegetable Consumption among Young Adults: An Application of the Theory of Planned Behaviour. Nutrients. 2015; 7: 7633–7650. Publisher Full Text\n\nNational Bureau of Statistics: 2018 Statistical Reports on Men and Women.2019. Reference Source\n\nNational University Commission, (NUC): Nigerian University Systems Statistical Digest. Slough UK and Delhi, India: NUC; 2017. 978-978-965-138-2. Reference Source\n\nOdu I: UNN, Shehu Musa Yar’Adua Foundation, launch ‘Whistle Blowing Portal’ to fight sexual harassment.2021, Nov. 19. https://www.vanguardngr.com/2021/11/unn-shehu-musa-yaradua-foundation-launch-whistle-blowing-portal-to-fight-sexual-harassment/#google_vignette\n\nOgunfowokan AA, Titilayo A, Adeleke AG, et al.: Sexual Violence Whistleblowing Intention by Higher Education Students and Staff. [Data set]. Zenodo. 2023a. Publisher Full Text\n\nOgunfowokan AA, Ayotunde T, Samson-Akpan PE, et al.: Intention of Staff and Students to Use Internal Whistleblowing to Report Sexual Violence: A Case Study of a Nigerian University. Journal of Interpersonal Violence. 2023b; 38: 9765–9794. PubMed Abstract \| Publisher Full Text\n\nOnoyase A: Prevalence of Sexual Harassment of Female Students of Tertiary Education in Taraba State, North East Nigeria: Implications for Counseling. International Journal of Higher Education. 2019; 8(1): 77–83. Publisher Full Text\n\nStahl NA, King JR: Expanding approaches for research: Understanding and using trustworthiness in qualitative research. Journal of Developmental Education. 2020; 44(1): 26–28.\n\nTella A: Electronic and paper based data collection methods in library and information science research: A comparative analyses. New Library World. 2015; 116(9/10): 588–609. Publisher Full Text\n\nYesufu A, Adimula B: What can be done to curb sexual harassment in schools? The Punch Newspaper.2018; April, 23. Reference Source\n\nZakaria M, Abdul Razak SNA, Wan Mohd Noor WNB: Effects of Planned Behaviour on Whistle Blowing Intention: Evidence from Malaysian Police Department. Middle East Journal of Scientific Research. 2016; 24(7): 2352–2365. Publisher Full Text" }	[ { "id": "231267", "date": "04 Mar 2024", "name": "Anna Bull", "expertise": [ "Reviewer Expertise Sexual harassment", "sexual violence", "higher education", "gender inequalities", "class inequalities", "music 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\nThis data note provides a transparent overview of many aspects of the data collection and curation process for this study. It is helpful to see such a comprehensive study being carried out of sexual violence prevalence and reporting intention across a wide range of institutions. I applaud the authors for the ambition of this study as well as its scale. However, I have two major concerns, as well as a number of minor concerns, that mean that I can’t as yet approve it.\nThe data note states that an adapted version of the SEQ-SFV is used to explore prevalence. However, the survey design itself does not use any aspect of the SEQ-SFV and instead asks participants directly if they have been raped. This goes against good practice in sexual violence research and is likely to lead to the findings being inaccurate (see further detail below). This point needs amendment, critical discussion and explanation. There is no information given relating to the ethics of carrying out research on sexual violence specifically, such as what support information was given to participants; how focus groups were held in a way to make them safe for survivors of sexual violence to participate; and what training/support was given to staff working on the project (see further detail below).\nBelow, I go through various points that I suggest should be addressed in this data note, including the two major issues identified above as well as various lesser concerns.\nUse of language In order for the article to be in dialogue with international literature in this area, there are some points of language that could be clarified. Most notably the terms ‘blow the whistle’ and ‘whistleblower’ appear to be used synonymously with reporting.\nI assume that the term ‘whistleblowing’ is the term used in Nigeria to describe reporting sexual violence to an institution. However, whistleblowing has quite a different meaning from reporting in some contexts; for example in the UK whistleblowing is a protected act, meaning that there are legal protections for whistleblowers, but speaking out only counts as whistleblowing if it is deemed to be ‘in the public interest’. Reporting individual experiences of sexual violence might not necessarily be deemed to be in the public interest. As such, further information about terminology is needed to clarify what is meant by this term.\nThere are also some instances of inaccurate language or claims that could be framed more carefully:\n‘the magnanimity of sexual violence in educational institutions in Nigeria’ (paragraph 1). I don’t think magnanimity is the right word here. ‘In cases of sexual violence, being a culturally sensitive issue, a reprisal attack on the whistleblower is inevitable.’\nWhile reprisal is probably not uncommon, to say that it is inevitably is a very strong claim. I would suggest the authors qualify this claim, explain why they are taking such a strong position, or add a citation.\n\nTheoretical framework\nThe statement that ‘we are of the opinion that an individual must have intention to blow the whistle to report sexual violence before carrying out the task’ needs more explanation and needs to be positioned within wider research on reporting sexual violence. More generally, this could contribute to a justification of the use of the Theory of Planned Behavior that is used to frame the study. I’m not yet convinced that this theory is helpful in the context of this study. In fact, reporting sexual violence is sometimes opportunistic, or occurs by accident or is taken by someone other than the survivor (Lievore D, et. al. 2005 [ref 4]; Bull A, et. al. 2022 [ref 2]; Brooks-Hay et. al. 2020 [ref 1]). Furthermore, ‘intention’ in this sentence is perhaps glossing over some of the complexities of reporting; as I have outlined (Bull, 2022), there are both immediate catalysts as well as underlying rationales for reporting sexual violence or harassment to higher education institutions; this term ‘intention’ could therefore be critically discussed in more detail.\nSimilarly, the claim that ‘for an individual to have intention to blow the whistle for reporting sexual violence act, he/she must have a positive attitude towards whistleblowing as an effective mechanism’ is also questionable in relation to existing literature; studies (as cited above) show that people report sexual harassment and violence to their institution primarily to protect themselves and others from further harm. Therefore it is possible that reporting parties are taking the step of reporting as they have no other options, rather than because they have a positive attitude towards reporting as an effective mechanism.\nMethods\nQualitative methods The methods are clearly explained but could benefit from a rationale as to why focus group discussions were seen as appropriate, and why mixed-gender focus groups were chosen. For such a sensitive topic, as the authors note, perhaps women-only focus groups or interviews might have been more appropriate, allowing interviewees to speak more openly? This would also have overcome the issue of having more male focus group participants in the focus groups.\nIn addition, the decision to hold a hypothetical discussion about whether participants would report, while a reasonable approach to take, has some limitations. The authors could therefore justify the decision to include hypothetical discussions about reporting only, and critically discuss the implications of this decision for the findings.\nQuestionnaire The description states that the article adapted the Sexual Experiences Short Form Victimization (SES-SFV) scale. However, the questions in the questionnaire (linked at the bottom of the article) are not from the SEQ-SFV and they do not follow good practice in sexual violence research, as they use the word ‘rape’ rather than behaviorally-specific language.\nAs such, it is inaccurate to state that they are an adaptation of the SES-SFV. Furthermore, the questions used will heavily underestimate prevalence of sexual violence as sexual violence survivors will often not use the term ‘rape’ even when they have experienced behaviors that do indeed fall under legal definitions of rape. This is a very serious issue in the research design which needs critical discussion and explanation.\nThe Sexual Violence Whistleblowing Intentions Questionnaire needs further information; was this developed/adapted by the authors themselves? If so, could they include more detail about its development. If not, could they link to where they have obtained it from. The questionnaire only asks about participants’ intentions to ‘blow the whistle’ relating to third party incidents of sexual violence that they hear about. However, it is not the norm for HEIs to take action on third party reports. Therefore, it is important to explain why the authors chose to ask only about third party reporting rather than reporting by victim-survivors themselves.\nThe authors state that ‘the vignettes represented cases of rape, attempted rape and sexual harassment and were rated on a scale of 1 to 5’. It is not clear what the vignettes were rated for; this becomes clear on reading the questionnaire in the linked document but it needs to be explained here.\nEthics The discussion of ethical issues is very brief and omits any discussion of the ethics of sexual violence research. Questions to address include:\nWhat support was offered for participants who might have experienced sexual violence and found the research participation triggering? More reflection on the use of paper questionnaires in relation to ethics is needed. For example, if class representatives collected the questionnaires that were returned at a later point, how was confidentiality assured? What training did the facilitators for the focus group discussions have in carrying out research in this area (see Campbell et al., 2019 [ref 3]) What protocols or mechanisms did the focus group discussion facilitators and organisers put in place to ensure that the discussion was safe for survivors of sexual violence? (even though the study was not directly recruiting survivors, there will of course have been some people in the sample who will have experienced sexual violence). Was the option to withdraw from the study available at any point, either to survey or FGD participants? How was the FGD schedule amended after the pilot, and were there any issues with the mixed gender groups?\nData member checking\n‘During and after the interview, participants were regularly instructed to confirm their statements as true reflections of their opinions by listening to the recordings’\nThis point needs further explanation. Was this standard practice for all FGDs? How many members of the FGD participated in the data member checking, and what proportion of the recording did they listen back to? Were there any instances where participants’ opinions had changed since the FGD?\n\nReflexivity statement\nThe authors state that ‘In order to eliminate any form of bias, information about the researchers was also given alongside the research information at the point of obtaining informed consent from the participants’.\nThis statement seems surprising. Eliminating any form of bias in qualitative research is not possible; rather the study design and methods should be transparently discussed so that readers can assess how the methods might influence the findings. I would recommend removing claims to avoid bias in qualitative work.\n\n** I hope that these comments are helpful in enhancing the transparency and robustness of this study.\n\nIs the rationale for creating the dataset(s) clearly described? Partly\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? Yes", "responses": [ { "c_id": "11262", "date": "05 Apr 2024", "name": "Adesola Ogunfowokan", "role": "Author Response", "response": "Dear Dr. Bull, Thanks for taking the time to review this manuscript. Find below our comments on the review. Main concerns The study is not a sexual violence prevalence study but rather an intention study. There are many studies in Nigeria that have explored the prevalence of sexual violence among higher education students (Onayase, 2019; Duru et al., 2018; Akinbode & Ayodeji, 2018; Adogu et al., 2014; and Ado et al., 2010, to mention a few); hence, we did not see the need to conduct a full prevalence study on sexual violence using the full SES-SFV. We adapted from the scale using the response options ‘How many times in the past 12 months – 0, 1, 2, 3+. Three questions were then constructed similar to Question 10 on the scale: Have you been raped before? The three questions were constructed to represent rape, attempted rape, and sexual harassment. The essence of this was to confirm in our study that sexual violence still occurs among higher education students. The participants were briefed on the study as a whistleblowing intention study. They were assured of their privacy and the confidentiality of their information. The consent forms also contained information on how their privacy and confidentiality would be assured. They were given the option of withdrawing from the study if they felt very uncomfortable during the process of data collection. During the planning phase of data collection, the team had a relationship with each of the University Health Centres via the institutions’ administrators. There was a plan to refer any student or staff who may be emotionally unstable as a result of their past sexual violence experience to the school health centre, where they would be managed appropriately. Luckily, we didn’t record any of such events; however, we got a particular questionnaire where a student wrote on it, “Ma, thank you for conducting this study; I had an experience of this with my father about two years ago.\" Unfortunately, we could not trace this participant because the questionnaire was de-identified. The staff working on the project were selected across the six regions of the country. The field supervisors were trained by the research team, and our interaction with them showed that they were excited about the study, and none of them expressed any emotional disturbance resulting from their past victimisation experience. During the training of the field supervisors, efforts were made to inform them of the likely emotional reactions of some participants, who must have been survivors of sexual violence. They were encouraged to refer such participants to the University Health Centre, where they would be managed appropriately. The field supervisors in turn trained the field workers that worked under them. Whistleblowing context in Nigeria Whistleblowing is a term that is just gaining ground in Nigeria. The whistleblowing policy was officially launched by the Federal Ministry of Finance on December 22, 2016, for the purpose of recovering several billions of stolen public funds (Ogbu, 2017). Following the success of the policy in financial systems, it was then recommended in various quarters as a mechanism that could be effective for reporting corruption and other wrongdoings, including sexual violence, in the country. Reporting sexual violence in the Nigerian context is always ‘in the public interest’, especially among young people. We are quite aware that whistleblowing is a legal issue. Whistleblower protection bill was passed in Nigeria on December 14, 2022 (Angbulu, 2022; Dec 14). As of today, in Nigeria, the understanding of whistleblowing is that anyone who is aware of the incident can blow the whistle. However, at the writing stage of the research proposal, we were not aware of any higher education institutions that had domesticated the whistleblowing policy. This particular study was then designed to explore the intention of students and staff in HEIs to use whistleblowing strategies for sexual violence if finally deployed in educational institutions. Looking through the manuscript, we shall ensure that the synonymous use of the terms ‘blow the whistle', 'whistleblower', and' reporting’ is corrected appropriately. Theoretical Framework Drawing from the porous nature of the security systems in Nigeria, the stigmatisation of sexual violence survivors, and the victim-blaming attitude in some quarters, it is assumed that whoever wants to blow the whistle for sexual violence must count the cost. Hence, the assertion by the authors that having a positive attitude towards the effectiveness of whistleblowing mechanisms could be a basis for intention for whistleblowing. Whistleblowing has been referred to as a planned behaviour, and the Theory of Planned Behaviour has been used by several authors, such as Tarjo et al. (2019), Zakaria et al. (2016), Owusu et al. (2020), and Wahyuni et al. (2021), to support whistleblowing intention. Since our study looked at intention for whistleblowing for sexual violence and also assessed the subjective norm and self-efficacy of the participants, which are precursors to planned behaviour, we are of the opinion that the Theory of Planned Behaviour is the best framework for the study. Methods Qualitative methods The mixed-gender focus group discussion was adopted because, in class settings in higher education institutions, sexual violence is usually discussed among the students irrespective of their gender. We did not record any issues with the mixed-gender group. The homogeneity of the group is based on participants being officers of students’ and staff’s associations. It is a general observation that males take on more leadership roles than females, which explains why there were more males in the group than females. The questions in the FGD guide are not personal to the participants but, general questions. Hence, we are of the opinion that personal interview is not relevant in this case. Questionnaire We adapted the questionnaire as stated in the data note: “The questions on attitude, subjective norm, and self-efficacy were adapted from the work of Zakaria et al. (2016). The sexual violence experiences component was adapted from the Sexual Experiences Short Form Victimization (SES-SFV) scale developed by Koss et al. (2006). The SES-SFV scale assessed sexual violence victimisation in the past 12 months and the number of occurrences. The whistleblowing intention component of the questionnaire was formulated using three vignettes, which were adapted from the work of Ahmad (2011). The response to ‘Main Concern 1’ above also explains the use of the SES-SFV. Vignette The vignette section of the questionnaire depicted the participants as third-party whistleblowers and not as survivors. It is assumed that survivors will report when they are victimised, but a third-party report is not the usual practice in HEIs. Whistleblowing action can be taken by a third party and not necessarily the survivor, and we are of the opinion that the HEIs should be getting used to third party whistleblowing and also take action when there is evidence. The rating for the vignette will be explained in the next revision of the manuscript. Ethics The class representatives collecting filled-out questionnaires from participants was not a study option but an individual option. The questionnaires were administered to the students in their classrooms, but some insisted they could not fill and submit them immediately; hence, they requested that they would submit to their class representatives for onward submission to the field workers. All efforts to dissuade them from this proved abortive, and we needed to respect their decisions. However, our observation on the field is that some of the participants did not see their responses as so confidential that their colleagues could not have access to them, more so that the bulk of the questions were on whistleblowing intention. Other ethical issues are addressed under ‘Main Concern 2’ above. Pilot Study During the pilot study, the officers of the academic staff association did not participate in the FGD despite various efforts put in place as documented in the published reports (Ogunfowokan et al., 2023). What we did then was to recruit academic staff members who were not necessarily officers to participate in the study. After the pilot study, we planned to use this method in any of the schools in case we ran into similar problems. Fortunately, we never experienced such problems except for a particular school where the entire officers of the association, both academic and non-academic, did not participate hence, we did not conduct FGD in the school. Member Checking While the discussion was ongoing, the facilitator reflected on the statements given by the members to confirm their true position. After the discussion, members were asked to exercise some patience while they listened to the selected part of the interview as deemed fit by the facilitator. In fact, in a particular school, the staff group agreed and insisted that a participant must be allowed to record the discussion before the discussion can commence so that if peradventure anything went wrong, they would have evidence of what the discussion was all about. Reflexivity statement The essence of giving information about the researchers was to ensure that the participants were rest assured that the researchers were university staff and not policymakers or groups of people who may use their responses to indict them. The claim ‘to avoid bias’ will be removed from this section. Language use Observed inaccurate languages will be corrected in the manuscript. References Ado, D. G., Anthonia, E. N. & Babagana, B. (2010). Prevalence and Nature of Sexual Assault among Female Students in a Tertiary Institution in Maiduguri, Nigeria – A Cross Sectional Study. International Journal of Health Research, 3(4), 199-203. Adogu, P. O., Adinma, E. D., Onyiaorah, V. I., & Ubajaka, C. F. (2014). Perception, Prevalence and Predictors of Rape among Female Students in a Tertiary Institution South East Nigeria. International Journal of Clinical Medicine, 5(14), 819. Akinbode, G. A. & Ayodeji, F. (2018). Sexual Harassment: Experiences, Prevalence and Psychopathology in some Selected Higher Institutions in Lagos, South-West Nigeria. African Journal of the Psychological Studies of Social Issues, 21 (3). Angbulu, S. (2022, Dec. 14). FG approves new whistle-blower bill. Punch. https://punchng.com/fg-approves-new-whistle-blower-bill/ Duru, C. B, Aguocha, C. M., Iwu, A. C., Oluoha, U. R., Okedo-Alex, I. N., Ikechi, O., & Nwaigbo, E. (2018). Sexual Abuse among Female Undergraduates in Tertiary Institutions in Imo State, Southeast Nigeria: Prevalence, Pattern and Determinants. Open Access library Journal 5(4), ISSN Print:2333-9705; ISSN Online: 2333-9721. Retrieved from: http://m.scirp.org/papers/83742 Ogbu, S. U. (2017). Whistle Blowing Policy as a Mechanism for Energizing The ‘War Against Corruption’ In Nigeria. International Journal of International Relations, Media and Mass Communication Studies Vol.3 (4) pp.16-32. ISSN 2059-1845(Online); ISSN 2059-1853(Print) Onoyase, A (2019). Prevalence of Sexual Harassment of Female Students of Tertiary Education in Taraba State, North East Nigeria: Implications for Counseling. International Journal of Higher Education. 8(1): 77–83. Publisher Full Text Tarjo, T., Suwito A., Aprillia, I. D. and Ramadan, G. R. (2019). Theory of planned behavior and whistleblowing intention. Jurnal Keuangan dan Perbankan https://api.semanticscholar.org/CorpusID:150581853 Zakaria, M., Abd Razak, S. N. A., & Yusoff, M. S. A. (2016). The Theory of Planned Behaviour as a Framework for Whistle-Blowing Intentions. Review of European Studies; 8(3); 2016ISSN 1918-7173 E-ISSN 1918-7181 Wahyuni, L., Chariri, A., & Yuyetta, E. A. (2021). Whistleblowing Intention: Theory of Planned Behavior Perspectives. The Journal of Asian Finance, Economics and Business, 8(1), 335–341. https://doi.org/10.13106/JAFEB.2021.VOL8.NO1.335 Owusu, G. M. Y., Bekoe, R. A., Anokye, F. K. and Okoe, F. O. (2020), \"Whistleblowing intentions of accounting students: An application of the theory of planned behaviour\", Journal of Financial Crime, Vol. 27 No. 2, pp. 477-492. https://doi.org/10.1108/JFC-01-2019-0007 Ogunfowokan, A. A., Ayotunde, T., Samson-Akpan, P. E., et al.: Intention of Staff and Students to Use Internal Whistleblowing to Report Sexual Violence: A Case Study of a Nigerian University. Journal of Interpersonal Violence. 2023b; 38: 9765–9794. PubMed Abstract \| Publisher Full Text" } ] }, { "id": "219037", "date": "17 Apr 2024", "name": "Florence Okoro", "expertise": [ "Reviewer Expertise Behavioral science" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is a robust study that covers all aspects of whistleblowing and sexual violence in higher institutions in Nigeria. The study framework - Theory of Planned Behavior aligns with the objectives of the study and the methods of data collection of the quantitative and qualitative arms of the study The method is sound as it covers qualitative and quantitative strands. Sampling is adequate - multistage stratified sampling to cover the six geopolitical zones of Nigeria. The data collection instruments are adequate. The SeVWIQ was administered to students and staff. The focus group discussion guide was appropriately used to facilitate the focus group discussions. The procedure for data collection was adequately described and appropriate for the study. The study and the report writing meet the criteria of a scientific project.\n\nIs the rationale for creating the dataset(s) clearly described? Yes\n\nAre the protocols appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and materials provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a useable and accessible format? Yes", "responses": [] } ]	1	https://f1000research.com/articles/12-1351
https://f1000research.com/articles/11-1511/v1	13 Dec 22	{ "type": "Case Report", "title": "Case Report: Ludwig's angina - 'The Dangerous Space'", "authors": [ "Satish Vasanth", "Satheesh Chandran", "Deepak Abraham Pandyan", "Padmashini Gnanam", "Sinouvassane Djearamane", "Ling Shing Wong", "Siddharthan Selvaraj", "Satheesh Chandran", "Deepak Abraham Pandyan", "Padmashini Gnanam", "Siddharthan Selvaraj" ], "abstract": "Background: Ludwig's angina is a potentially life-threatening disease characterized by diffuse bilateral cellulitis with an odontogenic origin. This unique infection is now rare owing to the antibiotic era. Case: This patient presented to the emergency room with trismus, jaw and neck swelling, mild respiratory distress with tachypnea, hyperthermia, and panic. Clinical examination and radiographic evaluation confirmed the diagnosis of Ludwig's angina. As it is a quickly spreading infection, the patient was taken up for immediate surgical decompression leading to pus drainage, removal of the offending tooth, bacterial culture and sensitivity, and administration of empirical antibiotics. As we had operated promptly, there was no need for emergency airway intervention, and the patient had immediate relief from airway distress. Conclusions: Early accurate diagnosis with conservative surgical decompression, thereby negating the need for airway intervention, was vital to avoiding mortality which is always possible in such an expeditious infection.", "keywords": [ "Ludwig's angina", "odontogenic space infection", "surgical decompression", "incision", "drainage", "case report" ], "content": "Introduction\n\nLudwig's angina, diffuse cellulitis on the floor of the mouth, was first described by a German physician, Wilhelm Frederick von Ludwig, in 1836.1 The old terminology describes it as “angina maligna” in Latin (angere-to strangle, Morbus strangularis).2 Ironically, Ludwig passed away at 75 from the same illness he had earlier described.3 The most prevalent etiology seems odontogenic in origin.4 Systemic illnesses such as diabetes mellitus, malnutrition, alcoholism, and AIDS may be risk factors.5 The incidence has recently dropped from 60% to 10% due to antibiotics and better oral hygiene practices.2 The objective of this case report was to raise awareness and facilitate the detection of similar occurrences, given their rarity.\n\n\nCase report\n\nA 40-year-old Indian male patient working as an electrician reported to the department of Oral and Maxillofacial Surgery with a chief complaint of inability to open the mouth, along with pain and swelling in the lower jaw and neck region for the past three days [Figure 1].\n\nNo relevant medical history was noted. The patient reported hyperthermia (100° F), pulse rate of 99 beats per minute, respiratory rate of 25 breaths per minute, and oxygen saturation fluctuating between 88 to 90 SP02. On clinical examination, he reported a restricted mouth opening of only 19 mm (about 0.75 in), a tongue deviation [Figure 2], and evident dysphagia and dyspnea. Extra orally, the swelling was indurated, non-fluctuant, with bilateral involvement of the submandibular and sublingual spaces. His dentate status revealed root stumps in relation to 36 and 46 regions, which were tender on percussion. The obliteration of the mucogingival junction was also noted. Radiographic examination with orthopantomogram (OPG) revealed periapical radiolucency concerning 36,37 and 38 with locules in the submandibular region (more on the right side than the left side), indicating air or pus [Figure 3].\n\nIt was diagnosed as Ludwig's angina, and Hilton's incision and drainage were administered promptly. Separate stab incisions were placed with the No. 11 BP blade on the bilateral submandibular and submental regions. The bilateral submandibular spaces were connected to the midline through blunt dissection. The root stumps were extracted with the evacuation of inflammatory exudate. An intra-oral incision was made along the lingual sulcus in relation to 36 and 37, along with two extraoral incisions in the submandibular region combined with superficial dissection; the pus was evacuated [Figures 4 and 5] along with copious povidone-iodine and saline irrigation.\n\nExtra orally corrugated rubber drain tubes were positioned and secured to the skin with silk sutures [Figure 6]. The patient subjectively experienced a reduction in dyspnea. The pus was collected with a sterile swab and sent for culture and antibiotic sensitivity test. The patient was prescribed empirical antibiotics of Tablet amoxicillin and potassium clavulanate 625 mg twice daily, Tablet metronidazole 400 mg thrice daily for five days orally, and the drain tubes were disconnected after five days.\n\nThe culture sensitivity report revealed the sensitivity to prescribed empirical antibiotics; therefore, the same medicines were continued for a week. After one week, the patient's re-evaluation revealed adequate wound healing and an increased mouth opening of 36 mm (about 1.42 in). The infection had nearly resolved with the disappearance of the symptoms. Post operative results showed adequate mouth opening and the infection was resolved [Figure 7].\n\n\nDiscussion\n\nLudwig's angina is a plausible life-threatening connective tissue infection of the floor of the mouth and neck, characterized by bilateral brawny supra hyoid swelling over bilateral sublingual and submandibular spaces. It can either lead to airway obstruction or, at a later stage, cause dissemination of the infection, which then spreads through several other adjacent spatial planes.6 The most cultured organisms include staphylococcus, streptococcus, and Bacteroides species of either aerobic or anaerobic origin.1 Ludwig's angina is often correlated with the region between the second and third lower molars. Since the apices of these teeth are positioned directly below the mylohyoid ridges, the submandibular space is proximal. If these teeth are infected, the infection will progress and perforate the lingual plate. The infection may rapidly spread into the submandibular, sublingual, and submental tissue spaces.7 According to the literature, four significant signs indicate the diagnosis of Ludwig's angina: (a) bilateral involvement of more than a single deep-tissue space (b) gangrene with serosanguinous, putrid infiltration but little or no frank pus (c) involvement of connective tissue, fasciae, and muscles but not the glandular structures (d) spread through fascial space continuity rather than by the lymphatic system.8 If not diagnosed early, complications include thrombophlebitis of the internal jugular vein, mediastinitis, empyema, pericardial effusion, osteomyelitis, aspiration pneumonia, and pleural effusion.1\n\nTypically, the infection begins at the floor of the mouth and progresses to the submandibular space rapidly, leading to elevation and posterior displacement of the tongue.2 The physical examination usually reveals aggressive gangrenous cellulitis, including fever, tachycardia, brawny induration and swelling of a tender submandibular space, and an elevated, protruding tongue. Trismus irritates the muscles of mastication.7 The enlargement of the anterior soft tissues of the neck above the hyoid bone sometimes leads to the characteristic “bull's neck” appearance of affected patients.8 Some signs of impending airway distress are hoarseness of voice, stridor, respiratory distress, decreased air movement, cyanosis, and a “sniffing” position (upright posture with the neck being put forward with the chin elevated).8 Patients may lean forward in the tripod posture as respiratory distress intensifies to enhance airway diameter and obtain relief.1\n\nThe risk factors such as age over 65 years old, immunocompromised conditions, diabetes mellitus, and alcoholism are said to increase the mortality and complications in Ludwig's angina. In addition, extended hospital stays, diabetes, and hemodialysis increases the risk of methicillin-resistant Staphylococcus aureus (MRSA) infection.1 The parameters used to analyze the risk factors leading to life-threatening complications are age, sex, diabetes, type and side of submandibular involvement, anterior visceral space involvement, type of infection, and symptoms like trismus and fever. According to one study, diabetes mellitus is commonly associated with Ludwig's angina. Logistic regression analysis confirmed the other co-morbidities and bilateral submandibular swelling as predictors for mortality in Ludwig's angina.9 Radiographs of the neck and chest often reveal the degree of soft tissue edema and gas accumulation in the tissues, especially in cases of anaerobic infection. The presence of air in the neck or mediastinum is diagnostic of the intrathoracic extension of the infectious process.10 According to some authors, ultrasonography may be beneficial in diagnosing early cases of abscess and cellulitis.5 In addition, computed tomography (CT) and magnetic resonance imaging (MRI) may be proposed to detect airway edema and identify mediastinal fluid collections. CT is accurate in evaluating deep neck and mediastinal collections of pus. By contrast, MRI generates higher resolution images, but imaging time is longer, so CT is the recommended investigation of choice.1\n\nAlthough there are no current guidelines for managing acute Ludwig's angina, the mainstay of the treatment includes airway maintenance, where the patency of the airway must be evaluated. The administration of broad-spectrum antibiotics follows evaluation, incision, and drainage removal of the infectious foci, i.e., mandibular molar, pus culture, and sensitivity test. Literature suggests that the inappropriate use of drugs like antibiotics, steroids & nonsteroidal anti-inflammatory drugs may affect the clinical signs and symptoms of infection and slow the progression of the disease, thereby potentially delaying the precise diagnosis of the condition.2 However, these medications are still provided to reduce the risk of airway derailment.4 Despite the use of steroids, most patients in the research (71%) were treated with surgical decompression and drain insertion, demonstrating that steroids are not the primary treatment mechanism. However, it is still debatable whether the usage of steroids necessitates surgical intervention.4 Corticosteroids are reported to decrease facial edema and airway edema, as well as facilitate antibiotic penetration. The steroid of choice is dexamethasone (IV 10 mg). Furthermore, nebulized epinephrine (1 mL of 1:1,000 diluted to 5 mL in 0.9% normal saline) reduces airway blockage: However, evidence is scarce. Despite contradictory findings, early surgical intervention improves airway conditions.1 Penicillin is the antibiotic of choice for empirical antibiotic coverage, which targets gram-positive cocci predominantly. Considering the increasing prevalence of penicillin resistant Bacteroides strains, metronidazole is recommended for the anaerobic cover.4 Clindamycin alone is not advocated, as resistance rates for streptococcal species and MRSA exceed 30%.1\n\nSurgery is usually accomplished by decompressing the submental, sublingual, and submandibular spaces by external incision and drainage. Significant airway compromise, characterized by stridor and the use of accessory muscles for breathing, necessitates a definitive airway, which can be attained via endotracheal intubation or tracheostomy, depending on the clinical scenario: Mask breathing will be complicated owing to neck swelling; thus, it is essential to pre oxygenate these patients using any suitable methodology. Blind oral or nasotracheal intubation can culminate in airway damage, increasing edema, and severe laryngospasm; hence, this technique is not advised. Additionally, supraglottic airway devices should be discouraged since they cannot be positioned correctly when the edema progresses. Ideally, patients should be treated with nasotracheal intubation while seated utilizing a flexible intubating endoscope and an awake intubation approach, anticipating a surgical airway (i.e., cricothyrotomy) if necessary.1 However, emergency cricothyroidotomy or tracheostomy is preferred in patients in the late stages.2 In a retrospective study comparing the conservative (antibiotics alone) and surgical decompression with antibiotics, the conclusion was that the latter is superior as there is always a possibility of antibiotics failure.6 A review of 29 cases over nine years by Greenberg et al., showed that 21 cases (72%) were managed conservatively, one case required emergency intubation, six cases (24%) were intubated using fiberoptic Naso endoscopy, and one case (3%) required tracheostomy under local anesthesia.10 In the present case report, the patient was treated conservatively, with the extraction of the mandibular molar, incision and drainage of the involved spaces, and administration of broad-spectrum antibiotics without airway intervention. One week after surgery, adequate mouth opening was achieved with the support of mouth opening exercises.\n\nIn the present case, air pockets in the neck alerted us to the likelihood of a deadly infection progressing fast9,11 [Figure 3]. We have attempted to eliminate the observer's subjective bias by employing many well-trained observers to document the case independently. In the research about Ludwig's angina, there are voids concerning risk factors such as smoking, drinking, and inadequate antibiotic coverage. Additionally, there are no data on this illness in COVID-19 patients, particularly in this pandemic era. According to our research, there needs to be a precise treatment plan and agreement for Ludwig's angina that could serve as a future reference. The literature on steroids' effects on this illness is still ambiguous; therefore, additional research is required.\n\n\nConclusions\n\nThe clinician should be familiar with the presentation of Ludwig's angina since prompt diagnosis and investigation, administration of antibiotic therapy, and possible surgical management is required to prevent the associated morbidity and mortality.\n\nI am willing to share my experience if it helps others. It only started as a small swelling in my jaw but later became big and made me uncomfortable as breathing became difficult. I should have come before. But thank God I am better now.\n\nWritten informed consent for publication of their clinical details and clinical images was obtained from the patient.", "appendix": "Data availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\n\nReferences\n\nBridwell R, Gottlieb M, Koyfman A, et al.: Diagnosis and management of Ludwig's angina: An evidence-based review. Am. J. Emerg. Med. 2021; 41: 1–5. PubMed Abstract \| Publisher Full Text\n\nDowdy RAE, Emam HA, Cornelius BW: Ludwig's Angina: Anesthetic Management. Anesth. Prog. 2019 Summer; 66(2): 103–110. PubMed Abstract \| Publisher Full Text\n\nWasson J, Hopkins C, Bowdler D: Did Ludwig's angina kill Ludwig? J. Laryngol. Otol. 2006; 120(5): 363–365. PubMed Abstract \| Publisher Full Text\n\nTami A, Othman S, Sudhakar A, et al.: Ludwig's angina and steroid use: A narrative review. Am. J. Otolaryngol. 2020; 41(3): 102411. PubMed Abstract \| Publisher Full Text\n\nVallée M, Gaborit B, Meyer J, et al.: Ludwig's angina: A diagnostic and surgical priority. Int. J. Infect. Dis. 2020; 93: 160–162. PubMed Abstract \| Publisher Full Text\n\nEdetanlen BE, Saheeb BD: Comparison of Outcomes in Conservative versus Surgical Treatments for Ludwig's Angina. Med. Princ. Pract. 2018; 27(4): 362–366. Publisher Full Text\n\nBarakate MS, Jensen MJ, Hemli JM, et al.: Ludwig's angina: report of a case and review of management issues. Ann. Otol. Rhinol. Laryngol. 2001; 110(5 Pt 1): 453–456. PubMed Abstract \| Publisher Full Text\n\nDavid M, Lemonick MD: Ludwig's Angina: Diagnosis and Treatment. Hosp. Physician. 2002; 38: 31–37.\n\nSnow N, Lucas AE, Grau M, et al.: Purulent mediastinal abscess secondary to Ludwig's angina. Arch. Otolaryngol. 1983; 109(1): 53–55. PubMed Abstract \| Publisher Full Text\n\nBoscolo-Rizzo P, Da Mosto MC: Submandibular space infection: a potentially lethal infection. Int. J. Infect. Dis. 2009; 13(3): 327–333. Publisher Full Text\n\nVasanth S, Gnanam P, Selvaraj S: Ludwig’s Angina- a Forgotten Crisis in the Field of Dentistry? J. Dental Sci. 2022; 7(3): 000344." }	[ { "id": "158065", "date": "22 Dec 2022", "name": "Abedelmalek Tabnjh", "expertise": [ "Reviewer Expertise Oral Epidemiology", "Biostatistics", "Oral Hygiene", "and Dental Materials." ], "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 is a well prepared case report. In the introduction the authors were covered the Ludwig's angina's definition, history, etiology, risk factors and the objective of the report. Then, they described patient's details, symptoms, diagnostic procedure, and treatment. The discussion section covered all aspects of the topic very well with good details.\nJust one point for improving: It will be better if the authors added if the patient had any risk factors or not. Yes they mention that he didn't have any medical history, but what about other risk factors such as alcoholism and malnutrition?\nOver all this is a good case report.\n\nIs the background of the case’s history and progression described in sufficient detail? Yes\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Yes\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Yes\n\nIs the case presented with sufficient detail to be useful for other practitioners? Yes", "responses": [] }, { "id": "272616", "date": "10 May 2024", "name": "Paramjot Kaur", "expertise": [ "Reviewer Expertise oral and maxillofacial surgery" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors have failed to reference any established protocols for the management of Ludwig's angina. What course of action should be pursued if the administration of steroids and epinephrine are contraindicated for a case of Ludwig's angina? The authors have neglected to include citations of recent publications. Is Ludwig's angina the most perilous type of facial and submandibular space infection? Justify the designation of 'dangerous space' in this context. The primary cause for the development of this condition in a 40-year-old male remains unspecified. Which specific diagnostic procedures were employed in the examination of this particular case? No details have been provided regarding the utilization of laboratory tests and radiographic imaging in the assessment. What are the respective roles of the first and second authors in the execution of this research? Was consent obtained from the patient prior to the capture of clinical photographs? The deficiency of comprehensive details in both the case presentation and subsequent deliberations is evident.\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? 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? Yes", "responses": [ { "c_id": "11592", "date": "27 Jun 2024", "name": "Siddharthan Selvaraj", "role": "Author Response", "response": "Dear Reviewers, We would like to thank the reviewers for taking their valuable time to provide their insightful queries, we have provided our explanation for the same. Once again thank you for your feedback. 1.The authors have failed to reference any established protocols for the management of Ludwig's angina. Answer: Although there are no current guidelines for managing acute Ludwig's angina, the mainstay of the treatment includes airway maintenance and following the principles of infection control which we have already discussed. 2. What course of action should be pursued if the administration of steroids and epinephrine are contraindicated for a case of Ludwig's angina? Answer: Maintaining patent airway is the most important consideration. Removing the source of infection, antibiotics and Incision and drainage would be course of action. 3.The authors have neglected to include citations of recent publications. Is Ludwig's angina the most perilous type of facial and submandibular space infection? Answer: yes, it is highly perilous but in this antibiotic era it has become a rare infection which makes recent publications little difficult. 5.Justify the designation of 'dangerous space' in this context. Answer: It can either lead to airway obstruction or, at a later stage, cause dissemination of the infection, which then spreads through several other adjacent spatial planes. 5.The primary cause for the development of this condition in a 40-year-old male remains unspecified. Answer: yes the patient wasn’t immuno compromised or medically compromised at the time of diagnosis and it still happened 6.Which specific diagnostic procedures were employed in the examination of this particular case? Answer: There is no specific diagnostic test which gives the diagnosis for Ludwigs angina. It’s a combination of clinical examination, symptoms and radiographic examination. The patient reported hyperthermia (100° F), pulse rate of 99 beats per minute, respiratory rate of 25 breaths per minute, and oxygen saturation fluctuating between 88 to 90 SP02. On clinical examination, he reported a restricted mouth opening of only 19 mm (about 0.75 in), a tongue deviation [and evident dysphagia and dyspnea. Extra orally, the swelling was indurated, non-fluctuant, with bilateral involvement of the submandibular and sublingual spaces. His dentate status revealed root stumps in relation to 36 and 46 regions, which were tender on percussion. The obliteration of the mucogingival junction was also noted. Radiographic examination with orthopantomogram (OPG) revealed periapical radiolucency concerning 36,37 and 38 with locules in the submandibular region (more on the right side than the left side), indicating air or pus 7.No details have been provided regarding the utilization of laboratory tests and radiographic imaging in the assessment. Answer: Radiographic examination with orthopantomogram (OPG) revealed periapical radiolucency concerning 36,37 and 38 with locules in the submandibular region (more on the right side than the left side), indicating air or pus. The pus was collected with a sterile swab and sent for culture and antibiotic sensitivity test. The culture sensitivity report revealed the sensitivity to prescribed empirical antibiotics; therefore, the same medicines were continued for a week. 8.What are the respective roles of the first and second authors in the execution of this research? Answer: The first author did the surgical procedure while the second author provided assistance. 9.Was consent obtained from the patient prior to the capture of clinical photographs? Answer: yes. We obtained consent for treatment and for capturing clinical photographs." }, { "c_id": "11601", "date": "25 Jun 2024", "name": "Siddharthan Selvaraj", "role": "Author Response", "response": "1.The authors have failed to reference any established protocols for the management of Ludwig's angina. Answer: Although there are no current guidelines for managing acute Ludwig's angina, the mainstay of the treatment includes airway maintenance and following the principles of infection control which we have already discussed. 2.What course of action should be pursued if the administration of steroids and epinephrine are contraindicated for a case of Ludwig's angina? Answer: Maintaining patent airway is the most important consideration. Removing the source of infection, antibiotics and Incision and drainage would be course of action. 3.The authors have neglected to include citations of recent publications. Is Ludwig's angina the most perilous type of facial and submandibular space infection? Answer: yes, it is highly perilous but in this antibiotic era it has become a rare infection which makes recent publications little difficult. 4.Justify the designation of 'dangerous space' in this context. Answer: It can either lead to airway obstruction or, at a later stage, cause dissemination of the infection, which then spreads through several other adjacent spatial planes. 5.The primary cause for the development of this condition in a 40-year-old male remains unspecified. Answer: yes the patient wasn’t immuno compromised or medically compromised at the time of diagnosis and it still happened 6.Which specific diagnostic procedures were employed in the examination of this particular case? Answer: There is no specific diagnostic test which gives the diagnosis for Ludwigs angina. It’s a combination of clinical examination, symptoms and radiographic examination. The patient reported hyperthermia (100° F), pulse rate of 99 beats per minute, respiratory rate of 25 breaths per minute, and oxygen saturation fluctuating between 88 to 90 SP02. On clinical examination, he reported a restricted mouth opening of only 19 mm (about 0.75 in), a tongue deviation [and evident dysphagia and dyspnea. Extra orally, the swelling was indurated, non-fluctuant, with bilateral involvement of the submandibular and sublingual spaces. His dentate status revealed root stumps in relation to 36 and 46 regions, which were tender on percussion. The obliteration of the mucogingival junction was also noted. Radiographic examination with orthopantomogram (OPG) revealed periapical radiolucency concerning 36,37 and 38 with locules in the submandibular region (more on the right side than the left side), indicating air or pus 7.No details have been provided regarding the utilization of laboratory tests and radiographic imaging in the assessment. Answer: Radiographic examination with orthopantomogram (OPG) revealed periapical radiolucency concerning 36,37 and 38 with locules in the submandibular region (more on the right side than the left side), indicating air or pus. The pus was collected with a sterile swab and sent for culture and antibiotic sensitivity test. The culture sensitivity report revealed the sensitivity to prescribed empirical antibiotics; therefore, the same medicines were continued for a week. 8.What are the respective roles of the first and second authors in the execution of this research? Answer: The first author did the surgical procedure while the second author provided assistance. 9.Was consent obtained from the patient prior to the capture of clinical photographs? Answer: yes. We obtained consent for treatment and for capturing clinical photographs." } ] } ]	1	https://f1000research.com/articles/11-1511
https://f1000research.com/articles/11-1061/v1	16 Sep 22	{ "type": "Research Article", "title": "Community social responsibility of continued and appropriate use of silver amalgam as dental restorative material in southern India: A cross-sectional study", "authors": [ "Ramprasad Vasthare", "Nidambur Vasudev Ballal", "Prajna P Nayak", "Pujan Kamath", "Nishu Singla", "Thrisha Hegde", "Ramprasad Vasthare", "Nidambur Vasudev Ballal", "Pujan Kamath", "Nishu Singla", "Thrisha Hegde" ], "abstract": "Background: For more than 150 years, dental amalgam (DA) has been popular as a dental restorative material. Yet, many organisations oppose its use due to perceived toxicity and environmental concerns. Hence, this study aimed to explore the continued use of DA from a South Indian dental practitioners’ perspective.\nMethods: This cross-sectional study was conducted among fifty-two private and public dental practitioners of Udupi district in Southern India. A self‑administered questionnaire was distributed, that involved assessment of their preferences, continuation of use and concerns of using DA as a restorative material. Percentage contribution of each variable was calculated. Preferences for continuation of use of silver amalgam based upon the age, experience and mercury toxicity as a risk factor were analysed using Students-t test and Chi-square test.\nResults: The majority of dentists were satisfied (87%) with the results of the DA, found minimal failures (96%) and found DA more economical (89%). More than half (54%) of the participants reported that they would not continue the use of DA owing to mercury toxicity and environmental concerns. Dentists with higher age and longer clinical experience preferred continuation of DA.\nConclusions: In spite of satisfaction with DA for its minimal failure, longevity and affordability, the authors found that a majority of practitioners did not prefer its continued usage. This highlights their concerns over mercury toxicity and soft tissue lesions and accentuates their community social responsibility. There is also an urgent need to educate dentists on mercury hygiene, mercury waste management and disposal.", "keywords": [ "dental amalgam", "mercury toxicity", "social responsibility", "dental material", "waste management", "dental education", "affordability" ], "content": "Introduction\n\nDental amalgam (DA) is popular as a restorative material for more than 150 years particularly in large cavities, owing to tremendous mechanical properties and durability. It makes up for seventy-five percent of all dental restorations performed across the world [Bharti et al. 2010]. DA is a combination of alloy particles and elemental mercury. The usage of the “silver paste” was first found in the Chinese medical texts written by Su Kung in 659 AD [Hsi-T’ao 1958]. In early 1800s, D’Arcet Mineral Cement was developed in France, which is regarded as the first dental amalgam [Magkert, 1991]. The use of room temperature mixed amalgam as a dental restorative material was formerly advocated by Bell in England (1819) and Traveau in France (1826) [Frykholm,1957 and Greener, 1979].\n\nThis material has proven itself over time, although its limitations have also been acknowledged. Functionally and financially, DA has been a source of great comfort for the common man. The plasticity and strength of the restorative material is a quality that has made dental practitioners utilize it not just for regular restorative work, but also for the making of dental inlays and onlays.\n\nIn spite of this, in the recent times, there is a reduction in the dental amalgam usage as a restorative material. Spencer (2000) and Brennan and Spencer (2003) have reported reducing use of DA in recent times. The reduction is traced to an increasing use of alternative materials such as glass ionomer cements, composite resins, and ceramics. Alleged mercury toxicity and environmental concerns too are debated for the reduced use lately [Brennan and Spencer, 2003].\n\nWe observed that DA is receiving undue attention and controversies, but not just for the first time. In 1833, the Crawcour brothers introduced a newer version of dental amalgam “The Royal Mineral Succedaneum” to America that resulted in multiple failed amalgam restorations that sparked the “First Amalgam War” in 1845 [Molin, 1992]. The American Society of Dental Surgeons condemned amalgam usage as malpractice and if used, member would be expelled from the society [Mosteller, 1961]. The criticism of amalgam gradually muted with improved handling and performance of the amalgam versions put forth by Elisha Townsend, J Foster Flagg and G.V. Black [Flagg, 1843; Cannon et al., 1985]. The “Second Amalgam War” resulted from the writings of Dr Alfred Stock, who was poisoned with mercury through the twenty- five years of exposure to the metal [Weiner JA, Nylander M, Berglund F, 1990]. A committee was appointed to study allegations, which concluded that amalgam has a rightful place in dentistry and that there was no reason to stop its use [Eames, 1959]. The current controversy popularly known as “Third Amalgam War” stemmed from the words of HA Huggins in 1973 who suspected that everything from leukaemia to bowel disorders could be due to patient’s reaction to mercury [Huggins, 2007]. The Consumer Report of 1986 exposed this anti - amalgam movement that subsided this controversy. Again, the “60 Minutes” TV program re-intensified the issue again thereby creating considerable public alarm [Dodes JE, 2001].\n\nMercury is present in abundance in the natural environment and a substantial number of people are exposed to it in various ways [Dodes JE, 2001]. Yet, any symptoms of unknown aetiology have been frequently linked to water fluoridation and dental amalgam restorations [Boyd et al., 1991; Huggins, 2007].\n\nIn the recent times, various organisations around the world have attempted to reduce the usage of DA. One such major setback for dental amalgam usage is the Minamata convention, a global health and environment treaty that governs the mining, usage and trade in mercury. It entreats for “phase down of dental fillings using mercury amalgam”. It included various strategies like “aiming at dental caries prevention and use of mercury-free dental restoration alternatives and on promoting best management practices. As well as promoting the use of best environmental practices in dental facilities to reduce release of mercury and mercury compounds to water and land” [Minamata Convention, 2014].\n\nThe European Commission’s Scientific Committee on Health and Environmental Risks (“SCHER”) authenticates that “dental amalgam in the environment can methylate (forming methylmercury, which is the most toxic form of mercury)”. Consequently, “the acceptable level of mercury in fish is exceeded” resulting in “a risk for secondary poisoning due to methylation” [SCHER, 2014]. Even the European Commission’s Scientific Committee on Emerging and Newly Identified Health Risks (“SCENIHR”) initially revoked its claim that amalgam is safe. But, in 2015 they changed their stance from amalgam is “a safe and effective restorative material” to that amalgam is only “an effective restorative material” [SCENIHR, 2014; SCENIHR, 2015]. Based on these, the European Union has accorded the “Berlin declaration” in 2017 to end amalgam use in Europe by 1 July 2022 [Berlin Declaration, 2017].\n\nMany other organisations contradict with above standpoint [U.S. Food and Drug Administration, 2020; National Institute of Health, 2006; Alzheimer’s myths; Uçar and Brantley, 2017]. The U.S. Food and Drug Administration states, “We have reviewed the best available scientific evidence to determine whether the low levels of mercury vapour associated with dental amalgam fillings are a cause for concern. Based on this evidence, U.S. Food and Drug Administration considers dental amalgam fillings safe for adults and children aged six and above. Clinical studies in adults and children ages six and above have found no link between dental amalgam fillings and health problems” [U.S. Food and Drug Administration, 2020]. The National Institute of Dental and Craniofacial Research in the U.S. Dept. of Health and Human Services also states that “[Two] studies - one conducted in Europe, the other in the United States - independently reached the conclusion: children whose cavities were filled with dental amalgam had no adverse health effects. The findings included no detectable loss of intelligence, memory, coordination, concentration, nerve conduction or kidney function during the 5-7 years the children were followed” [National Institute of Health, 2006].\n\nGiven the stance of dental amalgam usage by various organisations around the world, we wanted to explore the continued usage of silver amalgam as a tooth restorative material, from South Indian dental practitioners’ perspectives in an unbiased manner.\n\n\nMethods\n\nThis study was initiated after approval from the Kasturba Medical College and Kasturba Hospital Institutional Ethics Committee [dated 12/2018; Reference No. 569], which is the ethical committee for MAHE University. The study was conducted in agreement with World Medical Association Declaration of Helsinki, 1975. Prior to the start of study, a signed informed consent for participating in the study and reuse of anonymised data was received from each participant.\n\nA cross-sectional study was conducted over a duration of sixteen weeks in 2019 from second week of January to second week of May across various dental practices in the district of Udupi in alliance with Indian Dental Association, Udupi district branch, in Southern India. The inclusion criteria for the study participants were (i) Government or private practitioners (ii) Dental practitioners who have the willingness and who consented to participate in the study. The exclusion criteria for the study were: (i) those practicing for less than 5 years; and (ii) inability/unwillingness to participate in the study.\n\nA total of one hundred and thirty-four dental practices encompassing all the seven ‘Taluks’ were identified and were assessed on questions relating their opinions of using DA.\n\nPrivate dental clinics: The list of registered practitioners in Udupi district as per the Karnataka State Dental Council Registration list was used as a reference document for contacting the clinics individually. Access to this list was granted after the authors submitted a request to the Karnataka State Dental Council. Names and mail addresses were also obtained from the list of the largest non-governmental dental organization in India, namely the Indian Dental Association, Udupi branch. Access to this list was granted after the authors submitted a request to the Indian Dental Association.\n\nPublic health care centres: Oral health delivery in public sector is unified into the existing public hospital setups and is available from community health centres and district hospitals. So, we included practitioners from six Community Health Centres (CHCs) and the district hospital, details of the same obtained from official portal of Karnataka State Health Ministry. (District wise Hospital details with facilities). After excluding those not fulfilling the inclusion criteria, ninety-two participants were available and included in the study.\n\nA self-administered questionnaire [Nayak, 2022] assessing the practitioners’ preferences, continuation of use and concerns of using DA as a restorative material was developed based on similar studies [Brennan and Spencer, 2003; Maciel et al., 2017; Espelid et al., 2006]. Four subject experts checked the face validity and content validity of questions and finalised the questionnaire. A pilot survey was conducted among 15 dentists working in an academic setting to confirm the needed background preparations and clarity of specific terms in questionnaire that could seem unclear. The findings and responses of pilot study were found to be favourable, facilitating the initiation of the larger planned study. Their responses, however are not included in the study results.\n\nThe questionnaire consisted of two sections: (a) Four questions on respondents’ demographic and professional particulars: age, gender, qualification and type of practice and (b) fourteen closed-ended questions regarding duration of DA usage and preferences for DA over other restorative materials, preferred type of cavity for DA usage, experiences regarding ease of use, longevity, failures, soft tissue lesions and mercury toxicity during DA usage as well as on patient affordability and satisfaction of DA.\n\nQuestionnaires were distributed through email and communication network of IDA Udupi District branch. We attempted to contact non-respondents during the conduct of four Continuing Dental Education programs for dental practitioners so as to ensure maximum participation of respondents.\n\nResponses were documented on Microsoft Excel and data analysis was performed using IBM Statistical Package for the Social Sciences (SPSS) version 26 (IBM Corp., Armonk, N.Y., USA). The percentage contribution was obtained for each significant variable. Perception and awareness for DA use as a risk factor had continuous variables, so analysis was done using Students t-test. Results of duration and satisfaction of usage of DA, experiences regarding longevity and patient satisfaction of restoration were fractionated into ordinal and nominal variables for which, chi-square test was used at 5% level of significance.\n\n\nResults\n\nNinety-two questionnaires were distributed out of which 52 dental practitioners responded (Response rate 55.9%). About the gender distribution, there were equal number of male and female participants (26 out of 52 each). The mean age group of study population was 34.9 years.\n\nTable 1 describes the experience and satisfaction for DA use among practitioners. About 77% participants reported that they have been using DA for less than ten years and 87% participants were very satisfied/satisfied with its use. The longevity of DA is highly appreciated by the dental practitioners as 44% and 48% participants found the longevity “Very Good” and “Good” respectively. Most of them reported that their patients were ‘very satisfied’ and ‘satisfied’ (76.9% and 15.4% respectively) of the DA restorations.\n\nTable 2 describes the opinions and preferences of practitioners for DA usage. Regarding the ease of use, equal number (48% each) of participants found it “easy to use” and “difficult and cumbersome”. When asked about the type of cavity for which they would prefer to use DA, 46 (59.6%) participants responded that they would use it for medium and large cavities. They also reported that dental amalgam is the material of choice economically as 89% participants found it economical and 98% found it affordable by patients. Yet, 54% of the participants reported that they would not suggest the use of DA compared to other tooth-coloured restorations.\n\nTable 3 elucidates the perception and awareness for DA use as a risk factor. It was found that nearly 94% were aware of mercury toxicity concerns. Moreover, 46% and 37% participants felt that using DA as a restorative material could pose a risk factor for pregnant women and children respectively.\n\nPreference for continued usage of DA based upon the age of dentists, showed statistically significant differences, with older practitioners preferring DA more (Table 4). Likewise, a significantly greater number of experienced practitioners preferred continued use of DA as well as very satisfied with DA usage (Table 5).\n\np value derived by student t test, p < 0.05 considered significant.\n\np value derived by chi square test, p < 0.05 considered significant.\n\n\nDiscussion\n\nSilver amalgam as a dental restorative material has survived time and has successfully competed with various tooth-coloured restorations in the market [Roulet, 1997; Antony et al., 2008]. The longevity of the restoration, an extensive record of minimal failures in addition to being one of the most economic dental materials in the market, makes dentists and patients opt for the product especially in developing nations like India [Ukrainian Religious Studies, 1996; Maciel et al., 2017; Peretz and Ram, 2002]. Hence, this study was conducted to explore the continued use of silver amalgam for dental restorations, from a South Indian dental practitioner’s perspective in an unbiased manner.\n\nIn our study we witnessed that although a majority of dentists were satisfied with longevity, minimal failures of DA restorations and cost-effectiveness, more than 50% of them reported that they would not suggest dental amalgam over other tooth-coloured restorations. Reported continuation of DA usage is lesser in our study as compared to previous studies [Maciel et al., 2017; Peretz and Ram, 2002]. This can be owed to their concerns over mercury toxicity, as 94% practitioners were aware of its impact on environment. Presence of environmental Mercury results in microbial antibiotic resistance, which in turn propounds health risk to humans and animals [Rahman and Singh, 2018]. This is in line with Minamata Convention that calls for reduction of DA usage [Minamata Convention, 2014].\n\nPreferences for DA usage among practitioners in the present study can be mainly due to ease of its use, cost effectiveness, minimal failures and patient affordability. These findings are comparable with other studies conducted by Maciel et al. (2017), Espelid et al. (2006), Peretz and Ram (2002). In our study, more than half of them preferred DA usage in medium and large cavities. This is in accordance with studies that show ineffectiveness of DA in very large cavities owing to higher chances of overhanging margins in proximal restorations [Ghulam and Fadel, 2018]. This could be due to the exceptional mechanical properties of DA over others as well as aggravation of pain and sensitivity with composite restorations in deeper cavities. However, a shift in concept of ‘extension for prevention’ to a modern ‘minimally invasive approach’ with newer self-adhesive materials has further reduced the use of DA. This could be the reason for significantly lower preference for DA among younger practitioners. Further, not being aesthetic as compared to other restorations, DA also causes local soft tissue lesions like amalgam tattoo and lichenoid reaction and can trigger hypersensitivity and autoimmune disorders [Ghulam and Fadel, 2018]. This was similar to the results in our study, where 40% of practitioners had experienced soft tissue lesions due to DA restorations.\n\nWe observed that in the government run CHCs, none of the dentists are currently using DA. This can be attributed to (i) low rates of dental auxiliary recruitment at the CHCs, who are very much needed for handling of DA. (ii) non-availability of amalgam triturators in the government hospitals, (iii) Government’s support for the Minamata convention. There is also an attempt to move towards phase-down of DA restorations in the governmental sector.\n\nMoreover, the study results show that the practitioners lacked extensive knowledge on mercury toxicity, as not many of them felt that they could pose a risk factor for pregnant women and children. However, more than 90% of them expressed their concerns over mercury toxicity.\n\nConsequently, as our study and various authors [Al-Asmar et al., 2019; Umesi, Oremosu and Makanjuola, 2020] report, a majority of dental practitioners across the globe do not advise the use of DA over other tooth-coloured restorative materials. There is a prevailing notion that placing dental amalgam restorations can cause adverse health effects like impairing kidney function [Eggleston, 1994 and decreasing T-lymphocyte counts [Boyd et al., 1991], although studies by Berglund, 1990, University of Umea in Sweden found no evidence of kidney impairment in subjects with amalgam restorations.\n\nAlso, the hype generated from the three Amalgam Wars [Molin, 1992; Weiner JA, Nylander M, Berglund F, 1990; Huggins, 2007] raised considerable concerns about mercury toxicity amongst the patients and dentists, in spite of being disproved repeatedly. This discussion is still a relevant debate and different countries have laid down their guidelines regarding the use or restriction of amalgam as a dental restoration with many places where amalgam phase down is moving from a debatable domain to a legislative domain [Al-asmar et al., 2019; Umesi, Oremosu and Makanjuola, 2020].\n\nHowever, our study had certain limitations; significant reduction in sample size occurred due to a minimum of five years of experience as inclusion criteria. Also, certain practitioners had completely shifted to tooth-coloured restorations, precluding them from the study. Among those included in the study, a significant number of participants did not respond, in spite of repeated reminders, citing busy patient schedules, making it a limitation of this study.\n\n\nConclusions\n\nTo draw inferences from this study, it is important to take a calculated decision while selecting the right restorative material based on individual case scenario and economics of the patient. India is a developing country where emphasis on oral health is minimal, and majority of the population is incapable of meeting increased expenses on dental treatment. Hence, dental amalgam still stands as a good restorative material for low-middle income countries.\n\nHowever, there is an urgent need to educate dentists about the precautions to be taken on mercury hygiene as well as mercury waste management and disposal. There is an imperative need to sensitize the dentists on the guidelines of Minamata Convention. Patients too have to be alerted about the dental materials based on evidence so that they do not instinctively believe in biased publicity of products. From this study insight, it is advisable to conduct similar large-scale studies across the country to carefully assess the current Indian dental market and cautiously curate a product that is appropriate to patients.\n\nThe continued and appropriate use of DA is a decision that needs careful consideration in the times of restorative materials like Ivoclar Cention N and the spectrum of Composites. DA is a material that has been tried and tested. The newer materials too will face the test of time and will have to prove their efficacy in the coming decades.\n\n\nData availability\n\nOpen Science Framework: Community Social Responsibility of continued and appropriate use of Silver Amalgam as dental restorative material in Southern India. https://doi.org/10.17605/OSF.IO/NUC5J [Nayak, 2022].\n\nThis project contains the following underlying data:\n\n- Udupi Amalgam study.xlsx (social responsibility of silver amalgam usage as a dental restorative material).\n\nOpen Science Framework: Community Social Responsibility of continued and appropriate use of Silver Amalgam as dental restorative material in Southern India. https://doi.org/10.17605/OSF.IO/NUC5J [Nayak, 2022].\n\nThis project contains the following extended data:\n\n- Questionnaire – Copy.docx\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).", "appendix": "Acknowledgements\n\nWe acknowledge Late Dr K. S. Bhat, Former Dean, Manipal College of Dental Sciences, Manipal, MAHE for being the motivation behind the conduct of the study. We appreciate Kasturba Medical College Health Sciences Library, Manipal, MAHE for all logistic Support. We acknowledge Indian Dental Association, Udupi district branch for all related support and participating Dental practitioners of Udupi District, Karnataka State, India.\n\n\nReferences\n\nU.S. Food and Drug Administration: About Dental Amalgam Fillings.2020. [Accessed on 2020 Dec 11].Reference Source\n\nAl-Asmar AA, Al-Khatib KM, Al-Amad TZ, et al.: Has the implementation of the Minamata convention had an impact on the practice of operative dentistry in Jordan? J. Int. Med. Res. 2019; 47(1): 361–369. PubMed Abstract \| Publisher Full Text\n\nAlzheimer's Myths:[Accessed on 2020 Nov 11].Reference Source\n\nAntony K, Genser D, Hiebinger C, et al.: Longevity of dental amalgam in comparison to composite materials. GMS. Health Technol. Assess. 2008; 13(4): Doc12.\n\nAyushman Bharat: Pradhan Mantri Jan Arogya Yojana:[Accessed on 2020 Nov 11].Reference Source\n\nBerglund A: Estimation by a 24-hour study of the daily dose of intra-oral mercury vapor inhaled after release from dental amalgam. J. Dent. Res. 1990; 69(10): 1646–1651. PubMed Abstract \| Publisher Full Text\n\nBerlin declaration to end amalgam use in Europe:1 July 2022. [Accessed on 2020 Oct 10].Reference Source\n\nBharti R, Wadhwani KK, Tikku AP, et al.: Dental amalgam: An update. J. Conserv. Dent. 2010 Oct; 13(4): 204–208. PubMed Abstract \| Publisher Full Text\n\nBoyd ND, Benediktsson H, Vimy MJ, et al.: Mercury from dental “silver” tooth fillings impairs sheep kidney function. Am. J. Phys. Regul. Integr. Comp. Phys. 1991; 261(4): R1010–R1014. Publisher Full Text\n\nBrennan DS, Spencer AJ: Restorative service patterns in Australia: amalgam, composite resin and glass ionomer restorations. Int. Dent. J. 2003 Dec 1; 53(6): 455–463. PubMed Abstract \| Publisher Full Text\n\nCannon MS, Kapes ED, Palkuti GA: Dr. Black and the “amalgam question”. J. Hist. Med. Allied Sci. 1985 Jul 1; 40(3): 309–326. PubMed Abstract \| Publisher Full Text\n\nDistrict wise Hospital details with facilities:Last accessed on 23.05.Reference Source2022\n\nDodes JE: The amalgam controversy: an evidence-based analysis. J. Am. Dent. Assoc. 2001 Mar 1; 132(3): 348–356. Publisher Full Text\n\nEames WB: Preparation and condensation of amalgam with a low mercury-alloy ratio. J. Am. Dent. Assoc. 1959 Apr 1; 58(4): 78–83. Publisher Full Text\n\nEspelid I, Cairns J, Askildsen JE, et al.: Preferences over dental restorative materials among young patients and dental professionals. Eur. J. Oral Sci. 2006 Feb; 114(1): 15–21. PubMed Abstract \| Publisher Full Text\n\nEuropean Commission Scientific Committee on Emerging and Newly Identified Health Risks (SCENIHR): Final opinion on the safety of dental amalgam and alternative dental restoration materials for patients and users (29 April 2015).p. 69. [Accessed on 2020 Nov 05].Reference Source\n\nEuropean Commission Scientific Committee on Emerging and Newly Identified Health Risks (SCENIHR): Preliminary opinion on the safety of dental amalgam and alternative dental restoration materials for patients and users (26 August 2014).p. 66 [Accessed on 2020 Nov 05].\n\nFlagg JF: Metallic pastes for filling teeth. Bost. Med. & Surg. J. 1843 Dec 13; 29(19): 382–384. Publisher Full Text\n\nFrykholm KO: On Mercury from Dental Amalgam: Its Toxic and Allergic Effects, and Some Comments on Occupational Hygiene. Almqvist & Wiksells boktr;1957.\n\nGhulam OA, Fadel HT: Can clusters based on caries experience and medical status explain the distribution of overhanging dental restorations and recurrent caries? A cross-sectional study in Madinah–Saudi Arabia. Saudi J. Biol. Sci. 2018 Feb 1; 25(2): 367–371. PubMed Abstract \| Publisher Full Text\n\nGreener EH: Amalgam--yesterday, today, and tomorrow. Oper. Dent. 1979; 4(1): 24–35. PubMed Abstract\n\nHsi-T'Ao C: The use of amalgam as filling material in dentistry in ancient China. Chin. Med. J. 1958; 76: 553–555.\n\nHuggins HA: Medical implications of dental mercury: a review. Explore. 2007 Mar 1; 3(2): 110–117. Publisher Full Text\n\nMaciel R, Salvador D, Azoubel K, et al.: The opinion of children and their parents about four different types of dental restorations in a public health service in Brazil. Eur. Arch. Paediatr. Dent. 2017 Feb; 18(1): 25–29. PubMed Abstract \| Publisher Full Text\n\nMagkert Jr: Dental amalgam and mercury. J. Am. Dent. Assoc. 1991 Aug 1; 122(8): 54–61. Publisher Full Text\n\nMinamata Convention:2014.Reference Source\n\nMolin C: Amalgam – Fact and fiction Scand J Dent Res. 1992 Feb; 100(1): 66–73. PubMed Abstract \| Publisher Full Text\n\nMosteller JH: Restoration of teeth with silver amalgam. J. Prosthet. Dent. 1961 Mar 1; 11(2): 288–297. Publisher Full Text\n\nNational Institute of Health: Studies Evaluate Health Effects of Dental Amalgam Fillings in Children.2006. [Accessed on 2020 Dec 21].Reference Source\n\nNayak PP: Community Social Responsibility of Continued and Appropriate Use of Silver Amalgam as Dental Restorative Material in Southern India. OSF. August 24. [Data set].2022. Publisher Full Text\n\nPeretz B, Ram D: Restorative material for children's teeth: preferences of parents and children. J. Dent. Child. 2002 Sep 1; 69(3): 243–248.\n\nRahman Z, Singh VP: Assessment of heavy metal contamination and Hg-resistant bacteria in surface water from different regions of Delhi, India. Saudi J. Biol. Sci. 2018 Dec 1; 25(8): 1687–1695. PubMed Abstract \| Publisher Full Text\n\nReddy P, Krithikadatta J, Srinivasan V, et al.: Dental caries profile and associated risk factors among adolescent school children in an urban South-Indian city. Oral Health Prev. Dent. 2020; 18(1): 379–386. PubMed Abstract \| Publisher Full Text\n\nRoulet JF: Benefits and disadvantages of tooth-coloured alternatives to amalgam. J. Dent. 1997 Nov 1; 25(6): 459–473. PubMed Abstract \| Publisher Full Text\n\nSpencer AJ: Dental amalgam and mercury in dentistry. Aust. Dent. J. 2000 Dec; 45(4): 224–234. Publisher Full Text\n\nSCHER, Opinion on Environmental Risks and Indirect Health Effects of Mercury from Dental Amalgam:2014; page 4. [Accessed on 2020 Dec 21].Reference Source\n\nUkrainian Religious Studies: The Final Act of the Conference on Security and Cooperation in Europe.1996 Sep 27; (2): 71. [Accessed on 2020 Dec 21].\n\nUçar Y, Brantley W:Biocompatibility of dental amalgams. Biocompatibility of Dental Biomaterials. Woodhead Publishing;2017; (pp. 95–111).\n\nUmesi DC, Oremosu OA, Makanjuola JO: Amalgam phase down: baseline data preceding implementation in Nigeria. Int. Dent. J. 2020 Jun 1; 70(3): 161–166. PubMed Abstract \| Publisher Full Text\n\nWeiner JA, Nylander M, Berglund F: Does mercury from amalgam restorations constitute a health hazard? Sci. Total Environ. 1990 Dec 1; 99(1-2): 18. PubMed Abstract \| Publisher Full Text\n\nVasthare R: Community Social Responsibility of continued and appropriate use of Silver Amalgam as dental restorative material in Southern India.2022, July 8. Publisher Full Text" }	[ { "id": "150726", "date": "06 Oct 2022", "name": "Manjunath P Puranik", "expertise": [ "Reviewer Expertise Public Health Dentistry" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nAbstract - \"In spite of satisfaction with DA for its minimal failure, longevity and affordability, the authors found that a majority of practitioners did not prefer its continued usage.\" - There is a contradiction in their practice, perceptions and preferences. This has to be explained in the discussion.\n\nAbstract - \"Dentists with higher age and longer clinical experience preferred continuation of DA.\" - Is it because of lack of awareness or any other reason? This has to be explained in the discussion.\n\nAbstract - \"There is also an urgent need to educate dentists on mercury hygiene, mercury waste management and disposal.\" - Will this help dentists with higher age and longer clinical experience who preferred continuation of DA? This has to be explained in the discussion.\n\nAbstract - \"This highlights their concerns over mercury toxicity and soft tissue lesions and accentuates their community social responsibility.\" - How does it accentuate their community social responsibility? This has to be explained in the discussion.\n\nIntroduction - is extensive and informative about the stance of dental amalgam usage by various organizations around the world. Since the study is among individual dentists, the review demands the addition of such information if there is any in the existing literature and justifies the need for the study.\n\nDiscussion - there is a need to discuss community social responsibility since it is mentioned in the title.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] } ]	1	https://f1000research.com/articles/11-1061
https://f1000research.com/articles/13-694/v1	26 Jun 24	{ "type": "Systematic Review", "title": "Impact on postoperative complications of combined prehabilitation targeting co-existing smoking, malnutrition, obesity, alcohol drinking, and physical inactivity: a systematic review and meta-analysis of randomised trials", "authors": [ "Line N Lydom", "Sofie Anne-Marie S Jensen", "Susanne V Lauridsen", "Mette Rasmussen", "Robin Christensen", "Ulla N Joensen", "Jacob Rosenberg", "Hanne Tønnesen", "Line N Lydom", "Sofie Anne-Marie S Jensen", "Susanne V Lauridsen", "Mette Rasmussen", "Robin Christensen", "Ulla N Joensen", "Jacob Rosenberg" ], "abstract": "Background This study aimed to compare the effect on postoperative complications of prehabilitation targeting predefined co-existing risky lifestyle factors with usual preoperative routines in surgical patients.\n\nMethods This systematic review followed the PRISMA 2020 guideline and the protocol (CRD42022282611). Five databases were searched from inception to November 7, 2022 for randomised controlled trials on prehabilitation targeting ≥2 predefined risky lifestyles compared with usual preoperative routines. Risky lifestyles included Smoking, Nutrition (malnutrition and/or BMI>25), risky Alcohol intake, and Physical inactivity (SNAP). Primary outcome was postoperative complications ≤30 days. Cochrane’s risk-of-bias tool 2 was used and meta-analyses were conducted. GRADE was used to assess certainty of evidence.\n\nResults The search resulted in 20,862 records. At full-text screening, only two (120 participants) of 24 identified trials on combined SNAP intervention had ≥2 predefined risk factors and were included. One (n=110) on intensive physical and brief nutritional intervention to frail patients with colorectal cancer resection reported complication rates of 45% in both groups (relative risk (RR) 1.00, 95% CI 0.66 to 1.51). The other study (n=10, subgroup) on intensive alcohol and smoking intervention in patients with bladder cancer undergoing radical cystectomy, reported complications in 3/7 vs 3/3 participants (RR 0.50, 95% CI 0.21 to 1.19). The meta-analysis estimated a RR of 0.79 (95% CI 0.41 to 1.51, I2 51%).\n\nConclusion Two small of the 24 trials on prehabilitation targeted co-existing and predefined risky SNAP factors and the effect on postoperative complications is very uncertain. Future prehabilitation research involving patient needs is warranted.", "keywords": [ "Prehabilitation", "Postoperative complications", "Surgery", "Lifestyle" ], "content": "Introduction\n\nSurgery is a pivotal part of the treatment of numerous medical conditions. The estimated global volume of surgical procedures was 313 million procedures in 2012 and this has since increased.1 Development of complications is still a major challenge worldwide2,3 despite the improvements in perioperative care in the last decades including improved surgical and anaesthesiologic techniques, preoperative interventions targeting co-morbidities, and enhanced postoperative recovery programmes.4–6 The consequences of complications include prolonged recovery, reduced quality of life and life expectancy, as well as increased health care costs.7–10\n\nPostoperative morbidity is in part related to preoperative modifiable risk factors such as smoking,11,12 nutrition (overweight/obesity, malnutrition),13–15 risky alcohol drinking,16 and physical inactivity17–19 (SNAP). The SNAP factors compromise several organ functions of importance for successful outcome after surgery.13,20–23 While daily smoking, risky alcohol intake, or malnutrition are followed by a general 50% increased complication rate across different types of surgery,11,13,16 overweight or obesity are associated with increased complications to a minor degree.24,25 Low physical activity level is associated with increased risk of complications, length of stay and postoperative mortality.18,26–29\n\nThe SNAP factors are modifiable by prehabilitation,20,22,30,31 but the impact on postoperative morbidity differs among the SNAP factors.32,33 Only the most intensive programmes targeting smoking, alcohol, and malnutrition reduce complication rates by half.13,32,33 Recent systematic reviews have shown an improvement after preoperative physical training programmes of functional capacity both pre- and postoperatively, however, no effect on postoperative complications has been shown.34,35 The effect of overweight or obesity interventions have only poorly been investigated outside bariatric surgery.36 Until now, the large majority of the evidence from SNAP interventions are based on investigating one risky SNAP factor intervention at a time.37,38 This is despite of up to half of hospital patients have co-existing SNAP factors,39–41 such as smoking and overweight or frailty involving both malnutrition and physical inactivity, which potentiate the risk at surgery.14,42 This calls for risk reduction through targeted combined prehabilitation.\n\nThe aim was to compare the effect on postoperative complications of prehabilitation targeting predefined co-existing risky SNAP factors with usual preoperative routines in surgical patients. We hypothesised the combined prehabilitation would reduce the postoperative complications compared to usual preoperative routines.\n\n\nMethods\n\nThis systematic review and meta-analysis was conducted and reported according to the Cochrane Handbook for Systematic Reviews of Interventions43 and in line with PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses)44 and AMSTAR (Assessing the methodological quality of systematic reviews)45 Guidelines. The protocol was registered on PROSPERO (CRD42022282611) before retrieval of data.\n\nWe included randomised controlled trials enrolling populations of adult patients (≥18 years) undergoing any surgical intervention and having at least two of the five predefined risky SNAP factors (daily smoking, alcohol intake > 2 drinks daily (= above 24 g ethanol) or 14 drinks weekly, malnutrition (defined as either weight loss of 10-15% within the last 6 months, BMI < 18.5, Subjective Global Assessment (SGA) Grade C, Nutritional Risk Screening (NRS) > 5, or preoperative serum albumin < 30 g/l), BMI > 25 and physical activity < 4 hours/week), or as described by the authors and receiving a combined intervention initiated preoperatively and targeting those lifestyles. Populations in need for combined frailty intervention were accepted if the frailty screening tool involved at least two of the predefined risky lifestyles of interest in this review. Studies were excluded if their population did not have predefined risky lifestyles. Only face-to-face interventions (physical or online) were included. Intensive interventions were defined as having at least four sessions, each lasting longer than ten minutes and including education, motivational and (if relevant) pharmaceutical support.32,46 The intervention was compared with usual preoperative routines.\n\nWe searched Medline, Embase, Web of Science, Cochrane Central Register of Controlled Trials, and CINAHL on March 3, 2021 with an update on November 7, 2022. Our search strategy for MEDLINE was developed in consultation with an information specialist from the Cochrane Anaesthesia Group. It was combined with the Cochrane Highly Sensitive Search Strategy, with use of the sensitivity- and precision-maximising version, for identifying RCTs47 (see extended data file). Similar strategies were developed for the other databases. The search was performed without restrictions for language or publication year. In addition, we performed a simple keyword search (“multimodal prehabilitation surgery RCT”) in Google Scholar with a check-up of the first 200 references and a snowball search by manually scanning the reference lists of included trials and of topic relevant systematic reviews.\n\nScreening of articles was conducted using Covidence® with an institutional subscription. Two reviewers screened all titles and abstracts, independently. Likewise, all full text articles were screened by two other reviewers. Any disagreements were discussed and resolved within the author group. with an institutional subscription. Two reviewers screened all titles and abstracts, independently. Likewise, all full text articles were screened by two other reviewers. Any disagreements were discussed and resolved within the author group.\n\nData extraction was performed in collaboration of two reviewers with all discrepancies discussed and resolved within the author group. The following data were extracted from all studies into a pre-defined Excel-sheet: authors, year of publication, country, number of patients, patient characteristics (age, sex, ASA-score, SNAP factors), type of surgery, indication for surgery, intervention characteristics (targeted risky SNAP factors, intensity of intervention, preoperative duration, compliance measured as meeting adherence, additional interventions), definition of control groups, drop-outs, and length of follow-up.\n\nThe primary outcome was complications within 30 postoperative days, defined by requiring treatment and categorised according to a standardised methodology e.g., the Clavien-Dindo classification,48 comprehensive complication index,49 or as described by the authors.\n\nWe only included published randomized controlled trials (RCTs) including cluster and pilot RCTs. Secondary outcomes were extracted if present in the studies: length of stay (LoS), readmissions, adverse events of the lifestyle intervention, successful risk reduction perioperatively and long-term, and effect on patient reported long-term (one year) quality of life (QoL).\n\nSuccessful risk reduction was defined as quit smoking, quit drinking, no overweight or obesity, no malnutrition, physical activity >4h/week as well as change of at least 1 step on the ASA-score50 regarding risky lifestyles or any change of at least 1 unhealthy lifestyle. For long-term successful risk reduction same definitions were applied except for alcohol which needed to be below risky limits instead of zero intake exclusively.\n\nWhen doubts about extraction of data, trial authors were contacted by email for clarification. For studies that included a subset of eligible participants, we obtained data for only the subgroup of interest.\n\nRisk of bias in the individual studies was assessed independently by two reviewers using the Cochrane Handbook’s risk-of-bias tool (RoB2) for RCTs.51 Any discrepancies or doubts were discussed and resolved together with a third reviewer. For each outcome in each study, all signalling questions were answered for the five bias domains: the randomization process, deviation from intended interventions, missing outcome data, measurement of the outcome, and selection of the reported result. For each domain the responses were collated to a final judgement. In addition, the overall judgement of either low risk of bias, some concerns or high risk of bias was assigned based on the five bias domains.\n\nTo reduce the impact of bias due to missing data in the synthesis, we contacted the authors of the studies in case of missing estimates. In addition, in the data extraction we adhered to the best of our abilities to the intention-to-treat principle.52 Meta-analyses were performed using Review Manager 5.4® (RevMan [Computer program]. Version 5.4. The Cochrane Collaboration, 2020). The effect measure of choice for the binary outcomes (e.g., postoperative complications) was the relative risk (RR) with 95% confidence intervals (95% CI) in order to assess the likelihood of the event happening in the experimental intervention group relative to the control comparator.53 Secondary outcomes were expressed similarly except LoS and quality of life (continuous outcome measures), which were estimated based on the difference between means.54 If data were presented as median and IQR, the assumption was that the mean approximately corresponded to the median while SD was estimated as IQR/1.35.55\n\nA meta-analysis for the relative risks of postoperative complications as well as for the secondary outcomes was conducted based on a random-effects model per default (DerSimonian and Laird)56 and the results presented in Forest plots. Clinical heterogeneity was considered and evaluated qualitatively, and the statistical heterogeneity was assessed as I2-values as well as from the poor overlap in the visualized 95% CIs in the Forest plots.56 In addition, we planned subgroup analyses on different combinations of the five risky lifestyles, intensive interventions, elderly patient groups, and different types of surgery as well as sensitivity analyses.\n\nAccording to the new guidelines by The Institute for Quality and Efficiency in Health Care (IQWiG) it is recommended to use a fixed-effect model in the case of very few studies, so we also conducted these for the purpose of sensitivity analysis on the primary outcome.57\n\nAccording to the original protocol, we also applied a network meta-analysis technique in order to simultaneously compare three or more interventions in order to enable a comparison between multiple interventions since direct comparisons are limited. We estimated the odds ratios by default from the random effects network meta-analysis model with binomial likelihood and logit link.58 For these (arm based) network meta-analyses, we used generalised linear mixed models combining a series of 2×2 tables, with the odds ratio modelled as a linear combination of study level covariates and random effects, representing variation between studies.59\n\nOn the basis of the comparison of the individual OR values to the overall event rate in the treatment as usual groups as a proxy for baseline risk, we would estimate the number needed to treat (NNT) in order to get an extra patient without complications with 95% CI. We considered two-sided P-values less than 0.05 and 95% CIs for the RR values for binary outcomes that did not include 1 to be statistically significant. Summary assessments of the quality of evidence for each important outcome were performed using the GRADE (Grading of Recommendations Assessment, Development and Evaluation) approach60,61 which includes four levels of quality of evidence (high, moderate, low, and very low) and presented in a summary of findings table.\n\n\nResults\n\nAs illustrated in the PRISMA flowchart, the literature search revealed a total of 20,863 different records identified from various sources; these were screened for eligibility based on title and abstract, and 188 studies were subsequently assessed in full text. A total of 24 studies apparently met the inclusion criteria except for the criterion of at least two predefined risky SNAP factors. Consequently, we were only able to include two RCTs fulfilling our stringent eligibility criteria62,63 (Table 1).\n\nOne of the two included studies was a multicentre RCT with stratification for smoking, alcohol and both had a small subgroup (n=10) investigating the effect of combined intensive smoking and alcohol cessation intervention for patients with these predefined risk factors undergoing radical cystectomy for bladder cancer.63 In total, the sub-group consisted of 13 (eight in intervention group + five in control group) patients, but three did not undergo surgery leaving ten patients (seven in intervention group + three in control group) (Table 2). The other included study (n=110) investigated the effect of a brief nutrition and intensive physical activity intervention on patients undergoing colorectal cancer surgery.62 They included their patients based on being frail preoperatively according to the Fried Frailty Index,64 which includes both elements of physical capability and malnutrition. Patients who were current smokers or had a risky alcohol intake were counselled regarding cessation, but no information regarding counselling content or lifestyle improvement were described (Table 2). None of the two included studies received funding from foundations involved in any part of the trials (designing of study, study conduction, dissemination of results etc) except the funding.\n\na Overall adherence to the programme (supervised and homebased; exercise and nutritional components).\n\nb Attendance rate at the 5 planned meetings\n\nc Subjective global assessment. B indicates nutrition risk and C malnutrition.\n\nd Weight loss > 5% in the last month or food intake 0-25% of normal requirement in preceding week or BMI <18.5 + impaired general condition\n\ne For men: (>15 standard drinks per week) and women: (>10 standard drinks per week).\n\nf ≥ 3 units of alcohol (36 g) daily.\n\nRisk of bias assessment for the two included studies are presented in Figure 1. Being behavioural intervention studies blinding of patients and study personnel was not possible. Otherwise, both studies were judged to have a low risk of bias in almost all domains for both primary and secondary outcomes. Exceptions were the secondary outcomes of successful risk reduction at the end of intervention in Carli et al.62 and at 12 months in Lauridsen et al.63 In Carli et al. less than 80% of the control group attended follow-ups. Furthermore, most of the non-attendances at follow-up were not justified. One could wonder whether the non-attendances at follow-up were the patients in the worst physical shape/with the least improvement, thereby inducing bias due to missing results. Therefore, the domain of missing outcome data was assessed as having a high risk of bias. The problems with follow-up data in Lauridsen et al. was explained by death of patients. One patient in each group died within 90 days due to complications, the rest due to recurrence of their bladder cancers, therefore the domain received some concerns instead of high risk of bias. To identify publication bias we planned to produce funnel plots but too few studies were identified for this.\n\n+: low risk of bias, !: some concerns, -: high risk of bias, D1: randomization process, D2: deviations from the intended interventions, D3: missing outcome data, D4: measurement of the outcome, D5: selection of the reported result.\n\nNone of the two included studies reported a statistically significant difference in postoperative complications within 30 days between intervention and control groups. Carli et al.62 reported complications in 25 of 55 (45.5%) participants in both intervention and control group entailing a relative risk of 1.00. Lauridsen et al.63 reported complications in three of seven participants and three of three participants, respectively. The relative risk was 0.5. The meta-analysis based on a random-effects model estimated a weighted relative risk of 0.79 (Figure 2). The meta-analysis based on a fixed-effect model estimated a weighed relative risk of 0.92, 95% CI [0.63, 1.34]; I2: 51%.\n\nCI: confidence interval, P: p-value, SD: standard deviation, Z: z-value.\n\nAccording to the protocol, we performed a network meta-analysis comparing all intervention groups as if it had been compared in one large trial. When comparing an intensive (I) physical activity and brief (B) nutrition, smoking and alcohol cessation intervention (PINSAB) with an intensive smoking and alcohol cessation intervention (SAI) the risk of complications could potentially be unfavorable for PINSAB (OR = 1.19 [0.26 to 5.45]). SAI on the other hand might reduce the risk of complications when compared to treatment as usual (TAU) (OR = 0.79 [0.17 to 3.60]), but when TAU was compared to PINSAB there was no reason to suspect any difference in risk of complications (OR = 0.94 [0.46 to 1.92]).\n\nCarli et al. reported an identical length of stay in both groups of 4 days (mean difference 0.00, CI 95% [-1.38, 1.38]) while Lauridsen et al. reported length of stay of 7.3 days in the intervention group versus 11.7 days in the control group. The mean difference was -4.40 with CI 95% [-9.10, 0.30] pointing towards a shorter length of stay in the intervention group but still not statistically significant. Meta-analysis estimated a weighted mean difference of -1.60 days (Figure 3).\n\nCI: confidence interval, P: p-value, SD: standard deviation, Z: z-value.\n\nIt was not possible to conduct meta-analyses for the remaining secondary outcomes due to less than two studies reporting the outcomes. Carli et al. reported readmissions within 30 days in two of 55 (3.6%) participants versus five in 55 (9.1%) participants in the intervention and control groups, respectively (RR 0.40 [0.08, 1.97]). Lauridsen et al. reported readmissions within 90 days in five of seven participants versus two in two participants, respectively (RR 0.71 [0.45, 1.14]). Carli et al. did not report on long-term quality of life. Lauridsen et al reported one-year QoL and VAS QoL measured by the EQ-5D instrument. Mean difference for one-year QoL and VAS QoL was 0.06, 95% CI [-0.19, 0.32] and 2.4, 95% CI [-33.8, 38.6], respectively.\n\nRegarding successful risk reduction, data were sparse and reported on few SNAP factors. All available results are reported as intention to treat in Table 3. Both studies reported no adverse events due to the interventions. The data available did not allow for any subgroup analyses to be made.\n\nThe GRADE assessments of the quality of evidence for the meta-analysis outcomes for postoperative complications and length of stay are summarized in Table 4, including descriptions for downgrading the quality of the evidence.\n\n* The risk in the intervention group (and its 95% confidence interval) is based on the assumed risk in the comparison group and the relative effect of the intervention (and its 95% CI).\n\na Moderate statistical heterogeneity assessed as no serious inconsistency.\n\nb Downgraded for indirectness. Different SNAP-interventions being compared.\n\nc Downgraded for imprecision. Few patients and the confidence interval encompass both benefit and harm.\n\nd Downgraded for inconsistency. Substantial statistical heterogeneity.\n\n\nDiscussion\n\nSurprisingly, this systematic review identified only two randomized trials of prehabilitation before surgery targeting two or more co-existing and predefined risky SNAP factors (like physical activity below four hours per week and daily smoking) compared to treatment as usual or no treatment. More than 20 randomized trials on multimodal SNAP factor prehabilitation has been published and all but two had only one or no predefined risky SNAP factor as inclusion criteria. The lack of preidentified risk factors may result in populations with mixed needs for prehabilitation, thus, offering prehabilitation to both patients with and without risky SNAP factors thereby with or without a need for prehabilitation. We found no significant effect on postoperative complications in the two included studies.\n\nThe large majority of RCTs evaluating combined interventions mainly involved physical training and nutritional support, but they did not deliver the prehabilitation based on specified risky SNAP factors presented in the inclusion criteria (Table 2). This contrasts with other prehabilitation programmes, e.g., to quit smoking and alcohol prior to surgery, which would not be offered to persons without risky alcohol or tobacco use.\n\nMost of the excluded studies recruited participants on the basis of diagnosis or type of surgery rather than identified individual needs for prehabilitation.65–80 Another six studies on combined interventions included participants based on only one predefined risky SNAP factor; overweight81–83 or limited physical activity, function, or sedentary lifestyle.84–86 In the 22 excluded studies, there seems to be a discrepancy between the patients’ needs for prehabilitation and the programmes delivered. This may explain the inconsistency in impact on postoperative complications.\n\nFrailty is a medical syndrome characterized by “diminished strength, endurance, and reduced physiologic function”,87 which leaves the individual with decreased tolerance of stressors and vulnerable to adverse outcomes.88 Numerous screening tools exist, however, we have only included randomized trials using tools that include two or more of the predefined risk factors of relevance for this systematic review e.g. the Fried Frailty Index,64 which involves weight loss and reduced physical activity in addition to muscular weakness, slow walking, and exhaustion.42 The Fried Frailty Index is used in the included study by Carli et al.62 and this frailty diagnosis is closely related to the development of postoperative complications.42 However, the evidence from RCTs of frailty intervention is sparse,89,90 but studies are ongoing.91,92\n\nThe included randomized trial on intervention for co-existing risky alcohol and tobacco use prior to major surgery is based on the major risk reducing effect on the separate preoperative intensive smoking or alcohol intervention.12,32,33 It is only a minor subgroup from a larger study, but we have not been able to identify other studies of combined intervention for these risk factors. However, studies on non-surgical patients have shown successful quitting with the combined intervention, thereby indicating that this could be successful in relation to surgery.93\n\nA strength in this review is the substantial search of electronic databases using a highly sensitive search strategy developed in consultation with an information specialist. Another strength is that we only included studies where participants were selected and offered interventions based on five predefined risk factors associated with increased risk of postoperative complications, specifically according to the individual patient’s risk profile. One may consider the inclusion of any type of surgery as a weakness, however, several of the risky SNAP factors have been shown to increase complication rates with around 50% across different kinds of surgery.11,13,16\n\nThe limited number and the small size of the included studies are weaknesses. Especially, the combined alcohol and smoking cessation intervention constitutes a very small sub-group with unequal allocation to intervention- and control group despite of stratification, probably due to recruitment from five centres.63 The other included study evaluated frailty intervention based on Fried Frailty Index with five parameters in total. However, it is not clear to which degree the two SNAP factors weight loss and low physical activity were present in the included participants.62 None of the two included studies intervened or reported outcomes on all the risky SNAP factors identified in baseline data. The biases above further impact the limitation of this review. In addition, both studies were conducted on patient groups with specific cancers in Western high-income countries (Canada and Denmark). Therefore, the results must be interpreted with caution, and the generalisation should be carefully considered.\n\nPrehabilitation aiming at combined risky SNAP factors seems to have potential to abate postoperative complications, and probably long-term health. This untapped potential has not been defined yet, which may have impact for the individual patients and their families as they will continue suffering from potentially avoidable complications after surgery.\n\nComplications are also resource consuming, adding to the workload of the health professionals, the economic burden on the healthcare system and the society at large. Furthermore, offering effective interventions only to those in need of risk reduction will lessen the socio-economic expenses of prehabilitation.\n\nConduction of high-quality large-scale studies on combined interventions targeting individual co-existing and predefined risky SNAP factors are strongly requested. The combined intervention programmes should build upon the individual patient needs from preoperatively identified SNAP factors and establish new evidence regarding impact on surgical outcome at short term and health on longer term.\n\n\nConclusion\n\nThis review only identified two small trials that did not demonstrate statistically significant effects on postoperative complications after prehabilitation targeting co-existing and predefined risky SNAP factors. There is a lack of randomised trials evaluating the effect of individualised, combined prehabilitation programmes delivered in accordance with individual patients’ preoperative risky SNAP factors. While the meta-analysis did not demonstrate statistically significant effects on postoperative complications in this context, the study underscores the importance of involving patient needs in future research and evidence-based strategies to optimize surgical outcomes.\n\n\nAuthor contributions\n\nThe corresponding author attests that all listed authors meet the ICMJE authorship criteria and that no others meeting the criteria have been omitted.\n\nWe have used the repository Open Science Framework for the PRISMA checklist and flowchart. The name of the project is ‘Impact on postoperative complications of combined prehabilitation targeting co-existing smoking, malnutrition, obesity, alcohol drinking, and physical activity: a systematic review and meta-analysis of randomised trials’. https://doi.org/10.17605/OSF.IO/RKAVF\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\nEthics and consent statement\n\nEthics and consent not required.\n\n\nSoftware availability statement\n\nWe used Review Manager 5.4® (RevMan [Computer program]. Version 5.4. The Cochrane Collaboration, 2020). for the meta-analysis. Review Manager 5.4® is no longer available for download, but a web version can be used with a paid licence. However, an open access alternative is OpenMeta[Analyst].\n\nWe used Covidence for the screening of references with a paid institutional license. However, a limited open access alternative is the web tool Rayyan.", "appendix": "Data availability\n\nWe have used the repository Open Science Framework for extended data (complete search strings) and reporting guidelines (PRISMA checklist and PRISMA flowchart). 98 The name of the project is: Impact on postoperative complications of combined prehabilitation targeting co-existing smoking, malnutrition, obesity, alcohol drinking, and physical inactivity: a systematic review and meta-analysis of randomised trials. https://doi.org/10.17605/OSF.IO/RKAVF https://doi.org/10.17605/OSF.IO/RKAVF.\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\nWeiser TG, Haynes AB, Molina G, et al.: Size and distribution of the global volume of surgery in 2012. Bull. World Health Organ. 2016; 94: 201–209F. 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PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGram-Hanssen A: Impact on postoperative complications of combined prehabilitation targeting co-existing smoking, malnutrition, obesity, alcohol drinking, and physical activity: a systematic review and meta-analysis of randomised trials. Open Science Framework. (last accessed 31.05.2024). Publisher Full Text" }	[ { "id": "314669", "date": "24 Sep 2024", "name": "Tim Neumann", "expertise": [ "Reviewer Expertise perioperative medicine", "health promotion", "substance use and addiction medicine" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nLydom et al. conducted a systematic review and meta-analysis to examine the effect of combined prehabilitation in surgical patients targeting co-existing smoking, malnutrition, obesity, alcohol drinking, and physical inactivity (SNAP) on postoperative complications ≤30 days. Complications after surgery are highly relevant for patients as well as for the health system. Any reduction of complications is important. Studies addressing single SNAP risks with risk reducing interventions to patients undergoing operations have shown some benefit. It is unclear how two (!) or more interventions combined work for patients having two or more risk factor in comparison to treatment as usual or no treatment. This is a clinically relevant question for patients with two or more SNAP risk factors. It was of interest to learn from this study, that with this search strategy only two small randomized trials of prehabilitation before surgery targeting two or more co-existing and predefined risky SNAP factors were identified. This research question has not been addressed so far. Patients before surgery were frail in one study, and were small subgroup with risky substance use (alcohol and smoking) in the other study. The effect of combined SNAP interventions on postoperative complications was found to be very uncertain.\nThe following comments may be used to enhance the clarity and usefulness of this publication for the readers of this journal.\nAbstract Background, Introduction, Methods: Aim There is a difference between the aim as stated in Abstract’s Background, the aim as stated at the end of Introduction, and the aim as outlined by the search strategy. The “combined prehabilitation” is mentioned in the aim in the introduction chapter, not in the Abstract Background, (here: “…prehabilitation targeting predefined co-existing risky lifestyle factors with usual preoperative routines in surgical patients”), whereas in the eligibility criteria it is phrased “at least two of the five predefined risky SNAP factors” and “combined intervention initiated preoperatively”. It would be helpful, if the aim is stated identical at all places. Introduction: Devising the research question The rationale for comparing clinical pathways with interventions for patients with two or more factor and excluding those with only one SNAP risk factor might be better explained. Every patient with a defined risk should receive the appropriate intervention. Prehabilitation measures should be offered from a clinician’s point of view according to the patient needs and regardless of the number SNAP risks, and if provided, as intensive as needed. This systematic review addresses the clinical situation in which one needs the evidence that an offer of a combined intervention (regardless of SNAP risk combination) for those surgical patients only with 2 or more risk factors works better than treatment as usual (TAU). In this systematic review, studies reporting complications of one single SNAP factor only with one tailored intervention only were not considered and excluded from analysis. It is unclear why and whether two different interventions should work differently, when offered simultaneously. This might be discussed. Method: Data synthesis and statistical analysis data extraction and meta-analytical procedures were done extensively and excellent along the Cochrane Collaboration guidelines, although the number of studies (n = 2) and included patients N = 103) was small. Method/Results:\nThe method of Risk Ratio Mantel-Haenszel random-effects method Figure 2 should be explained in the method section: The RR calculation in in the Table 2 Forest plot with postoperative complications within 30 days in the Lauridsen et al (2022) study should be explained, as (3/7)/(3/3)=0.42. In the figure legends of the tables all abbreviations should be explained. Results, Table 1: On missing word “end” in Table 1: “Lauridsen 2022 Successful risk reduction at the end of intervention” Discussion: Future research strategies\nIt was called for conducting high-quality large-scale studies, especially RCTs on combined interventions targeting individual co-existing and predefined risky SNAP factors. Will the findings of this SR be helpful devising future research? How would one take such results into account when devising the research question? It was also stated that “the combined intervention programs should build upon the individual patient needs from preoperatively identified SNAP factors and establish new evidence regarding impact on surgical outcome at short term and health on longer term”. Before an ethical RCT a prior probability about roughly 50:50 is assumed that the intervention works better. How TAU should be defined? It would be of interest, how the authors would suggest a study design, especially the TAU control condition after this systematic review and in the light of the evidence about single interventions. In the times of ERAS pathways, the TAU is not the same anymore as it was when SNAP risks were followed by a general 50% increased complication rate. How would one integrate existing and developing ERAS concepts into high-quality large-scale studies? How would one deal with the narrowing effect of intervention gap (Lauridsen et al. 2022) when designing this study? Considering the variety of ERAS recommendations with outcome relevance, including the recommendation to address the SNAP risks, one must consider the intensity of each intervention, the reach into target population, the possible efficacy, effectiveness and efficiency, the staff’s adoption, settings, systems and communities variables, implementation consistency, costs and adaptions made during delivery, and maintenance/sustainment of intervention effects in individuals and settings over time. Very complex. When calculating sample size for future studies, would it be helpful to consider the findings of this review? Discussion: Socio-economic expenses of prehabilitation: only to those in need? It was stated in the conclusion that this study underscored the importance of involving patient needs in future research and evidence-based strategies to optimize surgical outcomes. It was also stated in the discussion, that “offering effective interventions only to those in need of risk reduction will lessen the socio-economic expenses of prehabilitation”. Is this a conclusion from the findings of the study? Is this meant as a general statement, and /or is it based on previous findings, such as the studies in the reference list “65–80” as mentioned on page 13: “Most of the excluded studies recruited participants on the basis of diagnosis or type of surgery rather than identified individual needs for prehabilitations65–80”? However, one has to keep in mind that in these studies the concept was to increase the functional capacity together with an evidence-based design to reduce perioperative stress and maintain physiological function and accelerate recovery after surgery and reduce complications. Activating patients in special holistic programs may also have other potential benefits. This should be to the benefit of all patients, regardless of whether individual risks exist. Clarification is recommended. Conclusion, last sentence: The importance of involving patient needs in future research and evidence-based strategies to optimize surgical outcomes is generally recognized. It does not become entirely clear how this study specifically underscores this.\nDiscussion: The limited number and the small size of the included studies is not a weakness, but an important finding: Research has not addressed this research question yet.\nMinor- Introduction: The authors called for risk reduction through targeted combined prehabilitation. This sentence might exclude those with a single SNAP risk in the context of this paper, which is most likely not intended by the authors. Rewording should be considered. Method: Concerning the outcome variable “overweight” or “obesity”: To become non-overweight, non-obese can take very long, even when weight loss was achieved, the patient would be still scored to be at risk. Not being at risk due to is difficult to achieve in severely obese patients, even when an intervention is effective, as weight reduction might take more time.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Partly\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Yes\n\nIs the statistical analysis and its interpretation appropriate? I cannot comment. A qualified statistician is required.\n\nAre the conclusions drawn adequately supported by the results presented in the review? Partly\n\nIf this is a Living Systematic Review, is the ‘living’ method appropriate and is the search schedule clearly defined and justified? (‘Living Systematic Review’ or a variation of this term should be included in the title.) Yes", "responses": [] } ]	1	https://f1000research.com/articles/13-694
https://f1000research.com/articles/13-693/v1	26 Jun 24	{ "type": "Research Article", "title": "Determinants of Household Resilience to Food Insecurity for Comparison: the Case of Chencha District, Southern Ethiopia", "authors": [ "Desta Dereje", "Temesgen Tilahun", "Teshome Yirgu", "Temesgen Tilahun", "Teshome Yirgu" ], "abstract": "Background Food insecurity is a historical global human challenge, but has yet remained a burning development agenda. The capacity to withstand and recover from food insecurity shocks and stresses refereed as resilience, which is determined by a strand of factors. This paper deals with measuring and; identifying major determinants of household resilience to food insecurity among weaving-based livelihood system in Chencha district.\n\nMethods Multi-stage sampling technique was employed to generate data from 303 sample households through household survey, focus group discussion, and key informant interviews. The collected data were analyzed by using descriptive statistics, household resilience index, chi-square test, one-way ANOVA and econometric model (probit regression).\n\nResults The household survey revealed that 59.04% households were non-resilient, 24.42% were moderately resilient, 10.89% resilient and 4.95% highly resilient. The Chi-square and one-way ANOVA tests have shown a meaningful and statistically significant difference among resilience categories. Finally, probit model analysis indicated that access to credit, average years of family education, crop diversity, income diversity, landholding size, TLU, expected crop harvest, expected cash income from fruit trees, frequency of extension contact, FCS, annual food expenditure, ownerships of Radio, Jewelry, furnished bed, membership in local associations, and distance to local market have positively influenced the likelihood of attaining higher household resilience at CI 95% or P<1%, 5% and 10%. Whereas; lack of access to mobile phone, inability to read and write, family business, formal employment, and transfers of payment have decreased likelihood of households to achieve higher resilience level.\n\nConclusions Therefore, improving household access to credit, education, income diversification, livestock and land, agricultural extension services, membership to local associations, mobile service, and income diversification would enhance household income and food security, which could in turn improve household resilience to food insecurity.", "keywords": [ "Household", "Resilience", "Determinants of resilience", "Food Insecurity", "Shock", "Stress" ], "content": "Background\n\nFood security is a multidimensional concept that is currently the political, economic, and social agenda of development. Its emergence dates back to some 50 years ago, in the 1970s, during 1996 world Food Summit (FAO, 2003). Currently, it is claimed that it has more than 200 definitions and many indicators of measurement (Maxwell and Smith, 1992). Definitions and conceptualizations of food security have undergone a series of modifications. However, food security is commonly understood as a condition where all people at all times have physical, economic, and social access to sufficient, safe, and nutritious food that helps to lead an active and healthy life (FAO, 1996). Basically, it can be conceptualized and examined at multiple levels (Anon, 2015).\n\nFood insecurity and undernourishment remained a burning development agenda in an ever uncertain world. A significant proportion of the world population is suffering from increasing hunger. In the year 2019, more than 820 million people were suffering from hunger (FAO et al., 2019). Its severity increasing over time, 828 million people were hunger in the year 2021, 924 million people were food insecure. Even an expected 670 million people will still be suffering hunger in the 2030 (FAO, 2022). Among 795 million food insecure people in 2015 worldwide, Africa comprises 28.05%, however, Sub-Saharan Africa constitute 95% of food insecure people in the whole Africa (USDA, 2022). Increasing climate change and resulting drought, successive shocks due to COVID-19 pandemic and war between Ukraine and Russia raised food insecure people to 123 million in 2022 (Baptista et al., 2022) take attributes for increased food insecurity problem in SSA.\n\nFood insecurity is a historical human challenge in Ethiopia since 1970s (Devereux, 2000; Kaluski et al, 2001; FAO, 2010). However, food insecurity and malnutrition are still a primary concern of Ethiopia. Currently, an estimated 20.1 million people need humanitarian food support, 7.4 million children and women were undernourished, malnutrition 41 percent of children between 6-59 months undernourished (WFP, 2023). For this, conflict during 2020-2022 in the northern part and associated displacement and historic drought in years 2020-2023 in the south and southeast part of the country has attributed to growing food insecurity (WFP, 2023; FWS NET, 2023). Hunger and malnutrition mainly caused by a combination of conflict and drought. Globally, conflict takes biggest driver of malnutrition where 70% of world hunger and food insecure people are found in areas affected by war and violence like; conflict of Ukraine and Russia, and conflicts in the northern part of Ethiopia (WFP, 2023). Climate change induced shocks (drought) are another important contributor next to conflict that destroy lives (human, crop and livestock), and decline people’s ability to feed them. Global market failure also caused raise to fertilizer price and declined food production and resulted in food price inflation. In Africa, population pressure, diminishing landholding size and farm productivity, limited adoption of technology, recurring droughts, conflict, rising food prices, and epidemics affecting humans and cattle considered as factors that attributed for food insecurity problem in Africa (FAO, 2015; Meskerem and Degefa, 2015). On the other hand, Ethiopia's food insecurity issue is linked to the country's increased reliance on rain-fed agriculture, drought, population pressure, and irregular rainfall (MoARD, 2009). Particularly, southern parts of Ethiopia are also encountering food insecurity in the form of chronic and seasonal forms despite its suitable and diverse agro-ecology. The area is highly exposed to soil erosion due to its mountainous topography. Particularly, the study area Chencha district is highly threatened by different forms of soil erosion (sheet, rill and gully) (CWARDO, 2014). The area is highly vulnerable to long-term seasonal food insecurity that lasts from April to May, and September to November (Tadesse et al., 2019; Abera et al, 2019). Declining landholding size, population pressure, drought, crop disease and pests, livestock and human disease, seasonal fluctuation, and resulting erratic rainfall are major causes of food and livelihood insecurity in the area (Engdawork, 2012; Shambel, 2017). To withstand this challenge, people practice income diversification, cultivating endogenous drought-resistant crops (Enset and Qoltso), weaving, and rural-urban migration (Abera, 2014; Abera et al., 2019). But it lacks empirical studies conducted on the status and determinant factors affecting household capacity to withstand food insecurity shocks and stresses (resilience).\n\nResilience is an important development discourse which has emerged as a novel and quickly expanding development topic in the past few decades (Bahadur et al, 2015; Winderl, 2014). It is defined as the capacity of a system to resist, absorb, accommodate to and recover from the effect of the livelihood shocks and stresses without being incurring irreversible damage on the structure and functions of a system (Olamide Bisi-Amosun & Lafayette, 2019). Resilience is a multidisciplinary concept, but, for the first time the work of Alinovi et al. (2009) has applied the concept in the context of food security analysis. However, its application depends on unit of analysis, type of shock, answering the question of resilience of what and resilience to what (Alinovi et al., 2009). Resilience of households to food insecurity depends on livelihood options available (assets, activities, services) to the household and its ability to manage. Unlike vulnerability, resilience analysis focus on measuring capacity of households to withstand and recover from expected shocks and stresses (Alinovi et al., 2009).\n\nHowever, resilience concept in food security study is newly emerging (Alinovi et al, 2009) and conceptualized as ability of household to maintain certain level of wellbeing (food security) in face of shocks and stresses. Basically, resilience analysis employs two data types; time series longitudinal data (longitudinal dynamics) and cross-sectional data (a static or current time) or a point in time data (Alinovi et al, 2009; Alinovi et al., 2010; Ciani & Romano, 2013; Adane, 2018 and Gebrerufael, 2019). However, analyzing longitudinal dynamics of resilience faces challenges of availability and access of time series data. As a result, very insignificant studies have used longitudinal data for resilience analysis (Alinovi et al., 2010; Mulat and Negussie, 2013). However, majority of resilience studies employ cross-sectional one time data (static data) (Carter et al., 2006; Keil et al., 2008; Adane Atara, 2018; Gebrerufael, 2019; Debebe, 2021). Using four building blocks, Alinovi et al. (2010) found that households' resilience to food insecurity varied among different sub-regions. Another study at Kenya using longitudinal from 2005-06 years data found large-holders are most resilient while pastoralist livelihood groups were found least resilient (Alinovi et al., 2010). While Ciani & Romano (2013) found smallholders and agricultural wage workers were less resilient than other livelihood groups in Nicaragua. The resilience study at Boricha woreda Sidama region found 61% of respondents as non-resilient and inter-livelihood zone variation (Adane Atara, 2018). Whereas Gebrerufael (2019) confirmed that half of the households in Ahferom woreda in the Tigray region were resilient, and the remaining half were non-resilient to food insecurity.\n\nIn a comprehensive evaluation of relevant empirical literature, the majority of studies focused on the ability of agriculture-based livelihood systems. This study, however, concentrated on assessing the resilience capacity of households that employ traditional weaving and spinning as a source of income for their livelihood. Though it is the most well-known alternative livelihood option in the country after agriculture, little research has been done on the benefits of weaving or its drawbacks. In Chencha district, the designated research area, the current study is novel because resilience studies there are the first of their sort. The current study examines the determinant factors of weaving-based households' resilience to food insecurity in the Chencha District using the revised version of the Alinovi (2010) resilience paradigm. Conceptualizing and analyzing household resistance to food insecurity within the context of sustainable livelihood thinking has also been shown to be an interesting approach. It differs from previous empirical research, though, in that it (1) examines how livelihood diversification affects household resilience and (2) concentrates on looking at weaving as a means of enhancing household resilience against food insecurity.\n\n\nMethod\n\nInformed written consent from respondents was obtained in order to conduct the data collection process for interviews, focused groups, and surveys. Ethical approval was granted by the Academic Commission of Addis Ababa University (approval number: 029/01/2023) on October 20, 2023. The Institutional Review Board (IRB) has three members: Amare Bantider (PhD), Adimasu Zerihun (PhD), and Teshome Tafese (PhD).\n\nThe study was conducted in Chencha district aiming to identify the determinants of household resilience to food insecurity shocks. The district is one of the ten woredas found in Gamo zone, Southern Ethiopia. The area is astronomically located between 6° 8’ 55” and 6° 25’ 30” North latitude and between 37° 29’ 57” to 37° 39’ 36” East Longitude with an elevation ranging from 1180 to 2732 meters above sea level. It is located about 521 kilometers South of Addis Ababa, the capital of Ethiopia and 37 kilometers away from Arba Minch, the administrative town of Gamo zone. The area has two agro-ecological zones, Dega (Highland) and Woyne Dega (midland) that account 82% and 18%, respectively. Currently, the district is shared by 33 kebeles and 3 transition towns (Figure 1). The district’s Agriculture and Natural Resource Office reports shown that the area is classified as 65% mountainous, only 13% plane, 5% gorges, and 17% sloppy lands (Essa, 2019). It is bordered by Arba Minch Zuriya woreda in the South and Southeast; Mirab Abaya in the East; the newly separated Kogota district in the North and Dita in the West. The district is one of the densely populated areas of the region with a 144, 918 people on 20,290 hectares of land with a population density of 388 persons per a square kilometer (CSA, 2011). From this, female population account 54.9 % of the population. The area receives bi-modal rainfall in the two production seasons of Tseday (spring) February to April and in the Meher (summer) production seasons in the months of June to September.\n\nSource: Ethiopia Mapping Agency 2007 Shape file.\n\nRain-fed subsistence agriculture is the main means of people livelihood. However, the area faces food shortage of 3-6 months in a year (CWARDO, 2014). This could be attributed to the high population growth, declining landholding size, severe land degradation due to continuous cultivation and steep slope, erratic rainfall, drought, crop disease and pest infestation, food price inflation, and weak market linkage due to road access problem. Due to shortage of grazing land; livestock holding and production pattern was also very minimal and homestead based. As a result, the people in the area are prone to both chronic and seasonal food insecurity. However, people adopt different types of mechanisms to withstand livelihood stress and shock. These include; livelihood diversification (agricultural intensification and out of farm), Enset production, migration, weaving, support from GOs and NGOs. Based on this reason, this study was designed to examine how resilient (withstand, react to, respond to and recover from) the households are to food insecurity causing shocks, and identify determinant factors that affect household resilience to various food insecurity inducing shocks and stresses. Households were used as a target group or unit of analysis who practice weaving as their livelihood income sources.\n\nBoth qualitative and quantitative data were employed in this investigation. To better understand the nature of livelihood conditions, food security, external shocks and pressures, and household resilience to food insecurity, quantitative and qualitative data from primary and secondary sources were acquired. Households, key informants, and focus group discussants were among the primary data sources used. Secondary data were gathered from national statistical reports, annual office reports, published and unpublished documents on livelihood conditions, food security status, food insecurity causing shocks and stresses, coping strategies, and potential sources of household resilience to food insecurity and its determinants in the area.\n\nChencha district is one of the food insecurity stressed areas found in southern Ethiopia in general and Gamo zone in particular. Food insecurity is exacerbated by fragmented and small landholdings, deteriorating soil fertility owing to protracted repeated agriculture, high population density, recurrent drought, irregular rainfall, and other factors. As a result, chronic and seasonal food insecurity is a critical development challenge in the area. However, the area has long been praised for its ability to endure the country's historical food crisis shocks without resulting in life losses (Desalegn, 1996; Abera et al., 2019). However, the causes and key sources of its ability to endure food instability and famine have yet to be empirically supported. In the Chencha district, weaving and spinning considered as the second most important livelihood activity following small-scale agriculture which complement the food and income shortage households encounter due to very low agricultural production. Weaving and spinning are regarded as the second most significant livelihood activity in the area, behind small-scale agriculture, and help to supplement the food and income shortfalls that households face due to low agricultural production. As a result, this study was designed to investigate household resilience to food insecurity, with weaving-based households as a target group assuming weaving as an important livelihood income alternative and household resilience to food insecurity.\n\nThe study used a multistage sampling technique to choose the study district and sample households. In the first stage, the Chencha district was purposefully chosen where weaving is the most prevalent livelihood activity in the zone in particular and the country in general. In the second stage, four kebeles were selected where weaving is dominantly practiced by running scatter plot for all kebeles in terms of the numbers of households involved in weaving activity. In this regard, Doko Danbo, Doko Loosha, Lakana Maldo and Setena Borcha were selected as a sample kebeles. The sample respondents were chosen in the third stage using systematic random sampling techniques. Finally, the sample size of respondents was determined using the following formula proposed by Israel (1992):\n\nWhere,\n\nN = the total population size,\n\nn = the sample size and\n\ne = the level of precision.\n\nIn this study, N = 2485 and e = 0.05 n = 303. Then, the representative sample respondents were identified based on probability proportion to population from four kebeles using systematic random sampling technique per each 8 household interval. The study data were collected in 2022 from 303 sample rural households, 20 in-depth key informants, 6 focus group discussions, and substantiated by field observations and secondary document analysis.\n\nTypes and methods of data collection\n\nThe study used cross-sectional data collection methods that included quantitative and qualitative data collection methods. This study relied on both primary and secondary data, which were quantitative and qualitative in character. As significant data gathering methodologies, household surveys, focused group discussions (FGD), key informant interviews, field observations, and secondary source analysis were used.\n\nKey Informant Interview\n\nBefore conducting household surveys, intensive key informant interviews were employed with food security and early warning officers, health, education, social affairs, and natural resource management officers. Accordingly, 20 in-depth Key Informant Interviews (KII) were held with household heads, kebele leaders, experts in agricultural extension, natural resource management experts, health extension, food security and early warning, water supply, and job creation and enterprise at kebele, woreda, and zone levels. Basically, the issues elaborated include: livelihood income sources in the area; food supply and adequacy; shocks and risks; vulnerability contexts; access to and availability of basic livelihood options and services; and challenges.\n\nHousehold survey\n\nHousehold survey has been conducted using semi-structured questionnaires. It has addressed the demographic, socio-economic, livelihood strategies, food security, household access to assets and basic services, livelihood shocks and stresses, challenges and household resilience sources that affect livelihood conditions of the sample households. The survey process has been managed by using trained enumerators under close follow up of the researchers. The household survey data collection was done on March and April, 2022 G. C from 303 weaving-based households.\n\nFocused Group Discussion (FGD)\n\nSix Focus Group Discussions were held on March 10-20, 2022, to supplement the data acquired from the household survey, two in Doko Danbo and two in Doko Loosha kebeles and one each in Setena Boricha and Lakana Maldo kebeles based on population size. It contains 6-10 people who have extensive knowledge in the area's livelihood conditions and accompanying difficulties. Members of the group discussion comprised elders, women, and teenagers, taking into account the group's diversity and managing the participation of all members. The FGD addressed problems such as livelihood possibilities, constraints, food security conditions, livelihood shocks and stress, and potential sources of household resistance to food insecurity in the area.\n\nField observations\n\nTransect walks were conducted throughout the research locations to observe people's livelihood patterns as well as the current opportunities and difficulties. Secondary data were gathered by analyzing numerous published and unpublished secondary documents. The household survey was conducted by researchers and professional enumerators.\n\nData analysis techniques\n\nData collected through household survey, focus group discussion, key informant interview and secondary document analysis were analyzed using relevant data analysis techniques. The main subject of this study, the household resilience to food insecurity problem majorly addressed with quantitative data collected through household survey. Thus, household resilience is examined through resilience analysis technique following RIMA-II approach (FAO &WHO, 2022). For this end, the data were analyzed by adopting quantitative data analysis model using multivariate analysis model. Among different multivariate analysis techniques, particularly principal component analysis method is applied. Various socio-economic explanatory variables (dummy, categorical and continuous) were used to examine their effects across the categories of household resiliencies (Tables 2, 3 & 4). Chi-square test is used to examine whether there exists meaningful difference among meaningful significant difference exists in various categorical variables across resilience categories of (non-resilient, moderately resilient, resilient and highly resilient categories). On the other hand, the existence of significant mean variation of continuous variables throughout the resilience categories was determined by using one-way ANOVA techniques.\n\nOn the other hand, qualitative data types collected through FGD, KII and field observation were analyzed by narrative inquiry, content analysis and interpretation. However, the detail of quantitative data analysis model was described in the following parts.\n\nTechniques of determining household resilience to food insecurity\n\nHousehold resilience conceptualized as the ability of a household to maintain a certain level of well-being (i.e., being food secure) by withstanding shocks and stresses and reorganizing while undergoing change so as to still retain essentially the same function, structure, and feedback (Alinovi et al., 2009; Daie & Woldtsadik, 2015). It can also be defined as a system's capacity to respond positively to surrounding changes, maintain, or improve function based on available options like assets, activities and services (Frankenberger, T., 2012). Household resilience is a complex system thinking that deals with vulnerability and changes considering households as basic components in a food system (Béné C.et al, 2016). In this regard, households are considered as main decision makers and main adaptive component having continuous interaction with its surrounding environment (Guyu & Muluneh, 2015; Dhraief et al., 2019). Regarding analytical techniques; resilience is a latent variable that cannot be directly observed. Hence, it is determined from covariate effects of hypothesized potential dimensions that are latent variables themselves (Alinovi et al., 2009). Following RIMA-II approach suggested by (FAO &WHO, 2022), household resilience to food insecurity was determined by covariates of eight components. These components include; access to Basic Services (ABS), Agricultural Assets (AA), Agricultural Technology and Practices (ATP), Income and Food Access (IFA), Non-agricultural asset (NA), Adaptive Capacity (AC), Social Safety Nets (SSN), and Stability (S). Final household resilience to food insecurity index was determined following a series of steps.\n\nThese include developing theoretical concept for understanding resilience, identifying and developing relevant variables, standardizing to allow comparison, weighting and aggregating the variables, and using uncertainty metrics to assess the robustness of the variables (Dhraief et al., 2019; FAO &WHO, 2022). The model for household resilience measurement can be expressed mathematically as:\n\nWhere RI is the resilience index, IFA is income and food access, ABS is access to basic services, AA is agricultural asset possession, NA is non-agricultural assets, ATP is agricultural technological and practices adoption, AC is adaptive capacity, SC is social capital, and S refers to household exposure to shocks or stability.\n\nDespite resilience’s multidimensional application and its dynamic nature, there is lack of consensus reached among scholars on how to measure it (Maxwell et al., 2013; Dhraief et al., 2019). It can be measured employing quantitative or qualitative techniques (Nelli, N., 2011). However, the current study used quantitative methods through applying a series of multivariate techniques (principal component analysis and optimal scaling). Optimal scaling is used to transform dummy and categorical data to standard continuous forms for ease of principal component analysis.\n\nTherefore, a two-stage factor analysis technique is used to determine the resilience index. First, an iterated principal component analysis (PCA) method is used to estimate an index for each component independently across a collection of observed variables. The interaction components that were calculated in the first stage are used as covariates in a PCA analysis to create the household resilience index in the second step. The components produced by Bartlett's (1937) scoring technique are then added up to form the resilience index, which is a weighted total. The weights correspond to the percentages of variation that each factor explains, as follows:\n\nWhere RI-Resilience index of the nth household, Wj-is the variance explained by factor j, and Fn is the factor retained based on eigenvalue greater than 1.\n\nThe compatibility of data for PCA analysis and sampling adequacy were checked by Bartlett’s test of Sphericity and Kaiser-Meyer-Olkin (KMO) criteria (Field, 2005). Accordingly, Bartlett’s test of Sphericity should be less than 0.05 (the cutting point), and Kaiser-Meyer-Olkin (KMO) tests of sampling adequacy should be equal to or above the recommended cutting point of 0.5. Resilience index scores range from negative to positive. However, there is a lack of consensus among the resilience literatures on using cutting points (Fikiru, 2016; Gebrerufael, 2019 & Debebe, 2021). In this regard, some categorize households into two; resilient (RI>0.000) and non-resilient (RI<0) (Gebrerufael, 2019; Debebe, 2021); others level them into four groups: non-resilience, moderately resilient, resilient, and highly resilient (Fikiru, 2016; Adane, 2018; Dhraief et al., 2019). This study categorized households into four groups following the suggestions by (Fikiru, 2016; Adane, 2018; Dhraief et al., 2019) namely; (1) non-resilient (RI≤0), (2) moderately resilient (0<RI≤0.50), (3) resilient (0.50<RI≤1.0), and (4) highly resilient (R>1.0). This helps us to make more descriptive comparisons among resilience groups rather than rough categorization into two groups.\n\nDeterminants of Household Resilience to Food Insecurity\n\nHousehold resilience to food insecurity refers to a household's ability to maintain food security despite shocks, stresses, and changes, ensuring its function, structure, identity, and feedback. The options accessible to the household and its capacity to withstand risks determine how resilient it is to food insecurity (Daie & Woldtsadik, 2015). Determinant factors must be identified in order to improve households' resilience to food insecurity. Therefore, it is critical to pinpoint the resilience-determining variables in order to implement programming and policy changes.\n\nHere the resilience level was used as a dependent variable with a negative to positive values. Based on the experiences of previous studies (Fikiru, 2016; Adane, 2019), the households were classified into four classes of resilience namely; Non-resilient (RI≤0.00), moderately resilient (0.00<RI≤0.50), resilient (0.50<RI≤1.00), and highly-resilient (RI>1.00). Since, the dependent variable has more than two outcomes, in our case four ordered outcomes. In this case, ordered probit regression model was most commonly recommended technique used with ordered classifications. Then, the differences across these categories can be affected by different explanatory variables at different levels. And the model was specified as follows;\n\nY = 1 if Y≤0\n\nY = 2 if 0<Y ≤0.50\n\nY = 3 if 0.50<Y* ≤ 1.0\n\nY = 4 if y>1.00\n\nWhere Y refers to the level of household resilience to food insecurity with an ordered outcomes of Y1 = Non-resilient, Y2=moderately resilient, Y3 = Resilient and Y4 = highly resilient. The Xij are the explanatory variables that are hypothesized to determine the household resilience status. The explanatory variables used in this model consist of dummy, categorical and continuous forms in their nature. And, β represents the parameters estimated and Uij is the disturbance term.\n\nBefore running the data analysis, the existence of bad correlation (multi-Collinearity) among potential explanatory variables should be tested using Variance Inflation Factor (VIF) for continuous variables and Contingency coefficient values for discrete variables. For acceptable multi-Collinearity test result, VIF should be less than 10. Similarly, in the case of discrete variables contingency coefficient value should be less than 0.75. The model fitness was also checked by using model fitting information (Nagelkerke pseudo R-square≥0.5 and significance of two log-likelihood chi-square). These confirm the existence of no strong association. The dependent and independent variables used in this model are described as follows.\n\nDefinition of variables and hypotheses\n\nFollowing the clear discussion of analytical techniques used for investigating the determinants of household resilience status, it is imperative to describe the dependent variable and the potential explanatory variables used in the model. For this end, the identification of the dependent variable and its potential explanatory variables was done based on previous literature and the authors’ experiences regarding resilience analysis. The descriptions of dependent and explanatory variables are shown in Table 1 below.\n\n\nResults and Discussion\n\nAs can be depicted in the Table 2 below, chi-square test is used to examine the statistical differences between household resilience across different socio-economic variables (dummy and categorical). Accordingly, the existence of statistical difference in terms of livelihood diversification categories was examined. In this regard, among non-diversified households only 15.9% were resilient to food insecurity at different levels. While 84.09% of the non-diversified (specialized at one livelihood option) households are non-resilient to food insecurity shocks. While about 58.42% of highly diversified households were found to be resilient to food insecurity at different levels. This may be explained by the fact that better household resilience to food insecurity requires greater household income diversification, and that there are significant differences in household diversification status among resilience categories (p = 0.000).\n\nA chi-square test is performed to determine whether household food consumption scores (FCS) vary throughout household resilience categories. According to the findings, 87.5% of poor (food-insecure) households are not resilient to food insecurity. About 46.93% of acceptable (food-secure) households were resilient to food insecurity to varying degrees. The results showed that there are significant differences in household food consumption scores between the categories of household resilience (p = 0.001). In similar ways, there is a significant difference across resilience categories in terms of livelihood strategy combinations (p = 0.000). More than 50% of households that combined on-farm, off-farm, and non-farm livelihood activities were resilient to food insecurity at different levels. Thus, adoption of diversified combination of livelihood activity is suggested for attaining more resilient livelihood.\n\nAs can be observed from Table 3, the chi-square test is used if there are meaningful differences across household resilience levels in terms of various dummy variables. The result revealed the existence of a significant and meaningful difference across household resilience in terms of access to basic services like education, credit, FTC, and utilizing Development Agent (DA) services in the area. For instance, in terms of access to education, a relatively large proportion of non-resilient households have no education at all compared to their resilient counterparts. In the cases of access to credit, only 15.18% of the total respondents have access to credit in different sizes and forms. However, the majority 65.2% of credit users were among the resilient categories of respondents. In a similar manner, there is less access to FTC and DA service utilization among non-resilient households than among the resilient categories of respondent households. Accordingly, only 3.96% and 5.61% non-resilient households have access to FTC and DA services, respectively. The differences across resilience categories are significant at p = 1%.\n\n* Significant at 1% and\n\n significant at 5%.\n\nIn general, the chi-square test result shown that there is a significant differences among the resilience categories of households in respect to access to education, household head ability to read/write or not, access to credit, utilization of FTC services and DA services, access to mobile, livelihood diversification status, access to government salary/wage, food consumption scores, livelihood diversification choices, on-farm participation and off-farm participation, availability of physical disability and ill members in the family, access to financial transfers in kind/cash, membership in Edir, whether the community was supportive or not in the cases of illness, and crop failure due to drought at probability of p<1 and p < 0.05 (Table 4).\n\n* Stands for significant at less than 1% and\n\n significant at less than 5%.\n\nA one-way ANOVA was employed to examine mean differences of various socio-economic characteristics of households. With regard to years of formal education, non-resilient households (m = 4.425) have relatively lower mean years of schooling than moderately resilient (m = 6.289), resilient (m =7.970), and highly resilient (m = 9.73) households. And, the difference is statistically significant at p = 0.000. Similarly, households with relatively higher mean family size, household productive labour, land holding size, non-food expenditure, agricultural expense, food expense, weaving income, total household income, and food consumption score have relatively higher household resilience attainment and the differences were significant at 1% and 5% (Table 4).\n\nIn addition to this, the post-hoc test is carried out to investigate if there are individual differences between groups. Accordingly, there exists group differences among non-resilient, moderately resilient, resilient and highly resilient groups in terms of years of household head years of formal education, total family size, number of working groups (Productive labour size), landholding size, annual non-food expenditure, annual agricultural expenditure, annual food expenditure, total livestock holding, weaving income, total household income from different sources, household diversification scores, food security status (using Food Consumption Score), and dependency ratio at probability of 5% and 1% levels. This result is in line with the study of Fikiru (2016) and Debebe (2021).\n\nThe ordered probit model was used to detect the determinants of household resilience to food insecurity. Here, the main focus is on carrying out the data analysis and identifying explanatory factors (continuous and discrete) that affect household resilience to food insecurity. Before running the data analysis, the existence of bad correlation (multi-Collinearity) among potential explanatory variables was tested using the variance inflation factor (VIF) and contingency coefficient values for continuous and discrete variables, respectively. Then, the test result revealed that there is no strong correlation among independent variables as shown in the Extended data (Dereje et al., 2024). Accordingly, the VIF values for all continuous variables were found to be small (i.e., VIF<10), with a mean value of 1.60744, which is far beyond the cutting threshold value of 10. In the same way, the multi-Collinearity test result for discrete explanatory variables revealed a contingency coefficient value of less than 0.75, which confirmed the existence of no strong association (see Extended data (Dereje et al., 2024)).\n\nAs shown in the previous sections, the existence of a statistically significant relationship between the status of household resilience to food insecurity and the potential explanatory variables was tested using chi-square and one-way ANOVA tests. Thus, these variables were used for ordered probit analysis using a 95% confidence interval (CI) or p<0.05 value. The model fitting information shows that it has high predictive power with a Nagelkerke pseudo-R-square value of 0.877, which indicates the model fits the data well with 87.7% of the dependent variable (household resilience to food insecurity) being determined by the independent variables. Besides, the difference between the two log-likelihoods, the chi-square has shown a significance level of less than 0.001. The parameter test results are shown in Table 5 below.\n\nBased on the probit model result, the following explanatory variables, which have significantly influenced the status of household resilience to food insecurity, are briefly interpreted. Accordingly, some explanatory variables were found to positively and significantly influence the likelihood of attaining from lower to higher household resilience to food insecurity (Table 5).\n\nAccess to credit services: access to credit services is an important engine to combat poverty and food insecurity through buying agricultural inputs for the purpose of agricultural intensification and livelihood diversification. However, households fear the high interest rates, and it needs pre-conditions like savings and collateral to get the loan. Despite the availability of some credit and saving institutions like Omo Microfinance and Vision Fund Micro-finance institutions; households in the area were not interested in getting the services. Besides this, the result indicated that access to credit has a positive influence on the resilience to food insecurity p<0.01. This implies that a unit increase in credit use increases the probability of a household falling into the higher category of resilience by 0.215 units more when other factors are kept constant. The odds ratio result shows that the probability of a household falling into the higher resilience level is 1.2398619 times greater for increased access to credit in comparison to low credit utilization. Therefore, this study suggests increasing access to credit for smallholder farmers to increase options, production and improve household resilience. This result is incongruent with Fikiru (2016) and Tesso et al. (2012).\n\nAccess to local market: Access to markets was expected to have a positive influence on household resilience to food insecurity by enabling ease of access to necessary agricultural inputs, food items, and agricultural products. However, the result confirmed that distance from the local market increased the probability of households attaining higher household resilience to food insecurity by 0.601 at p<0.01. This could be explained as the closer the household is to the market area, the less likely they are to participate in diverse agricultural production activities, resulting in decreased household resilience to food insecurity due to limited access to farmland. However, this result is in contrast with Debebe C. (2021).\n\nAccess to education (Average years of family schooling): education is one of the key factors in building household capacity to cope with shocks and stresses that could enhance individuals’ capacity to plan access, and utilize agricultural extension information, manage livelihood shocks, make better decisions on livelihood options, and more. The model result indicated that average educational attainment of the household positively and significantly affected resilience level at a 10% significant level. A positive sign with a household education coefficient of 0.054 would mean that with increasing education, there is a greater probability of falling into the higher resilience level. Regarding the odds ratio, the odds of improved resilience are 1.0554846 times greater for increased household education attainment than those with low educational status. This result is similar to the study conducted on the analysis of vulnerability and resilience to climate-induced shocks in North Shewa, Ethiopia (Tesso et al., 2012). Thus, the study advocates access to quality education considering intra-household equity.\n\nCrop diversity: Cultivating several crop species enables households to cope with the effects of both price and production risks, which can help them, ensure they have more food options and income alternatives. As a result, the sample households have grown a mean of 5.08 and a maximum of 11 types of crop species. The model result shows that a number of crop species cultivated in the area have positively and significantly affected household resilience, with a coefficient of 0.142 at p<0.05. Households with high crop diversity are more likely to fulfill improved dietary diversity and thereby attain a higher resilience level, with 1.19005557 times more than those with a low crop diversity level. In agreement with this result, the study conducted in Malawi reported positive contribution of crop diversification to the food consumption status of households (Mango et al., 2018; Adjimoti & Kwadzo, 2018).\n\nDiversity of income sources: Following diverse income sources is expected to have several livelihood implications, like enhancing household income sources, means of risk management, improving household wellbeing, and more. In this study, the number of income sources adopted by households has a positive influence on household resilience to food insecurity, with a coefficient of 0.174 at a significant level of p<0.01. This implies that households with diverse income sources will have a higher likelihood of falling into a higher resilience level at an odds ratio of 1.19005557 times greater than those with few income sources. This result is in agreement with Fikiru (2016).\n\nExpected crop harvest in cash (ETB): Resilience is about the capacity of an individual, a household, a community, or a subject to withstand the effect of a foreseen shock or the ability to recover from past shocks and stress using available and potential sources of capability. The model result shows that the expected crop harvest in monetary value has positively influenced household resilience with a coefficient of 0.00002802 at p<0.05. The odds ratio of falling to a higher resilience level is 1.0000280 times higher in cases of an increased expected crop harvest than a low expected crop harvest.\n\nExpected cash from fruit trees (ETB): Fruit production is an important cash crop in the study area and serves as a source of income to build household resilience. Study reports show that there are more than 60 varieties of apple fruit trees grown in the area, which serve as a basic income source in the form of seedlings and fruit products (Fetene et al., 2014). Apple fruit products reach during food deficit seasons of March, April, and May, which become food security buffering options. The probit result indicated that the amount of expected fruit income has a positive influence on household resilience and increases the likelihood of falling into higher resilience levels at P<0.05. The study report revealed that about 21.12 percent of respondents had incomes from apple fruit grown in their backyard. The FGD and KII results indicated the suitability of the area for apple cultivation and its high income-generating capacity, but theft due to its high economic value was stressed as the main threat.\n\nAccess to Development Agent contact (DA contact): Access to development agent contact has a positive influence on household resilience to food insecurity by providing agricultural production information. Households with a higher frequency of DA contact are more likely to fall into the higher category of resilience at p<0.05. Keeping other factors constant, a unit increase in access to DA contact will increase the probability of households being at a higher resilience level by 0.136 units. This, in turn, improves household resilience to food insecurity.\n\nFood Consumption Score (FCS): As expected, food consumption status in the form of FCS has a positive association with household resilience to food insecurity at p<0.05. This positive influence refers to the fact that the higher the food consumption status of the household, the greater its capacity to withstand food insecurity-related shocks. The model result indicated that a unit increase in FCS increases the likelihood of the household falling into the higher resilience category by 0.011 units, considering other factors constant.\n\nAccess to non-agricultural assets: In rural areas, ownership of non-agricultural assets is a sign of wealth status and is considered a means of livelihood risk management (Abbassi et al., 2020). As expected, the model result shows that access to and ownership of physical assets like jewelry, radios, and furnished beds are positively associated with household resilience to food insecurity at probability of less than 0.05, 0.05, and 0.01. A household with increased ownership of the physical assets is more likely to fall into the better resilience category than its counterparts.\n\nAccess to formal employment: Access to formal employment (government or non-government employment) is one of the major non-farm income sources adopted in the area, having the highest average income that accounting for more than 18 percent of the total household income of the respondents. Ceteris paribus, as expected, the probability of a household falling into the higher resilience level decreases by 0.644 units if the household has no access to formal employment at p<0.1.\n\nAccess to transfers payment (Dummy): Access to transfers in different forms, formal or informal, in-kind or in-cash, is considered one of the major sources of social safety nets. These include; donor agencies based support services (PSNP), aid, and remittances. Thus, the probit result indicated that lack of access to cash transfers decreases the likelihood of achieving higher resilience level by 2.154 units if other things kept constant at p<0.01. Hence, transfers help households in cases of food deficit seasons and help create assets, thereby enhancing household resilience to food insecurity.\n\nParticipation in family business activities: practicing non-farm livelihood diversification is believed to contribute to improved household food security and, in turn, strengthen household resilience to food insecurity. In the rural areas of Gamo zone in general and Chencha district in particular, weaving, trade, small-scale food item enterprises, hairdressers, and barber services were reported as the major out-of-farm business activities. Considering other things being constant household ability to attain higher resilience level decreases by 0.690 if the household has not participated in out-of-farm business activity p<0.05. Therefore, this study suggests creating a conducive environment for youth and able groups to enter into rural business activities is inevitable to create job opportunities for others, improve income, and thereby increase their resilience to food insecurity (Fikiru, 2016).\n\n\nConclusion and Recommendation\n\nThis work has aimed to examine the factors that determine household resilience status across different categories and understand the dynamics of household resilience across differing socio-economic characteristics. Hence, the result confirmed the proposed notion that household resilience depends on the resources and livelihood options available and the effects of external shocks and stresses. A thorough analysis of household resilience status has categorized households into four categories: non-resilient, moderately resilient, resilient, and highly resilient. Broadly, the study results show that the majority, about 59.76% of the households were non-resilient to the expected food insecurity shocks and stresses; the remaining 40.24% of the respondent households were found to be resilient at different levels.\n\nA close examination of household resilience across different socio-economic and demographic characteristics of households using a chi-square test indicated significant differences. As a result, there is a significant and meaningful difference across household resilience categories in terms of access to education, credit use, access to FTC and DA services, livelihood diversification categories, food consumption score categories, livelihood diversification choices like; participation in on-farm, off-farm, and non-farm options, access to mobile use, household head ability to read and write, disable household member availability, access to formal employment, access to transfers and assists, Edir membership, and whether encountered crop failure due to drought or not at 5% and 1% significant levels. The one-way ANOVA result revealed that there is a meaningful difference among household resilience categories in terms of years of education, total family size, productive labor, landholding size, annual non-food expense, annual agricultural expense, food expense, total livestock holding, weaving total income, total household income, and dependency ratio at less than 1%, 5%, and 10% significance levels.\n\nThe probit model confirmed that access to credit, average years of family education, diversity of crop types grown, number of income sources adopted, land holding size, livestock holding size, expected crop harvest, expected cash income from fruit trees, frequency of DA contact, FCS, annual food expenditure, radio ownership, jewelry ownership, ownership of a modern furnished bed, membership in local associations, and distance to a nearby local market have positively influenced the likelihood of attaining higher household resilience at 1%, 5%, and 10% significant levels. Whereas, lack of access to a mobile phone, inability of the household head to read or write, lack of family business, lack of formal employment, and lack of access to transfers of payment in the form of remittances and support have decreased the likelihood of households achieving a higher resilience level at 1%, 5%, and 10% significance levels.\n\nBased on the result of household resilience to food insecurity using one-time cross-sectional data, it has pinpointed areas and factors to be stressed by concerned bodies to initiate, improve, and build household resilience to food insecurity. Accordingly, improving household resilience in the study area requires investing and improving access to available options and alternatives such as agricultural assets, non-agricultural assets, adaptive capacities, basic services, agricultural technologies and practices, social safety nets, and income and food access. Particularly, improved access to credit, education, livelihood diversification options, creating opportunities to get assets like land and livestock, and improved agricultural extension services will have a potentially positive impact on building household resilience in the area. Therefore, concerned bodies need to improve households’ access to basic livelihood assets, livelihood options, and services to enhance household capacity to withstand food insecurity-inducing shocks and stresses.", "appendix": "Data availability\n\nFigshare: Livelihood Diversifications, Food Security, and Household Resilience to Food Insecurity: the case of Weaving-Based Livelihood System in Chencha District, Southern Ethiopia, https://doi.org/10.6084/m9.figshare.25975252.v1 (Dereje et al., 2024).\n\nThis project contains the following underlying data:\n\n• Access to Agricultural assets (AA).csv\n\n• Access to Agricultural Assets (AA).dta\n\n• Access to Basic services (ABS).csv\n\n• Access to Basic Services (ABS).dta\n\n• Adaptive Capacity (AC).csv\n\n• Adaptive Capacity (AC).dta\n\n• Agricultural Technology and Practices (ATP).csv\n\n• Agricultural Technology and Practices (ATP).dta\n\n• Income and Food Access (IFA).dta\n\n• Income and Food Access (IFA).xlsx\n\n• Livelihood Diversity and Demographic data.sav\n\n• Non-agricultural Asset (NNA).csv\n\n• Non-agricultural Asset (NNA).dta\n\n• Social Safety Net or Social Capital (SSN).csv\n\n• Social Safety Net or Social Capital (SSN).dta\n\n• Stability (S).dta\n\n• Stability (S).xlsx\n\nFigshare: Livelihood Diversifications, Food Security, and Household Resilience to Food Insecurity: the case of Weaving-Based Livelihood System in Chencha District, Southern Ethiopia, https://doi.org/10.6084/m9.figshare.25975252.v1 (Dereje et al., 2024).\n\nThis project contains the following extended data:\n\n• Household Survey Questionnaires, Focus Group Discussion and Key Informant Interview Results.docx\n\n• Supplementary Information- VIF and CC.docx.\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\n\nAcknowledgements\n\nWe authors are very grateful to the College of Development Studies at Addis Ababa University for ethical clearance and necessary support. 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Reference Source\n\nTadesse Y, Conny JMA, Schulte RPO, et al.: Potatoes and livelihoods in Chencha, southern Ethiopia. NJAS: Wageningen Journal of Life Sciences. 2019; 88(1): 105–111. Publisher Full Text\n\nTesso G, Emana B, Ketema M: Analysis of vulnerability and resilience to climate change induced shocks in North Shewa, Ethiopia.2012; 3(6): 871–888.\n\nUSDA: Economic Research Service. United States Department of Agriculture; 2022.\n\nWFP: WFP Ethiopia Country Brief. WFP; 2023.\n\nWinderl T: Disaster Resilience Measurements: Stocktaking of ongoing efforts in developing systems for measuring resilience.United Nations Development Programme (UNDP). 2014. Reference Source" }	[ { "id": "296749", "date": "06 Aug 2024", "name": "Kibrom Adino Abate", "expertise": [ "Reviewer Expertise PhD in Development studies (Rural 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\nI have tried to review the details of this manuscript. I found this paper can be indexed and contribute its role in the areas of resilience to food insecurity in the context of rural areas.\n\nMy comments - - In the introduction section much has been said about food security and undernutrition. Instead the authors need to give details about resilience contexts. - The theoretical ground of the study shall be indicated in the background and also should be connected with the conclusion section. - How this research is different from the previous studies shall be discussed boldly to demonstrate its uniqueness from previous resilience related studies. - On the methodological section, there shall be evidence for the use of PCA over MCA. In this regard, empirical works must be also included. - In the discussion part, each result demands triangulation with previous empirical works. - it also requires language editing by professionals\nDecision: - The manuscript deserves publication with the consideration of comments given to the manuscript.\nPlease also refer to the reviewed article document and comments here - https://f1000research.s3.amazonaws.com/linked/668134.Reviewed_Document.pdf\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] } ]	1	https://f1000research.com/articles/13-693
https://f1000research.com/articles/13-692/v1	26 Jun 24	{ "type": "Research Article", "title": "Digital Transformation and Its Relationship to the Job Performance of Employees at a Private University in Peru", "authors": [ "Arias Gonzales Hilda Paola", "Rogger Orlando Morán Santamaría", "Nikolays Pedro Lizana Guevara", "Morales Salazar Pedro Otoniel", "Salazar López Yasser Jackson", "Yefferson Llonto Caicedo", "Francisco Eduardo Cúneo Fernández", "Percy Junior Castro Mejía", "Milagros Judith Pérez Pérez", "Arias Gonzales Hilda Paola", "Nikolays Pedro Lizana Guevara", "Morales Salazar Pedro Otoniel", "Salazar López Yasser Jackson", "Yefferson Llonto Caicedo", "Francisco Eduardo Cúneo Fernández", "Percy Junior Castro Mejía", "Milagros Judith Pérez Pérez" ], "abstract": "Background Private universities in Peru still need to implement digital transformation models to enhance the job performance of faculty and staff, achieving consistent improvement in the performance levels of university teachers by deploying technological and didactic tools for students. Therefore, the study aims to determine the relationship between digital transformation and the job performance of employees at a Private University.\n\nMethods The research approach was quantitative, employing a non-experimental, longitudinal correlational design. The technique used was a survey, applied to a sample of 104 employees (school heads, faculty, and a director) from the university on a national level from a total population of 144.\n\nResults Descriptive results reveal that the university has regularly adopted tools related to digital transformation. In particular, it has efficiently employed agile technologies, Big Data, and various technological means, benefiting 90% (52% and 38%) of the staff. The study also showed a high positive correlation (0.92>0.7) between digital transformation and the job performance of staff at the Private University, confirming that there is a significant connection between the variables studied.\n\nConclusions Therefore, creating an innovative culture across all hierarchical levels and identifying key technologies that add value to the learning flow can meet the needs of an increasingly demanding society.", "keywords": [ "digital transformation", "job performance", "virtual education", "digital tools", "educational quality." ], "content": "Introduction\n\nCurrently, a high percentage of companies have perceived the need to create innovative models due to the COVID-19 pandemic, with the intent to add value to the end consumer and ensure business continuity (Marchesani et al., 2023; Acciarini et al., 2023). Consequently, the educational sector cannot escape this transformation, as it is a highly attractive sector that needs to be at the forefront of tools and digital channels to compete and offer professional profiles that meet the demands of the job market and successfully ensure their integration; at this stage of the study, the goal is for teachers to utilize technology and educational applications to enhance attention and teaching improvement (Kang & Park, 2023; Valdés & Gutiérrez, 2023; Chigbu et al., 2023).\n\nAn innovative business model allows for the adoption of technology to efficiently offer products or services, optimizing costs and time, making it more sustainable and responsive in the long term to challenges posed by external forces (Rojas et al., 2024; Afawubo & Noglo, 2022). Under this context, the business environment has drastically transformed, leading to the adoption of agile technologies that enable the continued competitive performance within the sector (Shahiduzzaman & Kowalkiewicz, 2018).\n\nDigital transformation in Peru is an ongoing process of cultural change supported by the intensive use of digital technologies, systematization, and data analysis to generate economic, social, and value impacts for individuals (Aurazo & Vega, 2021; Gupta et al., 2020). It is important to note that the Secretary of Government and Digital Transformation of the Presidency of the Council of Ministers (PCM) leads the coordination, implementation, and evaluation of the National Digital Transformation Policy, as well as its strategies, policies, plans, regulations, directives, projects, and corresponding platforms (Single Digital Platform of the Peruvian State, 2023). Therefore, private companies are acting in relation to the four main key aspects: strategy, customer interaction, business model transformation, and digital talent acquisition; on the other hand, in the public sector, the lack of organizational continuity prevents coordinated action in these areas (ESAN, 2022; BID, 2023).\n\nOn the other hand, universities are a main part of economic development globally, which is why many Latin American countries have adopted virtual reality as a key element to foster innovation and provide educational quality accessible to all, achieving social inclusion in the process (Maliqueo et al., 2021). According to UNESCO (2018), the job performance of teachers forms a solid and influential part of the journey to quality education. Thus, adopting digital transformation facilitates a quick response to the constant ups and downs posed by the market; however, it requires a review and change in the company culture, its operations, and a shift to agile technologies with the aim to replace and improve existing resources (Delgado, 2020).\n\nIt is important to note that the application of digital tools must be managed by specialists, as such technological products must serve a specific purpose and not be adopted merely for appearing innovative (Bindra, 2018). For this reason, companies view technology as a tool that encourages the creation of current models (Mamabu, 2017) and allows facing challenges posed by the market (Valderrama, 2019). In this regard, education will have a better response if implemented correctly in the digitalization processes, thereby improving productivity (Musaxonovna, 2022). At this point, Nwaiwu (2018) stated that education should not be limited to a physical space but rather promote the breakdown of barriers, giving teachers and students new roles in which they can interact virtually effectively and securely. For Ledahawsky (2022), digital transformation is a business opportunity as it allows the development of a technological vision in companies.\n\nWith this in mind, there is a need to categorize digital transformation as a process that must be prioritized in all organizations and not as an option for using digital tools. Likewise, the search for innovative business models that make a difference from conventional industries is evident (Bindra, 2018; Amarista, 2005). With this, it is evident that a large number of companies around the world use digital transformation as a means to be categorized as “digital companies,” hence the importance of adopting technology at all business levels.\n\nAs revealed, the research seeks to optimize the proper job performance of teachers, as they are the direct channel with the end consumers, who at this point are the students, through the use of digital transformation, thus ensuring the improvement of economic and social conditions. In this way, it seeks to reduce the gaps of inequality in quality education nationwide. For this reason, the general objective is to determine the relationship between digital transformation and the job performance of employees at a Private University.\n\n\nTheoretical framework\n\nTo deepen the foundation of the literature review for this study, a review of scientific articles was conducted based on two relevant areas: a) digital transformation and b) job performance. Initially, international scientific articles were considered; Nunes & Malagri (2023) provided a documentary review in Brazil, setting key parameters for student development in a modern and changing society. Following this, Bazzo et al. (2022) through their correlational study with a qualitative focus involving 104 participants highlighted the lack of digital tools and the poor performance of teachers, illustrating the impact of technology on teachers' job performance. Furthermore, Granda & Bermeo (2022) in their empirical and analytical study emphasized the importance of mindset change in organizational culture to adapt technologies in business process management. Townsend & Figueroa (2022) in their correlational-inductive article evaluated the quality of digital transformation on methods and labor productivity. De Matos et al. (2020), in their exploratory-qualitative study of 68 teachers at a Brazilian university, demonstrated that education in Brazil requires technologies for better student performance. Similarly, Cuenca et al. (2020) in their correlational study conducted at seven educational institutions in Spain showed that digital transformation is influenced by organizational climate, leadership, and employee profiles.\n\nNationally, Huamán & Medina (2022) in their correlational descriptive study showed that closing gaps in communication and response are inherent to the use of digital transformation. Collantes & Collantes (2022), in their correlational study involving 70 employees from the government sector, found a direct relationship between public policies and the use of digital transformation tools. Laurente (2021) in his documentary review of 54 technology sector companies demonstrated that digital transformation improves productive processes and fosters a culture based on technology and innovation. Moreover, Tippe & Soto (2021) in their hermeneutic-heuristic method study with 50 teachers from an institution argued that the government has the task of closing inequality gaps so that through internet access and various technologies, a quality education accessible to all Peruvians can be achieved. Guzmán et al. (2020), in their explanatory-deductive study at four Peruvian educational institutions, demonstrated the implications of digital transformation on customer-oriented attention and the performance of assigned tasks. Lastly, Ramirez & López (2018) highlighted the importance of converting traditional educational enterprises into purely virtual ones, stating that in the long term, this promotes better teaching performance and better response to market demands.\n\nRegarding the study variables, we have\n\nA) Digital Transformation\n\nRegarding the theoretical bases, we define digital transformation as the digital capability applied to internal processes to increase efficiency. Regarding the theoretical foundations of digital transformation, according to Matt et al. (2015), the term digital transformation evolves from the concept of “digitization,” that is, processes that support business transformation. Ramirez & López (2018) stated that digital transformation “is a model that focuses on the digital approach as a strategy that identifies the value proposition of the organization, considering having elements to innovate and respond to market demands and analyses. Ultimately, it seeks to concentrate a correct operational structure in order to achieve and maintain excellent processes.” (p.12). For Cueva (2020), the term digital transformation refers to all digital technology adopted by organizations to improve the performance and capabilities of the employees; Alonso (2017) described it as the induction of all technology for the improvement of internal processes in companies.\n\nB) Job Performance\n\nAccording to theories related to the variable of job performance, these are based on a procedure that evaluates, measures, and influences human behavior, generating attributes and outcomes related to work. Regarding the foundational theories of job performance, according to Klehe & Anderson (2007), this theory involves the specific ability required by the position, the level of effort required and demonstrated, and the proper application of discipline and moral values (avoiding counterproductive behaviors), ultimately these core aspects could apply to any position. Additionally, according to the adaptive performance theory, performance has defined the quality of work performed by employees within a company. Mamani & Cáceres (2019) suggested that job performance is about achieving objectives through strategies accompanied by patterns of behavior, competencies, and skills of the workers; Bellot (2011) indicated that it is important to measure job performance as it provides greater competitiveness and productivity among employees. Thus, it is defined as any skill or ability of the worker that leads to an efficient outcome.\n\n\nMethods\n\nThe methodology of the article was developed under a methodological process called “Quantitative Approach,” as it involved statistical analysis of the selected sample from the study object. Furthermore, the research scope is of an applied, quantitative, correlational, and non-experimental type (Maxwell & Reybold, 2015; Aarsman et al., 2024). Non-experimental, as the behavior of both variables was not altered; in other words, only the variables were observed under a natural context. Correlational scope, because the purpose of the research was to find relationships between the variables in question.\n\nThe population consisted of 144 employees, with a sample size of 104 employees (Otzen & Manterola, 2017; Stratton, 2021), including managers, directors, and teachers from the Professional Business School at the following campuses: Lima Este, Lima Norte, Chiclayo, Trujillo, Ate, Callao, and Piura. Below is the distribution of the sample across branches:\n\nFor sample selection, various eligibility criteria were employed. Inclusion criteria included employees with more than 6 months of tenure in the organization and employees with subordinates. Additionally, employees of both genders, regardless of age, were considered. Finally, exclusion criteria did not include employees whose tenure in the organization is less than 6 months (new hires), thus ensuring a more homogeneous learning curve for the activities.\n\nAccording to the research design, it follows rational or logical and systematic steps, which facilitated the resolution of the research problem. The most important steps of the research included the following points: conception of the idea, problem statement, research design, sample selection, data collection, data analysis, data interpretation, and discussion of results.\n\nIt is important to note that the technique applied, considering the dimensions and indicators of the study, is the survey, which was developed through a questionnaire. Regarding the Digital Transformation variable, 32 questions were considered (with 5 options structured on a Likert scale), while for the Work Performance variable, 26 questions were considered (also with 5 options structured on a Likert scale). It is worth mentioning that the survey was administered to the sample, and interviews were conducted with school heads for greater accuracy in the results (Story & Tait, 2019; Vaske, 2019).\n\nThe validity of the survey instrument was established through the informed opinion of individuals with extensive experience and legitimacy to provide information, testing, and judgment. Additionally, the reliability of the instrument was assessed through the Cronbach's Alpha coefficient, where the questionnaire for digital transformation obtained a score of 0.973 and for work performance, 0.976, both considered highly reliable (Kimberlin & Winterstein, 2008; Wyse et al., 2016).\n\nData analysis was conducted using IBM SPSS Statistics 26 software. This has allowed for efficient descriptive results of each variable, enabling the testing of hypotheses proposed in the research. In the results obtained from the “Normality Test,” the Kolmogorov-Smirnov test was employed, as the sample size exceeded 104 participants. The non-parametric Spearman's Rho correlation coefficient was also used, as the significance level is considered less than 0.05 (Bryman, & Cramer, 2011; Pallant, 2020; Saiyidi & Hadrian, 2024).\n\nDuring the research process, the participation of the 104 selected participants was obtained, who provided authorization and consent to obtain timely information for the development of the research. Considering the general principles governing ethics in scientific research, including intellectual honesty, truthfulness, transparency, human integrity, respect for intellectual property, justice, and responsibility, the study aims to comply with “The Code of Ethics in Research of César Vallejo University, version 01; through University Council Resolution No. 0340-2021-UCV”.\n\n\nResults\n\nThe study aimed to determine the relationship between digital transformation and the job performance of employees at a University. A quantitative study was conducted based on the survey data; according to the digital transformation variable, the following was observed:\n\nAccording to Table 2, the percentage of the independent variable and its dimensions regarding satisfaction levels related to processes, organizational culture, strategic vision, and business model are as follows: for the digital transformation variable, 38% good level, 45% regular level, and 16% poor level. For the process dimension, 29% good, 49% regular, and 22% poor. For the organizational culture dimension, 33% good, 52% regular, and 15% poor. For the strategic vision dimension, 33% good, 50% regular, and 17% poor. Lastly, for the business model dimension, 50% good, 27% regular, and 23% poor. Teachers believe that the university is not investing correctly in agile technologies for better performance, as the use of technology would offer better and correct decision-making and a flexible response to external events. Furthermore, it is evident that the digital channels and tools being applied by the university are not significantly impacting educational management, necessitating improvements and providing tools that change or modify the current business model and foster a culture of innovation.\n\nNote: Prepared based on questionnaire data. R2 is the coefficient of determination.\n\nIn Table 3, the percentage of the dependent variable and its dimensions regarding satisfaction levels related to the influence of personality, productivity, learning, and perception are: for the job performance variable, 62% good level, 33% regular level, and 6% poor level. For the personality dimension, 44% good, 33% regular, and 23% poor. For the productivity dimension, 50% good, 13% regular, and 37% poor. For the learning dimension, 57% good, 43% regular, and 0% poor. Finally, for the perception dimension, 50% good, 20% regular, and 30% poor. It is evident that the university does not influence the motivation of teachers, and the existence of job pressure generates stress events, thereby reducing performance. Teachers also consider the task demands excessive relative to their available time, adding to the authoritarianism of school heads. However, it was also found that teachers possess the necessary skills and competencies to meet demands, provided the weaknesses are addressed.\n\nThe hypothesis testing was performed using Pearson's correlation, which, as shown in Table 5, indicates a significant relationship between the study variables, as the observed significance level (bilateral sig.) is 0.001; being less than 0.05, the alternative hypothesis is rejected.\n\nAs per Table 4, the Kolmogorov-Smirnov test for normality is conducted as the sample size exceeds 50, aiming to observe the behavior of the variables and their distribution, concluding at this point that the distribution is not normal. Subsequently, it was analyzed whether there is a correlation between the components, through a scatter plot with Job Performance on the ordinate axis and Digital Transformation on the abscissa axis, as illustrated below.\n\nA higher level of digital transformation corresponds to better job performance, interpreting that the behavior of digital transformation explains 89% of the behavior of job performance; in its linear regression equation, there is a 79% likelihood that a higher propensity for digital transformation (variable x) generates better job performance (variable y). Therefore, Spearman's Rho needs to be calculated, as the study variables are ordinal (see Table 5 and Figure 1).\n\n* The correlation is significant at the 0.01 level (two-tailed).\n\nA high, statistically significant positive correlation is shown (0.92>0.7), rejecting the null hypothesis, thereby accepting the alternative hypothesis (There is a significant relationship between digital transformation and the job performance of employees at a Private University, 2023), indicating a significant relationship between the study variables.\n\n\nDiscussion - Conclusions – Recommendations\n\nDescriptive results suggest that the university implements digital transformation tools moderately, effectively utilizing agile technologies, BigData, and technological applications or media for 90% (52% and 38%) of employees. According to Granda & Bermeo (2022), a continuous change through the implementation of innovative and agile technologies is envisioned for optimal process improvement. It is concluded that processes are automated through platforms and tools aimed at reducing or optimizing time through the same.\n\nOn the other hand, job performance is affected by the organization's motivation for high performance. While there is existing pressure to achieve results, this must be managed along with its tolerance, as over 90% of teachers contend that these demands provide a sense of urgency, but in many cases, they exceed the attitudes of the employee. The organization must address the deficiencies in stress management and motivation and how a job under pressure can dramatically diminish individual and group performance. Thus, Taghipour & Dejban (2013) reaffirms our refined critique that job performance consists of the motivation that the worker has to perform the function.\n\nFinally, the research recommends redefining the university's business model, creating an innovative culture at all hierarchical levels, and identifying key technologies that add value to the learning flow. Additionally, feedback on the application of the same is important, and if necessary, training sessions should be coordinated with the teacher to ensure that the information provided is applied correctly. Equally important, a subsequent study on leadership is necessary, as the information received indicates poor practices by authorities that prevent teachers from responding adequately or feeling motivated in their daily tasks and/or duties.\n\nDuring the research process, 104 selected participants from the population took part. The procedures for obtaining results began with an email invitation to each participant, receiving their informed consent in writing via email. Additionally, each participant was provided with a detailed description of the study, its objectives, and the procedures involved. Data collection employed various digital strategies, notably live meetings via the Zoom platform and Google Forms, ensuring the confidentiality of responses for the researchers at all times. “The development of the research article was based on the guidelines established in the “Code of Ethics in Research of the Universidad César Vallejo, version 01”; by Resolution of the University Council N° 0340-2021-UCV, which was approved on 19 July 2022.\n\nReporting guidelines: 10.5281/zenodo.11322516\n\nCreative Commons Zero v1.0 Universal (CC0 License)", "appendix": "Data availability statement\n\nZenodo. Evaluation of the administrative management model in a municipality in Peru, incorporating the Intelligent Organization Theory. 10.5281/zenodo.11322516 (Arias et al., 2024).\n\nThis project contains the following underlying data:\n\n• Data SPSS.sav\n\n• Rectoral Resolution N° 760-2007_UCV_CODE OF ETHICS.pdf\n\nThis project contains the following extended data:\n\n• Figure 1_Scatter Illustration.png\n\n• Informed Consent.pdf\n\n• Instrument_F1000.pdf\n\nCreative Commons Zero v1.0 Universal (CC0 License)\n\n\nReferences\n\nAarsman SR, Greenwood CJ, Linardon J, et al.: Enhancing inferences and conclusions in body image focused non-experimental research via a causal modelling approach: A tutorial0. Body Image. 2024; 49: 101704. PubMed Abstract \| Publisher Full Text\n\nAcciarini C, Cappa F, Boccardelli P, et al.: How can organizations leverage big data to innovate their business models? A systematic literature review. Technovation. 2023; 123: 102713. 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Publisher Full Text\n\nTaghipour A, Dejban R: Job Performance: Mediate Mechanism of Work Motivation. Procedia. Soc. Behav. Sci. 2013; 84: 1601–1605. Publisher Full Text\n\nTippe S, Soto S: Política educacional para una modalidad e-learning en la universidad a partir de la pandemia. Revista Digital de Investigación En Docencia Universitaria. 2021; 15(2). Publisher Full Text\n\nTownsend J, Figueroa J: Los modelos de transformación digital en la gestión de las empresas comerciales. Cooperativismo y Desarrollo. 2022; 10(2): 407–429. Reference Source\n\nUNESCO: ¿Qué determina el buen desempeño de un docente?. UNESCO; 2018, 11 de abril. Reference Source\n\nValderrama B: Transformación digital y organizaciones ágiles. Arundu-Utic – Revista científica internacional. 2019; 6(1): 15–50. Reference Source\n\nValdés V, Gutiérrez-Esteban P: Challenges and enablers in the advancement of educational innovation. The forces at work in the transformation of education. Teach. Teach. Educ. 2023; 135: 104359. Publisher Full Text\n\nVaske JJ: Survey Research and Analysis. Sagamore-Venture; 2nd ed.2019. Reference Source\n\nWyse D, Suter LE, Smith E, et al.: The BERA/SAGE Handbook of Educational Research. London: SAGE Publications Ltd; 2016. Reference Source" }	[ { "id": "296617", "date": "09 Jul 2024", "name": "James Sunney Quaicoe", "expertise": [ "Reviewer Expertise Educational leadership and administration", "digital transformation and lifelong learning", "institutional-based digital transformation and padegogical innovation in schools", "digital lteracy development and digital divide interventions." ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe paper reports on a study that explored the relationship between digital transformation and job performance in higher education institutions.\n\nThe authors set the stage for the article by presenting a very well-composed introduction section.\n\nThe instruction is made up of relevant literature that defines the background of the research.\n\nThe paper presents a clear and concise theoretical underpinning of the study, providing a solid framework for the research, though skeletal, enough to situate the primary focus - i) digital transformation and ii) job performance into the research structure.\nThe paper meticulously addresses the study's methodology, including the sample, the instruments, the data collection procedure, and the analysis. Further steps were taken to test the instrument's validity and reliability, instilling confidence in the study's rigor. The authors also reported on steps taken to address the study's ethical requirements. The results establish the insightful correlations between digital transformation and job performance.\nOverall assessment, the research is topical, and the paper is well written. The language used in the article is scholarly. The paper can 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? Partly\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] }, { "id": "316917", "date": "24 Sep 2024", "name": "Ricardo Fernando Cosio Borda", "expertise": [ "Reviewer Expertise International business", "management", "sustainability and economy." ], "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 article complies in substance and form. It presents a review of relevant literature, based on current sources and essentially on scientific articles that contribute to a solid theoretical framework.\nThe methodology has been clearly detailed and supported by statistical elements, essentially the validation and reliability of the instrument used for data collection. The conclusions are relevant according to the objective of the study and at a thematic level it is a quite pertinent contribution.\nAs an opportunity for improvement for future research, the object of study can be broader and not only applied to a single institution; it could be of greater contribution to carry out a similar study but considering different institutions in emerging countries.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] } ]	1	https://f1000research.com/articles/13-692
https://f1000research.com/articles/13-691/v1	26 Jun 24	{ "type": "Research Article", "title": "Comparison of image quality between Deep learning image reconstruction and Iterative reconstruction technique for CT Brain- a pilot study", "authors": [ "Obhuli Chandran M", "Saikiran Pendem", "Priya P S", "Cijo Chacko", "Priyanka ,", "Rajagopal Kadavigere", "Obhuli Chandran M", "Priya P S", "Cijo Chacko", "Priyanka ," ], "abstract": "Background Non-contrast Computed Tomography (NCCT) plays a pivotal role in assessing central nervous system disorders and is a crucial diagnostic method. Iterative reconstruction (IR) methods have enhanced image quality (IQ) but may result in a blotchy appearance and decreased resolution for subtle contrasts. The deep-learning image reconstruction (DLIR) algorithm, which integrates a convolutional neural network (CNN) into the reconstruction process, generates high-quality images with minimal noise. Hence, the objective of this study was to assess the IQ of the Precise Image (DLIR) and the IR technique (iDose4) for the NCCT brain.\n\nMethods This is a prospective study. Thirty patients who underwent NCCT brain were included. The images were reconstructed using DLIR-standard and iDose4. Qualitative IQ analysis parameters, such as overall image quality (OQ), subjective image noise (SIN), and artifacts, were measured. Quantitative IQ analysis parameters such as Computed Tomography (CT) attenuation (HU), image noise (IN), posterior fossa index (PFI), signal-to-noise ratio (SNR), and contrast-to-noise ratio (CNR) in the basal ganglia (BG) and centrum-semiovale (CSO) were measured. Paired t-tests were performed for qualitative and quantitative IQ analyses between the iDose4 and DLIR-standard. Kappa statistics were used to assess inter-observer agreement for qualitative analysis.\n\nResults Quantitative IQ analysis showed significant differences (p<0.05) in IN, SNR, and CNR between the iDose4 and DLIR-standard at the BG and CSO levels. IN was reduced (41.8-47.6%), SNR (65-82%), and CNR (68-78.8%) were increased with DLIR-standard. PFI was reduced (27.08%) the DLIR-standard. Qualitative IQ analysis showed significant differences (p<0.05) in OQ, SIN, and artifacts between the DLIR standard and iDose4. The DLIR standard showed higher qualitative IQ scores than the iDose4.\n\nConclusion DLIR standard yielded superior quantitative and qualitative IQ compared to the IR technique (iDose4). The DLIR-standard significantly reduced the IN and artifacts compared to iDose4 in the NCCT brain.", "keywords": [ "Deep learning image reconstruction", "iDose4", "Image quality", "Filtered back projection", "CT Brain" ], "content": "Introduction\n\nComputed tomography (CT) is the primary imaging modality used to evaluate patients suspected to have central nervous system disorders. The ability to visualize brain regions quickly and thoroughly is one of their main advantages. This helps in the timely assessment of problems, including stroke, trauma, and intracranial lesions. Non-contrast CT (NCCT) brain scans are widely used in a variety of therapeutic contexts because of their accessibility, speed, and efficacy, which are vital for the early diagnosis and treatment of neurological diseases.1–3\n\nOne notable development in CT reconstruction technology is the use of iterative reconstruction (IR) techniques. iDose4 is a 4th generation IR method released by Philips Healthcare that offers improved image quality (IQ) with a reduced radiation dose. IQ and diagnostic precision are improved through IR, which uses sophisticated mathematical techniques to optimize and refine image data. A significant reduction in image noise (IN) allows for clearer visualization of anatomical structures, especially in regions of low contrast, which is the main advantage of the IR technique. IR allows the acquisition of high-quality images with a decreased radiation dose (RD) for patients. For vulnerable groups such as children or those who are radiation-sensitive, this is especially important.4,5 The IR technique results in a plastic or blotchy appearance at higher reconstruction levels.6–8\n\nDeep learning image reconstruction (DLIR) algorithms represent a transformative leap in image reconstruction and dose reduction in CT. DLIR in Philips Healthcare is called a Precise Image (PI). Philips PI is the latest and most reliable way to reconstruct high-quality CT images using artificial intelligence (AI) techniques. A trained deep learning neural network was used in the PI reconstruction process. With the fastest reconstruction speed in the market, PI preserves the traditional view of FBP photos.9 By harnessing the capabilities of artificial intelligence (AI), particularly convolutional neural networks (CNNs), these algorithms revolutionize image reconstruction by learning intricate patterns from raw CT data. These algorithms learn complex relationships between sparse or noisy input projections and corresponding standard-dose reference images, enabling the generation of clinically acceptable reconstructions even when using a reduced radiation dose. By leveraging the inherent information within the data and learning intricate patterns, DLIR contributes to the advancement of dose reduction strategies in CT. The DLIR technique yields an image texture reminiscent of FBP, even at low-dose strengths.10–12 There are limited studies on the usefulness of DLIR on IQ in the NCCT brain. Hence, the aim of this study was to compare the IQ between the new Precise Image (DLIR) and IR (iDose4) techniques for the NCCT Brain.\n\n\nMethods\n\nThis is a prospective study. The Institutional Ethical Committee (IEC 400/2022) was obtained from Kasturba Medical College and Hospital, Manipal, India, on 1st July 1, 2023, followed by the Clinical Trial Registry - India (CTRI) registration (CTRI/2023/07/055310) on 18th July 2023. Written informed consent was obtained from all the participants for publication and participation in the study.\n\nEligibility criteria: Thirty patients referred for the NCCT brain were included. Patients referred to the NCCT brain for various clinical indications such as trauma, seizures, stroke, headache, vomiting, fever, chills, and breast carcinoma were included. Patients who were uncooperative and who underwent CT scans with motion artifacts were excluded. The patients included in the study had neuropathological findings on CT, including hemorrhage (n=10), infarct (n=10), tumor (n = 5), VP shunt (n = 1), arachnoid cyst (n = 1), metastases with edema (n=1), cerebral atrophy (n=1), and encephalomalacia (n=1).\n\nCT Image acquisition: This study was performed at the Department of Radiodiagnosis, Kasturba Medical College and Hospital. Patients referred for NCCT brain examinations underwent 128 slice CT (Incisive, Philips Healthcare). The technical parameters for the NCCT brain acquisition are listed in Table 1. The images were reconstructed using iDose4 (level 3)4 and the DLIR reconstruction9 level standard.\n\n“Qualitative Image quality analysis”: Two radiologists [reader 1 (R1) and reader 2 (R2)] with over 15 years of experience in neuroradiology imaging evaluated the CT images. Both the readers were blinded to the reconstruction level. The readers assessed the “Overall image quality” (OQ), “Image noise” (IN), “Artifacts” using 5-point Likert scale (Figure 1).\n\n“Quantitative Image quality analysis”: CT attenuation (HU) and image noise (IN) of gray matter (GM) and white matter (WM) at the level of the basal ganglia (BG) and centrum-semiovale (CSO) regions were measured. To calculate attenuation (HU) at the GM and WM of the BG, an ROI of 0.1-0.2 cm2 was placed in the thalamus and posterior limb of the internal capsule (PIC). For calculating attenuation at GM and WM of CSO, the ROI of 0.1-0.2 cm2 was placed in the region of frontal WM and adjacent cortical GM (Figure 2a-b).\n\nThe posterior fossa index (PFI) was calculated as the image noise (Standard deviation-SD) of the HU values in the pons. To calculate the PFI, an ROI of 0.2-0.3 cm2 was placed in the pons region of the posterior cranial fossa (Figure 2c).\n\nThe signal-to-noise ratio (SNR) at the BG and CSO levels was calculated as mean CT attenuation (HU)/standard deviation (SD) (SD: Image noise).\n\nThe contrast-to-noise ratio (CNR) at the BG and CSO levels was calculated using the following formula:\n\nRadiation dose metrics such as “CTDIvolume (CTDIvol), dose length product (DLP), and size-specific dose estimate (SSDE)” were recorded from the display of the console monitor.\n\nSPSS (IBM, V20.0) was used for statistical analysis. Paired t-tests were performed for qualitative and quantitative IQ analyses between the iDose4 and DLIR-standard. “Kappa (k) statistics” were used to check the interobserver agreement for qualitative analysis. The k-value was considered as follows: <0.20, poor agreement, 0.21-0.40 - Fair agreement, 0.41-0.60 - Moderate agreement, 0.61-0.80 - Good agreement, 0.81-1.00 - Excellent agreement”. Statistical significance was set at P < 0.05.\n\n\nResults\n\nA total of thirty patients with 22 males and 8 females with mean age of 55.46±15.38 years referred for NCCT brain were included (Table 2). The mean CTDIvol, DLP, and Size specific dose estimate (SSDE) were 46.36±0.20 mGy, 1157.5±64.23 mGy.cm and 44.10 mGy respectively.\n\nQualitative IQ analysis showed an increase in scores for OQ, IN, and artifacts with DLIR-standard compared to iDose4 for both readers (Table 3) (Figure 3a-b).\n\nThe OQ showed a significant difference (<0.05) between the iDose4 (3.2±0.4; R1) and DLIR-standard (4.2±0.49; R1). IN showed a significant difference (<0.05) between iDose4 (3.03±0.41; R1) and DLIR-standard (4.16±0.46; R1). Artifacts showed significant differences (<0.05) between iDose4 (3.3±0.59 R1) and DLIR-standard (4.23±0.67 R1) (Table 3).\n\nFor OQ, the agreement between the readers was excellent for iDose4 (0.902) and the DLIR-standard (0.821). For IN, the agreement between readers was excellent for iDose4 (1.00) and the DLIR-Standard (0.837). For artifacts, the agreement between the readers was good for iDose4 (0.80) and excellent for the DLIR-Standard (0.943).\n\nCT Attenuation (HU) at the BG and CSO levels did not show significant differences (<0.05) in the GM thalamus, WM PIC, adjacent cortical GM, and frontal WM between the iDose4 and DLIR-standard (Table 4). IN showed significant differences (<0.05) between iDose4 and DLIR-standard at the BG level (GM thalamus, WM PIC) and CSO level (adjacent cortical GM, frontal WM). IN showed 42.8% and 43.47% decreases in GM thalamus and WM PIC, respectively, with DLIR-standard compared to iDose4. IN showed 41.86% and 47.61% decrease in adjacent cortical GM and frontal WM, respectively, with DLIR-standard compared to iDose4. PFI showed significant difference (<0.05) between iDose4 and DLIR-standard with 27.08% IN reduction in the pons region with DLIR-standard compared to iDose4. SNR at BG and CSO levels showed significant differences (<0.05) for the GM thalamus, WM PIC, adjacent cortical GM, and frontal WM between the iDose4 and DLIR-standard. SNR showed 67.60% and 76.78% increases in GM thalamus and WM PIC, respectively, with DLIR-standard compared to iDose4. SNR showed 65% and 82.81% increases at adjacent cortical GM and frontal WM, respectively, with DLIR-standard compared to iDose4. CNR at BG and CSO levels showed significant differences (p < 0.05) in GM thalamus and WM PIC differentiation, adjacent cortical GM, and frontal WM differentiation between iDose4 and DLIR-standard. CNR showed 68% and 78.8% increases in BG and CSO, respectively, with DLIR-standard compared to iDose4.\n\n\nDiscussion\n\nIn the present study, we compared the qualitative and quantitative IQ between the DLIR-standard (Precise Image) and IR (iDose4) techniques for the NCCT brain. Our study noticed that both qualitative and quantitative IQ improved significantly with the DLIR-standard compared with the iDose4. The new DLIR technique, Precise Image, outperformed the IR technique (iDose4). Our study found that the DLIR standard showed a significant reduction in IN and an increase in SNR and CNR at BG and CSO levels. The DLIR-standard showed higher subjective IQ scores with excellent agreement between readers compared to the iDose4. The lower IN, higher SNR, and CNR might allow for lowering the radiation dose with the DLIR-standard compared to iDose4 for the NCCT brain.\n\nStudies by Kim et al.13 and Alagic et al.14 showed 24-52% and 3.5-43% reduction in IN for NCCT brains with DLIR (True Fidelity; GE) reconstruction levels of low, medium, and high compared with ASIR-V (Adaptive statistical iterative reconstruction-Veo) at BG and CSO levels. DLIR-standard in the present showed a 41.8-47.6% reduction in IN at BG and CSO levels, which is similar to the results of Kim et al.13 and Alagic et al.14 Another Two studies by Oostveen et al.15 and Cozzi et al.16 reported a 9.6% and 13% reduction in IN for NCCT brains with DLIR (AiCE) compared with “hybrid-iterative reconstruction (Hybrid-IR)” and “model-based iterative reconstruction” (MBIR), “Adaptive iterative dose reduction” (AIDR-3D), which is slightly less IN reduction compared to our study. The slight variation in the reduction of IN across CT vendors might suggest the need for further research comparing different reconstruction algorithms.\n\nFor the NCCT brain, diagnostic evaluation of the posterior fossa in emergency situations to identify hemorrhagic and ischemic events is important. However, the posterior cranial fossa often experiences beam hardening, streak, and partial volume artifacts due to the presence of bony structures surrounding the cerebellum, pons, and medulla, which leads to diagnostic challenges in identifying hemorrhage and infarct in this region. The artifact index could indicate the extent of CT number fluctuations resulting from artifacts, along with intrinsic image noise linked to factors related to both the scanner and the patient.17,18 Our study noticed a 27.08% reduction in IN and artifact index in the pons region of the posterior fossa with DLIR-standard compared to iDose4 which was similar to the artifact index reported by Kim et al.13 (17-38%) and Alagic et al.14 (6.8-32.8%). However, Cozzi et al.16 reported a higher artifact index (median 8.4; interquartile range 7.3-9.2) with DLIR (AiCE) than with AIDR-3D (median 7.5; interquartile range 6.9-8.3) in thin sections, which is contrary to the study reported by Oostveen et al.15 with the same DLIR technique. The reason for this could be the difference in the placement of the ROI and slice thickness used between the two studies.\n\nOur study observed higher SNR (65-82%) at BG and CSO levels with DLIR-standard, which suggests better gray and white matter differentiation compared to iDose4. The findings of our study were similar to the results of Alagic et al.14 (2-89%) with DLIR-low, medium, and high levels, and Pula et al.19 (46-59%) with DLIR-High compared to IR techniques. A study by Oostveen et al.15 reported a slightly lower reduction in SNR (5-26%) compared to our study because of the difference in the formula used for calculating the SNR. Our study observed an increase in CNR (68-78.8%) with DLIR-standard at BG and CSO levels, which suggested better gray and white matter differentiation compared to iDose4. The results of our study were similar to the findings reported by Alagic et al.14 (2.4-53%) and Cozzi et al.16 (28-39%). However, Kim et al.13 reported an increase in CNR of 99% with DLIR-high DLIR.\n\nOur study found no significant difference (p>0.05) in CT attenuation (HU) between DLIR-standard and iDose4 at the BG and CSO levels. The findings of our study are similar to the results of Kim et al.13 which showed no significant difference in CT attenuation of GM between DLIR levels and IR technique. However, a study by Alagic et al.14 reported significant differences in CT attenuation between DLIR levels and IR technique at the PLIC WM and adjacent cortical GM, which might suggest that DLIR could lead to minor changes in attenuation values; however, this finding is unlikely to have significant clinical consequences.\n\nThe DLIR-standard showed higher qualitative scores for OQ, IN, and artifacts compared to iDose4 which is similar to the findings reported by Oostveen et al.15 and Pula et al.19 Studies by Kim et al.13 and Alagic et al.14 reported an increase in qualitative scores with an increase in the strengths of DLIR from low to high compared to IR techniques.\n\nOur study has a few limitations. First, the study involved a small sample size, and it is necessary to conduct further research with a larger patient cohort to confirm our study findings. Second, the study did not directly evaluate the diagnostic efficacy, which is a crucial step in understanding the complete clinical advantages of DLIR. Third, CT scanning was performed using a standard dose protocol, making it challenging to directly ascertain the potential dose-reduction benefits of DLIR.\n\n\nConclusion\n\nThe New DLIR Precise Image (DLIR) technique offers improved image quality with reduced image noise and higher SNR and CNR than iDose4. The DLIR standard also showed higher qualitative image quality scores than the iDose4. The reduction of posterior fossa artifacts with the DLIR standard for the NCCT brain improves the diagnostic accuracy of identifying hemorrhages/infarcts in emergency cases. Our current study may provide implications for performing low-dose scans with reduced radiation doses using DLIR in the NCCT brain.\n\n\nEthics and consent\n\nThe Institutional Ethical Committee (IEC 400/2022) was obtained from Kasturba Medical College and Hospital, Manipal, India, on 1st July 1, 2023.\n\nWritten informed consent was obtained from all the participants for publication and participation in the study.", "appendix": "Data availability\n\nFigshare: F1000 Data DLIR NCCT Brain, https://doi.org/10.6084/m9.figshare.25658829.v7. 20\n\nThis project contains following underlying data:\n\n• Anonymous brain (CT images of all 30 patients -JPEG images)\n\n• F1000 Final excel (demographic characteristics of patients, Qualitative and Quantitative analysis - spreadsheet)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nAbbasi B, Ganjali R, Akhavan R, et al.: The accuracy of non-contrast brain CT scan in predicting the presence of a vascular etiology in patients with primary intracranial hemorrhage. Sci. Rep. 2023; 13: 9447. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nClooney M, Brettig T, Kerr D, et al.: Compliance with guidelines for urgent head CT in an emergency department. EM. Aust. 2006; 18: 26–32.\n\nHill MD, Demchuk AM, Tomsick TA, et al.: Using the baseline CT scan to select acute stroke patients for IV-IA therapy. Am. J. Neuroradiol. 2006; 27(8): 1612–1616. PubMed Abstract\n\nScibelli A: iDose4 iterative reconstruction technique. Philips Healthcare Website.Reference Source2011.\n\nChhetri S, Pendem S, Bharath JL, et al.: Low kilovoltage and low contrast volume neck CT protocol using iterative reconstruction techniques: A comparison with standard dose protocol. Radiat. Phys. Chem. 2022; 193: 109935. Publisher Full Text\n\nStiller W: Basics of iterative reconstruction methods in computed tomography: A vendor-independent overview. Eur. J. Radiol. 2018; 109: 147–154. PubMed Abstract \| Publisher Full Text\n\nSaiprasad G, Filliben J, Peskin A, et al.: Evaluation of Low-Contrast Detectability of Iterative Reconstruction across Multiple Institutions, CT Scanner Manufacturers, and Radiation Exposure Levels. Radiology. 2015; 277(1): 124–133. PubMed Abstract \| Publisher Full Text\n\nSolomon J, Mileto A, Ramirez-Giraldo JC, et al.: Diagnostic Performance of an Advanced Modeled Iterative Reconstruction Algorithm for Low-Contrast Detectability with a Third-Generation Dual-Source Multidetector CT Scanner: Potential for Radiation Dose Reduction in a Multireader Study. Radiology. 2015; 275(3): 735–745. PubMed Abstract \| Publisher Full Text\n\nWhite Paper—AI for Significantly Lower Dose and Improvement Image Quality—Precise Image. Philips-Comput. Tomogr. 2021. Reference Source\n\nGreffier J, Hamard A, Pereira F, et al.: Image quality and dose reduction opportunity of deep learning image reconstruction algorithm for CT: a phantom study. Eur. 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PubMed Abstract \| Publisher Full Text\n\nAlagic Z, Diaz Cardenas J, Halldorsson K, et al.: Deep learning versus iterative image reconstruction algorithm for head CT in trauma. Emerg. Radiol. 2022; 29(2): 339–352. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nOostveen LJ, Meijer FJA, de Lange F , et al.: Deep learning–based reconstruction may improve non-contrast cerebral CT imaging compared to other current reconstruction algorithms. Eur. Radiol. 2021; 31: 5498–5506. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCozzi A, Ce M, De Padova G, et al.: Deep Learning-Based Versus Iterative Image Reconstruction for Unenhanced Brain CT: A Quantitative Comparison of Image Quality. Tomography. 2023; 9(5): 1629–1637. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGoldman LW: Principles of CT: radiation dose and image quality. J. Nucl. Med. Technol. 2007; 35(4): 213–225. Publisher Full Text\n\nRozeik C, Kotterer O, Preiss J, et al.: Cranial CT artifacts and gantry angulation. J. Comput. Assist. Tomogr. 1991; 15(3): 381–386. PubMed Abstract \| Publisher Full Text\n\nPula M, Kucharczyk E, Zdanowicz A, et al.: Image Quality Improvement in Deep Learning Image Reconstruction of Head Computed Tomography Examination. Tomography. 2023; 9(4): 1485–1493. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPendem S: F1000 Data DLIR NCCT Brain. Dataset. figshare. 2024. Publisher Full Text" }	[ { "id": "296709", "date": "01 Jul 2024", "name": "SENTHIL MANIKANDAN", "expertise": [ "Reviewer Expertise Radiological Physics" ], "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 recent years, significant advancements have been made in CT image reconstruction technology, particularly with the introduction of deep learning-based image reconstruction (DLIR) algorithms. One notable development is the \"Precise Image\" by Philips Healthcare, which aims to reduce image noise and enhance overall image quality for Non-contrast CT brain scans. Key Findings and Analysis The study provides a comprehensive comparison of image quality parameters, both qualitative and quantitative, which are crucial for radiographers, technologists, and radiologists seeking to understand the tangible benefits of DLIR over traditional iterative reconstruction methods in CT brain examinations. A particularly compelling aspect highlighted in the article is the measurement of the posterior fossa artifact index. Historically, posterior fossa beam hardening artifacts have posed challenges in CT brain examinations, particularly in assessing conditions such as posterior fossa contusions and infarcts. The reduction in artifacts observed in DLIR images compared to previous methods like iDose4 represents a significant advancement that aids radiologists in making more accurate diagnoses. Moreover, the article suggests that DLIR has the potential to lower radiation doses while maintaining diagnostic quality, which is critical for the safety and effectiveness of follow-up head CT scans. Minor Comments and Future Directions While the study is commendable in its depth and scope, minor adjustments such as limiting the use of quotation marks in the manuscript could enhance clarity and readability. Future research avenues could explore the application of DLIR in other body parts and in low-dose CT examinations to further elucidate its benefits and effectiveness across different clinical scenarios.\nThis research article contributes valuable insights into the applications and benefits of AI-based technologies in CT for improving image quality and optimizing radiation dose. The adoption of AI techniques such as DLIR, as reported in this study, represents a significant advancement in enhancing patient care through more precise diagnostic imaging.\n\nIs the work 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": "296703", "date": "02 Jul 2024", "name": "Jerald Paul Immanuel", "expertise": [ "Reviewer Expertise CT", "MRI", "AI based techniques and digital X rays systems" ], "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\nMajor Comments: This is an interesting study dealing with CT image quality using DLIR and iDose4 for non-contrast CT brain. The study concludes that DLIR showed higher qualitative scores and reduced image noise (41.8-47.6%) with higher SNR (65-82%) and CNR (68-78.8%). The innovation of the study is good. The authors clearly describe the scientific rationale or hypothesis of this study in the manuscript. Methods section is described well with various image quality measurements and its formula. Results explained clearly. Discussion compared the image quality measures from present study with references from literature. Conclusion explained the benefits of DLIR in Non-contrast CT brain.\nMinor comments: The Methods section can include more details about DLIR. Reference for using CNR formula can be provided. Abbreviations like SPSS in statistical section can be provided. The article is very attractive and provides deep insights about deep learning-based reconstruction techniques in CT.\nÂ\n\nIs the work 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": "296708", "date": "03 Jul 2024", "name": "Dr. Tamijeselvan S", "expertise": [ "Reviewer Expertise Competency based radiography education", "CT Studies", "Imaging Technology", "Radiography", "Radiation Physics" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn this article the author(s) compared the image quality obtained by 2 reconstruction methods namely DLIR standard and IR technique (iDose4). The findings revealed that DLIR-standard gives the better quality image by reducing the image noise and artifacts compared to iDose4 in the NCCT brain. Major comments This research article provides a comprehensive comparison of image quality parameters, such as diagnostic value, image noise and artifacts. of DLIR over traditional iterative reconstruction methods in Non contrast CT brain examinations. This will benefit the technologist and the radiologist to understand the various benefits using various available reconstruction method in Computed Tomography particularly in the Non contrast CT brain. Since this research was done in a mixed method (both qualitative and quantitative), it reveals a valuable result to upgrade the reconstruction algorithm in future. The biggest challenge in avoiding the base of skull artifacts in CT brain examinations is taken into account for the comparison. Any technical advancement which reduces the patient dose and improve the diagnostic value is always useful in diagnostic radiology. At this view this comparison study is very much appreciable and need of the hour. Minor comments Method of sample selection (how the researcher select the sample from the population) can be included in the Methods section. Instead of 2 radiologist more number can be used to get more appropriate results. Otherwise as a whole, this research article provides valuable data which will lead to quality imaging with less patient dose\n\nIs the work 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": "296706", "date": "03 Jul 2024", "name": "Shashi Kumar Shetty", "expertise": [ "Reviewer Expertise Medical imaging", "radiography", "radiation protection" ], "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\nPlease find the comments for the article Major comments Introduction: Well-structured. It explained the current reconstruction techniques of CT available in the market and the disadvantages of iDose4. Deep learning-based reconstruction techniques are currently being validated for various applications in CT for image quality improvement and radiation dose reduction. Hence the aim and research gap addressed here is very much relevant to the current context of issues to be addressed while using DLIR techniques for clinical use. Methodology: It clearly explains the key concepts such as inclusion, exclusion criteria, qualitative and quantitative image analysis. Statistical analysis: The tests used for comparing the image quality measures and interobserver agreement appear appropriate. Results: Well-explained with descriptive statistics as well as p-values. The tables provided are informative and easy to understand. Discussed: Clearly explained the results and implications of DLIR in image noise and artifact reduction with clinical relevance. Conclusion: It summarizes the key findings and applications of new precise image technique in clinical aspect for CT brain Minor comments Are there any additional costs required for installing these DLIR techniques in CT machines? Abbreviations needs to be provided at its first use\n\nOverall, the original research paper provides a significant contribution to the field of advancements in image reconstruction techniques in CT.\n\nIs the work 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": "296712", "date": "11 Jul 2024", "name": "Mustapha Barde", "expertise": [ "Reviewer Expertise Image analysis and processing", "CT Dosimetry" ], "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 revealed the effectiveness of deep learning iterative image reconstruction (DLIR) as compared to iDose4 (iterative reconstruction) in terms of qualitative and quantitative image quality (IQ) in non-contrast brain CT studies. DLIR presented better signal-to-noise ratio, contrast to noise ratio and reduced image noise. it enhances radiation dose optimization by using low radiation dose for purpose of image acquisition. The article is worthy of being published upon addressing the below minor corrections Minor corrections\nThe abbreviation FBP used in the introduction and VP in the eligibility criteria part should be written in full for the first time, and subsequently they can be used. In figure 2. The numbers 1 and 2 (ROIs) should be defined on either the image or the figure description. Formula should be written in a standard format, where superscripts is required, they should be correctly inserted. Based on the qualitative IQ analysis results of the different observers, the second observer R2 results should be explained with the corresponding P-value as well, as shown in Table 3. Try to modify the table to indicate the P-values based on each observer.\n\nQuantitative image analysis: the CT attenuation (HU) reported p-value in the result, did not correspond to Table 4. check for Possible sign error in the p-value stated.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] } ]	1	https://f1000research.com/articles/13-691
https://f1000research.com/articles/12-1196/v1	25 Sep 23	{ "type": "Review", "title": "Dissecting Loneliness in the Digital Age: An Insight into the Experiences of Medical Students Amid and Beyond the COVID-19 Pandemic", "authors": [ "Abdulqadir J. Nashwan", "Rawan Alahmad", "Ghazi Abu Afifeh", "Nour Abu Afifeh", "Rawan Alahmad", "Ghazi Abu Afifeh", "Nour Abu Afifeh" ], "abstract": "In this review, we explore the multifaceted issue of loneliness among medical students, with particular emphasis on the unique challenges posed by the COVID-19 pandemic and the digital age. Medical students face an especially demanding academic environment, and the pandemic has significantly exacerbated feelings of isolation and distress. The review examines distinct loneliness profiles and risk factors and emphasizes the urgent need for targeted interventions to support mental well-being. We also probe into the complex relationship between loneliness and the use of digital platforms, assessing the nuances of social media interactions pre- and post-pandemic. This includes an evaluation of both the positive and negative impacts of virtual medical teaching and the role of passive and active social media use in mitigating or exacerbating feelings of loneliness. The review provides insights into the psychological impact of the pandemic on medical students and how it intersects with loneliness, revealing a multifaceted problem that requires careful consideration and tailored support. This narrative review contributes valuable perspectives to medical education and mental health by synthesizing current research and highlighting gaps in our understanding. It calls for further research and the development of specific interventions that recognize medical students' unique needs, especially in the context of a post-COVID era. Overall, the findings presented here offer a foundational guide for educators, policy-makers, and mental health professionals seeking to address loneliness and foster well-being among medical students in our rapidly changing world.", "keywords": [ "Medical students", "Loneliness", "COVID-19", "Digital age", "Social media", "Well-being" ], "content": "1. Introduction\n\nIn December 2019, an outbreak of pneumonia with an unknown cause was reported in Wuhan, China. Investigation revealed that the cases were linked to the Huanan Seafood Wholesale Market.1 Scientists were able to isolate a novel respiratory virus from respiratory samples, which was later identified as a new coronavirus belonging to the same family as the virus causing severe acute respiratory syndrome (SARS).2 This new coronavirus was named SARS-CoV-2 and is responsible for the disease known as COVID-19. The rapid global spread of SARS-CoV-2 and the significant number of deaths led to the declaration of a pandemic by the World Health Organization in March 2020.2 Beside the increased morbidity and mortality that resulted from the spread of this virus, the impact of the COVID-19 pandemic has been immense; as governments around the world have implemented lockdown measures to isolate the infection, resulting in economic consequences, and increased poverty worldwide.3 In addition to that, extended periods of social isolation led to persistent feelings of loneliness and boredom, which can possibly have negative impacts on both physical and mental well-being on the long run.4\n\nThe lives of numerous individuals have been profoundly affected by the emergence of COVID-19 and the subsequent measures done to control its transmission. Among these impacted groups are medical students. A study conducted in the US revealed that a substantial number of students had their clinical rotations cancelled or shortened by COVID-19.5 Additionally, most students did not have in-person patient contact during the study period. Approximately, 75% of students acknowledged that their medical education had been significantly disrupted by the pandemic, and 84.1% of students agreed that COVID-19 pandemic affected their stress or anxiety levels.5 Despite these challenges, students were able to find valuable learning opportunities through alternative methods such as telehealth, online courses, research, volunteering, and independent study.5 But also, according to the study, 61.3 % of the respondents thought that medical students should continue with normal clinical rotations during this pandemic. In Saudi Arabia, a study found that 94.4% of medical students reported experiencing moderate to high perceived stress. Additionally, two-thirds of the students reported experiencing generalized anxiety symptoms, with 47% of them falling into the moderate to severe range.6\n\nLoneliness is defined by subjective feelings of social pain and isolation. It is considered a universal phenomenon in human experiences, and its emotional distress can have serious consequences.7 Loneliness showed medium to large effects on all health outcomes according to a comprehensive review and meta-analysis conducted in 2020.8 Those effects included physical and mental health outcomes, with the strongest impact being on mental health and well-being (i.e., depression, anxiety, suicidality, general mental health); it is especially crucial to prioritize the proper training of healthcare providers, enabling them to recognize and address their own feeling of loneliness. Given the fact that among medical residents, suicide ranks as the primary cause of death among males and the second leading cause among females.9\n\nAs per a recent study examining loneliness among medical students, physician trainees, and faculty physicians, the findings indicate that loneliness is prevalent amongst people in the medical health industry, and that indeed includes medical students.10\n\nThe COVID-19 crisis has resulted in the usage of digital platforms not only for entertainment purposes but also for educational and corporate reasons.11 Several studies looked at the role of social media use during the COVID-19 pandemic. A Pakistani study had shown that while using social media during the COVID-19 crisis can be beneficial for emotional support, information gathering, and connecting with peers, it also takes a toll on mental health due to excessive usage.12\n\nAnother study on Chinese college students revealed a connection between higher social media use and poorer mental health outcomes. Participants with high levels of disaster-related stress experienced greater depression when exposed to more disaster news on social media. Additionally, the relationship between social media use and mental health was mediated by negative affect, indicating that negative emotions played a role in this association.13\n\nIn this review, we focus on the issue of loneliness as experienced by medical students, which is a significant concern, especially during the COVID-19 pandemic, considering the demanding nature of their studies and the impact of the pandemic on their education and well-being. The review also focuses on the digital age, by specifically examining loneliness in the digital age pre- and post- pandemic. It also gives insights into the psychological impact of the COVID-19 pandemic on medical students and how it intersects with loneliness. Overall, this narrative review holds importance by exploring an important topic, considering the digital age and the COVID-19 pandemic, and providing valuable insights for intervention, support, and future research.\n\n\n2. Literature search\n\nA systematic search strategy was employed that adhered to the SANRA guidelines.14 PubMed, Scopus, PsycINFO, and Google Scholar, were searched using a combination of keywords and Boolean operators, such as “medical students,” “loneliness,” “mental well-being,” “virtual education,” “COVID-19 pandemic,” and related synonyms. The search was conducted in titles and abstracts, with inclusion criteria focusing on studies that specifically addressed aspects of loneliness, mental health, and virtual education among medical students, published in English, and peer-reviewed within the last ten years. Exclusion criteria ruled out studies not directly related to the topic. The screening process involved an initial review by title and abstract, followed by a full-text review.\n\n\n3. The pre-COVID state of loneliness among medical students\n\nLoneliness is a personal and psychological state that is linked to factors like social isolation, depression, introversion, or inadequate social skills. Studies have revealed that loneliness is most experienced among various social groups, including young adults (aged 18-29 years), older adults, individuals with physical or mental health conditions, those with low income, and people with different marital statuses, such as single, separated, widowed, or divorced individuals.15\n\nMedical students represent an important group deserving attention regarding the prevalence of loneliness and the factors influencing it. In a recent study focusing on loneliness among various medical professionals, including medical students, it was found that 20.9% of the participants of the medical students reported experiencing intense loneliness, indicated by scores of 2 or 3 on a scale ranging from 0 to 3.10 In a study that looked at loneliness at universities, the average emotional loneliness score in medicine/health care study discipline was 0.847, while the mean social loneliness score was 0.302 (The general loneliness scale ranged from 0 to 6 (0–1 = not lonely, 2–4 = moderately lonely, 5–6 severely lonely).16\n\nA recent meta-analysis was conducted and revealed some risk factors of mental problems in medical students, and the results indicate that female medical students are at a higher risk for mental health issues, possibly due to pre-existing gender differences in mental distress.17 Junior or preclinical students, who are at an early stage of medical education, are also at a higher risk for mental distress. Factors such as low social support, bad family relationships, economic troubles, pre-existing mental or physical illnesses, and COVID-19 infection or exposure are associated with mental problems among medical students. Unhealthy lifestyles, increasing substance use, irregular diet and sleep, and problematic smartphone and internet use are emerging risk factors that need further investigation.17 Another study that involved Chinese medical students revealed that sophomores and junior students, neuroticism, high arousal symptoms, and the quality of support from friends were the risk factors for high loneliness profile.18\n\nUndoubtedly, social media stands as one of the most extensively utilized interactive technologies, so it is important to study how those social connecting platforms affect loneliness.19 The primary purpose behind the development of social media was to establish connections between individuals in various parts of the world.20 However, as technology brings people closer, the “alone together” phenomenon arises, where individuals feel isolated despite constant technological connections, and this can lead to serious problems such as depression, especially for people who have the -so called-, social network site (SNS) addiction.21\n\nSNS addiction is a phenomenon where individuals are so highly motivated to use social networking sites that it adversely affects their social activities, studies, work, relationships, and overall psychological health and well-being.22 According to a meta-analysis that studied the SNS addiction problem in medical students, the prevalence of Internet addiction among medical students was five times higher than that of the general population.23\n\nAccording to a Chinese study, approximately 33.18% of the participating medical students were found to have an addiction to SNSs. Most of these students used social media platforms daily, with around half spending more than one hour per day on them. Among various demographic factors, the only influencing factor was the students' grade level. In addition, the study demonstrated that SNS addiction has the potential to impact depression by affecting feelings of loneliness and unmet interpersonal needs.24\n\nAddressing loneliness among medical students is crucial to ensure their overall well-being and academic success. Loneliness can result in a sense of isolation and detachment, exerting adverse effects on a student's mental health. This, in turn, may induce stress, potentially leading to detrimental impacts on academic performance. According to a study’s results, there was a positive association between loneliness and academic stress, meaning that as loneliness increased, so did academic stress.25 On the other hand, there was a negative association between loneliness and psychological well-being, suggesting that higher levels of loneliness were linked to lower levels of psychological well-being.25 In another study that exclusively evaluated the influence of family loneliness on medical professionalism measures (i.e., empathy, teamwork, and lifelong learning) among medical students, the findings revealed an inverse correlation between family loneliness and those measures; meaning that as family loneliness increased, the levels of empathy, teamwork, and learning measures tended to decrease among the medical students.26\n\n\n4. The impact of COVID-19 on loneliness among medical students\n\nA study aimed to investigate the psychological challenges related to COVID-19 quarantine faced by medical students, with a focus on loneliness.18 The researchers surveyed 1,478 participants using face-to-face online questionnaires, incorporating the University of California, Los Angeles (UCLA) Loneliness Scale and psychological characteristic scales.27 The results revealed three distinct loneliness profiles: low loneliness (52.3%), interpersonal sensitivity loneliness (3.5%), and high loneliness (44.1%). Risk factors for high loneliness included being a sophomore or junior student, neuroticism, high arousal symptoms, and the quality of support from friends, while predictors of interpersonal sensitive loneliness were sophomore and junior students, openness, and conscientiousness personality traits. Conversely, good peer relationships and other support acted as protective factors for the low loneliness profile. However, limitations in the study, such as the single medical university's participant selection, may affect the generalizability of the findings. In conclusion, targeted interventions addressing loneliness based on identified profiles and predictors in medical students are suggested, with timely support and strategies playing a crucial role in enhancing their mental wellbeing during challenging times like the COVID-19 pandemic.\n\nOther researchers present a review of the advantages and disadvantages of virtual medical teaching for medical students during the COVID-19 pandemic, focusing on the shift to remote learning.28 The study involved analyzing 201 articles, with 34 included, and conducting manual searches for additional references. Strengths of virtual teaching were identified, including improved access to diverse web-based resources, interactive teaching facilitating remote patient interactions, and open-access teaching with medical experts for staying updated on medical advancements. Peer mentoring also proved valuable. Conversely, weaknesses encompassed technical challenges, confidentiality issues, reduced student engagement, loss of assessments, and negative impacts on students' mental well-being. Global inequalities in virtual teaching services further affected medical education. Participants strongly agreed that virtual learning increased their knowledge and stimulated learning, with most indicating a willingness to recommend and continue with this form of teaching. The advantages included the ease of accessing educational materials in preferred environments, accessibility to experts globally, and an opportunity to enhance virtual medical education. However, disadvantages included technical issues with audio and video, lack of clinical experience, loss of networking opportunities, cost and time burdens for faculties, potential boundary issues between work and home, and increased risks of isolation, anxiety, and boredom. As a researcher, this comprehensive analysis sheds light on the benefits and drawbacks of remote learning, underlining the significance of optimizing virtual medical education while addressing associated challenges for improved outcomes during unprecedented times.\n\nFurthermore, a systematic review with meta-analysis aimed to investigate the potential increase in loneliness during the COVID-19 pandemic, considering the impact of measures like physical distancing.29 The review identified 34 high-quality primary studies with 215,026 participants, including longitudinal and pseudo longitudinal designs. The meta-analysis revealed a small but significant increase in loneliness scores and prevalence rates compared to pre-pandemic times. The findings underscore the importance of addressing the issue of loneliness during the ongoing health crisis and highlight the need for further investigation into risk and protective factors to develop targeted interventions for mental and physical health support.\n\n\n5. The role of social media during the COVID-19 era\n\nA study investigated the impact of social media use during the COVID-19 pandemic, utilizing both quantitative and qualitative surveys with 307 participants.30 The findings demonstrated that passive social media use was linked to increased loneliness and decreased life satisfaction. However, certain active social media engagement led to a rise in positive affect, while other active uses resulted in heightened feelings of loneliness. Platform-specific differences were also observed, with Twitter use being associated with increased feelings of loneliness. The qualitative results indicated a surge in social media use during the pandemic, providing opportunities for digital reconnection with old friends and family. These findings shed light on the diverse effects of social media use during COVID-19 and highlight the importance of understanding the nuances of online interactions on individuals' emotional well-being.\n\nIn another investigation, a study explores the impact of COVID-19 on communication and collaboration in distance learning environments, along with the role of social media in this context.31 The study collected data through an online survey from 234 students and tested research hypotheses. The findings indicate that increased use of Facebook for professional purposes enhances students' communication and collaboration during distance learning. High activity on Facebook and LinkedIn is crucial for communication with educators. Active participation in distance classes and positive assessment of online tools also positively influence communication and collaboration among students, aligning with engagement theory. The research contributes to the distance learning literature by shedding light on the pandemic's effects through the lens of engagement theory, and it offers practical implications for all participants in the educational process.\n\nFurthermore, the COVID-19 pandemic and its containment measures have had a significant impact on mental health, especially during adolescence, a critical period for social and cognitive development.32 Studies have shown that social deprivation during this time can lead to diverse mental health problems.33 Lockdown measures during the early months of the pandemic threatened the mental health of youth due to distant learning, closure of leisure environments, decreased outdoor activities, and distress related to the pandemic. Several reviews have highlighted the immediate impact of the pandemic on young people's mental health, showing increased anxiety, loneliness, stress, and depressive symptoms.34 Adolescents responded to social distancing by spending more time online, particularly on social media platforms, to alleviate negative experiences. This increased screen time, along with digital technology use, has both positive and negative impacts on mental well-being. However, the specific link between digital media use and adolescents' mental health during the COVID-19 pandemic has not been systematically studied. The present review aim to address this gap by focusing on the relationship between digital media use, mental health, and adolescents during the COVID-19 pandemic.\n\nMoreover, another study examined the impact of social media use on mental health and well-being.35 High frequency social media users, who used it several times daily, were found to have poorer mental health, overall quality of life, higher loneliness, and lower well-being compared to low-frequency users who used it daily or less frequently. Among those using social media daily or less frequently, 24.2% experienced emotional distress and poor overall quality of life. However, for high-frequency users, the proportions experiencing emotional distress and poor overall quality of life were significantly higher at 75.8% and 75.6%, respectively. The findings suggest that excessive use of social media may be associated with negative effects on mental health and overall well-being.\n\n\n6. The post-COVID scenario and the evolving role of social media\n\nIn the post-COVID era, loneliness continues to be a prevalent and concerning issue among medical students. Approximately 44.1% of medical students fall into the high loneliness profile, indicating a significant proportion experiencing profound feelings of isolation and disconnection. Moreover, 3.5% of students are categorized under the interpersonal sensitivity loneliness profile, suggesting a subgroup struggling with interpersonal interactions.36 This could be attributed to the pandemic's impact on campus closures, limited social interactions, and increased academic pressure. Consequently, there is a pressing need for targeted support and interventions to address the mental health struggles of medical students in the post-pandemic era. By understanding and addressing loneliness, we can promote their overall well-being and ensure their success in both academic pursuits and future medical careers.\n\nWhile numerous studies have explored the immediate impact of COVID-19 loneliness on the mental health of medical students, there is a lack of research on the long-term effects, this could be due to the temporal proximity of the lockdown termination. Regarding the short-term consequences, one study conducted in the United States found that medical students faced elevated levels of stress, burnout, and loneliness.36 Students with preexisting mental health conditions are at a significantly higher risk, as they might encounter restricted availability of crucial treatments and services, leading them to adapt their care delivery methods, such as transitioning to virtual sessions.37\n\nThese findings align with another study's results, which indicated that students living alone during the pandemic were more prone to experiencing moderate to severe levels of anxiety and post-traumatic stress disorder (PTSD).38\n\nAdditionally, the repercussions of pandemic-induced loneliness extended to sleep patterns. Strict social distancing measures and reduced interpersonal communication have intensified feelings of loneliness, exacerbating insomnia during the pandemic.39\n\nDue to quarantine measures, the role of social media has become more apparent. One finding suggests that social media may play a dual role in affecting loneliness during the pandemic.40 For older adults, using social media may serve as a tool to prevent or reduce loneliness, particularly when faced with reduced social contact due to various factors related to aging. On the other hand, among younger individuals, excessive social media use may be associated with higher emotional loneliness, possibly due to social comparison tendencies and presenting a “liminal self” online.41 Another study found that excessive and prolonged social media use, adopted as a coping strategy, resulted in negative consequences for mental health.42\n\n\n7. Mitigation strategies and interventions\n\nAs medical students face increased social isolation, it becomes crucial to identify effective interventions to address loneliness and promote student wellness and resilience.43 Various coping mechanisms have emerged, but focused interventions can significantly contribute to mitigating loneliness and enhancing students' mental well-being. Figure 1 illustrates facts and figures about loneliness among medical students.\n\n[This figure is an original figure produced by the authors for this review article.]\n\nPsychological interventions including cognitive-behavioral therapy (CBT), mindfulness-based interventions, social skills training, gratitude interventions, and reminiscence therapy have proven to be effective in reducing loneliness compared to control groups, with an overall effect size of 0.43; which would indicate that the psychological interventions (like CBT, mindfulness-based interventions, etc.) had a positive and moderate effect on reducing loneliness when compared to control groups.44\n\nProlonged social isolation measures during the COVID-19 pandemic may have deprived individuals of the need to belong and connect with others, leading to increased feelings of loneliness. Correspondingly, having a robust network of peer support is essential in reducing the feeling of loneliness, as well as improving emotional well-being.45,46\n\nMedical schools play a crucial role in supporting student wellness.47 They can incorporate evidence-based interventions into their programs to address loneliness effectively.48 Group-based approaches, such as support groups, social interaction activities, and group-delivered psychoeducation, provide opportunities for students to connect, share experiences, and develop a sense of belonging.43 Moreover, incorporating reflective exercises like mindfulness, meditation, or journal writing can be beneficial in reducing loneliness by promoting self-awareness and emotional well-being.43\n\nFurthermore, medical schools can harness the potential of online platforms, such as chat rooms or smartphone apps, to facilitate virtual connections and support, especially in situations where face-to-face interactions are limited. Social skills training can address maladaptive social cognition associated with loneliness by improving students' ability to initiate and maintain social connections.43\n\nIn addition to addressing loneliness directly, medical schools should focus on enhancing student resilience, which builds a protected personality that is able to tolerate challenging situations. programs may include workshops on stress management, coping strategies, and fostering a growth mindset. Encouraging a culture of open communication and emotional support among faculty and students can further contribute to enhancing student resilience.49\n\n\n8. Conclusions\n\nSeveral studies have underscored the importance of addressing loneliness among medical students, particularly during the COVID-19 pandemic. The findings identified various loneliness profiles and risk factors among medical students, emphasizing the need for targeted interventions to improve mental well-being. Virtual medical teaching has been found to have both advantages and disadvantages, with some negative impacts on students' mental health. More evidence further demonstrated an increase in loneliness during the pandemic, highlighting the necessity for mental and physical health support. Unique loneliness experiences of medical students compared to other students stress the need for specific understanding and support. The role of social media in loneliness is multifaceted. Passive use is linked to increased loneliness, while some active engagement can have positive effects. However, platform-specific differences exist, and excessive use, especially during adolescence, can have negative mental health effects. Understanding online interactions and promoting healthy social media usage is vital. Longitudinal studies to investigate the long-term impact of pandemic-induced loneliness on medical students' mental health, career choices, and overall functioning are essential. There is an urgent need to develop specific interventions targeting medical students' unique needs in the post-COVID era, as current interventions remain insufficient.", "appendix": "Data availability\n\nNo data are associated with this article.\n\n\nReferences\n\nZhu N, Zhang D, Wang W, et al.: A novel coronavirus from patients with pneumonia in China, 2019. N. Engl. J. Med. 2020; 382(8): 727–733. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCiotti M, Ciccozzi M, Terrinoni A, et al.: The COVID-19 pandemic. Crit. Rev. Clin. Lab. Sci. 2020; 57(6): 365–388. Publisher Full Text\n\nShadmi E, Chen Y, Dourado I, et al.: Health equity and COVID-19: global perspectives. Int. J. Equity Health. 2020; 19(1): 1–16.\n\nBanerjee D, Rai M: Social isolation in Covid-19: The impact of loneliness. London, England: SAGE Publications Sage UK; 2020; vol. 66. : 525–527. Publisher Full Text\n\nHarries AJ, Lee C, Jones L, et al.: Effects of the COVID-19 pandemic on medical students: a multicenter quantitative study. BMC Med. Educ. 2021; 21: 1–8.\n\nAlJhani S, Alateeq D, Alwabili A, et al.: Mental health and online learning among medical students during the COVID-19 pandemic: a Saudi national study. J. Ment. Health Train. Educ. Pract. 2022; 17(4): 323–334. Publisher Full Text\n\nDoman L, Le Roux A: The causes of loneliness and the factors that contribute towards it: a literature review. Tydskrif Vir Geesteswetenskappe. 2010; 50(2): 216–228.\n\nPark C, Majeed A, Gill H, et al.: The effect of loneliness on distinct health outcomes: a comprehensive review and meta-analysis. Psychiatry Res. 2020; 294: 113514. PubMed Abstract \| Publisher Full Text\n\nYaghmour NA, Brigham TP, Richter T, et al.: Causes of death of residents in ACGME-accredited programs 2000 through 2014: implications for the learning environment. Acad. Med. 2017; 92(7): 976–983. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKeiner C, Nestsiarovich A, Celebi J, et al.: Loneliness Among Medical Students, Physician Trainees and Faculty Physicians. Acad. Psychiatry. 2023; 1–7. Publisher Full Text\n\nAggarwal K, Singh SK, Chopra M, et al.: Role of social media in the COVID-19 pandemic: A literature review. Data mining approaches for big data and sentiment analysis in social media. 2022; 91–115. Publisher Full Text\n\nAbbas J, Wang D, Su Z, et al.: The role of social media in the advent of COVID-19 pandemic: crisis management, mental health challenges and implications. Risk Manag. Healthc. Policy. 2021; 14: 1917–1932. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZhao N, Zhou G: Social media use and mental health during the COVID-19 pandemic: Moderator role of disaster stressor and mediator role of negative affect. Appl. Psychol. Health Well Being. 2020; 12(4): 1019–1038. 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PubMed Abstract \| Publisher Full Text\n\nZhang MW, Lim RB, Lee C, et al.: Prevalence of internet addiction in medical students: a meta-analysis. Acad. Psychiatry. 2018; 42: 88–93. PubMed Abstract \| Publisher Full Text\n\nGong R, Zhang Y, Long R, et al.: The impact of social network site addiction on depression in Chinese medical students: A serial multiple mediator model involving loneliness and unmet interpersonal needs. Int. J. Environ. Res. Public Health. 2021; 18(16): 8614. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMunir T, Shafiq S, Ahmad Z, et al.: Impact of loneliness and academic stress on psychological well being among college students. Academic Research International. 2015; 6(2): 343.\n\nBerduzco-Torres N, Medina P, Choquenaira-Callañaupa B, et al.: Family loneliness: its effects in the development of empathy, teamwork and lifelong learning abilities in medical students. Front. Psychol. 2020; 11: 2046. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRussell DW: UCLA Loneliness Scale (Version 3): Reliability, validity, and factor structure. J. Pers. Assess. 1996; 66(1): 20–40. PubMed Abstract \| Publisher Full Text\n\nWilcha R-J: Effectiveness of virtual medical teaching during the COVID-19 crisis: systematic review. JMIR medical education. 2020; 6(2): e20963. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nErnst M, Niederer D, Werner AM, et al.: Loneliness before and during the COVID-19 pandemic: A systematic review with meta-analysis. Am. Psychol. 2022; 77(5): 660–677. Publisher Full Text\n\nPennington N: Communication outside of the home through social media during COVID-19. Comput. Hum. Behav. Rep. 2021; 4: 100118. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBruguera C, Guitert M, Romeu T: Social media in the learning ecologies of communications students: Identifying profiles from students' perspective. Educ. Inf. Technol. (Dordr). 2022; 27(9): 13113–13129. Publisher Full Text\n\nMarciano L, Ostroumova M, Schulz PJ, et al.: Digital Media Use and Adolescents' Mental Health During the Covid-19 Pandemic: A Systematic Review and Meta-Analysis. Front. Public Health. 2022; 9: 9. Publisher Full Text\n\nCheshmehzangi A, Zou T, Su Z: The digital divide impacts on mental health during the COVID-19 pandemic. Brain Behav. Immun. 2022; 101: 211–213. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKauhanen L, Wan Mohd Yunus WMA, Lempinen L, et al.: A systematic review of the mental health changes of children and young people before and during the COVID-19 pandemic. Eur. Child Adolesc. Psychiatry. 2023; 32(6): 995–1013. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGeirdal AØ, Ruffolo M, Leung J, et al.: Mental health, quality of life, wellbeing, loneliness and use of social media in a time of social distancing during the COVID-19 outbreak. A cross-country comparative study. J. Ment. Health. 2021; 30(2): 148–155. PubMed Abstract \| Publisher Full Text\n\nZhang H, Yang J, Li Y, et al.: The Patterns and Predictors of Loneliness for the Chinese Medical Students Since Post-Lockdown to New Normal With COVID-19. Front. Public Health. 2021; 9: 679178. Publisher Full Text\n\nGuo AA, Crum MA, Fowler LA: Assessing the Psychological Impacts of COVID-19 in Undergraduate Medical Students. Int. J. Environ. Res. Public Health. 2021; 18(6). Publisher Full Text\n\nLee CM, Juarez M, Rae G, et al.: Anxiety, PTSD, and stressors in medical students during the initial peak of the COVID-19 pandemic. PLoS One. 2021; 16(7): e0255013. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZhang M, Qin L, Zhang D, et al.: Prevalence and factors associated with insomnia among medical students in China during the COVID-19 pandemic: characterization and associated factors. BMC Psychiatry. 2023; 23(1): 140. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLisitsa E, Benjamin KS, Chun SK, et al.: Loneliness among young adults during COVID-19 pandemic: The mediational roles of social media use and social support seeking. J. Soc. Clin. Psychol. 2020; 39(8): 708–726. Publisher Full Text\n\nBonsaksen T, Schoultz M, Thygesen H, et al.: Loneliness and Its Associated Factors Nine Months after the COVID-19 Outbreak: A Cross-National Study. Int. J. Environ. Res. Public Health. 2021; 18(6). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBoursier V, Gioia F, Musetti A, et al.: Facing Loneliness and Anxiety During the COVID-19 Isolation: The Role of Excessive Social Media Use in a Sample of Italian Adults. Front. Psych. 2020; 11: 586222. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nEllard OB, Dennison C, Tuomainen H: Interventions addressing loneliness amongst university students: a systematic review. Child Adolesc. Mental Health. 2022. PubMed Abstract \| Publisher Full Text\n\nHickin N, Käll A, Shafran R, et al.: The effectiveness of psychological interventions for loneliness: A systematic review and meta-analysis. Clin. Psychol. Rev. 2021; 88: 102066. PubMed Abstract \| Publisher Full Text\n\nSun Y, Lin SY, Chung KKH: University Students' Perceived Peer Support and Experienced Depressive Symptoms during the COVID-19 Pandemic: The Mediating Role of Emotional Well-Being. Int. J. Environ. Res. Public Health. 2020; 17(24). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNashwan AJ, Mathew RG, Anil R, et al.: The safety, health, and well-being of healthcare workers during COVID-19: A scoping review. AIMS Public Health. 2023; 10(3): 593–609. Publisher Full Text\n\nNguyen M: Why medical school is depressing and what we should be doing about it. Australian Medical Student Journal. 2011; 2(1): 65–68.\n\nSmith KE, Norman GJ, Decety J: Increases in loneliness during medical school are associated with increases in individuals’ likelihood of mislabeling emotions as negative. Emotion. 2022; 22(4): 740–750. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLabrague LJ, Jaad S, Falguera C: Social and emotional loneliness among college students during the COVID-19 pandemic: the predictive role of coping behaviours, social support, and personal resilience.2021." }	[ { "id": "229584", "date": "20 Dec 2023", "name": "Henok Dagne", "expertise": [ "Reviewer Expertise Public Health", "Epidemiology", "Reviews (Scoping", "methodological", "systematic and meta-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\nOverall comments While the review raises important and relevant topics, evidence from qualitative studies is lacking. As experience is better captured using qualitative studies, including qualitative studies would have enriched the findings of this study. There are concepts that need definition in the review. These include concepts such as pre-covid era and post-covid era, the digital age, engagement theory, healthy social media use, excessive social media use and others which are confusing unless appropriately defined. Detailed transparent search strategy: one limitation of this review is the lack of rigorous methodology. Although it is not expected to have every detail of the search strategy as a systematic review, the review could have benefited from a detailed method section. Authors may include the search strategy and search terms used as an appendix in the revised version. As long as the search strategy is systematic, a clear description of how the articles have been screened, who screed them, and how disagreements have been solved has to be described. The review did not include limitations. Including review limitations will strengthen the review so that readers will be able to read the findings keeping in mind the limitations.\n\nSpecific comments Abstract: The abstract failed to summarise the review results. What is written in the abstract section is too general. Introduction: The introduction lacks focus. Authors may reduce significant portion of the following \"In December 2019, an outbreak of pneumonia with an unknown cause was reported in Wuhan, China. Investigation revealed that the cases were linked to the Huanan Seafood Wholesale Market. Scientists were able to isolate a novel respiratory virus from respiratory samples, which was later identified as a new coronavirus belonging to the same family as the virus causing severe acute respiratory syndrome (SARS).2 This new coronavirus was named SARS-CoV-2 and is responsible for the disease known as COVID-19. The rapid global spread of SARS-CoV-2 and the significant number of deaths led to the declaration of a pandemic by the World Health Organization in March 2020.2 Beside the increased morbidity and mortality that resulted from the spread of this virus, the impact of the COVID-19 pandemic has been immense; as governments around the world have implemented lockdown measures to isolate the infection, resulting in economic consequences, and increased poverty worldwide. \" and focus more on the impact of the pandemic on loneliness. Lots of information is cited from a single study reference #5. This may not always be wrong, but authors could have included other studies, too. The definition provided in paragraph 3 is misplaced. Authors may define the concept before the last statement of the first paragraph. The introduction should show the relevance of the review by uncovering the reasons that led to undertaking the narrative review. Along with this, why authors have opted for narrative reviews over the other types of reviews could have been justified. Literature search: SANARA guideline is not a guide lane for search strategy it is a reporting quality appraisal tool. \" systematic search strategy was employed that adhered to the SANRA guidelines.\" is confusing. Authors may clearly show how many articles were screed for full text and how many of them were included in the last narrative review. 3. The pre-covid state of loneliness The first statement is repetition. The next statement \"Studies have revealed that loneliness....\" cited a single reference 15. 6. The post-COVID scenario and the evolving role of social media \"While numerous studies have explored the immediate impact of COVID-19 loneliness on the mental health...\" cite at least some of these studies. Figure 1: How did the authors reach at numbers displayed in the figure as 30%, 45%, 60%, 70% etc. ? 8. conclusion \"Unique loneliness experiences of medical students compared to other students stress the need for specific understanding and support.\" This needs to be supported with evidence in the main text. While the authors mentioned medical students are more prone to loneliness as compared to the general population, the case is not well developed for comparing medical students with students of other disciplines.\n\n\"Longitudinal studies to investigate the long-term impact of pandemic-induced loneliness on medical students' mental health, career choices, and overall functioning are essential. this statement has a number of issues; first, is it really unique for medical students? second, whether studies on the long-term effect of loneliness on career choice are available from the main text. It appears in the conclusion section out of nowhere. Also \"There is an urgent need to develop specific interventions targeting medical students' unique needs in the post-COVID era, as current interventions remain insufficient.\" The literature in the main text did not show current interventions remain insufficient.\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? No", "responses": [ { "c_id": "11642", "date": "27 Jun 2024", "name": "Abdulqadir Nashwan", "role": "Author Response", "response": "Response to Overall Comments: - We acknowledge the importance of qualitative evidence in capturing experiential aspects. However, this is not a systematic review and is not meant to capture all the published literature. - We agree that clarity is essential for understanding. However, this will be beyond the aim and focus of this review. - We appreciate the feedback on our search strategy and methodology. Again, this is a narrative review and not expected to follow a systematic search strategy same as systematic reviews. We will add a section on our review's limitations. \"This narrative review has several limitations that should be considered when interpreting the findings. Firstly, while the review aims to synthesize a broad range of literature, including primarily English-language studies may have omitted relevant findings published in other languages, potentially introducing language bias. Secondly, the narrative approach, although beneficial for a comprehensive overview, does not allow for the quantitative synthesis of data which might lead to less precise conclusions compared to systematic reviews or meta-analyses. The reliance on published literature may also introduce publication bias, as studies with significant or positive results are more likely to be published than those with null or negative outcomes. Moreover, the definitions of key concepts such as \"loneliness\" and \"social media use\" were broadly interpreted and might vary between studies, potentially affecting the consistency of the results. Finally, the evolving nature of research on COVID-19 means that more recent studies or emerging data might not have been included, which could affect the review’s comprehensiveness and relevance over time.\" Abstract: We will revise the abstract to ensure it concisely summarizes the key results of the review, focusing more on specific findings rather than general statements. \"This narrative review explores loneliness among medical students, particularly heightened during the COVID-19 pandemic. This review aims to narratively describe how the digital age, both pre- and post-pandemic, influences loneliness and to assess the psychological effects of the pandemic on medical students. Our literature search, adhering to SANRA guidelines, scrutinized studies published in the last ten years focusing on loneliness among medical students. Our findings reveal that medical students experienced significant loneliness during the pandemic, attributed to virtual learning environments and decreased social interactions. Notably, the transition to online education has mitigated and exacerbated feelings of isolation. The review also highlights the dual role of social media in either alleviating or intensifying loneliness, depending on usage patterns and platform types. Overall, our study underscores the need for targeted interventions and support systems to address the mental well-being of medical students in the digital age and beyond, providing crucial insights for future research and policy-making in educational and psychological support frameworks.\" - The introduction will be sharpened to focus specifically on the pandemic's impact on loneliness, reducing the background details on COVID-19’s origins and global impact, which, while informative, detract from the main topic. - We will broaden our citation base to include multiple sources, ensuring a more robust representation of existing research and reducing the reliance on single study references. - We will rearrange the placement of key definitions to appear earlier in the text, ensuring they are established before extensive discussion. - The rationale for opting for a narrative review over other review types will be clearly articulated, highlighting its relevance and effectiveness in addressing the research questions. - We will correct the confusion regarding the SANRA guidelines and clarify the actual process used in the literature search, including the number of articles screened and included. - Figure 1 Clarification: we mainly relayed on several estimates such as https://www.sciencedirect.com/science/article/pii/S0165032722012319#t0005 and https://www.ingentaconnect.com/content/ben/cpsr/2015/00000011/00000002/art00003. - We will ensure that statements in the conclusion about the unique experiences of medical students are well-supported with evidence from the main text. We will also clarify the scope and necessity of proposed longitudinal studies and interventions tailored to medical students, ensuring the discussion is directly tied to evidence presented in the review." } ] } ]	1	https://f1000research.com/articles/12-1196
https://f1000research.com/articles/12-655/v1	13 Jun 23	{ "type": "Research Article", "title": "In silico screening for potential inhibitors from the phytocompounds of Carica papaya against Zika virus NS5 protein", "authors": [ "Kishore Krishna Kumaree", "Naga Venkata Anusha Anthikapalli", "Anchalee Prasansuklab", "Kishore Krishna Kumaree", "Naga Venkata Anusha Anthikapalli" ], "abstract": "Background: The Zika virus (ZIKV) infection has emerged as a global health threat. The causal reasoning is that Zika infection is linked to the development of microcephaly in newborns and Guillain-Barré syndrome in adults. With no clinically approved antiviral treatment for ZIKV, the need for the development of potential inhibitors against the virus is essential. In this study, we aimed to screen phytochemicals from papaya (Carica papaya L.) against NS5 protein domains of ZIKV. Methods: Approximately 193 phytochemicals from an online database (IMPACT) were subjected for molecular docking using AutoDock Vina against NS5-MTase protein domain (5WXB) and -RdRp domain (5UO4). Results: Our results showed that β-sitosterol, carpaine, violaxanthin, pseudocarpaine, Δ7-avenasterols, Rutin, and cis-β-carotene had the highest binding affinity to both protein domains, with β-sitosterol having the most favorable binding energy. Furthermore, ADME analysis revealed that selected compounds had good pharmacokinetic properties and were nontoxic. Conclusions: Our findings suggest that papaya-derived phytochemicals could be potential candidates for developing antiviral drugs against ZIKV. However, further experimental studies using cell lines and in vivo models are needed to validate their efficacy and safety.", "keywords": [ "Molecular docking", "Zika virus", "Papaya", "AutoDoc Vina" ], "content": "Introduction\n\nZika virus (ZIKV), belonging to the family Flaviviridae, is a mosquito-transmitted virus that infects humans through the biting of Aedes mosquitos (Aedes aegypti).1 Though the ZIKV was first reported in 1947 in Uganda, the severity of this virus was globally noticed during its outbreak in the years 2015–2017 in Brazil, and later the infection spread to 46 other countries.2,3 Furthermore, the recent outbreak was associated with severe neurological abnormalities such as microencephaly in foetuses, Guillain-Barré syndrome in adults and newborns due to infected mothers.4–6\n\nZIKV is an enveloped virus characterized by the presence of a single-stranded RNA genome.5,7 The genome of ZIKV encode a single polyprotein (~3400 amino acids), which is translated to three structural proteins (capsid-C, pre-membrane/membrane-prM, and envelope–E) and seven non-structural proteins (NS1, NS2A, NS2B, NS3, NS4A, NS4B, and NS5) using host and viral proteases (Figure 1).8 Despite the significant efforts of the scientific community, there is currently no specific therapy available for treating ZIKV infection, making developing such antivirals a critical priority.9,10 Antivirals that could target protein structures involved in genome replication, viral fusion, and RNA synthesis can be highly effective against the ZIKV. Among all the proteins expressed by ZIKV, the most significant and most conserved protein is the non-structural-5 or NS5, which is the polymerase enzyme; it consists of two major domains: RNA methyltransferase (MTase) at its N-terminus and RNA-dependent-RNA polymerase (RdRp) at its C-terminal.11 RdRP is an essential protein domain for initial viral replication, whereas the MTase domain is responsible for RNA capping of the viral genome. The structure of NS5 is exclusive to ZIKV and has no similarity with the host system, which makes it a unique target for inhibitors against ZIKV.12\n\nThe ZIKV polyprotein is composed of seven non-structural proteins (NS1, NS2A, NS2B, NS3 protease and helicase domains, NS4A, NS4B, NS5 methyltransferase, and RNA polymerase domains) and three structural proteins (C, M, and E). In addition, NS5 methyltransferase and RNA polymerase domains’ structures were retrieved from PDB databases.\n\nContinued clinical research is necessary to discover new antivirals. Considering the lower toxicity of plant-derived compounds,13,14 they serve as promising leads for the development of novel antiviral agents against various viruses, including Zika, through various mechanisms involving inhibition of viral replication, modulation of host immune response, and blocking viral entry into host cells.15–19 Molecular modelling techniques are widely used to study the dynamics, energy, and interactions between biomolecules, including proteins. These techniques are used extensively to study protein-ligand interaction and to predict the drug’s binding mode within the protein’s binding site. Through in silico analysis, several studies have identified potential phytochemicals and their impact on target proteins of humans.20–23\n\nHenceforth for this project, we have carried out in silico molecular docking analysis for potential anti-ZIKV compounds from Carica papaya (commonly referred to as papaya), an edible tropical fruit well-known for its many medicinal properties.24 Papaya contains bioactive substances, including alkaloids, flavonoids, and phenolic acids, which have been reported to exhibit various pharmacological effects, including antioxidant, anti-inflammatory, immunomodulatory, and antiviral activities.25,26 Previous in silico studies have documented the potential therapeutic effects of papaya in various human diseases,27–29 including an earlier study on identifying inhibitory compounds (e.g., luteolin) that targeted the dengue virus’s NS2B/NS3 protease (DENV).30,31 Given that ZIKV and DENV are members of the Flaviviridae family, we proposed to virtually investigate small molecules from papaya with possible targeting ZIKV NS5 protein domains, and to the best of our knowledge, no prior studies have investigated this possibility.\n\nThe paper aims to conduct a virtual screening of bioactive molecules from papaya, followed by ADMET assessment. Through molecular docking analysis using Autodoc Vina, we identified compounds that showed a promising binding affinity with the ZIKV’s NS5 protein domains (MTase and RdRp). Thus, they constitute potential drug targets, and our results may contribute toward developing effective treatments against this public health priority.\n\n\nMethods\n\nPhytocompounds of Carica papaya were selected from the plant database IMPACT and previously published literature (see the Underlying data, Supplementary Table S1).31–35 The ligands’ 3-dimensional (3-D) structures were retrieved from the PubChem database. The ligands underwent a series of adjustments, such as the addition of polar hydrogens, adding charges, and conducting energy minimization using PyRx Virtual Screening Tool software (v-0.8) (RRID:SCR_018548) with the default parameters.36\n\nThe crystal structures of the ZIKV proteins were retrieved from the PDB database. These included the SAH-binding site of NS5-MTase, and NS5 RNA-dependent RNA polymerase with their PDB entry 5WXB37 and 5UO4,38 respectively. Sinefungin and Sofosbuvir were included as the reference inhibitors for NS5-MTase and NS5 RdRp, respectively. In accordance with standard protocol, the protein structures were treated as receptors. At the start of docking, the receptor protein was optimized by removing any unrelated substructure. Then, the side chains in the protein structure were corrected using default settings like addition of hydrogens and removal of water molecules. The Molprobity server evaluated selected proteins’ stereo-chemical properties and Ramachandran graph.39 Chimera 1.16 (RRID SCR_004097) generated any residues missing in the selected target protein. After removing nonstandard heteroatoms, polar hydrogens, and Gasteiger charge were added. Next, the structural aspects of all targets were enhanced using the steepest decent (100 steps) and conjugate gradient algorithms (0 steps) with an Amber force field (Amber Ff14SB).39 The energy-minimized proteins were then converted into ‘pdbqt’ format using AutoDock Tools 1.5.7 (RRID SCR_012746) by AutoDock.\n\nDocking was performed with Autodock Vina,40,41 as described in a previous study.42 Briefly, the grid box’s dimensions were fixed at XYZ = 30 Å × 30 Å × 30 Å XYZ = 30 Å × 30 Å × 30 Å which was found to be the best size for the default exhaustiveness (= 8), and the ligand binding site was positioned in the middle of the grid box. AutoDock Vina version 1.1.2 (RRID:SCR_011958) was used to calculate each ligand’s binding energy and pose against the selected protein receptors. Each ligand’s best interaction energy scores (kcal/mol) were ranked and plotted against the reference inhibitor. The results obtained are limited to nine binding modes. The log file included a list with increasing binding energies and binding modes. The binding modes were viewed using the BIOVIA Discovery Studio visualizer - v21.1.0.20298 (Dassault Systemes BIOVIA, Discovery Studio, 2021, SanDiego).43\n\nThe compounds’ molecular properties and drug-like characteristics were assessed using “Lipinski’s Rule of Five” as the basis of analysis.44 First, 19 phytocompounds were analyzed regarding their physicochemical properties, drug-likeness, toxicity, and ADME properties (including absorption, diffusion, metabolism, and excretion) using ADMETlab 2.0 and SwissADME. In addition, the physicochemical features of compounds, including lipophilicity (log P), solubility (log S), and polar surface area and volume (PSA), were predicted. The mentioned parameters are necessary as they influence how a drug interacts with transport proteins and enzymes involved in drug clearance.\n\n\nResults molecular docking\n\nFor the molecular docking analysis, around 193 compounds found in papaya were docked against the two domains of ZIKV protein NS5 MTase (5WXB) and RdRp (5UO4).32 As positive ligands, Sinefungin against NS5-MTase and Sofosbuvir against NS5-RdRp were docked. Sinefungin had a binding affinity of -8.1 kcal/mol, whereas the binding affinity for Sofosbuvir was -7.4 kcal/mol.\n\nBinding affinity is an essential preliminary parameter for assessing a potential candidate drug. Therefore, first of all, we assessed the binding affinity of the candidate drug and compared it with the positive controls (Sinefungin and Sofosbuvir against 5WXB and 5UO4, respectively). The initial docking analysis helped in narrowing down to 19 shortlisted compounds which showed higher affinity compared to their respective positive ligands, mentioned in Figure 2. Figure 3A shows the heat map of the binding affinity of the ligands, lowest energy/highest affinity corresponding to red color, whereas the blue color indicates the highest binding energy or/lowest affinity.\n\nFor the MTase domain (5WXB), rutin has the strongest binding affinity with a binding energy of -9.80 kcal/mol, followed by Δ7-avenasterol (-9.20 kcal/mol), β-sitosterol (-9.10 kcal/mol), cis-β-carotene (-8.90 kcal/mol) and pseudocarpaine (-8.90 kcal/mol). On the other hand, the weakest binding affinity is shown by γ-carotene, with a value of -7.00 kcal/mol. Whereas for the RdRp domain of NS5 (5UO4), the ligand Δ7-avenasterol shows the highest binding affinity, followed by dehydrocarpaine-II and pseudocarpaine. Several ligands (rutin, carpaine, Δ7-avenasterol, β-sitosterol, pseudocarpaine, cis-β-carotene, violaxanthin) showed a better binding affinity with both the domains of NS5- protein (Figure 3B). Figure 4 shows the 3D and 2D structure of the common ligands, which showed higher docking ability towards both the domains of NS5 protein; however, the remaining ligand complexes are mentioned in the Underlying data, Figures S1 and S2.32 Among these bispecific compounds, rutin showed the highest binding affinity for both protein domains, followed by carpaine.\n\nHydrogen bonds and hydrophobic interactions play a critical role in molecular docking, and these interactions are key components in identifying potential drugs. As mentioned in Table 1, rutin forms the highest number of hydrogen bonds involving 14 amino acid residues (ARG84, GLY86, LYS182, ARG213, CYS82, GLU218, GLU149, GLU149, GLY109, THR104, GLU111, HIS110, HIS110, LYS61) and the bonding distance ranging from 2.27 to 3.08 Å; however, rutin had no hydrophobic interaction with the MTase domain (Figure 4). In hydrophobic interactions, Δ7-Avenasterol and cis-β-Carotene form the highest number (5) bonds with the MTase domain. Ligands interaction with the RdRp domain of NS5 (Table 2, Figure 4) shows that rutin has formed the highest number of hydrogen bonds (ARG794, ARG794, THR795, THR796, GLY793, SER798) and three hydrophobic interactions. α-Carotene forms the highest number of hydrophobic interactions with the RdRp domain and has no hydrogen bonding.\n\nADMET and drug-likeness evaluation provide insight into the properties of drugs based on their chemical structure. The best docked ligands (Figure 2) were analyzed for their pharmacokinetic properties. The evaluation criteria were based on solubility, gastrointestinal absorption (GI), blood-brain barrier (BBB) permeability, and Lipinski’s rules violation.\n\n(BBB - permeability = YES or > 0.1); (GI - absorption = high); (Carcinogenicity = 0 to 0.3); (PAINS alert = 0) and (Lipinski’s violation = 0).\n\nAll the compounds mentioned in Figure 2 were screened through ADMET for their suitability as a drug. The screening through ADMETLab 2.0 revealed that several compounds were approved under Lipinski criteria. BBB values reflect the ability of the ligands to cross the brain barrier, with a higher score value indicating greater permeability. β-Sitosterol has the highest BBB penetration with a score of 0.84, suggesting effective crossing. Carpaine showed to have poor penetration with a BBB score of 0.01. BBB values ranged between 0.01 and 0.001, indicating poor barrier crossing. Riboflavin, rutin, and all-trans-neoxanthin displayed moderate BBB permeability values ranging 0.111 to 0.444, while several had BBB penetration below 0.1, suggesting the limited ability to cross the BBB (see the Underlying data, supplementary Table S2.32\n\nTable S2 (Underlying data32 also signifies the ligands’ permeability based on Caco-2 cell permeability values, which translates to intestinal epithelium permeability. For example, β-sitosterol had the highest Caco-2 cell permeability value at -4.756, signifying improved intestinal permeability. On the other hand, carpaine showed poor intestinal epithelium permeability of -4.985. Table S2 (Underlying data32) suggests ligands and their respective Lipinski’s rule of five compliance. Among these ligands, β-sitosterol, violaxanthin, riboflavin, all-trans-neoxanthin, dehydrocarpaine-I, dehydrocarpaine-II, and β-carotene are Lipinski’s-rule-of-five compliant and are considered to be drug-like compounds.\n\n\nDiscussion\n\nEmerging viruses such as Dengue, Zika, Ebola, SARS-CoV2, and other infectious viruses demonstrate that the current antiviral therapeutic regimen is insufficient for these pathogens.45 The coronavirus 2019 (COVID-19) pandemic further highlighted this inadequacy. Vaccine development is a time-consuming and lengthy process, which also faces the challenges of large-scale administration. Moreover, the faster-evolving attribute of RNA viruses also makes it challenging to develop a particular antiviral treatment,46 one such RNA virus, Zika, continues to remain a global concern. Zika-related disorders are mainly found in infants but can also affect adults. Zika-related disorders reported in adults were the cases of Guillain Barre’ Syndrome,47 Myelitis,48 Meningoencephalitis,49 and Uveitis.50 Currently, no approved drugs nor vaccines are available for treating ZIKV infection.\n\nPlant-derived natural compounds are promising alternatives for treating infections with minimal side effects. Medicinal plants are the richest source of new drugs, including antivirals targeting several human ailments. Previous clinical studies have demonstrated the successful inhibition of Dengue infection by papaya extract.51,52 Phytochemical screening of papaya has been reported to constitute several compounds, including alkaloids, terpenoids, flavonoids, saponins, steroids, tannins, and phenols, which have potent therapeutic effects against several human diseases, such as inflammation, oxidative stress, antiviral and hypoglycemia.53,54 Since Zika and Dengue belong to the same Flaviviridae family of viruses, we hypothesized that papaya could also serve as the source for identifying potential inhibitors against ZIKV infection. In this context, in the present study, we have performed molecular docking to identify possible lead compounds from papaya against NS5 protein domains of the ZIKV.\n\nInitially, we screened 193 papaya-derived phytochemicals to know their molecular docking potential with the NS5 protein domains of the ZIKV. Our analysis revealed seven compounds (β-sitosterols, carpaine, violaxanthin, rutin, β-carotene, pseudocarpaine, and Δ7-avenasterol) that exhibited bispecific docking activity against both NS5 domains, with higher docking scores compared to their respective positive ligands (Sinefungin and Sofosbuvir against 5WXB and 5UO4, respectively) (Figure 3A). The MTase activity of the ZIKV NS5 protein plays a crucial role in the replication and spread of the virus.55 Hence, inhibiting this activity can be an effective strategy to prevent the virus from spreading. Previous studies explored small molecule inhibitors and RNA-based inhibitors against ZIKV infections. For instance, Sinefungin is a small molecule that has been shown to inhibit the MTase activity of several flaviviruses.56 However, the study showed a low potency of Sinefungin on NS5 of ZIKV compared to other flaviviruses’ MTase domain; additionally, the toxicity associated with the particular drug had raised concern about its use.57\n\nHydrogen bonding and hydrophobic interactions are crucial in facilitating significant ligand binding at the active site residues of the receptor in docked complexes.58 The bioactive compounds in this study were found to form hydrogen bonds and hydrophobic interactions with MTase. In the present study, flavonoid compounds, like rutin, showed the highest binding affinity to the NS5-MTase domain (5WXB), followed by riboflavin. Rutin formed a complex that entirely occupied the protein through 14 hydrogen bonding interactions with no hydrophobic interactions, and riboflavin interacted with NS5-MTase through nine hydrogen bonds (Table 1, Figure 4). Moreover, the interacting residues were identified as essential residues of the substrate binding of the MTase.59 The observed hydrogen bonding interactions between the selected compounds from papaya and MTase suggest that these compounds may effectively occupy the substrate binding site of MTase, making them promising lead compounds for drug development against ZIKV infection. Furthermore, the present study also indicates that phytocompounds from papaya showed several forms of strong and stable bonds like carbon-hydrogen, pi-alkyl, van der Waals, covalent, hydrophobic, and electrostatic bonds with the receptor ligands (Tables 1 and 2).\n\nThe ZIKV RdRp constitutes another important target for inhibiting ZIKA viral replication.60 ZIKV RdRp consists of two binding sites, the first one being the active site (formed by Asp535, Trp797, and Ile799), while the other site is the allosteric or N pocket, which contains the priming loop that is essential for stabilizing the initiation complex and releasing new dsRNA.61 In this study for docking to the RdRp domain (5UO4), the result reveals that rutin, has the highest number of hydrogen bond interactions (with ARG794, ARG794, THR795, THR796, GLY793, SER798) and hydrophobic interactions (involving ARG794, MET806, ALA408 amino acids) compared to the positive ligand, Sofosbuvir (Table 2, Figure 4).\n\nPhytosterols are naturally occurring plant molecules with a structure similar to cholesterol,62 and they have been demonstrated to possess antiviral activity of several sterols against the spike protein of the COVID-19 virus and influenza-A virus.56,63 Our study identified several phytosterols, including β-sitsterol and Δ7-avenasterol, demonstrating potent inhibitory affinity (Figure 3A). Earlier studies have also shown the potential health benefits including antiviral effects of β-sitosterol, which has been shown to reduce the infectivity of the hepatitis-B virus and HIV, possibly by hindering the attachment of viruses to host cells.64 Another study on HIV patients found that the combination of β-sitosterol and β-sitosterol glycoside helped maintain stable CD4 cell counts and significantly reduced plasma viral loads.65\n\nAlkaloids have also been shown to inhibit DNA and/or RNA synthesis in multiple viruses, including human coronavirus and herpes simplex virus.66–68 Our docking studies identified alkaloids like carpaine and pseudocarpaine (Figure 3A) with higher binding affinity to both target protein domains compared to positive ligands. Besides, another alkaloid dehydrocarpaine-II had a good binding score (-8.8 kcal/mol) only towards the protein NS5- RdRp domain. Therefore, binding to the RdRp domain may help inhibit normal virus replication. Whereas in the carpaine-5UO4 complex, it completely had no interaction with the protein through hydrogen or hydrophobic bonding.\n\nApart from it, several carotenoids had also shown good binding affinity to both domains of NS-5. Especially, caretenoids such as α-carotene, β-carotene, citroxanthin, β-cryptoxanthin, γ-carotene, violaxantin, zeaxanthin showed higher binding affinity to NS5-RdRp than NS5-MTase. Carotenoids have a variety of applications, including anticancer, anti-inflammatory, and antioxidant properties, as well as anti-obesity.69–71 Moreover, carotenoids also possess antiviral properties.72–74 Also, recent studies have proven the antiviral properties of carotenoids against COVID-19.75\n\nAs part of drug development, conducting in silico analyses on compounds to assess their absorption, distribution, metabolism, and excretion (ADME) properties is critical.76 Failure to accurately simulate these attributes or assess any toxicities may cause inhibitors to fail the screening process and thus fall outside its criteria for approval.77 An important consideration when developing drugs to treat central nervous system (CNS) conditions is BBB penetration.78 Cytochrome P450 (CYP) isozymes metabolize drugs, fatty acids, steroids, bile acids, and carcinogens.79 Approximately 75% of phase-1 drug metabolism processes involve CYP enzymes.80 Various CYP inhibitor and substrate scores were calculated in this metabolism, and the result shows that the shortlisted compounds are non-substrates and non-inhibitors of CYP enzymes (Underlying data, supplementary Table S232). Our ADME analysis (Underlying data, supplementary Table S232) demonstrated that 19 of the best docked compounds (Figure 2) had nontoxic properties. Lipinski’s rule of five was violated for 10 compounds (Underlying data, supplementary Table S232). However, the remaining compounds (carpaine, dehydrocarpaine I, dehydrocarpaine II, pseudocarpaine, Δ7-avenasterol, all-trans-neoxanthin, riboflavin, β-sitosterol, and violaxanthin) were found to be acceptable candidates based on Lipinski’s rule of five.\n\nBased on our in silico virtual screening study, we can state that Carica papaya has several bioactive compounds that could exert potent antiviral activity against ZIKV. The spread of ZIKV poses a global public health concern. In addition, ZIKV infection can result in neurological illnesses, with no FDA-approved antiviral therapy currently available. Computational approaches offer cost-effective and time-efficient drug development alternatives. Therefore, we screened for antiviral compounds derived from Carica papaya against ZIKV’s non-structural protein NS5 to find potential inhibitors for this virus. Through molecular docking, we identified seven compounds showing favourable binding energy against both ZIKV N5 -MTase and -RdRp domains, indicating their potential as antiviral drugs for ZIKV. Future studies should evaluate the safety and efficacy of these compounds in preclinical and clinical trials. These findings offer a promising path for developing and producing safe, natural antiviral drugs against the ZIKV.", "appendix": "Data availability\n\nProtein Data Bank: crystal structure of ZIKV MTase in complex with SAH. Accession number 5WXB; https://doi.org/10.2210/pdb5WXB/pdb .\n\nProtein Data Bank: Structure of human neuronal nitric oxide synthase heme domain in complex with 3-[(2-amino-4-methylquinolin-7-yl)methoxy]-5-(2-(methylamino)ethyl) benzonitrile. Accession number 5UO4; https://doi.org/10.2210/pdb5UO4/pdb .\n\nZenodo: In silico screening for potential inhibitors from the phytocompounds of Carica papaya against Zika virus NS5 protein. https://doi.org/10.5281/zenodo.7920519 . 32\n\nThis project contains the following underlying data:\n\n• 3D structure-Papaya compounds-IMPACT.zip (3D structures of all the compounds downloaded from IMPACT database)\n\n• NS5- protein.zip (3D structures of both the protein domains of NS5 protein)\n\n• supplementary Figures.docx\n\n• Supplementary Table S1.xlsx (Molecular docking result of all the downloaded compounds)\n\n• supplementary Table S2.xlsx (ADMETlab 2.0 information of the shortlisted compounds)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgements\n\nKishore K. 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Metab. 2008; 5: 1–10." }	[ { "id": "214337", "date": "18 Oct 2023", "name": "Arumugam Vijaya Anand", "expertise": [ "Reviewer Expertise Phytotherapeuics", "Clinical Biochemistry", "Medical Genetics" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors have put effort to evaluate the “In silico screening for potential inhibitors from the phytocompounds of Carica papaya against Zika virus NS5”. The authors describe the research undertaken with this in an organized manner, emphasizing the results obtained by them. The article needs modification for better cohesion of information to achieve the goal and the shortcomings which need to be considered. Hence, the paper can be approved after MAJOR REVISIONS are carried out.\n1. The English need improvement since there are some grammatical and syntax errors in the manuscript. For example, the words “subjected for” may be as “subjected to”; “NS5-MTase” as “the NS5-MTase”; “by ADMET” as “by an ADMET”; “addition of” as “the addition of”; “removal of” as “the removal of”; “ranging 0.111” as “ranging from 0.111”; “zeaxanthin” as “and zeaxanthin”. The grammar mistakes which are not mentioned here are also to be checked and corrected properly.\n2. There are some typing mistakes as well, and authors are advised to carefully proof-read the text. For example, the words “encode a” may be as “encodes a”; “decent” as “descent”; “Ligands” as “Ligand”; “best docked” as “best-docked”; “nor vaccines” as “no vaccines”; “other site” as “other side”; “rutin, has” as “rutin has”; “β-sitsterol” as “β-sitosterol or check correct spelling”; “caretenoids” as “carotenoids”. The typos not mentioned here are also to be checked and corrected properly.\n3. Check the abbreviations throughout the manuscript and introduce the abbreviation when the full word appears the first time in the abstract (The use of abbreviations in the abstract (ADME) section may distract readers who wish to quickly skim through several publications before deciding to read one in full) and the remaining part of the manuscript (For example, PDP, FDA, etc.,). Make a word abbreviated in the article that is repeated at least three times in the text, not all words to be abbreviated.\n4. The full form of the species should be given when the first time appears in both the abstract and in the remaining part of the manuscript and it should be followed by only the first letter of the genus (For example, Carica papaya when the first time appear and followed by C. papaya).\n5. The authors should use uniformly either “ZIKA” or “Zika” all over the manuscript for better understanding.\n6. The authors may cite recent prevalence or incidence data Zika virus (ZIKV) infection and it should be at-least of 2022 or 2023.\n7. The introduction part appears less informative about Carica papaya, thus this section should be indicated as detailed to understand the manuscript in clear since the main objectives is focused on Carica papaya. The botanical description, family name and different plants of the plant with it medicinal uses.\n8. The authors should rewrite the following “The paper aims” as “The present work or study aims”.\n9. The authors should avoid the repetition some content in the manuscript and also it affect the flow of reading. It should be carefully checked and removed. For example, the family name “Flaviviridae” of ZIKA has been mentioned in three times.\n10. The conclusion seems in general. All conclusions must be convincing statements on what was found to be novel, impact based on the strong support of the review. Moreover, the authors may also be included the limitation of the present findings for a better understanding of the manuscript.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\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": "11803", "date": "25 Jun 2024", "name": "kishore krishna kumaree", "role": "Author Response", "response": "1. The English need improvement since there are some grammatical and syntax errors in the manuscript. For example, the words \"subjected for\" may be as \"subjected to\"; \"NS5-MTase\" as \"the NS5-MTase\"; \"by ADMET\" as \"by an ADMET\"; \"addition of\" as \"the addition of\"; \"removal of\" as \"the removal of\"; \"ranging 0.111\" as \"ranging from 0.111\"; \"zeaxanthin\" as \"and zeaxanthin\". The grammar mistakes which are not mentioned here are also to be checked and corrected properly. Answer: Thank you for your detailed feedback regarding the grammatical and syntax errors in the manuscript. We have thoroughly reviewed the entire manuscript to identify and correct any other grammatical and syntax errors that were not mentioned. 2. There are some typing mistakes as well, and authors are advised to carefully proof-read the text. For example, the words \"encode a\" may be as \"encodes a\"; \"decent\" as \"descent\"; \"Ligands\" as \"Ligand\"; \"best docked\" as \"best-docked\"; \"nor vaccines\" as \"no vaccines\"; \"other site\" as \"other side\"; \"rutin, has\" as \"rutin has\"; \"β-sitsterol\" as \"β-sitosterol or check correct spelling\"; \"caretenoids\" as \"carotenoids\". The typos not mentioned here are also to be checked and corrected properly. Answer: Thank you for your detailed feedback 4in the manuscript. We have thoroughly reviewed the entire manuscript to manage necessary corrections. 3. Check the abbreviations throughout the manuscript and introduce the abbreviation when the full word appears the first time in the abstract (The use of abbreviations in the abstract (ADME) section may distract readers who wish to quickly skim through several publications before deciding to read one in full) and the remaining part of the manuscript (For example, PDP, FDA, etc.,). Make a word abbreviated in the article that is repeated at least three times in the text, not all words to be abbreviated. Answer: Thank you for your suggestion. We have reviewed the manuscript to ensure that abbreviations are introduced upon first use and are only applied to terms repeated at least three times in the text, to maintain clarity and readability. 4. The full form of the species should be given when the first time appears in both the abstract and in the remaining part of the manuscript and it should be followed by only the first letter of the genus (For example, Carica papaya when the first time appear and followed by C. papaya). Answer: Thank you for your suggestion. The corrections are made in the manuscript. 5. The authors should use uniformly either \"ZIKA\" or \"Zika\" all over the manuscript for better understanding. Answer: Thank you for your feedback. We have revised the manuscript to use \"Zika\" uniformly throughout the text for consistency and better understanding. 6. The authors may cite recent prevalence or incidence data Zika virus (ZIKV) infection and it should be at-least of 2022 or 2023. Answer: Thank you for your suggestion. We have updated the manuscript to include recent prevalence and incidence data on Zika virus infections from 2022 and 2023 to provide current and relevant information. 7. The introduction part appears less informative about Carica papaya, thus this section should be indicated as detailed to understand the manuscript in clear since the main objectives is focused on Carica papaya. The botanical description, family name and different plants of the plant with it medicinal uses. Answer: Thank you for your kind suggestion. We have updated the manuscript on the medicinal and botanical significance of papaya. 8. The authors should rewrite the following \"The paper aims\" as \"The present work or study aims\". Answer: Thank you for your suggestions. We have updated the manuscript. 9. The authors should avoid the repetition some content in the manuscript and also it affect the flow of reading. It should be carefully checked and removed. For example, the family name \"Flaviviridae\" of ZIKA has been mentioned in three times. Answer: Thank you for your feedback. We have carefully reviewed the manuscript and have reduced the redundant mentions of the family name \"Flaviviridae\" to improve clarity and coherence. 10. The conclusion seems in general. All conclusions must be convincing statements on what was found to be novel, impact based on the strong support of the review. Moreover, the authors may also be included the limitation of the present findings for a better understanding of the manuscript. Answer: Thank you for your valuable feedback. We have revised the conclusion to highlight the novel findings and their impact, ensuring that our statements are well-supported by the review. Additionally, we will include the limitations of the present study, such as the reliance on in silico methods, which need further validation through experimental and clinical studies." } ] }, { "id": "228783", "date": "29 May 2024", "name": "Luis Marquez-Dominguez", "expertise": [ "Reviewer Expertise virology", "antiviral design", "rational drug design", "and enzyme kinetics", "molecular biology." ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe quest for compounds exhibiting antiviral activity against diseases such as Zika is of paramount importance, given the absence of a definitive treatment for this ailment. However, I have several suggestions and reservations regarding the manuscript's content. Among the significant revisions required, it is observed that one of the receptors does not correspond to the Zika virus. Until the authors clarify this discrepancy, the integrity of the results, discussion, conclusions remains questionable.\n\n1. In Figure 1, the depiction of structural and non-structural proteins aligns with the complete genome. Therefore, I recommend that the box should encompass the entire genome in the virus diagram, rather than just a segment of it.\n2. Concerning the selection of receptors, the NS5 RdRp with PDB key 5UO4 corresponds to the Structure of human neuronal nitric oxide synthase heme domain in complex with 3-[(2-amino-4-methylquinolin-7-yl)methoxy]-5-(2-(methylamino)ethyl) benzonitrile, and not to the NS5 RdRp of the Zika virus. This discrepancy is also evident in the supplementary data. Was all docking and figure rendering performed using the 5UO4 structure, which does not represent the Zika NS5 RdRp? If so, a substantial portion of the results may not be reflective. I recommend a thorough verification. When compared with NS5 RdRp structures with PDB codes 5Wz3 or 5U0B, there appears to be no similarity.\n3. The methodology mentions obtaining 9 coupling results, yet it fails to specify the criteria used to select the optimal molecular coupling model. Please provide clarity on the selection process.\n4. In the section on \"Ligand and receptor molecular docking,\" the size of the grid is redundantly stated.\n5. In the \"Result Molecular Docking\" section, the references for the positive ligands (controls) do not support their selection. For example, concerning sinefungin, it is mentioned that they were designed by HVC, but there is no information related to flavivirus or Zika. The same applies to sofosbuvir. I suggest modifying the references to accurately reflect their relevance.\n6. The images exhibit low resolution, hindering effective structure visualization. Therefore, I recommend enhancing clarity for better interpretation. Specifically, in Figure 4, the sharpness is insufficient for clear visualization of 2D diagrams, and the residues interacting with molecules are not distinguishable from the representation of alpha helices and beta sheets. The legend of interactions is unreadable, and the figure caption lacks information on the meaning of each color. For improved comparison, I suggest including controls (sofosbuvir and sinefungin) in Figure 4. Additionally, consider incorporating a surface representation with electrostatic charges to highlight hydrophobic regions or regions with electrostatic charges interacting with molecules.\n7. In Figure 3, in the 5UO4 table, the control -7.40 should be white as it serves as the reference. It appears blue, possibly due to incorrectly taking the positive ligand of 5WXB as a reference. This is inaccurate, as it is a receptor and a distinct molecule.\n8. Table 1 in the docking results mentions different types of non-covalent interactions without justifying why only hydrogen bond bonds and hydrophobic interactions were considered. The discussion also lacks insights into the differences or importance of various interactions such as alkyl-alkyl, pi-alkyl, etc. I recommend ordering the amino acids in ascending order for clarity.\n9. In the discussion of interactions between molecules (rutin) versus sofosbuvir, there is mention of a greater number of interactions, but the explanation on how these interactions lead to blocking the active site is lacking. Consider discussing whether this blocking results from size or other characteristics inherent to enzymatic activity inhibition. A more in-depth discussion of the results is suggested.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [ { "c_id": "11804", "date": "25 Jun 2024", "name": "kishore krishna kumaree", "role": "Author Response", "response": "1. In Figure 1, the depiction of structural and non-structural proteins aligns with the complete genome. Therefore, I recommend that the box should encompass the entire genome in the virus diagram, rather than just a segment of it. Answer: Thank you for your suggestion, We have replaced the figure 1 with a new figure in the manuscript. 2. Concerning the selection of receptors, the NS5 RdRp with PDB key 5UO4 corresponds to the Structure of human neuronal nitric oxide synthase heme domain in complex with 3-[(2-amino-4-methylquinolin-7-yl)methoxy]-5-(2-(methylamino)ethyl) benzonitrile, and not to the NS5 RdRp of the Zika virus. This discrepancy is also evident in the supplementary data. Was all docking and figure rendering performed using the 5UO4 structure, which does not represent the Zika NS5 RdRp? If so, a substantial portion of the results may not be reflective. I recommend a thorough verification. When compared with NS5 RdRp structures with PDB codes 5Wz3 or 5U0B, there appears to be no similarity. Answer: Thank you for your meticulous review and valuable feedback. I sincerely apologize for the oversight regarding the receptor used in our study. There was indeed a typographical error in the manuscript. The correct PDB code for the Zika virus NS5 RdRp that we used for our analyses is 5U04, not 5UO4. I assure you that all docking and technical analyses were conducted using the 5U04 structure, which accurately represents the Zika NS5 RdRp. The incorrect PDB code in the text was an unfortunate typographical mistake, and we will promptly correct this in the manuscript and the supplementary data to reflect the accurate PDB code. We greatly appreciate your diligence in pointing out this discrepancy and apologize for any confusion it may have caused. Your feedback is crucial for maintaining the integrity of our work, and we will ensure that such errors are rectified to convey our research findings accurately. 3. The methodology mentions obtaining 9 coupling results, yet it fails to specify the criteria used to select the optimal molecular coupling model. Please provide clarity on the selection process. Answer: The selection of the optimal molecular model was done based on the lower binding energy (more negative value), a higher number of hydrogen bonds, and other nonbonded interactions, including hydrophobic and electrostatic interactions. In addition, conserved binding pocket interactions were also considered and compared with the known control inhibitors for the respective target proteins.We believe this multifaceted approach provides a more robust optimal model selection. 4. In the section on \"Ligand and receptor molecular docking,\" the size of the grid is redundantly stated. Answer:The redundancy mentioning of grid size has been corrected in the revised manuscript. 5. In the \"Result Molecular Docking\" section, the references for the positive ligands (controls) do not support their selection. For example, concerning sinefungin, it is mentioned that they were designed by HVC, but there is no information related to flavivirus or Zika. The same applies to sofosbuvir. I suggest modifying the references to accurately reflect their relevance. Answer: Thank you for your careful review and for highlighting the need to ensure the references for our positive control ligands are accurate and relevant. We apologize for any oversight in the current references and appreciate your suggestion to provide more relevant citations. In response to your concern and to support our selection, we have updated the manuscript and have included the following references: Sinefungin and Sofosbuvir were the reference inhibitors for NS5-MTase and NS5 RdRp, respectively. References: Hercik, K., et al., Structural basis of Zika virus methyltransferase inhibition by sinefungin. Archives of virology, 2017. 162: p. 2091-2096. Lin, Y., et al., Identification and characterization of Zika virus NS5 RNA-dependent RNA polymerase inhibitors. International journal of antimicrobial agents, 2019. 54(4): p. 502-506. Sacramento, C.Q., et al., The clinically approved antiviral drug sofosbuvir inhibits Zika virus replication. Scientific reports, 2017. 7(1): p. 40920. Tao, Z., et al., Design, synthesis and in vitro anti-Zika virus evaluation of novel Sinefungin derivatives. European Journal of Medicinal Chemistry, 2018. 157: p. 994-1004. 6. The images exhibit low resolution, hindering effective structure visualization. Therefore, I recommend enhancing clarity for better interpretation. Specifically, in Figure 4, the sharpness is insufficient for clear visualization of 2D diagrams, and the residues interacting with molecules are not distinguishable from the representation of alpha helices and beta sheets. The legend of interactions is unreadable, and the figure caption lacks information on the meaning of each color. For improved comparison, I suggest including controls (sofosbuvir and sinefungin) in Figure 4. Additionally, consider incorporating a surface representation with electrostatic charges to highlight hydrophobic regions or regions with electrostatic charges interacting with molecules. Answer: Thank you for your constructive feedback regarding the visualization quality of the images in Figure 4. We have considered your recommendations and replaced the images with higher-resolution versions to enhance clarity and facilitate better interpretation. However, at this stage, we have not incorporated surface representations with electrostatic charges to highlight hydrophobic regions and regions with electrostatic interactions. We will consider including these enhancements in future revisions to improve the visualization quality further. Additionally, we have included controls (sofosbuvir and sinefungin) in Figure 4 for improved comparison. We appreciate your valuable feedback, which has significantly improved the quality and clarity of our manuscript. Thank you for your continued support in refining our research. 7. In Figure 3, in the 5UO4 table, the control -7.40 should be white as it serves as the reference. It appears blue, possibly due to incorrectly taking the positive ligand of 5WXB as a reference. This is inaccurate, as it is a receptor and a distinct molecule. Answer: Thank you for pointing out the issue with the color assignment in Figure 3. We have redone the color mapping for the complexes 5U04 and 5WXB table in Figure 3. The new figure has been added to the manuscript. 8. Table 1 in the docking results mentions different types of non-covalent interactions without justifying why only hydrogen bond bonds and hydrophobic interactions were considered. The discussion also lacks insights into the differences or importance of various interactions such as alkyl-alkyl, pi-alkyl, etc. I recommend ordering the amino acids in ascending order for clarity. Answer: Thank you for your insightful feedback regarding the non-covalent interactions mentioned in Table 1 of the docking results. In our study, we focused on hydrogen bonds and hydrophobic interactions due to their significant roles in stabilizing ligand binding within the receptor's active site. Hydrogen bonds are essential for providing specificity and strong directional interactions, while hydrophobic interactions contribute to binding affinity by facilitating the burial of non-polar surfaces and reducing desolvation penalties. Although other non-covalent interactions such as alkyl-alkyl, pi-alkyl, and pi-pi interactions also play important roles in ligand-receptor binding, we prioritized hydrogen bonds and hydrophobic interactions due to their dominant influence in many docking studies. We have also included an explanation in the manuscript's discussion section. Furthermore, we have arranged the amino acids in Table 1 in their chronological order of occurrence within the protein sequence and structure, reflecting the sequential interaction pattern and spatial context, which is crucial for understanding the binding interactions. This arrangement aids in visualizing the interactions as they occur along the protein's active site and aligns with standard conventions in protein interaction studies. 9. In the discussion of interactions between molecules (rutin) versus sofosbuvir, there is mention of a greater number of interactions, but the explanation on how these interactions lead to blocking the active site is lacking. Consider discussing whether this blocking results from size or other characteristics inherent to enzymatic activity inhibition. A more in-depth discussion of the results is suggested. Answer: Thank you for your valuable feedback and suggestion for a more in-depth discussion of the interactions between rutin and sofosbuvir To address the interactions between rutin and sofosbuvir with the active site, we provide a more detailed discussion on how these interactions contribute to the inhibition of enzymatic activity. Rutin exhibits a greater number of interactions compared to sofosbuvir, which enhances its ability to effectively block the active site. This blocking is not solely a function of the number of interactions but also their nature and strength. The larger size of rutin allows it to span a broader area of the active site, facilitating multiple points of contact through hydrogen bonds, hydrophobic interactions, and aromatic stacking. These interactions collectively stabilize the binding of rutin within the active site, thereby preventing substrate access and subsequent enzymatic activity. In contrast, while sofosbuvir also forms stable interactions, the fewer number and potentially weaker nature of these interactions may result in less effective blocking. Thus, rutin's increased binding affinity and comprehensive interaction profile contribute to its potential as a more effective inhibitor of the enzyme's active site." } ] }, { "id": "273118", "date": "10 Sep 2024", "name": "Tiratha Raj Singh", "expertise": [ "Reviewer Expertise Bioinformatics and Systems 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 article titled \"In silico screening for potential inhibitors from the phytocompounds of Carica papaya against Zika virus NS5 protein\" by Kumaree et al is an interesting piece of work where authors have utilized in details all the structural bioinformatics components to analyze and annotate data utilized for the design of novel inhibitors for Zika virus protein. They also proposed that their studies results will be confirmed if experimental validations could be done in future. There are some typos and minor grammar issues along with the abbreviations used in the manuscript. Authors are suggested to rectify all these issues. There is no separate conclusion added, it should be added with specific outcomes of the study. Use of either “ZIKA” or “Zika” all over the manuscript be a better idea for making it uniform? Are there any other phytocompounds in the mentioned plant, which could be used for further studies.As the used compounds are naturally available, are their IC50 values available. If yes authors may compile this information for the readers, will add value to the research. There are some good articles such as: [ ref 1 ], which can also help the authors to look for technical contents for the refinements of the overall process.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] } ]	1	https://f1000research.com/articles/12-655
https://f1000research.com/articles/10-1082/v1	25 Oct 21	{ "type": "Systematic Review", "title": "An examination of the structural linkages between households and community health services in realization of accelerated primary healthcare delivery in Kisumu County, Kenya: a systematic review", "authors": [ "James M. Wakiaga", "Reginald Nalugala", "Reginald Nalugala" ], "abstract": "Background: The provision of community health services (CHS) is critical in accelerating primary health care delivery to vulnerable and deprived populations. However, the structural linkages between households and the CHS being provided by community health workers (CHWs) or volunteers in Kisumu County, Kenya, remains weak and inefffective. Methods: This study applied a descriptive approach using a systematic review technique to provide context and substance to the two main research questions: (1) how does the interaction between households and CHWs affect utilization of CHS to promote equity and right to health? (2) How do health-seeking behaviours of households influence their decision-making regarding choices of CHS? We screened the literature from Google scholar, JSTOR, SAGE and EBSCO based on our inclusion criteria, resulting in 21 studies. These studies were assessed for quality and eligibility and data extracted based on relevance to the research study. Results: Households place primacy on trust and confidentiality in the interaction with CHWs and this affects uptake of CHS. The social determinants of health are also critical in influencing the health-seeking behaviour of households and individuals and their choice of CHS. The successful models of CHS share the characteristic of community ownership and participation and provides for comprehensive health care teams. Conclusion: CHS are critical for the acceleration of primary health care delivery. It forms an important pathway for the achievement of universal health coverage, which is an outcome required for Sustainable Development Goal 3 on health.", "keywords": [ "community health services", "community health workers", "primary healthcare", "Kisumu County", "universal health coverage" ], "content": "Introduction\n\nThe provision of community health services (CHS) is critical in accelerating primary health care (PHC) delivery to the most vulnerable and deprived populations. According to the World Health Organization (WHO),1 community health workers (CHWs) have been widely used to deliver key health care and health promotion interventions in under-served populations in resource-limited settings and communities. In fact, The Alma Ata Declaration signed in 1978 declared PHC as the official health policy of member states. It defined PHC as ‘essential health care based on practical, scientifically sound and socially acceptable methods and technology made universally accessible to individuals and families in the community through their full participation and at a cost that the community or country can afford to maintain at every stage of their development in the spirit of self-reliance and self- determination’.2\n\nThis notion of PHC was further reinforced by the 2008 WHO report entitled ‘PHC: Now, more than Ever’, which underscored the case for universal health coverage (UHC) as an instrument to improve health equity, health systems strengthening, being people-centred and purposed to promote and protect the health of communities. The 2008 report of the WHO Commission on Social Determinants of Health3 underlined that social determinants such as income, education and political conditions of countries and societies are critical for health improvement.5 Today UHC has become a critical policy imperative to advance the ideas of social justice, human rights, and equity.\n\nAt the global level, the policy imperative for PHC and the role of community health system is anchored on the Alma Ata Declaration and most recently on the 2018 Astana Declaration in marking the 40th Anniversary since the Alma Ata. The Astana Declaration provides an opportunity to take stock of the global progress in supporting community health systems and to rekindle global interest on PHC and the centrality of community health systems to achieving UHC. Held under the banner “From Alma-Ata towards Universal Health Coverage and the SDGs”, it calls for the strengthening of PHC to be inclusive, effective and efficient to realize a sustainable health system that guarantees the achievement of UHC and health-related Sustainable Development Goals (SDGs).\n\nAgarwal et al4 observe that the Astana Conference provides a shift from whether CHW programmes are effective to identifying what makes the CHW programmes effective. Regretfully, world governments have been slow in formulating national policies, strategies and plans of action to launch and sustain PHC, especially in developing countries, as part of a comprehensive health system.3 Underlining this argument is the notion that the success of PHC will, among others, be driven by empowering individuals and communities through their participation in the development and implementation of policies and plans impacting on health outcomes.\n\nAfrica has an enormous task to achieve an inclusive and transformation growth unless it invests in sustainable health systems. The WHO estimates that investing an additional $21 to $36 per capita per year over the next five years in Africa would save 3.1 million lives, out of which 90% would be mothers and children. It would also prevent 3.8 million to 5.1 million children from stunting with anticipated economic gains in five years amounting to $100 billion from additional investments in health.53 According to Rifkin,5 it is estimated that by 2030, nearly 9 out of 10 of the extreme poor will be found in sub-Saharan Africa. The WHO6 gives an even more stark picture, pointing out that while the African region constitutes 11% of the world population, it has 60% of people living with HIV/AIDS and constitutes 300-500 million malaria cases occurring every year globally. The continent faces many other health challenges such as polio, rising cases of non-communicable diseases (NCDs), and high maternal and child mortality rates. Most countries did not meet the health-related Millennium Development Goals (MDGs) by 2015 and are not on track to achieve SDG3 on good health and well-being.\n\nThe dwindling fiscal space for health financing in Africa has further accentuated the challenge of meeting the health goals. Most countries are failing to meet the 2001 Abuja Declaration target of allocating 15% of total government expenditure to the health sector, and only five countries (Botswana, Rwanda, Zambia, Madagascar and Togo), have met the Abuja target so far.53 Data from the World Bank7 shows a significant increase in out-of-pocket expenses in almost all countries, and the regional average peaked from US$15 per capita in 1995, to US$38 in 2014. This translates to 11 million Africans falling into poverty every year due to high out-of-pocket payments. The fragility of Africa’s health system provides for a policy imperative to strengthen CHS to give impetus to the role of CHWs to accelerate PHC delivery and reduce disease burden. The Third Global Forum on Human Resources held in 2013 recognized that CHWs programmes could play a critical role in accelerating MDGs/SDGs and achieving UHC.8 The WHO Africa region has argued the case for increased scale up of access to PHC services and progress towards UHC by promoting the expansion and implementation of CHW programmes.8 This position is in fact a build up to the 1987 Bamako Initiative adopted by the African Ministries of Health on increasing access to essential drugs and other health care services by strengthening the PHC services9 and that of the African Union of deploying 2 million CHWs across sub-Saharan Africa.10\n\nIn Kenya, both the 2010 Constitution and the Vision 2030 policy blueprint commit to improving the health of the population by declaring health as a basic human right, and have now devolved health services to the counties. In addition, The Kenya Health Policy (2014-2030) seeks to achieve UHC by 2030.11 Despite this policy articulation and existence of robust strategies, the country is far from achieving the health goals. Available data, show that maternal mortality rate remains as high at 362 per 100,000 births, malaria incidence per 1000 population stood at 225, while infant and under-5 mortality remains high at 39 per 1000 live births and 52 per 1000 live births, respectively. Kenya is also grappling with communicable diseases such as HIV/AIDS and tuberculosis, with new HIV infections per 1000 infected estimated at 146 despite a drop in prevalence rate from 6.7% in 2003 to 5.9% in 2015.12 Tuberculosis incidence per 1000 population stood at 90 in 2015. NCDs are increasingly becoming a burden to the health system with rising cases of cancer causing an estimated 21,000 deaths annually.13\n\nTo improve health outcomes, especially for poor and vulnerable populations, the Government of Kenya prioritized a community health strategy. The second National Health Sector Strategic Plan (NHSSP II) (2005-2010) adopted the Kenya Essential Package for Health (KEPH), which underlined the policy imperative for community health. The KEPH was operationalized in 2006 as a package for the community health strategy – “Taking the Kenya Essential Package for Health to the Community: A Strategy for the delivery of Level One Services” and further revised in 2014 into the current Community Health Strategy (2014-19). The community strategy is geared towards enhancing community access to health care as an intervention to improve productivity and address poverty in Kenya. The communities have the responsibility to manage their own health while PHC provides the basis for CHS as a fundamental human right, social justice and equity. The implementation of the CHS in Kenya has been less than optimal and the CHWs and volunteers who form the bulk of the workforce for the level one services have weak linkages with households/wards and communities.\n\nMost written studies on challenges facing the CHS have narrowly focused on skill development for CHWs. Therefore, this research study looks at some of the functional and behavioural gaps, the structural linkages between households and CHS delivered by the CHWs, the health-seeking behaviour of the households demanding the CHS, and examines some of the successful community health models with a view to proposing a functional model of community health for PHC delivery in Kenya.\n\nThis systematic review is part my Doctorate thesis that focusses on Kisumu county, which has been selected due to its heavy disease burden as well as progress made in the roll-out of CHS. Available data from Kisumu County profile54 shows some progress, albeit slowly, in infant mortality at 54 per 1000 live births, maternal mortality rate of 495 per 100,000 births and under-5 mortality rate of 79 per 1000 live births. Communicable diseases such as HIV/AIDS and tuberculosis remain a major challenge to the health with HIV prevalence rate of 14.6%. The Kisumu County Health Sector Strategic and Investment Plan (KCHSSIP) (2013-2017) forms the main framework/strategy for the roll-out of the community health services under which the community health volunteers (CHVs) and community health extension workers (CHEWs) play an important role as intermediaries of CHS. However, the community health strategy model has been hampered by the weak linkages between households, village and community healthcare systems, which is key to accelerating PHC. The study therefore seeks to examine this challenge and has selected two main questions as follows:\n\n(a) How does the interaction between households and CHWs affect utilization of CHS to promote equity and right to health in Kisumu County?\n\n(b) How do health-seeking behaviours of households influence their decision-making regarding choices of CHS offered in Kisumu County?\n\nThe health equity, social justice and Sen’s human capability approach constitute the main theoretical underpinnings of the study, as well as for the guiding questions. The health equity theory underlines the prevailing differences in the quality of health and healthcare across different populations. It is about fair and just opportunities to accessing health by eliminating disparities that impact on health outcomes. For the two major proponents of health equity theory, Black14 looked at two primary mechanisms to explain how the social determinants influence health: cultural/behavioural and materialist/structuralist. The materialist/structuralist explanation looks at people's material living conditions and explains how social determinants influence health. Whitehead15 expanded on the concepts and principles of equity and health asserts that different social groups have differences in health where the disadvantaged group suffer a heavier burden of diseases.\n\nAmartya Sen’s theory of development that views development as freedom using the capability approach considers health equity as a matter of social justice. Sen et al16,17 posits that health equity is about broader issues of fairness and justice that pays attention to the role of health in human life and freedom. At the centre of the health equity theory is the idea that access to health is a right and a matter of social justice for the poor and the vulnerable segment of the population who need to be empowered and build their capability. This injustice can be seen from limited opportunity to achieve health outcomes arising from the social arrangements. Rasanathan et al18 observes that the focus on health inequities has renewed interest in PHC and the social determinants of health asserting that by ignoring the social determinants of health will be exacerbating health inequity.\n\nThe study also considers Rawl’s theory (1971) of social justice by espousing the theory of social justice as a framework for fairness and distributive justice that permeates the basic structure of society.19 The theory perceives justice as the first virtue of social institutions and that it must percolate at all levels of society. Hence, access to health must be seen as social justice to the citizens and, as Rawl would argue, ‘the rights secured by justice are not subject to political bargaining or to the calculus of social interests’.19 This theory postulates that the primary concern of justice is the functioning of social structure in a way that major institutions proffer fundamental rights and duties and the privilege and the division of advantages through social interactions.\n\nIn summary, health equity must be viewed as a plausible theoretical framework that encompass the principles of social justice, human rights (choice), participation and capability approach through empowerment of the people to make rational choices. This means viewing health equity and social justice as central to community empowerment for health promotion.20 The Rawlsian theory of justice provides a good framework for assessing social inequalities in health that are rooted in the society’s socio-economic institutions and this ties with Sen’s idea of capable institutions. Even though some authors16–21 critiques of Rawl’s distributive approach to social justice have underlined that capabilities are more relevant on justice matters and provide for a more normative conception of social justice.\n\n\nMethods\n\nThe systematic review targets both qualitative and quantitative conceptual and empirical studies. The study applies a descriptive approach by using narrative review22 to provide context and substance to the two main research questions:\n\n(1) How does the interaction between households and CHWs affect utilization of CHS to promote equity and right to health in Kisumu County?\n\n(2) How do health-seeking behaviours of households influence their decision-making regarding choices of CHS offered in Kisumu County?\n\nFor purposes of searching the literature, the study used the operational terms “CHW/V” defined as ‘members of the community selected from the area with the task of improving the community’s health and well-being and linking the people to primary care services’ and “CHS” operationally defined as ‘provision of community healthcare services to a client or patient usually at home or residential setting’.\n\nThe literature search involved screening articles from peer reviewed journals mainly targeting the year 2009 to the present. Exceptional cases were the historical literature. The following databases were used: Google Scholar, JSTOR, Kenya National Bureau of Statistics (KNBS) register, Kisumu County website, SAGE publications and EBSCO. The following search terms were used: “CHS”, “CHW/V”, “PHC”, “UHC” and combined with the terms used in the main research questions such as “CHW models”, “health equity”, “health-seeking behaviour”, “households and choice of community health services” by using the Boolean operators “AND” or “OR” accordingly.23 Zotero software version 5.0.89 was used to collect and collate the data and to assist in the citation and referencing.\n\nBoth conceptual and empirical studies were selected based on the title and abstract bearing relevance to the central role of the “CHW/Vs” and the relationship between households and CHWs, as well as the health-seeking behaviour of the households and how this influences their choice and decision-making on use of community health services provide by the CHW/Vs. These were mainly published studies and ranged from global, regional or Africa in particular, and then Kenya, accordingly, using the funnel approach. Studies not pertinent to the two research questions were excluded. The selection was confined to studies published in English language and the papers were screened by the main Author and then independently reviewed by the co-author based on the criteria of (i) relevance and applicability to the themes; and (ii) consistency of the results.\n\nThe data was extracted using the narrative analysis synthesis approach and clustered based on the thematic areas of the research questions. This is a technique used to identify, evaluate and then synthesize the available empirical evidence.55 The papers were clustered based on the research questions and using the funnel approach by systematically looking at studies that are global, from Africa, and then Kenya, and the relevance of the content to the themes of the research questions. The quality assessment was done by categorizing the screened papers into the two thematic areas of the research questions. The authors gauged the strength of the empirical evidence adduced and absence of bias using the criteria listed in Table 1. This enabled the authors to independently rate the papers as high, medium or low and settling on the 21 selected papers.\n\n\nResults\n\nThe process of the selection of the studies involved an electronic search identified 366 records, from which 21 studies were retained (Figure 1). The 21 studies included 19 qualitative and 1 mixed-methods and one randomised control trial. The studies were conducted in India, Cambodia, Uganda, Ethiopia, Burkina Faso, South Africa, Ghana and Kenya. Table 1 lists all studies included in this study.\n\nThe quality of the studies was good in terms of providing evidence and application of the methods though the authors offer a critique in terms of relevance to the research questions to determine a research gap. Hence it is important to underline that most of these studies have been narrow in scope and limited to analysing the role of CHWs in the health system and less on community and systemic issues that impact on their performance. The studies have also not focused on the contextual relations between the health volunteers and communities they serve especially from the perspective of the recipient of the services in this case the households.24\n\nFindings from the narrative synthesis of the systematic review of the study shows that the issue of community/household perception of the CHWs as an emerging thematic factor. Most of the studies have cited how the community perceives the CHWs has a positive correlation to the uptake of the CHS. Kok et al25 has identified three areas as key to the effectiveness of CHS: attitudes of the health personnel and communities towards CHWs, the management and structure of health systems and resource allocation guided by the principle of equity, and the quality of community participation. Hence forging a stronger linkage between CHWs and households/community will improve the uptake of the CHS and contribute to accelerated PHC delivery for poor and vulnerable populations.\n\nThe quality of interaction between households/communities and the CHWs impact on the effectiveness of the CHW interventions. Kok et al25 posits that policymakers of CHW interventions must take into consideration the socio-cultural, economic and political contextual matters when designing the programmes in order to optimize performance. Two studies25,26 have indicated that the socio-cultural factors influence the perceptions and relationship between CHWs and households or community. Other pertinent factors influencing the interaction is lack of alternatives to health service delivery that caters for the disadvantaged population and the dissatisfaction of CHWs that may arise due to lack of essential medicines and limited referrals.25,27\n\nOne of the selected studies also considers at length the effectiveness of community structures, such as the village/ward committees or community organizations specifically on leadership capacities and participation of interest groups. For instance, people living with disabilities or women are in some cases not represented in these committees responsible for decision-making on CHS. The studies selected have also cited several other factors that influence this relationship/interaction including the lack of confidence in CHWs, lack of relationship-building with households/community, inability of communes/communities to provide resources to support the work of the CHWs, lack of community mobilization skills and misunderstanding on the role of the CHWs by the community.28\n\nAn emerging theme from the selected studies is the importance of trust and confidentiality in improving interactions between CHWs and the household/community. Studies have cited examples from Philippines, Brazil, India and South Africa28–30 and all demonstrate that issues of trust, bonding, social capital and relationship-building as paramount in establishing linkages with communities and enhancing the uptake of CHS.31\n\nThe selected studies at global, regional and local levels based on the narrative synthesis review have highlighted how the health-seeking behaviour influences the choices of households/communities in utilizing the CHS provided by the CHWs.32–38 Findings show that a total of seven studies focussing on the role of social and cultural factors shows the impact on the choice of CHS from detection of illness to choosing the health care services.39 In Pakistan, Mushtaq et al35 found that the low position of women from a cultural perspective undermines their freedom to make health choices for themselves and their children without the consent of the head of household. In some cases, the limited number of female health workers limits the women’s access to health care and influences their decision on whether to deliver children at home or in a facility using skilled personnel.32,35,36\n\nThree key selected studies looked at geographical factors and how distance from the health facility could influence the health-seeking behaviour and the choice of CHS.40–42 For instance, the study by Mazzi et al,42 conducted in Uganda, examined the geographical factors that influence health-seeking behaviour by looking at proximity to the health care services. Even though this study could not explicitly explain whether the effect of bringing health facilities closer to the people would make them prefer seeking primary health care directly and avoid CHWs.42\n\nThe issues of trust and confidentiality in the interaction between households/community and CHWs equally featured when it comes to the health-seeking behaviour. Some of the selected studies explored how trust influences the health-seeking behaviour and towards selection of CHW as a first point of service. A study by Akeju et al32 in Ogun State, Nigeria, revealed that women utilized multiple caregivers during pregnancy, which was influenced by entrenched trust in traditional birth attendants who live among the community and have established trusted relationships. Studies also show that in Kenya choice of CHWs for PHC support in most disadvantaged households was hinged on trust/confidentiality. For example, mothers in rural Kenya trusted that the CHVs could increase their knowledge of maternal and newborn health.33 The studies analysed reinforced the idea that most qualitative studies on the impact of CHW programmes have narrowly focused on direct CHW management and less attention to how clients or beneficiary communities of the CHW programmes perceive services provided by CHW/Vs as part of the structural linkage of optimizing the CHS to vulnerable populations.24\n\n\nDiscussion\n\nThis systematic review has explored the structural linkages between community/households and the CHS by examining some select studies from the global, regional and local level to understand the interaction between households and CHWs. The systematic review has examined two dimensions that affect this linkage in terms of how the interaction between households and CHWs affect the uptake of CHS and how the health-seeking behaviour of households influence their choices of CHS being delivered by CHWs in the acceleration of PHC services. Evidence from the 21 selected studies show that improving this structural linkage is critical for the uptake of the CHS and towards subsequent acceleration of PHC delivery. The achievement of the SDG3 on good health, and well-being target 3.8 to achieve UHC will depend on the acceleration of PHC for poor and vulnerable populations.\n\nEvidence from the studies show that the relationship between household/communities and CHWs is important in strengthening the interaction and optimize the utilization of CHS.31 Important factors that impact on this relationship includes the social determinants of health, socio-cultural influences, importance of trust and confidentiality, and building on the social capital. A study conducted in Odisha, India, for example, observed that trust-building with the community is a critical determinant on utilization of CHS. This was also corroborated by the outcome of similar studies conducted in Kenya, Malawi, Mozambique and Ethiopia by Kok et al46 on factors shaping the relationship between households/community, CHWs and the health sector. These authors observed that this relationship is particularly important since CHWs act as intermediaries with the health facilities given their understanding and familiarity of the socio-cultural context. The findings from this particular empirical study re-affirms the importance in the trusting relationship for CHW/Vs as key to performance and also establishes that the bond of relationship between CHW/Vs and their supervisors’ impact on their relationship with the communities.\n\nTrust and confidentiality are very important in fostering strong linkage between the households/community and CHWs and this has an impact on the uptake of the community health services. Most of the selected studies underlined the role of perception and attitudes that influence the interaction. This is corroborated in the study by Rachlis et al28 on community perceptions of CHWs specifically for HIV, tuberculosis and hypertension patients in western Kenya. Their findings showed that some participants’ perceptions of CHWs act as an impediment in the management of chronic diseases, especially issues related to lack of confidentiality or information/knowledge on the subject matter. A study by Grundy & Annear29 in Kwa-Zulu-Natal, South Africa, on the role of CHWs in delivering maternal and child health services, observed that the lack of trust and confidentiality was perceived to be the most singular barrier to CHW acceptability and those CHWs with reputation of confidentiality were trusted by the individuals, households and communities. Evidence from the studies also observed that the interaction between the households and CHWs was in some instances influenced by the ability or inability to provide extra resources, especially to needy households. Some poor households see the CHWs not just as a medical aide support but that they should be able to meet their financial needs.27,43,44\n\nThis systematic review of the studies shows that health-seeking behaviour of household and communities influence their health care preferences.34 This is important for the poor and vulnerable communities who suffer from catastrophic health expenditure and rely on CHWs as their best preference. Using the Pathways model developed by Ref. 38, the social and cultural factors affect the steps of the process from the detection of symptoms to choosing health care services. A study by Mushtaq et al35 in Pakistan provides evidence to show that issues of gender and NCD burden are critical in influencing the health-seeking patterns of households.\n\nStudies are also showing that women are disadvantaged due to cultural reasons from making health choices for themselves and their children without the consent of the head of household.32,35 In some contexts, the limited number of female health workers limits the women’s access to health care and accounts for the growing burden of the NCDs, such as hypertension. This is also corroborated in a qualitative study conducted in North Eastern Kenya by N’Gbichi et al,36 which observed that women will prefer home-delivery by a skilled attendant if there are no female nurses to attend to them in a hospital facility. This buttresses the point that while delivery in a health facility is the preferred choice, culture could act as a disincentive against using the facility and home delivery is preferred to avoid male nurses or doctors.\n\nThe households/community perception on issues of trust and confidentiality does affect the choices they make on whether to utilize the CHWs.41 Other factors that influence the uptake of the CHS include distance to reach communities, infrastructure of geographical location, credibility, lack of awareness of the CHW services or poor engagement amongst the community.41,45\n\nThis systematic review has demonstrated that fostering sustainable linkage between households and community health services provided by the CHWs programmes is key to optimal functioning of the community health strategies and models. This is also in line with the Alma Ata Declaration that has been implementing community health strategy to accelerate the delivery of PHC and achieve UHC. This means putting in place an integrated system that has the people and community at the centre of the governance structure of health models to accelerate PHC delivery. Bitton et al47 posits that in most low and middle-income countries, what individuals and community receive from the community health models is not on par with effectiveness and care delivered.\n\nBased on the successful experience of developed models like Brazil’s FHS and Ethiopia’s Health Extension Programme, there is no “one-size-fits-all” approach and implementation has to be driven by local context-specific ways that respond to the socio-economic and political realities as well as health system imperatives.48 For example, in a study of contextual factors affecting integration of CHW into the health system in Limpopo, South Africa, Jobson et al49 identified six critical contexts: geographical context in terms of distance between PHC facility and households, socio-economic context with regard to high levels of poverty in Limpopo in relation to ill-health, community context associated with HIV stigma, cultural beliefs, local governance as a supportive role and organization contexts in the form of competitive interests between national health officials, NGOs, operational environment for CHWs, and leadership challenges.\n\nStudies show that Kenya has undertaken the implementation of the community health strategy in the different national counties with varying results. In pastoral nomadic areas of Northern Kenya, findings show a high cost of attrition for CHVs, per capita coverage by CHVs across the different geographical contexts due to population density, livelihoods opportunity cost and benefit, and the social opportunity cost.50 In Mwingi district, while the model was successful in providing maternal and child health services, socio-cultural and economic factors impeded on the progress.51 Kisumu county which forms case study of this research paper has identified weak linkages between households, village and community healthcare systems, which is key to accelerating primary healthcare. Other findings cited the low participation of the community during the program design, recruitment and implementation and hence the need to enhance linkages between community, CHEWs and CHWs right from the onset.52\n\n\nConclusions\n\nCommunity health services are critical for the acceleration of PHC delivery amongst vulnerable and deprived populations. It forms an important pathway for the achievement of UHC, which is an outcome of SDG3 on health. Fostering strong structural linkages between the households/wards and CHS being provided by the CHWs/Vs would therefore accelerate the achievement PHC delivery.\n\nThe findings from this systematic review study have demonstrated that PHC delivery is critical for better health outcomes and to achieve UHC. The studies have revealed that CHS could significantly contribute to the acceleration of PHC and the agency role of CHW/Vs is paramount at a community level. There is an imperative for strengthening the linkages between households/community and CHW/Vs to foster the uptake of CHS. Evidence from the systematic study pinpoints that understanding the health-seeking behaviour of the households is critical as this influences the choices households make on whether to utilize the health services provided by the CHW/Vs.\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-S checklist for ‘An examination of the structural linkages between households and community health services in realization of accelerated primary healthcare delivery in Kisumu County, Kenya: a systematic review’, https://doi.org/10.6084/m9.figshare.16798072.56\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\nWorld Health Organization: Primary health care: report of the International Conference on Primary Health Care Alma Ata, USSR, 6–12 September 1978. 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Africa Health Agenda International Journal. 2018; 1(4).\n\nDruetz T, Ridde V, Kouanda S, et al.: Utilization of community health workers for malaria treatment: results from a three-year panel study in the districts of Kaya and Zorgho, Burkina Faso. Malar. J. 2015; 14(1): 71. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKok MC, Ormel H, Broerse JE, et al.: Optimising the benefits of community health workers’ unique position between communities and the health sector: a comparative analysis of factors shaping relationships in four countries. Glob. Public Health. 2017; 12(11): 1404–1432. PubMed Abstract \| Publisher Full Text\n\nBitton A, Ratcliffe HL, Veillard JH, et al.: Primary health care as a foundation for strengthening health systems in low-and middle-income countries. J. Gen. Intern. Med. 2017; 32(5): 566–571. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSchneider H: The governance of national community health worker programmes in low-and middle-income countries: an empirically based framework of governance principles, purposes and tasks. Int. J. Health Policy Manag. 2019; 8(1): 18–27. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJobson G, Naidoo N, Matlakala N, et al.: Contextual factors affecting the integration of community health workers into the health system in Limpopo Province, South Africa. Int. Health. 2020; 12(4): 281–286. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWafula CO, Edwards N, Kaseje DC: Contextual variations in costs for a community health strategy implemented in rural, peri-urban and nomadic sites in Kenya. BMC Public Health. 2017; 17(1): 224.5. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNzioki JM, Onyango RO, Ombaka JH: Efficiency and factors influencing efficiency of community health strategy in providing maternal and child health services in Mwingi district, Kenya: An expert opinion perspective. Pan Afr. Med. J. 2015; 20(1). Publisher Full Text\n\nMireku M, Kiruki M, McCollum R, et al.: Context analysis: close-to-community health service providers in Kenya. Nairobi:Reachout Consortium;2014.\n\nUNECA: Healthcare and economic growth in Africa. Preview of the report at the High-Level Dialogue on Africa’s Health and Financing: Pathways to Economic Growth and Prosperity. New York.2018. 27 September 2018.\n\nKisumu County: Kisumu County Profile.2018. November, 2018.Reference Source\n\nMadden A, Bailey C, Alfes K, et al.: Using narrative evidence synthesis in HRM research: An overview of the method, its application, and the lessons learned. Hum. Resour. Manag. 2018; 57(2): 641–657. Publisher Full Text\n\nWakiaga J, Nalugala R: An examination of structural linkages between households and community health services in realization of accelerated primary healthcare delivery in Kisumu County, Kenya: a systematic review. figshare. J. Contribution. 2021. Publisher Full Text" }	[ { "id": "147526", "date": "12 Sep 2022", "name": "Henry Perry", "expertise": [ "Reviewer Expertise Primary health care", "community health", "community heath workers" ], "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\nMajor comments:\nI found this article troubling on several counts.\nThe title of the article and the research questions indicate that Kisumu County, Kenya, is the focus of the research, but there is nothing in the findings that pertain directly to Kisumu County. And, there is no description of the community health services in Kisumu County.\n\nThe authors state that they are interested in examining structural linkages between households and community health services, but they never clearly state what they mean by “structural linkages.” This should be defined at the outset. In fact, much of the literature they identify from their systematic review focuses on “soft” features of community health services (trust, confidentiality), on the context (social, cultural, economic and geographical factors), or the features of the health system (material support available to CHWs, available of essential services, including referral services). None of these findings provide any insights into actual structural linkages between households and the community health system.\n\nMost of the Introduction, while interesting, does not clearly relate to the research question that the authors pose.\n\nThe authors’ principal conclusion (from the Abstract), “CHWs are critical for the acceleration of primary health care delivery” is not supported by the evidence presented in the Results section. In the Conclusions section, the authors state that their findings “have demonstrated that PHC delivery is critical for better health outcomes and to achieve the UHC [Universal Health Coverage].” However, in fact, their findings do not demonstrate this.\n\nOn p. 8 middle the authors state “…most of these [included] studies have been narrow in scope and limited to analysing the role of CHWs in the health system and less on community and systemic issues that impact their performance.” This raises the question of why in fact these articles were included?\nMinor comments:\nThere is no mention of to what degree the article selection methodology meets the standard criteria for a systematic review.\n\nWhat is the “funnel approach”?\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? No\n\nAre sufficient details of the methods and analysis provided to allow replication by others? No\n\nIs the statistical analysis and its interpretation appropriate? Not applicable\n\nAre the conclusions drawn adequately supported by the results presented in the review? No", "responses": [ { "c_id": "10841", "date": "17 Jan 2024", "name": "James Wakiaga", "role": "Author Response", "response": "I have taken note of the comprehensive comments by the reviewer and especially pertaining to the title of the research paper. The central focus of the study is Kisumu County, Kenya and the systematic review was mainly to draw out the existing literature review around the structural issues of relationship between the CHVs and households in accelerating primary healthcare delivery, as well as, the health-seeking behaviour of households. The systematic review was partly to draw out the secondary research information that would guide the framing of the primary research. I also agree on the imperative of defining conceptually what \"structural linkages\" means for purposes of the research study and this will be addressed in the introduction in the revised draft." } ] }, { "id": "223647", "date": "27 Nov 2023", "name": "Beverly Marion Ochieng", "expertise": [ "Reviewer Expertise HEALTH SYSTEMS RESEARCH & COMMUNITY HEALTH" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nREVIEW\nTitle: An examination of the structural linkages between households and community health services in realisation of accelerated primary healthcare delivery in Kisumu County, Kenya: a systematic review\nMajor comments: In reference to your topic, it will be advisable to put into context the meaning of structural linkages between households and community health services in your introduction.\nAbstract\nKeep the abstract as brief as possible, with a precise, to-the-point example on critical issues that need to be highlighted in the abstract\nBackground: the context and purpose of the study; Method: how the study was performed and statistical tests used; Results: the main findings (Focus on Kisumu County) Conclusion: a brief summary and potential implications\n“Methods: This study applied a descriptive approach using a systematic review technique to provide context and substance to the two major research questions:\n(1) How does the interaction between households and CHWs affect the utilisation of CHS to promote equity and the right to health? (2) How do health-seeking behaviours of households influence their decision-making regarding choices of CHS? ”\nThe review has not answered the stated research questions, especially regarding Kisumu County.\n\n“We screened the literature from Google Scholar, JSTOR, SAGE, and EBSCO based on our inclusion criteria, resulting in 21 studies. These studies were assessed for quality and eligibility, and data was extracted based on relevance to the research study.\"\n*Unnecessary sentence in the abstract*\nThe introduction\nHelp the reader understand the interpretation of structural linkages between households and community health services from your research point of view. The introduction does link to the title of the study and the research question of the paper mostly sounds more like a world review of CHW services as opposed to what is stated in the research title. At what point do we narrow down the area of study?\nWhat is the statement of the problem with a focus on Kisumu County? What studies have been done based on your research topic on Kisumu County? What are the policy implications in relation to this study?\nInformative policy documents for your reading\n1) Community health Strategy document 2) Kisumu Health Strategic Plan 3) KDHS (Current)\n\nResults: contradict what is stated as the research questions; no systematic flow.\nThe results do not highlight studies that have been done on structural linkages between households and community health services, especially in this study, which begs the question: have we answered the research questions and are we linking our findings to the research topic?\nThe highlighted studies are focusing on the different aspects of community health services and not structural linkages, as stated in the research topic\n\nConclusion: not well thought through, not coherent with the findings, no mention of studies done in Kisumu in terms of structural linkages between households and community health services\nRecommendations based on findings from Kisumu County based on empirical evidence are conspicuously missing, which is obviously not stated in this paper.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? No\n\nAre sufficient details of the methods and analysis provided to allow replication by others? 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? No", "responses": [ { "c_id": "10838", "date": "17 Jan 2024", "name": "James Wakiaga", "role": "Author Response", "response": "The comments are well received and will attempt to respond to some of the issues raised in reviewing the draft. Notably the issue of conceptualizing \"structural linkages\" in the introduction, contextualizing the findings based on the Kisumu study as well as the abstract. Important to note is that this is systematic review study and focus was mainly on the available literature that respond to the 2 research questions that form the basis of the research study. hence the literature review could not just be confined to evidence derived from peer-reviewed studies conducted in Kisumu County but also global, regional and at national/local level. I will submit a revised paper based on the comments and open to any further suggestions." } ] } ]	1	https://f1000research.com/articles/10-1082
https://f1000research.com/articles/13-688/v1	25 Jun 24	{ "type": "Research Article", "title": "Identification of Biomarkers for Severity in COVID-19 Through Comparative Analysis of Five Machine Learning Algoritms", "authors": [ "Juan P. Olán-Ramón", "Freddy De la Cruz-Ruiz", "Eduardo De la Cruz-Cano", "Sarai Aguilar-Barojas", "Erasmo Zamarron-Licona", "Juan P. Olán-Ramón", "Eduardo De la Cruz-Cano", "Sarai Aguilar-Barojas", "Erasmo Zamarron-Licona" ], "abstract": "Background COVID-19 is a global public health problem.\n\nAim The main objective of this research is to evaluate and compare the performance of the algorithms: Random Forest, Support Vector Machine, Logistic Regression, Decision Tree, and Neural Network, using metrics such as precision, recall, F1-score and accuracy.\n\nMethods A dataset (n=138) was used, with numerical and categorical variables. The algorithms Random Forest, Support Vector Machine, Logistic Regression, Decision Tree, and Neural Network were considered. These were trained using an 80-20 ratio. The following metrics were evaluated: precision, recall, F1-Score, and 5-fold stratified cross-validation.\n\nResults The Random Forest algorithm was superior, achieving a maximum score of 0.9727 in cross-validation. The correlation analysis identified ferritin (0.8277) and oxygen saturation (-0.6444). The heuristic model was compared with metaheuristics models. Models obtained through metaheuristic search could maintaining the metrics with 3 variables and stable weight distribution. A perplexity analysis it allows to differentiate between the best models. The features of creatinine and ALT are highlighted in the model with the best CV score and the lowest perplexity.\n\nConclusion Comparative analysis of different classification models was carried out to predict the severity of COVID-19 cases with biological markers.", "keywords": [ "Biological markers", "Cross-validation", "Ferritin", "Machine learning", "Metaheuristics", "Oxygen saturation", "Random forest." ], "content": "1. Introduction\n\nThe coronavirus disease COVID-19 is a significant global public health problem. Given the ease with which new strains can emerge, it is essential to investigate and understand their pathophysiology using precise techniques.1 Machine learning (ML) emerges as a promising tool, offering the possibility of improving precision and reducing the time of variable analysis to deeply understand the pathophysiology induced by COVID-19,2 and, consequently, improve patient treatment.\n\nWhen using machine learning in the study of this clinical condition, it is necessary to choose between supervised or unsupervised learning and determine the appropriate algorithm, such as Random Forest, Support Vector Machine, Logistic Regression, Decision Tree, Neural Network (MLP), among others. Various studies3,4,5 have demonstrated the effectiveness of these algorithms in biomedical problems. In relation to COVID-19, there is also evidence6 that precise biological markers can be decisive in the patient's prognosis.\n\nRegarding the prediction of COVID-19 based on biomarkers in the study by Gharib et al.,7 inflammatory biomarkers were evaluated in 150 Egyptian patients and risk factors associated with the severity of COVID-19 patients. The study found a significant negative correlation between percent oxygen saturation and serum levels of inflammatory markers, including ferritin.\n\nAnother study with 50 patients infected with COVID-19 conducted in Peshawar by Khan et al.,8 an increase in the levels of CRP, ferritin, and IL-6 was detected, as well as changes in the count of neutrophils and lymphocytes. The authors concluded that elevation in CRP and ferritin are linked to secondary bacterial infections and adverse clinical outcomes. Findings from a meta-analysis suggest that serum ferritin levels correlate with the severity of COVID-19. Specifically, COVID-19 patients showed markedly higher ferritin levels compared to controls, with a SMD (Standardized Mean Difference) of -0.889 and a 95% CI of (-1.201, - 0.577).\n\nFurthermore, patients with severe to critical COVID-19 symptoms showed elevated ferritin levels compared to those with mild to moderate symptoms, with an SMD of 0.882 and a 95% CI of (0.738, 1,026). Also significant was the finding that nonsurvivors had a pronounced increase in ferritin levels compared to survivors, with an SMD of 0.992 and a 95% CI of (0.672, 1.172). These observations emphasize the potential usefulness of serum ferritin as a biomarker in the management of COVID-19, although the presence of other comorbidities and confounding factors require cautious interpretation of the results.9\n\nA study conducted in Alexandria, Egypt by Abdelhalim et al.,10 analyzed 210 non-hospitalized patients with confirmed COVID-19, aged between 14 and 75 years (mean age 44.5 ± 30.5). It was observed that 71.4% of these patients had high levels of serum ferritin, identifying ferritin as a significant biomarker for the diagnosis of COVID-19 in this population, with a value p = 0.014738. A comprehensive review of databases, including MEDLINE, EMBASE and others, identified relevant studies related to laboratory parameters in COVID-19 cases of different severities. Of 9,620 records, 40 studies with a total of 9,542 patients were included in the final analysis. The results showed that lymphopenia, thrombocytopenia and elevated levels of interleukin-6, ferritin, among other biomarkers, were associated with severe and fatal cases of COVID-19. In particular, elevated levels of interleukin-6 and hyperferritinemia were identified as indicators of systemic inflammation and a poor prognosis in patients with COVID-19.11 In a study conducted at the Department of Pathology and Laboratory Medicine, Aga Khan University (AKU), Karachi by Sibtain et al.,12 medical records of patients hospitalized with confirmed COVID-19 from March 1 to August 10, 2020 were reviewed. 157 patients were included in the final analysis, of which 108 were men and 49 were women. The analysis revealed a significant difference in ferritin levels between categories based on COVID-19 severity and mortality. Through binary logistic regression, ferritin was identified as an independent predictor of all-cause mortality in patients with COVID-19, with an AUC of 0.69 in the ROC analysis. The study concludes that serum ferritin concentration appears as a promising predictor of mortality in cases of COVID-19. In the work of Samprathi et al.,13 an extensive research protocol was designed for patients with COVID-19 that varies depending on the severity of symptoms and the presence of comorbidities. For those asymptomatic or with mild symptoms without comorbidities, no further investigations were requested. Patients with mild or moderate comorbidities, upon admission, needed tests such as CBC, CRP, serum creatinine, and liver function tests. In the presence of abnormalities, additional investigations were requested.\n\nFor severe cases, tests such as PT, APTT, INR and specific biomarkers were added, while for critical cases serial IL-6 and lactate levels were requested. Monitoring for hospitalized patients was performed using CBC and CRP every 48 to 72 hours. However, serum ferritin is not recommended to monitor response to treatment. For children with suspected MIS-C, a stepwise testing strategy is suggested, including cytokine testing and SARS-CoV-2 serology.\n\nTo predict the outcome in patients with COVID-19, AI techniques were successfully used, specifically the Random Forest and AdaBoost algorithms. These algorithms, using varied patient data, achieved a precision of $0.94$ and an F1 Score of $0.86$. A correlation between gender and mortality was also highlighted, with the majority of patients between 20 and 70 years.14 In the work of Ahmed et al.,15 machine learning methods (Random Forest, Support Vector Machine, Logistic Regression, Decision Tree and k Nearest Neighbors) were compared. Balancing of the dataset is not mentioned in this study. In the study by Wang et al.,16 the use of Random Forest to predict the severity of Covid-19 is reported, reaching an accuracy of 0.9905. For this purpose, they applied balancing using the SMOTE technique, achieving an AUC of 0.846.\n\nSimilarly, Elif et al.,17 used the SMOTE technique to balance their data. The Random Forest model they developed in their research returned a precision of 0.9796 and an AUC of 0.959. It is highlighted that some classes in their study had predictions lower than 90%, while others achieved perfect metrics. Among the biomarkers they identified as significant were LDH, high leukocyte count and C-reactive protein. On the other hand, Patterson et al.,18 also made use of the SMOTE balancing technique and developed a model that presented perfect metrics in all evaluated categories. Although they do not explicitly detail the cross-validation process in their study, they mention having used 10-fold CV (without specifying whether it was stratified) to perform an exhaustive search (grid-search) and determine the best hyperparameters. Additionally, it is noted that this validation was used exclusively for feature selection and not for dimensionality reduction.\n\nIn the work of Cui et al.,19 it is highlighted that its Random Forest model was able to predict the severity of the condition with a precision of 84.2% and an AUC of 0.874 for the first group and 0.842 for the second, both with an interval of confidence of 95%. LDH, D-Dimer and Fibrinogen stand out as key biomarkers. The main focus of their study, which included 437 patients, was to analyze the differences in these biomarkers between young (≤ 70 years) and older (≥ 70 years) people.\n\nIn the scope of the feature selection problem, metaheuristic algorithms have demonstrated effective addressing even in their most primitive versions on local and/or heuristic search mechanisms. In the work of Kabir et al.,20 used genetic algorithms for variable selection. In particular, this work uses a variant of the algorithm that allows reducing redundancy during the search for variables to improve performance.\n\nIn the work of Guha et al.,21 mentions the effectiveness that simulated annealing has had in multidimensional variable selection problems. Like the previous work, it proposes an improvement to the algorithm through its hybridization with another search mechanism that allows it to improve general performance. In the work of Chen et al.,22 it is described that the crow search algorithm was applied to variable selection problems. The authors faced late-stage diversity challenges, which are effectively addressed by a hierarchical adaptive approach. In a study by Bandyopadhyay et al.,23 on the detection of COVID-19 in radiological images, a two-stage pipeline consisting of feature extraction and selection was proposed. A CNN model based on the DenseNet architecture was used for feature extraction. To filter out non-informative and redundant features, the Harris Hawks optimization (HHO) algorithm with Simulated Annealing (SA) and chaotic initialization was used. When evaluating on the SARS-COV-2 CT-Scan dataset (2482 CT-scans), an accuracy of 98.85% was achieved with the inclusion of chaotic initialization and SA. The study reports a reduction in the number of selected features by 75%.\n\nThe main objective of this research is to evaluate and compare the performance of the algorithms: Random Forest, Support Vector Machine, Logistic Regression, Decision Tree, and Neural Network, using metrics such as precision, recall, F1-score and accuracy. With the models developed from these algorithms and metrics, we seek to identify which biological markers are affected in the pathophysiology of COVID-19 in order to monitor the clinical evolution and make medical decisions that contribute to the patient's recovery.\n\nThe structure of this document is as follows: section 2 details the methodology used in this research and the experimental design, section 3 presents the results. Section 4 focuses on discussing these results. Section 5 concludes the study. Section 6 shows some recommendations for future work.\n\nWhat are the laboratory biomarkers to predict the severity of SARS-CoV-2 infection in patients from southeastern Mexico?\n\n\n2. Methods\n\nIn this study, a comparative analysis of different classification models was carried out to predict the severity of COVID-19 cases.\n\nThe Python programming language was used for all calculations. For the classification models, the sci-kit learn suite was used in all cases.\n\nAuxiliary libraries:\n\n• DEAP: Allows the rapid construction and prototyping of genetic optimization algorithms.\n\n• Simmaneal: Contains tools for building simulated annealing algorithms.\n\n• Pandas: visualization and data management.\n\n• Seaborn: Data visualization.\n\n• Matplotlib: Data visualization.\n\n• Tabulate: Tabulation of data.\n\n• Scipy: Calculation of statistics. It comes integrated into Numpy.\n\n• Numpy: Calculation of statistics. NumPy is a library for the Python programming language, adding support for large, multidimensional arrays and arrays, along with a large collection of high-level mathematical functions for operating on these arrays.\n\n• Imblearn: Data balance for MLP with SMOTE. Imbalanced-learn offers resampling techniques.\n\nThis study includes patients diagnosed with COVID-19 according to the World Health Organization (WHO) guidelines for the clinical management of severe acute respiratory infections due to SARS-CoV-2,24 who were admitted to the Intensive Care Unit (ICU) at the “Dr. Desiderio G. Rosado Carbajal” general hospital in the time period between April 1st and July 31st, 2021 in Comalcalco Tabasco, Mexico. The ethical and legal guidelines considered for sampling are described in De la Cruz-Cano et al.25\n\nThe dataset has 138 entries that correspond to patients and 60 columns that represent different features. The features encompass a wide range of data, including demographic information, laboratory test results, vital signs, symptoms, pre-existing conditions, and the severity of the COVID-19 illness divided into three classes that are considered mild, moderate and severe.\n\nNext, the study population contained in the dataset used is characterized. In the dataset, there is a greater number of male patients (84) compared to female patients (54). It is also observed that the average age of the patients is approximately 59.9 years, with an age range that goes from 41 to 82 years, and a median of 58.\n\nThe severity of COVID-19 presents a significant proportion of patients (44.93%) with moderate severity of the disease (count of 62 and proportion of 0.4493), while mild and severe cases constitute 20.29% (count of 28 and proportion of 0.2029) and 34.78% (count of 48 and proportion of 0.3478) of the total respectively. Based on these data, it can be seen that the dataset is moderately unbalanced. Regarding comorbidities, presented in Table 1, the most prevalent is Heart Disease (Heart disease) with 97.10%, followed by Chronic Kidney Disease (CKD) with 94.20%. On the other hand, the least prevalent is Obesity, presented in only 34.06% of patients.\n\nTable 2 shows that the most common symptom among patients is Diarrhea, present in 94.93% of cases, while the least common symptom is Fever, reported only in 8.70% of patients.\n\n2.4.1 Experimental design\n\nThe research strategy focused on two primary objectives. The first objective was to identify the most effective algorithm for analyzing the dataset, and to conduct a correlation analysis of the variables to provide a suitable context. This was illustrated in Figure X (referenced as Figure 1). The second objective was to conduct a thorough analysis of various optimization methods to identify the key variables for a simplified model. This model should maintain a minimum reduction in its predictive capabilities while providing insight on the importance of each feature. The methodology used to achieve these objectives is explained in detail below:\n\n2.4.2 Data processing\n\nThe dataset was processed to contain a subset of 40 feature columns. The subset used in this work was generated from the first set by removing several features not directly related to the biomarkers. All variables were normalized, putting them on the same scale to facilitate analysis. The exclusion of certain variables is justified due to the analysis's focus on biomarkers and their importance in detecting the severity of COVID-19, which are features that can be objectively measured and that provide an assessment of a health condition.\n\n2.4.3 Evaluation of algorithms and metrics\n\nFive classification algorithms were evaluated and compared: Random Forest, Support Vector Machine, Logistic Regression, Decision Tree and Neural Network (Multi Layer Perceptron or MLP). To compare the performance of the models, evaluation metrics such as precision, recall, F1 score, and accuracy were used. The test used to discern the robustness of the methods was stratified five-segment cross-validation. During subsequent variable reduction experiments, an average of these metrics was employed as objective functions for the metaheuristic search algorithms.\n\n2.4.4 Model selection\n\nThe selection of the optimal model depends on the analysis of variables and the analysis of variable reduction that provide indications of the importance of the biomarkers. Given that there is an imbalance in the dataset, the models that will be selected for these analyzes will be those that are balanced by weights (or SMOTE in the case of the MLP). This ensures that uneven distribution of data is taken into account and more reliable and representative results are provided.\n\n2.4.5 Correlation analysis\n\nThrough correlation analysis, the variables (biological markers) associated with the severity of COVID-19 (COVID19_Severity) were identified. The correlated variables or biological markers are represented in a Table and a heat map of correlations.\n\n2.4.6 Variable reduction\n\nHeuristic experiments were carried out to progressively reduce the variables and the model performance was evaluated for each set of selected variables to obtain a model with a reduced number of variables without significantly compromising accuracy. In addition, variable selection experiments were performed using the following algorithms: genetic, simulated annealing, and crow search. These methods introduced variety to the models, ensuring that parameters were selected equitably to achieve similar time durations.\n\n2.4.7 Overfitting analysis\n\nTo evaluate the possibility of overfitting in the generated models, difference tests between the training and validation sets were implemented through learning curves. The curves, produced with the learning_curve() function from the sklearn library, illustrate the performance of the model when varying the size of the training set. A threshold of 0.05 (or 5%) was set for the difference between training and validation scores. If the difference exceeded this threshold, the model was considered overfitted. This methodology facilitated the identification of feature sets that provided an optimal balance between accuracy and generalization., illustrate the performance of the model when varying the size of the training set. A threshold of 0.05 (or 5%) was set for the difference between training and validation scores. If the difference exceeded this threshold, the model was considered overfitted. This methodology facilitated the identification of feature sets that provided an optimal balance between accuracy and generalization.\n\n\n3. Results\n\nIn this section, the results obtained in the study of predicting the severity of COVID-19 cases using different classification algorithms are presented. The algorithms evaluated include Random Forest, Support Vector Machine, Logistic Regression, Decision Tree and Neural Network (MLP). To evaluate the performance of each algorithm, the following metrics were used: precision, recall, F1-score and CV-Score (cross-validation).\n\nThe results in Table 3 provide a comparative view of the performance of machine learning algorithms based on various metrics.\n\nThis Table shows the basic metrics of the algorithms. It can be seen that all algorithms exhibit solid performance, with the precision, recall, F1-score, and ROC AUC value of each algorithm all exceeding 0.9. The Random Forest stands out as the best algorithm, which reaches the maximum value of 1.0000 in all metrics, with the exception of the cross-validation score, which is 0.9727. It's worth noting that, natively, Gradient Boosting (including XGBoost) and k Nearest Neighbors (kNN) do not allow balancing of classes and therefore they have not been considered in the comparison with the purpose of evaluating the models under equal conditions, in the same way, all the models have been initialized in random_state=42).\n\nTable 4 shows the accuracy, recall and F1 scores for each class of each algorithm. Random Forest achieves scores of 1,000 in all classes, but other algorithms, such as SVM and Logistic Regression, also show high performance in several classes, reaching scores of 1,000 in several metrics. The results reported for each metric with respect to the Random Forest algorithm select it as the best algorithm and it is subsequently used for the variable reduction experiments and other comparisons used.\n\nThe characterization analysis of the variables contained in the subset of data under study and the correlation analysis are presented below. The features are ordered by correlation. Table 5 contains the averages and range of all features, the correlation value and the Pearson P value with interpretation to provide context of the dataset.\n\nAdditionally, a bar graph of these correlations is shown in Figure 2.\n\nIn the original heat map, correlations clusters are distinguished that are characterized by variables with magnitudes greater than or close to 0.5. These magnitudes suggest a potential impact on the subsequent phase of feature selection. In particular, in the upper left corner of the map, a grouping stands out where variables such as ferritin and oxygen saturation present an absolute correlation greater than 0.5 with each other. Closely, fibrinogen shows a correlation of 0.47. Likewise, in the lower corner of the map, a strong correlation is observed between the variables Na, Creatinine, Urea and Cl. In addition, in relation to these, the variables ALT and AST also stand out.\n\nFigure 3, presents a refined version of this heatmap. In it, significant correlations with the target variable are evident (> 0.45). It can be deduced from this heat map that these correlations should, with high probability, be the ones selected in the variable reduction procedures.\n\nFour different approaches were used for feature selection: heuristic, genetic algorithm, simulated annealing algorithm and crow search algorithm. The two best models for each approach were identified (ranked based on cross-validation and number of variables). In the case of the heuristic approach, 3 and 4 variables were considered for the models. Once these models were found, it was decided that for metaheuristic approaches, the models would be encouraged to produce 3- and 4-feature solutions. The metaheuristic search algorithms were run ten times each and the two best models in each case were evaluated and compared at the end.\n\nSeveral progressively generated models were trained by adding the features that were found to have statistical significance during the correlation analysis. Below is a brief description of them for context.\n\n• Ferritin: Protein that stores iron in the body.\n\n• Oxygen Saturation (Sat.O2): Percentage of hemoglobin that carries oxygen.\n\n• Fibrinogen: Protein that helps in blood clotting.\n\n• D-Dimer (DDimer): Fibrin degradation product in coagulation.\n\n• Glucose: Blood sugar level.\n\n• Respiratory Rate: Number of breaths per minute.\n\n• Procalcitonin: Marker of inflammation and immune response.\n\n• Interleukin 6 (IL6): Protein involved in the inflammatory response.\n\n• Sodium (Na): Essential electrolyte for fluid balance.\n\n• Creatinine: Muscle waste product eliminated by the kidneys.\n\n• Urea: Waste that is formed when proteins are metabolized.\n\n• Chloride (Cl): Chloride level in the blood.\n\n• LDH: Enzyme that indicates tissue damage.\n\n• ALT: Enzyme indicating liver damage.\n\n• CRP: Protein that indicates inflammation in the body.\n\n• AST: Enzyme indicating liver damage.\n\n• Heart Rate: Number of heartbeats per minute.\n\n• Albumin: Protein produced by the liver and found in blood plasma.\n\n• Hemoglobin: Protein in red blood cells that transports oxygen.\n\nAs mentioned before, a limited set of variables within such a list (see heatmap in Figure 3) are expected to be displayed during variable selection. The models were trained progressively and the graphical results can be seen in Figure 4.\n\nThe values of the models represented in said graph are found in Table 6.\n\nDuring the training experiment with progressive addition of variables, 39 models were trained. The intermediate models, 20 to 38, have been omitted from Table 6 since their metrics were identical or inferior to subsequent models and the added variables did not show statistical significance during the correlation analysis. From this Table, procalcitonin and AST are highlighted as variables that increase the performance of the models; models were generated and analyzed with the progressive addition of these features. These models are referred to in this research simply as “Model 1” and “Model 2”.\n\nIn Table 7, a redistribution of the weights of the variables between Model 1 and Model 2 is observed. The inclusion of the variable AST in Model 2 entails a redistribution of the weight, especially with a notable reduction in the weight of procalcitonine from 0.2235 to 0.1140. However, despite the lower correlation of AST with severity (-0.2116), the inclusion of AST in Model 2 appears to contribute to a marginal improvement in the cross-validation accuracy of 0.9546 compared to 0.9636 for Model 1.\n\nIt is notable that both models achieve perfect accuracy and perfect F1-score, indicating their effectiveness in classification. The main difference between them lies in their performance in cross-validation, where Model 2 outperforms Model 1 with an increase of approximately 0.007 when including the variable LDH. This suggests that the inclusion of LDH may improve the robustness of the model and its generalization ability.\n\nDespite the marginal improvement, the decrease in cross-validation metrics in Model 2 compared to Model 1 suggests that the inclusion of the AST variable could be adding additional complexity without necessarily improving the generalizability of the model. The apparently unequal distribution of weights in the second model compared to the first could be a sign of overfitting.\n\nA joint superficial analysis of Tables 7 and 8, as well as the behavior of the metrics between models in Figure 4, suggests that although the Models 1 and 2 show excellence in their metrics, with a precision, F1-score and AUC of $1.0000$, this perfect performance could indicate a possible overfitting to the training data. To this end, subsequent evaluations are based on cross-validation as an indicator of performance and generalization (see Figure 6).\n\nThe algorithm used as an optimization function a combination of all the scores on average, so that it found the model that best satisfied all the metrics at the same time. The specifications of the genetic algorithm are as follows:\n\nIndividual Representation: Binary string of length equal to the number of features.\n\nAptitude Function: Average precision, recall, accuracy and F1 score.\n\nCrossing: Two point crossing.\n\nMutation: Bit flip mutation with probability 0.05.\n\nSelection: Tournament selection with size 3.\n\nPopulation Size: 50.\n\nNumber of Generations: 20.\n\nHall of Fame: Best individual through all generations.\n\nThe performance of the best models found with the metaheuristic method is shown below in Table 9.\n\nThis algorithm used a similar objective function as the previous algorithm. The specifications of the simulated annealing algorithm are as follows:\n\nIndividual Representation: Binary string of length equal to the number of features.\n\nPower Function: Negative of the average of the F1 scores obtained through cross-validation.\n\nMovement: Selects and deselects features randomly until the total of selected features equals 4.\n\nState Initialization: Random binary string with exactly 4 selected features.\n\nInitial temperature: 10.0.\n\nFinal Temperature: 0.01.\n\nNumber of Iterations: 150.\n\nThe performance of the best models found with metaheuristic method 2 is shown below in Table 10.\n\nThis algorithm used a similar objective function as the previous algorithms. The specifications of the crow search algorithm are as follows:\n\nIndividual Representation: Binary string of length equal to the number of features.\n\nAptitude Function: Average of cross-validation score and F1 score.\n\nCrow Movement: If the probability of consciousness is less than 0.2, it moves towards the target, otherwise it moves randomly.\n\nMutation: Flip bit with probability 0.2 (probability of consciousness).\n\nPenalty: Penalizes solutions with less than 3 features or 5 or more features.\n\nPopulation Size: 50.\n\nNumber of Iterations: 30.\n\nHall of Fame: Better individual through all iterations.\n\nThe performance of the best models found with metaheuristic method 3 is shown below in Table 11.\n\nTables 12 and 13 show the effectiveness and weighting of the features of the models under study (AUC and Specificity values are omitted as they are identical in all cases and equal to 1.0000).\n\nCertain clear patterns were observed in feature selection and its impact on model performance.\n\nIn Table 13, the models M3, M4, and M5, which have a cross-validation (CV) score of 0.9727, you can see the distribution of assigned weights of 0.5650 (M3), 0.4826 (M4) and 0.4920 (M5) respectively, for the Ferritin feature. This corroborates the importance of the variable in predicting the severity of COVID-19. In this table it can be seen that the ferritine feature is repeated in all models, and its weight is considerable in those with the best CV Scores (Models M3, M4, and M5), reinforcing its relevance in prediction. The variable sat. O2 is also selected consistently across almost all models, suggesting its predictive value, although its weight in the models varies, which could have implications for unbalancing the performance of each model.\n\nFeatures such as urea, creatinine, LDH, ALT and procalcitonine are selected in certain models, with variations in their weights. This could suggest that its importance may fluctuate depending on the context of the other features in the model. Although all models achieve high accuracy, CV Scores vary, suggesting differences in their ability to generalize to new data. Models M3, M4, and M5 stand out and tie with the CV Score of 0.9727, an indicator of better generalization ability than the rest of the models generated in the list.\n\nOn the other hand, models M7 and M8 have the lowest CV Scores (0.9545 and 0.9455, respectively), which could indicate a lower robustness in generalization or even overfitting (see Figure 5 in the overfitting analysis). We can relate these results to the weights assigned to their features and the selection method used. In the model M4, the additional features creatinine and ALT are included with weights of 0.07377 and 0.1113 respectively. In contrast, model M3 uses urea and Cl with weights of 0.2660 and 0.1690. Despite these changes, the CV score remains the same at $0.9727$ for both models.\n\nAny model suspected of overfitting is represented with a grid.\n\nModel M5, which also has a CV score of 0.9727, includes LDH and ALT with weights of 0.06770 and 0.1069, respectively, instead of creatinine which is found in the model M4. Despite this change, the weights assigned to ferritin and O2 saturation are very similar to those of the M4 model. A small difference of 0.006070 is shown when LDH is replaced by Creatinine. Models M4, M2 and M6 have CV scores of 0.9636. Despite sharing ferritin and O2 saturation with comparable weights with models M3, M4 and M5, these models also include procalcitonin, AST and fibrinogen with weights of 0.2235 (M1), 0.1191 (M2) and 0.1175 (M6) respectively.\n\nModels M7 and M8 have the lowest CV scores (0.9545 and 0.9455) and include urea and Na with weights of 0.1019 and 0.09156. Although urea is in the best model and both urea and Na are highly correlated between the variables with statistical significance and with others, its performance is lower than that of other models. One possible reason is the interaction with the oxygen saturation variable, which unbalances the weight distribution, which could lead to overfitting.\n\nA better qualitative comparison perspective and the importance of features can be appreciated in Table 14. In this table, the distribution of features in the models can be seen, where it can be observed that ferritine is present in all prediction models, due to its high correlation with the target variable and its high Pearson correlation. Following ferritine, oxygen saturation is present in almost all models, except the third one (which, according to Table 13, has a reasonable weight distribution and a high CV Score, so it could be possible to predict the disease severity without necessarily using oxygen saturation). Both features (ferritin and oxygen saturation) are considered as main features because they are present in all or almost all models, and this observation coincides with the calculated correlation for these features with the target feature. In addition, for the rest of the features, the complementary behavior of them with respect to the most frequent features can be seen. It is believed that those \"secondary features\" can be implicitly selected under diversity and cross-correlation criteria. It does not seem, in the first instance, to have any preferential distribution of secondary features, as the frequency values for these features fluctuate between 1 and 3 appearances. Being the secondary features most frequently appearing the LDH and ALT, whose target variable correlations are not necessarily the highest, but their interpretation with the p-value is deemed as \"significant\" (see Table 5).\n\nAn overfitting analysis was performed to evaluate the ability of the Random Forest model to generalize to new data. The overfitting analysis was carried out using two complementary approaches.\n\nLearning curve: Learning curves are generated using code:\n\nIn this code snippet, the learning_curve() function creates a set of training and validation scores for different training set sizes. An overfitted model will show a large discrepancy between training and validation scores, especially for larger training sets. In Figure 6 you can see these curves (the red one represents validation and the green one represents training).\n\nDifference between training and validation scores: The overfitting test is performed using the following code:\n\nThis code snippet calculates the difference between the mean training and validation scores for the largest training set size. If this difference is greater than 0.05, the model is considered to be overfitting.\n\nThe training and cross-validation results that were used to determine if the model is overfitted are presented in Table 15.\n\nThe perplexity parameters of the best models are presented below in Table 16 and models 9, 10 and 11 have been added, generated progressively and reporting the biomarkers Ferritin + Oxygen saturation + Fibrinogen because they are the three with the highest correlation with the target variable. In addition, model 12 has been added, which contains all the variables. The specificity is the average of the three classes for this case.\n\nA minimal difference between models can be noted in this table. One of the models from the heuristic algorithm presents the least perplexity of the set, closely followed by one of the best models according to the CV score. The one that is considered the best algorithm in Table 15 does not have the slightest measure of perplexity. Even so, in second place is one of the best models found in said table, which is also the only one of those at the top of the table that has a perfect Train Score. These results could indicate that by reducing model variables, there is a possibility of a slight degradation in performance, which could go unnoticed compared to classical accuracy tests.\n\nThis particular measure was adopted with a pragmatic consideration, since the probability distribution could be used experimentally as an indicator of the improvement or worsening of the condition in the absence of data of a temporal nature. This is because this distribution exhibits the proximity and similarity of a sample between different categories. It is suggested that perplexity can play a significant role as a metric to perform a differential analysis between the most prominent models.\n\nThe model highlighted in the table in question (determined by its CV score and its lower perplexity) stands out for a choice of biomarkers of a varied nature, which could suggest greater robustness of the model itself.\n\n\n4. Discussion\n\nThis study supports the conclusions presented by Gharib et al.,7 which emphasizes the relevance of negative correlations with oxygen saturation and positive correlations with ferritin when investigating biomarkers of inflammation related to the severity of COVID-19. Furthermore, it highlights the importance of biomarkers such as IL-6, LDH, CRP and D-dimer. The correlations with the variables mentioned in the study by Khan et al8., are also corroborated during the analysis phase in this study, especially regarding ferritin (highly significant), IL-6 (highly significant) and CRP (slightly significant). Similarly, the study conducted in Alexandria by Abdelhalim et al10. found that 71.4% of non-hospitalized patients had elevated levels of serum ferritin, reaffirming its relevance as a biomarker in the diagnosis of COVID-19.\n\nThe results obtained could indicate that, beyond the individual impact that each variable may have, the interaction between various biomarkers could be of especially significant importance. Most of the models investigated integrate fundamental features, such as ferritin levels and oxygen saturation, along with other secondary features, such as fibrinogen, sodium (Na) levels, creatinine, urea, chloride (Cl), as well as the levels of the ALT and AST enzymes. In the differential analysis of perplexity, the three outstanding models were identified, and it was observed that the model that presented the best performance (determined by its highest score in the CV Score and its lowest perplexity) uses variables that reveal liver damage (represented by ALT), kidney damage (evidenced by creatinine), biomarkers that denote immunoinflammatory alterations (such as ferritine), as well as the balance in oxygenation (sat.02). These observations could suggest that feature diversity could play an important role in decreasing model perplexity and granularly increasing overall prediction performance. Within the focus of the study, it has not been found whether this importance of diversity has already been reported previously.\n\nA point to highlight is the indication of Samprathi et al.13 on the non-recommendation of serum ferritin to monitor treatment response, despite its prominence in predictions. Additionally, a comprehensive review11 identified lymphopenia, thrombocytopenia, interleukin-6, ferritin, among other biomarkers, as associated with severe and fatal cases of COVID-19. In particular, hyperferritinemia was highlighted as an indicator of systemic inflammation and a poor prognosis.\n\nThese findings, together with the identification of ferritin as an independent predictor of COVID-19 mortality in the study by Sibtain et al.,12 highlight the need to continue investigating and evaluating the function and predictive value of these biomarkers in the disease using the interaction between variables as a framework.\n\nThis work is similar to the approach used in the work of Ahmed et al.15 However, there are fundamental differences in methodology. One of these is the deliberate exclusion of models that do not easily admit balance, as is the case of kNN. This choice was made despite the fact that many studies, including the recently mentioned,15 included it among their compared methods, along with Random Forest, Support Vector Machine, Logistic Regression and Decision Tree, such as the study by14 which used Random Forest and AdaBoost.\n\nThe current work has prioritized a preselection of biomarkers based on the Pearson p-value, facilitating the reduction of the search space for the metaheuristic algorithms that were used for subsequent feature selection. This preselection is consistent with the study by Elif et al.,17 which identified significant biomarkers with a similar method, agreeing with this study in biomarkers such as LDH, high leukocyte count and C-reactive protein. The models presented in said study achieved an accuracy of 0.9796 and an AUC value of 0.959, it can be suggested that the high prediction values may indeed be related to the selection of statistically significant features, given that this study reports exceptional metrics and AUC. A relevant aspect is that in the current work, unlike,26 the data used during the correlation analysis have been used for subsequent variable reduction experiments. In other similar works26,15 the 5-fold stratified cross-validation, considered fundamental in the analysis of this work to evaluate the performance of the models, has not been implemented. In the work of Patterson et al.18 A 10-fold CV approach is used which appears to be quite effective. This approach is feasible in this work given the magnitude of the dataset (n=225).\n\nIt is suggested that data balancing could present a significant improvement in model construction. Xiong et al.,26 carried out an analysis that is similar to the approach of this study. Despite working with a more extensive dataset (n=287) and having a notable diversity in features, they do not mention a specific balancing process. From the analysis of its results, the Random Forest model stood out with an AUC of 0.970, while the SVM model recorded the highest precision, with 88.5%. However, despite its extension, our study, with a sample of n=138, delves deeper and expands on the features of said data, in addition to using balancing techniques. For their part, Gok et al.17 worked with a larger dataset (n=863), which was balanced using the SMOTE technique. Of the 8 trained models, Random Forest had the best performance, achieving an accuracy of 0.98, similar to the results of our study. A key difference between the work of Gok et al.17 and ours lies in the nature of the variables used for prediction. While Gok et al.17 they did not use laboratory results that contained biomarkers such as IL-6, LDH or Ferritin, in this study they have been essential in the analysis. The latter can make prediction difficult because the biomarkers are not very specific, which highlights the high precision of the models generated in said study. It is vital to highlight that the study by Gok et al.17 emphasized how data preprocessing and balancing positively influence the accuracy and robustness of the model.\n\nIt should be noted that although Xiong et al.26 does not detail its balancing process, other studies, such as that of Wang et al.,27 have adopted the SMOTE technique successfully. Specifically, Wang et al.27 they achieved an exceptional precision of 0.9905 and an AUC value of 0.846. Given the performance results of the models, this study has recognized RandomForest as one of the best classifiers, aligning with observations in.15,26 It is relevant to mention that this work has obtained an AUC value that slightly exceeds that reported by,17 but as the dataset is smaller, more tests must be performed before reaching definitive conclusions. When looking at other metrics, such as accuracy, this work has achieved comparable results to studies such as,14 which achieved an accuracy of 0.94 and an F1 Score of 0.86, and with an accuracy19 of 84.2 % and an AUC value of 0.874 for the first group (age ≤ 70) and 0.842 for the second (age ≥ 70).\n\nFinally, while studies such as that of Iwendi et al.,14 which highlighted a correlation between gender and mortality, and that of Cui et al.,19 focused on the differences in biomarkers according to age, have provided unique perspectives, the present work has focused on validating and comparing techniques based on clinical analyzes with the aim of identifying the most appropriate approach to predict outcomes in patients with COVID-19. Future work could include the participation of these variables in the models.\n\nFeature selection has notably benefited from the use of metaheuristic algorithms, which have shown consistent improvements over traditional heuristic techniques, especially in high complexity areas such as COVID-19 severity prediction. In this work, we sought to use diverse algorithms inspired by evolution, physical mechanisms and collective intelligence, as mentioned in the work of Agrawa et al.28 It should be noted that the algorithms applied were quite simple, trying to preserve the minimum version of each one to encourage equality of conditions, so they cannot be directly comparable with those of other works that present cumulative improvements said algorithms.20,29,21,22,23 Relevant differences with said works will be discussed below.\n\nThe genetic algorithm has proven effective in several contexts, including the work of Kabir et al.,20 which introduced a redundancy reduction approach. In our study and in that of Hayet et al.,29 the genetic algorithms provided remarkable results, although the choice of appropriate objective functions could have improved the performance. Focusing on the detection of COVID-19, the study by Hayet et al.,29 highlights the importance of specific variables, such as CRP, Respiratory Rate, Oxygen Saturation, and LDH. The consistency in the selection of these variables between different investigations highlights their relevance, although differences have also been observed, such as the elimination of certain variables due to insufficient quality of the data.\n\nSimulated Annealing, analyzed by Guha et al.,21 has proven to be useful for multidimensional problems. This work mentions a hybridization with a recently developed optimization algorithm called equilibrium optimization (Equilibrium Optimizer) which, according to said work, is capable of working during the exploitation phase to obtain better results than just simple simulated annealing, for this it is considered that simulated annealing works as a local preseeker. Additional mention is made of the work of Bandyopadhyay et al.,23 where a two-stage pipeline was proposed for the detection of COVID-19 in radiological images. They used a DenseNet-based CNN for feature extraction and combined the Harris Hawks Optimization (HHO) algorithm with Simulated Annealing (SA) and chaotic initialization for selection. The study achieved an accuracy of 98.85% and reduced the number of features by 75%.\n\nDespite efforts to use crow search, highlighted by Chen et al.,22 in our work, this algorithm showed limitations, including the potential for overfitting. In this study, the search is improved using a hierarchical approach that reports favorable results. In all previous works, an improvement in the results can be seen by hybridizing the algorithms with pre-optimization during the search phase that allows a better exploitation phase.\n\n\n5. Conclusions\n\nIn this study, a comparative analysis of different classification models was carried out to predict the severity of COVID-19 cases with biological markers. The results obtained provide relevant information for the understanding and management of the disease. Below are the main conclusions of the study:\n\n• Model evaluation: Five classification models (Random Forest, Support Vector Machine, Logistic Regression, Decision Tree and Neural Network) were compared using metrics such as precision, recall, F1-Score and accuracy. Most models showed similar performance across all metrics evaluated. The Random Forest model showed exceptional performance with cross-validation of 0.9727 and perfect metrics for the rest.\n\n• Correlation of variables: A correlation analysis was carried out between the variables and the severity of COVID-19. It was observed that the biological markers ferritin and oxygen saturation (sat. O2) showed the highest correlations (0.8277, -0.6444) in absolute value with the target variable (COVID19_Severity). These findings may be useful in understanding factors (biological markers) related to disease severity.\n\n• Feature Selection: Experiments were conducted to evaluate the efficiency of the model when using different sets of predictor variables (biological markers). The experiments were carried out with genetic algorithms, simulated annealing and crow search. It was found that even with only two biological markers (variables), ferritin and oxygen saturation, the model maintained a high level of accuracy (0.9636). This suggests that it is possible to reduce the number of variables without a significant loss in the predictive ability of the model. The best model (fewer variables and more precision) was found to be one that included the features ferritine, urea and Cl without losing any of the metrics.\n\n• Overfitting evaluation: Cross-validation was performed and the importance of features in the Random Forest model was examined. The results indicated a stable performance of the model, with a small standard deviation and a prominent importance of the variables ferritin and oxygen saturation.\n\n\n6. Recommendations\n\n\n\n• Expansion of the dataset: It is considered that the dataset is relatively small and a larger sample would be preferred for better generalization of the model's classification patterns.\n\n• Validation with external datasets: Although cross-validation allows us to better perceive the generalization of the models, it would be good to be able to validate said model with public datasets. However, many of these datasets do not have the diversity of features necessary to fully use the models in this work. It should be noted that public datasets require a lot of preprocessing and exhaustive research would be necessary for such an experiment. If it is not possible to completely make these data sources compatible, the number of features to be used could be limited in order to homogenize the data.\n\n• Feature Selection: Although experiments were performed with fairly minimalist versions of the algorithms, it is possible to use some of the variants mentioned during the discussion. Its implementation would require a lot of experience in the subject but could suggest significant improvements in the convergence of said selections.\n\n• Overfitting evaluation: With a homogenized external dataset or more cases, you could have a better idea of the overfitting of the generated models.\n\n\nEthical considerations\n\nThe ethical and legal guidelines considered for sampling are described in De la Cruz-Cano et al.25\n\n\nAuthor contributions\n\nEduardo de la Cruz-Cano - collect the dataset studied in this research and data curation.\n\nFreddy de la Cruz-Ruiz - project administration, experimental study design.\n\nJuan Pablo Olán-Ramón - software, wrote code, conducted experiments and wrote the manuscript draft.\n\nSarai Aguilar-Barojas - review and approved the manuscript to be submitted.\n\nErasmo Zamarron-Licona - review and approved the manuscript to be submitted.", "appendix": "Data availability\n\nThe dataset studied in this research was already made available through De la Cruz-Cano et al. 25 Harvard Dataverse: Comorbidities and laboratory parameters associated with SARS-CoV-2 infection severity in patients from the southeast of Mexico: A cross-sectional study. https://doi.org/10.7910/DVN/DFALL683\n\nThis project contains the following files:\n\n• - COVID19_Database (v1).tab (Data on clinical features and laboratory parameters of COVID-19 patients).\n\n• - Data key.docx (Data key for variables and abbreviations in the tab file)\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\n\nAcknowledgements\n\nWe thank the doctors and nurses assigned to the COVID-19 area for the data provided to carry out this research.\n\n\nReferences\n\nZumla A, Niederman MS: The explosive epidemic outbreak of novel coronavirus disease 2019 (COVID-19) and the persistent threat of respiratory tract infectious diseases to global health security Current opinion in pulmonary medicine.2020.\n\nRamadijanti N, Muarifin, Basuki A: Comparison of Covid-19 Cases in Indonesia and Other Countries for Prediction Models in Indonesia Using Optimization in SEIR Epidemic Models. 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PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWorld Health Organization: Clinical management of severe acute respiratory infection (SARI) when COVID-19 disease is suspected: interim guidance, 13 March 2020 (No. WHO/2019-nCoV/clinical/2020.4).\n\nDe la Cruz-Cano E, del C Jiménez–González C, Díaz-Gandarilla JA, et al.: Comorbidities and laboratory parameters associated with SARS-CoV-2 infection severity in patients from the southeast of Mexico: a cross-sectional study. F1000Res. 2022; 11. Publisher Full Text\n\nXiong Y, Ma Y, Ruan L, et al.: Comparing different machine learning techniques for predicting COVID-19 severity. Infect. Dis. Poverty. 2022; 11(1): 1–9. Publisher Full Text\n\nWang J, Yu H, Hua Q, et al.: A descriptive study of random forest algorithm for predicting COVID-19 patients outcome. PeerJ. 2020; vol. 8: pp. E9945. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAgrawal P, Abutarboush HF, Ganesh T, et al.: Metaheuristic Algorithms on Feature Selection: A Survey of One Decade of Research (2009-2019). IEEE Access. 2021; 9: 26766–26791. Publisher Full Text\n\nHayet-Otero M, García: Extracting relevant predictive variables for COVID-19 severity prognosis: An exhaustive comparison of feature selection techniques. Plos one. 2023; 18(4): e0284150. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "296235", "date": "28 Jun 2024", "name": "Maitham Ghaly Yousif", "expertise": [ "Reviewer Expertise immunology", "Medical Microbiology", "and AI" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nAssessment and Recommendations for the Study: Strengths:\nAlgorithm Selection and Evaluation: The study effectively utilised a variety of machine learning algorithms, evaluating them comprehensively using multiple accuracy metrics, which enhances the credibility of the results. Correlation Analysis: The detailed correlation analysis provided deep insights into the relationships between variables and the severity of COVID-19, contributing significantly to the field.\nWeaknesses:\nSample Size: The relatively small sample size (n=138) may limit the generalisability of some machine learning algorithms used in this study. Class Balance: The study does not clearly detail how class balance was addressed, which is crucial for ensuring the accuracy of machine learning model outcomes.\nRecommendations:\nIncrease Sample Size: To improve generalisability and enhance the robustness of the findings, it is recommended to increase the sample size in future studies. Detailed Class Balance Analysis: A more detailed analysis of how class balance affects model performance is recommended, including exploring strategies such as SMOTE for improving class balance.\nUnassessed Aspects of the Study: The technical specifics related to data configuration and preprocessing were not assessed due to a lack of detailed information on the methods used for initial data preparation and analysis. Mandatory Reviewer Questions:\nClarity and Precision of Writing: The study is clearly written, providing sufficient detail about the algorithms and methodologies employed. Relevance to the Field: The study is highly relevant to COVID-19 research and innovatively applies machine learning techniques. Originality and Contribution to Knowledge: The study makes a valuable contribution by identifying potential biomarkers for the severity of COVID-19.\nApproval Status: Approved with Reservations - The study is recommended for revision to address issues related to class balance and sample size to strengthen the research and its generalisability.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] }, { "id": "322245", "date": "09 Oct 2024", "name": "Gustavo Sganzerla Martinez", "expertise": [ "Reviewer Expertise Artificial intelligence", "immunology." ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nI read with interest the work from Olan-Ramon et al. In their work, the authors compared different machine learning algorithms to predict severity in COVID-19 patients based on laboratory biomarkers.\nOverall, the introduction is extensively long and fails to describe what are the biomarkers the authors have actually considered for their work.\n\nPlease indicate the version of python and the libraries used.\nReading the methods, tt is not clear whether the authors used an already collected dataset of patients or they did their own data collection. If the authors collected their own data, the authors need to provide additional details regarding their cohort such as inclusion/exclusion criteria, how the data was collected, the laboratory procedures used to collected data, and much more.\nWhat is the criteria that defines mild, moderate, and severe COVID-19 infection?\nThe authors should pay attention to the spelling and writing consistency/quality throughout their text (e.g. title of section 2.3 - 'dataset characterizationc', the presence of $ when describing the performance in the eighth paragraph of the introduction, \"this was illustrated in Figure X\").\nIn tables 1 and 2, the authors should show the comorbidities and symptoms based on their groups (severe, mild, moderate).\nThe authors need to provide which are the 40 columns they used in their prediction (methods 2.4.2).\nDid the authors used a multi-class classification?\nThe authors need to provide more details on their algorithm selection process. What was the ratio of train and test data points? What was the architecture of the models? I understand this is an initial process to determine the algorithm with best likelihood of correctly predicting, but for models such as neural networks, random forest, SVM, a few parameters need to be defined (number of neurons, layers; SVM kernel; number of estimators for RF, etc).\nThe correlations described in section 3.2 need more details. I assume (from the title of Table 5) the authors are correlating the continuous values of the biomarkers with COVID19 severity. How was severity treated as a continuous value rather than a class?\nIs it really necessary to show code snippets along with the paper?\nThe chosen model by the authors (with best performance) was a random forest. The authors have provided an extensive feature selection process. I wonder what would have been the outcome if the authors have run the random forest with all the input variables and analyzed the feature importance of each. There is a built-in function based on gini importance of RF models in scikit learn (model.feature_importances_).\nThe authors have proposed models composed of different input variables with the best prediction score (table 15). It is clear that variables such as ferritin and sat 02 are ubiquitous in different subsets. I feel the authors should have provided an analysis of how these variables were treated by the RF model in characterizing each class of data (e.g. higher ferritin in severe patients, etc).\nOverall, the authors well documented most of their machine learning application. However, the study is filled with several points that need to be revisited prior to its indexing so it can be scientifically sound and reproductible.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? No\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] } ]	1	https://f1000research.com/articles/13-688
https://f1000research.com/articles/10-883/v1	02 Sep 21	{ "type": "Method Article", "title": "Hospital quality monitoring and evaluation system using linked spreadsheets on Microsoft SharePoint", "authors": [ "Francis Kiroro", "Majid Twahir", "Daniel Kiura", "Ann Kamuyu", "Ann Wanyoike", "Majid Twahir", "Daniel Kiura", "Ann Kamuyu", "Ann Wanyoike" ], "abstract": "Background Establishment of a systematic way of measurement and utilization of indicators for improvement is one of the most challenging issues in monitoring and evaluation of indicators in healthcare settings. In realizing these fundamental challenges, we designed a monitoring and evaluation system incorporating a hospital-wide quality variance report (QVR) system using linked Microsoft Excel® spreadsheets on Microsoft SharePoint®.\nMethods Indicators were determined at the departmental/unit level in line with the institutional goals, departmental functions, quality expectations, inputs/outputs, clinical priorities, compliance to policies/procedures/protocols/guidelines/pathways as well as in response to gaps in service delivery picked during root cause analyses. The sample design was determined in accordance with the characteristics of the population. Drawing of sample units was done using a simple random sampling technique without replacement or systematic random sampling. The indicator’s monitoring was enhanced visually by allocating colour codes based on performance across the months and quarters. The action plan tab consisted of a platform that aids in documenting corrective actions arising from the performance reviews. Results and discussion The QVR reporting system ensured a standardized format of monitoring throughout the institution with a reduced turnaround time from data collection to analysis. Further, continuity of the monitoring and evaluation (M&E) system was guaranteed even if an individual left the institution. The analysis of the QVR allowed hospital-wide trending on cross-cutting indicators with consequent ease of communication to multiple stakeholders. The automation has saved time and increased accuracy which has enhanced credible engagements during quality meetings. Conclusions\nUse of this system greatly enhanced quality performance monitoring in the hospital, identification of major bottlenecks that warranted hospital-wide projects or departmental-level projects. The QVR system enhanced the efficiency and accuracy of quality monitoring from data collection through to performance reviews. The QVR structure allows for customized development of an M&E database application software.", "keywords": [ "QVR", "quality variance reports", "monitoring and evaluation", "hospital quality", "key performance indicator", "Microsoft SharePoint", "Microsoft Excel" ], "content": "Introduction\n\nMonitoring and evaluation encompasses a systematic establishment of indicators, data collection and analysis as well as periodic reviews to identify suitable action plans for improved performance of ongoing processes (Fajardo Dolci, Aguirre Gas, and Robledo Galván 2011). Indicators refer to specific metrics that enable evaluation of goals’ and objectives’ achievements, they are specifically referred to as key performance indicators (KPIs). It is imperative that the KPIs are SMART (specific, measurable, achievable, relevant and time-bound) and linked to inputs, activities, outputs, outcomes and goals (Kusek and Rist 2004). A profound monitoring and evaluation system ought to incorporate mixed research approaches (Bamberger, Rao, and Woolcock 2010). All relevant stakeholders’ involvement is necessary in determination of indicators to be tracked (Emberti Gialloreti et al. 2020, Malone et al. 2014, Diallo et al. 2003, Guijt 1999). Participatory monitoring and evaluation involves incorporation of all the stakeholders in all stages and processes of the M&E system, and the engagement helps in determination of the way forward and what modifications are needed for better M&E (Izurieta et al. 2011, Estrella et al. 2000, Guijt 1999, Estrella and Gaventa 1998).\n\nThe most challenging issue in monitoring and evaluation of indicators in healthcare is the development of a systematic way of measurement and utilization of indicators for improvement, development of such a system which incorporates variance reporting requires concerted effort and inclusion of each team member (Brown and Nemeth 1998). There are myriad challenges towards the design, development, and implementation of an effective M&E system; such as stakeholder buy-in, knowledge gap, time constraints, logical frameworks, resources available, and the validity of data, sampling techniques, and the indicator measurements (Emberti Gialloreti et al. 2020, Anderson et al. 2019, Mthethwa and Jili 2016, Cameron 1993). Emberti Gialloreti et al. (2020) concluded that multiple stakeholder involvement is necessary for a successful and timely system in collection and monitoring of health information. Participatory M&E systems promote efficiency, relevant and effective processes leading to an elaborate corrective action (Guijt, 1999). In realizing these fundamental challenges, we designed and developed a monitoring and evaluation system incorporating hospital wide key performance indicators. We named the system; quality variance report (QVR) system, and it is developed by use of linked Microsoft Excel 2010 (Microsoft Excel, RRID:SCR_016137) spreadsheets on a Microsoft SharePoint 2010 on-premises (intranet). SharePoint being a Microsoft product, it has new and exciting features in every new release, among the functions available are; web content management, social media functionality, and search features, among others (Perran et al. 2013). Utilization of SharePoint fosters centrality of online access to collaborative information (Ennis and Tims 2012). Knowledge sharing via various media is possible through SharePoint (Weldon 2012). A well constituted SharePoint implementation strategy enables an institution to enhance collaboration, communication, and storage (Diffin et al. 2010) and in addition enables flexibility of spreadsheet data linkage (Prescott et al. 2010).\n\nThis was an improvement on the previous KPI’s monitoring process which entailed submission of hard copies of filled data collection tools to the monitoring and evaluation unit. This was a time-consuming process confounded with challenges, including lost forms, late submission, illegible handwriting, and transcription errors. In a study conducted by Jordans et al. (2019), illegible information was considered as incorrect which was similar to our experiences. Automation of data collection tools was one way our project intended to reduce the challenge of illegible handwriting.\n\nThe previous system was heavily dependent on individual quality focal points from the departments who maintained data on standalone computers and data were shared by use of emails. This presented another challenge during staff turnover, or cases where some data and related literature would be lost if the machines crashed or the data got accidentally deleted. There was also a lack of standardization on how the data was maintained among various quality focal points. The Microsoft SharePoint server hence came in handy, albeit its utilization bringing about need for elaborate training to ensure maximum utilization (Dahl 2010). Initially utilization of SharePoint was limited to document management, where staff working on policies updated the drafts in a dedicated folder on Microsoft SharePoint enhancing collaboration which was later extended to indicator monitoring.\n\nThis article presents a description of the system that we designed and implemented at the quality department of the Aga Khan University Hospital, Nairobi and rolled out across the entire hospital. It started as a basic standard system design which was improved with various features over time to address the emerging challenges experienced in monitoring and evaluation of quality indicators.\n\n\nMethods\n\nThe QVR monitoring and evaluation (M&E) system refers to a mechanism that enables KPI’s dashboards appearance and availability to be standardized and linked using spreadsheets on a Microsoft SharePoint server. The QVR adopted its name from the ability of the quality monitoring dashboards generated to show the difference between achievement and targets/benchmarks (variance). The quality indicators are gathered from the smallest unit level to the highest institutional level. The highest hierarchy of classification of the hospitals’ quality leadership includes institutional leadership, divided into; clinical and non-clinical departments that are branched further into various sub-sections and units. KPIs dashboards are aligned in the same order from the smallest unit to the highest in the echelon. A Microsoft SharePoint server anchored in the institution’s intranet configuration enables data capture and access through spreadsheets to be done centrally to everyone with rights of access. Rights of access are obtained from the institution’s Information Communication and Technology’s (ICT) administrator. The spreadsheets are linked allowing similar indicators to be grouped together at a higher level of departmental structure up to the institutional level which enhances comparisons. The linking of data from data-entry screens allows seamless real-time tracking of indicators. The spreadsheets are saved in folders which are arranged in line with departmental organograms, with sub-folders equivalent to all sub-units, the data entry sheets (templates) are placed in each of the unit folders. Figure 1 demonstrates how QVRs are linked from a unit level to institutional level. Several units comprise a department or a section/program of which several of these form a department. X in the illustration indicates the possibility of multiple available departments/units.\n\n\nDetermination of indicators\n\nThe indicators are determined at the departmental/unit level in line with the institutional goals, departmental functions, quality expectations, inputs/outputs, clinical priorities, compliance to policies/procedures/protocols/guidelines/pathways as well as in response to gaps in service delivery picked during root cause analyses. The committee that prepares the quality plans and indicator measures are referred to as departmental quality improvement and patient safety (DQIPS) committees. It is usually essential to incorporate all stakeholders in the formulation of indicator measures (Diallo et al. 2003). Each department has a quality advisor attached to it, from the quality department, who acts as a required liaison between the department’s needs and quality expectations. The indicators are then presented by the institutional quality improvement and patient safety (QIPS) committee to the joint staff committee (JSC) for reviews and approval. Figure 2 portrays the data aggregation process flow we developed to guide the practice; the process begins with identification of what needs to be measured; a review of the literature is undertaken to find out appropriate research questions and benchmarks if available (where benchmarks are not available internal targets are set up after the pilot phase), a research design is determined through which data collection tools are designed and developed, sample determination follows, data collection methods and analysis plan are established, tool validation is done during the pilot phase. When data tools and data collection teams are deemed appropriate, collection and processing of data is done, and trends are monitored over time. Frequency of data collection is dependent on the indicator being monitored; the data entry sheets are designed in such a way that data is collected continuously. The data is networked/mapped in an orderly manner where similar indicators are aggregated together at a higher level which leads to better monitoring (Abdi, Majdzadeh, and Ahmadnezhad 2019). For information to be useful, data gathering ought to be collected at well-defined frequency (Prennushi, Rubio, and Subbarao 2002, Guijt 1999).\n\n\nSampling\n\nSample design is determined in accordance with the characteristics of the population. Specifically, sample size is determined by considering factors such as the design, sampling method, the indicator/outcome being measured, design effect and variance, power, level of significance as well as the level of precision desired for the indicator estimates (Chander 2017). Drawing of sample units is done using either a simple random sampling without replacement or systematic random sampling. Microsoft Excel provides users with functions such as random number generator (=RAND(),=RANDBETWEEN(x,y)) and an add-on such as ‘Data Analysis Toolpack’. Either of these are used during determination of the sample units. A sample guideline had been developed to help the users for easier implementation with assistance by a statistician.\n\n\nQVR structure\n\nData collection tools were designed specifically to suit the measurement criteria of each indicator in a format that ensured easier entry and linkage with other indicators for results aggregation. The data entry sheets were created in user friendly formats so as to provide a platform for easier data entry, for instance, use of drop down lists where applicable, restrictions were also applied to ensure specified data were entered correctly in the cells. Customized error messages emerge if incorrect data type or format was entered. The excel functions in the data entry screens were locked for editing (using passwords that were only accessible to the M&E unit) to prevent alteration by users during data entry. Figure 3 portrays an example of a data entry sheet used to collect data on compliance towards the requirement for correct patient identification while administering treatment or when giving any other service to a patient. Columns B, G, H and J have drop down lists for easier data entry, all columns have restrictions such that only data in the specified format is entered, column E contains the medical record numbers of the patient sampled, column F provides a description of the procedure or the service audited, column J the category of staff observed, name of staff observed as well as that of the auditor is also captured. The data from the sheet, in which this snapshot is obtained, is aggregated into a dashboard by use of a formula separating the numerator (the opportunities complied to) against the total number of opportunities observed and a proportion of compliance is computed.\n\nQVR is a workbook that comprises several sheets as shown in Figure 4. The tab named QVR contains the master KPI dashboard described under the QVR master sheet section. The Definitions tab contains a sheet that presents explanations about the indicators and how they are measured. The dashboard tab presents data in terms of absolute numbers as well as in terms of ratios, proportions and rates, and obtained data (linked) from the data entry sheets. An action plan tab provides the users with a platform for documenting gaps, root causes and the resulting action plans.\n\n\nThe QVR master sheet\n\nThe QVR master sheet comprises various components. As demonstrated in Figure 5, the sheet has the first column containing an indication of the current year of tracking and the indicators measured, the second column defines how the indicators are measured. The third column contains either a target or benchmark corresponding to each indicator; a benchmark is derived from literature sources or from other hospitals’ accomplishments (whereas in the absence of these, internal targets are determined). The previous year’s average performance is presented to facilitate comparisons with the current year’s performance. Monthly performance is directly linked to data entry sheets and populates automatically as the data are entered. Quarterly performance has functions that compute the performance levels from the monthly data. The trends column uses sparklines which portray monthly trends from January to December. Variance indicates the percent difference between the benchmark/target and the quarterly performance. The annual column indicates performance from the beginning of the year up to the current date. Literature references provide the literature sources from which benchmarks are derived. Hazard vulnerability analysis provides rating metrics for the risk score based on the likelihood of risk occurrence as well as the consequences/severity of occurrence as per the guide obtained from institution’s risk program.\n\n\nColour codes configuration\n\nThe KPI’s monitoring is enhanced visually by allocating colour codes to various performances across the month and quarters. The conditional formatting feature available on Microsoft Excel is utilized to promote visual assessment of indicators. In the configuration, green portrays an indicator that has met benchmark or target set or exceeded. The colour red appears if the indicator measure’s level is below the benchmark/target. Amber appears if the performance is below benchmark but higher than the average performance of the previous year. White is present if for that particular period, the indicator is not applicable and finally the colour grey represents ‘grey areas’, where data is due but not yet populated. These entire colour codes are set to change automatically as the data is input into the linked data entry sheets. The final indicator measure on each QVR master sheet is the measure of timeliness of data provision expressed as a proportion of all the indicators which have data populated by the 5th of each subsequent month out of all indicators measured by the unit/department. The illustration of the colour code configuration is as shown in Figure 6.\n\n\nAction plan tab\n\nAction plan tab consists of a platform that aids in documenting corrective actions arising from the performance reviews/evaluation. Reviews are made at least once a month and gaps listed down in the action plan’s sheet. The gaps are identified by checking the colour codes, the trends column as well as the variance columns (see Figures 5 and 6). If an indicator presents more reds compared to other indicators this suggests a gap that needs to be dealt with, similarly, if the trends column shows a poorly performing trend or a sudden change either upwards or downwards this presents an opportunity for root cause analysis. Finally, in the variance column, a greater percentage variance presents an opportunity for further action. Figure 7 portrays the components of the action plan tab. It has a serial number column, month, the indicator with undesired performance, gaps and why as identified through a root cause analysis, the action plan containing the corrective action, a timeline for closure, the individual responsible for follow-up, and review date as well as the additional comments. The process of evaluation hence takes both the quantitative component and qualitative one.\n\nIn order to ensure effective utilization of various components and features, training was provided to each new user. The previously taught users were intended to pass on the knowledge, skills, and competencies acquired to their colleagues within departmental units. Advanced training needs identified were provided by the Quality department through the M&E unit in collaboration with the ICT training unit. Gaining the right competences enhances the success of the M&E. Successful training refers to proper acquisition of competencies, skills, and knowledge which are imperative in achieving a working M&E system (Fletcher et al. 2014).\n\n\nData security and back-up\n\nThe hospital’s Information Communication Technologies’ (ICT) department developed a framework of maintaining back-ups daily on hard disk separate from the server hosting the SharePoint data. In addition, offsite archiving of the data happened monthly which enabled recovery of any loss, in case a user deleted an item erroneously. Every user underwent basic training on how to access and update items on the Microsoft SharePoint platform. A request for rights to access to the Microsoft SharePoint server by any new potential user was sent to the ICT in order for the access rights to be provided. This ensured coordinated control of who accessed at any time. The Microsoft SharePoint also indicates the access logs, thus the last person who accessed a certain document on the server can be determined. Once a new user was allowed access to SharePoint, passcodes for the files they need to access were provided and this ensured that only the relevant files were accessed by the appropriate SharePoint users. Access to SharePoint data was further enhanced by document-level control where each department set passwords for their own documents. The quality department M&E unit also instituted document protection passwords that prevented the structure of the QVR and the formulae contained in the worksheets from being altered. Data are not entered directly into the QVR but are fed in through primary data entry sheets with enhanced data validation restrictions ensuring only the required type of data is entered. As such, the QVR dashboards are accessible to user departments with passcodes that grant them read only rights.\n\n\nResults and discussion\n\nThis section provides a review of the accomplishments observed since adoption of the QVR as a hospital quality monitoring and evaluation system.\n\nContinuity of the Monitoring and Evaluation System: Before implementation of the QVR reporting system, there was a major challenge in regard to data collection and sharing with the M&E unit for processing. In a situation where a data provider was away, data would not be available until such a data provider resumed work and shared it. The situation was worse in cases of service interruption through either staff dismissal or resignation, since some instances, a replacement would not be available immediately or the incoming staff might have been in need of an elongated period to adapt. After implementation of the QVR system, each unit head was required to be actively involved in the entire process. In addition, they were meant to involve their staff from the determination of the indicators, design of data collection and entry sheets as well as linking to the QVR spreadsheets on Microsoft SharePoint. The unit leaders were required to ensure availability of resources for continuous data collection and entry. Appointed staff from each unit were taught how to collect and enter the data which ensured continuity enough to withstand the effects of staff turnover. Adoption of the QVR system has increased tremendously since initial implementation; the initial year of implementation was 2017 where a total of 50 departmental units had functional QVRs which increased in year 2018 and 2019 with 60 departmental units having functional QVR dashboards. The participatory approach adopted in M&E enabled communication of results which enhanced sharing of information within the departmental units, as well as across the departmental units. Guidance was provided on what information was meant to be shared during the multidisciplinary meetings, leading to increased motivation to participate due to clarity on the expectations (Guijt 1999). The QVR system having been developed through Microsoft Excel formulae and linked across related units to departmental level, several departments linked to form institutional QVR dashboard provides an essential blueprint for a customized database system. Due to flexibility of Microsoft Excel formulae which can easily be handled, this provides a framework that can be adopted by others to improve automation through customized systems.\n\nReduced turnaround time from data collection to analysis: the QVR’s were monitored every beginning of the month i.e. by the 5th of each month to ensure that all the requisite data were collected and entered in good time hence impacting on utilization of the results. A score was allocated every month based on the availability of data as a proportion of all the KPIs in each unit/department’s QVR. Similarly, utilization of various features such as determination and review of an action plan, was further considered during establishment of the best performing departmental unit of the year. Utilization of the feature of the action planning increased from <10% in 2017 to 78.4% in 2018. A similar challenge had been experienced in Iran when a framework for M&E was being set-up, many indicators were noted to have stayed for long periods having not been updated leading to many gaps in health information monitoring (Abdi, Majdzadeh, and Ahmadnezhad 2019). A well-defined frequency of data gathering promotes the usefulness of information gathered (Guijt 1999).\n\nStandardized format of monitoring throughout the institution: prior to the implementation of the QVR system, reports were prepared on standardized PowerPoint slides by respective departments with the assistance of the statistician. This was a time consuming exercise since the data had to be provided via email and then analysed. The QVR system provided a ready and standardized format of outputs that were not alterable and enhanced aggregation, tracking and comparisons which worked throughout the year after setting up. Creation of a standardized monitoring framework promotes comparability and usability (Abdi, Majdzadeh, and Ahmadnezhad 2019). It is also possible to obtain hospital wide trends on cross cutting indicators: arising from the standardized format of reporting that was made possible by the QVR system it became possible to aggregate data on indicators such as compliance towards hand hygiene practice, patient identification monitoring, client feedback gathering, etc. which were monitored across many hospital departments.\n\nSaving man hours: Prior to the deployment of the QVR system there was plenty of time spent in transcribing data from paper forms into the M&E database. There was also time lost in the collection and transportation of primary (paper) data collection sheets from the source departments to the M&E unit. The QVR system provides a platform of networked dashboards which allows continuous monitoring of performance any time, as data is continually populated. Data validation commands customized in the dashboards prevent erroneous data entry cases. Before implementation of the QVR system, a data collector would spend over three days entering monthly data which would increase the chances of erroneous entries, a situation that was rectified by the QVR system, where data entry happens every day at a proportion of an hour 10% (5 to 6 mins), this also further facilitates easier monitoring and decision making through trend analysis at any time of the month.\n\nEase of communication to multiple stakeholders: data on matters of quality is communicated to various stakeholders who require different levels of data granulation in order to make decisions. As described above, this was previously done by the use of Microsoft Excel then exported into Microsoft PowerPoint slides and this lengthened the process of critical analysis and action planning. The effectiveness of this was altered dependence on extra labour force and technical knowhow in dealing with the multiple softwares involved. Currently through the use of QVR colour coded “traffic lights system” (Red, Green and Amber) trending and detection of low performing indicators has been simplified allowing decision makers to quickly focus on undesirable trends for corrective action.\n\nTime saving in quality meetings: The use of the QVR has enabled quicker discussion and shorter quality meetings regarding monitoring of indicators. This is because the agenda gets focused around the salient results on the QVR dashboards. This improves efficiency and effectiveness in decision making (Izurieta et al. 2011).\n\nDetermination of Quality Improvement Projects: Each year the departments were meant to select a quality improvement (Q.I) project that would have a great impact on quality. The hospital departments in conjunction with the M&E unit were able to narrow down on quality improvement (Q.I) projects from a review of the trends in KPI performance. Hospital wide Q. I improvements were easily selected from the combined set of institutional indicators (institutional QVR). An example of this was the consulting clinics no-show project that sought to reduce the number of booked patients who did not appear for their scheduled clinics due to various reasons. The selected project was conducted in the year that followed in a bid to reduce chances of no-show cases.\n\nEase of data access: as mentioned previously, before rolling out the QVR system data were stored on local drives and accessing the same was a laborious process of sending email requests and phone call follow-ups. The QVR system made data availability easy through the Microsoft SharePoint platform; any authorised staff could access the data from the comfort of their workstations.\n\nData processing: through the use of built-in formulae, data are processed in real time enhancing efficiency and usability of the results. This reduces time lag of data processing as well as workload on the part of the M&E unit.\n\nElimination of redundancy: The previous system was rife with instances of multiple copies of reports residing with different users as the review was not centralized and the reports were forwarded from one user to their seniors for reviews which at times same wouldn’t be reverted back. Often the quality reports would have variations due to editing. The QVR system now assures a single and most up-to-date copy of data sheets and reports that are widely accessible to all users.\n\nAutomatic back up: The Microsoft SharePoint server enables automatic backup of the input data as long as the internet connection remains uninterrupted.\n\n\nConclusions\n\nMonitoring and evaluation is fundamental in quality performance of a hospital through an elaborate system of establishment, measurement and assessment of key performance indicators over time. A quality system that allows for participatory development of indicators from the smallest unit/department to the highest hierarchy in the institution ensures exhaustive coverage of scope of quality monitoring. A spreadsheet program, despite its simplicity, allows for flexible linking and computation of the chosen indicators. The Microsoft SharePoint server platform enables users to access and update indicators with ease via intranet, made possible through linked spreadsheets. Pointers such as colour codes, sparklines, and benchmark-achievement variance computation allows for identification of performance gaps. Timely identification of these gaps enhances propitious reviews coupled with a well-designed standardized root cause analysis and action plan all-inclusive in the system. Use of this system greatly enhanced quality performance monitoring in the hospital, identification of major bottlenecks that warranted hospital wide projects or departmental level projects. The QVR system enhanced efficiency and accuracy of quality monitoring from data collection through to performance reviews/evaluation. Development and setting up of the QVR system required seamless internet connectivity, a deeper understanding of Microsoft SharePoint server and spreadsheets program by the technical team, and a trained manpower for data entry and utilization of results. Due to flexibility of the spreadsheet programme and ease with which dashboards can be manipulated coupled with availability and low cost of acquiring the software, institutions mounting a framework of monitoring KPIs may adopt their use. The framework also provides an opportunity to understand how well various indicators can be measured and monitored. The system provides a blueprint for a customized M&E database system.\n\n\nLimitations\n\n\n\n1. Knowledge gap in technology, it took some time for some users to become acquainted with the Microsoft SharePoint access and utilization. This was overcome through continued training and having always an M&E and ICT staff member reachable to sort out any emerging issues.\n\n2. Limited knowledge in Microsoft Excel usage; this was overcome through rigorous training between the quality department’s M&E unit and the ICT department’s training unit.\n\n3. Staff turnover affected seamlessness with which data were captured. Some newly recruited staff encountered challenges before they were acquainted with the system.\n\n4. Server downtime - during server downtimes access to the Microsoft SharePoint and documents saved therein was a big challenge until the server functioning was restored.\n\n5. Limitation to access documents (essentially) Microsoft Excel files with data validation features or those which were password protection were not easily accessed using several browsers with the exception of Internet Explorer. This was sorted by setting the default browser to Internet Explorer for users’ easier access and creation of desktop shortcuts to the SharePoint folders.\n\n6. Only a single user at a time could edit a document on Microsoft SharePoint at any given time, during this time other users could only access the document on “read only” mode. For this reason we created multiple data entry sheets to allow many users to continue doing data entry seamlessly and encouraging them to close the data entry screens as soon as they completed accessing or updating.\n\n\nAvailability of data and materials\n\nAll data underlying the results are available as part of the article and no additional source data are required.", "appendix": "Acknowledgments\n\nFirst and foremost we would like to thank the almighty God. Special thanks to each and every author who took part in the compilation of this paper. The quality department, ICT department as well as the entire fraternity of the Aga Khan University Hospital, Nairobi for their continued support since inception of the QVR system.\n\n\nReferences\n\nAbdi Z, Majdzadeh R, Ahmadnezhad E: Developing a framework for the monitoring and evaluation of the Health Transformation Plan in the Islamic Republic of Iran: lessons learned.2019. Publisher Full Text\n\nEastern Mediterranean Health Journal = La Revue De Sante De La Mediterranee Orientale = Al-Majallah Al-Sihhiyah Li-Sharq Al-Mutawassit. 2000; 25(6): 394–405. Publisher Full Text\n\nAnderson M, Schulze K, Cassini A, et al.: A governance framework for development and assessment of national action plans on antimicrobial resistance. The Lancet. Infectious Diseases . 2019; 19(11): e371–e384. Publisher Full Text\n\nBamberger M, Rao V, Woolcock M: Using mixed methods in monitoring and evaluation: experiences from international development. Policy Research working paper; 2010; no. WPS 5245Washington, D.C.: World Bank Group 1.\n\nBrown SW, Nemeth LS: Developing a variance reporting system to facilitate quality improvement. Outcomes Manag Nurs Pract . 1998; 2(1): 10–15. Publisher Full Text\n\nCameron J: The challenges for monitoring and evaluation in the 1990s. Project Appraisal . 1993; 8(2): 91–96. Publisher Full Text\n\nChander NG: Sample size estimation. J Indian Prosthodont Soc . 2017; 17(3): 217–218. Publisher Full Text\n\nDahl D: An unexpected ally: Using Microsoft's SharePoint to create a departmental intranet. J. Web Librariansh . 2010; 4(2-3): 207–224. Publisher Full Text\n\nDiallo K, Zurn P, Gupta N, et al.: Monitoring and evaluation of human resources for health: an international perspective. Hum Resour Health . 2003; 1(1): 3. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDiffin J, Chirombo F, Nangle D, et al.: A Point to Share: Streamlining Access Services Workflow Through Online Collaboration, Communication, and Storage with Microsoft SharePoint. J. Web Librariansh. 2010; 4 (2-3): 225–237. Publisher Full Text\n\nGialloreti E, Leonardo FB, Basa SM, et al.: Supporting Iraqi Kurdistan Health Authorities in Post-conflict Recovery: The Development of a Health Monitoring System. Public Health Front. 2020; 8: 7. Publisher Full Text\n\nEnnis LA, Tims RS: Help Central: Creating a Help Desk and Knowledge Portal in SharePoint. Computers in Libraries . 2012; 32(2): 6–10.\n\nEstrella M, Gaventa J: Who Counts Reality? Participatory Monitoring and Evaluation: A Literature Review-IDS Working Paper 70. Inst. Dev. Stud. 1998; 70.\n\nEstrella M, Blauert J, Gonsalves J, et al.: Learning from change: Issues and experiences in participatory monitoring and evaluation. IDRC Books; 2000.\n\nDolci F, Germán HG, Aguirre G, et al.: Monitoring evaluation system for high-specialty hospitals. Gac Med Mex. 2011; 147 (5): 411–419. PubMed Abstract\n\nFletcher G, Peersman G, Bertrand W, et al.: M&E competencies in support of the AIDS response: A sector-specific example. Can J Program Eval . 2014; 28(3).\n\nGuijt I: Participatory monitoring and evaluation for natural resource management and research . Natural Resources Institute Chatham, United Kingdom: Socio-economic Methodologies for Natural Resources Research Best Practice Guidelines; 1999.\n\nIzurieta A, Sithole B, Stacey N, et al.: Developing indicators for monitoring and evaluating joint management effectiveness in protected areas in the Northern Territory, Australia. Ecol. Soc. 2011; 16(3). Publisher Full Text\n\nJordans M, Chisholm D, Semrau M, et al.: Evaluation of performance and perceived utility of mental healthcare indicators in routine health information systems in five low- and middle-income countries. BJPsych open . 2019; 5(5): e70. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKusek JZ, Rist RC: Ten steps to a results-based monitoring and evaluation system: a handbook for development practitioners. In: Washington, DC: World Bank; 2004. (accessed 2004). Reference Source\n\nMalone N, Mark L, Miller K, et al.: Program monitoring: The role of leadership in planning, assessment, and communication (REL 2014–034) . Washington, DC: US Department of Education, Institute of Education Sciences; 2014.\n\nMthethwa RM, Jili NN: Challenges in implementing monitoring and evaluation (M&E): The case of the Mfolozi Municipality. African J Public Affairs . 2016; 9(4): 102–113.\n\nPerran A, Perran S, Mason J, et al.: Beginning SharePoint 2013 Building Business Solutions eBook and SharePoint-videos. com Bundle. John Wiley & Sons; 2013.\n\nPrennushi G, Rubio G, Subbarao K: Monitoring and evaluation. A sourcebook for poverty reduction strategies . 2002: 107–130.\n\nPrescott B, Downing J, Di Maio M, et al.: Using SharePoint to manage and disseminate fusion project information: An ITER case study. Fusion Eng. Des. 2010; 85(3): 571–578. Publisher Full Text\n\nWeldon LSJ: Knowledge Sharing Through MS SharePoint. Collaborative Librarianship. 2012; 4(1): 9. Publisher Full Text" }	[ { "id": "129078", "date": "12 Apr 2022", "name": "Khara M. Sauro", "expertise": [ "Reviewer Expertise Quality Improvement", "Implementation Science", "Health Services Research", "Administrative Data Analysis", "Systematic and Scoping Review" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThank you for the opportunity to read this work. The authors describe the process and outcomes of implementing a quality monitoring system at their centre. The authors should be commended for a very thorough description of the monitoring approach and system, which was developed in a collaborative fashion. I have some comments to the authors regarding the details related to the indicators included, the methods for measuring their outcome variables and the flow of the manuscript.\nFirst, I would recommend the authors use the SQUIRE reporting checklist to guide the format of the manuscript.\nIndicator development: I appreciate that this system is being designed to be flexible and reflexive of the needs of the units; this is a strength. However, could the authors provide some examples of indicators and how they will be operationally defined and measured to help the reader understand potential options for the indicators? Could the authors also clarify the specific criteria required to determine the indicators? Will quality indicator or key performance indicator development methodology be used?\nOutcome measures: In the results section there is some description of the outcome measures of this study (continuity of the monitoring and evaluation system, turnaround time, etc.). Could the authors elaborate on how these measures were determined to be the outcomes measures (rationale for choosing these variables) and how the data were collected for these measures?\nFlow: The flow of the manuscript is challenging to follow. I appreciate the authors are trying to follow the formatting suggested by the journal, which may be the source of the issue. I wonder if might help to describe the “intervention” (the QVR) in the method section then have another section in the methods section for the outcome measures (continuity of the monitoring and evaluation system, turnaround time, etc.), then the results can be dedicated solely to the changes in the outcome measures after implementing the QVR?\nMinor comments:\nThe middle 3 paragraphs of the introduction are better suited to the methods section. I am unclear what the sampling section refers to – is it the sampling for this study or for other studies using the dataset?\n\nIs the rationale for developing the new method (or application) clearly explained? Yes\n\nIs the description of the method technically sound? No\n\nAre sufficient details provided to allow replication of the method development and its use by others? No\n\nIf any results are presented, are all the source data underlying the results available to ensure full reproducibility? No\n\nAre the conclusions about the method and its performance adequately supported by the findings presented in the article? Yes", "responses": [ { "c_id": "11737", "date": "25 Jun 2024", "name": "Francis Kiroro", "role": "Author Response", "response": "Reviewer: Indicator development- I appreciate that this system is being designed to be flexible and reflexive of the needs of the units; this is a strength. However, could the authors provide some examples of indicators and how they will be operationally defined and measured to help the reader understand potential options for the indicators? Could the authors also clarify the specific criteria required to determine the indicators? Will quality indicator or key performance indicator development methodology be used? Author’s response - We have provided additional information on the criteria followed including examples of some indicators monitored. Reviewer: The middle 3 paragraphs of the introduction are better suited to the methods section. Authors: We moved two of the three recommended paragraphs to the methods section, we retained one since it provides information that is more relatable to the background section. Reviewer: I am unclear what the sampling section refers to – is it the sampling for this study or for other studies using the dataset? Authors: The sampling section describes the sampling strategy that was recommended to the users of the QVR system for each key performance indicator considered. Reviewer: Is the description of the method technically sound? No Authors: We have included further details to add more clarity. Reviewer - Are sufficient details provided to allow replication of the method development and its use by others? No Authors: The additional details we have included may be helpful to facilitate replication. Reviewer - If any results are presented, are all the source data underlying the results available to ensure full reproducibility? No Authors - As a methodology paper, we intended rather to provide a description of how they developed the QVR innovation and how it facilitated the quality monitoring. Therefore, no accompanying raw data." } ] }, { "id": "138577", "date": "08 Jun 2022", "name": "Ahmad Aburayya", "expertise": [ "Reviewer Expertise Business Management", "Operation Management", "Quality Management", "Total Quality 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\nThank you very much for this opportunity to read this research paper. The paper provides a description of a quality system that developed and implemented at the quality department of the Aga Khan University Hospital, which intends to mentor and evaluate hospital's performance indicators. While the research topic is interesting, the research objective and its question are not clear. Furthermore, the perspective that the authors used to examine the phenomenon needs further explanation and clarification. Overall, this submission suffers from several major issues in terms of theoretical gap, theoretical contributions, research novelty, and research methodology. In addition, the paper was written as a business case study rather than a research paper.\n\nTitle: the study title is vague and causes confusion for the readers. In essence, the current literature in the healthcare context conceptualized M&E as the basis of further understanding the key components of M&E and M&E systems as an important public management tool used to demonstrate results. In healthcare the M&E system is a huge \"comprehensive concept\". Moreover, monitoring the healthcare outcomes or performance indicators \"clinical and non-clinical\" is considered only one part from a comprehensive quality monitoring system. Hence, i would suggest to change the study title to reflect the main aspect of the work by specifying KPI within the title.\n\nAbstract: while the study problem statement was well explained at the beginning of this section, still the study abstract is uninformative in terms of providing useful or interesting information related to study objective, methodology used, data analysis tools, major study findings, and study implications. Therefore, the authors need to rewrite the whole section in a proper way.\n\nIntroduction: (a) Overall, I would recommend the authors use the journal instruction checklist to prepare the manuscript. (b) Although this section explained the practical need of the use of spreadsheets on a Microsoft SharePoint server, the authors need to provide more details and explanation on the study novelty, for example: \"the M&E system using spreadsheets and even using more advanced systems such as IBM been tackling in the healthcare context several times: so what is new?\". (c) This section extremely suffers from lack of information related to the study theoretical gap. (d) The authors need to clearly mention the study objective and how its linked to the study gap that was found. (e) This section needs to provide more detail, background and information relevant to the study.\n\nMethodology: this section is totally confused and needs to be fully rewritten. The study methods used are not clear and all the results presented do not match the methods described; for example: what is the research design used? Is this paper aimed to develop a KPIs tracking system or to investigate the effect of implementing the QVR reporting system in hospitals? What is the philosophical stand of this study \"positivism or interpretivism\"? Is it qualitative or quantitative? More explanation on the data collection method is needed. Moreover, further explanation on the study sampling approach is required - study sampling design, technique, target population or the unit of analysis. In addition, what were the main data analysis tools used? For example: if its a qualitative study that used interviews, did the authors use the thematic analysis to come up with the accomplishments observed since adoption of the QVR? The authors need to operationally define the determined KPIs and how they were measured. Also, more explanation on the criteria selection used to determine the indicators.\n\nResults: All the results presented do not match the methods described. Indeed, the main reason of this outcome is the confusion made by the study objective. The study results are discussing the accomplishments observed since adoption of the QVR as a hospital quality M&E system which is not correlated with the study objective and its design.\n\nDiscussion & Conclusion: Overall, the conclusions are not correlated to the results found. In addition, the discussion section needs to be supported by several studies relevant to its findings.\n\nIs the rationale for developing the new method (or application) clearly explained? Yes\n\nIs the description of the method technically sound? No\n\nAre sufficient details provided to allow replication of the method development and its use by others? No\n\nIf any results are presented, are all the source data underlying the results available to ensure full reproducibility? No\n\nAre the conclusions about the method and its performance adequately supported by the findings presented in the article? No", "responses": [ { "c_id": "11738", "date": "25 Jun 2024", "name": "Francis Kiroro", "role": "Author Response", "response": "Reviewer - Title: The study title is vague and causes confusion for the readers. In essence, the current literature in the healthcare context conceptualized M&E as the basis of further understanding the key components of M&E and M&E systems as an important public management tool used to demonstrate results. In healthcare the M&E system is a huge \"comprehensive concept\". Moreover, monitoring the healthcare outcomes or performance indicators \"clinical and non-clinical\" is considered only one part from a comprehensive quality monitoring system. Hence, i would suggest to change the study title to reflect the main aspect of the work by specifying KPI within the title. Authors - We have addressed this by rewriting the article title, we have also clarified that this is a methodology paper and not a research paper. Reviewer - Abstract: while the study problem statement was well explained at the beginning of this section, still the study abstract is uninformative in terms of providing useful or interesting information related to study objective, methodology used, data analysis tools, major study findings, and study implications. Therefore, the authors need to rewrite the whole section in a proper way. Authors - The abstract has been revised, however, as a methodological paper, our key interest was to explain how the innovation was designed and the way it is currently being utilized. Reviewer - Introduction: (a) Overall, I would recommend the authors use the journal instruction checklist to prepare the manuscript. (b) Although this section explained the practical need of the use of spreadsheets on a Microsoft SharePoint server, the authors need to provide more details and explanation on the study novelty, for example: \"the M&E system using spreadsheets and even using more advanced systems such as IBM been tackling in the healthcare context several times: so what is new?\". (c) This section extremely suffers from lack of information related to the study theoretical gap. (d) The authors need to clearly mention the study objective and how its linked to the study gap that was found. (e) This section needs to provide more detail, background and information relevant to the study. Authors - As a methodology paper we followed the instructions of writing a methodology paper rather than a research study article. We have provided more information about the gap that the innovation was intended to fill and linked these to objectives and provided further details to make the section complete. Reviewer - Methodology: This section is totally confused and needs to be fully rewritten. The study methods used are not clear and all the results presented do not match the methods described; for example: what is the research design used? Is this paper aimed to develop a KPIs tracking system or to investigate the effect of implementing the QVR reporting system in hospitals? What is the philosophical stand of this study \"positivism or interpretivism\"? Is it qualitative or quantitative? More explanation on the data collection method is needed. Moreover, further explanation on the study sampling approach is required - study sampling design, technique, target population or the unit of analysis. In addition, what were the main data analysis tools used? For example: if its a qualitative study that used interviews, did the authors use the thematic analysis to come up with the accomplishments observed since adoption of the QVR? The authors need to operationally define the determined KPIs and how they were measured. Also, more explanation on the criteria selection used to determine the indicators. Authors - As a methodology paper, the key intention of this paper was to provide a description of the design of our innovation and circumstances relating to its implementation, thus we did not intend to present the article in the usual research paper format. We have provided more details on the criteria for the indicator selection. Reviewer - Results: All the results presented do not match the methods described. Indeed, the main reason of this outcome is the confusion made by the study objective. The study results are discussing the accomplishments observed since adoption of the QVR as a hospital quality M&E system which is not correlated with the study objective and its design. Authors - We have added more details right from the background and restructured the results section in order to clear the confusion. Reviewer - Discussion & Conclusion: Overall, the conclusions are not correlated to the results found. In addition, the discussion section needs to be supported by several studies relevant to its findings. Authors - We have restructured these two sections (Discussion & Conclusion) to ensure the interconnections of the sections is maintained. Reviewer - Is the description of the method technically sound? No Authors - We have made amendments and made it clear that from the title and content that this is meant to be a methodology paper Reviewer - Are sufficient details provided to allow replication of the method development and its use by others? No Authors - the replication envisioned is of the innovation described not as a research study. Reviewer - If any results are presented, are all the source data underlying the results available to ensure full reproducibility? No Authors - The paper since it envisions to present a methodology, it did not intend to append datasets. Reviewer - Are the conclusions about the method and its performance adequately supported by the findings presented in the article? No Authors - We did restructure the results and conclusion sections so that they are aligned." } ] } ]	1	https://f1000research.com/articles/10-883
https://f1000research.com/articles/13-216/v1	22 Mar 24	{ "type": "Research Article", "title": "Network pharmacology and in silico approaches to uncover multitargeted mechanism of action of Zingiber zerumbet rhizomes for the treatment of idiopathic pulmonary fibrosis", "authors": [ "Bharath Harohalli Byregowda", "Krishnaprasad Baby", "Swastika Maity", "Usha Yogendra Nayak", "Gayathri S", "Shaik Mohammad Fayaz", "Yogendra Nayak", "Bharath Harohalli Byregowda", "Krishnaprasad Baby", "Swastika Maity", "Usha Yogendra Nayak", "Gayathri S", "Shaik Mohammad Fayaz" ], "abstract": "Background Idiopathic pulmonary fibrosis (IPF) is a disease with high mortality, and there are only two specific drugs available for therapeutic management with limitations. The study aims to identify comprehensive therapeutic mechanisms of Zingiber zerumbet rhizomes (ZZR) to treat IPF by using network pharmacology followed battery of in silico studies.\n\nMethods The protein-protein interaction network was developed using Cytoscape to obtain core disease targets involved in IPF and their interactive molecules of ZZR. Based on the pharmacophore properties of phytomolecules from ZZR, the drug targets in IPF were explored. Protein-protein interaction network was built in Cytoscape to screen potential targets and components of ZZR. Molecular docking and dynamics were conducted as an empirical study to investigate the mechanism explored through network pharmacology in relation to the hub targets.\n\nResults The network analysis conferred kaempferol derivatives that had demonstrated a promising therapeutic effect on the perturbed, robust network hubs of TGF-β1, EGFR, TNF-α, MMP2 & MMP9 reported to alter the biological process of mesenchymal transition, myofibroblast proliferation, and cellular matrix deposition in pulmonary fibrosis. The phytomolecules of ZZR act on two major significant pathways, namely the TGF-β-signaling pathway and the FOXO-signaling pathway, to inhibit IPF. Confirmational molecular docking and dynamics simulation studies possessed good stability and interactions of the protein-ligand complexes by RMSD, RMSF, rGyr, SASA, and principal component analysis (PCA). Validated molecular docking and dynamics simulations provided new insight into exploring the mechanism and multi-target effect of ZZR to treat pulmonary fibrosis by restoring the alveolar phenotype through cellular networking.\n\nConclusions Network pharmacology and in silico studies confirm the multitargeted activity of ZZR in the treatment of IPF. Further in vitro and in vivo studies are to be conducted to validate these findings.", "keywords": [ "Pulmonary fibrosis", "Zingiber zerumbet rhizome", "Network pharmacology", "Molecular dynamics", "Principal component analysis" ], "content": "1. Introduction\n\nNetwork pharmacology is a newer tool for discovering drug targets and identifying newer lead molecules to treat diseases with complex pathology.1 Idiopathic pulmonary fibrosis (IPF) is one such disease where currently there is no remedy and only two specific drugs available for the treatment, nintedanib, and pirfenidone.2 Nintedanib is a specific antifibrotic agent that inhibits transforming growth factor beta (TGF-β) and thereby prevents the progression of IPF. Pirfenidone has mixed antifibrotic mechanisms such as anti-inflammatory, antioxidant, and does not have specific antifibrotic activity; however, the main mechanism is found to be its antioxidant effect at the tissue level.3 IPF involves genetic and epigenetic mechanisms in pathogenesis and pathophysiology.4 There are multiple drug targets reported and many ongoing clinical trials, however, the priority is given in understanding the underlying molecular mechanisms and pathogenic factors would be the current focus.5 Hence, there is a need to discover new drugs for IPF and the most recent trends in literature for herbal products with multitargeted approaches.6–8 The network pharmacology tools are used to interpret Chinese traditional drugs for their mechanistic activity in IPF, such as Fei-Xian Formula,9 Qingfei oral liquid,10 Baofeikang Granules,11 Astragalus Polysaccharide,12 Isorhynchophylline,13 and Platycodon grandiflorum.14 The major pharmacological activity of these drugs is inhibiting TGF-β, multi-targeted molecular modulation of inflammation and antioxidant. We discovered many herbal drugs from traditionally used plants by literature search to screen for IPF. One such plant shortlisted was Zingiber zerumbet rhizome (ZZR) (Fam: Zingiberaceae) which has been reported for the ailment of multiple diseases.15–17 The ZZR contains volatile oils, flavonoids, and glycosides as pharmacologically active components. The major volatile constituent, a terpenoid reported, was zerumbone, which has multiple pharmacological activities in chronic diseases.18 ZZR prevented LPS-induced pro-inflammatory responses by NF-κB, MAPK, and PI3K-Akt signaling pathways.19 It also has immunomodulatory effects in rats.20 Zerumbone has been reported to inhibit the Epithelial mesenchymal transition (EMT) by acting on the TGF-β signaling pathway in epithelial A549 cells.21 The extract of ZZR was reported for a significant in vitro antioxidant activity.22 Further it was reported for antioxidant property was responsible for their anticancer activity in cell line.23 The active constituent of plant rhizomes are mainly terpenoids in volatile oil and many flavonoids.24\n\nNetwork pharmacology, systems pharmacology, and multiple bioinformatics tools can be used to evaluate the mechanistic therapy of ZZR,25 and in silico drug discovery can validate the findings from network pharmacology, especially for natural products.26 Several studies on IPF reported TGF-β1, EGFR, TNF-α, MMP2 and MMP9 are the major effectors in the progression of IPF, which plays a significant role in the modification of biological processes likely to be EMT, myofibroblast proliferation, and extracellular matrix (ECM) deposition.27 This study outlines the mechanistic interaction of ZZR bioactive constituents with perturbation IPF system by unexplored network pharmacology studies and confirmed the reported interactions of potential molecules and identified targets by molecular docking and dynamics simulation as an evidence approach to the study findings. Molecular docking is a computer technique that examines the pattern of binding of potential components to the recognised protein binding sites and predicts the three-dimensional (3D) structure of interest with the ideal position and orientation of the protein-ligand complex. Using scoring functions, interactions, and binding affinity, the components are then ranked. In order to determine the efficiency of the ligand, MD simulation explains how atoms and molecules move over time and under specific conditions in a protein-ligand complex.28,29 Following the post-simulation, principal component analysis (PCA) is used to evaluate the protein system’s conformational variations and movement correlation. Molecular interactions of multi-components with the multiple targets of fibrosis can be explored by utilizing the network pharmacological computational methods.\n\n\n2. Methodology\n\nThe active components reported in the ZZR were identified from the Traditional Chinese Medicine Systems Pharmacology (TCMSP)30 (https://tcmsp-e.com/tcmsp.php), database and by performing literature search.31\n\nThe 3D conformers of the bioactive phytomolecules were retrieved from PubChem in an SDF format. This was subsequently fed into “PharmMapper,”32,33 (http://www.lilab-ecust.cn/pharmmapper/) which predicted human targets. The predicted targets were uploaded to the UniProt database to get standard gene names and official gene symbols.34 The targets involved in IPF were found utilizing the “GeneCards”35 (https://www.genecards.org/) and “DisGeNET”36 (https://www.disgenet.org/home/) databases with efficient keywords “idiopathic pulmonary fibrosis” and “lung fibrosis” for finding the differentially expressed genes in the disease condition based on the disease score. The top targets were sorted to build a network. The overlapped gene symbols, referred to as targets of zingiber zerumbet in IPF were then obtained by uploading the component gene and the disease gene using the Venny 2.1 (https://bioinfogp.cnb.csic.es/tools/venny) duplication method mapping tool.37\n\nStep 1: The target proteins of the phytomolecules in IPF were used to construct the Protein-Protein interaction networks using String app embedded in Cytoscape 3.9.1 software.38 Cytoscape software served as a platform with multiple inbuilt applications, that are needed for the interaction network and analysis through the application manager. Using the string protein query, 1.7.139,40 and the selection of the homo sapiens species, the targets of ZZR in IPF were imported to the Cytoscape, with the confidence score cut-off limited to a minimum of 0.40 and no further extra interactions. Each component was sorted based on the number of nodes and edges, and more than 300 edges and 40 nodes were considered for additional virtual screening.\n\nStep 2: The hub genes were found using the Cytohubba 0.1 built-in programme.41 The hub targets were built in a separate subnetwork, and the components with the highest degree, closeness centrality, and betweenness were chosen for further potential component screening.42\n\nStep 3: Screening was done with the new technique to bring the highly disease-specific targets. From the Cytoscape, by selecting a string disease query from the dropdown box and entering a specified confidence score, highly expressed disease-specific targets were imported into the Cytoscape. The top 30 hub genes based on the degree were identified by employing the analyse network tool.43\n\nStep 4: The core targets and potential components (phytomolecules) were identified by merging the top 30 disease query target and enriched targets of ZZR using a merge tool in Cytoscape. The potential phytomolecules which interact with all the identified core targets were selected for molecular docking.\n\nEnriched hub targets of 30 nodes obtained from the subnetwork and were uploaded to the database for Annotation, Visualization, and Integrated Discovery (DAVID) database for bioinformatic analysis of KEGG (Kyoto Encyclopedia of Genes and Genome) pathway enrichment and GO (Gene Ontology) functional annotation to elucidate biological functions (biological process, molecular function, and cellular components) of targets of ZZR components in treating IPF, with significant screening criteria of P-value and enrichment score.44–46 The enrichment bubble chart and bar chart were obtained from the bioinformatics tool (https://www.bioinformatics.com.cn/).\n\nThe Compound-Target-Pathway network was built by merging the Compound-Target and Pathway-Target networks in order to better understand the interactions among the phytomolecules, targets, and pathways.37 Based on the pathway analysis, the top 20 key pathways were considered with the enriched hub targets to build and analyse the pathway-target network. The relationship between the primarily screened compounds with their top subnetwork targets was developed and analysed.\n\nIn silico docking was carried out using the Glide module of Schrodinger software.47 Alternatively, free software such as AutoDock and Gromacs could also be used. Protein information regarding the docking was considered from the UniProt with the best PDB (protein data bank) having high resolution and screening criteria.\n\n2.6.1 Protein and Ligand preparation\n\nThe structural coordinates (Solved by X-Ray crystallography) for the core targets were identified and downloaded to Schrodinger Maestro from the RCSB Protein Data Bank. These proteins were prepared by a three-step process via the protein preparation wizard of Schrodinger software.48–50 Alternatively, AutoDock 4 software can be used which is freely available. The imported structure was pre-processed, hetero atoms and crystallographic waters were removed from the structure, H-bond was optimized to obtain the low energy state of protein at pH 7.4 using OPLS3e force-field.51,52 Using the LigPerp programme, the structures of phytomolecules retrieved previously for biological target prediction were optimised to yield 3D coordinates.53 The ligands’ possible ionisation states were generated using the Epik tool at pH 7.4, generated tautomeric states for each ligand, and the output was saved in maestro format.54\n\n2.6.2 Extra precision (XP) glide dock and binding free energy\n\nA site map tool was utilised to determine and evaluate the druggable pocket in proteins that did not have binding ligands.55 Subsequently, the receptor grid generation tool was used to generate a receptor grid around the co-crystalized ligand by picking it from the workspace. For the proteins, without any co-crystalised ligand-receptor grid generation tool with an entry option was used to generate a grid around the site with the highest SiteScore and bearing necessary amino acid residue to modulate protein activity. To determine and rank the potential components, rigid with XP-docking was performed and presented in an XP-visualizer, where we interpret the pose viewer file in a table and 3D visualization of the pose to interpret changes in the complex internal geometry.47 Pose with a better favourable interaction score when an H-bond forms, rewards of the electrostatic and hydrophobic enclosure, lipophilic chemscore, and penalties at various conditions were all taken into account while choosing an MD simulation. In rigid docking, the hydrogen bond interaction with the important amino acids was evaluated as an independent quality measure. The Prime MM-GBSA of all the docked protein-ligand complexes was performed to identify the binding-free energy.56,57 Subsequently, the protein-ligand complex exhibited a good docking score, binding free energy, and XP-dock results with the interactions were considered for the molecular dynamics (MD) simulation.\n\n2.6.3 Molecular dynamics (MD) simulation\n\nMD simulations have become an effective method for identifying the crucial residues in biomolecular interaction and assessing the stability of protein-ligand complexes. In order to examine the conformational stability and steady state of the protein-ligand complexes, 100 ns MD simulations were run using the Desmond module.58 Alternatively, NAMD molecular simulation along with VMD software can be used. By using the SPC (simple point charge) solvent tool, the system builder tool was employed to develop an orthorhombic-shaped simulation box around the docked ligand complex, with a buffer distance of 10 Å from any side of the complex to keep water molecules around to prevent false interference from occurring on active sites.59 By adding the necessary quantity of Na+ or Cl- salts, the water-solvated system was neutralised and iso-osmolarity was maintained by adding the 0.15M salt concentration. The system was relaxed and minimised to a 100 ps local energy minimum and achieved by a gradient threshold till it reaches 25 kcal/mol/Å using the steepest descent (SD) method and the limited memory Broyden-Fletcher-Goldfarb-Shanno (LBFGS) algorithm. The custom seed MD simulation was performed with the 300K temperature and 1.0315 bar pressure, using the Nose-Hoover chain thermostat and Martyna-Tobias-Klein Barostat method coupled to an isotropic style for 100 ns using NPT.60,61 At the end of the MD simulation, a simulation interaction diagram (SID) was generated to analyse the MD simulation parameters like root mean square deviation (RMSD) of protein α-carbon atoms to measure the average change in the superimposition of the selected atoms at a particular frame on the first frame, and protein root mean square fluctuation (RMSF) of the ligand fragment fluctuating while binding with the protein, and the hydrogen bonding plays a crucial role in the biomolecular interactions of the protein-ligand complex, which are then followed by hydrophobic interactions and are necessary for the drug’s metabolization, specificity, and adsorption. The strong binding of molecules to proteins preserves the protein’s compactness, as assessed by the radius of gyration (rGyr), and Solvent Accessible Surface Area (SASA) was calculated to quantify the surface area of a molecule accessible by a water molecule.62\n\n2.6.4 Principal component analysis (PCA) and Domain cross-correlation map (DCCM)\n\nThe PCA was employed to evaluate the dynamic motion of the protein affected by the K3R and 4AFZ binding required for the biological function to calculate eigenvectors and eigenvalues. The Desmond simulation trajectory was converted to dnd format using the VMD v1.9.4 programme.63 The PCA was carried out using the BioEdit R package64,65 and the interaction pattern of the binding site of ligand was analysed by performing the DCCM during the overall equilibrium period.66\n\n\n3. Results\n\nThe TCMSP and literature search yielded a list of the 39 active components that were reported in ZZR (Table 1).\n\nUsing the keywords “idiopathic pulmonary fibrosis” and “lung fibrosis” as input, the databases “GeneCards” and “DisGeNET” yielded a list of 6696 and 803 disease targets, respectively. Overall, 416 potential targets in IPF were identified by performing duplication analysis and combined based on the disease score from both databases with a score above 50 in GeneCards and a disease score above 400 in DisGeNET. Candidate targets were identified from Venny 2.1 by uploading disease and compound targets of PharmMapper. kaempferol derivatives like kaempferol-3-O-rhamnoside (K3R), kaempferol-3-O-methylether (K3ME), kaempferol-3,4,7-O-trimethylether (K374TME), kaempferol-3,4-O-dimethylether (K34DME), kaempferol-3-O-(2,4-di-O-acetyl-α-L-rhamnopyranoside) (K3(23DARP)), kaempferol-3-O-(2″-O-acetyl) rhamnoside (K32AR), 4-O-acetyl afzelin (4AFZ) and 3,4-O-diacetylafzelin (34DFZ) were shared more than 60 common targets as shown in Table S1 (Supplementary file 1, Extended data67).\n\nStep 1: A network of 76 nodes and 1010 edges was obtained for a component K3R and represented in Figure 1; similarly, networks were built for all the components and screened primarily using the criteria to obtain 25 components (Table S1, Supplementary file 1, Extended data67), based on the topological parameters of networks. Targets with more than a 50-degree score are represented in gradient green colour and gradient light blue between 20-50 degrees. Targets with thick borders (more than 15) represented good betweenness centrality. A circular shape represented good closeness centrality of more than 0.666, hexagon represents closeness centrality score between 0.595 to 0.666, and octagon represented lesser than 0.595 closeness centrality.\n\nStep 2: Table 2 lists the hub targets for all components based on the degree, betweenness centrality, and closeness centrality using Cytohubba.\n\nStep 3: To identify significant targets, the top 200 disease-specific targets for IPF (DOID: 0050156) were imported into the Cytoscape as a new screening method with a minimum confidence score of 0.90. After examining the network, the top 30 targets with the greatest degrees were chosen (Table 2).\n\nStep 4: Overall, seven significant components were identified with a minimum of six nodes and six edges after merging the disease-specific network and enriched targets of ZZR for molecular docking, these components with common targets were considered. According to Table S2 (Supplementary file 1, Extended data67) and Figure 2, compounds such as K3R, K3ME, K374TME, K34DME, K3(23DARP), K32AR, and 4AFZ have shared common targets of TGFB1, MMP9, MMP2, EGFR, AKT1, SRC, and TNF.\n\n3.4.1 Pathway enrichment\n\nDAVID database was the keen gene ontology (GO) and pathway enrichment analysis tool with a significant P-value <0.05. The KEGG pathway was enriched by performing the enrichment analysis. Targets are enriched in 147 pathways, and the top 20 entries were considered based on enrichment score (Table S3, Supplementary file 1, Extended data67), as shown in Figure 3 and 4, which comprise the TGF-β signaling pathway, PI3K-Akt signaling pathway, MAPK signaling pathway, FoxO signaling pathway, and TNF signaling pathway in IPF (Figure S1-S5, Supplementary file 1, Extended data67).\n\n3.4.2 Functional annotation\n\nThe enriched targets were uploaded to get specific functional annotations in every discipline. The biological process includes collagen degradation with the highest 51.8 enrichment scores, as represented in Figure 5 and Table S4 (Supplementary file 1, Extended data67). Among the cellular components, the ECM was mostly investigated with a 6.9 enrichment score, and the molecular functions of the included entry targets consisted of the tyrosine-protein kinase with a 17.8 enrichment score.\n\n3.4.3 Compound-Target-Pathway network\n\nEach gene interacts with several active components, while each component targets several genes. The Compound-Target-Pathway network in Figure 6 shows compounds such as K3R, K3ME, K374TME, K34DME, K3(23DARP), K32AR, and 4AFZ interact with multiple targets. These targets disrupt the pharmacological activities of many pathways involved in the progression of IPF. The Compound-Target-Pathway (C-T-P) network was built with multi-components, multi-targets, and multi-pathways interaction, which can be correlated with a clear understanding of the pharmacological activity of ZZR.68\n\nThe identified components of ZZR were docked with 3KFD(TGFB1); 4XCT(MMP9); 3POZ(EGFR); 1QIB(MMP2); 2AZ5(TNF); 2UVM(AKT1) and 4HXJ(SRC) PDB IDs. Proteins were prepared by updating the missed side chains or loops to generate states and generated a receptor grid. The proteins without bound ligand SiteMap was used and generated a grid, with a site score of 0.976, a D-score of 1.024, and a volume of 302.18 Å3, the binding site of the 3KFD was visualised and assessed as a druggable pocket at site 1. The amino acids implicated in latent TGF-β1 activation are found at this Site. The site score 0.995, D-score 0.987, and volume 395.48 Å3 were found in 1QIB site 1 with the essential amino acid residues to inhibit the protein (Table S5, Supplementary file 2, Extended data67).\n\nAs illustrated in Table S6 (Supplementary file 2, Extended data67) and Figure S6, K3R formed a hydrogen bond with GLY 46 and ALA75 residues of TGF-β1 dimer and residues play a major role in activating latent TGF-β1. It also includes hydrophobic interaction with the reported inhibitory amino acid residues.69,70 K3R interacts with ASN842 and LYS745 by hydrogen bond, and MET793 interacted by hydrophobic with EGFR.71 K3R interacts hydrophobically with MMP9 amino acids of LEU188 and ALA189 residues, creating hydrogen bonds with PRO246, GLU227, and GLY186 residues.72 K3R interacts with TYR119 with pi-pi interaction, SER60 with hydrogen bond and other hydrophobic interactions with LEU57, and TYR59 residues of TNF-α dimer.73 Hydrogen bond interaction was noted between the K3R and GLU202 and hydrophobic interaction with LEU164, ALA165, and HIS201 residue of MMP2.74 K3R exhibited higher binding free energy (∆G); -34.22, -57.35, -66.37, -48.20, and -57.85 with MMP9, TGF-β1, EGFR, TNF-α, and MMP2 respectively (Table 3).\n\nAs demonstrated in Table 3 and Table S7 (Supplementary file 2, Extended data67), 4AFZ provided a decent docking score and binding free energy, however specific amino acid residual interactions were only seen with the MMP9, MMP2, and TNF-α. Following glide docking, the reported 2D interactions of 4AFZ with MMP9, MMP2, and TNF-α were shown in Figure S7 (Supplementary file 2, Extended data67). 4AFZ shared two hydrogen bonds with the residues GLU227 and ALA191, as well as other significant hydrophobic interactions with MMP9.72,75 The MMP2 inhibitory amino acid residues of GLU202 and ALA165 have formed hydrogen bond interaction with the 4AFZ.74 Ligand formed hydrogen bond interaction with SER60 and GLN61 as well as hydrophobic contacts with TYR119 residues in TNF.76 4AFZ displayed a decent binding free energy (∆G); -59.52, -45.62, and -49.94 with MMP9, TNF-α, and MMP2 respectively.\n\nThe structure of K3R and 4AFZ were illustrated in Figure S8 (Supplementary file 2, Extended data67) and considered for dynamics simulation at 100 ns based on good docking score except for AKT1 and SRC, hydrogen bond interaction scores obtained from the XP-visualizer (Table S8, Supplementary file 2, Extended data67), good binding free energy, and substantial interaction with the desired amino acid residues of all proteins to inhibit their activity.77 The hydrogen bonds were formed within the geometric criteria of 2.5 Å in all the protein-ligand complexes as shown in Table S9 (Supplementary file 2, Extended data67) except EGFR-K3R of GLY791 (2.68 Å) and MMP2-4AFZ of ALA165 (2.79 Å). The pi-pi interactions were observed within the geometric criteria of 4.5 Å between the TNF-K3R and TNF-4AFZ complexes.\n\nTGFB1: Moderate hydrogen bond interactions were formed from the K3R to GLY46 (chain A), ASN66 (chain A), and CYS44 (chain A and B) with occupancy of 44%, 46%, and 47%, respectively, as shown in Figure 7a.69 Figure 8a shows that ALA75 had hydrogen bond and hydrophobic interactions in the binding pocket. RMSD Figure 9a illustrates the stable interaction of K3R with the binding pocket of the protein within 3 Å up to 43 ns, thereafter, fluctuated for 2 ns due to conformational changes that occurred during the spatial ligand fitting and maintained continuous equilibrium till the end of the simulation period. Even during the 2 ns fluctuation, ALA75 (chain A) and CYS44 (chain B) maintained a consistent contact, but some interactions were shifted between the dimer and exposed to the solvent system. Protein RMSD is stably within 2 Å throughout the MD simulation. Inhibition of TGF-β1 suppresses mesenchymal transition, angiogenesis, ECM deposition, and myofibroblast differentiation.78\n\nEGFR: MD simulation retains the stability of protein and ligand interaction by succeeding to keep the molecular docking interactions within the RMSD limit. As represented in the Figures 7b & 8b, strong hydrogen bond interactions were retained in the MD simulation of K3R to residues such as LYS745, GLN791, ASP800, MET793, and ALA722 with occupancy of 90%, 99%, 87%, 64%, and 31% respectively and bridged hydrogen bonds were noted with ARG841, ASN842, and ASP855 (occupancy of 39%, 58%, and 61%).71 Amino acid residues LEU844, CYS797, and ALA743 formed hydrophobic interaction, as illustrated in Figure 8b. The ligand fitting to the protein remained consistent throughout the simulation, as illustrated in Figure 9b, with 2Å RMSD being the same as protein RMSD. Inhibition of EGFR helps to decrease mucus secretion, collagen deposition, fibroblast proliferation, and disrupts lung morphogenesis.79\n\nMMP9: The protein and K3R interaction stabilised at the binding pocket. A strong and direct continuous hydrogen bond interaction was observed between K3R and GLU227 and ALA191 residues with 99% and 61% of occupancy (Figures 7c and 8c). The continuous Pi-Cation (Zn) interactions were observed with HIS226, HIS230, HIS236 and GLU227. While ALA189 and LEU188 interact via bridging interactions with water molecules to K3R with occupancy of more than 50%.72 From Figure 9c, the RMSD of the ligand and protein resides within 2Å. Because MMP9 is a zinc-dependent, the compound interaction required a pi-cation binding to inhibit the protein. Figures 7f and 8f illustrated 4AFZ to PRO246 formed a continuous and strongest hydrogen bond interaction at an 83% occupancy, along with the 100% Pi-Cation interactions of HIS226, GLU227, HIS230, and HIS236 via a Zn coordination, which is required for a compound’s potency to inhibit MMP9.72 Figure 9f illustrates the RMSD of the 4AFZ and MMP9 within the limit of 2.5 Å and maintained the phase of stabilization throughout the period of simulation. Inhibition of MMP9 decreases the activation of latent TGF-β1 and extracellular matrix deposition.80\n\nTNF: From the Figures 7d and 8d, K3R displayed continuous binding stability in the binding pocket of TNF due to strong hydrogen bond interactions with TYR151 (Occupancy of 53%), moderate H-bond with SER60, and GLN61 through a bridge contact (Occupancy of 54% and 34%) and a strong 93% Pi-Pi interaction with TYR119, as well as other important hydrophobic interactions involving LEU55 and TYR59.73 RMSD of ligand-protein interaction resides within 2 Å, and interaction was stabilized during the simulation (Figure 9d).\n\nFigures 7h and 8h show a moderate hydrogen bond formed from the 4AFZ to SER60 via a water bridge with a 36% occupancy and other key hydrophobic contacts to TYR59 and LEU57.73 Figure 9h depicts the first 10 ns of fluctuation and maintains 1.5 Å RMSD for the remainder of the 90 ns simulation time to remain stable. Inhibition of TNF-α decreases inflammatory reactions and activation of macrophages.81\n\nMMP2: From Figure 7e, a strong hydrogen bond interaction was observed between ILE222 residues and K3R through the water bridge at an occupancy of 55%.74 Hydrophobic interaction was observed in Figure 8e between the residue GLU202, GLY162, LEU164, TYR193, and TYR223 and the ligand. From Figure 9e, the RMSD was found to be within 2 Å for the Ligand and protein interaction.\n\nModerate water-bridged hydrogen bond interactions were formed from 4AFZ to ILE222 at 44%, ALA220 at 57%, HIS201 at 40%, and PRO221 at 35% occupancy as represented. The continuous Pi-cation interactions were seen to HIS201, GLU202, HIS205, and HIS211 through a Zn, which is required to inhibit MMP2 (Figure 7g and 8g). The ligand fitting to the MMP2 remains consistent throughout the simulation at 2.5 Å RMSD (Figure 9g) and maintains constant contact with the residues as depicted in the Figure 8g.74 Inhibition of MMP2 suppresses β-catenin and lowers the TGF-β1 levels which favors the EMT. Inhibition promotes ECM degradation by affecting collagen degeneration.82\n\nWith the exception of a few individual residues that fluctuated in the range of 40–50 and 150–160 of the EGFR–K3R complex, and 90-100 residues of the TNF-4AFZ complex, all other complexes exhibited good and lower RMSF values (Figure S13, Supplementary file 2, Extended data67). The RMSF of K3R and 4AFZ ligands were stabilized at lower levels of less than 1-2 Å to their respective protein complexes (Figure S14, Supplementary file 2, Extended data67), whereas the RMSF of K3R fluctuated considerably more with the TGF-β1 complex. In most of the complexes, an intramolecular hydrogen bond was observed. The rGyr of K3R and 4AFZ ranged between 4.00 ± 0.08 Å and 4.44 ± 0.10 Å respectively and maintained stability. The SASA of K3R was shown to be very less in TNF and MMP9, at 70 and 120 Å2 respectively, while the other complexes with K3R and 4AFZ had an equilibrium of 240-260 Å2 (Figure S15 & S16, Supplementary file 2, Extended data67).\n\nThe three principal components are represented in the Figure 10 for all the complexes of K3R with TGFB1, EGFR, MMP9, TNF, and MMP2, and 4AFZ with MMP9, TNF, and MMP2. The complex conformational variations are shown in the 2D PCA scatter plot to indicate system fluctuations by eigenvectors of PC1, PC2, and PC3. The biological functions are governed by the motion mode of 20 PCA patterns and represented in three PCA modes. The density of the distribution of the dots demonstrated stable system conformations. According to the Figure 10, except for TGFB1-K3R, PCA of all complexes exerted denser conformation, but EGFR-K3R has a small variance in the eigenvalue rank. The first three eigenvalues (PC1, PC2, and PC3) of TGFB1-K3R contributed 62.15, 31.74, and 2.09% of variables, respectively, while the other systems generated lower eigenvalues of variance (Figure 10), indicating higher stability.\n\nDCCM analysis was used to examine the movement correlation of the protein complex system. When there is a positive value, the same direction emerges (positive correlated movement), however, when there is a negative value, the opposite way appears (anti-correlated movement). Except for TGFB1-K3R, the protein-ligand complex systems were shifted in the same direction as they shifted towards the cetacean blue, and dark cornflower blue implies the positive values in the Figure 11.66 TGFB1-K3R correlated negatively by moving in the opposite direction towards the negative value. The colour distribution of the TNF-K3R was demonstrated to deflect the residual strength.\n\n\n4. Discussion\n\nIPF is a disease characterised by remodelling lung architecture due to abnormal deposition of myofibroblasts, and ECM in interstitial space by upregulation of matrix metalloproteinases (MMP2 and MMP9), resulting in respiratory failure.83 As a result of a lung injury followed by an EMT brought on by TGF-β1 and differentiates myofibroblast with the growth factor receptors activation to increase the ECM deposition.84,85 Chinese traditional medicines are considered over Western medicines, and many of them have been clinically shown effective in treating several diseases with a patent approach, and when treating the condition, these drugs interact with multiple pathways and targets.86 In traditional medicine practices, a wide range of diseases was treated using natural products such as Chinese and Indian traditional medicine. Pertaining network pharmacology to the Indian system of medicine helps to overcome snags confronted in exploring the mechanistic effect through multi-component and multi-target by acting over a few major pathways involved in disease perturbation.68 Functional analysis of hub targets by their annotation network provides a great strategy for finding the mechanism of action. Network pharmacology has prospective inferences for understating disease conditions and treatment mechanisms, and generating new avenues for investigating novel pharmacological treatments.87 Here we considered rhizomes of Zingiber zerumbet to treat IPF with the functional hub targets, multi-component interaction analysis, confirmational molecular docking, and dynamics studies to bring forward into the new drug therapies. Network pharmacology aided in the comprehension of phytoconstituent multi-target impact, where the ‘goldilocks’ principle is followed to restore the perturbation robust network of pulmonary fibrosis.88\n\nThe identified 416 disease targets from the two disease-specific databases that were screened with all components of ZZR targets and built a protein-protein interaction network. Top-25 components were found to be effective based on the higher node and edge connection as they attribute and annotate.89 Targets were identified to analyse the functional annotation and pathways that interact. The course of the present study used an algorithm innovatively to screen high pulmonary fibrosis-specific targets, top disease targets were imported to Cytoscape through a string disease database and identified the overlapping component targets, and based on the degree, closeness centrality, and betweenness proximity of the network, components were selected for molecular docking.90\n\nPathway analysis interprets, ZZR components effectively interact with the EGFR tyrosine kinase inhibitor resistance pathway to inhibit fibroblast growth, proliferation, and differentiation by acting on the epidermal growth factor receptor followed by downstream effector PI3K/AKT pathway.91 MAPK signaling pathway inhibition occurs from the ZZR components to inhibit inflammation, proliferation, and differentiation-related responses through the TNF signaling pathway.91 ZZR acts on the TGF-β signaling pathway by inhibiting TGF-β1 to interfere with the process of EMT, angiogenesis, ECM neogenesis, myofibroblast formation, immunosuppression, and protection from apoptosis.78 The main collagen-degrading enzymes, MMP-9 and MMP-2, are likely to leave a permanent scar in lung tissue, network pharmacology and molecular docking approach to ZZR components have shown the inhibition of these matrix metalloproteinases prevent ECM deposition and scar formation.92 Figure 4 interprets the inhibition of the aforementioned pathways from ZZR restrains the FoxO signaling pathway and regulates the expression of several downstream genes to improve its therapeutic effect through several aspects of the network.83\n\nThe pharmacological activity of ZZR has been explained in the Compound-Target-Pathway network Figure 6 with multi-interactions. The network interactions show stable “network responses” and more effective multi-component activity than a single substance.93 Illustrations of Figures 1, 2, and 6 explore TGF-β1, MMP9, MMP2, EGFR, AKT1, SRC, and TNF-α as core targets in treating IPF. The reported targets come under various stages in the development of fibrosis; inflammatory mediators release, EMT, proliferation and differentiation, and matrix accumulation.27\n\nAll identified potential components exerted a good docking score of more than -4 with all core targets except AKT1 and SRC. K3R and 4AFZ had shown higher docking scores in Table 3 compared to other components K3ME, K374TME, K34DME, K3(23DARP), and K32AR. K3R and 4AFZ had specific interactions with the proteins to inhibit their activity with the hydrogen bond interactions (Table S6 and S7, Supplementary file 2, Extended data67).77 Based on the docking, binding free energy, and interaction analysis K3R and 4AFZ were considered for the MD simulation. Except in a few cases, the kind of hydrogen bonds formed during the molecular docking study was conserved in most of the MD simulation complexes. K3R and TGF-β1 complex conformation suffered due to the shift between the dimers. The flexibility of individual residues did not change much throughout the simulation period and preserved RMSF at lower values of complexes, except in a few cases as reported in the result section. As shown in the Figure S15 and 16 (Supplementary file 2, Extended data67), the compound achieved stable RMSD, preserved structural compactness of proteins by lowering ligand rGyr fluctuation, and ligand intact in the binding pocket of protein was detected with less solvent exposure predicted from the SASA. The rigidity of the amino acids was seen in the binding pocket of the ligand-protein complexes.94 Protein-ligand contacts timeline throughout the 100ns simulation period and 3D ligand-protein interactions remain stable, and data were included in Figure S9-S12 (Supplementary file 2, Extended data67). K3R and 4AFZ have a potential hydrogen atom on the oxygen atom at position 28 that forms a donor hydrogen bond with the inhibitory amino acid residues of the protein targets. The donor and acceptor hydrogen bond interaction formed by the scaffold H and O atoms at positions 21, 29, 30, and 31 significantly increased the inhibitory effect of K3R and 4AFZ towards TGF-β1, EGFR, MMP9, TNF-α, and MMP2 targets in the aforementioned pathways. The connection between the TGFB1-K3R was disrupted due to opposite direction moves and varied eigenvalue. In 2D PCA scatter analysis, the coordination motion of the molecules provided lower eigenvalues of all the other complexes and demonstrated stable conformation to exert an inhibitory effect of K3R and 4AFZ to their respective complexes. DCCM examination of all other systems revealed that the good strength of the residues was achieved through positive correlation. Network pharmacology predictions had shown good therapeutic effects and scrutinized the therapeutic “multi-compound multi-target” mechanism of ZZR, and the activity was confirmed by molecular docking and MD simulation of K3R and 4AFZ.95\n\n\n5. Conclusion\n\nPhytomolecules from the rhizomes of Zingiber zerumbet impact core targets TGF-β1, EGFR, MMP9, TNF-α, and MMP2 in IPF are expected to release immediate injury mediators, mesenchymal transition to secret ECM, fibroblast proliferation, and differentiation at various stages of idiopathic pulmonary fibrosis progression. The FoxO signaling pathway, which is connected to numerous other important pathways including PI3K/AKT, MAPK, TNF signaling pathways, and EGFR tyrosine kinase inhibitor resistance pathway, whereas the TGF-β signaling pathway has been profoundly enriched and is the pathway where phytomolecules interrupt the IPF progression along with FoxO signaling pathway. Structure-based molecular docking had emerged as a realistic approach to support and confirm the outcomes of network pharmacology with network-target by multi-component, and multi-target therapeutic understandings in the study with reliable MD simulations of K3R and 4AFZ with the core targets. Based on the proposed and confirmed affinity and stability of protein-ligand complex throughout the MD simulation period with good RMSD, RMSF, Protein-ligand contacts, rGyr, PCA, DCCM, and SASA activity of K3R and 4AFZ in ZZR is expected to better and enhance the therapeutic effect over the existing therapies to treat pulmonary fibrosis by performing preclinical and clinical studies.", "appendix": "Data availability\n\nFigshare: Data of in silico studies on Zingiber zerumbet rhizomes for idiopathic pulmonary fibrosis. https://doi.org/10.6084/m9.figshare.24113343.v1 67\n\nThis project contains the following underlying data:\n\n- Cytoscape used to build networks of Z.z.cys\n\n- Disease Targets_idiopathic pulmonary fibrosis.xlsx\n\n- Disgenet_IPF targets.xlsx\n\n- GeneCards-IPF targets.csv\n\n- glide-dock_XP_1QIB_Zz_pv.maegz\n\n- glide-dock_XP_2AZ5_Zz_pv.maegz\n\n- glide-dock_XP_2UVM_Zz_pv.maegz\n\n- glide-dock_XP_3KFD_Zz_pv.maegz\n\n- glide-dock_XP_3POZ_Zz_pv.maegz\n\n- glide-dock_XP_4HXJ_Zz_pv.maegz\n\n- glide-dock_XP_4XCT_Zz_pv.maegz\n\n- Molecular dynamics data.zip\n\n- PCA _Output.zip\n\n- Z.z. all components targets for Cytoscape.xlsx\n\n- Z.z. David database KEGG and Functional annotation.xlsx\n\n- Z.z. sitemap result.csv\n\nFigshare: Data of in silico studies on Zingiber zerumbet rhizomes for idiopathic pulmonary fibrosis. https://doi.org/10.6084/m9.figshare.24113343.v1 67\n\nThis project contains the following extended data:\n\n- Supplementary file 1.docx\n\n- Supplementary file 2.docx\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CCBY 4.0)\n\n\nAcknowledgments\n\nThe authors thank the facilities – Schrodinger Centre for Molecular Simulations, Manipal College of Pharmaceutical Sciences, Manipal and Department of Pharmaceutics, Manipal College of Pharmaceutical Sciences for providing computer simulations (SERB DST, New Delhi, India EMR/2016/007006). Thanks, are also for TMA Pai Fellowship supported to Bharath H B by Manipal Academy of Higher Education, Manipal, India, and Indian Council for Medical Research, India for ICMR-SRF (Mr. Krishnaprasad and Ms. Swastika Maity). Authors are also thankful to Manipal Academy of Higher Education for supporting for Open Access Funding.\n\n\nReferences\n\nHopkins AL: Network pharmacology: The next paradigm in drug discovery. Nat. Chem. Biol. 2008; 4(11): 682–690. PubMed Abstract \| Publisher Full Text\n\nSpagnolo P, Sverzellati N, Rossi G, et al.: Idiopathic pulmonary fibrosis: An update. Ann. Med. 2015; 47(1): 15–27. Publisher Full Text\n\nHan M, Song Y, Liu S, et al.: Engineering of Stimulus-Responsive Pirfenidone Liposomes for Pulmonary Delivery During Treatment of Idiopathic Pulmonary Fibrosis. Front. Pharmacol. 2022; 13: 13. Publisher Full Text\n\nVelagacherla V, Mehta CH, Nayak Y, et al.: Molecular pathways and role of epigenetics in the idiopathic pulmonary fibrosis. 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Divers. 2021; 25(1): 233–248." }	[ { "id": "273633", "date": "29 May 2024", "name": "Jingcheng Dong", "expertise": [ "Reviewer Expertise Network pharmacology； Chinese medicine therapy" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\n1. The identification of bioactive ingredients with mass spectrometry data is more reliable. 2. What is the research support for selecting Zingiber zerumbet rhizome (ZZR) (Fam: Zingiberaceae) for the treatment of pulmonary fibrosis? The author lacks clinical evidence, and there is no animal experiment to support the exact curative effect. 3. The author searched the active ingredients according to the literature, but the literature source was not shown. 4. The pictures in Figure 3 are not fully displayed. The axis of enrichment score needs to be improved. 5. The author should at least add animal experiments and molecular biology experiments to verify the efficacy of this drug and whether these targets of online analysis have really changed.\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": [ { "c_id": "11733", "date": "25 Jun 2024", "name": "Yogendra Nayak", "role": "Author Response", "response": "Reviewer Comment 1: The identification of bioactive ingredients with mass spectrometry data is more reliable. Answer to Comment 1: While we agree that mass spectrometry data provides highly reliable identification of bioactive ingredients, our study utilized existing data from a well-established Traditional Chinese Medicine Systems Pharmacology (TCMSP) database and literature search. We used databases and literature based on comprehensive and validated data availability in these resources. By comparing the mass spectra of detected compounds with reference spectra from databases or published literature, TCMSP can identify known phytoconstituents present in a plant. It relies on a combination of analytical techniques and data sources to provide a holistic view of the chemical composition of medicinal plants. Reviewer Comment 2: What is the research support for selecting Zingiber zerumbet rhizome (ZZR) (Fam: Zingiberaceae) for the treatment of pulmonary fibrosis? The author lacks clinical evidence, and there is no animal experiment to support the exact curative effect. Answer to Comment 2: The selection of Zingiber zerumbet rhizome (ZZR) for the treatment of pulmonary fibrosis is based on its documented pharmacological properties and traditional medicinal uses. While we acknowledge the current limitations in clinical and animal studies specifically addressing pulmonary fibrosis, there is supportive data from related research areas. Traditionally, ZZR has been utilized to treat respiratory disorders such as asthma, cough, and inflammatory reactions. We have included reference articles detailing these traditional uses and have expanded the hypothesis to explore its potential in treating pulmonary fibrosis, alongside its recent applications observed in preclinical studies. In summary, the direct clinical evidence is currently lacking, the existing pharmacological data and traditional use, provided a strong rationale for further investigation. The following references are added: 18. Tushar, Basak S, Sarma GC, Rangan L. Ethnomedical uses of Zingiberaceous plants of Northeast India. J. Ethnopharmacol. 2010;132(1):286-96. https://doi.org/10.1016/j.jep.2010.08.032 21. Chaung HC, Ho CT, Huang TC. Anti-hypersensitive and anti-inflammatory activities of water extract of Zingiber zerumbet (L.) Smith. Food Agric. Immunol, 2008;19(2), 117–129. https://doi.org/10.1080/09540100802047783 22. Hong TY, Tzeng TF, Liou SS, Liu IM. The ethanol extract of Zingiber zerumbet rhizomes mitigates vascular lesions in the diabetic retina. Vascul. Pharmacol. 2016;76:18-27. https://doi.org/10.1016/j.vph.2015.08.015 Reviewer Comment 3: The author searched the active ingredients according to the literature, but the literature source was not shown. Answer to Comment 3: We want to clarify that while we extensively searched the literature to identify active ingredients, the specific literature sources were incorporated into the methodology section. Furthermore, in addition to the literature search, we utilized the TCMSP database to identify components. We apologize for any oversight in clearly indicating the literature sources within the manuscript. Reviewer Comment 4: The pictures in Figure 3 are not fully displayed. The axis of enrichment score needs to be improved. Answer to Comment 4: We have addressed the issue of incomplete display in Figure 3 and improved the axis of the enrichment score. The revised figure now includes a complete image of the KEGG pathway analysis. We have utilized an enrichment score instead of an enrichment fold to denote pathways in the figure. The top three enrichment scores indicate that adipocytokines have the highest score, followed by Leishmaniasis and TGF-beta, with the third top enrichment score encompassing the remaining pathways shown in the figure. Pathways with lower scores are depicted in the supplementary file. The axis of the enrichment score was enhanced by reducing the length of the pathway names, ensuring better readability and clarity. Reviewer Comment 5: The author should at least add animal experiments and molecular biology experiments to verify the efficacy of this drug and whether these targets of online analysis have really changed. Answer to Comment 5: We understand the importance of in vivo and molecular biology experiments in verifying efficacy and confirming changes that may occur. However, the current study is mainly a computational prediction study. To establish a foundational understanding of the effects based on the docking studies that have shown promising results, indicating potential efficacy and target specificity, providing a strong basis for further investigation. Based on this study, we will focus on in vitro studies. These findings will be critical first steps to guide subsequent in vivo studies." } ] } ]	1	https://f1000research.com/articles/13-216
https://f1000research.com/articles/13-685/v1	24 Jun 24	{ "type": "Research Article", "title": "Unravelling the devaluation puzzle: Empirical insights into the transmission channel on balance of payments and output in Ethiopia", "authors": [ "Yigermal Maru Ayinewa", "Mesele Belay Zegeye", "Tesfahun Ayanaw Alemu", "Abate Belaye Tefera", "Mesele Belay Zegeye", "Tesfahun Ayanaw Alemu", "Abate Belaye Tefera" ], "abstract": "Background Empirical studies on the impact of devaluation in developing countries, including Ethiopia, have revealed diverse and mixed results. The effects can be positive or negative depending on the specific economic context and policies in place.This study addresses the devaluation puzzle by providing a more comprehensive and nuanced understanding of how devaluation affects the balance of payments and output.\n\nMethods To achieve this, we employ a recursive structural vector autoregressive (SVAR) model focusing on Ethiopia from 2001Q1 to 2023Q4.\n\nResults The findings reveal that exchange rate shocks negatively affect the balance of payments in both the short and long run, with a greater impact observed in the short run. Shocks in other variables, such as foreign exchange rate reserves, inflation, and interest rates, exert a stronger influence on the balance of payments than the exchange rate itself in the long run. In addition, shocks in the exchange rate significantly impact foreign exchange rate reserves in the long run, highlighting the complex dynamics of exchange rates and the indirect nature of the exchange rate channel. Exchange rate shocks also negatively impact output growth in both the short and long run.\n\nConclusion The study concludes that devaluation has a contractionary effect through various channels. Devaluation increases the money supply, leading to inflationary pressures and a decline in output. It also increases interest rates, which further reduces output. In addition, devaluation reduces foreign exchange reserves, resulting in a fall in the balance of payments and a decrease in output. We suggest policymakers prioritize exchange rate stability through practical monetary and fiscal policies. In general, International financial institutions, particularly the National Bank of Ethiopia, should reconsider their devaluation-focused policies, considering the complexities and potential negative consequences associated with devaluation.", "keywords": [ "Devaluation", "Balance of Payments", "Output growth", "SVAR Model", "Transmission Channels" ], "content": "1. Introduction\n\nThis study examines the complex dynamics between devaluation, the balance of payments, and output in Ethiopia. Devaluation, a decline in the value of a country’s currency relative to foreign currency, is recognized as a tool for stabilizing the foreign sector of an economy.1–3 During the 1970s and 1980s, many developing countries faced severe balance of payments deterioration due to overvalued currencies and high unemployment rates.4 Consequently, these countries sought assistance from international organizations, such as the International Monetary Fund (IMF) and the World Bank (WB), both of which were cautious in providing aid without specific conditions, including the implementation of structural adjustment programs (SAPs).5,6 As a result, numerous African countries, including Ethiopia, agreed to implement SAPs and fulfil the World Bank and IMF requirements.\n\nThe impact of exchange rate movements in developing countries varies depending on the nature of their principal exports. It is governed by the Marshall-Lerner condition, which determines the effect of exchange rate depreciation or appreciation on the balance of payment.7\n\nSince 1992, Ethiopia has followed a managed floating exchange rate system, which has resulted in significant fluctuations in the official exchange rate. One notable instance of devaluation occurred when the exchange rate surged from 2.07 birr/dollar to 5 birr/dollar, representing a remarkable devaluation rate of 142%, the highest in Ethiopian history. In September 2010, there was another significant increase in the exchange rate, with a rise of 16.7% from 13.6 birr/dollar to 16.3 birr/dollar. Additionally, in November 2017, the Ethiopian birr was officially devalued by 15% against the US dollar, causing the exchange rate to shift from 23.3 birr per dollar to 27 birr per dollar. To provide a broader perspective, it is important to highlight the overall trend in Ethiopia’s exchange rate. For example, in 1973, the exchange rate was 2.1 birr/dollar, and by 2024, it had increased to 56.559 birr/dollar on average, demonstrating an average annual growth rate of 7.4%.3,8–10\n\nEmpirical studies conducted in developing countries in general, and in Ethiopia in particular, the impact of devaluation on the balance of payments, and output growth reveals diverse perspectives and mixed results, which is positive and negative effect. Studies such as,6,11–18 devaluation affects positively the balance of payment trough improving trade balance, current account balance and output growth. However, several other studies19–24 suggest that devaluation negatively affect trade balance in the short run and had no any significant gain in the long run, and output is negatively affected both in the short run and short run, contractionary impact. This contractionary impact is attributed to reduced aggregate demand, income redistribution from domestic to foreign sectors, and deterioration of the trade balance.25 In addition, devaluation does not have a significant impact on Ethiopian economy because it increases the rate of growth of imports and decreased the rate of growth of export.26\n\nHence, this study aims to make the following contributions to the existing literature: first, while previous studies have primarily focused on examining the individual effects of devaluation on trade balance, balance of payment, and output growth; (e.g., Refs. 3, 7, 11, 13, 16, 18–21, 27–32), it has been observed that there are dynamic relationships among devaluation, balance of payment, and output growth. Thus, this study seeks to provide empirical evidence on the dynamics of devaluation, the balance of payment, and output growth. Second, prior studies have primarily concentrated on illustrating the transmission mechanism of monetary policy while neglecting to investigate the transmission of devaluation on the balance of payments and output growth (e.g., Refs. 4, 33, 34). Thus, further investigation is needed to explore the complex channels through which devaluation influences the balance of payments and output growth. Third, many previous studies have revealed inconclusive results regarding the dynamics of devaluation, balance of payment, and output growth. Therefore, this study contributes by providing more critical insights into these dynamics. Finally, this study resolves the devaluation puzzle by offering a more comprehensive and nuanced understanding of the transmission channels through which devaluation impacts the balance of payments and output growth. In addition to the exchange rate, this study considers other crucial variables such as foreign asset reserves, interest rates, money supply, and inflation, thereby providing a more comprehensive picture of the transmission channel. This study employs a structural VAR model and uses a comprehensive dataset covering the period from 2001Q1 to 2023Q4 to enhance our understanding of the complex dynamics between devaluation, balance of payments, and output growth in the Ethiopian context.\n\nThe remaining section of the paper is structured as follows; Section 2 presents data description and methodology, Section 3 reports results and discusses the study’s results, and Section 4 provides the conclusion and policy recommendations of the study.\n\n\n2. Methods\n\nThis study uses quarterly data obtained from the National Bank of Ethiopia (NBE) to investigate the effects of devaluation on the balance of payments and output. The dataset comprises seven variables: exchange rate, balance of payments, money supply, inflation, interest rates, foreign asset reserves, and real gross domestic product (GDP). To ensure consistency, the real GDP data initially available only annually from the NBE are interpolated to quarterly data using the quadratic-sum approach of E-views 12. The dataset covers a period of 92 observations from 2001Q1 to 2023Q4. The use of quarterly data facilitates the identification of structural shocks, reduces the likelihood of structural breaks, and captures important intra-year dynamics.35\n\nIn line with established economic theories and empirical literature, this study builds a model that enables exploration of the transmission channels through which the exchange rate affects the balance of payments and output. By employing rigorous econometric techniques and a sound theoretical framework, this study provides valuable insights into the dynamics of exchange rate transmission in relation to the Ethiopian economy.\n\nThe model specification begins with the identification and determination of independent variables based on economic theory.36 In accordance with the theoretical framework and empirical evidence, models can be specified to capture the impact of devaluation on the balance of payments and output growth by introducing structural shocks. The theoretical model examines the transmission channels of devaluation in the balance of payments and output. The model incorporates both the demand and supply sides of the economy to analyse the effects of devaluation.37 On the demand side, the model considers the national income identity equation and aggregate supply.\n\nThe balance of payment channel: devaluation can improve the current account of an economy in equilibrium if the combined elasticities of foreign demand for exports and domestic demand for imports exceed unity, known as the Marshall-Lerner condition.37–39 This indicates that devaluation has both a price effect, making exports more competitive and imports more expensive, and a volume effect, leading to increased export volumes and decreased import volumes. Moreover, devaluation can impact the current account balance by influencing the marginal propensity to absorb, income levels, and direct absorption. Furthermore, the imbalance in the money market, as explained by the monetary approach, contributes to the disequilibrium in the balance of payments. In addition, shocks in the money supply, central bank’s foreign exchange reserves, inflation, domestic interest rates, and real output levels influence the balance of payments, and are specified in Eq. (1).\n\nWhere, bop - is balance of payment, e - is nominal exchange rate, Ms - is money supply (M2), inf - is inflation, I - is domestic interest rate, fxre - is foreign asset reserve, and rgdp - is real GDP.\n\nThe exchange rate channel: in a small open economy with free capital mobility, the domestic interest rate must equal the world interest rate in equilibrium.37 Therefore, by equating the domestic interest rate with the world interest rate, we can determine the equilibrium level of the current account. However, in our economy, the interest rate is not determined through this mechanism but is instead fixed by the central bank. A higher domestic interest rate encourages domestic savings and reduces firms’ investment in physical capital. As a result, the domestic interest rate itself affects the current account by reducing exports. The relationship between the interest rate and the exchange rate, regardless of whether devaluation is expansionary or contractionary, is influenced by the type of shock.40 This relationship between the domestic interest rate and investment demonstrates that the domestic interest rate has its own impact on the balance of payments.\n\nThis study also considers the inclusion of the price level in the balance of payment equation to account for the price environment of an economy. This is crucial in determining whether devaluation is inflationary or not, as inflation has a significant impact on output.41 An inflationary environment can have negative effects on output.14,42 This is because it can lead to inefficient allocation of resources due to distortions in relative prices and increased administrative costs for firms37,38; clearly indicate the interaction between the balance of payments and the exchange rate. According to the elasticity approach of exchange rate determination, the exchange rate is determined by the flow of currency through the exchange rate market affecting trade balance, which affects the balance of payments component. In the portfolio view of exchange rate determination; the change in asset prices in the stock market through changes in the price of bonds and money affects the exchange rate.\n\nTherefore, we include BOP in the exchange rate model. We have also understood that an increase in the money supply lowers interest rates, reduces borrowing costs, and promotes investment, which might enhance domestic output. In addition, a higher money supply will reduce the value of the currency. This relationship shows that money supply affects investment and output.40 As in the quantity theory of money, the nominal exchange rate is determined by the quantity of money printed by the central banks that is money supply. This is seeing the exchange rate from the viewpoint of the monetary approach; interest rate and money supply influence exchange rate determination. There is a long run relationship between foreign reserves and exchange rate.43 Moreover; any changes in foreign reserves would lead to fluctuations in the exchange rate but not vice versa. On the basis of these theoretical foundations, we can develop the following exchange rate model, which is specified in Eq. (2):\n\nFrom the above theoretical framework, we can develop the model that fulfills one of the objectives of this paper, and is specified in Eq. (3):\n\nThe existence of exchange rate devaluation has both contractionary and expansionary effects on output through the employment effect and the terms of trade balance effects.38 To show which effect will happen when the country devalues its currency; adding nominal exchange rate into the model is necessary. An increase in money supply lowers interests, reduces borrowing costs, and promotes investment which might enhance domestic output. The improvement in investment leads to increase output which intern promotes a country to export more. In addition, a higher money supply will reduce the value of currency. This relation shows money supply affects the balance of payment.40 Thus, we include the money supply in the model. Table 1 summarizes the contractionary effect of devaluation on the basis of various theoretical and empirical studies, highlighting the transmission channels.\n\n2.2.1 Structural Vector Autoregressive model (SVAR)\n\nThe Structural Vector Autoregressive (here after, SVAR) model is a widely used tool for analysing the monetary transmission mechanism45 and for empirically studying the impact of structural shocks empirically.46,47 The SVAR model is constructed from the reduced form of the VAR (p) model, which represents the data generated by the structural VAR (p) model, as specified in Eq. (4);\n\nWhere, αi,j is an (n×2) matrix constants and linear trends, Bi, i=1,…,p, is a K×K matrix of autoregressive slope coefficients, the K×K matrix B0 reflects the instantaneous relations among the model variables, and the K×1 vector of mean zero structural shocks wt is serially uncorrelated with a diagonal covariance matrix Σw of full rank such that the number of shocks coincides with the number of variables. The endogenous variable,yt, that we include the VAR is the first difference of nominal exchange rate (∆et), output growth (∆yt), consumer inflation (∆pt), broad money supply (∆mst), nominal interest rate (∆it), foreign exchange reserve (∆fxre), and balance of payment (bop). These variables are assumed to be a covariance stationary vector process. For (∆et,∆yt,∆pt, ∆mst, ∆it, and ∆fxre, we can reject the hypothesis of the existence of a unit root at the 10% level (using Augmented Dickey-Fuller and Phillips-Perron tests). We can, however, not reject the hypothesis of a unit root inbop. Given the low power of these tests in relatively small data sets, we follow48–50 and assume that bop is stationary since the balance of payment cannot have a unit root at level.\n\nThe reduced-form representation of the model in Eq. (5) can be obtained by pre-multiplying both sides of Eq. (4) byB0−1, results in the model.46,51,52\n\nWhere; Ai = B0−1Biandut=B0−1wt, λ = B0−1α and it can be estimated by maximum likelihood (ML) estimation methods.\n\nEstimation of the matrix B0 requires additional restrictions on the data generating process (DGP) based on economic theory. If the matrix B0can be solved for, given these restrictions and the data, we say that the structural VAR model parameters, (B0,B1,…,Bp,Σw), are identified or, equivalently, that the structural shocks wt=B0ut are identified. In compact form, an SVAR system relates to the following relations as specified in Eq. (6):\n\nThe equation (6) is known as the AB model53; Where A0is (n×n)matrix of contemporaneous relations between endogenous variables, B is (n×n)matrix that linearly relates the SVAR residuals to the structural innovations, utis vector of reduced-form residual, and wtis vector of structural shocks. The residual utin the reduced form is presumed to be white noise. Therefore, we can estimate the AB model by OLS (ordinary list square).\n\nThe structural innovations wt can be derived from errors ut of the reduced form, but certain restrictions must be placed on the system. In details,n(n−1)2 [1] Where n is the number of variables in the model; restrictions must be imposed on A0 matrix to be able to identify the structural shocks.54\n\n2.2.2 Recursively identified structural VAR model\n\nIn this study, based on the work of,46 the response of economic variables to temporary shocks was estimated using a recursively identified structural model. This approach assumes that the current structural shocks are not influenced by the preceding ordering variables. Instead, it is assumed that the variables are affected by a sequential chain of shocks, or alternatively, the matrix A0 is diagonal, indicating that the structural shocks are orthogonal. Specifically, the matrix A0 takes the form of a lower triangular matrix, as illustrated below:\n\nWhere, (ute,uti,utms,utinf,utfxre,utbopandutrgdp), are the structural disturbance, that is, exchange rate shocks, interest rate shocks, money supply, the price shocks, foreign asset reserve shocks, the balance of payment shocks, and output shocks respectively; and (wte,wti,wtms,wtinf,wtfxre,wtbop,andwtrgdp), are the residuals in the reduced form equations, which represent unexpected movements (given information in the system) of each variable.\n\nIn certain scenarios where a fully developed theoretical model is unavailable, the process of identification can be achieved through the incorporation of extraneous information and the selective utilization of insights from economic theory. In line with,46 we present the construction of a recursive form of the SVAR (Structural Vector Autoregressive) model, as demonstrated above.\n\nOnce the structural shocks have been identified, a rigorous analysis and interpretation of these macroeconomic shocks become imperative. This analysis is conducted within the framework of structural VAR models and involves the examination of structural impulse responses as well as the implementation of forecast error variance decompositions. These analytical techniques provide valuable insights into the dynamics and impacts of the identified shocks.\n\n\n3. Results and Discussion\n\nTo enhance the robustness of the test, the presence of a unit root was assessed using the Augmented Dickey–Fuller (ADF) and Phillip-Perron (PP) tests. The results of the unit root tests conducted using the Augmented Dickey–Fuller and Phillip-Perron methods are summarized in Table 2. Based on the results of the ADF and PP tests, it is evident that all variables in the VAR model, except bop, are nonstationary at this level. This implies that the null hypothesis of a unit root, including both trend, and trend and intercept, cannot be rejected for these variables. However, upon considering their first differences, these variables exhibit stationarity.\n\no determine the lag length of VAR/SVAR, the study employs different lag-length selection criteria, including the likelihood ratio test statistic (LR), Final Prediction Error (FPE), Akaike Information Criteria (AIC), and the Hannan-Quinn Information Criterion (HQ). In Table 3 the lag length selection criterion is tabulated. The AIC lag length section test indicates that the appropriate lag length for the VAR model is three (3).\n\n* Optimal lag length selected by the criterion.\n\nPrior to estimating the parameters of the SVAR model with the optimal lag length, it is essential to assess the stability conditions of the VAR model by examining the AR roots. The obtained results, which are reported in Table 4, indicate that all eigenvalues in the proposed model lie within the unit circle, signifying values that are either less than one or equal to unity. Consequently, it can be concluded that the VAR/SVAR model satisfies the requisite stability condition.\n\nThe unit root test reveals that the model in our study consists of a mixture of I(1) and I(0) variables. To investigate whether these variables are cointegrated at the same order (only I(1) variables) and at different orders (I(0) and I(1)), we employ Johansen’s cointegration technique.36 Our analysis is based on an SVAR model with a mixture of I(1) and I(0) variables, as described previously.48,55,56 The results of Johansen’s cointegration test in Table 5 indicate the presence of multiple cointegrating equations and vectors in the case of I(1) variables, whereas for the mixture of I(0) and I(1), evidence suggests the presence of three cointegrating relationships. These findings contribute to a deeper understanding of the long-run dynamics and interdependencies among the macroeconomic variables studied.\n\n* Selected rank.\n\nThe study investigated the presence of serial autocorrelation (Table 6) before discussing the impulse response function. The selected lags in the VAR model exhibit no significant serial autocorrelation at the 5% level, and the parameter estimates remain stable. As a result, the SVAR models with three lags satisfy the stability condition and can be reliably estimated.\n\n3.5.1 The response of the balance of payment to shocks\n\nFigure 1 illustrates positive shocks on the exchange rate and other variables included in the balance of payment channel in the long run. In both short run and long run, devaluation negatively affects the balance of payment. Contrary to initial expectations, our findings indicate that devaluation does not have a significant long-run impact. Therefore, we reject the null hypothesis suggesting that devaluation enhances the balance of payments in the long run. Interestingly, we discover that a positive shock exchange rate actually has a negative effect on the balance of payments. The success of devaluation as a strategy to improve the balance of payments depends on the elasticities of exports and imports. In the context of Ethiopia, where elasticity is significantly low, devaluation is not expected to lead to an improvement in the balance of payments. These findings align with those of previous studies conducted by.57,58\n\nAdditionally, we find that an initial positive shock in interest rates improves the balance of payments, but this effect diminishes after the fourth quarter in both the short and long run. On the other hand, in the short run, a positive innovation in money supply negatively affects the balance of payments up to the fourth quarter, and after the fourth quarter, its effect is positive. However, in the long run, a positive shock in the money supply initially enhances the balance of payments, but the effect diminishes after the fourth quarter in the long run. Furthermore, the response of the balance of payments to a positive innovation in inflation is negative in the short run and positive up to the third quarter. However, after the fourth quarter, the balance of payments worsens in the long run, which contradicts the findings of.59 This divergence highlights the need for further investigation into the dynamics of inflation and its impact on the balance of payments in Ethiopia. Lastly, a positive shock in foreign asset reserves affects negatively up to the third quarter and positively after the third quarter in both the short and long run. Initially, a positive shock on real output has a negative impact on the balance of payments both in the short and long run up to the second quarter; thereafter, its impact is positive.\n\n3.5.2 The response of real GDP (output growth) to shocks\n\nFigure 2 presents empirical evidence on the contemporaneous response of output to various macroeconomic shocks, including positive innovations in the nominal exchange rate, interest rate, money supply, inflation, foreign asset reserves, and balance of payments in the long run. Our analysis reveals that the nominal exchange rate has a negative impact on output in both short run and long run, indicating a contractionary effect. These findings are consistent with prior research by,15,32,60 providing further support for the hypothesis that positive shocks to the exchange rate adversely affect output. Additionally, we find empirical evidence supporting the null hypothesis, confirming that devaluation has a contractionary effect on output.\n\nFurthermore, our study reveals that positive innovations in interest rates have a negative effect on output both in the short and long run, providing empirical support for the monetary theory. This finding strengthens the existing literature by confirming the negative relationship between output and interest rates. Moreover, our analysis reveals that a positive shock in the money supply leads to a positive response in output. This observation suggests that an increase in money supply stimulates output, thereby contributing to economic growth in both the short and long run.\n\nIn line with the research conducted by59 our study highlights the adverse impact of inflation on output against the findings of.12 Specifically, we find that an increase in inflation significantly and negatively affects output in both the short and long run, emphasizing the detrimental consequences of rising inflation for overall economic performance. Regarding foreign asset reserves, our analysis indicates that an initial positive shock in these reserves adversely affects output in both the short and long run. However, after three quarters in the long run, the effect becomes positive, suggesting a gradual recovery and the potential for long-term benefits. This dynamic nature of the relationship between foreign asset reserves and output in the long run underscores the importance of considering the timing and persistence of shocks when assessing their effects. In addition, our study reveals a positive contemporaneous response of output to positive shocks in the balance of payments. Specifically, a surplus in the balance of payments improves the level of output, indicating a favourable impact on the economy.\n\nIn summary, the findings confirm the contractionary effect of positive shocks in the nominal exchange rate, the inverse relationship between output and interest rates, and the positive impact of money supply shocks on output. Furthermore, our study emphasizes the negative effects of inflation on output and highlights the dynamic nature of the relationship between foreign asset reserves and output.\n\n3.5.3 The response of money supply to shocks\n\nFigure 3 illustrates the response of the money supply (M2) to contemporaneous positive shocks in macroeconomic variables. Specifically, we examine the response of the money supply to positive innovations in the nominal exchange rate, interest rate, inflation, foreign exchange reserves, balance of payments, and output. In the case of a positive innovation in the nominal exchange rate, our findings reveal that the response of the money supply is positive during the first three quarters in both the short and long run. This implies that an initial positive shock to the nominal exchange rate leads to an increase in the money supply in Ethiopia. However, after the third quarter, the response of the money supply declined, although it remained positive. This suggests a diminishing effect over time. Consistent with economic theory, our analysis supports the inverse relationship between the interest rate and money supply in Ethiopia. A positive innovation in the interest rate leads to a decrease in the money supply, aligning with the expected relationship.\n\nFurthermore, our findings indicate that a positive innovation in inflation has a significant effect on increasing the money supply in Ethiopia. This suggests a positive relationship between inflation and money supply, highlighting the impact of inflation on the monetary dynamics of the Ethiopian economy. Regarding foreign exchange reserves, our analysis reveals a dynamic response of money supply. A positive shock in foreign exchange reserves initially leads to an increase in money supply. However, similar to the response to the nominal exchange rate, the effect gradually declines over time. Moreover, our study finds that a positive shock in the balance of payments leads to an increase in money supply in Ethiopia. This implies a positive relationship between the balance of payments and money supply, indicating the influence of external factors on the domestic money supply dynamics in the Ethiopian context in both short run and long run.\n\nFinally, our analysis demonstrates a positive response of money supply to positive shocks in output. This implicates that a positive shock to output leads to a rise in money supply in Ethiopia, highlighting the relationship between output and money supply dynamics in the country.\n\n3.5.4 The response of inflation\n\nFigure 4 presents the impulse response analysis of inflation to exogenous shocks in the innovations of other variables within the system. Specifically, we examine the effects of a positive shock in the exchange rate, interest rate, and money supply on inflation dynamics. Our findings reveal that a positive shock in the exchange rate, indicative of devaluation in the domestic currency, exerts a positive impact on inflation in both the short and long run. This outcome suggests the presence of inflationary pressures resulting from exchange rate movements, whereby devaluation in the domestic currency contributes to higher import costs and subsequently increases domestic prices.6 In contrast, the response of inflation to a positive random shock in the innovation of the interest rate demonstrates a negative relationship. This observation implies that an increase in interest rates reduces inflationary pressures within the economy. Moreover, a positive random shock in the money supply is associated with an increase in inflation. This result suggests that an expansionary monetary policy, as reflected by an increase in the money supply, contributes to higher inflationary pressures.\n\nOverall, these findings underscore the interconnectedness and dynamics of inflation with respect to exogenous shocks in the exchange rate, interest rate, and money supply. The implications of these relationships provide valuable insights for policymakers in managing inflationary pressures and devising appropriate monetary and exchange rate policies.\n\n3.5.5 The response of foreign exchange reserve\n\nFigure 5 presents the impact of devaluation and other macroeconomic variables on foreign asset reserves. Devaluation of the domestic currency leads to a decline in foreign asset reserves. The response of reserves to positive innovations in the interest rate initially exhibits a negative relationship, but after a few quarters of adjustment, it results in an increase in reserves. Moreover, the response of foreign asset reserves to changes in the money supply is positive, indicating that an expansionary monetary policy contributes to an increase in reserves.\n\nThis study also highlights the positive relationship between inflationary shocks and foreign asset reserves. When inflationary pressures arise, the central authority takes measures to collect funds to mitigate inflation. Consequently, the reserve in banks increases. Furthermore, lagged positive innovations have a significant impact on the current performance of foreign asset reserves. These findings shed light on the dynamics and interplay among currency devaluation, interest rate innovations, money supply changes, inflationary shocks, and foreign asset reserves. The implications of these relationships provide valuable insights for policymakers in managing and optimizing foreign asset reserves in response to various economic shocks and policy interventions.\n\n3.5.6 The response of interest rate\n\nFigure 6 shows the responses of the interest rate to positive shocks in the innovations of other variables in the system. Initially, positive shocks on the exchange rate have a positive effect, but the effect declines after the second quarter. The response of the interest rate to the money supply is negative. An increase in inflation leads to a decline in the interest rate, and the effects of foreign asset reserves initially increase the interest rate, but the interest rate declines a few quarters later. The balance of payment surplus influenced the domestic interest rate to decline. Responses to positive innovation in output led to an increase in the lending interest rate.\n\n3.5.7 Estimation results of Variance decomposition\n\nThe variance decomposition analysis of the balance of payment (bop) and output (lrgdp) is used to examine the strengths of various devaluation channels. The study includes forecast horizons ranging from 1 to 10 quarters. The first column of the results displays the forecast periods, while the second column represents the standard error (SE), indicating the forecast error at different quarters. Shocks denoted as Shock1 (e), Shock2 (i), Shock3 (lnms), Shock4 (inf), Shock5 (lnfxre), Shock6 (bop), and Shock7 (lrgdp) are used to represent each variable. Furthermore, the decomposition values for the 1st to 10th forecast horizons are presented in Tables 7 and 8.\n\nThe results of our variance decomposition analysis in the short-run shocks on the exchange rate significantly affect the balance of payment next to the foreign exchange reserve. In the long run, foreign exchange rate reserve shocks (Shock 5) have more significant explanatory power in accounting for balance of payment (bop) fluctuations than nominal exchange rate shocks (Shock 1) and output shocks (Shock 7). Thus, the foreign exchange rate reserve channel emerges as a dominant factor in the context of exchange rate policy and its influence on balance of payment dynamics. In contrast, the impact of the exchange rate channel alone appears to be ineffective in the long run, as indicated by its contribution to the balance of payment fluctuations in Table 7. However, the exchange rate channel indirectly affects the balance of payment through other channels, such as the foreign exchange reserve, output, and money supply channels. This highlights the interdependencies and interconnectedness of these channels in shaping balance of payment dynamics in the long run.\n\nThe results of our variance decomposition analysis in Table 8 indicate that balance of payment shocks (Shock 6), interest rate shocks (Shock 2), exchange rate shocks (Shock 1), and money supply shocks (Shock 3) have a significant impact on output variations in the long run. Among these shocks, the exchange rate channel emerges as a crucial factor that interacts with the balance of payment and interest rate channels, shaping the dynamics of output fluctuations.\n\n\n4. Conclusion and policy recommendations\n\nThis study addresses the devaluation puzzle by providing a more comprehensive and nuanced understanding of how devaluation affects the balance of payments and output. To achieve this, we employ a recursive structural vector autoregressive (SVAR) model focusing on Ethiopia from 2001Q1 to 2023Q4. In addition to examining the exchange rate, we incorporate other essential variables such as foreign asset reserves, interest rates, money supply, and inflation. By including these variables, we provide a more complete depiction of the transmission channel. This study also demonstrated unit root tests using the ADF and PP tests, model stability, and other necessary assessments.\n\nThe findings of this study lead to the following key conclusions: first, a shock to the exchange rate hurts the balance of payments in both the short and long run. The effectiveness of exchange rate movements on the balance of payments is greater in the short run than eventually. Second, shocks to other variables such as foreign exchange rate reserves, inflation, and interest rates exert a stronger influence on the balance of payments than the exchange rate itself in the long run. Moreover, in the long run, shocks in the exchange rate have a significant impact on foreign exchange rate reserves. The impact of devaluation on the balance of payments, particularly through the exchange rate channel, is limited when considered in isolation over the long run. Instead, its influence is observed indirectly through interactions with other channels, such as the foreign exchange reserve channel, highlighting the complex dynamics of exchange rates. Third, shocks to the exchange rate hurt output growth, both in the short and long run. Fourth, in the long run, the exchange rate responds negatively to shocks in the balance of payments and output growth (appreciation of domestic currency). Changes in the balance of payments and output explain a significant portion of the variability in exchange rate movements. Finally, the study concludes that devaluation has a contractionary effect through various channels. Devaluation increases the money supply, leading to inflationary pressures and a decline in output. It also increases interest rates, which further reduces output. Additionally, devaluation reduces foreign asset reserves, resulting in a fall in the balance of payments and a decrease in output.\n\nBased on the findings of this study, several policy recommendations arise: first, given the negative impact of exchange rate shocks on the balance of payments and output growth, policymakers should prioritize maintaining exchange rate stability. This can be achieved through prudent monetary and fiscal policies that avoid excessive exchange rate volatility and promote economic stability. Second, because shocks in the exchange rate significantly affect foreign exchange rate reserves, the National Bank of Ethiopia should diversify its reserve holdings. Holding a diversified portfolio of currencies and assets can help mitigate the adverse effects of exchange rate fluctuations and enhance the resilience of the balance of payments. Third, while the exchange rate plays a role in the balance of payments, policymakers should adopt a broader perspective by considering the interplay of other variables such as foreign exchange rate reserves, inflation, and interest rates. Implementing comprehensive economic policies that address these factors can significantly impact the balance of payments in the long run. Fourth, policymakers should prioritize effective inflation control.\n\nThis involves implementing appropriate monetary policies to control money supply growth, ensuring price stability, and minimizing the inflationary pressures associated with devaluation. Fifth, given the negative impact of exchange rate shocks on the balance of payments, policymakers should focus on enhancing the competitiveness of domestic industries in global markets. This can be achieved by investing in infrastructure, providing targeted support to export-oriented sectors, and implementing policies that foster innovation and productivity improvements.\n\nFinally, it is recommended that international financial institutions such as the International Monetary Fund (IMF) and the World Bank revisit their policy advising developing countries to devalue their currencies. In addition, the National Bank of Ethiopia should reassess its policies that prioritize currency devaluation as the preferred approach for the development of the economy. These revisions should consider the complexities and potential negative consequences associated with devaluation.", "appendix": "Data availability statement\n\nZenodo: Unravelling the Devaluation Puzzle: Empirical Insights into the Transmission Channel on Balance of Payments and Output in Ethiopia https://zenodo.org/doi/10.5281/zenodo.11190281.\n\nThis project contains the following underlying data:\n\n- data.xlsx\n\n\nReferences\n\nUpadhyaya KP: Currency devaluation, aggregate output, and the long run: an empirical study. Econ. Lett. 1999; 64(2): 197–202. Publisher Full Text\n\nHayes A: 3 reasons why countries devalue their currency. Investpedia; 2016.\n\nElias A, Dachito A, Abdulbari S: The effects of currency devaluation on Ethiopia’s major export commodities: The case of coffee and khat: Evidence from the vector error correction model and the Johansen co-integration test. Cogent Econ. Finance. 2023; 11(1): 2184447. Publisher Full Text\n\nStambuli P: Revisiting a policy of currency devaluation in African countries. Surrey Institute of Global Economics Research, Vos Mises University, Alabama; 2002.\n\nAleto AA: The Economy Wide Impact of the Devaluation of Ethiopian Currency: A Recursive Dynamic Computable General Equilibrium Approach. Ethiopia: Addis Ababa University Addis Ababa; 2018.\n\nTafesse B: The impact of currency devaluation on the Ethiopian economy.2019.\n\nAllen M: Exchange rates and trade balance adjustment in emerging market economies. Washington, DC, United States: International Monetary Fund; 2006.\n\nEthiopia NBo: National Bank of Ethiopia Annually Bulletin. In: NBE, editor. Addis Ababa, Ethiopia NBE; 2021/22. pp. 1–120.\n\nKidane A: Indices of effective exchange rates: a comparative study of Ethiopia. Nairobi, KE: Kenya and the Sudan. AERC; 1994.\n\nHausmann R, O’Brien T, Cheston T, et al.: Development in a Complex World: The Case of Ethiopia. CID Faculty Working Paper Series.2023.\n\nHaile F: The exchange rate: Why it matters for structural transformation and growth in Ethiopia. The World Bank. 2019. Publisher Full Text\n\nAyanaw T, Godadaw S, Maru Y, et al.: The empirical analysis on dynamics of currency devaluation, external debt to GDP ratio, and output growth: evidence from Ethiopia. Cogent Soc. Sci. 2024; 10(1): 2319373. Publisher Full Text\n\nOladipupo AO: Impact of exchange rate on balance of payment in Nigeria. African Research Review. 2011; 5(4). Publisher Full Text\n\nAn L, Kim G, Ren X: Is devaluation expansionary or contractionary: Evidence based on vector autoregression with sign restrictions. J. Asian Econ. 2014; 34: 27–41. Publisher Full Text\n\nAyen YW: The effect of currency devaluation on output: The case of Ethiopian economy. J. Econ. Int. Finance. 2014; 6(5): 103–111. Publisher Full Text\n\nAsmamaw H: The Impact of devaluation on trade balance: The Case of Ethiopia.2008.\n\nMaru Y: Devaluation, balance of payment and output dynamics in developing countries: (the case of Ethiopia). Addis Ababa University; 2018.\n\nGelana D: The Effect of Real Exchange Rate on the Trade Balance of Ethiopia: Does Marshal Learner Condition Holds? Evidence from (VECM) Analysis.2019.\n\nDamoense MY, Agbola FW: Estimating the Long Run Effects of Exchange Rate Devaluation on the Trade Balance of South Africa. maylene damoense@ busco monash edu. 2004.\n\nGebeyehu AB: Exchange rate and trade balance; J curve effect in Ethiopia. Exchange. 2014; 5(24).\n\nGenemo KB: Effect of exchange rate on trade balance in major east African countries: Evidence from panel cointegration. Eur. Bus. Manag. 2017; 3(6): 95–104. Publisher Full Text\n\nNguse T, Oshora B, Fekete-Farkas M, et al.: Does the exchange rate and its volatility matter for international trade in Ethiopia? J. Risk Financial Manag. 2021; 14(12): 591. Publisher Full Text\n\nFeyissa S, Garomsa T: Narrowing trade deficit through increased import substitution. Chamber of Commerce and Sectoral Association; 2011.\n\nHailu T: Determinants of Ethiopian Foreign Direct Investment Inflows: Bounds Testing Approach.2019.\n\nKrugman P, Taylor L: Contractionary effects of devaluation. J. Int. Econ. 1978; 8(3): 445–456. Publisher Full Text\n\nTafesse B: The impact of currency devaluation on economic growth: its benefits and costs on Ethiopian economy. st. mary’s University; 2019.\n\nFufa GB: Analysis Of The Determinants Of Relative Trade Balance In Ethiopia: Econometric Time Series Application. Int. J. Inf. Bus. Manag. 2022; 14(2): 58–68.\n\nGebremariam TK, Batu MM, Tola S: The effect of real effective exchange rate on balance of payments in Ethiopia: A co-integrated VAR approach. J. Econ. Int. Finance. 2018; 10(12): 156–165. Publisher Full Text\n\nGemechu H: determinants of trade balance in Ethiopia. St. Mary’s University; 2018.\n\nKamin SB, Klau M: Some multi-country evidence on the effects of real exchange rates on output. FRB International Finance Discussion Paper.1998; 611.\n\nKemoe L, Mbohou M, Mighri H, et al.: Effect of Exchange Rate Movements on Inflation in Sub-Saharan Africa.2024.\n\nUmer MM: devaluation and its impact on Ethiopian economy. Sosyal Bilimler Enstitüsü; 2015.\n\nAbate Y, Koteswara R, Nagaraja G: Transmission mechanisms of monetary policy in Ethiopia: evidence from structural VAR approach. Int. J. Adv. Res. 2019; 7(2): 576–587.\n\nOnaga IF, Arize AC, Onwumere JUJ, et al.: Monetary policy transmission channels and the performance of the real sectors in selected sub-Saharan African countries: a system-GMM approach. Future Bus. J. 2023; 9(1): 49. Publisher Full Text\n\nBlanchard O, Perotti R: An empirical characterization of the dynamic effects of changes in government spending and taxes on output. Q. J. Econ. 2002; 117(4): 1329–1368. Publisher Full Text\n\nLütkepohl H: New introduction to multiple time series analysis. Springer Science & Business Media; 2005.\n\nSchmitt-Grohé S, Uribe M, Woodford M: International macroeconomics: A modern approach. Princeton University Press; 2016.\n\nPilbeam K: International finance. Bloomsbury Publishing; 2006.\n\nAbbas Ali D, Johari F, Haji Alias M: The effect of exchange rate movements on trade balance: A chronological theoretical review. Econ. Res. Int. 2014; 2014: 1–7. Publisher Full Text\n\nShahbaz M, Islam F, Aamir N: Is devaluation contractionary? Empirical evidence for Pakistan. Econ. Chang. Restruct. 2012; 45: 299–316. Publisher Full Text\n\nIhsan I, Anjum S: Impact of money supply (M2) on GDP of Pakistan. Glob. J. Manag. Bus. Res. Finance. 2013; 13(6): 1–8.\n\nMejía-Reyes P, Osborn DR, Sensier M: Modelling real exchange rate effects on output performance in Latin America. Appl. Econ. 2010; 42(19): 2491–2503. Publisher Full Text\n\nFang Y, Lu L: Does a correlation exist between the foreign exchange reserves and the exchange rate?: An empirical study of China.2011.\n\nBach TNT: An evaluation of monetary policy in Vietnam, 1998-2016: a SVAR approach.2017.\n\nChristiano LJ, Eichenbaum MS, Evans C: Monetary policy shocks.1998.\n\nKilian L, Lütkepohl H: Structural vector autoregressive analysis. Cambridge University Press; 2017.\n\nPham T: Monetary policies and the macroeconomic performance of Vietnam. Australia: Queensland University of Technology Queensland; 2016.\n\nPeersman G: What caused the early millennium slowdown? Evidence based on vector autoregressions. J. Appl. Econ. 2005; 20(2): 185–207. Publisher Full Text\n\nGali J: How well does the IS-LM model fit postwar US data? Q. J. Econ. 1992; 107(2): 709–738. Publisher Full Text\n\nGerlach S, Smets F: The monetary transmission mechanism: evidence from the G-7 countries.1995.\n\nGottschalk J: An introduction into the SVAR methodology: identification, interpretation and limitations of SVAR models. Kiel working paper.2001.\n\nHamilton JD: Time series analysis. Princeton University Press; 1995.\n\nAmisano G, Giannini C, Amisano G, et al.: From var models to structural var models. Topics in structural VAR econometrics. 1997; 1–28. Publisher Full Text\n\nMcCoy D: How useful is Structural VAR Analysis for Irish economics? Central Bank of Ireland; 1997.\n\nPagan AR, Pesaran MH: Econometric analysis of structural systems with permanent and transitory shocks. J. Econ. Dyn. Control. 2008; 32(10): 3376–3395. Publisher Full Text\n\nOuliaris S, Pagan A, Restrepo J: Quantitative macroeconomic modeling with structural vector autoregressions–an EViews implementation. IHS Global. 2016; 13.\n\nAlemayehu G: Why is the World Bank Bothering the Government of Ethiopia on Devaluation. Addis Ababa University; 2014.\n\nDorosh P, Robinson S, Hashim A: Economic implications of foreign exchange rationing in Ethiopia. Ethiop. J. Econ. 2009; 18(2): 1–30.\n\nTafere K: The sources of the recent inflationary experience in Ethiopia. Addis Ababa University; 2008.\n\nGenye T: Currency devaluation and economic growth: The case of Ethiopia. Departments of Economics, Stockholm University; Reference Source\n\n\nFootnotes\n\n1 The contemporaneous matrix requires (7(7−1)2=24) restrictions for exact identification more than 24 restrictions were imposed, leading to over identification." }	[ { "id": "297002", "date": "19 Jul 2024", "name": "Michael Connolly", "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\nFirstly, it is hard to think of the nominal exchange rate as an exogeneous variable, though in Ethiopia there seem to have been large devaluations. The issue is that under fixed or crawling exchange rates, the authorities often sell reserves to defend the exchange rate while the price of non-traded goods rises due to money base expansion to finance the fiscal deficit. So, the devaluations may be \"catch up\" to an overvaluation. Indeed, they may get closer to the equilibrium where M/E, M/P, and interest rates are in equilibrium (though with expected devaluation and possibly default, there are risk premia).\nDear The exercise has some interest though since it reaches sensible long run results. The article is too long winded and this SVAR methodology crunches out all sorts of stuff. When the authors say exchange rate shocks negatively affect foreign exchange reserves in the short and long run, they presumably mean devaluations, since a shock could also be an appreciation. The exposition is a bit sloppy. Reliance on the Marshall Lerner condition is an old partial equilibrium elasticity result. The table is interesting and the real cash balance effect of Alexander is mentioned. I like the table, but in light of all these channels and not that many degrees of freedom, it would behoove the authors not to overinterpret causation and results. In any case, as in Mundell's analysis you either set the money supply and the exchange rate adjusts or you set the exchange rate and the money supply adjusts (unless you have exchange controls). So this is sort of a chicken and egg issue, is the exchange rate the control variable or is the money supply the control variable.\nStill, I found the results interesting and would consider a revision. However the authors have submitted 8 tables and 5 figures (each containing 7 impulse figures for a total of 35 figures altogether) T In theory, money is neutral, the exchange rate is neutral, departing from an equilibrium. Real variables should not be affected for unanticipated one time shocks. In the case of Ethiopia, though the expectations of devaluation can change much both before and after the devaluation.\n\nThe authors do not have clean cut tests in my view, nor do they have clear causations. If they found no major long run changes to real variables, that would be interesting. But money or the exchange rate should be the long run determinant of nominal variables. Table 1 is good, but in any case, if the authors resubmit, I would constrain them to two sets of tables, and two sets of figures. The other results can be explained in text form, if necessary.\nAt the end of the day, I feel the authors claim too much. The model obviously does not start in equilibrium nor reach equilibrium in the short or even long run. Further, it is sort of a kitchen sink model, several factors working in different directions at the same time on the dependent variables. In statistical analysis, the idea is to test hypotheses where an exogeneous variable changes and the hypothesized change is not rejected. The model could instead have had the exchange rate as the dependent variable and the money supply as the independent variable.\nSo this could be treated as such and if the long run outcomes are not significant this would not reject the hypothesis that changes in nominal variable do not affect long run real variables. That would be useful and less speculative. The authors would not need to report every single page of the SVAR program. Have fewer objectives that can be analyzed. Unravelling the details of the channels is not done nor can it be done with these techniques. I would suggest a less enticing title.\n\nIs the work 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? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] }, { "id": "305323", "date": "28 Sep 2024", "name": "Florencia Médici", "expertise": [ "Reviewer Expertise Macroeconomics" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address 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 paper is to empirically study the effects of currency devaluation on output and the balance of payments (BoP), considering other relevant macroeconomic variables.\np.4 The authors: “By employing rigorous econometric techniques and a sound theoretical framework, this study provides valuable insights into the dynamics of exchange rate transmission in relation to the Ethiopian economy…. The model specification begins with the identification and determination of independent variables based on economic theory.”\nFrom my point of view, the paper presents both theoretical and empirical issues that require further attention.\nFirstly, the theoretical framework needs to be more clearly articulated. While I assume the authors adopt a New Keynesian approach, the transmission mechanisms of the variables of interest are not explicitly defined, nor is it clear which variables are treated as independent.\nOne key omission is the role of international financial flows, which is crucial when discussing balance of payments in underdeveloped countries. I recommend the authors review the relevant literature on this topic to address potential omitted effects, such as the interaction between interest rates, financial flows, and the real exchange rate. For instance, an increase in the domestic interest rate may attract capital inflows, resulting in a short-run balance of payments surplus and currency appreciation. This could potentially reduce inflation, improve real wages, and ultimately have a positive impact on GDP.\np.3 “In addition, devaluation does not have a significant impact on Ethiopian economy because it increases the rate of growth of imports and decreased the rate of growth of export.”\nWhat is the mechanism behind this assertion? Devaluation typically has a contractionary effect, at least in the short run, which would generally lead to a reduction in imports. laiming that devaluation \"increases the rate of growth of imports and decreases the rate of growth of exports\" seems to imply that the country in question set international prices—a challenging assumption for a developing country. This reasoning needs to be supported by a clear explanation of the transmission mechanism at play. (Also, please refer to transmission channel 1 in Table 1 for further clarification.)\np.4 The authors consider the money supply to be exogenous (determined by the central bank), making the interest rate endogenous. However, both variables are included in the VAR as independent variables. While this may be theoretically acceptable, it creates ambiguity in the model structure. If the money supply is exogenous, the interest rate should be excluded from the set of independent variables, or a new equation should be added to represent the determination of the money supply (M). Alternatively, the model should account for endogeneity by employing appropriate techniques to address this issue.\nMoreover, assuming that money is exogenous while the interest rate is endogenous requires a more robust theoretical discussion to support this assumption.\np.4 “This is seeing the exchange rate from the viewpoint of the monetary approach; interest rate and money supply influence exchange rate determination. There is a long run relationship between foreign reserves and exchange rate. Moreover; any changes in foreign reserves would lead to fluctuations in the exchange rate but not vice versa.”\nForeign reserves are a stock variable derived from flow variables, specifically the outcome of the balance of payments (BoP). If the exchange rate affects the BoP, it is inconsistent to assume that variations in the nominal exchange rate (NER) do not influence foreign reserves. This concept needs to be reconsidered in light of the interdependencies between these variables.\nSo far, the theoretical framework is not well articulated, making the transmission mechanisms confusing. This, in turn, limits the specification of the empirical model\nEMPIRICAL EVIDENCE\nThe inclusion of both the interest rate (i) and money supply (Ms) as independent variables, as mentioned earlier, raises some concerns. These variables need to be more carefully justified within the model. I recommend providing clearer definitions of the variables used, along with the sources from which this data was collected. This will enhance the transparency and replicability of the study.\nUnit Root Tests:\nClarification is needed on the variable “inf.” Is this inflation measured as consumer price variation? Since \"inf\" is presented as the difference of the price variable, this suggests that prices might be treated as an I(2) variable. If this is the case, further explanation is necessary. It would also be helpful if Table 2 included information on the significance of the trend and constants for each variable. This is important for understanding the behavior of the variables and for assessing the stationarity assumptions used in the model.\nCointegration:\nIn Table 5, the results indicate the presence of 2 cointegration relationships, not 3. This discrepancy should be addressed for accuracy. On p.9, the authors state, “These findings contribute to a deeper understanding of the long-run dynamics and interdependencies among the macroeconomic variables studied.” However, it is unclear what specific dynamics are revealed by the cointegration test. A more detailed explanation of the nature of these long-run relationships would strengthen the paper's contributions. Additionally, please note that if \"Ms\" (money supply) and \"BoP\" (balance of payments) are removed from the set of independent variables, as previously suggested, the cointegration relationship may no longer hold. This could significantly alter the interpretation of the long-run dynamics and should be carefully reconsidered.\nImpulse Response and Variance Decomposition:\nBy definition, a VAR model is used to analyze short-run relationships. How do the authors define the “long run” in this context? Typically, in econometric analysis, when persistent relationships between variables (i.e., long-run relationships) are present, a Vector Error Correction (VEC) model is employed. The VAR model, on the other hand, is generally built with I(0) stationary variables that do not exhibit long-run relationships. Regarding the impulse response functions, it is unclear what specific shock each graph in Figures 1 and 2 represents, making it difficult to follow the results. Additionally, many of these results indicate no significant relationships, even in the short run, as the impulse response functions—including the confidence intervals—hover around zero.\nConclusion: In conclusion, while the empirical study on the macroeconomic effects of exchange rates is relevant and timely, the paper requires significant revisions to improve its consistency, both in the theoretical framework and the development of the empirical section.\nArestis P. 2009. Ref 1\n\nBahmani M. H. Harvey and S. W. Hegerty. 2013. Ref 2\nBorio C. and P. Disyatat. 2015.Ref 3\nKohler K. 2022. ‘Ref 4\n\nKrugman, P., & Taylor, L. (1978). Ref 5\nLavoie, M. (2014).Ref 6\nReinhart C. 1995. ‘Ref 7\nRey H. 2015. ‘Ref 8\nRey H. 2016. Ref 9\nSerrano, F., & Summa, R. (2015) Ref 10\nSerrano, F., Summa, R., & Aidar, G. (2021). Ref 11\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/13-685
https://f1000research.com/articles/11-1054/v1	15 Sep 22	{ "type": "Research Article", "title": "The impact of spinal fusion of adolescent idiopathic scoliosis in Salah (Islamic Prayer) movement: a case-control study", "authors": [ "Komang Agung Irianto", "Naufal Ranadi Firas", "Carlos Gracia Supriantono Binti", "Damayanti Tinduh", "Yudha Mathan Sakti", "Brigita De Vega", "Naufal Ranadi Firas", "Carlos Gracia Supriantono Binti", "Damayanti Tinduh", "Yudha Mathan Sakti", "Brigita De Vega" ], "abstract": "Background: Corrective spine surgery is widely accepted for treating severe adolescent idiopathic scoliosis (AIS). Postoperative spinal range of motion (ROM) could be affected after such surgery. In certain populations, such as Muslims, this ROM change can impact daily life, as it may affect the five-times-a-day prayer (Salah). This study aims to assess the influence of spinal fusion (SF) in Adolescent Idiopathic Scoliosis (AIS) during the daily Islamic prayer (Salah). Methods: SF-AIS patients were videoed while performing Salah prayer. The kinematic documentation was assessed and compared to Salah movements of a control group of age-matched Muslim AIS patients, who had not had surgery. The prayer quality changes were subjectively classified into improved, no change/remained, and worsened, according to the Global Perceived Effect (GPE). Functional outcome and pain were assessed by the Scoliosis Research Society Questionnaire Version 30 (SRS-30). Results: Thirty-nine women and five men (mean age±SD: 14.8±2.3 years) met the inclusion criteria, and unoperated AIS patients were used as control (twenty-two women, mean age±SD: 15.32±1.43 years). The prostrations ROM of the SF-AIS group differed significantly from the control group (p<0.05). The GPE of the prayer movement showed improvement in 36.4%, no change in 59.1%, and worsening in 4.5% of the SF-AIS patients. The worsened group had a significantly lower bowing ROM and higher prostrations ROM compared to all groups of prayer quality changes (p<0.05). SRS-30 scores showed good outcomes (function 4.0±0.2, pain 4.2±0.5), along with the overall bowing ROM and prostrations ROM (84.2±12.0o and 53.4±9.6o, respectively). Moreover, a significant moderate positive correlation between the bowing ROM and pain (r=0.417, p=0.007) was also found. Conclusion: Spinal fusion positively affects AIS Islamic patients in maintaining their daily Salah movement, ROM and prayer quality. Prayer quality assessment should be given extra attention as an adjuvant of the SRS-30 questionnaire to evaluate Muslim patients.", "keywords": [ "Adolescent", "Scoliosis", "Adolescent Idiopathic Scoliosis", "Spine", "Spinal Fusion", "Islam" ], "content": "Introduction\n\nCorrective spine surgery is widely accepted to improve the overall quality of life (QOL) for adolescent idiopathic scoliosis (AIS). Maximal deformity correction in achieving the coronal and sagittal balance while retaining the spine flexibility will attain the desired cosmetic look and potentially bring back patient’s lost self-esteem.1,2 A study by Weiss and Goodall, discovered that patients’ ability to perform flexion was reduced by 20–60% following scoliosis correction surgery.3 Meanwhile, physical impairment in any disease corresponds to physiological abnormalities. In AIS, self-esteem is one of the most important aspects that build the patient’s courage to endure a serious high-risk spinal surgery. Likewise, physical function is an important outcome that could portray a meaningful individual’s QOL.4\n\nInterestingly, pain is not the primary reason for patients seeking treatment. Patients can move and perform daily activities without pain before the surgery. Disability, defined as the diminished capacity for everyday activities and gainful employment, is a common cause for a patient seeking medical attention. Nevertheless, pain and disability assessments are highly personal; thus, they may differ among individuals.5,6 Patients also demand information regarding the continuation and possible improvement following corrective surgery, which this study emphasized in performing daily prayer (Salah) for Muslims.\n\nFor decades, the AIS surgical treatment has encompassed pedicle screw fixation to fuse vertebral segments while maintaining growth preservation in the immature AIS. However, the older Harrington instrumentation technique has a higher risk of loose correction.1 Studer et al., studied 157 AIS patients who underwent spinal fusion surgery. Although they reported minimal complications with no revision surgery, they did not relate to the outcome of QOL. Therefore, an additional evaluation of clinical and patients’ health-related QOL as a reliable outcome is needed rather than solely radiologic or curve measurement.5\n\nFurthermore, Helenius et al., learned that in the five years of follow-up, scoliosis correction surgery in AIS could reduce back pain and improve QOL compared to untreated AIS patients. The QOL outcome was similar to healthy patients.1 Therefore, utilizing an objective assessment to measure functional outcomes is essential, in addition to subjective questionnaires. Scoliosis Research Society Questionnaire Version 30 (SRS-30) has been used in many studies to objectively measure the functional outcome of scoliosis patients.6,7 The questionnaire contains 30 questions covering five domains, including 1) function/activity, 2) pain, 3) self-image/appearance, 4) mental health, and 5) satisfaction with management. Nevertheless, existing tools used to assess post-surgery impacts on the activities of daily living (ADL) could not portray an important activity for Muslim patients, for instance, practicing five-times-a-day prayer. In Indonesia, the largest Muslim-populated country, it is essential to have AIS patients fully informed about the possible impact of the post-surgery spinal fusion on their Salah (Islamic prayer).\n\nIslamic prayers consist of a certain number of Rak’ah, which involves several repetitive movements and postures. Every day, Muslims are obligated to perform 119 postures from 7 to 10 years old.8,9 These gave numerous physical and physiological benefits since almost all body muscles and joints are exercised during prayers.9–11 The Salah movements are composed of standing upright, bowing, prostration, and sitting with knees bent; these movements need maximum extension and flexion of the spine.10,11 The flexors and extensors of weight-bearing joints are also involved during various Salah positions.10,11 Islamic prayer has a similar effect as gentle exercises that cause muscles to contract isometrically and isotonically. These movements are beneficial in maintaining joint mobility and elasticity of its surrounding structures.9,10 Although Salah involves continuous gentle muscle contraction and relaxation with perfect harmony and balance, it may be modified depending on certain medical conditions.8,9 AIS patients expect their ADL (including the compulsory prayers for Muslims) to be unaffected following the spinal fusion corrective surgery. To the best of our knowledge, the evaluation of Islamic prayer (Salah) movements in scoliotic patients and the possible impact of corrective spinal fusion on practicing Salah movements has not yet been studied. Therefore, this study aims to primarily assess the influence of spinal fusion (SF) in AIS during the daily Islamic prayer (Salah) by assessing the Salah prayer quality changes following spinal fusion surgery. By comparing the postoperative Salah movement ROM to age-matched Muslim unoperated AIS patients, this study aims to identify whether spinal fusion surgery affects the Muslims’ quality of life (including their prayer quality).\n\n\nMethods\n\nEthical clearance was approved by the Ethical Review Committee of Faculty of Medicine, Airlangga University (institutional review board approval no. 285/EC/KEPK/FKUA/2020). The research team obtained written informed consent from participants before study commencement. All participants consented to be video recorded and photographed during one Salah movement. The participants also consented to having their videos/images and data (excluding name/contact details) published.\n\nThis case-control study was conducted in three orthopedic centers in Surabaya and Yogyakarta, Indonesia, by retrieving data from physical and electronic medical records from 2010 to 2020. The three orthopedic centers were chosen due to their roles as the main referral centers and prime affiliated teaching hospitals in the region. Four research team members (KAI, NRF, CGS, and YMS) screened patients’ data for their eligibility with a predefined form (containing the patient’s personal information such as name and phone number, age during surgery, sex, religion, medical history, pre-operative Cobb angle, post-operative Cobb angle, fusion level, Lenke classification, and follow-up duration). No additional authorization (in addition to the ethical clearance) was required to access patients’ records because the researchers involved in data collection were the relevant orthopedic surgeons in the respective centers. Patients who met the inclusion criteria were telephoned by the authorized research team members (KAI, NRF, CGS, and YMS) to be invited to the research program.\n\nThe inclusion criteria for this study were: 1) patients suffering from AIS alone (without any neuromuscular deficit), who underwent spinal fusion corrective surgery; 2) completed at least two years of follow-up post-surgery; 3) are Muslim; 4) consented to be video recorded during one Salah movement. The surgery was offered by all three orthopedic centers using freehand technique and fluoroscopy assistance for final confirmation. Posterior spinal fusion surgery was conducted by bilateral segmental pedicle screw instrumentation following a combination of vertebral column derotation and selective translation, compression, and distraction maneuver.\n\nEligible patients were invited to the outpatient clinic in all three orthopedic centers and asked to perform one Salah movement, during which they were videoed and photographed by orthopedic residents. The range of movement (ROM) during the Salah were evaluated and analyzed via video recordings and photos using the Kinovea software application (version 0.8.15).12 This tool can track computed points, distances (up to 5m distance from an object), and measure angles. The Salah’s movement consisted of four postures (Figure 1).8,9 The first and second postures, namely standing upright (Qayyam) and bowing (Ruku), comprise a series of movements involving: the standing position (Figure 1A) and bowing (approximately 90 degrees), while the fingers are stretched with two knees clasped firmly, elbows are extended and facing inwards, back is flattened, and the head is not tilted nor bent (i.e., parallel to the back) (Figure 1B). Next, sitting with knees bent (Taashahhud) is performed by kneeling and sitting on the top of the left foot while the right foot rests on the toes. The toes should face forward towards the Qibla (the direction in which the Muslims are praying) (Figure 1C). Finally, prostration (Sajdah) places both palms, knees, feet, forehead, and nose on the floor (Figure 1D). The ROM of standing-to-bow (i.e., bowing ROM) movement was measured by obtaining the angle difference between Figure 1A and Figure 1B. The ROM of the sitting position between two prostrations to prostration (i.e., prostrations ROM) was measured by obtaining the angle difference between Figure 1C and Figure 1D. Figure 2 shows the incorrect Salah movement.\n\nThe position of the Salah movement involves: (A) standing position, (B) bowing, (C) sitting between prostrations, and (D) prostration. The ROM of standing-to-bowing movement was measured by obtaining the angle difference between A and B. The ROM of the sitting position between two prostrations to prostration was measured by obtaining the angle difference between C and D. Image source: authors.\n\n(A) The back is overly bent; (B) the back is too upright. Image source: authors.\n\nThe patients were then asked to fill out the SRS-30 questionnaire as an assessment for their QOL. Among five assessment categories in the questionnaire (pain, function or activity, self-image, mental health, and satisfaction with management), we only utilized two of them (pain and function or activity) as these are the most relevant assessment categories to our study. The score ranges from 1 to 5, with a higher SRS score showing a better outcome. The patients were also categorized based on their subjective perception of their prayer quality changes, which were classified into 1) Improved, 2) No change/remained, and 3) Worsened. This subjective perception is based on global perceived effect (GPE), a commonly used tool to assess patients’ own viewpoint on how much their condition has improved or deteriorated since a particular time point in interest.13 In the present study, the GPE was used to assess the overall situation concerning their prayer movement compared to pre-surgery conditions. To acquire an objective comparison, 22 age-matched Muslim unoperated AIS patients were recruited as a control group.\n\nWe analyzed several outcomes, such as postoperative SRS-30 (pain and functional outcome) and postoperative Salah prayer ROM (bowing and prostrations) of the SF-AIS patients, which were compared to the control group. The patients in the intervention (operated) group were grouped based on their prayer quality changes perception/GPE (improved, no change/remained, worsened) and compared. We also conducted a correlation analysis to identify whether the outcomes (including some variables such as Cobb angle correction and total fused level) affect one another.\n\nAll statistical analyses were performed using SPSS software version 23.0 (IBM, Chicago, USA). The normality test was performed using the Shapiro-Wilk test.14 Discrete data were presented in frequency and percentage (%), while continuous data were presented in mean and standard deviation (mean±SD). When the data were normally distributed, the outcome comparison among the groups was analyzed using the ANOVA parametric test. In contrast, the non-normally distributed data were analyzed using the non-parametric Kruskal-Wallis test.14 Differences between group means were compared using appropriate Post Hoc tests (Post hoc Games-Howell test following ANOVA, post hoc Mann-Whitney test following Kruskal Wallis).15 The correlation analysis among the outcomes was calculated using the Spearman rank test.14 A p-value of <0.05 was considered to be statistically significant.\n\n\nResults\n\nForty-four SF-AIS Muslim patients met the inclusion criteria, consisting of 39 women (88.6%) and five men (11.4%). Moreover, unoperated AIS patients were included in the control group (22 women). The summary of demographics, characteristics, and outcomes of the AIS patients is presented in Table 1. In contrast, a detailed description of the included patients is provided in Extended data.40 Overall, the average SF-AIS patients’ age at surgery was 14.8±2.3 years (range 10-18 years), with an average follow-up time of 4.4±1.9 (range 2-9) years.\n\n* Detailed description is available in Appendix 1 and 2.\n\na Mann-Whitney test p=0.466.\n\nb Fisher’s exact test p=0.160.\n\nc Independent t-test p=0.000\n\nSimilarly, the average age of the control group was 15.32±1.43 (range 13-18) years. Although the preoperative Cobb angles between the two groups differed significantly (67.1±16.2° and 52.3±14.0°, respectively), it does not necessarily reflect a non-homogeneity between them. The nature of this study is to compare the operated and unoperated patients. Those who underwent surgery would generally have a higher degree of Cobb angle, though the clinical significance of 14.9° mean difference is debatable. Moreover, the mean Cobb angle correction of the intervention (operated) group was 34.8±12.8°, with an average total fused level of 11.4±2.8. The highest spinal fusion level was T1, and the lowest was L5, with L3 being the most frequent lowest fused level (31.8%).\n\nDespite the overall relatively good postoperative SRS-30 score (4.0±0.2 for function and 4.2±0.5 for pain), the quality of prayer movement, which was subjectively expressed by the patients as a global perceived effect (GPE), improved only in fifteen women and one man (36.4%) (Table 1). Figure 3 shows the example of Salah movements from a patient who expressed an improved prayer quality following surgery. Whereas the majority of the patients (22 women and four men) reported the same prayer quality compared to preoperative condition (no changes/remained) (59.1%). Two women (4.5%) felt that their prayer movement worsened due to the difficulties in bowing and bending properly. Interestingly, the SRS-30 scores of both worsened patients were reasonably good, i.e., 3.7 and 4.1 for functional outcome and 3.2 and 4 for pain (maximum score of 5) (see Extended data).\n\nROM measurement of the prayer movement: (A) standing position (179.6o); (B) bowing position (86.4o); (C) sitting between prostrations (90.4o); to (D) prostration (40.4o). The patient’s radiographs showed the preoperative (E) and postoperative (F) conditions of the spine. In these radiographs, the preoperative Cobb angle was 50o, and the postoperative Cobb angle was 18o (Cobb angle difference: 32o). Image source: authors.\n\nThe mean postoperative bowing ROM in SF-AIS patients was lower than the control group (84.2±12.0°, range 26-101° vs. 87.8±9.3°, range 71.5-106.4°, respectively) (Table 2 and Extended data). One SF-AIS patient (in the “worsened” group) had lower bowing ROM than the control group. Moreover, the mean prostrations ROM in SF-AIS patients was also lower (53.4±9.6°, range 39.6-100°) compared to the control group (58.5±4.7°, range 49.2-66.4°). Twelve SF-AIS patients (five in the “improved” group, seven in the “no change” group) had lower prostrations ROM compared to controls. Interestingly, there was one SF-AIS patient who complained of an overall “worsened” prayer quality (Patient 43), but their bowing and prostrations ROM were within the normal range (Figure 4). Moreover, the other patient who also reported “worsened” prayer quality (Patient 44) had a strictly limited bowing ROM but excessive prostrations ROM instead (26° and 100°, respectively) (see Extended data). None of the operated patients had revision surgery or complication.\n\n* Statistically significant (p<0.05).\n\n(A) The patient’s bowing movement ROM was within the normal range: (178o to 73o), but she experienced a worsened prayer quality because of pain. (B) She can perform sitting motion between two prostrations and prostration as good as normal (108o to 45o) but accompanied by pain. (C) Preoperative radiograph showing Cobb angle 45o. (D) Postoperative radiograph showing Cobb angle 20o (Cobb angle difference: 25o). Image source: authors.\n\nWe compared bowing and prostration ROM between SF-AIS patients and the control group (Table 2) and the outcomes across the three GPE prayer quality (improved, no change/remained, worsened) groups (Table 3). The prostrations ROM of the SF-AIS group differed significantly from the control group (p=0.000). However, the bowing ROM differences between the SF-AIS and control groups were insignificant (p=0.366). Although the Cobb angle correction was lower and the total fused levels were higher in the “worsened” group than the “improved” and “remained” group, their differences were insignificant (p=0.678 and 0.115, respectively). Similarly, the “worsened” group showed worse SRS-30 function and pain than the other two groups, but the differences were insignificant (p=0.253 and 0.700, respectively).\n\na Analyzed using ANOVA.\n\n* Statistically significant (p<0.05).\n\nIn general, the “remained” group had the highest bowing ROM while the “worsened” group had the lowest (50.5±34.6°) (Table 3). Surprisingly, the “worsened” group showed the highest prostrations ROM compared to the other groups of prayer quality changes (as high as 81.7±26.0°), with a significant mean difference (p=0.040). The pairwise comparison post hoc tests (Tables 4 and 5) showed that the “worsened” group had a significantly lower bowing ROM and higher prostrations ROM compared to all groups of prayer quality changes.\n\n* Statistically significant (p<0.05).\n\n* Statistically significant (p<0.05).\n\nThe correlation analyses (Table 6) showed that the Cobb angle correction and total fused levels did not correlate with either the quality of life (SRS-30 function and pain) or Salah ROM (bowing and prostrations ROM). Likewise, we found that SRS-30 function and pain did not correlate significantly with Salah ROM, except for bowing ROM. Our study showed a significant moderate positive correlation between bowing ROM and pain score (r=0.401, p=0.007).\n\n* Statistically significant (p<0.05).\n\n\nDiscussion\n\nPosterior spinal fusion is a primary surgical treatment for adolescent idiopathic scoliosis, which led to QOL improvement.1,3,5,12,13 A Bayesian meta-analysis study on the effectiveness and safety of surgical interventions for treating AIS revealed that posterior spinal fusion is a primary surgical treatment due to the lower complication rate.16 Our present study showed surgical outcomes following single-stage reconstruction to objectively measure values for the quality of Islamic prayer (Salah) range of motion (ROM) following spinal fusion in adolescent idiopathic scoliosis (AIS). The world’s Muslim population as of 2021 is estimated as high as over 1.9 billion people, making 24.7% of the world’s total population today.17 This number is projected to increase at a rate of 1.5% annually. By 2030, a study approximated that Muslims will make 26.4% (2.2 billion people) of the world’s total population.18 Muslims inhabit almost all countries (over 70 countries) globally, with Asia-Pacific and Africa being the largest populated regions (60% and 35%, respectively). As the country with the single largest Muslim population, Indonesia is home to over 242 million Muslims (making over 87% total population of the country and 12.5% world’s Muslim population) in 2021.18,19 In Indonesia, the scoliosis prevalence in secondary school screening was 2.9%.20 Indeed, most Indonesian AIS patients are presumably Muslims. Thus, they will need all the information about the postoperative outcomes for their lifelong quality of life. However, the quality of Islamic prayer practiced regularly (five times a day) concerning spinal ROM as a crucial part of practicing the whole serial movement is not covered by all generic surgical outcome evaluations for health-related QOL.\n\nIn general, we found that spinal fusion surgery did not negatively affect the Salah prayer quality, as 95.5% of the operated patients reported improved or similar prayer quality as the preoperative condition. The quality of life, including daily prayers five times a day, could improve after the surgery. Although the ROM improvement may only be modest, spinal fusion surgery still enhances patients’ quality of life.21 Only two patients (4.5%) reported a worsened prayer quality following surgery, one of whom showed a somewhat extreme value of bowing and prostrations ROM (26° and 100°, respectively). There are several possible factors contributing to this phenomenon.\n\nFirstly, despite longer fused levels (15.0±1.4), the Cobb angle correction in the “worsened” group is less than in the other groups (28.0±4.2°), which might partly explain the restricted bowing ROM. A study by Cho et al., reported that longer fused levels were associated with significantly better Cobb angle correction than shorter fused levels (72% and 39%, respectively, p=0.001).22 Secondly, the excessive prostration ROM is probably due to the hyperextended lumbar condition. Longer fused levels could restore lumbar lordosis better; however, hypercorrection might lead to lumbar hyperextension.23 Thirdly, the patient could only make a sitting position between the two prostrations and could not proceed to the prostration movement. Thus, the prostration ROM might have seemed greater.\n\nDuring the bowing movement, one should maintain the lower back flexed, followed by resting the forehead gently on the floor (i.e., prostration movement), activating postural neck muscles to control the neutral head position when lowering down and lifting it from the floor.11 The stretch felt along the spine as the individual curls the torso over the legs also creates a space between the dorsal surfaces of the vertebra, aiding spinal distraction, allowing neural glides and nerves lengthening.11 Our findings showed insignificant differences (p≥0.05) in bowing ROM between treated AIS patients in comparison to the controls but not prostrations ROM (Table 2), implying that bowing ROM following surgery is comparable to the unoperated AIS patients. This distinct finding might be caused by the difference in muscles used during the two movements. Ruku’ (bowing) uses neck extensors (NE), deltoid (DT), triceps brachii (TB), and rectus abdominal (RA) muscles; in contrast, Sajdah (prostration) uses sternocleidomastoideus (SCM), trapezius (TRP), biceps brachii (BB), and erector spinae (ES) muscles.21 Since the ES and other paraspinal muscles are retracted for long hours during surgery, ischemia may occur and cause degeneration.24 Nonetheless, further studies might be needed to thoroughly understand the differences in each specific muscle used in Ruku’ and Sajdah to understand the effect on muscle after spinal fusion surgery.\n\nInterestingly, we obtained a positive correlation between the bowing ROM and pain (Table 6). During Ruku’s (bowing) movement, the surgical wound along the spinal axis will be stretched, causing pain and restricted motion. This finding needs to be informed to the AIS Muslim patients because their prayers and QOL might be affected due to pain. Moreover, Bastrom et al., who investigated the prevalence of postoperative pain in AIS and its association with preoperative pain, reported a 7% prevalence of unexplained postoperative pain within two years of follow-up. The unexplained pain was significantly correlated with preoperative pain.25 Likewise, other studies have confirmed that increased baseline pain and psychological factors such as anxiety and helplessness are significant factors contributing to persistent pain (months to years) in 36-41.8% of SF-AIS patients, although gene expression HLA-DRB3 and surgery duration may also play a role.26–28 Altogether, proper patient education is required since patients expect less pain and return-to-normal activities after corrective surgery.\n\nThe results of this study showed that the scoliosis surgical outcome indicators (SRS-30; function and pain domain) in the three orthopedic centers were within good scores for all patients. The functional outcome and pain after posterior spinal fusion in our study were comparable to the SRS score reported by existing literature.7 The SRS-30 questionnaire score for the normal population ranged from 4.1–4.6, while our patients’ score was 4.0±0.2 for function and 4.2±0.5 for pain. However, the GPE, which values the patients’ perception about the quality of their prayer’s movement, seemed to be not affected by SRS-30. Although the patients who reported a worsened prayer quality showed an overall lower SRS-30 score, the differences were insignificant (Table 3). This finding could imply that the SRS-30 score (especially function and pain domain) might have different aspects for particular daily activities in a certain population. The quality of prayer has not been reflected in the SRS questionnaire, which warrants further consideration for orthopedic surgeons in explaining to Muslim scoliotic patients.\n\nPatient number 44, who complained of pain in prostration posture while praying, scored 4 for pain, and the ROM was very limited compared to normal control. Patient 43 scored 3.2 for pain; nonetheless, the ROM for praying was within the normal range (Figure 4). This was possibly due to her determination to pray as perfectly as possible to gain “normal” ROM, reflecting her coping mechanism. Several studies have reported that spinal fused-AIS patients (SF-AIS) have adapted to the fused condition to maintain the demanded posture in performing particular physical activities.29,30 A case-control study by Kakar et al., which investigated the kinematics of the spine and lower extremity during high-effort running, found that SF-AIS patients expressed a significantly excessive lower trunk (by 6.1°) and pelvis (by 6.3°) segmental axial rotation while running compared to healthy controls but reduced ankle plantarflexion (by 9.2°) in the support phase; implying their compensatory mechanisms are possibly due to increased lumbar muscle stiffness and reduced proprioception.29 Another study by Holewijn et al., who performed gait analysis on SF-AIS at increasing walking speeds (0.45 to 2.22 m/s), revealed that transverse plane thoracic-pelvic ROM was significantly diminished following spinal fusion surgery, with higher walking speeds showing more obvious differences. However, the lower body ROM, step length, and cadence remain unaffected, and SF-AIS patients could still walk with somewhat unaltered spatiotemporal parameters.30\n\nMany studies about the lumbar stiffness as the side effect of the spinal fusion in AIS have reported that the frontal plane of thorax-pelvis mobility improved, the volitional weight shifting that gave them postural control also improved, and the SRS score did not correlate with the outcome motion of the fused level.31–33 However, these phenomena could not be covered by SRS-30 and its variants. The evaluation of scoliosis treatment comprises the surgical aspects, radiology aspects, and the most important is the quality of life (function, pain, and deformity).7,34 The outcome instruments must be proven reliable, standardized, and validated to be applicable worldwide.35 The generic instruments used to assess health-related quality of life (HRQL) are the SF-36 questionnaire, SRS 30, SRS 22, and the EuroQol5D instrument.7 In spite of that, previous studies have reported that it is preferable to assess the condition of specific populations with certain needs.30,35,36 As the SRS questionnaire and its variants could not fully portray important aspects of physical functioning such as mobility in praying for individuals with AIS, we suggest orthopedic surgeons incorporate prayer quality assessment as an adjuvant of QOL measurement in Muslim patients.\n\nOur study found no significant nor strong correlation between Cobb angle correction and total fused level with prayer quality changes (Table 3), quality of life (SRS-30 function and pain), and Salah ROM (bowing and prostrations) (Table 6). To our knowledge, we are the first to identify whether curve correction and total fused levels are associated with Muslim prayer quality and Salah ROM. It seems that in the sagittal plane, the spine-pelvic-hip alignment following spinal fusion is well achieved regardless of the degree of curve correction and total fused level; hence, they are not associated with the ROM of Salah movements. Moreover, our findings are in agreement with previous studies that have reported the irrelevance of Cobb angle correction degree with postoperative SRS-30 function and pain.6,37 A study by Ghandehari et al., revealed that the percentage of radiographic correction was positively correlated only with the total SRS-30 score (r=0.52, p<0.001) and the satisfaction domain (r=0.386, p=0.026) but not with the function and pain domains.6 Likewise, Chaudhary et al., reported similar findings (p-values of SRS-30 function and pain correlation analyses with curve correction: 0.688 and 0.453, respectively).37 Moreover, our results showed that total fused levels were not associated with function or pain. Likewise, existing literature has reported that despite resulting in better ROM, fewer fusion levels did not correlate with SRS-22 function and pain in 2-10 years of follow-up.2,38,39\n\nRendering the limitation of our study in which the samples were relatively small, using patient’s perception (GPE), using a newly proposed standardized prayer movement ROM evaluation, not to mention the possibility of incorrect landmark identifying when measuring the ROM, we suggest that future studies should address these issues. Moreover, spine surgeons in largely Muslim countries should start evaluating the impact of spinal fusion on the Salah movement as part of the daily activity functional outcome. However, we believe that we are the first to assess the Islamic prayer ROM following spinal fusion surgery and attempt to identify whether spinal fusion surgery affects the Muslims’ quality of life (including their quality of prayer).\n\n\nConclusion\n\nOur study found that spinal fusion positively affects AIS Islamic patients in maintaining their daily Salah movement ROM and prayer quality. Orthopedic surgeons should consider incorporating prayer quality assessment as an adjuvant of the SRS-30 questionnaire to evaluate Muslim patients’ specific functional outcomes and quality of life.\n\n\nData availability\n\nFigshare: The Impact of Spinal Fusion of Adolescent Idiopathic Scoliosis in Salah (Islamic Prayer) Movement. DOI: https://doi.org/10.6084/m9.figshare.20380635.40\n\nThis project contains the following underlying data:\n\n• Appendix 1. docx (A detailed description of the AIS patients’ demographics, characteristics, and outcomes).\n\n• Appendix 2. docx (A detailed description of demographics and characteristics of the control group (i.e., age-matched unoperated AIS patients).\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).", "appendix": "References\n\nHelenius L, Diarbakerli E, Grauers A, et al.: Back Pain and Quality of Life after Surgical Treatment for Adolescent Idiopathic Scoliosis at 5-Year Follow-up: Comparison with Healthy Controls and Patients with Untreated Idiopathic Scoliosis. J. Bone Jt. Surg. - Am. 2019; 101(16): 1460–1466. Publisher Full Text\n\nFan H, Wang Q, Huang Z, et al.: Comparison of functional outcome and quality of life in patients with idiopathic scoliosis treated by spinal fusion. 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PubMed Abstract \| Publisher Full Text\n\nMarks M, Newton PO, Petcharaporn M, et al.: Postoperative segmental motion of the unfused spine distal to the fusion in 100 patients with adolescent idiopathic scoliosis. Spine. 2012; 37: 826–832. Publisher Full Text\n\nBago J, Climent JM, Pérez-Grueso FJS, et al.: Outcome instruments to assess scoliosis surgery. Eur. Spine J. 2013; 22(Suppl 2): S195–S202. PubMed Abstract \| Publisher Full Text\n\nDu C, Yu J, Zhang J, et al.: Relevant areas of functioning in people with adolescent idiopathic scoliosis on the international classification of functioning, disability and health: The patients’ perspective. J. Rehabil. Med. 2016; 48(9): 806–814. PubMed Abstract \| Publisher Full Text\n\nAlamrani S, Rushton A, Gardner A, et al.: Outcome measures evaluating physical functioning and their measurement properties in adolescent idiopathic scoliosis: A protocol for a systematic review. BMJ Open. 2020; 10(4). PubMed Abstract \| Publisher Full Text\n\nChaudhary RK, Kaucha D, Banskota B, et al.: Correlation between Radiological Outcome and Health Related Quality of Life after Posterior Spinal Fusion for Adolescent Idiopathic Scoliosis. J. Nepal Health Res. Counc. 2021; 19(1): 44–47. PubMed Abstract \| Publisher Full Text\n\nUehara M, Takahashi J, Ikegami S, et al.: Correlation of Lower Instrumented Vertebra with Spinal Mobility and Health-related Quality of Life after Posterior Spinal Fusion for Adolescent Idiopathic Scoliosis. Clin. Spine Surg. 2019; 32(7): E326–E329. PubMed Abstract \| Publisher Full Text\n\nOhashi M, Bastrom TP, Marks MC, et al.: The Benefits of Sparing Lumbar Motion Segments in Spinal Fusion for Adolescent Idiopathic Scoliosis Are Evident at 10 Years Postoperatively. Spine. 2020; 45: 755–763. Publisher Full Text\n\nIrianto KA, Firas NR, Binti CGS, et al.: The Impact of Spinal Fusion of Adolescent Idiopathic Scoliosis in Salah (Islamic Prayer) Movement. Extended Dataset: figshare.2022. Publisher Full Text Reference Source" }	[ { "id": "156368", "date": "20 Feb 2023", "name": "Yasser Allam", "expertise": [ "Reviewer Expertise spine 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\nIt would be interesting to include the whole 5 items of SRS 30 in this study and not only pain and function.\n\nControl group degree of scoliosis is less than study material. It would be better if the control group has nearly the same degree of scoliosis as patient group.\n\nIn Fig. 3, it was mentioned that the patient had got 50° scoliosis and in Fig. 4, 45° scoliosis which from my point of view can be treated conservative. what were the measures for patient selection i.e. degree of scoliosis\n\nI would prefer to write muscle fibrosis instead of muscle degeneration (4th paragraph in discussion)\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "9419", "date": "24 Jun 2024", "name": "komang irianto", "role": "Author Response", "response": "Dear Dr. Yasser Allam, Thank you for your kind review of this manuscript, which has been very helpful in improving the manuscript. We also thank the reviewer for the careful reading of our text. Here we present our reply to each suggestion separately as the following: 1. \"It would be interesting to include the whole 5 items of SRS-30 in this study and not only pain and function.\" Answer: We only utilized two of five assessment categories in the SRS-30 questionnaire (pain, function or activity, self-image, mental health, and satisfaction with management). The self-image, mental health, and satisfaction items are not directly relevant to our study. This study focuses on the daily Islamic prayer function (Salah activity), which needs a series of complex movements involving the spine, hip, and knee. The prayer activity itself is believed ought to be performed with the correct movements as mandated by their religion within the correct timeframe (5 times a day at certain hours), which makes patients worry if they cannot perform it after corrective surgery. Hence, we deem the two chosen items (pain and function) to be the two most critical and relevant tools to evaluate patients’ quality of life relating to their ability to fulfill their religious obligation. However, we acknowledge the reviewer’s suggestion as our limitation. We have added the reviewer’s suggestion in our limitation section: “Another drawback is that we only assessed two items of the SRS-30 questionnaire (pain and function), as we deem the most critical evaluation tools for performing the Islamic Salah prayer activity. Future studies should attempt to assess all five items of SRS-30 for a more comprehensive evaluation.” 2. \"The control group's degree of scoliosis is less than the study material. It would be better if the control group has nearly the same degree of scoliosis as the patient group.\" Answer: We thank the reviewer for their comment. We also realized this as the limitation of this study, and we have previously justified this in the Results section, paragraph 2, as follows: “Although the preoperative Cobb angles between the two groups differed significantly (67.1±16.2° and 52.3±14.0°, respectively), it does not necessarily reflect a non-homogeneity between them. The nature of this study is to compare the operated and unoperated patients. Those who underwent surgery would generally have a higher degree of Cobb angle, though the clinical significance of 14.9° mean difference is debatable.” However, based on the reviewer’s suggestion, we have added this in our limitation section as follows: “Moreover, due to the nature of this study, the control group had a lesser Cobb angle value. This difference is unavoidable because the larger curves group would most unequivocally be offered surgery rather than conservative treatment; hence, this condition has become a natural limitation of this study.” 3. \"In Fig. 3, it was mentioned that the patient had got 50° scoliosis, and in Fig. 4, 45° scoliosis which from my point of view can be treated conservatively. what were the measures for patient selection i.e. degree of scoliosis\" Answer: We thank the reviewer for their meticulous review. There are several considerations for the treatment choice (explained below), which is specific for each patient. We have added our surgery indication in the Method section: “As for the surgical indication, we follow the indication outlined by the Scoliosis Research Society (SRS), namely when the curves exceed 45°-50°. Patients with less than 45° curvature are generally treated with conservative treatment, unless in skeletally immature patients who are at high risk of developing progressive deformity. In the “gray zone” cases (i.e., 45°-50°), the clinical complaints (pain, diminished capacity for activities) along with psychological state play a major role in determining the treatment choice. However, other contributing factors, such as the patient’s socioeconomic condition, willingness to undergo a surgical procedure, and family support, may also affect the final decision of treatment choice.” 4.\"I would prefer to write muscle fibrosis instead of muscle degeneration (4th paragraph in discussion)\" Answer: We agree with your opinion. We have replaced the degeneration with \"fibrosis\"." } ] } ]	1	https://f1000research.com/articles/11-1054
https://f1000research.com/articles/13-323/v1	23 Apr 24	{ "type": "Brief Report", "title": "Challenges of recruitment processes to a randomized dietary trial in irritable bowel syndrome", "authors": [ "Bodil Roth", "Bodil Ohlsson", "Bodil Roth" ], "abstract": "Background Irritable bowel syndrome (IBS) is common with a global prevalence of 4%. Dietary regimes with a low content of fermentable oligo-, di-, and monosaccharides and polyol (FODMAP) or a starch- and sucrose-reduced diet (SSRD) have proven to be efficient. The aim of the present study was to describe the recruitment process for a randomized dietary trial with low FODMAP or SSRD for 4 weeks with a follow-up period of 5 months.\n\nMethods The County of Skåne, with 1,41 million inhabitants, was used as a base to perform a dietary trial in which IBS patients, age 18-70 years, were randomized to either low FODMAP or SSRD for 4 weeks. The estimated number of IBS patients in the actual age span was approximately 32,000. The trial was announced through lectures, letters to all primary healthcare centers (n=203), social media (two campaigns), and invitations to IBS patients identified in medical records (n=744).\n\nResults Three referrals arrived from the healthcare system, 17 patients contacted the investigators in person after receiving information from their healthcare center, and four patients contacted the investigators after recommendations from friends. Of these, 14 were enrolled in the study. From social media, 218 names were delivered, of which 93 fulfilled the study criteria and were willing to participate when contacted by the investigators (42.7%). Of the 3587 identified IBS patients in medical records in close proximity to the hospital, 744 were randomly contacted. Forty-eight patients (6.5 %) were willing to be included in the study. Thus, 155 patients with IBS were included in this study.\n\nConclusions The inclusion rate for dietary intervention was very low considering the large population informed about the study. Announcements on social media seem to be the best way to recruit patients for intervention.\n\nTrial registration NCT05192603, 29/11/2021, ClinicalTrials.gov. The PRS URL is https://register.clinicaltrials.gov", "keywords": [ "dietary habits", "dietary intervention", "irritable bowel syndrome", "recruitment process" ], "content": "Background\n\nIrritable bowel syndrome (IBS) is the most common functional gastrointestinal disorder (FGID), with a global prevalence of 4% according to Rome IV criteria.1,2 The prevalence of any functional gastrointestinal symptom is 40% in the general population.2 Apart from bowel symptoms, extraintestinal symptoms and comorbidities are common, with a great impact on quality of life.3,4 Many patients with IBS do not seek medical care, but between 10% and 70% of patients are estimated to attend primary care; the prevalence depends on the country.5 Individuals who met the Rome IV criteria for any FGID were more likely to have visited healthcare at any time point than individuals without these diseases.2 Taken together, FGID/IBS is the most common gastrointestinal entity, leading to the most frequent healthcare visits.6 Due to the great healthcare burden, these diseases lead to both direct and indirect costs for the health service and society.7,8\n\nThe effect of drugs in FGID/IBS is moderate, with a therapeutic gain of 10%–15% over placebo.9 Most FGID patients report food-related symptoms,10 leading to dietary changes in approximately half of the patients due to their symptoms.11 Accordingly, the most efficient treatment for IBS is dietary accommodation, and 50%–75% is improved by a low content of fermentable oligo-, di-, and monosaccharides and polyol (FODMAP).12 A 70% effect on gastrointestinal symptoms has recently been described for a starch- and sucrose-reduced diet (SSRD) in IBS, with improved dietary intake and a healthier endocrine profile.13–15 Therefore, we aimed to perform a dietary intervention to compare low FODMAP diet and SSRD diets. However, motivating individuals to change their dietary habits is challenging. The aim of the present brief report was to describe the recruitment and inclusion processes of dietary interventions for IBS.\n\n\nMethods\n\nThe study was an open randomized, non-inferior trial, with two parallel groups, performed at the Department of Internal medicine, Skåne University Hospital. Malmö, Sweden. The study was registered at ClinicalTrials.gov (NCT05192603), date 29/11/2021. A dietary intervention was given for 4 weeks, followed by another 5 months when the participants were allowed to eat whatever they preferred, before a final appointment. Study questionnaires, diary books, blood samples and fecal samples were collected at each appointment and saved for later analyses. The primary study outcome was to measure the responding rate concerning gastrointestinal symptoms, and secondary outcomes to measure mechanisms behind the response.\n\nThe study inclusion criteria were diagnosis of IBS with abdominal pain at least weekly with a total irritable bowel syndrome severity scoring system (IBS-SSS) > 175, age 18–70 years, and ability to understand the Swedish language. The exclusion criteria were diagnosis of celiac disease, inflammatory bowel disease (IBD), bile acid malabsorption, infectious gastroenteritis, severe gastrointestinal surgery in the past, or enteric dysmotility. Participants were excluded if they had alcohol or drug abuse, severe food allergy, current eating disturbances, or any other severe organic or psychiatric disease. Pregnancy or a low FODMAP diet, low carbohydrate and high fat diet (LCHF), gluten-free diet, or vegan diet were also excluded.\n\nThe recruitment process was initiated 13/12/2021 and was ongoing throughout the study period until study recruitment was completed 13/09/2023. The first participant was allocated 03/03/2022. The study information was directed to the entire county of Skåne, with 1,41 million inhabitants. Divided into 5-year age classes, this rendered 793,914 inhabitants between 20 and 69 years old by the end of 2021.16 By calculating the prevalence of FGID (39%) and IBS (4%) in Sweden,2 the County of Skåne should have 309,626 subjects with FGID and 31,757 subjects with IBS according to Rome IV in the age range of 20–69 years.2 Owing to the inclusion criteria of 18–70 years, more IBS patients were expected to be available.\n\nIn all information distributed, it was clearly stated that all participants were randomized to a dietary treatment, either in the form of low FODMAP or SSRD.12,13 Furthermore, information on the study design and practical issues is provided.\n\nLectures\n\nThe principal investigator (PI) (BO) held two lectures at regular meetings for researchers from primary healthcare, representing several healthcare centers. The PI also held a digital lecture for primary healthcare in the whole region with invitations to all general practitioners (GP), as well as a physical lecture at the Department of Internal Medicine, Skåne University Hospital. Afterwards, the lecture was made available on the website of Region Skåne. The head of the dieticians in the region was informed about the study and forwarded the information to all dieticians. All dietitians in the environment of the PI were informed in person. The head of the Department of Gastroenterology was informed about the study, and a recommendation was stated orally and written at the Department, that all IBS patients admitted to the Department should be informed about the study. A physical lecture was also held for a local working group within the Region Skåne, working with the implementation of healthy lifestyle habits.\n\nAnnouncements\n\nAn information letter was sent to all primary healthcare centers (PCC) in the region (n=203). The letter contained study information and several study leaflets. The leaflets contained brief written information about the study, including contact details to the investigators. The staff at the centers were encouraged to distribute the leaflets in waiting rooms.\n\nA contract was signed with Trialy AB, Gothenburg, Sweden to recruit participants through social media from Region Skåne. A questionnaire was constructed in which the interested individuals had to reply to a few questions to test suitability for entrance into the study (Table 1). If individuals were not suitable according to any of the questions, they were automatically excluded from the system. However, they were able to complete the questionnaires as many times as they wanted. Two recruitment periods were performed: one during the summer/autumn of 2022, and one during the winter of 2022.\n\nPersonal invitations\n\nA data search was performed in March 2022 at the Clinical Studies Sweden-Regional node in Southern Sweden. The search was performed on all medical records from the County of Skåne for patients who had received any of the diagnoses K58.1, K58.2, K58.3, and K58.8 during 2019–2022. Initially, an information letter was sent randomly to the patients, and after a couple of weeks, the subjects were asked whether they were interested in participating. Because of the time-consuming routine with a few replying to the phone call and a few who wanted to participate, the information letter was changed, and the subjects were encouraged to call or email the investigators whether they were interested in participating in the study.\n\nEstimation of sample size\n\nThe power calculation was based on non-inferiority, where a new treatment for IBS (SSRD) was tested against standard treatment (low FODMAP). The primary outcome was the responder rate (RR = ∆Total IBS-SSS ≥ −50), which was assumed to be 65% in both treatment groups. A difference in responder rate as large as 20% in favor of the standard treatment low FODMAP would allow the new treatment SSRD to be non-inferior. The sample size was based on 80% power, a one-sided confidence level of 97.5%, and an expected loss to follow-up of 10% to confirm non-inferiority was calculated to be 100 patients in each group. Since very few of the included patients were lost to follow-up, a new contact was made with the statistician. After discussion, the study was concluded in September 2023, although only 155 and not 200 patients were included.\n\n\nResults\n\nReferrals from healthcare staff\n\nOne written referral from a private healthcare center and two phone call referrals from the Department of Gastroenterology were obtained. One patient from the Department of Gastroenterology had bile acid malabsorption, but the other two were eligible for inclusion (Figure 1).\n\nSelf-referrals from patients\n\nEight patients contacted the investigators because they were encouraged to participate by a dietician or GP at the PCC. Three of these were excluded because they fulfilled any of the exclusion criteria for the study (Figure 1). Nine patients contacted the investigators because of information leaflets in the waiting room at their PCC, and four patients after recommendations from friends or relatives. Some patients fulfilled any of the exclusion criteria (Figure 1).\n\nAdvertisements in social media\n\nTwo different recruitment campaigns on social media were performed by the professional company Trialy. The contract was to recruit 100 patients at each campaign, who were willing to participate in the study and who fulfilled the inclusion criteria without any of the exclusion criteria. The 218 assigned patients were contacted by phone by one of the investigators (BR). Upon calling, 66 participants did not answer or declined to participate, whereas 12 fulfilled any of the exclusion criteria. After exclusion, 140 patients (64.2%) were willing to participate in the study (Figure 1).\n\nMedical records\n\nFrom the medical records, 8999 IBS patients were identified from the whole county, and 3587 patients in the age group of 18–70 years in the area close to Malmö. Of these 3587 cases, 744 were randomly selected and contacted through a written letter to be informed about the study and contact details to both investigators. Of them, 58 (7.8%) were willing to participate in the study.\n\nPatients who were willing to participate in the study were randomized to either the low FODMAP or SSRD group by block randomization. After randomization, 53 patients did not attend the first meeting. After new contact, they declined participation if they answered the phone call. Three patients were excluded at the first visit because they did not fulfill the inclusion criteria of a total IBS-SSS score of 175, one suffered from cognitive failure, one suffered from severe heart disease with bile salt malabsorption, and one suffered from microscopic colitis. Finally, 155 patients with IBS (72.4% of randomized cases) underwent dietary intervention (Figure 1). This means an inclusion rate of 42.7% in the group recruited from social media and 6.5% in the group recruited from the medical records.17 Reporting guidelines for the study are available.18\n\nEight participants interrupted the intervention because they thought it was too difficult to adhere to the diet or because the symptoms were exaggerated by the diet. Of these, four were recruited from social media and four from medical records. One participant interrupted the intervention due to acute diverticulitis, one due to personal troubles, and one did not start the dietary intervention (Figure 1).\n\nDuring the consultations with the patients, both during the recruitment and inclusion processes, it was found that many patients had low knowledge about nutrition, the benefits of a healthy diet, or the risks associated with malnutrition. These dialogues were not formally structured or analyzed.\n\n\nDiscussion\n\nThe main finding in the present study was the great challenge in motivating patients with IBS to participate in a dietary intervention, although all patients were offered one of two efficient diets.12,13\n\nSeveral systematic reviews and meta-analyses have shown that a low FODMAP diet is efficient in IBS, with a marked improvement in global and specific gastrointestinal symptoms.19,20,21 However, quality of life has not improved in parallel with symptom reduction.21,22 The reason for unaffected quality of life may be the symptom burden of comorbidity and necessity of food avoidance.6,19,22 Despite evidence of the beneficial roles of dietary modifications in several studies, it is a great adjustment for individuals in daily life to change dietary habits. This may have an impact not only on themselves but also on their families, friends, working routines, and social life. It costs a lot of motivation to make pervasive changes to daily routines. Adherence to a strict diet may have equal or more adverse effects on their lives than bowel symptoms.22\n\nSince dietary risk factors largely contribute to diseases and death worldwide,23 work to support and improve the dietary habits of the population is extremely important to reduce the disease burden and healthcare expenses.24 Poor dietary intake of IBS has been reported in several studies, with a lower nutritional intake than recommended.15,25 This may have been due to dietary changes and food avoidance. However, SSRD reduced the symptoms in parallel with healthier dietary habits,13,15 which was not observed after low FODMAP.25 Thus, food avoidance does not necessarily mean impaired nutrient intake. A systematic review reported lower vitamin D levels in patients with IBS than in healthy controls.26 Accordingly, vitamin D supplementation has been shown to improve IBS symptoms.22,26 This suggests that some of the effects of low SSRD may be due to the elevation in vitamin D levels and other micronutrients.15\n\nSeveral studies have demonstrated that a high proportion of the population does not engage in health-promoting behaviors.27 This may be partly due to the lack of knowledge about the consequences of different lifestyle habits. The great disease burden of IBS on the healthcare system,7,8 in parallel with the difficulties in motivating patients to change their lifestyle habits to a healthier diet, rendering fewer symptoms,19,20,21,27 is a challenge for the system. Although healthcare centers were informed about the study through lectures and written letters, only a few referrals came from this resource. This may be because physicians and dieticians informed about the study, but the patients declined the opportunity for referral. Several methods have been used to increase awareness of healthy behaviors. Motivating interviewing is a method practiced in primary healthcare, which may be useful for achieving behavioral changes.24,28 It is also important to recommend dietary regimes that are simple to follow with a minimum of interference with daily life to increase quality of life in parallel with reduced symptoms and health risks.\n\nWe conclude from the current study that announcements on social media were the most efficient recruitment process.17 Still, more than one-third of the initially assigned patients were unwilling to participate when they were contacted by the investigator, and one-third of the randomized participants did not show up at the appointment for inclusion. Hiring a company for announcements on social media is expensive. However, it seems to be the most superior method for recruiting patients and is the least time-consuming for investigators. Furthermore, those included in this recruitment arm were motivated and interested in dietary habits. However, there is a risk that recruitment from social media attracts those who are already aware of dietary factors, and those who have the most benefits of dietary improvements are never included. When inviting patients randomly or consecutively, participants may be more representative of the patient group.\n\nIn conclusion, despite clear evidence of successful dietary programs, it is difficult to recruit IBS patients for dietary interventions/treatments. Announcement through social media seems to be the most efficient way to recruit patients for dietary interventions.\n\nThis study was conducted in accordance with the Declaration of Helsinki. Thus, all reported research has been conducted in an ethical and responsible manner and is in full compliance with all relevant codes of experimentation and legislation. This study was approved by the National Swedish Ethical Review Authority (https://etikprovningsmyndigheten.se/en/), 2021-05407-01, date of approval 10/11/2021. All participants provided written informed consent before participating in the study. The participants gave written consent for the inclusion of material pertaining to themselves in publications and acknowledged that they could not be identified via the paper.\n\n\nAuthors Contribution\n\nBO and BR were responsible for study design and data acquisition. BO was responsible for statistical analysis, interpretation of data, and drafting of the manuscript. BO obtained funding. Both the authors contributed to the manuscript and approved the submitted version.", "appendix": "Data availability\n\nFigshare: Underlying data for ‘Challenges of recruitment processes to a randomized dietary trial in irritable bowel syndrome’, https://doi.org/10.6084/m9.figshare.25562292. 17\n\nFigshare: CONSORT checklist for ‘Challenges of recruitment processes to a randomized dietary trial in irritable bowel syndrome’, https://doi.org/10.6084/m9.figshare.25399030. 18\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\n\nAcknowledgements\n\nThe staff at the Clinical Studies Sweden- Regional node in Southern Sweden and Trialy are acknowledged for their help in recruiting patients.\n\n\nReferences\n\nLacy BE, Mearin F, Chang L, et al.: Bowel disorders. Gastroenterology. 2016; 150: 1393–1407.e5. Publisher Full Text\n\nSperber AD, Bangdiwala SI, Drossman DA, et al.: Worldwide prevalence and burden of functional gastrointestinal disorders, results of Rome foundation global study. Gastroenterology. 2021; 160: 99–114.e3. PubMed Abstract \| Publisher Full Text\n\nParé P, Gray J, Lam S, et al.: Health-related quality of life, work productivity, and health care resource utilization of subjects with irritable bowel syndrome: baseline results from logic (longitudinal outcomes study of gastrointestinal symptoms in Canada), a naturalistic study. Clin. Ther. 2006; 28: 1726–1735. PubMed Abstract \| Publisher Full Text\n\nOhlsson B: Extraintestinal manifestations in IBS. A systematic review. Ther. Adv. Gastroenterol. 2022; 15: 175628482211145. Publisher Full Text\n\nCanavan C, West J, Card T: The epidemiology of irritable bowel syndrome. Clin. Epidemiol. 2014; 6: 71–80. 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PubMed Abstract \| Publisher Full Text\n\nBöhn L, Störsrud S, Törnblom H, et al.: Self-reported food-reported gastrointestinal symptoms in IBS are common and associated with more severe symptoms and reduced quality of life. Am. J. Gastroenterol. 2013; 108: 634–641. PubMed Abstract \| Publisher Full Text\n\nLahner E, Bellentani S, Bastiani RD, et al.: A survey of pharmacological and nonpharmacological treatment of functional gastrointestinal disorders. United European Gastroenterol J. 2013; 1: 385–393. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMitchell H, Porter J, Gibson PR, et al.: Review article: implementation of a diet low in FODMAPs for patients with irritable. APT. 2019; 49: 124–139.\n\nNilholm C, Larsson E, Roth B, et al.: Irregular dietary habits with a high intake of cereals and sweets are associated with more severe gastrointestinal symptoms in IBS patients. Nutrients. 2019; 11: 1279. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSaidi K, Nilholm C, Roth B, et al.: A carbohydrate-restricted diet for patients with irritable bowel syndrome lowers serum C-peptide, insulin, and leptin without any correlation with symptom reduction. Nutr. Res. 2021; 86: 23–36. PubMed Abstract \| Publisher Full Text\n\nRoth B, Larsson E, Ohlsson B: Poor intake of vitamins and minerals among patients with irritable bowel syndrome is associated with symptoms. J. Gastroenterol. Hepatol. 2022; 37: 1253–1262. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nReference Source (Downloaded 7 June 2023).\n\nOhlsson B, Roth B: Datasheet_Figshare_anonymized, which describes gender, age, type of recruitment process, and lost at follow-up.2024. Licence CC0. Publisher Full Text\n\nOhlsson B, Roth B: Challenges of recruitment processes to a randomized dietary trial in irritable bowel syndrome. Dataset. figshare. 2024. 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PubMed Abstract \| Publisher Full Text\n\nLim SS, Vos T, Flaxman AD, et al.: A comparative risk assessment of burden of disease and injury attributable to 67 risk factors and risk factor clusters in 21 regions, 1990-2010: A systematic analysis for the global burden of disease study 2010. Lancet. 2012; 380: 2224–2260. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMorton K, Beauchamp M, Prothero A, et al.: The effectiveness of motivational interviewing for health behaviour change in primary care settings: a systematic review. Health Psychol. Rev. 2015; 9: 205–223. PubMed Abstract \| Publisher Full Text" }	[ { "id": "272869", "date": "29 May 2024", "name": "Jari Punkkinen", "expertise": [ "Reviewer Expertise Functional gastrointestinal disorders" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis is an interesting study about the difficulty of recruiting IBS patients to a dietary trial. I have only some concerns.\nThe abstract background describes that this paper about the recruitment process is part of a larger randomized study, about FODMAP and SSRD in IBS patients. It would be clarifying to tell in the abstract that the results of the dietary trial itself are not included in this paper but will be presented in another publication.\n\nIn the methods section the authors tell that questionnaires, diary books, blood samples and fecal samples were collected as part of the dietary trial. It would be useful to describe these more in detail because if this caused a lot of effort and work for the patients, it might have hindered patients from participating in the study.\n\nIt would also be important to tell, how the FODMAP and SSRD diets were carried out. Were the patients provided the food they ate or did the patients only receive instructions how to prepare their meals and what food to buy ? Providing ready made meals is easier than only giving instructions and orders to prepare meals. Buying food to prepare a FODMAP/SSRD diet might also result expensive. All this might hinder patients from participating in the study.\n\nWhat did the FODMAP/SSRD diets consist of ? People have different tastes and not all are willing to commit to a restricting diet for four weeks. This should be described briefly\nis is an interesting and important finding regarding future studies that the easiest way to recruit patients for a dietary trial is through the social media.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate? Yes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "11796", "date": "25 Jun 2024", "name": "Bodil Ohlsson", "role": "Author Response", "response": "Jari Punkkinen, Helsinki University Central Hospital, Helsinki, Finland Comment: This is an interesting study about the difficulty of recruiting IBS patients to a dietary trial. I have only some concerns. Reply: Dear Reviewer, thank you for evaluating this manuscript. We do appreciate the constructive criticism given and have tried to answer the questions. All changes are marked as tracked changes. We think that the changes have improved the manuscript. On behalf of both authors, Bodil Ohlsson, Professor, Senior Consultant of Gastroenterology and Hepatology Comment: The abstract background describes that this paper about the recruitment process is part of a larger randomized study, about FODMAP and SSRD in IBS patients. It would be clarifying to tell in the abstract that the results of the dietary trial itself are not included in this paper but will be presented in another publication. Reply: Thanks for this comment that will make the intention of the publication much clearer. This is now added in both the abstract and in the last sentence of background, page 3. Comment: In the methods section the authors tell that questionnaires, diary books, blood samples and fecal samples were collected as part of the dietary trial. It would be useful to describe these more in detail because if this caused a lot of effort and work for the patients, it might have hindered patients from participating in the study. Reply: The number of physical visits as well as the time needed for each visit and completion of questionnaires are now given along with more details about the study design, page 3, second section. A new reference is added for IBS-SSS, ref No 16, which was unfortunately forgotten in the first version. Comment: It would also be important to tell, how the FODMAP and SSRD diets were carried out. Were the patients provided the food they ate or did the patients only receive instructions how to prepare their meals and what food to buy ? Providing ready made meals is easier than only giving instructions and orders to prepare meals. Buying food to prepare a FODMAP/SSRD diet might also result expensive. All this might hinder patients from participating in the study. Reply: The participants received oral and written information about the food. They had to buy and cook all the food themselves, but they received menu suggestions and recipes to make it easier for them, page 4, first section. However, since many people buy ready-to-eat food it was a great challenge for many of them to plan and cook the food on their own. It could also be more expensive to buy more fruits, vegetables and fish. On the other hand, to cook the food themselves could be cheaper than to buy food ready-to-eat, soda, candies and go to restaurants. This is now discussed in the discussion, page 8, third section. Comment: What did the FODMAP/SSRD diets consist of ? People have different tastes and not all are willing to commit to a restricting diet for four weeks. This should be described briefly Reply: The diets are now briefly described on page 4, first section. However, since this was only a methodological study about the recruitment process, we have kept this information short. Comment: It is an interesting and important finding regarding future studies that the easiest way to recruit patients for a dietary trial is through the social media. Reply: Yes, we think so" } ] }, { "id": "283692", "date": "14 Jun 2024", "name": "Tarek Mazzawi", "expertise": [ "Reviewer Expertise Assistant Professor", "MD", "PhD", "Gastroenterologist and Hepatologist. My research involves: IBS", "microbiota", "fecal microbiota transplantation", "intestinal ultrasound", "endoscopy and sedation." ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis research describes the challenges the researchers face while recruiting patient with IBS into research studies. This is a very important issue both for medical researchers and reviewers who demand high power and large study cohorts to understand that IBS patients are not easy to recruit.\n\nI have minor comments:\n1) Under Methods- personal invitations: please add the coding system used for setting the diagnosis : ICD 10\n\n2) Under discussion: The authors seem to drift from the main topic (challenges of recruitment processes) while writing in the discussion (the 3rd paragraph) about the different diets and low vitamin D supplements and their relations to IBS symptoms. The point is to discuss why IBS patients drop out, factors that influence their acceptance or withdrawal from the studies, any psychological issues that affect their motivations ,,etc. Also if there are solutions that can be suggested to solve these challenges . I suggest that the discussion should be edited to cover these 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? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate? Yes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "11797", "date": "25 Jun 2024", "name": "Bodil Ohlsson", "role": "Author Response", "response": "Tarek Mazzawi, Al-Balqa Applied University, Al-Salt, JOR, Jordan Comment: This research describes the challenges the researchers face while recruiting patient with IBS into research studies. This is a very important issue both for medical researchers and reviewers who demand high power and large study cohorts to understand that IBS patients are not easy to recruit. Reply: Dear Reviewer, thank you for evaluating this manuscript. We do appreciate the constructive criticism given and have tried to answer the questions. All changes are marked as tracked changes. We think that the changes have improved the manuscript. On behalf of both authors, Bodil Ohlsson, Professor, Senior Consultant of Gastroenterology and Hepatology Comment:I have minor comments: 1) Under Methods- personal invitations: please add the coding system used for setting the diagnosis : ICD 10 Reply: This has now been added on page 5, last section. Comment: 2) Under discussion: The authors seem to drift from the main topic (challenges of recruitment processes) while writing in the discussion (the 3rd paragraph) about the different diets and low vitamin D supplements and their relations to IBS symptoms. The point is to discuss why IBS patients drop out, factors that influence their acceptance or withdrawal from the studies, any psychological issues that affect their motivations ,,etc. Also if there are solutions that can be suggested to solve these challenges . I suggest that the discussion should be edited to cover these issues. Reply: You are completely right, and now we have changed the discussion accordingly. Hope you find this better and more relevant. See page 8, third section." } ] } ]	1	https://f1000research.com/articles/13-323
https://f1000research.com/articles/11-889/v1	04 Aug 22	{ "type": "Software Tool Article", "title": "Sapporo: A workflow execution service that encourages the reuse of workflows in various languages in bioinformatics", "authors": [ "Hirotaka Suetake", "Tomoya Tanjo", "Manabu Ishii", "Bruno P. Kinoshita", "Takeshi Fujino", "Tsuyoshi Hachiya", "Yuichi Kodama", "Takatomo Fujisawa", "Osamu Ogasawara", "Atsushi Shimizu", "Masanori Arita", "Tsukasa Fukusato", "Takeo Igarashi", "Tazro Ohta", "Hirotaka Suetake", "Tomoya Tanjo", "Manabu Ishii", "Bruno P. Kinoshita", "Takeshi Fujino", "Tsuyoshi Hachiya", "Yuichi Kodama", "Takatomo Fujisawa", "Osamu Ogasawara", "Atsushi Shimizu", "Masanori Arita", "Tsukasa Fukusato", "Takeo Igarashi" ], "abstract": "The increased demand for efficient computation in data analysis encourages researchers in biomedical science to use workflow systems. Workflow systems, or so-called workflow languages, are used for the description and execution of a set of data analysis steps. Workflow systems increase the productivity of researchers, specifically in fields that use high-throughput DNA sequencing applications, where scalable computation is required. As systems have improved the portability of data analysis workflows, research communities are able to share workflows to reduce the cost of building ordinary analysis procedures. However, having multiple workflow systems in a research field has resulted in the distribution of efforts across different workflow system communities. As each workflow system has its unique characteristics, it is not feasible to learn every single system in order to use publicly shared workflows. Thus, we developed Sapporo, an application to provide a unified layer of workflow execution upon the differences of various workflow systems. Sapporo has two components: an application programming interface (API) that receives the request of a workflow run and a browser-based client for the API. The API follows the Workflow Execution Service API standard proposed by the Global Alliance for Genomics and Health. The current implementation supports the execution of workflows in four languages: Common Workflow Language, Workflow Description Language, Snakemake, and Nextflow. With its extensible and scalable design, Sapporo can support the research community in utilizing valuable resources for data analysis.", "keywords": [ "workflow", "workflow language", "workflow execution service", "open science" ], "content": "Background\n\nModern experimental instruments that convert biological samples into digital data have lower costs and higher throughput than conventional ones.1 Those instruments have made it possible to conduct large-scale data-driven biology, not only in large projects but also in smaller studies. A DNA sequencer is one such technology in biology, which has shown a drastic improvement in throughput since the late 2000s.1 DNA sequencing technology highlighted the data science aspect of biology, sparking the demand for computation in biology.2\n\nRaw data, the fragments of nucleotide sequences for a DNA sequencer, often called “reads,” are not biologically interpretable in their unprocessed form. Researchers need to process the data using computational methods to obtain biological insights from the samples. The data processing includes, for example, estimation of sequence error rates, read alignment to a reference genome sequence, extraction of genomic features from aligned data, and annotation with the information obtained from public databases. Researchers develop and share the command-line tools for each step in an analysis. They use the raw data as the initial input data of the first tool and pass its output on as input for the next tool. This chain of processes, connecting a sequence of tools according to their inputs and outputs, is called a workflow.3\n\nWorkflow structure can be complicated as various sequencing applications require multiple steps of data processing. Combining many tools to construct a complex workflow that performs as intended is not straightforward. It is also not practical to fully understand the internal processes of all the tools. Thus, ensuring that every individual part of a workflow is working correctly depends heavily on the skills of the workflow developer. Even if a workflow runs successfully once, maintaining it is another issue. The tools in a workflow are often developed as open-source software and are frequently updated to improve performance and fix bugs. It is time-consuming to assess the impact of updates associated with individual tools. The tools in a workflow often work in an unintended manner for many reasons, such as changes in hardware, operating system (OS), software dependencies, or input data. Difficulties in building and maintaining workflows cause portability issues with workflows.4 Because of this, researchers have to spend a great deal of time building workflows similar to those that others have already created.\n\nTo address these issues, researchers have developed many workflow systems in bioinformatics.5 Each workflow system has unique characteristics, but generally, they all have a language syntax and a workflow engine. Workflow languages define a syntax to describe the inputs and arguments passed to tools and the handling of outputs. Workflow engines often take two arguments to execute a workflow: a workflow definition file that specifies the processes and a job file for input parameters. In many cases, techniques, such as package managers and container virtualization, make it easier to build, maintain, and share complex workflows by pinning down the versions of workflow tools.6\n\nOpen-source workflow systems help the research community work efficiently by reusing published workflows.7 However, having multiple systems has resulted in resources distributed across various workflow system communities. For example, the Galaxy community is known for being one of the largest for data analysis in biology.8 The community maintains a number of workflows and learning materials that users can run on public Galaxy instances. However, as the Galaxy workflows are only runnable on the Galaxy platform, users will face difficulties in running these workflows on other platforms. As another example, Nextflow, one of the most popular command-line-based workflow systems, has a mature community called nf-core to share standard workflows.9,10 The community has excellent resources, but these are usable only by Nextflow users. It is not reasonable to have a “one-size-fits-all” workflow system in science because various approaches have pros and cons.3 Learning the different concepts and features of each workflow system has a high cost associated with it. Thus, it is not practical to consider becoming familiar with a large number of workflow systems in order to be able to utilize the workflows shared by their community users.\n\nIn this paper, we introduce Sapporo, a platform for running multiple workflow systems in the same computing environment. Sapporo wraps the differences in the workflow systems and provides an application programming interface (API) for executing them in a unified way. Sapporo also provides a graphical user interface (GUI) that works as its API client. By enabling users to run multiple workflow systems on the same computing environment, Sapporo gives users the ability to reuse workflows without having to learn a new workflow system.\n\n\nMethods\n\nSapporo consists of two components: Sapporo-service and Sapporo-web (Figure 1). Sapporo-service is an API that receives requests for workflow execution from clients, then executes them in a specified manner. Sapporo-service has an API scheme that satisfies the Global Alliance for Genomics and Health (GA4GH) Workflow Execution Service (WES) standard.11 Sapporo-web is a workflow management client. It is a client of Sapporo-service and other GA4GH WES compatible API servers. The GUI is a browser-based application that does not require user installation.\n\nThe component at the bottom is Sapporo-service, a Global Alliance for Genomics and Health (GA4GH) Workflow Execution Service (WES) standard compatible application programming interface (API) to manage the workflow execution. The box at the top is Sapporo-web, the graphical user interface (GUI) client for WES implementations. Sapporo-service has the open specification of the API endpoints, which users can access programmatically.\n\nWe designed the Sapporo system based on the concept of microservices architecture.12 Unlike conventional computation server applications, we expect multiple Sapporo-service instances to be run on servers as independent endpoints on demand. To manage the runs on the different API servers, we separate the implementation of the server and its client, allowing clients to connect to multiple servers (Figure 2). One of the unique features of the Sapporo system is that it has no authentication mechanism on the application layer. Instead of having users’ information on the server-side, the user’s web browser stores the information, such as workflow execution history. The online documentation “Sapporo: Getting Started”, available in Extended data, shows the step-by-step procedures to deploy a Sapporo instance on a local computer to test the system.13,34\n\nResearchers often have multiple computing environments for their data analysis. We designed the Sapporo system to work with a distributed computation model. For example, users can deploy the application programming interface (API) on their local computer, remote computing server, and public cloud instances. As long as the API is running, the user can send a request to execute a workflow from a local client computer.\n\nThe source code, test code, and documentation for Sapporo-service and Sapporo-web are available from GitHub and archived in Zenodo.35,36\n\nThe WES has two layers: the API and the execute function (Figure 3). The API structure and the response are compliant with the GA4GH WES standard.14 The API specification defines the methods to manipulate workflow runs, such as execution, stop, and checking the outputs. In addition, Sapporo-service has its own unique features (Table 1). The key feature that makes Sapporo notable is the workflow engine selection. While the other workflow management systems accept one or a few workflow languages, Sapporo-service can accept any workflow language as long as it has a corresponding workflow engine.\n\nSapporo-service’s application programming interface (API) layer implemented in Python works as an API server to receive the request of a workflow run. Once the API receives the request, it creates a directory to store all the related information and execute run.sh. The run.sh script receives the arguments from the API request and runs the workflow with the specified workflow engine.\n\nThe execution layer executes the workflow system according to the request. It has a simple shell script named “run.sh” as its easily extendable core component. The number of workflow systems increased from just one at the beginning of the project to seven in the current version (Table 2). Once the system receives a workflow run request, it issues a universally unique identifier (UUID) and creates a directory named with the UUID, where the system stores all the necessary files. The workflow definition files, intermediate and final outputs, and the other metadata are stored in that directory. This per-run directory can act as a bundle of provenance for the workflow run (Figure 4).\n\nVarious types of information, such as run requests, execution results, and runtime information, are stored as a bundle of provenance for the workflow run.\n\nThe system has no backend database as it stores all the information in the file system. This architecture allows the system administrators to manage the data as they do for normal server operations. We also provide a Docker image of the application, which can completely separate the system into the application (container image) and data (file system) for better portability and scalability.21\n\nAnother feature not implemented in a standard WES server is a registered-only mode. By enabling it at the server start-up, users can execute only the workflows in the allowed list specified by the administrator. This function helps the administrators launch a public WES instance while preventing suspicious programs from running on the server. Instead of implementing user authentication on the application, we expect the administrators to do the required authentication to the server on the network layer, such as virtual private network (VPN).\n\nWe designed Sapporo-web as a browser-based GUI client for GA4GH WES endpoints. The system is a JavaScript application that runs on a web page, which users do not need to install on their computers. It stores user data in the browser’s local storage, so users do not need to sign up to start running workflows. No information other than the access log is preserved on the server-side. The Sapporo-web system is compliant with the GA4GH WES specification. We used Elixir WES, another WES implementation, to confirm Sapporo’s GA4GH WES specification compliance.22\n\nTo execute a workflow with Sapporo-web, users take the following five steps (Figure 5). Users can use a WES endpoint either running remotely or locally. Following the user’s connection request, Sapporo-web requests the service-info API of the WES to read the endpoint metadata and display the information (Figure 6). Users can select a workflow to run by entering a published workflow URL, uploading a workflow definition file, or selecting from the workflows registered on the WES server. Sapporo-web also can accept the GA4GH Tool Registry Service (TRS) protocol as a source of published workflows. Sapporo-web retrieves the content of the requested workflow definition file to generate a web form for entering input parameters (Figure 7). The type of web form depends on the workflow language. For example, loading a workflow described in Common Workflow Language (CWL) generates a typed input form per parameter because CWL specifies input parameters with a structured text form.23 In contrast, loading a workflow described in languages other than CWL generates a text editor to change the parameters in the corresponding format. After the edit, users can click “execute” to request the workflow to run on the server where the WES endpoint is running.\n\nSapporo-web provides a step-by-step user interface to help users set up a workflow run. First, users need to specify where to execute a workflow (Workflow Execution Service (WES) instance). Next, users select what to run (workflow) and then how it should be run (input parameters). The UI allows users to download a set of input parameters, which users can upload to re-run a workflow with the same parameters.\n\nThe Global Alliance for Genomics and Health (GA4GH) WES specification defines the scheme of the response of service-info. It has the basic information of the WES endpoint, such as supported workflow language and workflow engines. Sapporo-web reads the WES metadata and provides the interface to start composing a workflow run.\n\nSapporo-web automatically generates a typed input form for a given workflow. It is possible when the given workflow language has a structured job configuration file, for example, a YAML format file for a Common Workflow Language (CWL) workflow. The form has the type validation function for users’ input, such as a file, integer, or array of strings.\n\nWhile the workflow is running, users can check the execution log via Sapporo-web. The standard output and the standard error of the workflow run retrieved from the WES endpoint show up in the log history section. The running status becomes “complete” when the execution finishes on the server. Workflow outputs stored in the WES server are downloadable via a link in the Sapporo-web user interface. If the workflow run failed with an error, the status “executor error” would be shown. Users can visualize the error log in Sapporo-web.\n\n\nResults\n\nWe developed Sapporo as a WES implementation that allows developers to add new workflow systems. Developers only need to implement the command line procedure in the run.sh script, which is a simple bash script. The project was hosted on GitHub from its inception, with the intention to have other developers contribute with new workflow systems. A good example of this in practice can be seen in the pull request (https://github.com/sapporo-wes/sapporo-service/pull/29) that added a new workflow system called StreamFlow.20\n\nTo evaluate the usability with real use cases, we used Sapporo to run the public workflows that researchers frequently use. We successfully executed the following three workflows: Mitochondrial short variant discovery from the GATK best practice workflows (language: WDL), RNA-Seq workflow from the nf-core repository (language: Nextflow), and a GATK best practice-compatible germline short variant discovery workflow, which is used to process whole-genome sequencing data of the Japanese Genotype-phenotype Archive (language: CWL).24 We published the description of the test procedures for these workflows on GitHub,25 and the results of the test runs on Zenodo.26–28\n\n\nDiscussion\n\nIn the big-data era in biology, the demand for efficient data processing will never stop increasing.29 There are countless painful tasks in data processing, and researchers have developed methods to solve each of them, resulting in many different workflow systems.30 We appreciate that many options are available as open-source so that researchers can choose one for their specific needs. The situation strongly encourages open science: each workflow system community is there so that individuals can help each other by sharing resources.31 However, as each community grows, the gap between the communities also becomes larger. We developed Sapporo to bridge these gaps by providing a new layer to better utilize resources across communities. As the workflow systems are for the increased productivity of data scientists, improving resource interoperability must not interfere with researchers doing their science. An upper layer, the layer of workflow execution, can be a better solution than proposing a new language convertible to other existing languages. The concept of abstraction of workflow execution, as well as the idea of “bringing the algorithms to the data,” is also proposed by the GA4GH cloud work stream, which resulted in the development of the GA4GH Cloud standards. As of May 2022, the GA4GH WES specification supports only CWL and WDL for their workflow format. There is no official list of WES implementations; however, no other service that allows the addition of workflow systems is available as far as we investigated.\n\nAlthough Sapporo is a flexible system covering many use cases, we recognize that the current implementation has a few technical limitations. The main objective of Sapporo is to absorb the variance of the execution methods per workflow system. We achieved building a unified way to request a workflow run by providing the API and its client. However, there is still a challenge in the user experience with regard to the parameter editing function. This is caused by differences in the workflow system concepts. For example, some workflow systems, such as Nextflow or Snakemake, use Domain Specific Language (DSL) model in their syntax for better productivity, so users can write a workflow as they would write a script in their preferred programming language.9,18 However, this flexibility in describing the procedures often makes the required input parameters unparsable by other applications. It means that users need to learn how to edit the parameters for each workflow system they are using. Though often this is not too difficult, the workflow system communities need to lower the learning costs to use a workflow. For example, finding a more generic representation of workflow inputs between workflow language systems could alleviate the situation.\n\nSapporo is a unique WES implementation that accepts multiple workflow languages. Researchers can use the system to utilize community workflows without regarding what language they are written in. One downside of this flexibility is that errors reported by Sapporo from different workflow engines may not look familiar to users. Many well-maintained workflow registries are available, such as nf-core and WorkflowHub, but the quality of the workflows published in these registries relies on each community’s efforts.10,32,33 A system that validates and verifies the quality of workflows is also required for the sustainability of the resources published in the workflow registries.\n\nData processing methods vary greatly depending on the type of input data and the computational platform. In bioinformatics, the laboratory equipment and computers available drive changes. New computing applications for efficient data science, and new problems of resource portability may appear if variables such as input data, equipment, and computing resources keep changing in the future. Through its concept of abstraction, Sapporo can be a key player in assisting different communities in sharing and reusing workflows and other computing resources.\n\n\nData availability\n\nAll of these projects are licensed under the Apache License 2.0.\n\nZenodo: sapporo-wes/test-workflow: 1.0.1. https://doi.org/10.5281/zenodo.6618935.25\n\nThis project contains the following underlying data:\n\n• sapporo-wes/test-workflow-1.0.1.zip (description of the test procedures and results of the workflows described in section Use cases).\n\nThe results of the test runs are contained in the following projects:\n\n• Zenodo: Sapporo execution results - broadinstitute/gatk/MitochondriaPipeline: 1.0.0. https://doi.org/10.5281/zenodo.6535083.26\n\n• Zenodo: Sapporo execution results - nf-core/rnaseq: 1.0.0. https://doi.org/10.5281/zenodo.6534202.27\n\n• Zenodo: Sapporo execution results - JGA analysis - per-sample: 1.0.0. https://doi.org/10.5281/zenodo.6612737.28\n\nZenodo: sapporo-wes/sapporo: 1.0.0. https://doi.org/10.5281/zenodo.6462774.34\n\nThis project contains the following extended data:\n\n• Sapporo: Getting Started.md (step-by-step procedures for deploying a Sapporo instance on a local computer and testing the system).\n\n\nSoftware availability\n\nSapporo-service’s source code, test code, and documentation:\n\n• Source code available from: https://github.com/sapporo-wes/sapporo-service/tree/1.2.4\n\n• Archived source code at time of publication: https://doi.org/10.5281/zenodo.6609570.35\n\n• License: Apache License 2.0\n\nSapporo-web’s source code, test code, and documentation:\n\n• Source code available from: https://github.com/sapporo-wes/sapporo-web/tree/1.1.2\n\n• Archived source code at time of publication: https://doi.org/10.5281/zenodo.6462809.36\n\n• License: Apache License 2.0", "appendix": "Acknowledgements\n\nWe acknowledge and thank the following scientific communities and their collaborative events where several of the authors engaged in irreplaceable discussions and development throughout the project: the Pitagora Meetup, Workflow Meetup Japan, NBDC/DBCLS BioHackathon Series, Elixir’s BioHackathon Europe Series, GA4GH Cloud WorkStream, Common Workflow Language Community, Nextflow Community, Galaxy Community, and Open Bioinformatics Foundation Bioinformatics Open Source Conference Collaboration Fest. We would like to acknowledge Dr. Alexander Kanitz for his support of the collaboration with WES-ELIXIR. We also would like to thank Dr. Ivan Topolsky for his assistance with the implementation of Sapporo-service. We also acknowledge Prof. Kazuki Yoshizoe for his valuable comments on the project. We also would like to thank Ascade Inc. for their support with the software development. Computations were partially performed on the NIG supercomputer at the ROIS National Institute of Genetics.\n\n\nReferences\n\nGoodwin S, McPherson JD, McCombie RW, et al.: Coming of age: Ten years of next-generation sequencing technologies. Nat. Rev. Genet. 2016; 17(6): 333–351. PubMed Abstract \| Publisher Full Text\n\nStein LD: The case for cloud computing in genome informatics. Genome Biol. 2010; 11(5): 207–207. Publisher Full Text\n\nPerkel JM: Workflow systems turn raw data into scientific knowledge. Nature. 2019; 573(7772): 149–150. 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PubMed Abstract \| Publisher Full Text\n\nDi Tommaso P, Chatzou M, Floden EW, et al.: Nextflow enables reproducible computational workflows. Nat. Biotechnol. 2017; 35(4): 316–319. Publisher Full Text\n\nEwels PA, Peltzer A, Fillinger S, et al.: The nf-core framework for community-curated bioinformatics pipelines. Nat. Biotechnol. 2020; 38(3): 276–278. Publisher Full Text\n\nRehm HL, Page AJH, Smith L, et al.: GA4GH: International policies and standards for data sharing across genomic research and healthcare. Cell Genomics. 2021; 1(2): 100029. PubMed Abstract \| Publisher Full Text\n\nCerny T, Donahoo MJ, Trnka M: Contextual understanding of microservice architecture: Current and future directions. ACM SIGAPP Applied Computing Review. 2018; 17(4): 29–45. Publisher Full Text\n\nSuetake H, Ohta T: Sapporo: Getting started.2021.Reference Source\n\nThe Global Alliance for Genomics and Health Cloud Work Stream: Workflow Execution Service (WES) API.2017.Reference Source\n\nCommon Workflow Language: common-workflow-language/cwltool.2015.Reference Source\n\nVivian J, Rao AA, Nothaft FA, et al.: Toil enables reproducible, open source, big biomedical data analyses. Nat. Biotechnol. 2017; 35(4): 314–316. PubMed Abstract \| Publisher Full Text\n\nVoss K, Van Der Auwera G , Gentry J: Full-stack genomics pipelining with GATK4 + WDL + Cromwell.2017.Reference Source\n\nKöster J, Rahmann S: Snakemake—a scalable bioinformatics workflow engine. Bioinformatics. 2012; 28(19): 2520–2522. Publisher Full Text\n\nTanjo T: tom-tan/ep3.2019.Reference Source\n\nColonnelli I, Cantalupo B, Merelli I, et al.: Streamflow: Cross-breeding cloud with hpc. IEEE Trans. Emerg. Top. Comput. 2020; 9(4): 1723–1737.\n\nMerkel D: Docker: Lightweight linux containers for consistent development and deployment. Linux Journal. 2014; 2014(239): 2.\n\nHarrow J, Drysdale R, Smith A, et al.: ELIXIR: Providing a sustainable infrastructure for life science data at European scale. Bioinformatics. 2021; 37(16): 2506–2511. PubMed Abstract \| Publisher Full Text\n\nCrusoe MR, Abeln S, Iosup A, et al.: Methods included: Standardizing computational reuse and portability with the common workflow language. arXiv. 2021.\n\nKodama Y, Mashima J, Kosuge T, et al.: The ddbj japanese genotype-phenotype archive for genetic and phenotypic human data. Nucleic Acids Res. 2015; 43(D1): D18–D22. PubMed Abstract \| Publisher Full Text\n\nSuetake H, Ohta T: sapporo-wes/test-workflow: 1.0.1.2022. Publisher Full Text\n\nSuetake H: Sapporo execution results - broadinstitute/gatk/MitochondriaPipeline.2022. Publisher Full Text\n\nSuetake H: Sapporo execution results - nf-core/rnaseq.2022. Publisher Full Text\n\nSuetake H: Sapporo execution results - JGA analysis - per- sample.2022. Publisher Full Text\n\nPrins P, De Ligt J, Tarasov A, et al.: Toward effective software solutions for big biology. Nat. Biotechnol. 2015; 33(7): 686–687. Publisher Full Text\n\nAmstutz P, Mikheev M, Crusoe MR, et al.: Existing workflow systems.2021.Reference Source\n\nWilkinson MD, Dumontier M, Aalbersberg IJJ, et al.: The fair guiding principles for scientific data management and stewardship. Sci. Data. 2016; 3(1): 1–9.\n\nGoble C, Soiland-Reyes S, Bacall F, et al.: Implementing FAIR digital objects in the EOSC-life workflow collaboratory.2021.\n\nO’Connor BD, Yuen D, Chung V, et al.: The dockstore: enabling modular, community-focused sharing of docker-based genomics tools and workflows. F1000Res. 2017; 6. Publisher Full Text\n\nSuetake H, Ohta T: sapporo-wes/sapporo: 1.0.0. Zenodo. 2022. Publisher Full Text\n\nSuetake H, Ohta T, Tanjo T, et al.: sapporo-wes/sapporo-service: 1.2.4. Zenodo. 2022. Publisher Full Text\n\nSuetake H, Ohta T: sapporo-wes/sapporo-web: 1.1.2. Zenodo. 2022. Publisher Full Text" }	[ { "id": "185842", "date": "26 Jul 2023", "name": "Justin M. Wozniak", "expertise": [ "Reviewer Expertise workflows", "hpc", "distributed computing" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 presents a new abstraction layer (Sapporo) over existing workflow systems to support portability and interoperability. The paper is oriented around a bioinformatics workload. The paper is primarily focused on how Sapporo operates as a web service and runs underlying workflows using the other existing systems.\nThe paper provides a pretty good high-level state-of-the-art in the workflow ecosystem and the bioinformatics use case.\nThe paper spends most of its space describing the abstraction over workflow systems and figures that illustrate the corresponding architecture. It does not contain a deep dive into any challenges regarding workflow system interoperability.\nFrom a bioinformatics perspective, the description of support for the application workload is very high-level. There is no deep dive into what is really required to make this workload work. There are results posted for the run that are linked on the Internet, but they are not summarized in the text.\nThe architecture figures are very spacious and do not provide much technical insight.\nThere is an illustration of the web form used to run Sapporo, but it seems oversimplified and does not convey what the user would be faced with in a real-world problem.\nI downloaded the Sapporo source zip via the links in the paper. The source tree was not very revealing and I am not set up to run a new web service. The README pointed me to web-based docs that seemed quite good and included detailed installation notes.\nOverall, this is a good high-level introduction to Sapporo, but does not offer detailed technical insights into the problem space or the Sapporo solution. More details are necessary about these topics to provide insight to the community and allow for a better evaluation of the Sapporo contribution.\n\nIs the rationale for developing the new software tool clearly explained? Yes\n\nIs the description of the software tool technically sound? Partly\n\nAre sufficient details of the code, methods and analysis (if applicable) provided to allow replication of the software development and its use by others? No\n\nIs sufficient information provided to allow interpretation of the expected output datasets and any results generated using the tool? No\n\nAre the conclusions about the tool and its performance adequately supported by the findings presented in the article? Partly", "responses": [ { "c_id": "11768", "date": "24 Jun 2024", "name": "Tazro Ohta", "role": "Author Response", "response": "We deeply thank you for taking the time to review our manuscript. 1. The paper spends most of its space describing the abstraction over workflow systems and figures that illustrate the corresponding architecture. It does not contain a deep dive into any challenges regarding workflow system interoperability. We agree with your assessment. We added the text below in the Background section to emphasize the challenge in making the existing workflow systems: > Workflow systems have different language syntaxes and engines, each designed for specific purposes. For instance, Nextflow aims to boost developer productivity and scalability, while Snakemake focuses on flexibility and simplicity, using Python as its base. In contrast, the Common Workflow Language (CWL) project aims to promote interoperability by creating a standardized syntax that various workflow engines can understand. However, workflows written in different languages cannot be easily converted into each other automatically. The most popular workflow systems used in bioinformatics, such as CWL, WDL, Nextflow, and Snakemake, take a workflow definition and input parameters to produce output result files, while there are differences between these workflow systems in command-line options, workflow description syntax, methods for specifying inputs, and how expected output files are defined. > Creating a universal language converter isn't practical because some languages lack the necessary syntax parsers, or contain features that are not commonly found in other workflow engines (e.g. JavaScript evaluation as in CWL, loops in workflows or cyclic workflows instead of DAG-based systems). To bridge the gap between different workflow systems, we need a standardized way to specify workflows, input parameters, and expected outputs. Additionally, a system that supports various engines and selects the appropriate one for a given workflow is essential for smooth interoperability. 2. From a bioinformatics perspective, the description of support for the application workload is very high-level. There is no deep dive into what is really required to make this workload work. There are results posted for the run that are linked on the Internet, but they are not summarized in the text. We agree again with your assessment. To clarify the user's procedure for performing the analysis, we modified the paragraph in the Result section as follows: > To evaluate the practical applicability and robustness of Sapporo, we executed public workflows frequently used by researchers. Specifically, we chose the Mitochondrial Short Variant Discovery workflow from the GATK best practices (written in WDL), the RNA-seq workflow from the nf-core repository (written in Nextflow), and a Germine Short Variant Discovery workflow for processing whole-genome sequencing data from the Japanese Genotype-phonotype Archive (written in CWL). Users access Sapporo's endpoint specifying the input parameters following the WES specification. The required parameters are workflow_url, workflow_type, workflow_type_version, and workflow_params. The workflow_url argument specifies the location of the workflow definition file (e.g. CWL file) to be executed, typically hosted on a remote server, enabling the API to access and utilize the workflow's instructions. The workflow_params argument points to a JSON file containing input parameters essential for the workflow execution, facilitating customization and adaptation of the workflow's behavior. The arguments workflow_type and workflow_type_version arguments indicate the type and version of the workflow language being employed, ensuring compatibility and proper interpretation of the workflow instructions by engines supported inside Sapporo. Additionally, the workflow_engine_name argument specifies the execution engine to be used, while the default engine for the given workflow language is assigned when it is not specified. Lastly, another optional argument workflow_engine_parameters argument allows for the specification of additional parameters tailored to the execution engine, providing fine-grained control over the execution environment and behavior of the workflow engine. We published the detailed description of the test procedures for these workflows on GitHub, and the results of the test runs on Zenodo. We also added a detailed view of user's procedure to run a workflow with Sapporo as Figure 8. 3. The architecture figures are very spacious and do not provide much technical insight. The architecture figures presented in the paper aim to illustrate the concept of our approach, which is not a monolithic software but rather divided into multiple layers. The figure aims to focus on the concept itself, because the technologies employed for implementation may change in the future. While we implemented the Sapporo-service providing the Web API in Python Flask and the Web UI accessing the API in Vue.js to enhance our development efficiency, we do not claim technical superiority over them here. As the software stacks evolve, we acknowledge the possibility of changing technology choices in the future. The idea of decomposing components into functionalities, as exemplified by microservices architecture, is common in today's software engineering, and we do not consider it novel. However, in the field of bioinformatics where existing workflow systems tend to be monolithic, easily extensible and layered systems are not as prevalent. Thus, we argue in the paper that such a design is beneficial for solving the problem we raise. Nonetheless, from the series of comments received from the reviewer, we recognized that the main message of the paper might not have been as clear as we intended. We believe the paragraphs added in Background and Discussion according to your comments may help readers to understand the aim of our projects. 4. There is an illustration of the web form used to run Sapporo, but it seems oversimplified and does not convey what the user would be faced with in a real-world problem. We understand the reviewer's concern about the oversimplified depiction of the workflow in Figure 7, resulting in a very basic UI representation that may differ from what users may encounter when using Sapporo-web in real-world scenarios. The intention behind this illustration was to demonstrate the automatic rendering of the UI based on the input in the workflow definition file. We do not assume or claim here that highly complex workflows with complicated input parameter sets can be executed seamlessly through the generated Web UI. We added the following sentences in the Discussion section to claim the relationship between the user interface and the improvement of workflow usability: > As the complexity of the workflow increases, so does the difficulty of executing it. Sapporo's primary goal is to reduce the time and learning costs associated with deployment, parameterization, and execution due to changes in workflow languages or systems, not to reduce the inherent complexity of given workflows. The use of complex workflows requires complex input parameter specifications due to the intricacies of their internal processes, and using them without understanding them would not reflect scientific integrity in data analysis. Of course, some costs can be mitigated through UI enhancements, such as optimizing sets of multiple input parameters or streamlining iterations for numerous input files. However, it's not practical for Sapporo-web's default UI to cover all these scenarios, as web UIs are not one-size-fits-all. There is potential to solve this problem by semi-automatically generating a UI for each workflow, a concept we're exploring in another project. However, even in this scenario, the advantage of splitting our UI into standardized APIs remains apparent. 5. Overall, this is a good high-level introduction to Sapporo, but does not offer detailed technical insights into the problem space or the Sapporo solution. More details are necessary about these topics to provide insight to the community and allow for a better evaluation of the Sapporo contribution. In response to your comment; we believe that your previous points stressed this same point, and the content added there addresses this same issue. As outlined in our response to your first comment, we have added descriptions in the updated manuscript about the issues Sapporo aims to address. Additionally, we have incorporated the following passage into the Discussion section: > To support workflow developers and researchers conducting data analysis, multiple different workflow management systems have been developed. These systems enhance productivity and reproducibility in data analysis, enabling more effective science. However, the proliferation of multiple systems has revealed inefficiencies, leading to fragmentation within developer and user communities. While it is crucial to effectively leverage the assets of each system and community, it is not practical to provide the methods for syntax conversion between workflow systems and extending execution engines. Therefore, Sapporo aims to absorb differences between systems by wrapping multiple systems. Specifically, we provide an API that rewrites workflow definitions and runtime parameters into the command lines of each system based on the type of workflow definition received, enabling the execution of different workflows using the same client. Inside the API server, we use Docker containers to ensure the usability of different workflow engines. The use of containers also ensures future additions of workflow engines while maintaining the portability of the API server. The Web API adheres to the internationally defined GA4GH WES standard, ensuring interoperability with other GA4GH WES implementations. By developing and releasing Sapporo Web as an example of a GA4GH WES client, we demonstrate the readiness of our developed API for research use." } ] }, { "id": "185836", "date": "05 Oct 2023", "name": "Iacopo Colonnelli", "expertise": [ "Reviewer Expertise Workflows", "High Performance Computing", "Parallel Computing", "Distributed Computing" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIn this article, the authors describe Sapporo, a WES-compatible web-based interface to multiple workflow management systems (WMSs). Sapporo aims to act as a common interface to different underlying WMSs, abstracting product-specific details and complexities to the end users. This way, Sapporo fosters WMSs interoperability and lowers the technical barriers between domain experts and workflow execution.\nThe description of Sapporo is kept at a high level of abstraction, without many technical details about the implementation. However, it is detailed enough to let the reader capture all the crucial aspects of the software architecture, the frontend and backend structure, and the main limitations of the current version. A link to a Docker Compose manifest for quick evaluation would be a plus.\nFor implementers, the description is too high-level to understand how to replicate the software development. Additional material published on GitHub and Zenodo contains further details for the developers. However, having at least a high-level description of the `run.sh` script, which constitutes the core of the Sapporo backend, would improve the article's understandability.\nThe main flaw of the article in its current form is that the description of the experimental evaluation and the obtained results is left to external references. The authors describe three different experiments using three different workflow languages and datasets. Adding a detailed description of one of them directly in the article, together with the steps needed to reproduce it, would allow the reader to better understand the features Sapporo provided.\nAlso, there is no quantitative measure of achieved results in the article. Some quantitative measures of the Sapporo complexity (e.g., the percentage of product-specific lines of code that users are still forced to write to specify workflow parameters or the average lines of code needed to add support for a new WMS) would enable a more scientifically sound evaluation of the product.\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? No\n\nAre the conclusions about the tool and its performance adequately supported by the findings presented in the article? Partly", "responses": [ { "c_id": "11769", "date": "24 Jun 2024", "name": "Tazro Ohta", "role": "Author Response", "response": "We deeply thank you for taking the time to review our manuscript. 1. A link to a Docker Compose manifest for quick evaluation would be a plus. Thank you for the great suggestion. We added a line to indicate the location of the docker compose manifest for each of Sapporo-service and Sapporo-web. 2. For implementers, the description is too high-level to understand how to replicate the software development. Additional material published on GitHub and Zenodo contains further details for the developers. However, having at least a high-level description of the `run.sh` script, which constitutes the core of the Sapporo backend, would improve the article's understandability. We agree with your assessment. We modified the paragraphs in the subsection \"Workflow execution service\" in the Methods section to describe the run.sh function of Sapporo-service: > The system is designed to separate the execution layer from the handling of API requests, thereby enhancing modularity and extensibility. The execution layer operates through a well-structured shell script named \"run.sh.\" Upon receiving an API request, the system forks \"run.sh,\" which then generates command lines for the workflow system and executes them. This separation enables the addition of new workflow systems without changes to the API server's code. As a result, adding new workflows becomes straightforward, with the number of systems growing from just one at the beginning of the project to seven in the current version (Table 2). The flexibility of the \"run.sh\" also allows for specific adjustments for each workflow system, supporting pre- and post-execution processes, such as authentication, staging input files, and uploading results. Additionally, it is enabled to manage environment-specific requirements, including executing jobs on grid engines and handling file I/O with S3-like object storage. Once the system receives a workflow run request, it issues a universally unique identifier (UUID) and creates a directory named with the UUID, where the system stores all the necessary files. The workflow definition files, intermediate and final outputs, and the other metadata are stored in that directory. This per-run directory can act as a bundle of provenance for the workflow run (Figure 4). 3. The main flaw of the article in its current form is that the description of the experimental evaluation and the obtained results is left to external references. The authors describe three different experiments using three different workflow languages and datasets. Adding a detailed description of one of them directly in the article, together with the steps needed to reproduce it, would allow the reader to better understand the features Sapporo provided. In response to the comment by another reviewer (Dr. Justin M. Wozniak), we added the details of how users can specify the workflow condition in the Result section and the new figure Figure 8. We believe the addition can guide users to understand how they can run a workflow using our implementation. 4. Also, there is no quantitative measure of achieved results in the article. Some quantitative measures of the Sapporo complexity (e.g., the percentage of product-specific lines of code that users are still forced to write to specify workflow parameters or the average lines of code needed to add support for a new WMS) would enable a more scientifically sound evaluation of the product. We agree with the reviewer's feedback. Indeed, quantitatively evaluating how much the adoption of our system reduces the barrier to using different workflow management systems is challenging, which made this article posted as a software tool article. Methods such as user surveys could be considered for evaluation, but attempting to familiarize participants with multiple workflow systems without the assistance of our system or having learners of one language use a system in another language would not be practical. Demonstrating quantitatively that \"using workflow systems is inherently more productive than executing workflows built with shell scripts on job queuing systems via the command line\" poses a challenge for the entire developer community involved in developing workflow systems. Considering the challenges in the evaluation, with this paper we believe that providing the option of not only multiple different workflow management systems but also a system that can be used across them is our main contribution to the community." } ] } ]	1	https://f1000research.com/articles/11-889
https://f1000research.com/articles/13-678/v1	24 Jun 24	{ "type": "Study Protocol", "title": "Comparative study of the efficacy of volume control ventilation vs pressure control ventilation on patients undergoing laparoscopic surgeries under general anaesthesia", "authors": [ "Dr. Poornima Dhakshinamurthy", "Dr. Amol Singam", "Dr. Amol Singam" ], "abstract": "Background A variety of disorders are surgically treated with laparoscopy. Its benefits are frequently considered as being less intrusive, giving superior cosmetic outcomes, and needing a shorter hospital stay because they are based on surgical knowledge and cutting-edge technology. However, laparoscopic surgery under general anaesthesia and pneumoperitoneum may result in adverse pulmonary physiological alterations. This study will make choosing between volume control ventilation and pressure control ventilation for patients undergoing laparoscopic surgeries under general anaesthesia feasible.\n\nMethod 82 participants of both male and female gender and of the age between 18 and 70, with 41 in each group, will be randomly allotted with pressure control or volume control ventilation. The hemodynamic parameters and ventilatory parameters will be assessed. Data collection and analysis will be done.\n\nExpected outcomes To conclude if volume control ventilation or pressure control ventilation is effective in laparoscopic surgeries and which has less hemodynamic responses and better patient outcomes.", "keywords": [ "Pressure control ventilation", "volume control ventilation", "laparoscopic surgeries", "pneumoperitoneum", "general anaesthesia." ], "content": "Introduction\n\nAnalgesia, or the inability to feel pain, is one of the many goals of general anaesthesia, along with immobility (loss of reflexes), paralysis, amnesia (loss of memory), and unconsciousness (loss of awareness) (muscle relaxation).\n\nThe main ventilation mode used during surgery is volume-controlled ventilation (VCV). However, when dealing with elevated peak airway pressure, it is crucial to establish the tidal volume and respiratory rate beforehand to ensure effective ventilation. Although pressure-controlled ventilation offers better management of airway pressure, it is not the preferred choice for intraoperative use.1\n\nLung compliance, functional residual and vital lung capacity decrease during general anaesthesia. The pneumoperitoneum can increase intra-abdominal and intrathoracic pressure, whereas the Trendelenburg position, favoured during laparoscopic surgery, can further reduce these values. Atelectasis may result from recurrent minor airway closures. The majority of patients should be able to adapt to these changes without too much trouble if they are otherwise healthy, but obese patients and those with long-term respiratory issues are more likely to experience issues with intraoperative hypoxia, barotrauma, and volutrauma during laparoscopic procedures.2\n\nWith more surgeries being performed laparoscopically in the previous ten years our understanding of the effects of pneumoperitoneum on the cardiopulmonary physiology has also increased. Among the most noticeable ventilatory effects, along with cardiovascular consequences, is increased peak airway pressure (Ppeak). The anaesthesiologist could change the ventilation control mechanism from volume-controlled (VC) to pressure-controlled (PC) for the patient’s respiratory rate (RR), tidal volume, or both. PC ventilation is being employed regularly in operating rooms to handle patients with elevated Ppeak, despite a paucity of knowledge about its ventilatory and hemodynamic effects and potential downsides.3\n\nThe objective of this study is to compare volume control ventilation (VCV) and pressure control ventilation (PCV) in laparoscopic surgery patients, specifically examining their impact on ventilatory and hemodynamic responses. In PCV, the ventilator is responsible for regulating inspiratory flow and flow waveform to maintain a square inspiratory pressure profile while the physician adjusts the inspiratory pressure based on the measured tidal volume.\n\nVCV is commonly used in general anaesthesia to maintain steady minute ventilation during pulmonary resistance and compliance impact airway pressure. Volume-controlled ventilation (VCV) utilizes a steady flow to administer tidal volume. Nevertheless, this method can result in elevated airway pressures.4\n\nDuring laparoscopic surgeries, the presence of pneumoperitoneum can lead to decreased tidal volumes in patients. This is attributed to the increased pressure within the abdomen, which negatively affects the compliance of the chest wall and lungs. Consequently, the functional residual capacity decreases, leading to a reduction in alveolar ventilation.5\n\nThe study will assess the efficacy of ventilation by measuring various parameters such as end-tidal carbon dioxide (ETCO2), mean airway pressure (Pmean), peak inspiratory pressure (Ppeak), and expiratory tidal volume. Its primary goal is to determine whether VCV or PCV offers superior ventilation and preserves hemodynamic stability in patients undergoing laparoscopic procedures with pneumoperitoneum.\n\n\nProtocol\n\nThis study’s aim is to compare the efficacy of volume control ventilation with pressure control ventilation in patients undergoing laparoscopic surgery under general anaesthesia.\n\n\n\n1. The primary goal is to assess the effectiveness of ventilation by examining expiratory tidal volume, high peak pressure, and mean inspiratory pressure (Ppeak) (Pmean).\n\n2. The secondary goal is to compare the efficacy of hemodynamic response by evaluating variables such as heart rate (HR), oxygen saturation (SPO2), systolic blood pressure, diastolic blood pressure, and mean arterial pressure (MAP).\n\n\n\n▪ Study design:\n\n1. Study duration: Two years of research.\n\n2. Study area: JNMC and AVBRH’s anaesthesia department.\n\n3. Research design: Interventional parallel group randomised study\n\n4. Patients of either gender between the ages of 18 and 70 make up the study population.\n\n▪ Study setting\n\nThe research study has obtained ethical approval from the Ethics and Screening Committee of The Jawaharlal Nehru Medical College (JNMC), Datta Meghe Institute of Higher Education and Research, to be carried out at Acharya Vinoba Bhave Rural Hospital (AVBRH), Sawangi (M), Wardha. The study will involve 82 participants, and prior to their surgical procedures, all patients will be requested to provide written consent after receiving comprehensive information about the study.\n\n▪ Participants:\n\nCriteria for inclusion:\n\n1. Patients of any gender, ages 18 to 70.\n\n2. Patients in ASA Classes I and II.\n\n3. All patients who are willing to provide written, fully informed permission.\n\n4. The surgery duration is between 60 and 120 minutes.\n\nCriteria of exclusion:\n\n1. ASA Class III and higher.\n\n2. Patients’ rejection.\n\n3. Male or female, between the ages of 18 and 70.\n\n4. Patients who shouldn’t have laparoscopic procedures.\n\n5. People who experience allergic responses to anaesthetics.\n\n▪ Data analysis:\n\n1. Haemodynamic parameters, including heart rate, blood pressure, and blood oxygen level\n\n2. Mean inspiratory pressure (Pmean), Tidal volume, High peak pressure (Ppeak), and End-tidal CO2 (etco2)\n\n▪ Materials requirement:\n\n1. Appropriately sized cuffed endotracheal tubes and masks.\n\n2. Anaesthesia workstation Drager.\n\n3. Monitors with ECG, pulse oximetry, and non-invasive blood pressure.\n\n▪ Recruitment:\n\n1. Patient Counselling and Explanation: Prospective research volunteers will be identified and given in-depth counselling regarding the goals, methods, and possible advantages of the study during the pre-anaesthetic check-up. Patients will be made aware of the need for the study as well as its expected results.\n\n2. Informed Consent: A thorough informed consent form will be given to patients who indicate an interest in taking part. This form will provide a detailed description of the goals, methods, possible hazards, and advantages of the study. Patients will be able to voice any concerns and ask questions. Enrollment in the study will only be granted to individuals who furnish legitimate written consent.\n\n3. Patient Selection: Subjects must fulfil the required ASA and Mallampati classifications, fall within the given age range, and undergo laparoscopic procedures under general anaesthesia in order to be chosen for participation.\n\n4. Preoperative Evaluation: The day before surgery, every chosen patient will go through a thorough preoperative evaluation to determine their general health and suitability for the treatment. The study protocol contains specific measurements and assessments that will be part of this evaluation.\n\n5. Randomization: Subjects will be assigned at random to either Group A (pressure control ventilation) or Group B (volume control ventilation), which are the two study groups. To ensure impartial allocation, the randomization will be performed by staff members who are not directly involved in the study using a specified technique, such as computer-generated random numbers.\n\n6. Blinding: The patients and the anesthesiologist who records perioperative data will be unaware of the particular study medication that is given in order to preserve the study’s integrity.\n\n▪ Sample design & size:\n\nThe study will be conducted among 82 adult patients of both sexes (41 patients in each group) fulfilling all inclusion criteria. They will be allotted randomly using a computer generated sequence:\n\n•GROUP A (n=41): Patients receiving pressure control ventilation.\n\n•GROUP B (n=41): Patients receiving volume control ventilation.\n\n▪ Rationale for selected sample size:\n\nThe formula for sample size from the difference between two means was used to calculate the sample size of this study. The MAP after 15 mins of tracheal intubation was chosen to calculate the sample size.2\n\nZα: level of significance at 5%-95% confidence level\n\nZβ is the power of test = 80% = 0.84\n\nδ1 = SD of MAP in PCV = 15\n\nδ2 = SD of MAP in VCV = 10\n\nK = 1\n\nΔ = Difference between two means\n\nIn order to calculate sample size for comparing two means, data that was inputted.\n\n• Confidence Interval (2-sided): 80%\n\n• Power: 80%\n\n• The ratio of sample size (Group 2/Group 1): 1\n\n• MAP: 97 mmHg (Group A), 91 mmHg (Group B)\n\n• Standard deviation: 15 (Group A), 10 (Group B)\n\nSubstituting:\n\n• Zα = 1.28\n\n• Zβ = 0.84\n\n• δ1 = 15\n\n• K = 1\n\n• δ2 = 10\n\n• Δ = (97-91 = 6)\n\n\nMethods\n\nAfter giving written informed consent, 82 patients between the ages of 18 and 70 who will have laparoscopic surgery under general anaesthesia will be enrolled in the study. An intravenous line with an 18-gauge cannula will be started as soon as the patient enters the operating room, and monitors will be linked to them for continuous monitoring of their heart rate, ECG, non-invasive blood pressure, breathing rate, and oxygen saturation (SpO2). The baseline vitals will be noted. As part of a typical premedication protocol, patients will get 0.2 mg of Injection glycopyrrolate (Supplier: NEON; Catalogue Number: 6612; 0.004 mg/kg), 1 milligram of intravenous midazolam (Supplier: NEON; Catalogue Number: V304510; 0.05 mg/kg), and 1 milligram of injection butorphanol (Supplier: NEON; Catalogue number: KP094033; 0.04 mg/kg). Injection vecuronium 6 milligram intravenous (Supplier: NEON; Catalogue Number: 385376; 0.1 mg/kg) and injection propofol 100 milligram (Supplier: NEON; Catalogue Number: 338419; 0.2 mg/kg) will be used to induce anaesthesia in the patient.\n\nThe patient will be connected to a ventilator after being intubated with an acceptable internal diameter cuffed endotracheal tube. A total of 41 people will receive PCV (Group A), and a total of 41 people will receive VCV (Group B). Regular monitoring will be done periodically using the ET CO2 Pmean and Ppeak, NIBP, ECG, and pulse oximetry. Systolic blood pressure, Diastolic blood pressure, and respiratory parameters like respiratory rate, and saturation will be measured at the time of induction and every five minutes post-induction till 45 minutes (Table 1).\n\nThe Statistical analysis will be done using SPSS version 16. The statistical analysis conducted in this study will encompass both inferential and descriptive statistics. Inferential statistics, such as the chi-square test and unpaired t-test, will be utilized to analyze the data and make inferences about the broader population. Descriptive statistics, including measures like the mean, standard deviation, and standard error of the mean, will be computed to summarize and describe the data. A significance level of 5% will be applied to evaluate the statistical significance of the results.\n\n\nDiscussion\n\nIn 2011 Tyagi et al. did a study titled “A comparison between volume control and pressure control ventilation for laparoscopic cholecystectomy”, where they randomly assigned volume control ventilation and pressure control ventilation. The ventilator settings were assigned accordingly to match the parameters. The initial 5 minutes had no difference in peak and mean airway pressure. The peak airway pressure decreased after 10 and 30 minutes, and the mean pressure increased in PCV more than in VCV. This, they explained, is due to decelerating inspiratory flow rate. However, they could not see any differences in the ETCO2, gas exchange, or PaCO2.1\n\nIn a 2017 study conducted by Mihalj et al., the effects of pressure-controlled ventilation (PCV) and volume-controlled ventilation (VCV) on respiratory and hemodynamic parameters were examined during laparoscopic cholecystectomy. The study included 60 patients aged 18 to 70, with ASA scores ranging from 1 to 3, a body mass index (BMI) below 35 kg/m2, and no history of chronic respiratory disorders. The patients were randomly divided into two groups: one receiving protective pressure-controlled mechanical ventilation and the other receiving volume-controlled mechanical ventilation.\n\nInitially, no significant differences in respiratory and hemodynamic measures were observed between the two groups. However, when specifically comparing patients with a BMI of 25, it was found that the PCV group exhibited significantly lower peak inspiratory pressure (Ppeak) at 15, 30, and 45 minutes after tracheal intubation. Similar trends were observed in other measured parameters. The study concluded that PCV and VCV effectively maintained appropriate ventilation, oxygenation, and hemodynamic stability in the observed patient groups.2\n\nIn a 2007 study conducted by Balick et al., titled “Respiratory and hemodynamic effects of volume-controlled vs. pressure-controlled breathing during laparoscopy: a cross-over study with echocardiographic assessment,” the objective was to compare the respiratory and hemodynamic effects of volume-controlled (VC) and pressure-controlled (PC) ventilation in laparoscopic urological procedures. The study included twenty-one patients who underwent VC ventilation initially and then switched to PC ventilation. Tidal volume, respiratory rate, and fraction of inspired oxygen (FIO2) were maintained constant across both ventilation modes. The study findings indicated that pressure-controlled (PC) ventilation resulted in better outcomes in peak airway pressure, peak inspiratory flow, and dynamic compliance compared to volume-controlled (VC) ventilation. However, no significant differences were observed in static airway pressure, static compliance, or arterial oxygenation. The systolic and diastolic heart performance assessment also showed no notable changes. Therefore, the study concluded that PC ventilation had no immediate benefits over traditional VC ventilation in patients undergoing laparoscopic procedures with pneumoperitoneum.3\n\nIn a 2020 study conducted by Salah et al. titled “Comparison Between Volume Controlled Ventilation and Pressure Controlled Ventilation in Laparoscopic Bariatric Surgeries,” the researchers aimed to investigate how different ventilation modes impact respiratory parameters and the need for postoperative ventilation in laparoscopic bariatric surgeries.\n\nThe study revealed that pneumoperitoneum during these surgeries led to a significant increase of 68% in inspiratory resistance and a decrease of 30% in compliance among obese patients compared to normal-weight patients. These changes reduced arterial oxygenation due to decreased functional residual capacity, pulmonary shunting, ventilation-perfusion mismatch, and increased atelectasis, particularly in obese patients. However, no significant differences in oxygenation levels between volume-controlled and pressure-controlled ventilation modes were observed.\n\nInterestingly, the study showed that pressure-controlled ventilation resulted in significantly lower levels of arterial carbon dioxide (PaCO2) after pneumoperitoneum, at the end of the surgery, and in the postoperative period. This was the case despite similar preoperative PaCO2 levels between the two groups.\n\nIn another study from 2014 titled “Comparison of pressure and volume-controlled ventilation in laparoscopic cholecystectomy operations,” researchers specifically examined the effects of pressure-controlled ventilation (PCV) and volume-controlled ventilation (VCV) during the surgery. The study concluded that based on patient characteristics, surgical procedures, anaesthesia, pneumoperitoneum, and recovery period there were no significant changes. Hemodynamic data and blood gas values were also similar. However, both groups experienced decreased lung compliance after pneumoperitoneum, with a more pronounced effect observed in the PCV group. The VCV group showed a significant increase in tidal volume at 10 and 20 minutes after insufflation. According to the study, the group receiving pressure-controlled ventilation (PCV) exhibited higher values of alveolar dead space ventilation to tidal volume ratio before pneumoperitoneum and a higher alveolar-arterial oxygen gradient after pneumoperitoneum compared to the group receiving volume-controlled ventilation (VCV). However, the dynamic compliance of the respiratory system was similar between the two groups. The study results showed that by using volume-controlled ventilation for laparoscopic surgeries required tidal volumes to be on higher side and alveolar-arterial oxygen was less after pneumoperitoneum. These findings suggest that VCV may offer improved alveolar ventilation compared to PCV in laparoscopic cholecystectomy procedures.5\n\nPelosi et al.’s (1998) study, “The Influence of Body Mass on Gas Exchange, Lung Volumes, and Respiratory Mechanics,” looked at how body mass index (BMI) impacts respiratory variables under general anaesthesia. Their method entailed analysing compliance, resistance, gas exchange, and the effort needed to inhale one litre of air using the oesophageal balloon technique and rapid airway obstruction. At the same time, functional residual capacity (FRC) was calculated using the helium dilution technique. The study included 24 participants randomly selected in a supine position before surgery, divided into three groups based on BMI: normal BMI (<25 kg/m2), moderately obese (BMI between 25 and 40 kilograms per square metre), and severely obese (BMI >40 kilograms per square metre). The results of the study revealed the following changes as BMI increased:\n\nThe compliance of the chest wall was marginally impacted, while the compliance of the lung and the overall respiratory system dropped dramatically.6\n\n“Haemodynamic and respiratory outcomes for pressure-controlled ventilation versus volume-controlled ventilation in patients undergoing laparoscopic surgery” was a study by Martinez et al. conducted in 2007. This study involved 40 Class I/II ASA patients with elective laparoscopic surgery. The patients were given fentanyl (2 mg/kg), propofol (2 mg/kg), and atracurium (150 mg/kg) to produce anaesthesia while they fasted starting at midnight the night before the procedure. Following a thorough relaxation assessment, endotracheal intubation was carried out and scored with a train of four (TOF). Sevoflurane (1 MAC) was used to keep the anaesthesia in place. PCV or VCV was administered to patients at random. Both groups’ hemodynamic parameters during the various period records were comparable. Mean, systolic, and diastolic pressures were comparable. In comparison to 97.25 + 1.2 for VCV, SpO2 increased during pneumoperitoneum up to 97.61 + 1.29 for PCV. SpO2 levels for both groups remained identical ten minutes after insufflation. Both PCV and VCV were well-tolerated treatment options for individuals undergoing laparoscopic surgery.7\n\nIn a study by Gupta et al., the effects of volume-controlled ventilation (VCV) and pressure-controlled ventilation (PCV) on oxygenation8 in obese patients undergoing laparoscopic cholecystectomy were investigated. The study included 102 adult patients with a 30-40 kg/m2 BMI. Initially, all patients received VCV, but after pneumoperitoneum, they were randomly assigned to continue with VCV or switch to PCV. The results showed that the PCV group had significantly higher arterial oxygen partial pressure (PaO2) levels and lower alveolar-arterial oxygen gradient (PAO2-PaO2) values than the VCV group. The VCV group required higher tidal volume and minute ventilation to maintain appropriate CO2 levels. In contrast, the PCV group improved lung ventilation by using higher flow rates in the early inspiratory phase. Despite lower tidal volume and minute ventilation in the PCV group, adequate carbon dioxide elimination was achieved. PCV was found to reduce the adverse effects of high tidal volumes. Another study by Sen et al. also compared VCV and PCV in patients undergoing laparoscopic cholecystectomy and found that the PCV group had lower peak airway pressure levels, reduced systemic stress response, and improved oxygenation compared to the VCV group. Overall, these findings indicate that PCV might be an improved option for laparoscopic surgery in terms of oxygenation and lowering stress reaction.9\n\nBy comparing the effects of pressure-controlled ventilation (PCV) and volume-controlled ventilation (VCV) on oxygenation parameters in obese patients having laparoscopic cholecystectomy, Movassagi et al. conducted a randomised prospective trial. Seventy patients with ASA physical status I-II and a BMI of 30 to 40 were enrolled in the study.\n\nInitially, VCV was used, and after pneumoperitoneum was established, patients were randomly assigned to either the PCV or VCV group. The results revealed that the VCV group required larger tidal volumes and respiratory rates to maintain the necessary CO2 levels at specific intervals. Following pneumoperitoneum, the VCV group exhibited significantly higher peak airway pressure compared to the PCV group. However, the two groups had no significant changes in plateau pressure and mean airway pressure. Oxygenation parameters, such as PO2, PCO2, and pH, showed no significant differences between the two groups, except for a few instances after pneumoperitoneum, where the PCV group displayed higher PO2 levels.\n\nThe study concluded no clinically significant differences between PCV and VCV in obese patients undergoing laparoscopic cholecystectomy. Although PCV demonstrated some improvements in plateau pressure, mean airway pressure, and oxygenation parameters, it may be beneficial to consider using a dual-mode strategy to mitigate complications effectively.10\n\nThe ethics and screening committee has approved the research proposal at Jawaharlal Nehru Medical College in accordance with guidelines prescribed by Central Ethics Committee on Human Research (CECHR). Patients will be informed verbally at the time of hospital admission about the nature of the study. This will include a description of the procedures involved, potential discomforts and risks, anticipated benefits, alternative treatment options, monitoring and support methods, and the responsible staff members. The information will be conveyed in clear and accessible language.\n\nPatients will receive explanations both before and during the study about its methodology, explicitly stating that a placebo group will not be used and that participation in a control group is possible. They will be informed of their right to decline participation or withdraw from the study at any point without any penalties or negative impact on their care. They will be assured of the confidentiality of their data, the absence of expense reimbursement for participating in the research, and the forms of compensation available in case of any harm resulting from the study, following the ethical standards and regulations for human studies as outlined in the Helsinki Declaration (2014). Written informed consent will be obtained from all participants to ensure their understanding and voluntary participation in the research.\n\nREF NO.: DMIMS (DU)/IEC/2022/90\n\nDate: 20/07/2022\n\nThe findings of the study will be shared with participants and relevant organisations, as well as published in an acceptable scholarly journal.\n\nControl group data collection is ongoing.", "appendix": "Data availability\n\nNo data are associated with this article.\n\nReporting guidelines:\n\nRepository name: Zenodo,Checklist for Comparative study of the efficacy of volume control ventilation vs pressure control ventilation on patients undergoing laparoscopic surgeries under general anaesthesia: DOI: 10.5281/zenodo.11530839. 11\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgements\n\nThe writer wishes to thank the personnel at the Department of Anaesthesia in JNMC, AVBRH, Sawangi, Wardha, India, for their assistance.\n\n\nReferences\n\nTyagi A, Kumar R, Sethi A, et al.: A comparison of pressure-controlled and volume-controlled ventilation for laparoscopic cholecystectomy. Anaesthesia. 2011; 66(6): 503–508. PubMed Abstract \| Publisher Full Text\n\nMihalj M: Effects of Pressure-Controlled vs. Volume-Controlled Ventilation on Hemodynamic and Respiratory Parameters in Patients During Laparoscopic Cholecystectomy. Acta Clin. Croat. 2017 [cited 2023 May 17]; 56: 555–560. PubMed Abstract \| Publisher Full Text Reference Source\n\nBalick-Weber CC, Nicolas P, Hedreville-Montout M, et al.: Respiratory and haemodynamic effects of volume-controlled vs pressure-controlled ventilation during laparoscopy: a cross-over study with echocardiographic assessment. Br. J. Anaesth. 2007 Sep; 99(3): 429–435. PubMed Abstract \| Publisher Full Text\n\nSalah A, Shonoda AM, Khalaf K, et al.: Comparison between volume controlled ventilation and pressure controlled ventilation as regards effects on respiratory parameters and need of postoperative ventilation in laparoscopic bariatric surgeries. Ain Shams Med. J. 2020 Sep 1; 71(3): 635–646. Publisher Full Text\n\nAydın V, Kabukcu HK, Sahin N, et al.: Comparison of pressure and volume-controlled ventilation in laparoscopic cholecystectomy operations: laparoscopic cholecystectomy operations. Clin. Respir. J. 2016 May; 10(3): 342–349. PubMed Abstract \| Publisher Full Text\n\nPelosi P, Ravagnan I, Tredici S, et al.: The effects of body mass on lung volumes, respiratory mechanics, and gas exchange during general anesthesia. Anesth. Analg. 1998; 87: 654–660. PubMed Abstract\n\nMartínez-Leyva E: Haemodynamic and respiratory outcomes for pressure-controlled ventilation and volume-controlled ventilation in patients submitted to laparoscopic surgery.\n\nGupta S, Kundu S, Ghose T, et al.: A comparison between volume-controlled ventilation and pressure-controlled ventilation in providing better oxygenation in obese patients undergoing laparoscopic cholecystectomy. Indian J. Anaesth. 2012; 56(3): 276–282. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSen O, Umutoglu T, Aydın N, et al.: Effects of pressure-controlled and volume-controlled ventilation on respiratory mechanics and systemic stress response during laparoscopic cholecystectomy. Springerplus. 2016 Dec; 5(1): 298. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMovassagi R, Montazer M, Mahmoodpoor A, et al.: Comparison of pressure vs. volume controlled ventilation on oxygenation parameters of obese patients undergoing laparoscopic cholecystectomy. Pak. J. Med. Sci. 2017 Oct 9 [cited 2023 May 17]; 33(5): 1117–1122. PubMed Abstract \| Publisher Full Text \| Free Full Text Reference Source\n\nDhakshinamurthy P, Singam A: Comparative study of the efficacy of volume control ventilation vs pressure control ventilation on patients undergoing laparoscopic surgeries under general anaesthesia (Version 1). Zenodo. 2024. Publisher Full Text" }	[ { "id": "301211", "date": "25 Jul 2024", "name": "Dita Aditianingsih", "expertise": [ "Reviewer Expertise Anesthesiology and Critical Care 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\nThe manuscript entitled \"Comparative study of the efficacy of volume control ventilation vs pressure control ventilation on patients undergoing laparoscopic surgeries under general anaesthesia\" is written with an acceptable language, has a clear study objective and well-defined protocol is. A couple of things to consider: 1. In the first paragraph of background, \"muscle relaxation\" is the definition of paralysis, please place the definitions accordingly. 2. Please provide the values of intraabdominal pressure that will be applied during laparoscopic surgery, whether it is variable or as a set value for all patients, as it may have an effect on hemodynamics. 3. In the exclusion criteria you stated, \"Male or female, between the ages of 18 and 70\". Please confirm if you meant below 18 and above 70 years of age. 4. Please consider to include in your exclusion criteria, patients who undergo conversion to laparotomy during laparoscopy, or patients who encounter complication during surgery which may result in hemodynamic instability. 5. Will there be any monitoring of the depth of anesthesia and neuromuscular blocking, to make sure that it is constant throughout the duration of operation? 6. Please provide the hypothesis of this study.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Yes\n\nAre sufficient details of the methods provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable", "responses": [] }, { "id": "312147", "date": "11 Sep 2024", "name": "Frank Sterke", "expertise": [ "Reviewer Expertise Biomedical engineering", "abdominal dynamics and interaction with mechanical 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\nThis study aims to determine which ventilation mode is superior for patients undergoing laparoscopic surgery with a pneumoperitoneum.\nFirstly, I want to commend the authors for addressing an important issue in the context of laparoscopic surgery with pneumoperitoneum. The choice to compare volume-controlled ventilation (VCV) and pressure-controlled ventilation (PCV) is highly relevant given the increasing number of laparoscopic procedures and the potential for pulmonary complications. Overall, your protocol provides a strong foundation for an important study. These suggestions aim to further refine and clarify the research approach to maximize its potential impact.\nTo further enhance the study and its presentation, I have a few suggestions:\n1) Introduction: Emphasize it is a protocol paper. 2) Aim: focus on etCO2 to evaluate efficacy of ventilation. One would expect oxygenation as well to assess efficacy. 3) Methods and analysis: Study design, of either gender --> just all patients.\n\n4) Methods and analysis: Study setting, ethical approval statement is somewhat scattered over the paper. (Considerations in the discussion and in the protocol) I would advise to keep al the ethics in one section. 5) Methods and analysis: Participants, type in the criteria of exclusion 6) Methods and analysis: Data analysis. I would suggest to include Peak inspiratory pressure, respiratory frequency and I:E ratio. These are known to affect the mechanical efficiency.\n\n7) Methods and analysis: Data analysis. I would suggest to include evaluate lung compliance and airway resistance as patient characteristic. 8) Methods and analysis: Data analysis. I would suggest to include insufflation settings and body position. These can affect the interaction between surgical cavity and respiratory system. 9) Methods and analysis: Materials requirement: For repeatability one would expect the sizes types and brands of the used materials and measurement devices. 10) Methods and analysis: Recruitment, \"A thorough informed\". I would leave out thorough, not because I don't think it is being thorough but because it is an arbitrary/vague word. I think your description already emphasizes your thoroughness. 11) Methods and analysis: Recruitment, clarify the Randomization sections. It is somewhat unclear whether you intend to randomize or if/how you actually randomized. Specifying the technique is enough I would say. 12) Methods and analysis: Rationale for selected sample size, this one is important to me. If I understand correctly, the sample size is estimated based on MAP. Yet MAP is not a primary outcome in this study. I believe it is required to use primary outcome for sample size calculation. 13) Discussion: I believe the author has an excellent overview of the relevant literature. It would help the reader to summarize the discussion and evaluate the potential implications of this study and compare the strengths and limitations of the protocol to the existing protocols described in literature. This will help to emphasize the importance of this study. 14) Out of curiosity, perhaps worthy to add to the discussion, what outcome does the author hypothesize. Which mode does the author expect to be superior and what's the reasoning behind it. 15) References: \"Modeling intra-abdominal volume and respiratory driving pressure during pneumoperitoneum insufflation-a patient-level data meta-analysis\" by Mazzinari et al. [ref 1] could be of interest to you.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Partly\n\nAre sufficient details of the methods provided to allow replication by others? Partly\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable", "responses": [] } ]	1	https://f1000research.com/articles/13-678
https://f1000research.com/articles/13-238/v1	28 Mar 24	{ "type": "Research Article", "title": "How research consortia can contribute to improvements in PhD students’ research environment and progress in sub-Saharan African countries", "authors": [ "Taghreed El Hajj", "Neele Wiltgen Georgi", "Susie Crossman", "Nadia Tagoe", "Imelda Bates", "Neele Wiltgen Georgi", "Susie Crossman", "Nadia Tagoe", "Imelda Bates" ], "abstract": "Background The Africa Capacity Building Initiative (ACBI) programme aimed to ‘strengthen the research and training capacity of higher education institutions and support the development of individual scientists in sub-Saharan Africa through UK-Africa research collaborations’ including by funding PhD studentships. We conducted research to understand students’ experiences and to see how consortia-based programmes such as ACBI and their own institutions can enhance PhD students’ research environment and progress.\n\nMethods In-depth interviews with 35 ACBI-funded PhD students explored their perspectives about how their research and personal development benefitted from belonging to a research consortium. Questionnaires were used to corroborate interview findings.\n\nResults Students recognised that membership of a research consortium provided many benefits compared to less well-resourced peers. By drawing on the programme and consortiums’ resources, they were often able to overcome some limitations in their own institution’s systems and facilities. Through their consortia they could access a wide range of international expertise and support from mentors and colleagues for their technical and psychosocial needs. Multiple consortia opportunities for engaging with the international scientific community and for networking, gave them confidence and motivation and enhanced their career prospects.\n\nConclusion Our study and its recommendations highlight how the breadth and diversity of resources available to PhD students through research consortia can be harnessed to facilitate students’ progress and to create a supportive and conducive research environment. It also underlines how, through a multi-level approach, consortia can contribute to longer-term improvements in institutional research environments for PhD students.", "keywords": [ "Research capacity strengthening", "research environment", "PhD programmes", "research institutions", "natural sciences research", "sub-Saharan Africa" ], "content": "Introduction\n\nStrengthening research capacity in countries in the global south is a goal of many international research funders and development agencies because research can help to solve national problems and thereby drive socioeconomic development (UNESCO, 2015). Sustainable funding to conduct research and to enhance institutions’ research environments is important for training, motivating and retaining researchers (Colenbrander et al., 2015), yet most African research institutions continue to face serious funding shortfalls (Teferra, 2013). Increasingly this is being addressed through collaborative arrangements for joint support from external partners and governments (UKCDR, 2021). The UK spend on strengthening research capacity in low- and middle-income countries is vast. Between 2016-2021 the UK government and the Wellcome Trust alone spent £873M on dedicated research capacity strengthening schemes and £1.2B on projects that ‘add on’ capacity strengthening (UKCDR, 2021). 80% of this spend was on African institutions, predominantly universities, and much of this was through research consortia.\n\nBetween 2012-2022 the UK Government’s Foreign, Commonwealth and Development Office (FCDO), in partnership with the Royal Society funded the Africa Capacity Building Initiative (ACBI), a pilot study to ‘strengthen the research and training capacity of higher education institutions and to support the development of individual scientists in sub-Saharan Africa through UK-Africa research collaborations’ (Royal-Society, 2018). The ACBI programme focused on three research areas: i) water and sanitation, ii) renewable energy and iii) soil-related science and aimed to initiate lasting improvements in the research environment within the African host institutions. ACBI comprised ten research consortia, each involving one UK and three African institutions. Each ACBI-affiliated African institution hosted at least one PhD student: in total the ten ACBI consortia supported 38 PhD students based in 26 African institutions across 18 sub-Saharan African countries. Each consortium received funding for five years, including for PhD studentships which covered the students’ research expenses, travel and training and a contribution to equipment costs.\n\nThe Centre for Capacity Research (CCR) at the Liverpool School of Tropical Medicine was responsible for monitoring, evaluating and learning about capacity strengthening aspects of the ACBI programme and was not directly involved in any of the activities of the consortia or PhD students. As new learning emerged from the programme, this was disseminated to the ACBI management team, funders and consortia through regular meetings and presentations at programme conferences. In collaboration with all of the African and UK research leads, and with the PhD students themselves, CCR guided research in two phases to better understand and improve the capacity strengthening processes used within ACBI. In the first phase, and in partnership with the lead researchers in African institutions, we conducted qualitative baseline assessments of research capacity across eight ACBI-affiliated African institutions to identify existing capacity gaps and strengths, and to highlight examples of good practice and problem-solving strategies that could be shared within and beyond the programme. The assessments identified institutions’ strengths and gaps in postgraduate training and overall research environment against an evidence-informed benchmark (Bates et al., 2014). A detailed account of these findings has been published elsewhere (El Hajj et al., 2020). Whilst findings revealed significant differences in PhD programmes, institutions commonly experienced challenges with registration and induction, finances, communication, supervision, workload, infrastructure, research management and professional development and networking opportunities (El Hajj et al., 2020; Pulford et al., 2020).\n\nThese findings clearly indicated a need to strengthen PhD training programmes but before making recommendations for improvement, it was important to explore the perspectives of the African PhD students themselves. This was the focus of the second phase of the research and of this manuscript. In particular we aimed to understand how to improve a) consortium-based PhD training and b) PhD programmes provided by institutions, based on the challenges identified and experiences of the cohort of ACBI PhD students, including creating a constructive and supportive environment where everyone’s contributions to research are valued.\n\n\nMethods\n\nEthical approval for this study was granted by the Research Ethics Committee of the Liverpool School of Tropical Medicine (approval number: 17-061, approval granted 9th July 2018). Informed verbal consent was obtained from each student after explaining the purpose of the study, the type of questions that would be asked, research procedure, voluntary participation, recording purposes, anonymity, confidentiality and privacy, risks, benefits and dissemination of findings. They were free to withdraw at any time.\n\nWe used a mixed-methods approach with in-depth interviews as the primary source of data complemented by quantitative self-administered questionnaires to validate findings from the interviews. The PhD students were asked to consider the contributions made to their PhD experience by their institutions and their consortium at three levels – their individual development, the research infrastructure and support mechanisms, and their opportunities for interactions at the (inter) national level. To help ensure validity, the topics covered at each of these levels were based on discussions with the African lead researchers about the findings that emerged from the baseline assessment of institutions’ PhD programmes. We also took account of informal feedback from the PhD students themselves about their experiences, and publications about the organisation of PhD programmes. We invited all 38 doctoral students directly supported by the ACBI programme to participate. We focused on the challenges that hindered their research progress, and the role ACBI played in addressing the challenges and in improving their institutions’ research environment.\n\nInterviews\n\nIn-depth semi-structured interviews were conducted with 35 of the 38 ACBI-affiliated PhD students (92%): three students were absent at the time of the interviews or on maternity leave. All interviews, except one, were conducted in English and face-to-face between July 2018 and October 2019, either during site visits to ACBI-affiliated African research institutions or when students visited the UK. One interview was conducted online (in French) in October 2020 due to COVID-19 pandemic travel restrictions. Interview questions covered topics that were previously identified as challenges in the baseline assessment such as student satisfaction with stipend; overall PhD progress; supervision; research outputs; challenges that might hinder or delay progress (at the personal, institutional and consortium levels); benefits from involvement in the ACBI programme; and suggestions for improvements. For equity purposes and to ensure all the students remained engaged in the research, they were all interviewed although data saturation was achieved after approximately three-quarters of the interviews had been completed (i.e., no new information emerged from the later interviews).\n\nQuestionnaires\n\nQuestionnaires were provided to all 38 students to be completed online, electronically via email or in a hard copy format between May and December 2018. The overall response rate was 87% (33/38 students).\n\nInterviews were led by TEH supported by SC who observed and took notes during interviews; notes were then discussed and compared to clarify any discrepancies and to ensure and verify accuracy. All interviews, except one (at the student’s request), were digitally recorded after written and verbal consent was obtained. Recordings were transcribed, coded in NVivo software (under licence to Liverpool School of Tropical Medicine), and analysed using thematic analysis framework [supplementary file 1] in Excel. Data coding and thematic analysis were carried out and discussed by two researchers (TEH and NWG) for verification and to ensure research rigour. Preliminary themes were presented and discussed with other research team members for their input and feedback. Quantitative data were analysed using the Statistical Package for the Social Sciences (SPSS) software (under licence to Liverpool School of Tropical Medicine). For anonymity purposes, all quotes presented in this manuscript were given a unique number code to conceal the student’s identity.\n\nCharacteristics of the PhD students\n\nOf the 35 PhD students interviewed, 60% (21) were males and 40% (14) were females. Of the 33 students who completed the questionnaire, 58% (19) were males and 42% (14) were females (mean age 37 years). The majority of students (61%; 20) were conducting their research in a renewable energy related field; this reflects that five of the ten ACBI consortia (22/38 students) had a focus on renewable energy. The remaining students were doing research in soil-related sciences (21%; 7) or water and sanitation (18%; 6). The majority (79%; 26) were in their second (13) or third year (13) of studies at the time they filled the questionnaire, and were mainly hosted at a “public university” (85%; 28/33). The rest were hosted either at a “research institution” (9%; 3/33) or at a “private university” (3%; 1/33). Only one student reported “other” for their type of institution. 79% (26/33) of students had “English” and 21% (7/33) had “French” as the main language of instruction at their host institution.\n\nThemes that emerged from our analysis of the students’ interviews and questionnaire responses were divided into those that primarily focused on the infrastructure, facilities and research environment provided by students’ institutions and those that focused on the individual students’ supervision and personal development. We first describe the challenges experienced by the PhD students and then explain how many of these were mitigated by being part of a research consortium and, through the consortium, involved in the overarching ACBI programme.\n\nInadequate research infrastructure and facilities in students’ institutions occasionally hindered their PhD progress and also had implications for their motivation and longer-term retention.\n\n“… there are certain facilities that are not readily available to us and puts us at the downside when it comes to research because we may not be able to necessarily keep up with developed countries when it comes to cutting-edge research, mainly because of facilities. I do not want to attribute it to economic state of the country but unfortunately that plays a role too. I think we have a lot of technical know-how because most of the experts in the country are not trained here. They’re trained outside. But when they come back to help, they get frustrated because there are systems that don’t necessarily function and the facilities that you were trained with are not here…”\n\n[007, PhD student, male]\n\nInstitutional financial and procurement systems\n\nInadequate or slow financial and procurement systems within students’ institutions impacted on the processing of their stipends and procurement of equipment and consumables. In some instances the consortia intervened to process stipend payments, procure equipment and pay for travel through a UK or African institution to avoid delays.\n\nLaboratory facilities\n\n80% of ACBI’s PhD students needed laboratory facilities for their research so challenges with these featured highly in interviews with students. They had difficulties accessing the laboratory itself or the equipment because it was being used by another student, researcher or laboratory technician, or else the laboratory was occupied by undergraduate students or equipment had access restrictions.\n\n“Access to instruments. That’s the one thing I would say really becomes a challenge, because not only is it the limited resources, but also the number of students that get to use the same instruments. So, there’s quite a lot of waiting in-between.”\n\n[034, PhD student, male]\n\nMore than half the students reported that their laboratories had dysfunctional equipment that occupied vital space but was not disposed of or repaired. Some students sought alternative ways of accessing the equipment they needed such as through commercial laboratories or other academic institutions, mostly in the UK.\n\n“You see, for our work we use a lot of instruments for the analysis, which are missing. And in most of the cases it’s the work of the university to supply that, to have it. So, without the instruments for your work, you can’t do much. […] Okay, I try to do whatever I can do with the limited facilities I have… like, when I was there [in my home country] what I was able to do was to prepare the materials so that once I am here [in the UK], I can just characterise them using the facilities here.”\n\n[035, PhD student, male]\n\nStudents who had to access facilities in external laboratories also experienced delays, for example, while waiting for health and safety training, or academic or technical supervision.\n\n“I stayed three months [here at the UK institution] but last time, it was worse to me … because they arranged the adviser to be here. When I came here, my advisor told me ‘It’s not my area’. So, I attended a master course on two courses, and I tried to work myself, to talk with my lecturer because they suggested the course can help me for my design.”\n\n[028, PhD student, female]\n\nFrequent power outages which delayed their research were reported by some students.\n\n“Then the power, there’s no power. Sometimes I’m there for three weeks and there’s power maybe for five days out of those three weeks.”\n\n[024, PhD student, female]\n\nAlthough the ACBI programme provided for the purchase of research equipment and consumables to support PhD students’ research, a third of the students interviewed had encountered significant delays with procurement or sub-standard quality items.\n\n“Another challenge for the synthesis is that you will need the chemicals and when you order the chemical it takes six months, even one year, or they are never delivered at all. And, you see, the challenge is, most of these chemicals, you don’t need just one chemical - you need one, three or five chemicals and you need to use them all at the same time.”\n\n[035, PhD student, male]\n\nAccess to literature\n\nStudents often struggled to access journal articles and other e-resources through their institutional libraries so many found alternative sources. These included free, open access journals and platforms such as Sci-Hub and Google Scholar; requesting articles directly from authors; requesting articles through colleagues in institutions outside the country (including UK Principal Investigators); and by being granted library access through affiliation to a UK institution. Suggestions for improving access to literature included: provision of tutorials and support to students on how to retrieve literature and access resources (e.g., how to use search engines and literature databases); enhancing institutions’ subscription to scientific journals and databases; extending library opening times; improving access to computers, electricity and internet; and establishing collaborations with institutions with better access to literature.\n\nQuestionnaire results\n\nThe questionnaire findings from the 33 PhD students largely corroborated those from the interviews with the 35 PhD students from the same cohort. More than 80% of the students whose research was laboratory-based stated that new laboratory equipment purchased through ACBI was useful for the progress of their research work. More than half the students were “satisfied” or “very satisfied” with meeting rooms (66.6%), study area (60.6%), office space (54.5%) and teaching rooms/lecture halls (57.7%). Over half were also “very satisfied” with the power supply (60.6%), internet and IT/computer facilities (54.5%), library facilities (63.6%), and access to journals in their research field (54.5%). Barriers to accessing literature resources at students’ in-country institutions included lack of access to relevant databases/literature (64%), poor Wi-Fi/internet connection (45%), limited resources in general and in the repository (42%), and outdated resources in the library (36%). However, less than half (48%) were “satisfied/very satisfied” with their personal study space, access to relevant databases (45.4%), laboratory facilities (42%), and research software packages (39%). Lack of software packages caused particular frustration and delays for students doing computational research especially when combined with insufficient IT hardware, poor internet and interrupted power supply.\n\nProcesses and supervision\n\nStudents indicated that having a doctoral school (or equivalent) that had effective processes for admission, induction, progress monitoring and examinations, and which offered careers and financial advice, hardship funds and counselling and well-being services contributed to a positive experience. However, the students themselves had little or no involvement in framing policies and regulations at their institution relating to doctoral training programmes and student experiences.\n\nThe supervision experiences of the PhD students varied widely across the consortia; experiences that were supportive and encouraging were described as “motivating”.\n\n“Usually, it’s a reinforcement by supervisors. They are integrated in our lives. I don’t know how to put it not to sound weird but … These guys are always encouraging you, especially if you’re actually working. I’ve worked under a number of people where if you go with the problem, no attention is paid to you or very little attention is paid to you. But these guys are involved. They’re with you the whole time. And they’re quite available as well, especially [Prof X] - he reinforces the fact that he believes in you. That’s the main motivation aside from the fact that you have family as well that are relying on you.”\n\n[007, PhD student, male]\n\nStudents perceived good quality PhD supervision to be characterised by a having a supervisor with appropriate research expertise, and who was able to provide relevant technical and professional support. They also recognised that high-quality supervision also meant the supervisor provided timely responses and feedback to queries, was available for regular follow-up meetings, and provided clear and transparent communications and guidance. Four students mentioned that their lead supervisor lacked experience or knowledge in their research field. In a few cases, this led to the student having to repeat their work due to unreliable results leading to demotivation and lost time and resources.\n\n“Prof has supervised a lot of students from various fields, but I think it would still be very good if there’s someone who knows exactly what you’re doing. I think it takes longer if you are finding that information all by yourself, but if you ask someone who is ahead of you, who has done something similar, you can tap from that person’s knowledge and move forward. I think that is a little bit not there.”\n\n[019, PhD student, male]\n\nTwo students also reported inadequate support and unavailability of their main supervisor.\n\n“The challenge is getting them. Sometimes you write, you remind them like five times, no one is responding. Of course, it discourages you.”\n\n[014, PhD student, female]\n\nStudent-supervisor relationships\n\nDuring the interviews students indicated that the relationship dynamics between students and supervisors are complex and hierarchical. Students perceived that they were very reliant on their supervisors for successful progression on the doctoral programme. This was because it was the supervisors who had to review their thesis, and provide feedback and technical advice, and who also facilitated the students’ future research, work opportunities, and professional and scientific networks. These dynamics were mentioned in almost all interviews regardless of the students’ satisfaction level with their supervisors and their overall supervision experience.\n\nSome students acknowledged and accepted that “respect” for the supervisor’s position, knowledge, expertise and even age, was the basis of a “professional relationship”. A few students felt frustrated and anxious with the imbalance in student-supervisor power relations and expressed challenges in managing differences of opinion with their main supervisor, to the extent that most of the dissatisfied students were only willing to provide “off-the-record” information.\n\n“Clear guidelines guarding both students and supervisor must be made and communicated to both. Until you get into trouble, you sometimes do not know some guidelines exists.”\n\n[011, PhD student, male]\n\nJoint supervision\n\nUnder the ACBI scheme, the Royal Society strongly encouraged implementing a shared supervision between the UK and African institutions. In the vast majority of cases, this proved to be a successful approach that PhD students found valuable and constructive as it gave them access to diverse expertise, knowledge, resources and discussions and enriched the scientific input to their research work. However, for a few students this resulted in an overwhelming number of supervisors. For instance, four students reported having between four and six supervisors because their own institution allocated two to three local supervisors and they were also assigned external supervisors from their ACBI consortium. Whilst students acknowledged the value of having various supervisors with different areas of expertise to add richness to their research, they also stated that managing timely feedback and discrepancies in opinions and reaching a consensus on ways to move forward could be challenging and delay progress.\n\n“I have 6 supervisors … consulting with so many supervisors with different opinions gets me confused and sometimes delays my work progress …”\n\n[003, PhD student, female]\n\nMonitoring PhD progress\n\nAll students interviewed had formal or informal progress monitoring by their own institution (i.e., by their supervisor, department or graduate/doctoral school) or by their ACBI consortium. These included filling out progress forms (each semester or annually) which had to be signed by their supervisor and submitted to the graduate school at the university. A couple of students thought these processes not effective. Other mechanisms included meetings (weekly, monthly, ad hoc) with their primary supervisor or presentations at departmental and consortium meetings.\n\n“Every month … the last Friday of every month, I’m supposed to meet Prof. It doesn’t happen all the time because sometimes he’ll get busy and all that. I go to him, I tell him what I have done, what I’m doing – for example, some occasional informal outputs: I’ve made a couple of reports—presentations and groups of lectures …”\n\n[019, PhD student, male]\n\nStudents found presentations to groups to be useful because they stimulated debates and discussions which were learning opportunities not only for the student but also for other researchers and fellow students.\n\n“Yes, quarterly almost [student present their work progress to supervisors and department]. Then, as a consortium, every time we meet for consortium meeting, we have a presentation which show the way we progress our research. Also, apart from a consortium meeting, we have summer conferences where we have to give our presentation and then you have to let your supervisors know. It is also a way of monitoring your progress.”\n\n[026, PhD student, male]\n\nSome students were required by their institutions to provide regular written reports in order to obtain their stipend, or to present their progress to formal supervision panels convened by their institution or their ACBI consortium.\n\n“… Every six months we submit a six-month progress report to the faculty. We have to show the results, give the aim, objectives of the results.”\n\n[030, PhD student, female]\n\n“ … We have a committee that is organised by department where you have your supervisor, the student and two outsiders from your field. We do have a meeting every six months. [….] Yes, without the general meeting, we have a progress report every month, myself and my supervisors. Then the general one is every six months. That contains other groups beside the supervisors and students.”\n\n[006, PhD student, male]\n\nFor two students their consortium tracked their progress by monitoring their data inputs into a database:\n\n“[The UK PI] created a page [at UK University X] where almost every data you have finished, you submit it to that page. Yes, a format yes where almost all the data we are having for most of us it is still in a raw form but what we have been able to type and send, you send it to that page … No set monitoring system in place with the supervisor.”\n\n[011, PhD student, female]\n\nThe majority of students were confident that any delays in progress would first be discussed with their supervisor(s), then with the UK consortium lead before any further action was taken at a higher level (either by their institution or the ACBI programme).\n\nQuestionnaire results\n\nAlthough 58% of students reported being “satisfied” or “very satisfied” with communication by their graduate school, the majority reported that they did not receive any financial hardship (88%) or career advice (61%), or any counselling or well-being services (55%). Only 12% of students reported “ever participating in developing/updating post-graduate related policy and strategies at their department/institution”.\n\nThe vast majority of students (94%) had had “good” or “satisfactory” quality of PhD supervision and 82% described their relationship with their main supervisor as “good” or “very good”. Most students (79%) considered their lead supervisor to be an expert in their subject area and 67% “always” received enough support from their main supervisor(s). 64% “always” received timely feedback from their supervisor(s) with a turnaround time of two days to one week. Over half the students (52%) met with their supervisors at least once a month and 33% met with them at least once a week. 67% of the students were aware of the PhD progress monitoring processes/guidelines at their institution but only a few (21%) were aware of the institutional procedures and actions taken if progress was unsatisfactory.\n\nStudents’ enhanced knowledge and skills\n\nAlmost all the students were enthusiastic about their participation in ACBI recognising it as a great opportunity and a privilege. Many of the students interviewed were aware that professional development opportunities provided by their host institutions for PhD students were very limited due to the lack of funding. Almost all students considered themselves to be privileged because through their consortia and the ACBI programme they could access a wide range of technical and research skills training opportunities. They recognised that these opportunities would likely be unattainable and unaffordable for their colleagues who were self-funded, non-ACBI PhD students.\n\n“My research skills have been built in a lot of ways, I have learnt new research methodologies, I have learnt new statistical approaches, I have learnt new laboratory techniques.”\n\n[001, PhD student, female]\n\nStudents reported a significant increase in self-confidence, knowledge, and skills from their participation in ACBI. For instance, many PhD students felt equipped to mentor and train their peers, masters students and undergraduates within their home institutions, and felt empowered to progress into fellowship programmes and lectureship positions after graduation.\n\nAround a third of students were involved in teaching at their institution. Despite the additional workload they recognised that this improved their knowledge and skills, and positively contributed to their research work and career development.\n\n“I cannot complain because in our consortium we do most of the time visit other institution partner. Also, sometimes, we do organize - every year we have this consortium meeting. When we arrive, sometimes we present and organize some workshop with students in the department. That’s it. Sometimes we do have training, a lot of activities. In our case, I will say, so far, we got my team, I can say that the research capacity is going on well.”\n\n[020, PhD student, male]\n\n“I learnt a lot from sharing my knowledge with other students although this sometimes puts pressure during peak teaching times and during my fieldwork.”\n\n[002, PhD student, female]\n\nA couple of students even suggested making “teaching undergraduates” part of the requirements for PhD students under the ACBI programme.\n\n“Teaching experience has pushed me to mature from the stage of constantly being taught to a point where I can supervise undergraduate projects.”\n\n[007, PhD student, male]\n\n“I’ve benefited greatly with the interaction with [field technician X] I think…Also seeing somebody’s life improve because of this project has been very amazing. To watch [the field technician’s] confidence grow and just his life has just got better. [Principal Investigator X] often says that this that’s come out of this project is very ready to be celebrated because he cares so deeply about the project, he tried to understand it and everything.”\n\n[038, PhD student, female]\n\nSome UK PIs made efforts to engage students in other projects beyond the ACBI programme allowing students to learn how to manage projects, encouraging them and opening new opportunities for them.\n\n“One major benefit is networking with other PhD students and African researchers and researchers in the UK … I hope our relationship continues beyond the programme, and I think it will …”\n\n[003, PhD student, female]\n\nFrancophone students reported improved English language skills, especially for those who spent a few months in the UK and interacted with researchers and academics in English.\n\n“… Secondly, I improved my English. I learned English in secondary school but because I never communicate and I was not a part of an English programme, it is not something that matters for me to improve or to do any effort to communicate in English. From this program I’ve seen that we have to learn.”\n\n[010, PhD student, female]\n\nMentorship and peer support\n\nMost students had received mentorship, though only two described this as ‘formal’. Mentorship was provided by senior colleagues at their own institution (e.g., lecturers, postdoctoral researchers, laboratory technicians) or by ACBI-affiliated research fellows or PhD students. Mentors facilitated exchange of scientific ideas and involvement of students in training and consultations. They provided technical and moral support and encouragement. They gave advice on research opportunities and future career direction, reviewed documents and provided feedback on students’ scientific writing and overall research work.\n\n“I’ve got some informal mentorship, especially that we’ve already got to the writing [stage]. At [X] University, we’ve got two guys who used to deliver scientific writing sometimes …. When you write, you submit, and they can check it for you and to give a few feedback … It has been very helpful for me because I used to have it as a pre-processing of my writing before I submit to my school supervisor.\"\n\n[026, PhD student, male]\n\n“[They have a] mentor in a fellowship program that I was involved in …. So, she was my former mentor, because it’s a mentorship program, and I have since graduated from that program, but she has continued mentoring me morally, and also even […] she is one of those I can have a document and ask her to proof-read for me, or to go through it.”\n\n[001, PhD student, female]\n\nStudents valued the academic and professional support, and advice and problem-solving offered through their consortium, and from regional and international experts.\n\n“They [African and UK researchers in the consortium] bring in a very good level of expertise, so I have benefited through their expertise; and even the methods that I’m using through my study are quite new to me, and all that has been facilitated through this consortium.”\n\n[001, PhD student, female]\n\nTwo students stated that they would have benefited from having an “independent mentor” (outside their department and/or consortium) whom they could confide in and reach out to when faced with difficulties from their supervisor(s).\n\nA quarter of the students reported that positive interactions (e.g., sharing research ideas, peer reviews, support with methods and data analysis) with other students, colleagues and senior researchers contributed to a positive working and learning environment. However, a few students felt they lacked a supportive environment mainly due to a competitive research environment at their institutions. For instance, students indicated that some lead researchers did not encourage the advancement of PhD students and early-career researchers, particularly if they felt exposed or insecure about their own academic performance.\n\n“Spirit of collaboration needs to be enhanced and unhealthy competition among lecturers, and lecturers and students should be subdued.”\n\n[011, PhD student, male]\n\n“… maybe they [supervisors or lead researchers] feel threatened. They fear that the student might do better than the supervisor.”\n\n[030, PhD student, female]\n\nNetworking\n\nStudents indicated that opportunities for networking, and for establishing long-term professional partnerships and academic collaborations (such as shared publications, grant writing, knowledge sharing) were some of the most valuable benefits of belonging to ACBI. These opportunities included South-North and South-South exchange visits, scientific meetings and conferences, and training workshops. These enabled students to interact with a wide range of researchers, experts and scientists from within and outside their research field and to participate in joint research activities within and beyond their consortium.\n\n“… it’s giving me so much exposure just in terms of the conferences that I’ve been able to attend and the links that I’ve been able to establish. I know and communicate with people almost from every corner of the world just because of this one project.”\n\n[024, PhD student, female]\n\nThese activities allowed the students to strengthen their communication skills and confidence through networking and presenting research findings.\n\n“… presenting at the meetings and conferences, it gives you the chance to speak. You get more confidence in yourself in presenting and all [the networking].”\n\n[030, PhD student, female]\n\nImportantly this networking built a sense of solidarity among the whole cohort of African ACBI PhD students and enabled them to create African communities beyond their own consortium on specific research topics using WhatsApp.\n\n“The collaboration with the south-south has been really beneficial … We’ve been able to collaborate with each other, learn from each other and become inclusive with the research that we are doing, and even it’s kind of built this solidarity amongst the [African] nations … even amongst the students, apart from times when we meet during the consortia meeting, when we go back to our different countries, we are able to communicate with each other and talk about our projects and update on our progress.”\n\n[003, PhD student, female]\n\nAll students interviewed reported communicating with other PhD students “within their consortium” and around half reported communicating with PhD students “across other research consortia within ACBI”. These interactions were mostly perceived as beneficial for providing peer-to-peer support such as sharing and discussing the challenges they faced; discussing solutions and good practices; learning about new/innovative research methods and techniques; reviewing each other’s work (peer-review); and advising on ways to improve research work.\n\n“Our group, I’ll say, it’s a rainbow … Different colours all matched together. That’s what I love about it … Perfected by its colours - so like everybody is from their [own] discipline, but usually, even in the meetings you see that there’s no difference between [us] despite the [specialised work] that they are doing … [We communicate] a lot … WhatsApp, emails … I think we have moved from being colleagues to being siblings. Because I remember one time, I was having a problem with my [X] experiments, so I made a WhatsApp call, so we ended up having a video call training and it was three hours long… That’s how we are usually …”\n\n[008, PhD student, female]\n\nIn rare cases, competition between students within the same consortium hindered collaboration and communication between the students and created a feeling of isolation and discomfort at the beginning of the programme. However, as soon as their interaction and communication with each other and with students from other consortia increased, they started to open up, share information and help each other. This eventually created more solidarity, understanding and support for each other.\n\nQuestionnaire results\n\nQuestionnaire data supported the interview findings, showing that the vast majority of students (88%) felt “advantaged compared to other PhD candidates at their department/school”. More than half (58%) of students reported being “satisfied” or “very satisfied” with the access to personal development and skills training opportunities; and 70% reported being “satisfied” or “very satisfied” with their opportunities to participate in conferences, workshops and competitions. More than half the students (61%) had a mentor other than their supervisor (e.g., post-doctoral/senior researcher) and 67% received support from other PhD students. Students utilised their consortia for “participating in capacity building activities organised by the consortia” (76%); “knowledge exchange” (61%); “building network for career related reasons” (55%); and for visits to UK partner institutions (52%).\n\nOur findings indicate that students had identified several hinderances to progressing their PhD studies that were beyond their control and which were mostly related to inadequacies in their institutions’ research infrastructure and systems (Box 1). Many of these were recognised by consortium leaders and the ACBI management team and mitigated for the student through their own consortium within the overall ACBI programme. In particular, ACBI invested heavily in providing equipment for the research consortia and to support PhD student’s projects. This meant that some students no longer needed to travel to other laboratories to conduct their experiments. Some departments even used their own funds to refurbish their laboratories to accommodate the new equipment and instrumentation purchased through ACBI. The new laboratory equipment, computers and software also benefited other researchers, students, and research support staff such as laboratory technicians.\n\n\n\n\n\n▪ Delays in financing which affected equipment purchase and stipends\n\n▪ Slow procurement processes\n\n▪ Unreliable power supply\n\n▪ Lack of laptop/computer\n\n▪ Insufficient time allowances for maternity leave\n\n▪ Lack of access to up-to-date resources (e.g., books, manuals, research articles)\n\n▪ Lack of quiet study space\n\n\n\n▪ Laptop provided for each student\n\n▪ Improved access to scientific literature e.g., through granting access to UK university libraries during exchange visits, and consortia members providing articles on request\n\n▪ Advocated for better study and learning space that positively impacted on PhD studies\n\n▪ Research consortia processed funds/stipends and paid for travel which avoided payment interruptions and delays\n\n▪ Improved financial administration and procurement (e.g., faster turnaround of funding claims)\n\n▪ Extended PhD timelines to account for maternity and sick leave\n\n\n\n▪ Inadequate laboratory and field equipment including licences for computational software\n\n▪ Lack of, or sub-standard, laboratory consumables and reagents\n\n▪ Restricted access to laboratories and/or lack of laboratory availability to conduct research\n\n\n\n▪ Purchased quality consumables and new equipment (e.g., GPS, cameras, projectors, laptops, software, high-performance computers) that benefited the students and their institution\n\n▪ Granted PhD students access to sophisticated laboratory equipment unavailable in their own institutions, through exchange visits to other institutions in their consortium\n\n\n\n▪ Lack of the technical training to do research work\n\n▪ Inadequate PhD supervision\n\n▪ Security issues hindered fieldwork\n\n▪ Lack of professional development opportunities\n\n\n\n▪ Provided technical and generic training (including through exchange visits)\n\n▪ Provided PhD students with opportunities to present at scientific conferences and meetings – which enhanced their self-confidence and communication skills, and where they learnt about different research cultures/systems\n\n▪ Improved English language skills and networking with Francophone institutions, among Francophone students\n\n▪ Consortia provided academic and professional support, advice and guidance from a range of world-class experts and supervisors (including assigning supervisory panels and formal monitoring of progress)\n\n▪ Networking and collaboration between PhD students and their supervisors which fostered high quality research and research outputs\n\n* Note that laptops and training were provided but may not have been in place for all students at the time of this study.\n\n“… we’ve had funds to do some previously, say, impossible things. We’ve bought so much equipment, some of them we used to maybe dream about them. We’ve finally had the funds to buy this equipment. We’re doing some ground-breaking research.”\n\n[024, PhD student, female]\n\n33% of the students observed changes in the infrastructure and learning environment that they attributed to the ACBI programme, and which positively impacted on their PhD programme and experience.\n\n\nDiscussion\n\nThe overall aim of this study was to identify actions that were then used to improve the ACBI programme within its lifetime. More broadly - and using practical experiences and examples from a large UK-Africa research programme - we also aimed to explore how institutions and consortia-based programmes can help to create a constructive environment that supports PhD students’ progress and wellbeing. In close collaboration with senior African researchers and programme managers, we collected data focused on the perspective of 35 African PhD students. Using these data we have formulated recommendations that will be useful for institutions to improve their own doctoral programmes and for designing other large, multi-national, consortia-based research programmes. Creating a supportive research environment and a sense of belonging to a department is an important part of strengthening research capacity including for the progress, interest, empowerment and retention of PhD students (Langhaug et al., 2020; Pyhältö et al., 2009; Stubb et al., 2011; van Rooij et al., 2021). A supportive research environment is one which is inclusive and values everyone’s contributions to research; it encompasses the behaviours, values, expectations, attitudes and norms of research systems (Moran et al., 2020; Royal-Society, 2021; UK Government; Department for Business, 2021). The recommendations from this study focus primarily on the perspectives of the PhD students. Our complementary findings about PhD programmes from the institutional perceptive have been published previously (El Hajj et al., 2020).\n\nData for our study were obtained through interviews with the students during the course of their PhD programmes. The interview findings were corroborated using questionnaires completed by the same students. These provided an idea of the weighting behind each of the different perspectives expressed by the students. Our findings fell into three categories: factors affecting the infrastructure and systems of institutions hosting the students; the PhD processes and student supervision; and students’ professional development, though – since our participants were PhD students – most of the findings concerned the last two categories.\n\nPrevious studies of institutional research capacity (Pulford et al., 2020) and PhD programmes in low- and middle-income countries have shown that access to adequate research facilities and appropriate infrastructure is a major enabler for sustainable research capacity (Ogundahunsi et al., 2015; Pilowsky et al., 2016) and for timely completion of PhD programmes (Pitchforth et al., 2012). Consortia were able to circumvent several weaknesses in institutions’ infrastructure and systems thereby reducing hindrances to students’ progress. For example, they were able to arrange timely procurement of good quality equipment and consumables. Although ACBI did not fund building or infrastructure costs, the programme was able to advocate for improvements in internet access and power supplies for students, and for their need to have a quiet space in which to study and write.\n\nACBI’s focus on natural science research meant that accessing up-to-date research equipment (laboratory or computational) was commonly mentioned as essential to their successful progress. Through their consortium, many students were able to use world-class equipment for their research either because this was purchased for their own institutions or because they had funds to travel to other institutions within their consortium where such equipment – and training on its use – was available. Despite the support from ACBI, students still faced difficulties with their institutions’ slow procurement processes and unavailable or sub-standard consumables and equipment, and even when the equipment was procured internationally, there were often delays at customs. Issues with procurement delays and poor-quality equipment and consumables, despite funding from external programmes, have been found in previous studies (Pulford et al., 2020) suggesting that this is a widespread and intractable problem that is a substantial barrier to effective research, that would be a good target for a focused joint effort by institutions and their collaborators.\n\nAn innovative aspect of the ACBI programme was the formalisation of arrangements to transfer ownership of the equipment to the African partner institutions along with an agreed maintenance and sustainability plan. Access to scientific literature and up-to-date resources is essential for PhD students to learn about the latest discoveries, innovations, problems and methods in their research field (Colenbrander et al., 2015; Davis & Walters, 2011). Through their consortium, PhD students were able to have much better access to scientific journals than many of their own institutions were able to provide. Some students were even given access to the libraries of their UK partner institutions. For others, members of institutions within the consortium partnership were able to provide students with the articles they needed.\n\nPrevious studies have indicated that supervision quality, good communication and the relationship between the student and supervisor are vital for students’ motivation and progress (Ali et al., 2017; Cotterall, 2013; Ives & Rowley, 2005; Khozaei et al., 2015; Lee, 2008; Leijen et al., 2016; van Rooij et al., 2021; Welde & Laursen, 2008; Young et al., 2019). Positive supervision experiences motivate students, increase their self-confidence and create a constructive drive for their work progress. A negative supervision experience can lead to frustration, delays and demotivation. The PhD students in the ACBI programme benefited by having supervisors from within their own institution and from their consortium. This gave them access to a broad range of expertise in their subject area and more personal support than would have been possible for students who were not part of a large programme. The vast majority of students were satisfied with their PhD supervision and their relationship with their supervisors.\n\nA few students were dissatisfied with the quality of their supervision and attributed this to their supervisor having insufficient knowledge of the research topic, being unavailable or unable to provide clear guidance or timely feedback, and tensions in the supervisor-student relationship. Reasons for poor quality PhD supervision highlighted in previous studies (Lee, 2008; Leijen et al., 2016; Young et al., 2019) include supervisors’ overwhelming teaching and administrative workloads (Lee, 2008; Pulford et al., 2020), their styles and approaches to supervision (Lee, 2008), and lack of accountability and oversight of PhD supervision (Colenbrander et al., 2015). Students’ own characteristics, such as their research skills (Ali et al., 2017; Khozaei et al., 2015), knowledge and experience, communication and management skills, and their ability to write academically (Khozaei et al., 2015) and to critically reflect, also contribute to PhD supervision quality and progress (Lee, 2008).\n\nDespite the high levels of satisfaction with their supervision, the ACBI PhD students made several suggestions about how their supervision could be further improved. These included establishing clear roles and responsibilities for students and their supervisors, formalised tracking of progress, and training for supervisors in communication, leadership, management and supervisory skills. Such suggestions have been made previously along with clearly defined standards for programme admission and supervision of doctoral students, improving students’ critical thinking abilities, and enhancing supervisors’ skills so they can develop relationships in which students feel motivated, inspired and cared for (Ali et al., 2017; Duke & Denicolo, 2017; Lee, 2008).\n\nDevelopment of confidence and interpersonal skills is highly valued by doctoral students (Lindén et al., 2013) and is important preparation for their future whether it is within or outside academia (Duke & Denicolo, 2017; Lindén et al., 2013), but is often an overlooked component of PhD programmes (Lee, 2008). This was not the case in ACBI which provided multiple opportunities for students’ personal and professional development covering technical and soft skills such as academic writing and presentation skills. These opportunities included technical training, language skills (for French-speaking students), exchange visits, conference attendance and scientific discussions with world-class experts in their field.\n\nThrough ACBI, students had a large pool of colleagues and mentors they could turn to for academic and personal support during different aspects and stages of their programme. This support took various forms including reviews of data analyses and draft publications which improved their quality, discussions to help guide students’ careers, and personal and psychosocial support. Students recognised that their acquisition of new knowledge and skills, their expanded networks and collaborations, and all-round support provided by their consortium for their research and personal needs, had boosted their career prospects, self-confidence and motivation.\n\nBy working together and taking a multi-level approach to capacity strengthening, institutions and research consortia programmes can attain consortium goals as well as systemic and sustainable improvements in institutions’ PhD programmes. Below we have summarised the suggestions proposed by the African PhD students in this study about how their institutions and consortia can contribute to a conducive research environment, and how they can mitigate barriers to progress faced by the students (Box 2). In addition to promoting sustainable PhD training benefits, adoption of these suggestions would help to provide the kind of environment that the PhD graduates can thrive in beyond the consortium period.\n\n\n\nResearch facilities\n\n\n\n• Provide access to quality consumables and state-of-the-art equipment, and reliable power supply\n\n• Streamline and speed-up procurement processes for research equipment and supplies\n\n• Provide access to quiet study space and to research journals\n\n• Advocate for adequate IT capability\n\nSupervision and mentoring\n\n\n\n• Set out the role and responsibilities of supervisors and students, including reciprocal timely feedback\n\n• Ensure supervisors have expertise and research skills to match the students’ research topic\n\n• Ensure supervisors have adequate time to provide quality supervision and that they are held to clear and appropriate standards\n\n• Provide training and ongoing support for supervisors including in technical, communication, supervisory and management skills\n\n• Establish formal induction and progress monitoring processes for students\n\n• Ensure students have a manageable number of supervisors\n\n• Provide students with access to mentors (formal or informal) to provide additional research expertise, psychosocial support and careers and personal guidance\n\nPersonal development\n\n\n\n• Provide training in technical skills, critical thinking, and in research management and leadership; tailor this to meet students’ needs and career aspirations\n\n• Facilitate exchange visits for technical training and exposure to different research environments and systems\n\n• Foster supportive and inclusive collaborations among the PhD cohort and with other researchers and research support staff within and beyond their institution and consortium\n\n• Provide opportunities for (inter) national networking with peers and research topic experts, and facilitate collaborations to enhance career and research opportunities\n\nOur study highlighted areas for further research including:\n\n• How can consortia facilitate more efficient procurement systems in partner institutions, sustainably and in a way that does not undermine the institution’s own systems?\n\n• How to foster a sense of belonging to a department among PhD students?\n\n• How does the transfer of project equipment ownership to partner institutions, along with agreed maintenance and sustainability plans, impact institutions’ research performance (e.g., enhanced research opportunities and potential for income generation)?\n\n• How can inconsistencies in PhD supervision be minimised to ensure that all PhD students receive high quality academic support?\n\nSome of these research questions concerning the challenges faced by PhD students cannot be directly addressed by consortia because they depend on changes in institutions’ broader research environment and need long-term efforts and investments. Nevertheless, externally-funded research projects need to be cognisant of these and have a role to play in catalysing improvements. For example projects can:\n\n• Involve institutional leaders/stakeholders in their capacity strengthening plans and share emerging findings with them\n\n• Promote institutional investments (possibly with project co-funding) to address systemic challenges for PhD training (e.g., providing and refurbishing space for new equipment or study space, and for improved internet)\n\n• Facilitate PhD-relevant policy development and revisions, and the involvement of PhD students in these processes\n\n• Promote counselling and well-being services for PhD students\n\n• Facilitate strategic institutional collaborations with long-term potential beyond the project’s lifetime (e.g., through shared use of laboratory equipment)\n\n• Set up pilot institutionally-owned projects to tackle systemic challenges (e.g., concerning financial and procurement procedures) which are scalable beyond the project lifetime\n\nOur study had several strengths and limitations. Our participants were a large cohort of contemporaneous African PhD students who were part of the ACBI natural sciences research programme. The size of the cohort, the balanced gender mix, their diverse institutions and multiple countries meant that the students had many different perspectives which provided broad and deep data for the study. The students all belonged to the same programme (ACBI). This reduced confounders due to differences in management processes and access to resources that would have been present if they had all been affiliated with different programmes. However, as all the students were doing natural sciences research, there was a strong emphasis in this study on laboratory facilities; findings relating to these aspects may therefore not apply in the context of non-laboratory research. Despite ACBI’s natural sciences focus, the variety in types of studies and research topics (Royal-Society, 2018) means that the findings are likely to be applicable to science PhD students across sub-Saharan Africa and in other low- and middle-income countries. We were aware that students may have felt constrained in providing perspectives that may be construed as critical of their institutions or supervisors. We mitigated this by ensuring that all responses were anonymised, by assuring students of complete confidentiality and advising them they were able to withdraw their comments or participation at any time.\n\n\nConclusion\n\nOur study has highlighted several ways in which research consortia can contribute to conducive environments for PhD students, and how they can make the students’ experiences positive and fulfilling. Unlike more senior researchers, PhD students’ experiences are critically linked to their relationship with, and quality of support from, supervisors and mentors, and this was reflected in their interviews and in our recommendations. Since they were science students, the quality and availability of equipment and consumables was also a common focus of their recommendations. The networking and collaboration opportunities provided by consortia were highly valued by the PhD students with many intangible benefits such as confidence-building and enhanced career prospects. Our study findings provide valuable insights into how consortia can complement and contribute to improvements in the PhD programmes and facilities of their member institutions, and promote a conducive research environment in which the students can feel supported and flourish.", "appendix": "Data availability\n\nTranscriptions of interviews have not been made available as a dataset because they cannot be de-identified without compromising anonymity and the project’s ethical approval conditions. These limit the access to raw, unprocessed data strictly to the research team to safeguard the privacy and confidentiality of participants. Despite these constraints, the authors are open to discussing specific requests for further information (via the corresponding author) about the contents of the transcripts while strictly adhering to ethical obligations.\n\nHarvard Database: Extended Data - How research consortia can contribute to improvements in PhD students’ research environment and progress in sub-Saharan African countries, https://doi.org/10.7910/DVN/DRKNED (Centre for Capacity Research, 2024).\n\nThis project contains the following extended data:\n\n• ACBI Online Survey_PhD candidates 2018_Unrestricted_FINAL.docx\n\n• Interview Guide PhD Students-Phase 2-FINAL.docx\n\n• Participant Information Sheet_ PhD Candidates Interview.docx\n\n• RS-DFID Consent form_ACBI PhD students_Template.doc\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\n\nAcknowledgements\n\nWe are grateful to all ACBI-affiliated PhD students who agreed to take part in this research study and provided valuable information and insight about their personal experiences. We are also thankful to all ACBI lead and senior researchers who made the necessary logistical or administrative arrangements to allow a smooth data collection process, as well as the Royal Society grants’ management team for their continuous support and collaboration.\n\n\nReferences\n\nAli F, Shet A, Yan W, et al.: Doctoral level research and training capacity in the social determinants of health at universities and higher education institutions in India, China, Oman and Vietnam: a survey of needs. Health Res. Policy Syst. 2017; 15(1): 76. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBates I, Boyd A, Smith H, et al.: A practical and systematic approach to organisational capacity strengthening for research in the health sector in Africa. Health Res. Policy Syst. 2014; 12: 11. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCentre for Capacity Research: Extended Data - How research consortia can contribute to improvements in PhD students’ research environment and progress in sub-Saharan African countries. Harvard Dataverse. 2024; V1. Publisher Full Text\n\nColenbrander S, Lovett J, Abbo MS, et al.: Renewable energy doctoral programmes in sub-Saharan Africa: A preliminary assessment of common capacity deficits and emerging capacity-building strategies. Energy Res. Soc. Sci. 2015; 5: 70–77. Publisher Full Text\n\nCotterall S: More than just a brain: emotions and the doctoral experience. High. Educ. Res. Dev. 2013; 32(2): 174–187. Publisher Full Text\n\nDavis PM, Walters WH: The impact of free access to the scientific literature: a review of recent research. J. Med. Libr. Assoc. 2011; 99(3): 208–217. 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Publisher Full Text\n\nLanghaug LF, Jack H, Hanlon C, et al.: “We need more big trees as well as the grass roots”: going beyond research capacity building to develop sustainable careers in mental health research in African countries. Int. J. Ment. Heal. Syst. 2020; 14(1): 66. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLee A: How are doctoral students supervised? Concepts of doctoral research supervision. Stud. High. Educ. 2008; 33(3): 267–281. Publisher Full Text\n\nLeijen Ä, Lepp L, Remmik M: Why did I drop out? Former students’ recollections about their study process and factors related to leaving the doctoral studies. Stud. Contin. Educ. 2016; 38(2): 129–144. Publisher Full Text\n\nLindén J, Ohlin M, Brodin EM: Mentorship, supervision and learning experience in PhD education. Stud. High. Educ. 2013; 38(5): 639–662. Publisher Full Text\n\nMoran H, Karlin L, Lauchlan E, et al.: Understanding Research Culture: What researchers think about the culture they work in [version 1; peer review: 1 approved, 1 approved with reservations]. Wellcome Open Res. 2020; 5: 201. Publisher Full Text\n\nOgundahunsi OAT, Vahedi M, Kamau EM, et al.: Strengthening Research Capacity—TDR’s Evolving Experience in Low- and Middle-Income Countries. PLoS Negl. Trop. Dis. 2015; 9(1): e3380. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPilowsky DJ, Rojas G, Price LN, et al.: Building Research Capacity Across and Within Low- and Middle-Income Countries: The Collaborative Hubs for International Research on Mental Health. Acad. Psychiatry. 2016; 40(4): 686–691. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPitchforth J, Beames S, Thomas A, et al.: Factors affecting timely completion of a PhD: a complex systems approach. J. Scholarsh. Teach. Learn. 2012; 12(4): 124–135. Reference Source\n\nPulford J, Crossman S, Begg S, et al.: Strengthening research management and support services in sub-Saharan African universities and research institutions [version 2; peer review: 2 approved, 1 approved with reservations]. AAS Open Res. 2020; 3: 31. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPyhältö K, Stubb J, Lonka K: Developing scholarly communities as learning environments for doctoral students. Int. J. Acad. Dev. 2009; 14(3): 221–232. Publisher Full Text\n\nRoyal-Society: The Royal Society-FCDO Africa Capacity Building Initiative.2018. Reference Source\n\nRoyal-Society: The Royal Society-Research culture.2021. Reference Source\n\nStubb J, Pyhältö K, Lonka K: Balancing between inspiration and exhaustion: PhD students’ experienced socio-psychological well-being. Stud. Contin. Educ. 2011; 33(1): 33–50. Publisher Full Text\n\nTeferra D: Funding Higher Education in Africa: State, Trends and Perspectives. J. High. Educ. Afr. 2013; 11: 19–51.\n\nUK Government; Department for Business, E. I. S: Policy paper Research and development (R&D) people and culture strategy.2021. Retrieved 22 July 2022. Reference Source\n\nUKCDR: UK funding landscape for research capacity strengthening in low- and middle-income countries. Briefing paper. UK Collaborative on Development Research; 2021. Reference Source\n\nUNESCO: United Nations Educational Scientific and Cultural Organization. UNESCO Science Report: towards 2030.2015. Reference Source\n\nvan Rooij E , Fokkens-Bruinsma M, Jansen E: Factors that influence PhD candidates’ success: the importance of PhD project characteristics. Stud. Contin. Educ. 2021; 43(1): 48–67. Publisher Full Text\n\nWelde K, Laursen S: The “Ideal Type” Advisor: How Advisors Help STEM Graduate Students Find Their ‘Scientific Feet’. Open Educ. J. 2008; 1: 49–61. Publisher Full Text\n\nYoung SN, Vanwye WR, Schafer MA, et al.: Factors Affecting PhD Student Success. Int. J. Exerc. Sci. 2019; 12(1): 34–45. PubMed Abstract" }	[ { "id": "263540", "date": "30 Apr 2024", "name": "Julie Reeves", "expertise": [ "Reviewer Expertise Researcher development", "doctoral supervision", "research leadership and research capacity strengthening." ], "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 mixed method study provides an important insight into the perceptions and experiences of doctoral researchers in international consortia, and continues the research into the ACBI programme. The paper makes a critical addition to our understanding of international consortia and the benefits they are able to bring to doctoral researchers, and their institutions. We do not know enough about the experiences of researchers in international research partnerships - and this paper makes a very welcome contribution to the field. One that will be useful to other international research partnerships with doctoral and early career researchers. It is particularly notable that the voices and perspectives of the African PhD students in the consortia provide the central focus of this research and the paper.\n\nThe suggestions the authors make towards mitigating the challenges doctoral researchers face and their findings, are especially useful in encouraging consortia to be mindful of the impact they can have in leveraging resources and expertise to support individuals and institutions. .\nThe interview transcripts have not been made available as anonymity cannot be maintained if they were open source (i.e. No - the source data are not available). However, the interview questions and the questionnaire are available and make it possible for similar studies to be undertaken by other international research consortia.\n\nThe authors uniquely enquired into the perceptions of doctoral researchers in the consortium. The interview questions and the questionnaire used to corroborate the interview data, were comprehensive and will have yielded a rich range of data. The study design is consistent and builds on a baseline assessment and an established evidence informed benchrmark approach. The ACBI was a substantial programme and the authors have been able to draw on 35 of 38 doctoral researchers for interview purposes. The authors make excellent use of the qualitative data and quotations to illustrate their key points. This enables important points about the interviewees' experiences to unfold in their own words. The paper has a comprehensive structure and is well written.\n\nIn view of the above, there is a need for some more detail in a few places and to help situate the reader on occasion. For example, the 'Characteristics of the PhD students' indicates the gender makeup of respondents, but the paper does not indicate whether or not there were any areas of significant gender difference. There is a good summary of the field of study, the nature of the institutions, the stage of study and language in this section, yet the reviewer wondered if it was possible to offer any overall information about the countries in which the respondents are located without compromising anonymity. As 18 countries were involved in the consortia, were there any notable regional differences? It would be useful to have an indication of the common complaints, with percentages, among the interviewees to follow the demographic/characteristics information. An overall view (perhaps in a table against the key themes) would help to set the scene for the remainder of the paper and the detailed quotations. There are a few areas where an example would assist the reader and add to the paper. For instance, under the section 'Institutions' research infrastructure and facilities', an example to illustrate what is meant by 'inadequate research infrastructure and facilities' (is this lab equipment or research management offices, or both?) would help the reader to appreciate the comment that follows. Where some students reported delay due to power outages or those students undertaking computational research who were frustrated by software- are the authors able to say how many students were affected?\n\nA minor point - the Introduction paragraph says 'The UK spend on strengthening research capacity in LMIC is vast'. 'Vast' is a strong word and one would want to know how this spend compares with internal research funding or other countries' expenditure, to qualify the term.\nAn excellent study and enjoyable paper that will stimulate reflection on international research partnerships and the experiences of the researchers within them.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? No\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] }, { "id": "276503", "date": "06 Jun 2024", "name": "Donald Cole", "expertise": [ "Reviewer Expertise Historically research capacity strengthening among others", "methodologically mixed methods." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nGreat to see this work based on interviews with doctoral students, and relevant doctoral studies literature.\n\nAbstract provides a good summary of the article.\nMethods seem to start in the Ethics section, not sure why. The mixed methods design would appear to be overlapping based on the timelines identified. Reference to a typology of mixed methods designs would be helpful e.g. Cresswell and Plano's text.(Creswell et al., 2017)(Ref-3)\nMore information could be provided on the sources for questionnaire items i.e. prior questionnaires in the literature, conceptual framework of the parent study, etc. Reference to the availability of the questionnaire, and the interview guide in the extended data instruments and consent should be noted in the Methods section.\n\nSources of interview questions are more fully set out.\nWas analysis sequential i.e. questionnaires first as completed first, then interview data? or was it integrated as per the theme description? Currently interview analysis and themes are described prior to questionnaire analysis and results, though participant characteristics described jointly.\nPlease clarify each of these so Methods can be rated yes vs partly.\nFindings include some well known but some very exciting newer findings like solidarity among doctoral students in the networking section.\n\nBox 1 also helpful as a very positive statement on consortia impact.\nDiscussion includes some unnecessary repetition of methods. The links with literature are good, though some on other consortia experience in Africa would be worthwhile e.g. (Adedokun et al.,2014)(Ref-1) or (Ruhweza Katahoire A et l.,2023) (ref-2) The very recommendation focused discussion is important for the application of the study, including Box 2. Similarly some good further research questions. Among limitations, your note in findings that some interviewees asked that material be \"off the record\" is an indication of constraints that they felt. What proportion of interviewees indicated this?\nIn the conclusions, I would clarify that these were natural science students, as sciences include social and health sciences as well.\nThe terms \"underlying data\" and \" extended data\" are new to me. It would seem that the latter is really research instruments, data collection and ethics related. The former would seem appropriate for the interview transcripts. Not clear from the questionnaire data. Can you clarify?\n\nIs the work 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": "11776", "date": "24 Jun 2024", "name": "Susie Crossman", "role": "Author Response", "response": "1. Methods seem to start in the Ethics section, not sure why. The mixed methods design would appear to be overlapping based on the timelines identified. Reference to a typology of mixed methods designs would be helpful e.g. Cresswell and Plano's text.(Creswell et al., 2017) Was analysis sequential i.e. questionnaires first as completed first, then interview data? or was it integrated as per the theme description? Currently interview analysis and themes are described prior to questionnaire analysis and results, though participant characteristics described jointly. >> the ethics section has been moved to the end of the methods >> the timelines for conducting and analysing data from the different methods have been clarified, Briefly, the majority of the baseline questionnaires were completed in May 2018. A few students were unable to complete them online because of difficulties in accessing the form and were therefore given the opportunity to fill them in either offline (via email) or in-person prior to their face to face interviews which were held in either July/ August 2018 or December 2018. >> the description of, and rationale for, the mixed methods approach has now been expanded and supported by the helpful Cresswell reference [thank you] 2. More information could be provided on the sources for questionnaire items i.e. prior questionnaires in the literature, conceptual framework of the parent study, etc. Reference to the availability of the questionnaire, and the interview guide in the extended data instruments and consent should be noted in the Methods section. Sources of interview questions are more fully set out. >> more details about the sources for the questionnaire and interview items have been provided >> the link to the ‘extended data’ additional documents (questionnaire, interview guide, consent) has been inserted in the methods and reference to ‘supplementary file’ deleted. 3. Please clarify each of these so Methods can be rated yes vs partly. >> see responses above 4. Discussion includes some unnecessary repetition of methods. The links with literature are good, though some on other consortia experience in Africa would be worthwhile e.g. (Adedokun et al.,2014) or (Ruhweza Katahoire A et l.,2023) >> repetition of methods has been removed from the discussion >> additional references relevant to research fellows’ programmes and experiences in Africa have been added [thank you for these] 5. Among limitations, your note in findings that some interviewees asked that material be \"off the record\" is an indication of constraints that they felt. What proportion of interviewees indicated this? >> More information on this has been provided in the results section. Only one student did not want their interview recorded: instead running notes were taken during the interview. Three others asked for the recording to be turned off temporarily; this included two who did not want to share personal health information. Three did not request the recording to be stopped but at the end of the interview they asked for specific pieces of information not be to disclosed. Reasons for not recording/disclosing related to concerns about sharing their honest opinion on relationship (power) dynamics with supervisors or colleagues. Nevertheless, the vast majority of interview responses were recorded as the participants trusted that the information would be handled sensitively and anonymously. We have not gone into this level of detail in the text but have adjusted it to reflect that virtually all of the information provided during interviews was recorded. 6. In the conclusions, I would clarify that these were natural science students, as sciences include social and health sciences as well. >> this has been clarified 7. The terms \"underlying data\" and \" extended data\" are new to me. It would seem that the latter is really research instruments, data collection and ethics related. The former would seem appropriate for the interview transcripts. Not clear from the questionnaire data. Can you clarify? >> these are not our terms but are those used by the F1000 journal. Their guidelines state “we no longer host supplementary material. Instead, we ask that these be deposited in an approved repository and included in the article’s Data Availability section as “Extended data”.” In the methods section we have clarified the types of information that are provided as extended data (see response to #2)." } ] }, { "id": "263539", "date": "10 Jun 2024", "name": "Francesco Obino", "expertise": [ "Reviewer Expertise research capacity building", "social sciences", "international funding", "ethics of North-South research collaboration" ], "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 the results of an assessment of the impact of linking a doctoral track to an internationally-funded research consortium (ACBI) between UK and African higher education institutions. The study was carried out, and the paper was authored, by the Centre for Capacity Research (CCR) at the Liverpool School of Tropical Medicine as part of their role in monitoring and evaluating the capacity-strengthening components of the ACBI program. Specifically, the paper presents and discusses data relating to the experiences of the involved PhD students (38 in total, of which 33 participated in the study).\nThe content is well-structured, moving from background and general considerations to a presentation of results, organized by sub-topics, and then to a discussion. The paper uses adequate citations from interviews and basic statistical analysis of survey responses by the PhD students.\nOur main first comment (of two) focuses on the framing of the paper and its contribution. The title is catchy (for those interested in the topic), but it leads the reader to expect a comprehensive assessment of the impact of the program on A) PhD students' 'research environment and progress' and B) 'in sub-Saharan Africa.' We believe that the framing is too ambitious and does not reflect the content of the paper. Ultimately, the paper presents a 'user-side perspective' of a doctoral track integrated into an international research program. The title should reflect this more accurately and reduce the scope from an entire continent to the specific program at stake. The confusion is genuine, and we see no attempt to misguide the reader, but the title over-commits the authors to something much more ambitious than the available evidence.\nFollowing the first comment, it emerges from the paper that a separate publication and dataset exist on the perspective of the institutions participating in the program. We understand the incentives for producing separate papers, but it would have been very useful to use the two datasets to answer the broader question regarding the strengthening of doctoral tracks, which is one analytical level up from the experience of the PhD students, as the lens moves from the individual to the institutional level of analysis.\nUltimately, the paper argues that embedding PhD students 'by design' in an international research consortium can have benefits for the quality of doctoral training received, particularly as the consortium can mobilize resources that single institutions cannot. However, the shortfalls emerging from the PhD students' responses point to a number of more systemic obstacles that are proper to a) doctoral programs (i.e., uneasiness with supervision as a technology of capacity building when the personal match is not right; the bureaucratic nature of higher education institutions, etc.) and b) universities, particularly universities in many African countries (lack of resources, lack of career advisory services, etc.). The risk of this analysis is to implicitly reiterate the 'blanket' narrative about the 'weak' research and research training environment at a continental scale and to miss the critical nuances that, on such a small sample of people and institutions, could lead to opportunities and levers of change.\nIt would be very useful to correlate the experience of the students, based on their responses, to their own aspirations and personal trajectories, and to specific realities of their institutions. Ultimately, the paper describes the benefits of being part of an 'elite' PhD cohort, with access to more resources and opportunities for mobility and supervision compared to others and other doctoral tracks that remain undefined and are not described. The strongest asset of the paper is also its Achilles' heel: the idea that an international program is a variable in strengthening a process of research capacity building (such as a doctoral track) in isolation from the research systems from which and in which the students emerge. A mention of these broader 'systemic' aspects and a critical assessment of the normative bias of the program the paper describes towards the benefits of international consortia could help stir some debate on the paper itself.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? No source data required\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "11777", "date": "24 Jun 2024", "name": "Susie Crossman", "role": "Author Response", "response": "1. The paper presents a 'user-side perspective' of a doctoral track integrated into an international research program. The title should reflect this more accurately and reduce the scope from an entire continent to the specific program at stake. >>The title has been adjusted to address the reviewers’ concerns 2. It emerges from the paper that a separate publication and dataset exist >>This refers to the baseline study, please refer to El Hajj T, Gregorius S, Pulford J, et al.: Strengthening capacity for natural sciences research: A qualitative assessment to identify good practices, capacity gaps and investment priorities in African research institutions. PLoS One. 2020;15(1):e0228261. 31978119 10.1371/journal.pone.0228261 PMC6980527 3.…..analysis is to implicitly reiterate the 'blanket' narrative about the 'weak' research and research training environment at a continental scale and to miss the critical nuances that, on such a small sample of people and institutions, could lead to opportunities and levers of change. >>In the discussion we have replaced ‘likely to’ with ‘could’ to reduce the emphasis on the wider applicability of our findings. We hope the actions we have summarised in box 2 are potential ‘levers of change’ that can lead to opportunities to further enhance the research environment for doctoral students everywhere, not just in sub-Saharan Africa. 4. the paper describes the benefits of being part of an 'elite' PhD cohort, with access to more resources and opportunities for mobility and supervision compared to others……. >>We have added a statement in the discussion to highlight that these were ‘elite’ students. 5.…..an international program is a variable in strengthening a process of research capacity building (such as a doctoral track) in isolation from the research systems from which and in which the students emerge. A mention of these broader 'systemic' aspects and a critical assessment of the normative bias of the program the paper describes towards the benefits of international consortia could help stir some debate on the paper itself. >>We have emphasized in the discussion that it is important for such international consortia to discover and build on the strengths of their partner institutions, to avoid undermining their systems and to align their efforts with the vision, strategy and needs of partner institutions." } ] } ]	1	https://f1000research.com/articles/13-238
https://f1000research.com/articles/13-673/v1	21 Jun 24	{ "type": "Research Article", "title": "Association of cancer and outcomes of patients hospitalized for COVID-19 between 2020 and 2023", "authors": [ "Abdulai Tejan Jalloh", "Laura Merson", "Divya Nair", "Shermarke Hassan", "Ibrahim Franklyn Kamara", "Innocent Nuwagira", "Sia Morenike Tengbe", "Yusuf Sheku Tejan", "Mustapha Kabba", "Sulaiman Lakoh", "Donald S Grant", "Robert J Samuels", "Rugiatu Z Kamara", "Robert F Terry", "Laura Merson", "Divya Nair", "Shermarke Hassan", "Ibrahim Franklyn Kamara", "Innocent Nuwagira", "Sia Morenike Tengbe", "Yusuf Sheku Tejan", "Mustapha Kabba", "Sulaiman Lakoh", "Donald S Grant", "Robert J Samuels", "Rugiatu Z Kamara", "Robert F Terry" ], "abstract": "Background The coronavirus disease 2019 (COVID-19) has caused substantial morbidity and mortality on a global scale. A strong correlation has been found between COVID-19 treatment outcomes and noncommunicable diseases such as cancers. However, there is limited information on the outcomes of cancer patients who were hospitalised for COVID-19.\n\nMethods We conducted an analysis on data collected in a large prospective cohort study set-up by the International Severe Acute Respiratory and Emerging Infection Consortium (ISARIC). All patients with laboratory-confirmed or clinically-diagnosed SARS-CoV-2 infection were included. Cancer was defined as having a current solid organ or haematological malignancy. The following outcomes were assessed; 30-day in-hospital mortality, intensive care unit (ICU) admission, length of hospitalization and receipt of higher-level care.\n\nResults Of the 560,547 hospitalised individuals who were analysed, 27,243 (4.9%) had cancer. Overall, cancer patients were older and had more comorbidities than non-cancer patients. Patients with cancer had higher 30-day in-hospital mortality than non-cancer patients (29.1.3% vs 18.0%) and longer hospital stays (median of 12 days vs 8 days). However, patients with cancer were admitted less often to intensive care units than non-cancer patients (12.6% vs 17.1%) and received less invasive mechanical ventilation than non-cancer patients (4.5% vs 7.6%). The hazard ratio of dying from cancer, adjusted for age, sex and country income level was 1.18 (95%CI: 1.15-1.2).\n\nConclusions This study’s findings underscore the heightened vulnerability of hospitalized COVID-19 patients with cancer, revealing a higher mortality rate, longer hospital stays, and an unstructured pattern of care that reflects the complexity of managing severely ill patients during a public health crisis like the COVID-19 pandemic.", "keywords": [ "COVID-19", "cancer", "comorbidities", "mortality", "hazard ratio", "risk factor", "ISARIC", "SORT IT" ], "content": "Introduction\n\nEarly in the COVID-19 pandemic, data were collected to identify risk factors for poor outcomes that could inform a risk-based approach to health policy and patient management. Risk factors including age, sex, and several comorbidities were reported to be associated with an increased risk of death.1,2 The most common comorbidities identified in hospitalised patients during the first wave of the COVID-19 pandemic were chronic cardiac or cardiovascular diseases, diabetes mellitus, hypertension, non-asthmatic chronic pulmonary disease, obesity, and chronic kidney disease.1,3–6 Understanding which individuals are likely to have a poor prognosis could help inform vaccine prioritisation, shielding policies, or allocation of health care resources in future infectious disease outbreaks and pandemics.\n\nSeveral studies have reported COVID-19 patients with cancer to be at higher risk of adverse outcomes compared with COVID-19 patients without cancer.7,8 In a study from China, COVID-19 patients with cancer had higher observed increased rates of death, intensive care unit (ICU) admission, and need for invasive mechanical ventilation.9 A study of COVID-19 patients in the United States of America reported that cancer patients were at higher risk of death and hospitalisation but were not found to have significantly different rates of ICU admission or ventilator use compared to non-cancer patients.10 Data from the United States Centre for Disease Control showed that in 2020 and 2021 respectively, 2.0% and 2.4% of people who died of cancer had COVID-19 listed as the underlying cause of death.11 There is a dearth of evidence on the outcomes of patients with cancer in middle- and low-income countries.\n\nThe studies referenced above and other national studies have shown that patients with cancer have worse outcomes than those without cancer when hospitalised due to COVID-19.12,13 However, to our knowledge, no study has been conducted to evaluate the association between cancer and hospital outcomes among hospitalised COVID-19 patients using an international data set. This study, seeking to build on the collection of existing evidence, uses secondary COVID-19 patient data collected in 54 countries via the Clinical Characterisation Protocol designed by the International Severe Acute Respiratory and Emerging Infections Consortium (ISARIC) and the World Health Organisation (WHO).14 We investigated the association of cancer as a comorbidity with 30-day in-hospital mortality, ICU admission, length of hospitalization and receipt of higher-level care in COVID-19 patients with and without cancer.\n\n\nMethods\n\nThis was a prospective cohort study that utilised secondary data from the COVID-19 clinical database hosted by the Infectious Diseases Data Observatory (IDDO). The database contains individual patient data from more than 800,000 hospitalised patients in more than 1,200 institutions from 60 countries across 6 continents. The data were collected using the ISARIC-WHO case report form as a part of the ISARIC-WHO Clinical Characterisation Protocol.15,16\n\nWe included hospitalised patients of any age with clinically or laboratory-diagnosed SARS-CoV-2 infection. Patients were enrolled between 30th January 2020 and 10th January 2023. Patients with unknown cancer status were excluded. Patients were followed from the time of hospital admission to discharge or death.\n\nWe compared the differences in demographic characteristics, comorbidities, treatment with intensive interventions, length of hospitalisation, death (defined as 30-day in-hospital mortality), and hospital outcomes to characterise hospitalised COVID-19 patients with and without cancer.\n\nSevere disease was defined as treatment with higher-level care, including one or more of the following events: admission to an ICU, treatment with invasive mechanical ventilation (IMV), non-invasive ventilation (NIV), high-flow nasal cannula (HFNC), inotropes and/or vasopressors. Length of hospital stay was censored at 100 days.\n\nThe presence of cancer was self-reported by patients and recorded as a binary variable classified as malignant neoplasm in the ISARIC-WHO case report form. Cancer was defined as having a current solid organ or haematological malignancy. Malignancies that had been declared ‘cured’ ≥5 years with no evidence of ongoing disease, non-melanoma skin cancer and benign growths or dysplasia were not included in this definition.\n\nWe used international prospectively collected observational data on demographics, clinical features and outcomes of patients hospitalized with COVID-19 with or without cancer (coded as ‘malignant neoplasm’). Data were collected using the ISARIC-WHO Clinical Characterisation Protocol and contributed to a central repository at the University of Oxford, England. Participating sites used the ISARIC-WHO case report form to enter data onto a Research Electronic Data Capture (REDCap, version 8.11.11, Vanderbilt University, Nashville, TN) database or used local databases before uploading to the central data repository.15 Open Data Kit is a suitable open access alternative. Centrally collated data were wrangled and mapped to the structure and controlled terminologies of the Study Data Tabulation Model (version 1.7, Clinical Data Interchange Standards Consortium, Austin, TX) using Trifacta® software version 9.7.1. OpenRefine is a suitable open access alternative to using Trifacta®. The data collection, aggregation, curation, and harmonisation process has been previously described.16 Though more than 50% of the data were collected from low- and middle-income countries, most data on patients with cancer were collected from patients in higher income countries.\n\nContinuous variables such as age and length of hospital stay were summarised as means with standard deviations or medians with interquartile ranges depending upon the distribution of data. Categorical variables (sex, presence of cancer, hospital exit outcomes, etc.) were summarised as frequencies and percentages.\n\nCategorical variables such as death and treatment with intensive interventions between patients with cancer and those without cancer were compared using the chi-square test. Continuous variables such as length of hospital stay were compared between the two groups using the unpaired t-test or Mann Whitney U test depending on the distribution of data. A Kaplan-Meier curve was plotted to show the cumulative incidence of mortality during hospitalization. To assess the independent effect of cancer on mortality in hospitalized COVID-19 patients, a survival analysis model was fitted to the data. The model was adjusted for the following confounders: age, sex, and country income-level. Unadjusted and adjusted hazard ratios with 95% confidence intervals were reported as measures of association. Denominators on individual analyses differ due to availability of data on different variables across the dataset. A P-value of <0.05 was considered statistically significant.\n\nInformation on country income level was obtained from the World Bank (https://datacatalog.worldbank.org/search/dataset/0038543).\n\nAll analyses were performed using R version 4.2.2 (IDE PBC, Boston, MA, USA), an open access software. (R: The R Project for Statistical Computing)\n\nExecution of the ISARIC-WHO Clinical Characterisation Protocol was approved by the WHO Ethics Review Committee (RPC571 and RPC572, 25 April 2013) and by local or national ethics committees for participating sites. Approvals include the South Central—Oxford C Research Ethics Committee for England (Ref. 13/SC/0149), the Scotland A Research Ethics Committee (Ref. 20/SS/0028) for Scotland, and the Human Research Ethics Committee (Medical) at the University of the Witwatersrand in South Africa as part of a national surveillance programme (M160667), which collectively represent most of the data. Written patient consent for data to be collected and used in research was obtained or waived according to local norms determined by the responsible Ethics Committee. The data were collected using the ISARIC-WHO case COVID-19 report form, locally-tailored versions of the form, or independently designed forms. Arrangements surrounding the pooling, storage, curation and sharing of these data are covered by the IDDO Governance processes.17\n\nAll data were deidentified and ensured of low risk for identification of individuals by a statistical disclosure process prior to sharing. Data were shared under a Data Access Agreement following approval from the IDDO Data Access Committee.18 Execution of this secondary analysis was approved by the Union Ethics Advisory Group of the International Union against Tuberculosis and Lung Disease, Paris, France (EAG number 18/23, dated 8th September 2023).\n\n\nResults\n\nAmong 841,640 individual records in the dataset, 560,547 (66.6%) met the criteria for analysis. Of those that did not, 73,327 (8.7%) did not have clinical or laboratory confirmation of SARS-CoV-2 infection; a further 3,879 (0.5%) were not admitted to hospitals between January 30th 2020 and January 10th 2023; and 203,887 (24.2%) did not have information on cancer status available.\n\nOf the 560,547 individuals analysed, 27,243 (4.9%) had cancer. Furthermore, 219,922 (39.2%) individuals that met the criteria for analysis were hospitalised in high-income countries. There were differences in age, sex, country income level, and other comorbidities in the group of patients with cancer versus those without cancer. Those with cancer were older (84.4% versus 46.3% aged ≥60 years), were more likely to be male (58.1% versus 49.1%) and were more likely to come from a high-income country (90.6% versus 36.6%). Of the 10 comorbidities most common in the whole population, all except obesity were more prevalent in the group of patients with cancer (Table 1).\n\nPatients with cancer had higher 30-day in-hospital mortality (29.1% vs 18.0%) and longer duration of hospitalization (median of 12 days (IQR 6.0-22.0) vs 8 days (IQR 4.0-14.0)) compared with those without cancer (Table 2 and Figures 1 and 2).\n\nHowever, patients with cancer were reported to have received higher-level care slightly less often than those without cancer (28.9% vs 29.8%) including lower rates of ICU admission (12.6% vs 17.1%) and invasive mechanical ventilation (4.5% vs 7.6%). There were similar levels of treatment with high-flow nasal cannulas (17.5% vs 16.1%), extracorporeal membrane oxygenation (0.1% and 0.5%), non-invasive ventilation (11.6% vs 11.7%), and treatment with inotropes or vasopressors (3.5% vs 4.5%) across both groups (Table 2).\n\nThe effect of cancer and other comorbidities on 30-day in-hospital mortality among COVID-19 patients is reported in Table 3 and Figure 3. Hospitalised COVID-19 patients with cancer had a higher risk of 30-day in-hospital mortality compared to those without cancer. The hazard ratio of dying from cancer, adjusted for age, sex and country income level was 1.18 (1.15-1.2).\n\n* Adjustment made for age, sex and country income level.\n\nAdjusted hazard ratios were higher for age and gender compared with those for cancer. Adjusted for sex and country income level, individuals aged ≥ 60 years had the highest hazard ratio 2.43 (2.39-2.46). Adjusted for age and country income level, male sex had a hazard ratio of 1.19 (1.18-1.21).\n\nAmong all comorbidities, only diabetes mellitus (HR: 1.32, 95%CI: 1.31-1.34) and chronic pulmonary disease (HR: 1.30, 95%CI: 1.28-1.33) were more strongly associated with an increased risk of death compared with cancer, after adjusting for age, sex and country income level.\n\n\nDiscussion\n\nOur study findings underscore the heightened vulnerability of cancer patients hospitalized with COVID-19, revealing a higher mortality rate, longer hospital stays, and a nuanced pattern of care that reflects the complexity of managing severely ill patients during a public health crisis. These outcomes align with the existing literature on the association of cancer with COVID-19 prognosis and treatment approaches during the pandemic.13,19 In keeping with our findings, other studies conducted in high-income countries have also documented that the proportion of COVID-19 patients with cancer and other comorbidities is higher in the elderly (>60 years) as compared to the general population.13,20,21\n\nA meta-analysis of 4 studies (4691 non-cancer patients, 154 cancer patients) that looked at mortality in cancer patients versus non-cancer patients reported a pooled odds ratio of death of 3.91 (95%CI: 2.70-5.67).12 This is higher than reported in our study. This could be explained by the lack of adjustment for potential confounders in the meta-analysis. It is also unclear whether or not the patients in these studies were primarily admitted for COVID-19, for cancer, or for other reasons. When considering other significant risk factors for mortality, we observed that cancer ranked prominently. Cancer demonstrated a stronger association with mortality compared to all other comorbidities, except for diabetes mellitus and chronic pulmonary disease.\n\nDespite the higher mortality risk, cancer patients in our study were slightly less likely to receive higher-level care compared to patients without cancer (28.9% vs 29.8%). Specifically, cancer patients were less frequently admitted to the ICU (12.6% vs. 17.1%) and had invasive mechanical ventilation less often (4.5% vs. 7.6%). These findings diverge from the expectation that higher-risk patients would necessitate more aggressive treatment. Though these event rates align with other studies of cancer patients, few comparators with non-cancer patients hospitalised for COVID-19 are in the literature. Marta et al. (2020) reported ICU admission rates of 39.1% in cancer patients with COVID-19 and use of invasive mechanical ventilation in 84.4 %.22 Elgohary et al.’s (2021) systematic review and meta- analysis of cancer patients with COVID -19 reported an ICU admission rate of 14.5% (95% CI: 8.5-20.4) and a mechanical ventilation rate of 11.7% (95% CI: 5.5-18).12 When comparing cancer patients with non-cancer patients, Abuhelwa et.al (2022) found cancer patients hospitalized for COVID-19 had similar rates of invasive mechanical ventilation compared to those without cancer (10.14% vs 9.36.%).13\n\nWe found differences in mean hospital stay between patients with cancer and those without cancer. The longer hospital stay might be related to cancer patients having several other comorbidities and the management of the side effects of cancer treatment. However, we cannot explain why they stayed longer in hospital but received less high-level care compared to COVID-19 patients without cancer. Abuhelwa’s 2022 nation-wide study reported no difference in hospital stays between these patient groups (8.07 vs 7.46 days). The difference between these findings and ours may reflect differences in admission policy or availability of hospital beds. The lower mortality rates in Abuhelwa’s study as compared to our findings may indicate less severe disease, and therefore a population requiring less in-hospital care.\n\nOne key strength of our study was the use of a large sample size, orders of magnitude larger than most previous studies. Therefore, our estimates should be more generalisable and should have a higher power to demonstrate significant associations than previously published studies. We adhered to the STROBE (Strengthening the Reporting of Observational Studies in Epidemiology) guidelines for reporting study findings.\n\nThis analysis has several limitations. This study encompassed all patients with current cancer, but we couldn’t distinguish between various cancer types as detailed information on each patients’ cancer diagnosis, staging and treatment modalities were not available. However, other studies have highlighted lung cancer and haematological cancers as being those most closely linked to mortality in COVID-19 patients.13,23,24\n\nDifferences in reporting of the type and details of cancer diagnosis across the available literature make it challenging to make comparisons. Studies that analysed data through the use of electronic health records may have included patients in remission. Though enrolment to the ISARIC-WHO Clinical Characterisation Protocol focused on individuals admitted for COVID-19 illness, some individuals may have been admitted due to cancer related illness.\n\nIn order to enable future research to disaggregate cancer patients by the following characteristics i.e. type of cancer, staging of cancer and treatment modalities, - a more comprehensive case report form is needed. Having these data available would enable a more personalized risk assessment and a better understanding of how management strategies relate to patient outcomes. Additionally, the availability of vaccination data will allow the examination of the impact of COVID-19 vaccination status on outcomes in cancer patients. The majority of data on patients with cancer (90.6%) were collected from patients in high income countries. so no inferences could be drawn from patient outcomes linked with World Bank income classifications.\n\n\nConclusions\n\nOur study found that patients with cancer were older with more comorbidities. They had an increased risk of mortality with longer duration of hospital stay as compared to non-cancer patients but received less high-level care including ICU admission and invasive mechanical ventilation. This highlights the importance of collecting data in emerging infections to identify at-risk groups, facilitating appropriate resource allocation and informing policy decisions aimed at resource allocation during health emergencies. The availability and collection of data on our platforms were predominantly from high-income countries. To prepare for a future pandemic, data availability and coverage must be more universal. More must also be done to support data collection and the capacity to analyse those data within low- and middle-income countries.", "appendix": "Data availability\n\nThe data that underpin this analysis are available via a governed data access mechanism following review of a data access committee. Data can be requested via the IDDO COVID-19 Data Sharing Platform (http://www.iddo.org/covid-19). The Data Access Application, Terms of Access and details of the Data Access Committee are available on the website. Briefly, the requirements for access are a request from a qualified researcher working with a legal entity who have a health and/or research remit; a scientifically valid reason for data access which adheres to appropriate ethical principles. The full terms are at: https://www.iddo.org/document/covid-19-data-access-guidelines . These data are a part of https://doi.org/10.48688/cpwp-ft84\n\n\nAcknowledgements\n\nThis research was conducted through the Structured Operational Research and Training Initiative (SORT IT), a global partnership led by TDR, the Special Programme for Research and Training in Tropical Diseases hosted at the World Health Organization. The specific SORT IT program that led to this publication is a SORT IT partnership with the WHO Emergency Medical Teams (Geneva), WHO-AFRO (Brazzaville), WHO Country Offices and Ministries of health of Guinea, Liberia, Sierra Leone, and the Democratic Republic of the Congo, the Infectious Diseases Data Repository (IDDO); The International Union Against Tuberculosis and Lung Diseases, Paris, France and South East Asia offices, Delhi, India; The Tuberculosis Research and Prevention Center Non-Governmental Organization, Yerevan, Armenia; I-Tech, Lilongwe, Malawi; Medwise solutions, Nairobi, Kenya; All India Institute of Medical Sciences, Hyderabad, India; and the National Training and Research Centre in Rural Health, Maferinyah, Guinea.\n\nThe views expressed in this article are those of the authors and do not necessarily reflect those of their affiliated institutions.\n\n\nReferences\n\nDocherty AB, et al.: Features of 20 133 UK patients in hospital with covid-19 using the ISARIC WHO Clinical Characterisation Protocol: prospective observational cohort study. 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PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "295443", "date": "04 Sep 2024", "name": "Tom Fowler", "expertise": [ "Reviewer Expertise Public Heath", "Genomics", "Pandemics" ], "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 examining an important area of whether outcomes in hospitalized Covid 19 cancer patients compared to other hospitalized patients for Covid 19 have worse outcomes. It uses data from International Severe Acute Respiratory and Emerging Infection Consortium (ISARIC) and a substantial strength is the international nature of this cohort and its overall size.\nThe paper identifies demographic differences between those hospitalised for Covid 19 with Cancer and those without along with different outcomes in key measures (e.g. 30-day in hospital mortality).\nThere are however a number of major and minor issues that need to be addressed. In part areas of analysis may be restricted due to the availability of data - in which case this should be acknowledged and addressed in the discussion.\n1. It is unclear to me the extent to which individuals were hospitalised for a specific reason (e.g. due to their cancer ) and identified as having Covid 19 or were hospitalised for respiratory symptoms and identified as having another diagnosis such as cancer. This is particularly important as there are conclusions about different care between these groups and the demographic characteristics of those with cancer are substantially different from others admitted and this may be driven by the reason for admission. Additionally, the implications for the difference in demographic characteristics are not fully explored in the discussion\n2. The major results are the comparison of the outcomes of those with cancer versus those without cancer. The authors point out there are other individuals with conditions with increased risk in their comparison group. As such by combining all other groups the approach is likely to underestimate the increase in risk of those with cancer. This is possibly the output in figure 3, however this is not explicitly stated and the reporting of adjusted results for other variables (such as age and sex) appear to be without adjusting for this. In other results this is not addressed, e.g. Data in Table 2 seems to be a direct comparison between those with and without cancer only.\n3. The analysis does not include an examination of change over time of risk associated with cancer. It also does not look at the impact of vaccination on risk (which we become more prevalent over time). There is literature on changing risk over the course of the pandemic of individuals with cancer - e.g. Ref 1 and the impact of vaccination and vaccine response Ref 2\nAs such I would expect consideration of vaccination status to be part of the methods/ analysis.\n4. It is unclear on the rationale of covariates included in the analysis and why others have been omitted. For example, a key strength is the international nature of this dataset, which allows exploration of differences between countries. It is stated in the paper the authors are unaware of any other analysis looking at outcomes using and international data set. There is between countries differences in provision of health care, even of those with similar income level. However the rationale for why country income level was chosen and its implications is not discussed or why a more granular variable reflecting country could not be used. Rather it is stated that due to the predominance of cases from high income countries they were unable draw inferences, suggesting that using world bank income classification is not an appropriate variable to use. The authors need to reconsider what is used to assess international differences and include this in the analysis\nOther examples, including those mentioned above, vaccine status, other clinical comorbidities, likely variant (or time as a proxy), severity at admission (or length of hospitalization) etc,\n\n6. The presentation of results needs review to ensure it is clear. For example the Figure 2 Kaplan Meier plot references inclusion of people between 2020-2023 - this is the only reference to a time period, the x axis is labeled as time and is in days. I assume this is the risk from the date of admission, however that is not explicitly stated - as such the presentation is not clear.\nNote, If it is the number of days hospitalized, rather than the days since admission, part of the downward trend may be driven by those no longer hospitalized being removed from the analysis as time continues, leaving only those hospitalized for longer being included in survival risk at later timepoints . Without clear description in is challenging to determine if this is a relevant point.\nOther examples include Figure 3 - while the graphical representation is helpful - it is not possible to ascertain the exact hazard ratio and confidence intervals are omitted\n\n7. It is stated the presence of cancer was self reported, It may be that more detail of this process would clarify potential biases, however given findings that the cancer group were, for example, admitted less to ICUs it is conceivable that those presenting with more severe symptoms at the time of recruitment were unable to self report if they had cancer. Greater clarity on either the process of collecting relevant clinical details or discussion of potential implications of data collection approaches are needed.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] } ]	1	https://f1000research.com/articles/13-673
https://f1000research.com/articles/13-672/v1	21 Jun 24	{ "type": "Research Article", "title": "Factors associated with death in patients admitted with Ebola virus disease to Ebola Treatment Units in Guinea, Sierra Leone, and Liberia – December 2013 to March 2016", "authors": [ "Trokon Omarley Yeabah", "Ibrahima Kaba", "Gomathi Ramaswamy", "Prabin Dahal", "Alexandre Delamou", "Benjamin T. Vonhm", "Ralph W. Jetoh", "Laura Merson", "Adam C. Levine", "Pryanka Relan", "Anthony D. Harries", "Ajay M.V. Kumar", "Gomathi Ramaswamy", "Prabin Dahal", "Alexandre Delamou", "Benjamin T. Vonhm", "Ralph W. Jetoh", "Laura Merson", "Adam C. Levine", "Pryanka Relan", "Anthony D. Harries", "Ajay M.V. Kumar" ], "abstract": "Background The 2013-2016 West African Ebola Virus Disease (EVD) outbreak resulted in 28,600 cases and 11,300 deaths officially reported to the World Health Organization. Previous studies investigating factors associated with death had conflicting findings, interventions showing promising outcomes had small sample sizes, studies were often single- or dual-country based and most focused on laboratory-confirmed EVD and not on clinically-suspected EVD. We used the Ebola data platform of the Infectious Disease Data Observatory (IDDO) to review individual patient records to assess factors associated with death, and particularly whether there were differences between laboratory-confirmed and clinically-suspected cases.\n\nMethods This was a cohort study involving analysis of secondary data in the IDDO database. The study population included all patients classified as having either clinically-suspected or laboratory-confirmed EVD, admitted to 22 Ebola Treatment Units (ETU) in Guinea, Liberia and Sierra Leone between December 2013 and March 2016. Baseline characteristics and treatments were documented along with ETU exit outcomes. Factors associated with death were investigated by multivariable modified Poisson regression.\n\nResults There were 14,163 patients, of whom 6,208 (43.8%) were laboratory-confirmed and 7,955 (56.2%) were clinically-suspected. Outcomes were not recorded in 2,889 (20.4%) patients. Of the 11,274 patients with known outcomes, 4,090 (36.3%) died: 2,956 (43.6%) with laboratory-confirmed EVD and 1,134 (18.8%) with clinically-suspected EVD. The strongest risk factor for death was confirmed disease status. Patients with laboratory-confirmed disease had 2.9 times higher risk of death compared to clinically-suspected patients, after adjusting for other co-variables. Other factors significantly associated with death included a higher risk for patients aged ≥60 years and a lower risk for patients in Sierra Leone.\n\nConclusions Although laboratory-confirmed patients admitted to ETUs fared worse than clinically-suspected patients, the latter still had a substantial risk of death and more attention needs to be paid to this group in future EVD outbreaks.", "keywords": [ "West Africa", "Ebola", "mortality", "viral haemorrhagic fever", "filovirus", "SORT IT", "operational research", "pandemic preparedness" ], "content": "Introduction\n\nEbola virus disease (EVD) is a severe, often fatal, zoonotic, filovirus illness that was documented for the first time in the Democratic Republic of Congo (formerly Zaire) in 1976. Since then, there have been several outbreaks, with the largest and deadliest outbreak occurring in West Africa (primarily Guinea, Sierra Leone, and Liberia) between 2013 and 2016, with approximately 28,600 cases and 11,310 deaths officially reported to the World Health Organization (WHO) (WHO - emergencies).1 The disease remains a public health threat due to its high case-fatality ratio and the potential for the virus to lie dormant in animal reservoirs and then re-emerge. Recent outbreaks in the Democratic Republic of Congo in 2017-2022, Guinea in 2021, and Uganda in 2022 illustrate this ongoing concern (CDC - Ebola outbreaks). Despite recurring outbreaks, many aspects of EVD remain poorly understood.2 There remains a need to further understand the relationship between the signs and symptoms, the spectrum of illness, and outcomes, as well as the influence of co-existing infections and environmental factors on disease course and outcomes.3,4\n\nThe 2013-2016 West African EVD outbreak was associated with an overall case fatality ratio of 51% (95% CI, 46%-56%), pooled from 16 independent cohorts of over 6,000 patients.5 Various cohort studies investigated risk factors associated with death in adults and children, both separately and together. Demographic factors such as age (elderly and young children) and male gender appear to be important factors associated with increased risk of death.6–9 Clinical characteristics that include symptoms such as fever, diarrhoea, vomiting, dysphagia, cough, and dyspnoea, and physical signs such as skin rash, conjunctival injection, and haemorrhagic manifestations have been independently associated with high-case fatality in many studies,10–13 although these associations have not been consistent.9 Certain laboratory investigations such as hyponatraemia, hypokalaemia, hyperkalaemia, elevated liver enzymes, high serum creatinine, and high EVD viral load have been associated with high risk of death.7,14 Co-infection with malaria appears to be a risk factor for death.15 Finally, there are a few studies with small numbers of patients that have found various interventions beneficial in reducing case fatality: multivitamins or vitamin A given within 48 hours of admission,16,17 antibiotics such as third-generation oral cephalosporins especially cefixime,17 and use of empirical antimalarial treatment, especially artesunate-amodiaquine rather than artemether-lumefantrine.18,19\n\nWhile existing published studies have examined risk factors for mortality, several reasons justify the need for additional research in this area. First, there have been conflicting findings between studies, especially with respect to clinical characteristics associated with mortality.14 Second, interventions that have shown promising outcomes, such as the use of certain antibiotics, multivitamins, and antimalarial drugs, were based on small sample sizes. Third, many of the previous studies included data from one or two countries, limiting their generalizability. Lastly, most previous studies focused on mortality in patients with laboratory-confirmed EVD, and there is limited information about clinical characteristics and outcomes in patients with clinically-suspected EVD.6,9,20\n\nThe Infectious Disease Data Observatory (IDDO) hosts an Ebola Data Platform (EDP), the first multi-country repository for clinical, epidemiological, and laboratory data, on patients with suspected EVD. Data from over 14,000 individual patient records collected during the 2013–16 West African Ebola outbreak have been deposited with the aim of reducing the impact of EVD by generating new evidence to improve outbreak response and patient care. This resource allows the unique possibility of examining a large dataset, with data combined from three countries -- Guinea, Liberia, and Sierra Leone - to generate further evidence on risk factors for mortality and on interventions that can reduce mortality in patients with both clinically-suspected and laboratory-confirmed EVD.\n\nThe aim of this study was to assess factors associated with mortality during admission to Ebola Treatment Units (ETU) among patients with clinically-suspected and laboratory-confirmed EVD admitted to 22 ETUs in Guinea, Liberia, and Sierra Leone between December 2013 and March 2016. The specific objectives were to: i) describe the baseline socio-demographic and clinical characteristics, laboratory investigations, and treatments received; ii) determine the ETU exit outcomes, including the proportion who died during hospitalization and the median time from onset of symptoms to admission and admission to death; and iii) assess the baseline socio-demographic and clinical characteristics, and treatments that were associated with risk of death during hospitalization.\n\n\nMethods\n\nThis was a cohort study involving analysis of secondary data collected from Guinea, Liberia, and Sierra Leone.\n\nGeneral setting\n\nGuinea, Liberia, and Sierra Leone are Member States of the Mano River Union Basin located in West Africa, with an estimated population of 23.5 million inhabitants in 2015 (Figure 1).21\n\nGuinea is a country bordered by Guinea-Bissau to the northwest, Senegal to the north, Mali to the northeast, Côte d’Ivoire to the southeast, and Liberia and Sierra Leone to the south, with an estimated population of 11.6 million inhabitants.21 It has 8 administrative regions with 38 health districts and 936 health facilities.22\n\nLiberia is a country bordered by Sierra Leone to the northwest, Guinea to the north, Ivory Coast to the east, and the Atlantic Ocean to the south and southwest, with an estimated population of 4.6 million inhabitants.21 It has 15 counties with 98 health districts and 978 health facilities.23\n\nSierra Leone is a country bordered by Liberia to the southeast and Guinea to the northern half, with an estimated population of 7.3 million inhabitants.21 It has four provinces with 13 health districts and 1,280 health facilities.24\n\nSpecific setting\n\nAcross the three countries, ETUs were set up in hospitals and other external designated sites by Ministries of Health and Non-Governmental Organizations (NGOs) for the case management of patients with suspected and confirmed EVD. These ETUs were subdivided into sections for processing patients that included triage, admission, and treatment wards. Patients who arrived at the ETUs were triaged, and demographic and clinical characteristics, medical history, and environmental risk factors such as funeral attendance were collected.\n\nA polymerase chain reaction (PCR) test was then carried out for the determination of EVD. Patients were then transferred to separate treatment unit wards depending on whether they had laboratory-confirmed EVD or clinically-suspected EVD. For the purpose of this study, laboratory-confirmed EVD was based on a positive polymerase chain reaction (PCR) test or a cycle threshold of 36.1 or less, obtained within the first three days of reporting to the health facility. Clinically-suspected EVD was based on a negative/indeterminate PCR test and/or a cycle threshold greater than 36.1 or no laboratory information available in the dataset.\n\nIn ETU wards, additional data were collected routinely on clinical care and follow-up, including laboratory and epidemiological investigations. These data were often used for patient management and occasionally for observational or interventional research. Clinical trials on EVD therapeutics such as monoclonal antibody therapies and convalescent plasma were conducted at some ETUs. These sites had local and international medical doctors, nurses, laboratory technicians, epidemiologists, logisticians, and other support personnel. Data were collected on either paper-based or electronic forms using variables selected by the organization managing the respective clinical treatment centres and those undertaking studies. The data were submitted to the EDP by the organization responsible for primary data collection under the authority of the responsible Ministry of Health or National Public Health Institute.\n\nThe EDP team aggregated and standardized disparate datasets from the many organizations that collected individual patient-level data as a part of the care provided in ETUs. The data were hosted on the University of Oxford data repository server. The curation of the data was done using a Clinical Data Interchange Standards Consortium (CDISC) compliant model and the standardised data are stored across several study data tabulation model (SDTM) domains.\n\nTable 1 shows the total number of ETUs25 in each country, the number and proportion included in the study (IDDO - Ebola), the number of EVD cases reported to WHO,26,27 and the number and proportion included in the study.\n\nThe study population included all patients classified as having either clinically-suspected or laboratory-confirmed EVD who were admitted at the 22 ETUs in Guinea, Liberia and Sierra Leone between December 2013 and March 2016.\n\nThe data variables were extracted from the Ebola Database Platform (EDP) database (using the variable name from the respective SDTM Domains) according to the specific study objectives. The key exposure variable was ‘confirmed disease status’ (laboratory-confirmed or clinically-suspected). Socio-demographic characteristics included: country, age, sex, pregnancy status, healthcare worker, contact with an individual suspected of EVD infection, visit to a traditional healer and funeral attendance. Baseline clinical features included: general, gastrointestinal, respiratory, neurological, and ocular symptoms; a variety of physical signs such as fever, rash; vital signs such as temperature, pulse rate, respiratory rate and blood pressure; and investigations for diagnosis of malaria. The signs and symptoms data were extracted only if they were indicated as pre-specified variables (i.e. those variables that were actively solicited in the case report form). Baseline was defined as any clinical feature present at least once between the date of reporting to the health facility and 21 days before reporting to the health facility. Availability of laboratory tests varied between patients and ETUs and included serum sodium, serum potassium, blood urea, serum creatine and liver function tests such as aspartate transaminase and alanine transaminase. Treatments received included: multivitamins, antimalarial drugs, antibiotics, intravenous fluids and parenteral nutrition. ETU exit outcomes included: discharge, death, and other (withdrawn from clinical trial, transferred, lost to follow-up, still in hospital or unknown). We also measured number of days from symptom onset to ETU admission and number of days from ETU admission to discharge or death.\n\nThe variables of interest were extracted from the EDP database, cleaned, duplicates were removed, data elements were recoded including missing data and a standardised dataset was formulated to allow analyses to proceed. These data were then imported to Stata Statistical Software (Release 18.0, StataCorp. LLC, College Station, Texas, USA) and R Studio (version 2023.06.1 Build 524, IDE PBC, Boston, MA, USA) for further analysis. While Stata is a proprietary software, all the analyses presented in the manuscript can be replicated using R Studio, which is an open access software. Categorical variables such as socio-demographic baseline characteristics and ETU exit outcomes were summarised using frequencies and proportions while continuous variables were summarised using mean (and standard deviations) or median (and interquartile range), as appropriate.\n\nDifferences in proportion of deaths across the various sub-groups (based on laboratory-confirmed and clinically-suspected EVD, demographic and clinical characteristics and treatments) were assessed for statistical significance using the Chi-squared test or Fisher’s exact test, as appropriate. The strength of associations was measured using risk ratios (RR) and 95% confidence intervals (CI), with the level of significance set at P-Value <0.05. Univariable and multivariable predictors associated with death were assessed using modified Poisson regression with robust variance estimation using rqlm package in R Studio software.28 Variables found to be associated with hospital death on unadjusted analysis were further assessed in multivariable analysis, and adjusted RRs with 95% CI were calculated. Clinical signs and symptoms were not included in the multivariable model as they were highly correlated with each other and with the confirmed disease status. Patients who received treatments (such as antibiotics, antimalarials, IV fluids and multivitamins) often received them in combination and hence it was not possible to assess the effects of each of the treatments. A composite variable ‘receiving any treatment’ was created and used in the multivariable analysis.\n\nThe hosting of data and access to the EDP were approved by the Oxford Tropical Research Ethics Committee, UK, in 2018 and by the national ethics committees in each contributing country. The Guinea National Committee for Health Research Ethics (2018), the Sierra Leone Ethics and Scientific Review Committee (2018) and the Liberia National Research Ethics Board (2018) all approved the activities of the EDP. For the current study, approval was obtained from the Ethics Advisory Group (EAG) of the International Union against Tuberculosis and Lung Disease, Paris, France (date of approval 08/09/2023; EAG approval number 19/23). Approval was also obtained from the Liberia National Research Ethics Board (date of approval 27/09/2023; approval number 23-09-389). No identifiable data were included in the analysis. The study used anonymised secondary collected data and as such no informed consent was needed from patients.\n\n\nResults\n\nThere were 14,163 patients admitted to the study ETUs in Guinea, Liberia, and Sierra Leone during the study period. Of these, 6,208 (43.8%) were laboratory-confirmed and the remainder (n=7,955, 56.2%) were clinically-suspected. The proportion of laboratory-confirmed patients varied across the countries: 43.6% in Guinea, 50.0% in Liberia and 39.7% in Sierra Leone.\n\nThe distribution of socio-demographic characteristics of patients disaggregated by laboratory confirmation status is shown in Table 2. Overall, 51.8% of the patients were male – this was higher among clinically-suspected compared to laboratory-confirmed patients. Among 6,715 females, 195 (2.9%) were pregnant. The age distribution across the two groups was similar, barring a marginally higher proportion of under-five children in clinically-suspected patients. Nearly one in 10 patients were healthcare workers; this proportion was higher among laboratory-confirmed (15.0%) compared to clinically-suspected (7.0%) patients. 42.8% of patients had a history of contact with an EVD suspect, and 17.8% had a history of funeral attendance – these proportions were higher among laboratory-confirmed patients compared to the clinically-suspected cases. A higher proportion of clinically-suspected patients had visited a traditional healer compared to laboratory-confirmed patients (6.8% vs 3.3%).\n\nThe pre-specified clinical symptoms and signs presented by the patients at the time of admission are shown in Table 3. The most common symptoms were fever, fatigue/lethargy, myalgia/arthralgia, anorexia/dehydration, diarrhoea, nausea/vomiting, abdominal pain and neurological symptoms (which included headache, seizures/convulsions, agitation, disorientation, coma/unconsciousness, confusion, dizziness). Other symptoms included chest pain, difficulty breathing, difficulty swallowing, sore throat, hiccups and bleeding. The following symptoms were proportionately higher among the laboratory-confirmed cases: fatigue, nausea/vomiting, diarrhoea, anorexia & dehydration, fever, myalgia/arthralgia, neurological symptoms, hiccups, difficulty swallowing, sore throat, and ocular complaints. The proportion of patients with abdominal pain and bleeding (internal and external) was similar in laboratory-confirmed patients and clinically-suspected patients.\n\nThe following symptoms and signs occurred less among laboratory-confirmed cases compared to clinically-suspected cases: difficulty breathing (16.9% vs 27.7%) and rash (3.7% vs 6.6%).\n\nAltogether, only 2,145 (15.1%) EVD patients had malaria laboratory results available. Of these, 654 (30.5%) had a positive diagnosis, this being more common in those with clinically-suspected EVD (34.9%, 546/1,564) compared to those with laboratory-confirmed EVD (18.6%, 108/581).\n\nVital signs (respiratory rate, pulse rate, blood pressure etc.) and laboratory parameters such as serum electrolytes and renal or liver function tests were documented in <1% of the patients and hence were not included in the analysis (data not shown).\n\nIn patients with documented treatment information, the common treatments received included multivitamins, antimalarials, antibiotics, and intravenous fluids (Table 4). The proportions of patients who received cephalosporins and IV fluids were similar between laboratory-confirmed and clinically-suspected patients. The proportion of patients who received multivitamins and antimalarial drugs were slightly higher among clinically-suspected patients.\n\nOverall, 50.7% (7,184/14,163) of the patients were discharged, 28.9% (4,090/14,163) of patients died and in the remaining 20.4% (2,889/14,163), the outcome was unknown (which included withdrawn from a clinical trial, transferred, lost to follow-up, still in hospital or unknown) (Table 5). Death was substantially higher in laboratory-confirmed patients as compared to clinically-suspected patients (43.6% vs 18.8% among patients with known outcomes). The median duration from onset of symptoms to admission in the ETUs was 3 days (similar in both clinically-suspected and laboratory-confirmed patients). The median duration from admission to death was 4 days – this was higher at 4 days in laboratory-confirmed patients compared to 3 days in clinically-suspected patients. The median duration from admission to discharge was 4 days – this was higher at 13 days in laboratory-confirmed patients compared to 3 days in clinically-suspected patients.\n\nFactors associated with death are shown in Table 6, the denominator for this analysis being patients with known outcome. Overall, a total of 11,274 patients had their outcome recorded as death or discharged and of these, 4,090 (36.3%) died. In multivariable analysis, the factors significantly associated with death included confirmed disease status, age and country. The strongest risk factor was laboratory-confirmed disease status. Patients with laboratory-confirmed disease had 2.9 times higher risk of death compared to clinically-suspected patients, after adjusting for other co-variables. Patients aged 60 years and above had a significantly higher risk of death compared to that in ≤5-year-old children. Among the countries, Sierra Leone had the lowest risk of death compared to Guinea and Liberia.\n\nb The definition of confirmed disease status is outlined in the methodology section.\n\nc Any treatment with one or more of the following: antimalarials, any antibiotic, vitamins or multivitamins, nutritional intervention or intravenous fluids.\n\n\nDiscussion\n\nThis analysis used the largest available Ebola clinical database to explore factors associated with death in laboratory-confirmed and clinically-suspected EVD cases in the three West African countries of Guinea, Liberia and Sierra Leone. The key finding was that almost half of the patients with laboratory-confirmed EVD died which was almost three times higher than in patients with clinically-suspected EVD, although a higher proportion of clinically-suspected cases had unknown exit outcomes which may have masked additional deaths.\n\nThere were other important findings. There were some baseline differences between laboratory-confirmed and clinically-suspected EVD in terms of characteristics and treatments given. In particular, those with clinically-suspected EVD had a higher proportion of males and individuals who had recently visited a traditional healer, and a lower proportion of patients who came into contact with a suspected patient and funeral attendance. Symptomatology and physical signs in general were less prevalent in those with clinically-suspected EVD compared with laboratory-confirmed EVD. A positive diagnosis of malaria was more common in those with clinically-suspected EVD, although in over 80% of patients the malaria status was unknown. The time from symptom onset to admission was similar in both groups, but the median time from admission to death or discharge was higher in those with laboratory-confirmed EVD compared with clinically-suspected EVD. Finally, on adjusted analysis, the confirmed disease status (laboratory-confirmed or clinically-suspected) was the strongest risk factor for death. In the multivariable analysis, older age (≥ 60 years) was associated with increased risk of death while being treated in Sierra Leone was associated with a decreased risk of death.\n\nThese study findings are important for several reasons. First, they show that clinically- suspected EVD patients still have an appreciable in-hospital mortality and thus justify the need for better on-going care and support. We defined clinically-suspected EVD on the basis of negative PCR tests up to day 3 of inpatient admission, but our datasets showed that patients could become PCR-positive from day 4 onwards. On-going repeat PCR testing in this group of patients is necessary, not only to improve confirmatory diagnoses for reporting and epidemiological purposes but also to further direct care and treatment.\n\nSecond, the findings support previous studies that show old age is a risk factor for death.6,7,9,29 Older people with EVD thus need to be prioritised for ETU admission and targeted for appropriate care and support.\n\nThird, it was discouraging, to see the lack of documentation of malaria testing. West Africa is endemic for this parasitic infection, and in more than 30% of the small number of patients tested there was a positive malaria diagnosis. Malaria is common and is a risk factor for death in EVD17 and empirical antimalarial treatment may reduce case fatality.20,21 Empiric treatment with antibiotics is frequently used as a supportive care component in the clinical management of EVD, the rationale being to mitigate the potential risk of secondary bacterial infection and gram-negative bacteraemia that arises during EVD. Oral cephalosporins may reduce the case fatality,19 and should be explored further as treatment in patients ill with EVD.\n\nThere were several strengths to the study. There were large numbers of patients distributed between the three countries, giving enough power to test associations of baseline characteristics and treatments with exit outcomes. The conduct and reporting of the study adhered to STROBE (Strengthening the Reporting of Observational Studies in Epidemiology) guidelines.30\n\nThere were some limitations. First, data on vital signs and laboratory investigations were only documented in a limited number of patients and we therefore could not investigate these as potential factors for mortality. Furthermore, there were large numbers of missing data for clinical characteristics and treatment. Second, we did not explore the impact of treatment as it was impossible to unravel the individual effects of vitamins, antibiotics and antimalarial treatment on EVD outcomes, as patients usually received a combination of these treatments at the time of ETU admission. Third, nearly one fifth of patients had unknown exit outcomes, which reduced the reliability and precision around analysis of risk factors associated with death. Previous investigations have highlighted that case fatality estimates can be substantially affected by these unknown outcomes and this remains a major limitation of the analysis.31 It should also be noted that the findings on factors associated with death presented in our study should be interpreted solely as statistical associations which can be used for hypothesis generation; causal postulations remained beyond the scope of the current work. Fourth, we used a cycle threshold of 36.1 or less to define laboratory-confirmed EVD, while in other studies in West Africa and the Democratic Republic of Congo a cycle threshold >40 was considered negative when assessing various machine learning models to predict survival in children with suspected EVD.32 Different results might therefore be obtained depending on how that cycle threshold is set. Finally, extracting data from the large IDDO database was technically difficult as the database stores standardised data across multiple domains in a CDISC compliant format.\n\nDespite these limitations, there are a number of implications from this study. First, and as mentioned earlier, clinically-suspected EVD needs higher priority for treatment and care as there is a substantial mortality associated with this category. Second, large databases such as IDDO need to be better structured and planned right from the start so that it is easy to a) separate baseline variables from follow-up variables during data extraction and b) ensure that important information that might have a bearing on mortality such as vital signs and laboratory investigations at baseline can be easily teased out to enable front-line in-country staff faced with an epidemic/outbreak to access relevant and important data in real-time. Efforts are ongoing in this direction. Third, the extraction of data from the IDDO database was done within a structured operational research training (SORT IT) course, demonstrating once again that this is a useful way of equipping healthcare workers with an understanding about data and implementation research especially during outbreaks and pandemics.33,34\n\n\nConclusions\n\nIn conclusion, during the 2013-2016 EVD outbreak in Guinea, Liberia and Sierra Leone, 14,163 patients were admitted to ETUs and among the 11,274 (80%) patients with outcome recorded, 4,090 (36%) died. Patients with laboratory-confirmed disease had 2.9 times higher risk of death compared to clinically-suspected patients, after adjusting for other co-variables. Clinically-suspected patients nevertheless had a substantial risk of death and more attention needs to be paid to this group in future EVD outbreaks.\n\n\nData availability\n\nThe data that underpin this analysis are available via a governed data access mechanism following review of a data access committee. Data can be requested via the IDDO Ebola Data Platform (https://www.iddo.org/ebola/data-sharing/accessing-data). The Data Access Application, Terms of Access and details of the Data Access Committee are available on the website. Briefly, the requirements for access are a request from a qualified researcher working with a legal entity who have a health and/or research remit; a scientifically valid reason for data access which adheres to appropriate ethical principles. The full terms are at: https://www.iddo.org/ebola/data-access-guidelines These data are a part of https://doi.org/10.48688/cpwp-ft84.", "appendix": "Acknowledgements\n\nThis research was conducted through the Structured Operational Research and Training Initiative (SORT IT), a global partnership led by TDR, the Special Programme for Research and Training in Tropical Diseases hosted at the World Health Organization. The specific SORT IT program that led to this publication is a SORT IT partnership with the WHO Emergency Medical Teams (Geneva), WHO-AFRO (Brazzaville), WHO Country Offices and Ministries of health of Guinea, Liberia, Sierra Leone, and the Democratic Republic of the Congo, the Infectious Diseases Data Repository (IDDO); The International Union Against Tuberculosis and Lung Diseases, Paris, France and South East Asia offices, Delhi, India; The Tuberculosis Research and Prevention Center Non-Governmental Organization, Yerevan, Armenia; I-Tech, Lilongwe, Malawi; Medwise solutions, Nairobi, Kenya; All India Institute of Medical Sciences, Hyderabad, India; and the National Training and Research Centre in Rural Health, Maferinyah, Guinea.\n\nThere should be no suggestion that WHO endorses any specific organization, products or services. The views expressed in this article are those of the authors and do not necessarily reflect those of their affiliated institutions. The use of the WHO logo is not permitted.\n\n\nReferences\n\nJacob ST, Crozier I, Fischer WA, et al.: Ebola virus disease. Nat. Rev. Dis. Prim. 2020 Feb 20; 6(1): 13. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLeroy ÉM: The Emergence of Ebola virus in humans: a long process not yet fully understood. Bull. Acad. Natl Med. 2015; 199(4–5): 651–671. PubMed Abstract \| Publisher Full Text\n\nWorld Health Organization Team: WHO Guideline: Therapeutics for Ebola virus disease. Geneva: 2022 Aug [cited 2023 Jul 16]. Report No.: 32. Reference Source\n\nInstitute of Medicine; National Research Council: Research Priorities to Inform Public Health and Medical Practice for Ebola Virus Disease. Washington, D.C.: National Academies Press; 2014. Reference Source\n\nRojek AM, Salam A, Ragotte RJ, et al.: A systematic review and meta-analysis of patient data from the West Africa (2013-16) Ebola virus disease epidemic. Clin. Microbiol. Infect. 2019 [cited 2023 Jul 15]; 25: 1307–1314. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHaaskjold YL, Bolkan HA, Krogh KØ, et al.: Clinical Features of and Risk Factors for Fatal Ebola Virus Disease, Moyamba District, Sierra Leone, December 2014-February 2015. Emerg. Infect. Dis. 2016 Sep; 22(9): 1537–1544. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSchieffelin JS, Shaffer JG, Goba A, et al.: Clinical illness and outcomes in patients with Ebola in Sierra Leone. N. Engl. J. Med. 2014 Nov 27 [cited 2023 Jul 15]; 371(22): 2092–2100. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSow MS, Sow DC, Diallo ML, et al.: Ebola virus disease in children in Conakry and Coyah Ebola treatment centers and risk factors associated with death. Med. Mal. Infect. 2020 Oct 1 [cited 2023 Jul 15]; 50(7): 562–566. PubMed Abstract \| Publisher Full Text\n\nCherif MS, Koonrungsesomboon N, Diallo MP, et al.: The predictor of mortality outcome in adult patients with Ebola virus disease during the 2014-2015 outbreak in Guinea. Eur. J. Clin. Microbiol. Infect. Dis. 2017 Apr 1 [cited 2023 Jul 15]; 36(4): 689–695. PubMed Abstract \| Publisher Full Text\n\nBah EI, Lamah MC, Fletcher T, et al.: Clinical presentation of patients with Ebola virus disease in Conakry, Guinea. N. Engl. J. Med. 2015 Jan 1; 372(1): 40–47. PubMed Abstract \| Publisher Full Text\n\nKangbai JB, Heumann C, Hoelscher M, et al.: Sociodemographic and clinical determinants of in-facility case fatality rate for 938 adult Ebola patients treated at Sierra Leone Ebola treatment center. BMC Infect. Dis. 2020 Apr 21 [cited 2023 Jul 15]; 20(1): 293. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKangbai JB, Heumann C, Hoelscher M, et al.: Epidemiological characteristics, clinical manifestations, and treatment outcome of 139 paediatric Ebola patients treated at a Sierra Leone Ebola treatment center. BMC Infect. Dis. 2019 Jan 24 [cited 2023 Jul 15]; 19(1): 81. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDallatomasina S, Crestani R, Sylvester Squire J, et al.: Ebola outbreak in rural West Africa: epidemiology, clinical features and outcomes. Trop. Med. Int. Health. 2015 Apr 1 [cited 2023 Jul 15]; 20(4): 448–454. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLamontagne F, Fowler RA, Adhikari NK, et al.: Evidence-based guidelines for supportive care of patients with Ebola virus disease. Lancet. 2018 Feb 17 [cited 2023 Jul 16]; 391(10121): 700–708. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWaxman M, Aluisio AR, Rege S, et al.: Characteristics and survival of patients with Ebola virus infection, malaria, or both in Sierra Leone: a retrospective cohort study. Lancet Infect. Dis. 2017 Jun 1 [cited 2023 Jul 15]; 17(6): 654–660. Publisher Full Text Reference Source\n\nYam D, Aluisio AR, Perera SM, et al.: Association between multivitamin supplementation and mortality among patients with Ebola virus disease: An international multisite cohort study.2020 [cited 2023 Jul 15]; 10: 23–29. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAluisio AR, Perera SM, Yam D, et al.: Association between treatment with oral third-generation cephalosporin antibiotics and mortality outcomes in Ebola virus disease: a multinational retrospective cohort study. Trop. Med. Int. Health. 2020 Apr 1; 25(4): 433–441. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAbel L, Perera SM, Yam D, et al.: Association between oral antimalarial medication administration and mortality among patients with Ebola virus disease: a multisite cohort study. BMC Infect. Dis. 2022 Jan 20 [cited 2023 Jul 15]; 22(1): 71. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGignoux E, Azman AS, de Smet M , et al.: Effect of Artesunate-Amodiaquine on Mortality Related to Ebola Virus Disease. N. Engl. J. Med. 2016 Jan 7 [cited 2023 Jul 15]; 374(1): 23–32. PubMed Abstract \| Publisher Full Text\n\nWHO Ebola Response TeamAylward B, Barboza P, et al.: Ebola virus disease in West Africa--the first 9 months of the epidemic and forward projections. N. Engl. J. Med. 2014 Oct 16 [cited 2024 May 27]; 371(16): 1481–1495. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSchool of Applied Policy U of S. World Perspective: Educational tool of major global trends since 1945.2023 [cited 2023 Jul 16]. Reference Source\n\nProgramme National de Lutte Contre le Paludisme: Plan National de Suivi - Evaluation 2013-2017. REPUBLIQUE DE GUINEE; [cited 2024 May 27]. Reference Source\n\nDivision of Infectious Disease and Epidemiology: Liberia Early Warning Disease Surveillance Bulletin. Monrovia, Liberia: 2023 [cited 2024 May 27]. Reference Source\n\nMinistry of Health and Sanitation: Sierra Leone Basic Package of Essential Health Services 2015-2020. Freetown: Sierra Leone; 2015 [cited 2023 Jul 16]. Reference Source\n\nNyenswah TG, Kateh F, Bawo L, et al.: Ebola and Its Control in Liberia, 2014-2015. Emerg. Infect. Dis. 2016 Feb; 22(2): 169–177. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWorld Health Organization: EBOLA SITUATION REPORT. Geneva: 2016 Mar [cited 2023 Jul 19]. Reference Source\n\nWorld Health Organization: SITUATION REPORT: Ebola Virus Disease. Geneva: 2016 Jun [cited 2023 Jul 19]. Reference Source\n\nZou G: A modified poisson regression approach to prospective studies with binary data. Am. J. Epidemiol. 2004 Apr 1 [cited 2024 Mar 28]; 159(7): 702–706. Reference Source\n\nCherif MS, Dumre SP, Kasse D, et al.: Prognostic and Predictive Factors of Ebola Virus Disease Outcome in Elderly People during the 2014 Outbreak in Guinea. Am J Trop Med Hyg. 2018 [cited 2024 Mar 16]; 98(1): 198–202. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nvon Elm E , Altman DG, Egger M, et al.: The Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) statement: guidelines for reporting observational studies. Lancet. 2007 [cited 2024 Mar 16]; 370(9596): 1453–1457. Publisher Full Text Reference Source\n\nForna A, Nouvellet P, Dorigatti I, et al.: Case Fatality Ratio Estimates for the 2013-2016 West African Ebola Epidemic: Application of Boosted Regression Trees for Imputation. Clin. Infect. Dis. 2020 Jun 10 [cited 2024 Mar 16]; 70(12): 2476–2483. PubMed Abstract \| Publisher Full Text\n\nGenisca AE, Butler K, Gainey M, et al.: Constructing, validating, and updating machine learning models to predict survival in children with Ebola Virus Disease. PLoS Negl. Trop. Dis. 2022 Oct 12 [cited 2024 Mar 16]; 16(10): e0010789. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZachariah R, Berger SD, Thekkur P, et al.: Investing in Operational Research Capacity Building for Front-Line Health Workers Strengthens Countries’ Resilience to Tackling the COVID-19 Pandemic. Trop. Med. Infect. Dis. 2020 Sep 1 [cited 2024 Mar 16]; 5(3). Publisher Full Text Reference Source\n\nRamsay A, Harries AD, Zachariah R, et al.: The Structured Operational Research and Training Initiative for public health programmes. Public Health Action. 2014 Jun 19 [cited 2024 Mar 16]; 4(2): 79–84. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "323135", "date": "09 Oct 2024", "name": "Michael T Hawkes", "expertise": [ "Reviewer Expertise Pediatric infectious diseases and global health. Clinical EVD and social resistance to EVD control efforts." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 analysis of a large multinational database of Ebola virus disease (EVD) patients treated at ETUs in West Africa (2013-2016). The sample size is very large (strength) but the retrospective data are of limited quality (large proportion of missing data), such that biases are likely (weakness). There are many interesting observations that are consistent with past studies. We provide some suggestions to improve the manuscript below:\nHeterogeneity of the “clinically-suspected EVD” group The main comparison is between lab-confirmed and clinically-suspected EVD cases. The “clinically-suspected EVD” group is heterogeneous:\nNegative PCR Indeterminate PCR EVD positive but low viral load (cycle threshold greater than 36.1) No data (missing data)\nThere are likely cases of malaria, bacterial sepsis, community acquired pneumonia, and other acute infections in this group. There may even be non-infectious pathologies (see comment below on fever). There are likely also some cases of EVD (e.g., when the data were missing). Because cases with positive EVD PCR and low viral load were also included in this group, we may be looking at “mild EVD” in some patients (note that the viral load is a key determinant of mortality, as noted by the authors). It is not unexpected that severe acute non-EVD illness would be associated with some mortality (18.8% in this study). What makes this study difficult to interpret is the heterogeneity of the “clinically-suspected EVD” group. We don’t know what the etiology of their illness was, just that it resembled EVD clinically.\nThis is reflected in the study data. In Table 2, known risk factors for EVD transmission (funeral attendance, healthcare worker, contact with suspect case) were present in a higher proportion of lab-confirmed cases than “clinically-suspected EVD” cases. This is consistent with non-EVD etiology in a fraction of “clinically-suspected EVD” cases. For example, an alternative diagnosis of febrile illness, malaria, was found in 35% of “clinically-suspected” cases (versus 19% of laboratory confirmed cases).\nInclusion criteria ill defined The inclusion criteria (perhaps the same as ETU admission criteria) were not precisely defined for this retrospective database review, and may well be variable between ETUs. For example, one might expect fever to be universal in patients with suspected EVD admitted to an ETU, but it was present in only 77.6% overall and 75.7% of patients with clinically-suspected EVD. Why were afebrile patients admitted to the ETU? (this is actually dangerous as it exposes them to a significant risk of nosocomially-acquired EVD) Inclusion criteria are not clear, which further complicates the interpretation of the cases which were not lab-confirmed.\nRelated to the issue of inclusion criteria is the composition of the database itself. The large database is described in some detail. But several questions remain about who was included in this database and who was not included. This question arises, for example, in Table 1, in which the IDDO database had 5448 cases from Guinea while 3814 cases were reported to WHO (143%). One wonders how cases were reported to the IDDO but not the WHO and one questions if there might be duplications or inaccuracies in reporting. We suspect that the WHO records are also imperfect. The absence of any data from the DRC, which experienced the second largest outbreak in history (2018-2020) and has experienced multiple subsequent outbreaks also illustrates that the database (large and multinational) is not truly global and comprehensive. All this calls into question the representativeness of the database and whether the sample (though enormous) may be a selection of EVD patients. The authors are encouraged to provide more granular details on reporting to the IDDO database (mandatory or voluntary) and how the ETUs that contributed data were recruited. We suspect that this is related to the funders (MSF and Wellcome Trust) rather than any scientific sampling strategy.\n\nEtiology of illness in the “clinically-suspected EVD” group not examined/investigated Given this limitation (i.e., what exactly are these “clinically-suspected EVD” cases?), it seems reasonable to question and revisit the rationale behind the analysis. In the abstract (Conclusions subsection), and in the concluding paragraph of the article, the authors note that “clinically-suspected patients… still had a substantial risk of death and more attention needs to be paid to this group in future EVD outbreaks.” This does indeed seem to justify the present analysis and the conclusion does follow from the data. With this rationale in mind, it would seem important to try to identify the etiology of the illness when EVD is clinically suspected but not demonstrated by PCR. The authors have noted a high prevalence of malaria which could in part explain the clinical manifestations (although among adults in an endemic area with partial immunity, malaria is not typically lethal). It would be nice to know if the malaria positive patients were treated with an antimalarial, and if mortality was elevated when malaria was present and treatment was not documented. For malaria negative patients, bacterial sepsis is on the differential diagnosis. It would be interesting to know how many of these got antibiotics and whether that was associated with differences in mortality. A higher proportion of patients with “clinically-suspected EVD” had respiratory symptoms (difficulty breathing, Table 3), suggesting that pneumonia could contribute to mortality in the clinically suspected cases. It would be interesting to know which patients who were EVD negative, malaria-negative, with difficulty breathing, received antibiotics and if this was associated with a difference in mortality. Overall, we would would like to see more detailed analysis of the “clinically-suspected EVD” cases and an attempt to classify patients into possible etiologic categories (including mild EVD cases in this groups, as noted above). The large sample size may allow such probing subgroup analyses, which would be helpful to delineate the cause of the illness in the EVD-negative patients. This would go beyond a mere observation of high mortality, toward actionable hypotheses (i.e., treatable etiologies) for improved management of these patients. We don’t think it is satisfactory to identify a high mortality in this subgroup without any attempt to answer why they died. Clinical clues and limited microbiologic data should be leveraged to try to answer this question, recognizing that microbiologic tests were scant and a diagnosis won’t be definitive. After all, this is the difficult task faced by clinicians managing these suspected cases in resource-limited contexts.\nTable 3. Statistical versus clinical significance Despite the heterogeneity of the “clinically-suspected EVD” group, the authors’ analysis could be illuminating for clinicians facing diagnostic uncertainty with febrile patients during an EVD outbreak. One value of this analysis, comparing lab-confirmed and “clinically-suspected EVD,” could be to examine the clinical manifestations in each group to determine which are clinically informative. This is attempted in Table 3, but falls short of its goal. We acknowledge the statistically significant differences between lab-confirmed and clinically suspected cases in presenting signs and symptoms (Table 3). Because of the large sample size, these differences all reach statistical significance except for abdominal pain and bleeding (This point is interesting and perhaps unexpected! We would have thought bleeding would be a more specific sign of EVD, a hemorrhagic fever). However, there remains a question about whether the differences are clinically significant. Taking, for example, nausea and vomiting (62% in EVD vs 51% in non-EVD, p<0.001), the 11% absolute difference may not be very helpful in distinguishing EVD from other illnesses. The clinical utility (diagnostic accuracy) of clinical exam findings might be better expressed with sensitivity, specificity or likelihood ratios of positive/negative signs (see, for example, the JAMA series on The Rational Clinical Examination). These statistics will likely show that the small differences observed would be of little help in clinical decision-making, even though they are statistically significant. Taking the example of nausea and vomiting as a clinical sign of EVD positivity and using complete cases (ignoring missing data), we calculate a sensitivity of 62%, a specificity of 49%, a likelihood ratio of a positive sign of 1.1 and a likelihood ratio of a negative sign of 0.87. (A good “test” has a positive LR of >10 and/or a negative LR of < 0.1). Thus, nausea and vomiting discriminates poorly between lab-confirmed EVD cases and other illnesses. The same would be true for other clinical signs, even though they are statistically significantly different between the two groups. Our interpretation of the findings, therefore, is that the clinical signs are neither sensitive nor specific and are present in a substantial proportion of EVD-negative patients. Thus, the table as presented, with highly statistically significant differences, may mislead all but the most savvy reader knowledgeable in interpreting clinical epidemiology data. Readers will assume that “statistically significant” clinical signs may help identify EVD cases, whereas our interpretation of the findings is quite the opposite: these data show that nothing can replace a PCR. To address this limitation, the authors are encouraged to show (for example) sensitivity, specificity, negative and positive likelihood ratios which will make it clear that the clinical signs do not provide actionable information (not clinically informative).\nTable 6\n“Patients aged 60 years and above had a significantly higher risk of death compared to that in ≤5-year-old children.” The authors go on to note in the discussion that old age is a risk factor for mortality and cite other studies in support of this finding. The data do indeed show this, but the conclusion misses another major, important finding. The RR of death is significantly lower in the 6-18 year olds and lower in the 19-39 year olds relative to the reference group (<=5 years). Thus, the “U-shaped” mortality curve, with higher mortality at the extremes of age should be the “take-away” observation from the data, not just elevated mortality in the elderly. We request that the authors amend this sentence to include elevated mortality in children and infants under 5 years of age (relative to older children and young adults) as well as elevated mortality in the elderly.\nDiscussion -\nWe were perplexed by the following statement and citation in the Discussion: “Oral cephalosporins may reduce the case fatality…” (citation Gignoux E, Azman AS, de Smet M , et al.: Effect of Artesunate-Amodiaquine on Mortality Related to Ebola Virus Disease. N. Engl. J. Med. 2016 Jan 7 [cited 2023 Jul 15]; 374(1): 23–32.) The citation compares two artemisinin combination therapy (ACT) regimens and does not examine oral cephalosporins. Broad-spectrum intravenous (not oral) cephalosporins would seem to be indicated in critically ill EVD patients in whom a blood culture is not available (Plachouras D, Monnet DL, Catchpole M. Severe Ebola virus infection complicated by gram-negative septicemia. N Engl J Med. 2015 Apr 2;372(14):1376-7.). We request that the authors delete or modify this sentence and citation.\nMissing data The authors are to be congratulated on reporting the missing data transparently in the Tables. Missing data is acknowledged as a limitation in the Discussion. Nonetheless, this remains a major limitation which threatens the validity of the findings. When, for example, the chi-squared statistic was calculated (e.g. ,in Table 2), were the missing cases disregarded? Or was missing included as a category in a “three-level” categorical variable (yes/no/missing) in the contingency table? The “complete case” analysis (ignoring missing data) is actually a “naïve” approach that is prone to biases when the data are not missing at random. It would have been nice to see attempts to address data missingness through statistical analyses (e.g., multiple imputation).\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] }, { "id": "364685", "date": "08 Feb 2025", "name": "Aroop Mohanty", "expertise": [ "Reviewer Expertise Diagnostic 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\nAt the outset, I express my gratitude to the editorial team to have provided me the opportunity to review this paper in your prestigious journal. Ebola virus causes a very lethal disease and its endemicity in Africa has been found to be very lethal. This paper has been written in clear and simple language and with a proper methodology. The structure of the paper is clear and all the results have been compared very well with the other relevant papers. A bit more can be added on the testing methods deployed to diagnose Ebola as well as a bit more data of recent outbreaks.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] } ]	1	https://f1000research.com/articles/13-672
https://f1000research.com/articles/13-671/v1	21 Jun 24	{ "type": "Research Article", "title": "Analysis of associated scrotal anomalies in boys with hypospadias", "authors": [ "Vita Indriasari", "Felicia Felicia", "Rizki Diposarosa", "Yoni Fuadah Syukriani", "Dedi Rachmadi", "Felicia Felicia", "Rizki Diposarosa", "Yoni Fuadah Syukriani", "Dedi Rachmadi" ], "abstract": "Background Hypospadias is a common congenital anomaly of the penis characterized by ventral opening of urethra. This abnormality is often accompanied by scrotal abnormalities, where both penile and scrotal development occur at the same time during the fetal period. This study aims to analyze associated scrotal anomalies in children with hypospadias.\n\nMethods This is a retrospective cross-sectional study of boys diagnosed with hypospadias during a 6 years period. The age of patients, severity of hypospadias, and associated scrotal anomalies such as penoscrotal transposition (PST), bifid scrotum (BS), and scrotal hypoplasia were assessed. Scrotoplasty procedure was also recorded. The association between the severity of hypospadias, incidence of scrotal anomalies, severity of both PST and BF were analyzed using Chi-square test and alternatively Fisher exact test, p<0,05 considered significant.\n\nResults During the study period, there were 240 hypospadias patients, with a median age of 5,6 years. Most patients had severe hypospadias. Associated scrotal anomalies were found in 63,3% of patients. Incidence of scrotal anomaly was higher in patients with severe hypospadias (75%) compared to mild cases (75% vs 36.1%; p<0.001; PR= 2.08 (95% CI: 1.51 – 2.86)). Patients with severe hypospadias had a more severe PST, especially in bilateral minor and major forms compared to patients with mild cases (p<0.001); and was significantly associated with severe and partial type of SB (p<0.001). Patients with a more severe PST tend to have a more severe SB, on contrary, patients with minor PST tend to have a milder or even no BS (p<0.001). Scrotoplasty was performed in 35,4% of cases.\n\nConclusion Most hypospadias patients had associated scrotal anomaly, in which severe hypospadias was associated with the more severe type of PST and BS.", "keywords": [ "Hypospadias", "penoscrotal transposition", "scrotal anomalies", "scrotal bifid" ], "content": "Introduction\n\nHypospadias is the most common congenital anomaly of the penis characterized by the abnormal ventral position of usingthe urethral opening and associated penile curvature.1,2 Etiology of hypospadias is thought to be a combination of genetic defects and environmental factors that affect the developing male external genitalia.3–5 Disturbance of scrotal development can also occur at that time.6\n\nCongenital scrotal anomalies are rare clinical findings. The spectrum of these anomalies has been described, such as penoscrotal transposition (PST), bifid scrotum (BS), accessory scrotum, scrotal agenesis, hypoplasia, scrotoschisis, and scrotal calcinosis. Although rare, scrotal anomalies are often found together with hypospadias.5,7–9 Currently, studies discussing scrotal anomalies in hypospadias are limited and mostly reported through case reports. A study by Fahmi et al discusses scrotal position disorders in children comprehensively but not specifically for children with hypospadias.10 Spectrum and severity of scrotal anomalies are thought to be associated with the severity of hypospadias. This study aims to analyze associated scrotal anomalies in children with hypospadias who were treated in our institution.\n\n\nMethods\n\nThis is a retrospective cross-sectional study.\n\nThis study was conducted on all boys diagnosed with hypospadias treated in a pediatric surgical unit of a provincial referral hospital during 2018 – 2023. This study was approved by The Research Ethics Committee of Dr. Hasan Sadikin General Hospital Bandung, Indonesia (No: LB.02.01/X/6/5/67/2023). Data was collected from medical records including age, severity of hypospadias, scrotal anomalies, and scrotoplasty procedure. Severity of hypospadias was revaluated from preoperative clinical pictures, and was assessed according to the quality of glans, meatus, and shaft and scored as a GMS score, with a total score of 12.11 A score of ≤6 was considered as mild hypospadias, while >6 was assessed as severe type.\n\nAssociated scrotal anomalies such as penoscrotal transposition (PST), bifid scrotum (BS), and scrotal hypoplasia were recorded and reassessed from preoperative clinical picture. PST was classified as complete major if the penis is completely caudal to the scrotum and there is no scrotal tissue distal to the penis, while incomplete major PST cases had scrotal tissues completely surrounding the root of the penis. Minor PST had scrotal tissue creeping to one (unilateral) or both (bilateral) sides of the penis.10\n\nBS is an anomaly affecting the midline of the scrotum which can be differentiated as severe, minor, and partial forms. A severe BS has two scrotal sacs that are widely separated with a laid opened urethra in the form of proximal hypospadias and the scrotal raphe is not detectable. Minor form had a split or wide scrotal raphe, while a partial bifid scrotum may be seen as a pit at the proximal scrotal end or distally at the base of the scrotum. Scrotal hypoplasia refers to an incompletely developed scrotum, which looks smaller, non-pendant, with a few rugae.12 Scrotoplasty as a procedure for correction of scrotal anomalies was also recorded. Subjects with incomplete medical records and clinical photograph were excluded.\n\nMedian and range of age, as well as proportion of each degree of hypospadias, PST, BF, and scrotal hypoplasia were analyzed. The association between the severity of hypospadias, incidence of scrotal anomalies, severity of both PST and BF were analyzed using Chi-square test and alternatively Fisher exact test, p<0.05 considered significant.\n\n\nResults\n\nDuring the study period, there were 244 hypospadias patients. Four of them were excluded due to incomplete data in medical records. A total of 240 hypospadias patients were included in this study, with a median age of 5.6 years (range 0.8 – 18 years old). Most patients had severe hypospadias. Associated scrotal anomalies were found in 63.3% of patients; the spectrum of this anomaly is described in Table 1. Scrotoplasty was performed in 81,5% cases with scrotal anomalies.\n\nIncidence of scrotal anomaly was higher in patients with severe hypospadias (75%) compared to mild cases (75% vs 36.1%; p<0.001), as described in Table 2. Severe hypospadias had a significantly higher prevalence of scrotal anomaly compared to those with mild hypospadias (PR=2.08 (95% CI: 1.51 – 2.86)).\n\n* p<0.05 significant.\n\nMost patients with mild hypospadias (80.6%) did not have PST and SB. Patients with severe hypospadias had a more severe PST, especially in bilateral minor and major forms compared to patients with mild cases (p<0.001) (Table 3). Patients with severe hypospadias were significantly associated with severe and partial types of SB (p<0.001) (Table 4).\n\n* p<0.05 significant.\n\n* p<0.05 significant.\n\nPatients with a more severe PST tend to have a more severe SB, compared to patients with milder type of PST. On the contrary, patients with minor PST tend to have a milder BS or even no BS (p<0.001) (Table 5).\n\n* p<0.05 significant.\n\n\nDiscussion\n\nMost of our patients were presented at an older age compared to the other studies.13–15 Hypospadias can be corrected at any age but mostly recommended at 6 to 18 months. Scrotal abnormalities which may be associated with hypospadias, are usually corrected simultaneously.5,16,17 The late presentation may be due to various factors, such as socioeconomic problems, or difficulties in accessing our provincial hospital that covers a wide geographic area. We also found that severe hypospadias was more common than the mild type. This is in line with previous study at the same hospital, where the characteristics of our hypospadias patients had a worse penile biometry profile with a more severe degree of hypospadias.18\n\nHypospadias occurs due to cessation of penile development in the fetus. This process is divided into 2 phases: the hormone-independent phase (5th – 8th week of pregnancy) where the development of the genital tubercle occurs; and the hormone-dependent phase (8th – 12th week of pregnancy) where lengthening of the genital tubercle, fusion of the urethral folds to the midline to form the penile urethra, and development of the scrotum occur.2 Scrotal development begin early in the fifth week of gestation. A pair of swellings called urogenital folds develops on either side of the urogenital plate. Labioscrotal swellings, then appear on either side of the urethral folds. Starting in the fourth month of gestation, with the effects of dihydrotestosterone, labioscrotal folds fuse at the midline to form the scrotum.6 Depending on the severity of the disorder, mild and severe hypospadias as well as scrotal anomalies can occur.\n\nWe found a high incidence (63.3%) of scrotal anomalies in boys with hypospadias, with PST and BS as the most common spectrum. PST and BS were found together in 45.3% of all cases with scrotal anomalies. Scrotal development and urethral localization both take place during the first trimester.19 PST and BS arise from abnormal or arrested migration and fusion of labioscrotal swellings due to poor response to androgens.10,19,20\n\nIn this study, both PST and BS occurred more often in severe hypospadias (p<0.001). Contrary, 80.6% of patients with mild hypospadias had no PST or BS. It is consistent with findings from other studies where PST is usually accompanied by proximal hypospadias.10,21,22 A study by Swartz et al. also stated that 86% of patients with BS had severe hypospadias, but they did not classify the severity of BS.19 The greater proportion of PST and BS in severe hypospadias indicated that severe hypoplasia of the ventral penis and proximal urethral opening may influence the process of caudal migration and fusion of the scrotum. Apart from that, severe androgen defects also definitely have an influence.\n\nAll types of PST, especially bilateral minor and incomplete major types were more often found in severe hypospadias compared to the mild one (p<0.001). However, the most severe form which is complete major PST was found only in 7,1% of severe hypospadias cases. Complete major PST is a rare heterogeneous condition that result from abnormal genital tubercle development around the 6th week of gestation.7,23 In this study, the lower incidence of complete major PST reflects the small number of hypospadias patients who might have abnormal penile development starting at non-hormonal phase when the development of genital tubercle occurred. Severe form of BS was also found in the majority of severe hypospadias cases in this study. Further analysis showed that severe PST was associated with higher degree of BS. This supports the interrelated processes of scrotal migration and fusion.\n\nWe found only 3 patients with scrotal hypoplasia. The etiology of scrotal hypoplasia is multifactorial, which are localised androgen insensitivity, localised 5a-reductase deficiency, and failure of formation of the labioscrotal fold. It is also usually associated with undescended testes. In this study, two patients had unilateral scrotal hypoplasia with ipsilateral undescended testes (UDT). This number is very small considering that the etiology of hypospadias is also caused by androgen defects and this disorder is often accompanied by UDT. This may be due to the assessment of scrotal hypoplasia that are more challenging in patients with hypospadias because of the frequent PST and BS that accompany it.\n\nfPST necessitates a staged surgical repair for physiological and psychological reasons if associated with severe hypospadias.10 The goal of the surgery in PST is to achieve normal anatomic position of the penis and scrotum with concurrent correction of the severe hypospadias. In our institution, scrotoplasty was performed in 35,4% of hypospadias cases with associated PST. However, the type of PST indicated for scrotoplasty, timing of procedure (whether scrotoplasty performed with the first or subsequent stages of hypospadias repair), stages needed, and the techniques used were still varied among paediatrics surgeons in our institution. Scrotal procedure has been described for correction of PST, in which two halves of scrotum are mobilized as advancement flaps with relocation of scrotum caudal to the penis.24,25 Mori-Ikoma, Glenn Anderson, and buttonhole technique were among the most common procedures used in our centre. Inverted omega skin incision at the scrotal apex and the base of penis is used in Mori-Ikoma technique, closure of the flaps is in the form of zeta. In Glenn Anderson technique both halves of scrotum are fully mobilized as rotational advancement flaps, relocating the scrotal compartment to a normal dependent position, and constructing the neourethra during the same operation. In buttonhole technique, the degloved penis is brought out to the new dorsal site leaving the scrotum at caudal position. The transposed penis than delivered through a newly created window in the dartos tissue to achieve proper orientation with the shaft skin. In 12% of cases, we did scrotal fat mobilisation for PST repair without extensive scrotal skin roof incisions as in Mori-Ikoma and Glenn Anderson technique. Penoscrotal junction was divided, followed by mobilisation of the scrotal fat and penoscrotal skin flap caudally.\n\nThis study provides a thorough analysis of associated scrotal anomalies in children with hypospadias. However, it has some limitations. This is a retrospective study so that data collection was based on medical records, supported by clinical photos of the external genitalia of the patients. Although bias may occur, scrotal abnormalities should be easily assessed from clinical photographic data. We have not been able to comprehensively evaluate the scrotoplasty results due to the diversity of indications, techniques, timing, and performed by multiple surgeons.\n\n\nConclusions\n\nMost hypospadias patients had associated scrotal anomaly, in which severe hypospadias was associated with the more severe type of PST and BS.\n\n\nEthical considerations\n\nThis study has Ethical approval from The Research Ethics Committee of Dr. Hasan Sadikin General Hospital Bandung, Indonesia on 28 February 2023 and the ethical approval number: LB.02.01/X/6/5/67/2023. The research has been performed following the Declaration of Helsinki.\n\nConsent: All parents or guardians signed written informed consent to participate in this study.", "appendix": "Data availability\n\nThe underlying data has been deposited in the Zenodo Dataset repository and contains:\n\nRaw data of this study. Available at:\n\nZenodo Analysis of associated scrotal anomalies in boys with hypospadias [Data set]. https://doi.org/10.5281/zenodo.11497582\n\nData is available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0.1.0 Public domain dedication).\n\nRepository: STROBE checklist for “Analysis of associated scrotal anomalies in boys with hypospadias”. https://doi.org/10.5281/zenodo.11218363.\n\nData is available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0.1.0 Public domain dedication).\n\n\nReferences\n\nYu X, Nassar N, Mastroiacovo P, et al.: Hypospadias Prevalence and Trends in International Birth Defect Surveillance Systems, 1980–2010. Eur. Urol. 2019; 76(4): 482–490. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBouty A, Ayers KL, Pask A, et al.: The Genetic and Environmental Factors Underlying Hypospadias. Sex. Dev. 2015; 9(5): 239–259. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChang J, Wang S, Zheng Z: Etiology of Hypospadias: A Comparative Review of Genetic Factors and Developmental Processes Between Human and Animal Models. Res. Rep. Urol. 2020; 12: 673–686. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSuresh MS, Kattepura S, Yathindra N, et al.: Incidence of types of hypospadias in and around Tumkur district, Karnataka, India: an anatomical classification. Int. J. Res. Med. Sci. 2018; 6(4): 1161–1164. Publisher Full Text\n\nZhu XY, Feng DC, Han T: Hypospadias in male infants - a review. Eur. Rev. Med. Pharmacol. Sci. 2017; 21(4): 1–3.\n\nSchoenwolf GC, Bleyl SB, Brauer PR, et al.: Larsen’s Human Embryology. 6th ed.Philadelphia: Elsevier, Inc.; 2021.\n\nAyamba AM, Maalman RS-E, Donkor YO, et al.: Complete Penoscrotal Transposition with Other Extragenital Anomalies in a Neonate Delivered at Term. Case Rep. Urol. 2021; 2021: 1–4. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFitouri F, Chebil N, Ben Ammar S, et al.: Accessory Scrotum. Fetal Pediatr. Pathol. 2020; 39(1): 90–91. Publisher Full Text\n\nAladag Ciftdemir N, Vatansever U, Duran R, et al.: Accessory Scrotum with Bifid Scrotum and Hypospadias. Turkish J. Pediatr. Dis. 2013; 7(September): 38–40. Publisher Full Text\n\nFahmy MAB, El Shennawy AAA, Edress AM: Spectrum of penoscrotal positional anomalies in children. Int. J. Surg. 2014; 12(9): 983–988. PubMed Abstract \| Publisher Full Text\n\nMerriman LS, Arlen AM, Broecker BH, et al.: The GMS hypospadias score: Assessment of inter-observer reliability and correlation with post-operative complications. J. Pediatr. Urol. 2013; 9(6 PART A): 707–712. PubMed Abstract \| Publisher Full Text\n\nFahmy MAB: Normal and Abnormal Scrotum. Switzerland: Springer Nature Switzerland AG; 2022.\n\nArlen AM, Kirsch AJ, Leong T, et al.: Further analysis of the Glans-Urethral Meatus-Shaft (GMS) hypospadias score: Correlation with postoperative complications. J. Pediatr. Urol. 2015; 11(2): 71.e1–71.e5. PubMed Abstract \| Publisher Full Text\n\nHuang J, Rayfield L, Broecker B, et al.: High GMS score hypospadias: Outcomes after one- and two-stage operations. J. Pediatr. Urol. 2017; 13(3): 291.e1–291.e4. PubMed Abstract \| Publisher Full Text\n\nShoukry A, Abbas A, Abdelwahab M, et al.: Glans–urethral meatus–shaft score and penile parameters as preoperative assessment tools for hypospadias surgery outcome. Afr. J. Urol. 2021; 27(1): 1–8. Publisher Full Text\n\nvan der Horst HJR , de Wall LL : Hypospadias, all there is to know. Eur. J. Pediatr. 2017; 176(4): 435–441. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKeays MA, Dave S: Current hypospadias management: Diagnosis, surgical management, and long-term patient-centred outcomes. Can. Urol. Assoc. J. 2017; 11(1-2S): 48–53. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nIndriasari V, Suritno R: Biometry of Hypospadic Penis in Children: Study From a Tertiary Referral Hospital. Malays. J. Med. Health Sci. 2022; 18(SUPP10): 31–34.\n\nSwartz JM, Ciarlo R, Denhoff E, et al.: Variation in the clinical and genetic evaluation of undervirilized boys with bifid scrotum and hypospadias. J. Pediatr. Urol. 2017; 13(3): 293.e1–293.e6. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWong YS, Tam YH, Pang KKY, et al.: Incidence and diagnoses of disorders of sex development in proximal hypospadias. J. Pediatr. Surg. 2018; 53(12): 2498–2501. PubMed Abstract \| Publisher Full Text\n\nSarma DVP: Penoscrotal transposition for pre-penile scrotum in Hypospadias: Analysis of timing and outcome. J. Med. Sci. Clin. Res. 2018; 6(7): 46–49. Publisher Full Text\n\nMagdalena P, Kusuma Duarsa GW: Multi-stage repair surgery in combination with hormonal therapy for scrotal hypospadias with severe chordee, micropenis, and bifid scrotum. Neurologico Spinale Medico Chirurgico. 2019; 2(3): 47–50. Publisher Full Text\n\nBeyazıt F, Pek E, Aylanç H: A rare case of complete penoscrotal transposition with hypospadias in a newborn. Turk. J. Obstet. Gynecol. 2017; 14(1): 74–75. PubMed Abstract \| Publisher Full Text\n\nSmith JA, Howards SS, Preminger GM, et al.: Hinman’s atlas of urologic surgery. Amsterdam: Elsevier; 2019.\n\nHadidi AT: Penoscrotal Transposition. Hypospadias Surgery: An Illustrated Textbook, Second Edition. 2022; pp. 705–713. Publisher Full Text" }	[ { "id": "304407", "date": "10 Aug 2024", "name": "Priyank Yadav", "expertise": [ "Reviewer Expertise I am a Pediatric Urologist with expertise in hypospadias" ], "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 retrospective cross-sectional study examined the association between hypospadias severity and scrotal anomalies in 240 boys at an Indonesian referral hospital from 2018 to 2023. The authors used the Glans-Meatus-Shaft (GMS) score to classify hypospadias as mild or severe, finding that 63.3% of patients had associated scrotal anomalies, with a higher incidence in severe cases.\nI have the following comments:\n1) The use of the GMS score to classify hypospadias severity is problematic, as this system was designed to predict postoperative complications rather than differentiate between distal and proximal hypospadias. This misclassification may have led to biased results and potentially incorrect conclusions about the association between hypospadias severity and scrotal anomalies.\n2) The study overlooks the well-established connection between bifid scrotum and underlying urethral hypoplasia, often associated with more severe forms of hypospadias.\n3) The association between bifid scrotum and the degree of penoscrotal transposition (PST) is already well-known in the literature, and the study fails to contextualize this finding adequately.\n4) There are inconsistencies in the reporting of scrotoplasty rates, and the criteria for performing this procedure are unclear. This lack of clarity makes it difficult to interpret the surgical decision-making process and limits the generalizability of the findings.\n5) The paper focuses on statistical associations without adequately addressing the clinical significance of the findings. It does not provide sufficient information on how these results might impact clinical decision-making or patient outcomes, limiting its practical utility.\n6) The wide age range of patients (0.8 to 18 years) could introduce confounding factors related to age differences.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? No\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? No\n\nAre the conclusions drawn adequately supported by the results? No", "responses": [] }, { "id": "355190", "date": "16 Jan 2025", "name": "Ismail Selvi", "expertise": [ "Reviewer Expertise Pediatric urology" ], "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 aimed to analyze associated scrotal anomalies in children with hypospadias. They designed a retrospective cross-sectional study of boys diagnosed with hypospadias over a 6-year period. However, I do have some questions and concerns outlined below about their study.\nIt is also known that severe hypospadias is associated with the more severe type of penoscrotal transposition and bifid scrotum. Therefore, I'm not sure what this is going to add to the literature. The Chi-square test or Fisher exact test is not sufficient to evaluate the association between the severity of hypospadias, the incidence of scrotal abnormalities, the severity of PST and BF. Other statistical analyses are also required. I think the discussion section could be simplified a bit to better highlight the main focus.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] } ]	1	https://f1000research.com/articles/13-671
https://f1000research.com/articles/13-670/v1	21 Jun 24	{ "type": "Review", "title": "Recent advances in the design of SERS substrates and sensing systems for (bio)sensing applications: Systems from single cell to single molecule detection", "authors": [ "Sai Ratnakar Tadi", "Ashwini G Shenoy", "Anirudh Bharadwaj", "Sreelakshmi C S", "Chiranjay Mukhopadhyay", "Kapil Sadani", "Pooja Nag", "Sai Ratnakar Tadi", "Ashwini G Shenoy", "Anirudh Bharadwaj", "Sreelakshmi C S", "Chiranjay Mukhopadhyay" ], "abstract": "The Raman effect originates from spontaneous inelastic scattering of photons by matter. These photons provide a characteristic fingerprint of this matter, and are extensively utilized for chemical and biological sensing. The probability of generation, and hence the detection of these Raman scattered photons, is very low; hence, it is difficult to use this directly for sensing in complex matrices. To amplify this signal, surface-enhanced Raman spectroscopy (SERS) has been extensively investigated and has emerged as a powerful analytical tool for sensing diverse analytes, including ions, small molecules, inorganics, organics, radionucleotides, and cells. Plasmonic nanoparticles, called hotspots, exhibit localized surface plasmon resonance (LSPR). This amplifies the Raman signal and may offer up to a 1010-fold SERS signal enhancement. The development of SERS active substrates requires further consideration and optimization of several critical features such as surface periodicity, hotspot density, mitigation of sample or surface autofluorescence, tuning of surface hydrophilicities, use of specific (bio) recognition elements with suitable linkers and bioconjugation chemistries, and use of appropriate optics to obtain relevant sensing outcomes in terms of sensitivity, cross-sensitivity, limit of detection, signal-to-noise ratio (SNR), stability, shelf-life, and disposability. This article details the optimization of the aforementioned considerations in the use of disposable materials such as commercial grades of paper, textiles, glasses, polymers, and some specific substrates such as blue-ray digital versatile discs (DVDs) for use as SERS-active substrates for point-of-use (POU) sensing applications. The advancements in these technologies have been reviewed and critiqued for analyte detection in resource-limited settings, highlighting the prospects of applications ranging from single-molecule to single-cell detection.", "keywords": [ "Raman effect", "Surface Enhanced Raman Spectroscopy", "Disposable substrates", "Point-of-use", "Single-molecule sensing", "Bioreceptor." ], "content": "1. Introduction to Raman effect for sensing\n\nRaman spectroscopy is an analytical technique used to sense a diverse range of analytes by providing insights into their molecular structure and bonding. When illuminated with a suitable light source, the intra-and intermolecular vibrations of the sample result in a wavenumber shift of the scattered photons, generating a unique Raman fingerprint spectrum. In contrast to near-infrared (NIR) spectroscopy, Raman spectroscopy generates a unique fingerprint that is insensitive to the bulk properties of the matrix and masking effects of water in the aqueous phase. Raman spectroscopy relies on Raman scattering, experimentally discovered as a modified scattered radiation by Raman and Krishnan in 1928, initially annotated as “a new type of secondary radiation’ (Raman & Krishnan, 1928). Further studies indicated that Raman scattering of the incident light resulted in scattered radiation of a lower frequency than that of the incident light. Therefore, Raman scattering is mathematically calculated as a measure of the phase shift between incident and Raman-scattered photons.\n\nRaman spectroscopy is extensively used in research for industrial quality control applications, assessment of environmental safety, healthcare as diagnostics, and nutritional security owing to its characteristic fingerprinting ability for diverse analytes. Its use in healthcare is predominantly directed towards metabolite sensing (F. Hu et al., 2014; L. Wei & Vikesland, 2015), diagnosis of infectious diseases and carcinoma (Tipping et al., 2017), mapping of drug distribution (Tipping et al., 2016), and whole cell detection (Crawford et al., 2012) in other allied areas of bioscience (Benevides et al., 2005). Other prominent domains of application include pharmaceuticals (Choo-Smith et al., 2002), nanostructure characterization (Bensebaa et al., 1999), forensic studies, analytical chemistry (Doty et al., 2015), phase transitions (Elleuch et al., 2006), solid-state physics (Jawhari, 2000), and archaeology (Kiefer, 2007).\n\nMost asymmetric molecules display a weak Raman effect, thus requiring the use of strong illumination, such as lasers, to obtain measurable Raman-scattered photons. The use of appropriate optics such as lenses, notch filters, and monochromators as spectral filters, differently cooled detector arrays comprising charge-coupled devices (CCDs), complementary metal-oxide-semiconductor (CMOS) or avalanche photodiodes (APDs), and silicon photomultipliers (SiPMs) as detectors improves the sensitivity by several orders of magnitude (Mukhopadhyay, 2007). However, as the Raman effect is a weak phenomenon, its direct use in trace-level analysis of analytes is limited, and technologies for its amplification have been extensively studied.\n\nRaman scattering involves the inelastic transfer of momentum from photons of the incident light to molecules in the sample. The interaction of the external electromagnetic field with the electron subsystems of the molecule results in light scattering. These molecular energy transitions during scattering are shown in the Jablonski diagram, which illustrates the electronic states: ground state, singlet state (So), and triplet state (T), as shown in Figure. 1. A typical Jablonski diagram contains vertically stacked electronic states and horizontally grouped vibrational energy states, according to their spin multiplicity. Each energy state contains sublevels based on the vibrational energy of the molecule (Demtröder, 2015). According to Pauli’s exclusion principle, all electrons are paired in the ground state of the molecule, while a change in the spin of the energy state is observed in the singlet state (S0) due to half-filled molecular orbitals. The electronic transitions to higher singlet energy states are caused by photon energy absorption from the incident electromagnetic radiation, whereas the emission is a two-photon process, with single-photon emission to the lowest vibrational state (S1). A triplet state (T1) is a virtual triple-degenerate excited state for the relaxation of excited photons to the ground state by intersystem crossing (Prochazka, 2016). The standard expression for the energy of the photon transition is illustrated in (equation 1), where h = Planck’s constant = ~6.626 x10−34 J/s and c = speed of light = ~3 × 108 m/s\n\nThe standard expression for the energy of the photon transition is illustrated in (equation 1), where h = Planck’s constant = ~6.626*10−34 J/s and c = speed of light = ~3 ×108m/s\n\nHowever, in addition to optical absorption and emission, another process termed as scattering is often observed in the emission of a molecular photon owing to the absorption of an incident light photon. This photon scattering may be elastic or inelastic. Rayleigh scattering, an elastic scattering, is associated with energy conservation during photon emission, whereas the inelastic scattering associated with the transfer of energy between photons and molecular subsystems is termed Raman scattering. Furthermore, any Raman active molecule in the lowest vibrational state that absorbs the photon energy causes a decreased frequency and higher wavelength (λS > λL) of the scattered photon, resulting in a lower energy of the scattered photon (ES < EL), termed as the Stokes process, as shown in Figure 2(a). In contrast, the anti-Stokes process occurs because of the emission of excessive energy from the molecule in the excited vibrational state with a lower wavelength (λS < λL) and a higher energy (ES > EL) of the scattered photons (Eric Le Ru, 2009). Hence, the Stokes process results in a lower vibration energy (hωv), while the anti-Stokes process is associated with a higher vibration energy (hωv), as shown in Figure 2(b). The Raman shift is only dependent on the material subjected to the Raman effect; hence, a negative shift is associated with the anti-Stokes process, and a positive shift with the Stokes process. Hence, the anti-Stokes Raman scattering process is weaker than the Stokes process (Blackie et al., 2009).\n\n(b) Raman spectrum depicting Stokes scattering and anti-stokes scattering.\n\nHowever, the abundance of photons involved in Stokes and anti-Stokes processes was significantly lower. A comprehensive study by D.A. Long stated that one out of 107 photons incident on a sample may be scattered, resulting in the Stokes or anti-Stokes process. The Raman effect is also significantly affected by the components of the optical system, as it can limit the sensitivity with some major design considerations, such as the wavelength and power of the laser (Glass, 1967), spectral resolution (Meier et al., 1988), collection optics (Greenler & Slager, 1973), range and sensitivity of the detector (Allemand, 1970), and minimizing Rayleigh scattering (Cutler et al., 1980). Typically, near-infrared (NIR) laser-equipped Raman systems are employed to test organic (Košek et al., 2020) and biological specimens (Synytsya et al., 2014) in order to minimize fluorescence and facilitate easier penetration into the sample matrix. Efficient Raman scattering can be achieved only with optimum laser power, as lower power generates weak Raman signals, while high power can generate fluorescence, which in most cases may lead to sample degradation. In addition, spectrometers with a lower spectral resolution cannot distinguish between close Raman peaks. The light collection efficiency of a spectrometer is significantly affected by collection optics; hence, high-numerical-aperture (NA) lenses are commonly used in commercial Raman systems. Rayleigh scattered light is a significant consideration for producing better Raman signals, which can be mitigated with notch filters. Other considerations include the choice of optical components for minimal autofluorescence and the stable alignment of the optical components for the highest light throughput.\n\nHowever, despite these considerations, definitive fingerprinting ability can assist in the development of Raman-based optical sensing systems and their use in sensing diverse inorganic molecules (Mycroft et al., 1990), biomolecules (Larsson & Rand, 1973), and bacterial cells (Layne & Bigio, 1986). Most of the Raman spectrometers before the 1990s used low-energy argon ion lasers with a high laser power of 200–500 mW and silicon photodiodes as detectors, thereby producing fluorescence and a low signal-to-noise ratio (SNR). Hence, the use of plasmonic nanoparticle-modified substrates may amplify Raman scattering at low laser power, which enhances the Raman effect. The Raman shift observed in the presence of resonating electronic clouds around noble metal surfaces enhances molecular scattering, and this surface enhancement is called Surface-Enhanced Raman Scattering (SERS) (D.A. Long, 1977).\n\n\n2. Surface Enhanced Raman Spectroscopy (SERS)\n\nSERS involves the amplification of the Raman scattered signal of target analyte molecules in the presence of a resonating plasmonic field. The Raman effect states that the photon-molecule interactions may result in photon scattering, which generates a dipole moment (μind) that is directly proportional to the polarizability (αm) of the molecule, as shown in (equation 3).\n\nAs discussed in Section 1, Raman-based sensing systems require high laser power and longer exposure durations for analyte sensing at lower concentrations. In contrast, SERS-based sensing systems detect target analytes in complex samples at low laser powers and with minimal exposure durations. Typically, SERS systems use metal-based plasmonic nanoparticles to synthesize SERS-active substrates. The Raman scattering of the plasmonic nanoparticles was amplified using a laser with a similar range of excitation wavelengths. During the mid-1970s, Jeanmarie et. al., identified the SERS effect while studying the Raman effect of pyridine on a roughened silver electrode surface (Jeanmaire & Van Duyne, 1977), further widening its application in various fields of study up to single-molecule detection. Commonly seen SERS-active substrates are noble metal nanostructures, such as colloidal gold and silver nanostructures with sizes range from to 10-150 nm. These noble metal-based substrates were observed to improve the Limit of Detection (LoD) by amplifying the Raman signals; however, the mechanism of enhancement is not clearly understood (Fleischmann et al., 1974). Later studies indicated that silver (Ag), gold (Au), and copper (Cu) nanostructures can enhance signals by generating larger localized surface plasmons (LSPs) in the field of lasers. The SERS effect was identified as a dual effect, that is, chemical enhancement (CE) and electromagnetic enhancement (EM) of the molecule-metal nanostructure interaction. The physical basis of EM is clear and was successfully altered to obtain an enhancement of six to eight orders of magnitude, while the basis for CE is still not clear.\n\nSERS systems offer some potential advantages over conventional Raman systems, such as (i) higher signal enhancement owing to higher Raman scattering (Pérez-Jiménez et al., 2020), (ii) better signal-to-noise (SNR) ratio that detects weak Raman signals despite any background fluorescence (Pérez-Jiménez et al., 2020), (iii) distinction of spectra for multiplex detection of analytes, (Vo-Dinh, 1998) (iv) rapid real-time monitoring owing to greater Raman scattering (Etchegoin et al., 2003), and (v) imaging and chemical mapping by integration with microscopy techniques (McGuire et al., 2001). However, there are some important design considerations for the development of SERS systems for commercial purposes. Some important considerations include: (i) selection of an appropriate wavelength laser; shorter wavelength lasers require higher power, in contrast to common NIR lasers that possess better SNR, (ii) use of additional optical components, such as a high NA lens and mirrors for better collection of scattered light, (iii) anti-reflective coatings to avoid undesirable reflections and better SNR, (iv) use of edge filters to avoid transmittance of Rayleigh scattering to the detector, (v) use of a low-noise, high-sensitivity photodetector with minimal thermal noise during prolonged use of the laser, and (vi) alignment of the optical components to reduce the vibrations. The optimization of a SERS system with all specified considerations is utilized to develop commercial or point-of-use SERS sensing systems.\n\nChemical enhancement (CE) is defined as the amplified Raman scatter signal of a target analyte resulting from the interaction between the adsorbed analyte molecule and the plasmonic nanostructure. It is calculated as the sum of changes in Raman polarizability due to the adsorption of the molecule onto the metal surface and the charge transfer mechanism, given by equation (4). However, the basis of CE has been the subject of debate for decades, particularly the science that governs the SERS chemical enhancement factor (EF) (Eric C. Le Ru & Pablo G. Etchegoin, 2009). Molecular adsorption can be physisorption or chemisorption with a bond energy of ~40 kJ/mol (Aroca, 2006). Charge transfer in the metal-molecule complex is due to the incident light energy corresponding to the electronic transitions of the molecule with the underlying phenomenon of Resonance Raman Scattering.\n\nOne of the widely accepted theories for chemical enhancement is the Charge Transfer (CT) mechanism proposed by the SERS pioneer Andreas Otto, where the molecule is chemically adsorbed on the substrate, which subsequently changes the molecular polarizability, thereby enhancing the Raman spectrum (Otto et al., 1992). For example, an incident photon with a frequency νinc, in resonance with the surface-adsorbate complex, causes excitation and return of the metal electron to its ground state because of the CT mechanism. However, if the excited electron resides in the lowest unoccupied molecular orbital (LUMO) for a time period shorter than the absorbed photons, it will be scattered with dissimilar energy levels than the incident photons (ωs = ωinc − ωvib).\n\nChemical enhancement can be due to intramolecular resonance (Creighton, 1983), ground-state charge transfer, (Lippitsch, 1984) or resonant charge transfer (Lombardi et al., 1986). Intramolecular resonance assists in improving Raman scattering when the molecular vibrations of the analyte molecules match the frequency of the selected excitation wavelength. However, intramolecular resonance is affected by the area of the Raman cross-section, as larger cross-sections assist in the greater scattering of some weak scattering molecules (Tauber & Mathies, 2002). Other key parameters include the chemical structure of the analyte (Ryder, 2005) and the shape, size, and dielectric properties of the plasmonic nanostructure (Jensen et al., 2000) (Notingher & Elfick, 2005). Another cause of chemical enhancement is ground-state charge transfer, a process of electron transfer between the metal surface and the adsorbed molecules to generate charged species, which typically assist the formation of coordination compounds (Flamigni et al., n.d.) and redox reactions (Fukuzumi, 1997). However, the ground state charge transfer is associated with specific limitations, such as the selective enhancement of certain molecular vibrations of the analyte molecule, (Rurack et al., 2000) thereby limiting the uniform enhancement. Additionally, the charge transfer dynamics are affected by environmental factors (Fleming et al., 1988), the spectral overlap with other vibrational modes of the analyte (Blandamer & Fox, 1970) can limit the selectivity, and ground state saturation with the electrons of the analyte can limit any further enhancement. In the other chemical enhancement mode, resonant charge transfer was observed to overcome the limitations of ground-state charge transfer. This is the electron transfer from the resonating energy levels between the plasmonic metal and analyte molecule by charge transfer between the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO), which alters the local electromagnetic field of the analyte molecule, resulting in greater Raman scattering. The improvement in resonant excitation enhances the plasmonic metal nanostructure and analyte interaction (McNay et al., 2011) and facilitates enhanced Localized Surface Plasmon Resonance (LSPR) of the plasmonic substrates (Kleinman et al., 2013), thereby maximizing the enhancement effect. Despite these modes of signal improvement associated with chemical enhancement, their significance to the overall average enhancement factor was marginal. Hence, the use of noble metal substrates is also being explored to achieve better signal enhancement by altering the surface chemistry of substrates and modifiers.\n\nHowever, the contribution of the CE to the average SERS enhancement was not significant. Therefore, the choice of materials used for SERS substrate synthesis requires meticulous consideration of the nanostructure morphology, light absorbance range, stability, (Yamada et al., 1987) and hydrophobicity, which may be tailored to improve plasmonic resonance and electromagnetic enhancement.\n\nElectromagnetic (EM) enhancement refers to the amplification of Raman-scattered photons in the proximity of a resonating electron cloud at the metal-dielectric interface. Surface plasmon resonance (SPR) is generated by the cumulative resonance on the metal surface by the coherence of the electron cloud oscillation frequency at the metal-dielectric interface with the frequency of the excitation laser. In contrast, resonance localized at a position with plasmonic nanoparticles is termed LSPR. The LSPR effect can absorb or scatter the incident laser and potentially enhance the local electromagnetic field. Local field enhancement requires the molecule to be in proximity (within ~ 100 nm) to the metal surface, that is physisorption or chemisorption. The field enhancement factor is also prominently dependent on the laser power and Stokes and anti-Stokes effects (Ding et al., 2016). Similarly, EM enhancement is a coupling effect of the local field and the re-radiated (Raman) field of the SERS substrate, as shown in Figure 3. As previously discussed, the localized electromagnetic field for metals is higher if the excitation wavelength (λL) is close to the electromagnetic resonance of the system. Hence, the localized electric field (Eloc) is dependent on light polarization and its excitation wavelength. SERS hotspots are generated if the magnitude of │Eloc│ is greater than │Einc│. The local field intensity enhancement factor (Mloc (wL)) would be increased by a factor of:\n\nIn addition to local field enhancement, re-radiated field enhancement is also prominent for EM enhancement. In the electromagnetic model, the molecule is considered a dipole that responds to a greater local field near the surface (Kerker, 1984). The interaction of a metal nanostructure with light generates an LSPR effect on the nanostructure, which amplifies the incident EM field and scattered Raman field. Under SERS conditions, the radiation of the Raman dipole of a molecule in proximity to the metal surface modifies the exciting field, termed modified spontaneous emission (MSE). The enhancement of the EM field is a combination of the excitation field and the Raman scattered field, which is proportional to the fourth power of the field enhancement given by equation (7), where MLoc (ωL) is the local field enhancement, MLoc (ωR) is the re-radiated field enhancement, │Eloc (ωL)│4 is the magnitude of the local electric field amplitude, and │Eloc│4 is the magnitude of the incident electric field amplitude.\n\nThe maximum EM enhancement for isolated silver or gold nanostructures/nanoparticles was observed in the range of 109-1010 (Le Ru et al., 2007). This was further improved to approximately 1011 by roughening the substrate surface (Camden et al., 2008). However, some significant limitations associated with electromagnetic enhancement include the near-field effect of isolated plasmonic nanomaterials that require close presence of the analyte on the substrate (Chou et al., 2012), heterogeneous signal enhancement (Schlücker, 2014) on the substrate surface that can alter the reproducibility, and amplification of background signals that obscure the weak Raman signals (Larmour et al., 2012), thereby reducing the signal-to-noise ratio (SNR) of the SERS system. A low SNR was associated with low sensitivity, poor selectivity, fluorescence, higher Rayleigh signal scattering, and low reproducibility and reliability. Thus, some considerations for transcending the low SNR of a SERS system include the synthesis of plasmonic nanoparticles with uniform shape, size, and morphology to ensure sharp absorption peaks for signal enhancement (Berciaud et al., 2005), use of pulsed lasers with short duration that minimize photobleaching of the sample (H. F. Zhang et al., 2007), use of longer-wavelength lasers (Liu et al., 2020) and spectral filters (T. Murphy et al., 2000) to reduce fluorescence of biological samples, and minimizing photobleaching effects by optimizing the laser exposure time and laser power. Ongoing studies suggest that the use of these strategies can effectively improve the SNR of SERS systems and their applicability for on-site sensing in environmental monitoring, characterization, and diagnostics. SERS systems provide significant amplification of the scattered Raman signal, thus allowing trace-level fingerprinting in complex samples with a relatively simpler optical system that allows for point-of-use (POU). Hence, the basic building blocks of the SERS system were discussed.\n\n\n3. Optical assemblies for POU-SERS\n\nThe building blocks of a SERS system are similar to those of a Raman system with simpler optics, allowing for the construction of portable point-of-use (POU) sensing setups. However, the optimization and alignment of the elements used in the assembly of a POU SERS sensing system, which includes a laser, sample illumination system, photodetector and its associated electronics, and allied optics, is often tailored to a specific substrate of interest.\n\nLasers are commonly employed in modern Raman spectrometry because of the high coherence necessary to produce efficient Raman scattering with high SNR. However, the design of POU SERS systems mostly uses laser photodiodes because of their small footprints. Table I presents a list of laser diodes along with their corresponding emission wavelengths and samples that are typically tested using the respective SERS systems. Laser diodes are a common choice for light sources in SERS systems because of their high stability, electronic tunability, and wavelength precision. However, the choice of a laser diode in a POU-SERS system requires a comprehensive understanding of the plasmonics of the nanostructure or nanocomposite. Additionally, the physical and chemical properties of the substrate and the optical properties of the substrate material can determine the required laser power, laser diodes with low fluorescence, minimal photodamage to the target analyte, and match the substrate plasmonic resonance with the excitation laser. Hence, SERS systems with laser diodes can generate accurate and reproducible measurements.\n\nThe choice of excitation wavelength is a key consideration, as some solvents and colored sample matrices absorb the incident light or the Raman scattered radiation, thus requiring multiple wavelength laser sources. As discussed in Table I, the laser diodes are wavelength-specific, and higher-wavelength lasers can produce a different color with doubled frequency, such as the NIR (1064 nm) laser diode, which can produce green light at 532 nm with doubled frequency. Other considerations for the choice of laser are (i) absorbance and autofluorescence of the sample matrix, (ii) optimized laser power to avoid the generation of fluorescence and sample degradation, and (iii) inexpensive, compact, and easy to integrate with the sensing system.\n\nSERS sample illumination systems are equipped with laser diodes, as in the case of Raman systems; however, the choice of diode is based on the plasmonic absorbance wavelength of the nanostructure used in SERS systems. The sample illumination system also includes other optical components such as a beam expander to regulate the laser beam divergence, collimation optics to ensure a constant diameter of the laser beam, a dichroic mirror that separates laser light from the Raman-scattered light, and a few optical filters that ensure specific transmission of Raman-scattered light to the photodetector. The use of sample illumination systems for POU-SERS sensing applications requires device miniaturization by integration with nanostructure specific laser diodes or fiber optics probes coated with nanostructures, or integration with microfluidic channels for efficient transport of samples to the SERS-active substrate. In addition, the miniaturization of all optical components, such as mirrors, lenses, and spectral filters for specific applications, can also ease device miniaturization. They differ from conventional sample illumination systems in terms of compactness and portability, ease of integration with mobile electronic devices, ease of sample handling and transport to the laser transmission path, and the use of tailored SERS-active substrates for improved sensitivity and specificity.\n\nRaman spectroscopy is widely applied for the analysis of all forms of matter, including the liquid and gaseous phases. Sensing target analytes in solid samples may require manual preparation for accessible target analyte detection, sampling by swabbing or pressing the samples on the substrate, and appropriate instrumentation, such as sample holders or stages integrated with fiber optics or microscopes. Figure 4(i) depicts the optical configuration used for the analysis of solid samples and the staged sample holder attached to the stepper motor that facilitates continuous solid sample rotation (Paiva et al., 2020). Commonly tested solid samples include nanomaterials, pharmaceuticals, semiconductors, metals, alloys, food, biological samples, forensic analysis, and environmental samples. In contrast, liquid samples are typically sealed in capillaries, glass tubes, or ampoules for samples using volatile solvents or detected in standard cuvettes for aqueous samples, as shown in Figure 4(ii) (Kawahara-Nakagawa et al., 2019). Typically, in liquid samples, collection optics are placed perpendicular to the sample position for maximum light collection and transmission to the photodetector. Commonly tested liquid samples include organic solvents, acids, biological fluids, petroleum products, chemical reagents, food, and beverages. Consequently, gaseous samples were tested by filling a capillary or small cavity with a fine ground sample. As shown in Figure 4(iii) The gaseous samples are typically passed through specialized optically transparent chambers, where scattering is observed perpendicular to the sample chamber (Sänze et al., 2013). Some commonly tested gaseous samples include pollutants NOx and SOx, molecules that are IR inactive with zero dipole moment, such as H2, and hydrocarbons, such as methane, ethane, propane, and butane.\n\nOptic fiber bundles may be used to guide the laser and collect scattered Raman signals with minimal collimating optics, allowing the construction of simpler and more robust optical systems. The integration of fiber bundles allows for flexible optical transmission; hence, devising systems with SERS-enabled cartridges becomes easy (Milenko et al., 2020). Typically, a fiber optic probe integrated with a micro-Raman setup comprises an objective lens focused on a laser beam that brings excitation radiation towards the sample. This excitation fiber can be used to illuminate solid samples or immersed in liquid samples. The other terminal collects the scattered radiation from the aperture of the spectrometer. For example, as illustrated in Figure 5, the fiber-optic SERS probe was etched and modified using Ag nanostructures. The SERS-active probe was connected to a microscope objective and the other end was connected to a chamber with nanostructured Au substrates. Evaporation of a 2-napththalenethiol (2-NP) sample with Au nanostructures results in analyte adsorption onto the Ag film-coated SERS-active probe tip, which determines the analyte concentration. Time-based spectral measurements can determine the variation in sample matrix evaporation and thus facilitate the efficient detection of 2-NP (Agarwal et al., 2016).\n\nPhotodetectors used in optical systems include CCDs, CMOS, APDs, SiPMTs, and laser diodes, which are comprised of photoresponsive semiconductor materials. They are commonly used because of their spectral range, cost, and rapid capture and analysis. Photodiode arrays are the most commonly used photodetectors for the design of POU systems owing to their scalability and footprint. They offer high sensitivity and rapid responses that are detected in specific visible or near-infrared (NIR) regions. Semiconductor materials with customized bandgaps allow photodetectors to detect predefined wavelengths of light, thereby aiding in specific optical applications. These semiconductors operate based on the difference in bandgap energy, which determines the emitted light absorbance wavelength of the photodetector. Table II. discusses the types of photodiodes, detection ranges, specific characteristics, and commonly detected analytes. However, the tunability of photodiodes for specific applications requires the use of spectral filters for high SNR, optimizing the spectral response with signal processing tools, and miniaturization of photodiodes and allied electronics. Fourier Transform (FT) Raman spectrometers facilitate signal processing of the obtained spectral data by splitting the fundamental constituent frequencies of the signal. It also assists in high-frequency precision, enhancement of spectral resolution, data processing, image reconstruction, and the quantitative analysis of samples. Figure 6 illustrates a visible laser-based FT-Raman system, with optical elements such as parabolic mirrors to focus the excitation light, dielectric mirrors to collect the scattered light, long-pass filters to allow a specific wavelength of scattered light to reach the photodetector, a quartz beam splitter to simultaneously measure the reference and the sample, a pinhole to restrict unwanted light, and a photomultiplier tube that acts as a photodetector. The integration of this Raman system with FT assists in the classification of spectral patterns (Baeten et al., 1998) and multiplex analyte sensing from complex specimens.\n\nHowever, a significant consideration in developing a POU-SERS system is the intermittent cooling of the photodetector to reduce thermal noise and operate at longer wavelengths. The use of spectral filters, such as notch filters or bandpass filters, can prevent heating, and anti-reflective optics may minimize the laser light absorption and thus the heating of the photodetector. At higher temperatures, thermally generated noise can affect the efficiency of semiconductor materials used as photodetectors, which require intermittent cooling to ensure stability and high spectral resolution. The cooling of the photodetector in a Raman system reduces the dark noise, which can be attributed to the dark current (Stiff-Roberts, 2011). These dark currents influence the photodetector temperature, which requires intermediate cooling. Cooling the photodetector also aids in reducing background noise and improving the SNR of the sensing system. Most photodetectors employ thermoelectric coolers (TECs) or cryogenic cooling using liquid nitrogen. TECs utilize the Peltier effect, in which a voltage applied across two dissimilar semiconductors creates a temperature gradient. One side serves as a heat sink (at a higher temperature), while the other end cools where the photodetector is attached (Lundgaard & Sigmund, 2019). In the case of cryogenic cooling mechanism, liquid nitrogen at -196° C was utilized. A double-walled dewar flask with a vacuum between the two walls was filled with liquid nitrogen on the outer surface of the flask, and the photodetector was placed inside the chamber. The outer surface absorbed heat from the inner chamber until equilibrium was achieved. At equilibrium, the photodetector can operate efficiently at lower temperatures, resulting in reduced dark noise and improved SNR (Hubbs, 2000), which are crucial for achieving high-quality measurements in Raman spectroscopy and other applications.\n\nThe key components and alignment in Raman spectrometers can be optimized and miniaturized on the basis of the type of sample matrix, sensing application, and deployability. Some essential characteristic features of POU-SERS systems include portability, rapid analysis, multiplex detection, user-friendly interfaces, and customization and integration with intelligence-enabled technologies. Other considerations include the choice of stable excitation with high laser power and minimal photobleaching, the selection of optimal spectral filters, lenses and mirrors with higher NA, and a dispersion component, such as a prism. Spectral filters, such as bandpass filters and notch filters, are employed for light transmission of specific wavelengths. In POU-SERS systems, spectral filters are crucial for blocking Rayleigh scattered light, reducing background noise, and reliable detection. In addition, the high NA of the mirrors and lens assists in efficient light collection and precise focusing owing to their parabolic structure that minimizes the loss of scattered light. Furthermore, dispersion components, such as diffraction gratings and prisms, are used to split the incident light into its spectral components to obtain accurate and high-resolution Raman spectra to differentiate the Raman shift. Precise consideration and optimization of these challenges can assist in reliable, high-performance, and on-site sensing applications.\n\n\n4. SERS systems for point-of-use sensing\n\nConventional sensing strategies, such as mass spectrometry (MS), high-performance liquid chromatography (HPLC), gas chromatography (GC), enzyme-linked immunosorbent assay (ELISA), and polymerase chain reaction (PCR), are associated with significant limitations such as high cost, long assay time, need for sophisticated instrumentation, and trained personnel. Hence, there is an immediate need to develop SERS-based POU systems integrated with SERS to aid in rapid sample processing, ease of use, and on-site detection (Perumal et al., 2021). POU technologies are promising for the detection of whole analytes or their residual form, above the maximum residual limit (MRL) or the lethal dose (LD50), which by integration with SERS can provide a typical enhancement of 106-108 and aid in single-molecule detection. However, designing SERS-based POU systems requires the following considerations: (i) system compatibility and portability, (ii) user-friendly sample handling, (iii) integration with optical accessories and ensuring their compatibility, (iv) maintenance and recalibration without the need for extensive expertise or tools, (v) real-time analysis with rapid data acquisition and results, and (vi) robustness for deployability. A few other considerations include cost-effectiveness, data connectivity with cloud-based platforms, durable components, and application-specific features. Some recent novel SERS-based POU systems are discussed in Table III, with some critical insights for improvement.\n\nSERS sensing systems are widely used for the detection of analytes, such as metal ions (C. Song et al., 2020; Y. Zeng et al., 2016), organic (Ignat et al., 2009; Virga et al., 2012) and inorganic molecules (Alvarez-Puebla & Liz-Marzán, 2012; Y. Zhou et al., 2012), and small molecules, such as antibiotics, pesticides (Chan et al., 2003; Severyukhina et al., 2015; P. Guo et al., 2015; Y. Zhang et al., 2014), nucleic acids (Bell & Sirimuthu, 2006; Y. He et al., 2011; Prado et al., 2014), proteins, (Feliu et al., 2017; Kennedy et al., 2010; Y. Zhu et al., 2020) and radionuclides (X. He et al., 2019). Most of these POU-SERS systems are efficient for on-site use and have the potential for commercialization. A POU Raman system was developed by Choi et al. in 2017 for the colorimetric detection of thyroid-stimulating hormone (TSH) using a SERS-based lateral flow immunoassay (LFIA). Figure 7(i) shows a schematic illustration of the developed SERS-LFIA platform and the TSH detection mechanism. The image shows the use of SERS nanotags with gold nanoparticles (AuNPs) coated with malachite green isothiocyanate (MGITC), a Raman reporter, and immobilized with an anti-TSH antibody. The LoD of the proposed sensor was calculated to be 0.025 IU/mL in a 10-minute assay and a linear analyte detection range of 1–30 μIU/mL (Choi et al., 2017). However, the use of antibodies immobilized on gold nanoparticles (AuNPs) can affect the stability and reproducibility of the sensor because the activity of the antibody can be significantly affected by the temperature and pH of the sample. In addition, the use of a Raman dye such as 4-mercaptobenzoic acid (4-MBA) with terminal thiol groups for analyte detection can improve the reproducibility by covalent linking with the antibody.\n\nIn 2020, Song et al. developed a novel method for detecting mercury (Hg2+) levels in aqueous samples via a unique colorimetric/SERS dual-mode method using SERS-active peroxidase-like Au core-Pt shell nanoparticles (Au@AgPt NPs). Figure 7(ii) depicts the method of Au@AgPt NPs synthesis and laser-induced enzyme-based oxidation for Hg2+. The hexoctahedral core of the Au@AgPt NP had edges coated with Pt, which displayed enhanced catalytic activity and SERS effect. The developed sensor achieved an LoD of 0.28 nM, a linear detection range of 1–5 M with an unaided eye, and 1-10 nM using SERS-active peroxidase-like Au@AgPt NPs. However, this method relies on the catalytic activity of PtNPs and is not specific to the presence of Hg2+; therefore, it can adversely alter the result in the presence of a potent oxidizing molecule in the sample, resulting in false positive results. In addition, masking the PtNPs by any biological or non-biological molecule can inhibit the oxidation of 3,3′,5,5′-tetramethylbenzidine (TMB), thus affecting the sensitivity (C. Song et al., 2020). This approach may be used for the cumulative detection of heavy metal ions, thus enabling quick discard or remediation; however, for specific detection of Hg2+, receptors such as those illustrated (Sadani et al., 2019) may help improve sensor specificity and mitigate cross-sensitivity.\n\nExtensive research has been conducted on the development of microfabricated SERS-active substrates, such as those involving nanopillars, nanopyramids, nanoholes, and nanogratings. However, their cost-effective scalability for extensive use is limited and the development of frugal interventions for POU sensing in resource-limited settings is necessary. Thus, commercial-grade disposable materials with surface modifications can be used to develop robust, accurate, and reproducible SERS-active substrates (Ogundare & van Zyl, 2019). The choice of base materials for use as disposable substrates depends on a few characteristics, such as ease of synthesis and integration of plasmonic nanocomposites, compatibility with the target analyte, resistance to biofouling, and mitigation of noise due to background effects. Commonly used disposable substrates, including paper, fabrics, polymers, and silica-based materials, are briefly discussed. Table III presents the target analyte, substrate synthesis method, use of a (bio) receptor for specificity, linker chemistry of the substrate with (bio) receptor, sample matrix of the analyte, (LoD), and some critical insights for improvement.\n\n\n5. Considerations in design of disposable SERS substrates\n\nExtensive research is being conducted to develop disposable substrates for the sensitive and specific detection of various analytes of interest, as described in Section 6. Despite the use of commercial-grade disposable materials as SERS substrates, the development of SERS sensing platforms that offer repeatable utility is associated with a few important considerations such as hotspot uniformity, surface periodicity, and surface hydrophobicity. The optimizations involved in each of these methods are discussed.\n\nSERS hotspots are localized nanozones with intense plasmonic fields that enhance Raman scattering. The interaction of incident light with plasmonic nanostructures results in a highly concentrated EM field, and an exceptional enhancement in Raman scattering is termed a hotspot. This interaction requires the presence of a target analyte near the plasmonic field of the nanostructure. SERS hotspots assist in the amplification of Raman scattering by multiplicative enhancement of the plasmonic field of nanostructures, resulting in synergistic effects and spatial localization that facilitates selective enhancement of signals from the hotspot and reduces the background interference. The signal enhancement is affected by the structure and orientation of the nanostructure on the substrate and aggregate formation, which affects the dimensionality of the nanosubstrate. The enhancement factor in the hotspots was calculated as the ratio of the SERS intensity (ISERS) to the Raman intensity (IRaman). The Raman scattering intensity is mathematically expressed as the square of the electric field energy of the incident light (│E│2) and expressed as (│E│4) in the proximity of a plasmonic nanoparticle. The generation of hotspots is crucial for the design of SERS materials and platforms to improve nanoscale light confinement. Hence, extensive research is being pursued on the synthesis and incorporation of nanomaterials ranging from 0D to 3D for engineering hotspots. Table IV provides an overview of the common nanostructures used in hotspot generation, and some unique properties that assist in higher signal enhancement.\n\nHotspot engineering is crucial for the design of SERS-active substrates that improve nanoscale light confinement in specific localized regions on 0D to 3D materials. In the case of 0D materials, such as quantum dots, a plasmonic field structure with confined dimensionality is not possible. However, quantum confinement owing to discrete energy levels can generate localized EM fields that can be engineered to generate hotspots, and the near-field effect can tailor the plasmonic field structure to generate hotspots. The limited plasmonic field of 0D materials cannot detect larger analytes. Common domains of applications include the detection of small molecules and biomolecules. In the case of 1D materials, such as nanorods and nanowires, a greater plasmonic field is observed at the tips or edges, which contributes to longitudinal plasmon absorbance. Regularly ordered alignment, surface roughness, and tip engineering of 1D materials can be used to tailor plasmonic field structures. These materials are mostly employed for the detection of small molecules, inorganic molecules, and heavy metal ions in biological or non-biological samples. For 2D materials such as nanoparticle films, graphene, and graphene oxide, the plasmonic field structure is determined by the nanogaps or crevices of adjacent nanosheets or nanoparticles. Cumulative surface plasmon polaritons (SPP) can enhance the local field by coupling with 1D and 3D materials to tailor the plasmonic-field structure. 2D materials are commonly used for the label-free detection of biomolecules. In the case of 3D materials such as microfabricated nanoholes, nanopillars, and nanopyramids, the plasmonic field structure is generated by bulk plasmon resonance. Optimization of the 3D material geometry and customizing the dielectric environment can tailor the plasmonic field structure, and thus assist in hotspot engineering. Three-dimensional (3D) materials are commonly used in the detection of biological and non-biological organic molecules, food sample analysis, and forensic analysis.\n\n5.1.1 Hotspot engineering with 0D & 1D materials\n\nResearch in the past decades regarding hotspot engineering of 0D and 1D nanostructures has focused on the synthesis of shape-controlled metallic (Au/Ag/Cu) nanoparticles. 0D materials are nanostructures lacking dimensionality and show quantum confinement effects, whereas 1D materials are relatively larger or elongated nanostructures that generate hotspots partially by phonon scattering and electron confinement. Common 1D materials include nanorods, nanotubes, and nanowires with high aspect ratios that generate well-defined hotspots. The edges or vertices of 1D nanostructures exhibit the lightning rod effect by concentrating on the localized EM field. This results in a longitudinal enhancement mode of the plasmonic resonance (Cardinal et al., 2017) and absorbance at longer wavelengths (700-1000 nm). Arrays of 1D metal nanoparticles are promising nanoscale optical devices because they can guide electromagnetic energy (Quinten et al., 1998). An interesting study by Vaidya et al. al., the use of free-standing fibers of a Au(I)-based coordination polymer (CP) for 4-MBA detection was described. The [Au (SPh)]n CP flexible fibers are hydrophobic and exhibit high chemical stability under harsh acidic and basic conditions because of the phenyl rings and strong Au(I)–S interactions. Furthermore, calcination can produce a composite, resulting in the formation of AuNPs on CP fibers. Because of the plasmonic resonance of AuNPs, this composite material showed high sensitivity, as demonstrated by SERS (Vaidya et al., 2020a). Figure 8(i) shows the 1D gold(I)-thiophenolate [Au (SPh)]n deposition on a polymer, XRD patterns, and photographs of the modified coordination polymers. Despite the extensive use of electron-beam lithography (EBL)-fabricated 1D metal nanoparticle arrays with defined spacing, the large-scale fabrication of 1D arrays and organized structures is essential for practical applications. Other methods, such as chain assembly synthesis using solution-based protocols, exhibit interesting plasmonic properties. For example, hollow Au nanoparticle-based chains with cobalt nanoparticle (CoNP) chain templates have been assembled using magnetic fields (J. Zeng et al., 2007). Other examples of nanostructures assembly include the ligand exchange method using mercaptoethyl alcohol (MEA) (S. Lin et al., 2005) or cetyltrimethylammonium bromide (CTAB), a cationic surfactant (Dai et al., 2006). For example, as shown in Figure 8(ii), the etching of Ag nanowires using a H2O2/NH3 mixture roughens the nanowire surface resembling beads-on-a-string, which improves the SERS activity across the surface area by 10-fold, while (Goh et al., 2012) another common 1D nanostructure is face-to-face nanodisk arrays fabricated by on-wire lithography comprising cylindrical nanopores, using porous alumina membranes (J. Qin et al., 2005). Therefore, research suggests that the decrease in SERS enhancement is due to excitation in the crevices of nanostructures, for which field enhancement is associated with the nanoscale roughness of the metal surface. Despite significant progress in optimizing protocols for nanoparticle hotspot engineering, these nanoparticles do not possess the intrinsic property of serving as efficient SERS platforms because of the limited SERS active area and insufficient EM hotspot strength required for ultra-trace sensing. Future studies should aim to improve nanoparticle efficiency and enhance SERS signals by optimizing the interparticle distance or using nanostructures with high-order dimensionality.\n\n5.1.2 Hotspot engineering with 2D materials\n\nThe organization of plasmonic nanoparticles in ordered 2D arrays significantly initiates the plasmonic coupling of neighboring nanoparticles, which generates a homogenous EMF enhancement. This will likely enable the design of repeatable SERS systems. 2D hotspot engineering can be achieved using a top-down or bottom-up approach. A recent strategy for engineering hotspots with 2D materials is graphene-enhanced Raman scattering (GERS), which results from the deposition of exfoliated graphene on a SiO2/Si substrate. The characteristic electronic structure and high electron density of graphene can significantly improve EM interactions (Schultz et al., 2014). Additionally, the first layer effect of the molecules adsorbed on the graphene surface caused by its high surface area and charge transfer can substantially improve EM interactions (Ling & Zhang, 2010), thereby enhancing Raman scattering. In a study by Yu et al., mildly reduced graphene oxide (MR-GO) was drop-casted on a 300 nm SiO2/Si substrate for the detection of Rhodamine B (RhB), which displayed a good EF of 103 and LoD of 10−8M. Figure 9(i) Graphical abstract of the 2D MR-GO substrate for Rh B detection and corresponding SERS spectra (X. Yu et al., 2011). Another interesting strategy is the use of graphene-noble metal substrates that can provide substantial SERS enhancement by the coupling of GERS with the plasmonic effect of nanostructures. An interesting study by Xu et al. fabricated a novel SERS substrate by depositing Ag and Au nano-islands on the backside of a graphene monolayer (1LG) for the detection of R6G molecules on the non-coated side of graphene (W. Xu et al., 2012b). Furthermore, the geometry of plasmonic nanostructures deposited on graphene was found to alter the nanoparticle assembly. A recent study by Zhang et al., in 2017, demonstrated the fabrication of gold triangular nanoarrays (Au TNAs) on graphene for the detection of Hg2+ in water and sandy soil samples. The use of AuTNAs for substrate fabrication improved the thermal stability and further deposition on the graphene monolayer, which enhanced the SERS signal, facilitating improvement in SERS sensitivity with an LoD of 8.3 nM. A schematic representation of the Au TNA/graphene/Au NP fabrication process and its effect on the SERS spectra is shown in Figure 9(ii) (X. Zhang et al., 2017). Furthermore, other 2D materials, such as hexagonal boron nitride (h-BN), can also be used for hotspot engineering because of its structural analogy with graphite (Pakdel et al., 2014). Signal enhancement using h-BN was different from that of graphene, as variations in the charge transfer process of h-BN do not affect the Raman intensity. Kim et al., in 2016, utilized h-BN to insulate Au SERS substrates. R6G Raman signals were stronger for h-BN/Au/SiO2 than for h-BN/SiO2 and Au/SiO2 (G. Kim et al., 2016a). Therefore, the use of nanostructured sheets, graphene, and h-Bn as 2D materials assists in hotspot engineering and the enhancement of Raman signals. Although 2D materials possess unique benefits, the use of 3D materials for hotspot engineering is expected to provide further enhancements.\n\n5.1.3 Hotspot engineering with 3D materials\n\nHotspot generation with 3D materials differs from that with 2D materials in terms of dimensionality, spatial distribution, plasmonic field distribution, and accessibility to the analyte. Common 3D materials for hotspot engineering include nanoporous materials, such as nanoholes, nanoarrays, nanopillars, and nanoparticle aggregates. The integration of top-down and bottom-up strategies, as seen in 2D hotspot engineering, was identified to generate open 3D SERS platforms. In the case of a bottom-up approach, nanoparticle self-assembly is widely used to exploit the interface of two immiscible fluids to improve the assembly of 2D nanoparticle meta-crystals. Figure 10(i) shows the schematics of the developed interfacial self-assembly at the oil/water interface, varying configurations of the Ag octahedral nanostructures, Atomic Force Microscope AFM images of functionalized Ag octahedra, and length of octahedra immersed in the oil phase (Y. H. Lee et al., 2015). 3D hotspot engineering also focuses on designing open structures that improve the accessibility of the laser to the analyte to maximize the SERS response. For example, Udayabhaskararao et al. (2017) used non-close-packed gold nanoparticle arrays with Au and Fe3O4 building blocks that displayed improved analyte diffusion into the crystal lattice due to the selective etching of Fe3O4 nanoparticles and the resulting SERS signal enhancement, as shown in Figure 10(ii) (Udayabhaskararao et al., 2017). Another approach proposed by Lee et al. (2013) used polymeric films for nanoimprint molds to create porous microcylindrical structures and further used metal nanoparticles by electrostatic self-assembly to generate open SERS-active microcylinders with an EF of 6.5 × 104 (S. Y. Lee et al., 2013). The use of 3D porous microcylinders improves the AuNP loading ability, thus improving the SERS signal by 10-fold in comparison with AuNPs on non-porous substrates. Despite the advancements in hotspot engineering, some persistent considerations include: (1) inadequacy of target/analyte detection at the single-molecule level and (2) uniform hotspot density only with specific affinity of analyte molecules to plasmonic surfaces. Hence, most studies still use Raman probes that possess a greater affinity for plasmonic surfaces or larger cross-sectional areas. To overcome the limitations of hotspot engineering, surface fabrication techniques such as in situ growth of 3D nanostructures may be used by electrochemical deposition and bottom-up in situ growth for an enhanced SERS effect.\n\nHydrophobicity is the intrinsic property of a material to resist water owing to nonpolar interactions, resulting in poor water solubility. Substrate hydrophobicity can alter the contact angle, which defines the ability of the substrate to maintain contact with the liquid sample matrix. Hydrophilic surfaces possess a high affinity for aqueous sample matrices, thus decreasing the contact angle and increasing the surface contact area of the droplet, resulting in rapid sample evaporation (T. Smith, 1980). In contrast, hydrophobic surfaces have a higher contact angle with the substrate surface because of their quasi-spherical shape and require a longer time for solvent evaporation (Ko et al., 1981). Analyte detection with hydrophobic substrates generates a large EM enhancement owing to the high contact angle of the target analyte containing the sample matrix. The confinement of plasmonic nanostructures on a substrate can generate enhanced SERS signals. This behavior was not observed with hydrophilic surfaces owing to the low contact angles and no possible confinement of plasmonic nanostructures. Hydrophobic surfaces aid in the concentration of target analyte molecules near plasmonic nanoparticles within a confined region on the substrate (Sakai et al., 2006). The confinement of the analyte molecules with nanostructures generates an intense plasmonic field that assists in SERS signal enhancement. Common hydrophobic surface fabrication methods include silanization (Péron et al., 2009), fluorination (Y. Chen et al., 2009), vapor deposition (Y. Wu et al., 2007), sol-gel coating (Pilotek & Schmidt, 2003), chemical etching (B. Qian & Shen, 2005), and the use of hydrophobic nanostructures (Akagi et al., 2007).\n\nThe substrate wettability can be tailored for SERS-based applications by fabricating hydrophobic and hydrophilic surfaces. For example, a microcontact-printing-based hydrophilic surface was fabricated by Shin et al. in 2002 on a hydrophobic polydimethylsiloxane (PDMS) stamp using hydrophilic silver colloids. The hydrophilic nanostructure coated stamp was pressed against a gold-coated Si substrate with a self-assembled monolayer (SAM) of a thiol-containing moiety to develop silver colloidal patterns (Shin et al., 2002). However, the hydrophilicity of this substrate is dependent on electrostatic and van der Waals interactions, which can severely affect silver colloid adsorption on the gold-coated Si substrate. In another study by Wei et al. (2005), a hydrophilic substrate was fabricated on mica using CTAB-based silver colloids, forming a hydrophilic surface because of the -NH4+ cationic group of CTAB (G. Wei et al., 2005). However, CTAB concentrations lower than 10 μM resulted in no SERS signal, and a higher CTAB concentration may result in the formation of surfactant bilayers, resulting in minimal surface adsorption.\n\nAs discussed, hydrophobic surfaces can improve the retention time because of the increased contact angle with the sample matrix. An interesting study by Kyle C. Bantz and Christy L. Haynes in 2009, demonstrated the use of SAMs of alkanethiol and perfluoroalkanethiol on the silver film over nanospheres (AgFON) substrates for the detection of polychlorinated biphenyls (PCBs). Cleaned copper discs were deposited with silica nanospheres and vapor-deposited with Ag to form a 200 nm thick Ag film on the nanospheres. Further, it was treated with 1 mM decanethiol (DT) and perfluorodecanethiol (PFDT) to improve the hydrophobicity of the SAM layer. The sensor demonstrated an LoD of 50 pM PCB within 1 min of 532 nm laser exposure, thus facilitating the distinction of PCBs (Bantz & Haynes, 2009). However, manual agitation of the silica nanospheres cannot ensure homogeneous layer formation, which affects substrate repeatability. Rather, spin-coating the silica nanospheres and analysis with microscopic techniques, such as atomic force microscopy (AFM), may provide insight into substrate surface homogeneity. In addition, the SAM layer assists in the partitioning of PCBs from organic solvents, such as tetrahydrofuran (THF), rather than from an aqueous solvent. However, this may limit the use of AgFON substrates for on-site applications because they are abundantly found in aqueous environmental samples. An interesting study by Gentile et al. (2010) developed a micro/nanopatterned superhydrophobic sensor to detect and differentiate biomolecules. Figure 11(i) shows silver grains coated with regularly ordered disk patterns comprising cylindrical micropillars on a Si wafer obtained by optical lithography aiding in the SERS enhancement. A thin Teflon (C4F8) polymer film was coated on the Si wafer to ensure hydrophobicity, which increased the apparent contact angle from 150° °to 175°. This hydrophobic SERS sensor exhibited an LoD of 10−18 M with a sample volume of 5 μL of R6G (Gentile et al., 2010). However, the sensitivity may be significantly affected by the reactive-ion etching process, which in turn alters the diameter and height of the Ag mask. Hydrophobic metal surfaces are synthesized by the construction of a micro/nano-metered structure, followed by surface modification with low surface energy molecules (B. Su et al., 2010).\n\nThe contact angle of the substrate affects the analyte distribution around a plasmonic hotspot and thus determines the effective SERS enhancement. Another property of the substrate surface, superhydrophobicity, can be obtained with contact angles higher than 150° (Reyssat et al., 2006). Optical lithography-based superhydrophobic surfaces are created to adlayer plasmonic nanostructure arrays by micro/nanofabrication. The structured arrays were coated with a thin Teflon film via reactive ion etching. The deposition of a droplet of aqueous R6G solution on the superhydrophobic surface allows it to concentrate and precipitate to a confined area near the Ag nanostructures owing to substrate hydrophobicity. Figure 11(ii) depicts a droplet of a specific solute deposited on a hydrophobic substrate made of nanopillars. The use of a hydrophobic nanopillar substrate resulted in an increase in the SERS intensity, as shown in Figure 11(ii) and (f) (De Angelis et al., 2011). The use of a superhydrophobic plasmonic substrate such as silver-decorated polystyrene (PS) nanotubes is highly efficient, with an LoD of 400 ppt for crystal violet (Lovera et al., 2014). Jayaram et al. used a hydrophobic Ag-decorated ZnO nanostructure thin film with a contact angle of 163°. The as-prepared SERS substrate exhibited an LoD of 10−10 mol/L for the detection of R6G (Jayram et al., 2015).\n\nPeriodicity is defined as a highly ordered array or pattern on the substrate surface that ensures hotspot uniformity, with SERS enhancement up to several orders of magnitude higher than that of disordered metal-nanoparticle films. This section focuses on the use of ordered 1D and 2D SERS substrates and the corresponding SERS enhancements. Periodicity using larger metal nanoparticles is challenging because of the increase in long-range van der Waals forces due to the increase in particle size, thus preventing the formation of 2D periodic structures. The tuning of van der Waals attraction was observed using a proper surfactant, ensuring the close packing of larger nanoparticles. For example, the use of calixarene as a surfactant provides greater repulsive forces for the fabrication of highly ordered larger-sized AuNPs, as shown in Figure 12(ii) (A. Wei, 2006).\n\nThe periodicity of metafilms created by self-assembled nanostructures at the liquid-liquid interface owing to density differences can be utilized for signal enhancement. Metafilms are customizable nanofilms fabricated using precisely structured nanoparticles with unique optical properties that generate highly localized EM hotspots. Yang et al. synthesized a flexible SERS metafilm with self-assembled AuNPs at the water-toluene interface for the detection of thiram, a commonly used moderately toxic fungicide, on orange peel, as shown in Figure 12(i). The metafilm obtained after the evaporation of toluene exhibited high uniformity owing to its ordered nanostructure arrangement. The sensitivity of metafilm was tested using crystal violet as the SERS probe. The sensitivity of the metafilm with 1 mL and 6 mL was low because of the large vacant spaces and due to overspread and close packing, respectively. The metafilm with 3 mL showed the best enhancement, with an LoD of 0.5 ppm thiram (N. Yang et al., 2019).\n\nIn addition to chemical synthesis and self-assembled structures, surface fabrication techniques assist in the formation of 2D periodic substrates. Gong et al. employed plasmonic cavity lens lithography for the fabrication of graphene and silver nanohole arrays for the detection of R6G in standard samples. A 100 nm thick silver film was deposited on a quartz substrate, followed by spin coating of the photoresist and another layer of silver film. The substrate was UV-cured with a chromium (Cr) mask, followed by Ag film removal for photoresist development. The pattern was then transferred to the bottom Ag layer by dry etching. The developed SERS-active substrate exhibited an LoD of 10−11 mol/L of R6G and an EF of 107 (T. Gong et al., 2019). In another study by Bi et al., an SERS substrate was fabricated using electron-beam lithography (EBL) to detect crystal violet from standard samples. Polyvinylpyrrolidone (PVP) dissolved in ethanol was mixed with chloroauric acid and spin-coated onto the Si substrate. EBL was used to generate nanopatterns of AuNPs on the Si substrate. Polyvinyl alcohol (PVA) gel was then spin-coated onto the nanopatterns. Following the baking and solidification of PVA, the gel was peeled off with the AuNP pattern transferred onto the gel. The fabricated PVA gel with AuNP patterns was used to analyze the sensitivity of the Crystal Violet (CV) probe molecule, which showed an LoD of 10-5 M and an enhancement factor of 9.8 × 105 (Bi et al., 2019). In conclusion, the periodicity of the substrate was observed to improve the surface plasmonic field density and, thus, the EF of the substrate. Furthermore, specific optimizations with physical, chemical, or biological methods may ensure periodicity at the nanoscale, but may not ensure repeatability of the substrate owing to irregular distribution or uneven surface fabrication.\n\n\n6. Disposable SERS surfaces and substrates\n\nDisposable SERS substrates can be used for SERS and are discarded after single use. They are relatively inexpensive and can mitigate biofouling. Unlike reusable substrates, disposable substrates do not require pretreatment steps, as they are intended for single-use detection (Ferchichi et al., 2015). A few potential disposable substrates employed in SERS-based analyte detection are discussed here.\n\nPaper-based substrates are gaining attention owing to their customizable, biodegradable, and biocompatible properties, and their scalable use in the development of consumer-oriented products. Most paper-based substrates are made of cellulose polymer, which is composed of a linear structure of a few to hundred 1 of 4-linked D-glucose monomers (Shaik et al., 2022). Other common polymers in paper include hemicellulosic paper (Kaushik & Moores, 2016; Xiang et al., 2022), lignin-based paper (Klemm et al., 2005; Mahmoud & Zourob, 2013), and bacterial cellulose-based paper (Basta & El-Saied, 2009; Xiao et al., 2023). However, hemicellulose exhibits high water solubility, (Credou & Berthelot, 2014),whereas lignin-based paper undergoes rapid oxidation in the presence of air, leading to degradation of the substrate (Małachowska et al., 2020). Bacterial cellulose is known to lose its flexibility upon drying, which may serve as a potential limitation for its extensive use in paper-based sensor substrates (Provin et al., 2021). Therefore, cellulose-based paper has been extensively used for the development of paper-based substrates. For instance, in a study conducted by Romo et al. (2021), the intrinsic properties of cellulosic paper, such as porosity, hydrophilicity, and mechanical strength, were exploited to fabricate SERS-based substrates for cell culture applications. The inherent ability to absorb fluid by capillary action and its porous nature contribute to the adhesion and migration of cells (Romo-Herrera et al., 2021). These properties make cellulosic paper an excellent substrate for various applications, including the development of paper-based biosensors. In addition to low-cost, large-scale production and disposability are some major benefits of cellulose-based paper (S. Wang et al., 2012). The physical and chemical properties of cellulose paper have been utilized for the integration of nanoparticles and surface engineering to develop disposable paper-based substrates for SERS-based sensing applications. They are affordable, highly useful in resource-limited settings, and user-friendly alternatives with considerable sensitivity and specificity (W. Zhao et al., 2008). Additionally, the ease of loading liquid samples will further improve sensitivity by restricting the sample flow to a small sensing region, which will aid in lateral flow assay (LFA)-based sensing techniques (W. W. Yu & White, 2010).\n\nIn an interesting study by Dong-Jin Lee et al., in 2019, a method was developed for the detection of thiram, using paper as the sensor substrate. Initially, the surface of the filter paper was modified with a diluted PDMS solution to achieve hydrophobicity and confine the porosity, followed by drop-casting gold nanoparticles arranged on graphene oxide (AuNPs@GO) flakes to fabricate a hydrophobic paper (h-paper). The PDMS on the filter paper increased the contact angle (CA) to ~ 128.4 °and decreased the surface contact area with an extended retention time of the AuNPs@GO solution. The developed sensor showed an LoD of 1 μM and a linear detection range of 10−3-10−6M, using a Raman spectrometer equipped with a 785 nm excitation wavelength (λex) laser and a laser power of 2.4mW (Dong-Jin Lee & Dae Yu Kim, 2019). Figure 13. depicts the detailed synthesis of gold nanoparticles (AuNPs) and the steps involved in substrate modification. However, this study did not include validation using real samples. Additionally, the presence of interferents or other structurally analogous molecules can result in false positives. This limitation can be overcome by using a bioreceptor specific to the analyte, which can improve the specificity of the sensor, even in the presence of complex samples. However, all these cellulose-based paper substrates are associated with a major limitation of autofluorescence because of the presence of organic materials, lignin, and additives, such as calcium carbonate (CaCO3), alkyl ketene dimer (AKD), polyacrylamide-based resins, bleaching agents, and antioxidants. Autofluorescence may be mitigated by the use of higher-wavelength lasers and optics that block fluorescence or baseline autofluorescence. Other limitations include moisture sensitivity, flammability, and lower chemical and temperature resistance, which can be surpassed by other disposable substrates such as polymer-based and silica-based substrates. Recent advancements in analyte detection using paper-based substrates are presented in Table V.\n\nFabrics can serve as excellent substrates for SERS-based detection owing to their uniform interwoven fibers, durability, and resistance to wear and tear (Satani et al., 2023). They possess excellent porosity, microfluidic behavior, and enhanced surface area; thus, they (Ismail, 1991) make ideal materials for efficient contact with samples. In addition, the 300–500 μm coarse fibrous structure in plant fibers (C. H. Lee et al., 2021) can be modified by coating or trapping plasmonic metal nanoparticles for the development of a SERS-active substrate (Moon et al., 2011). However, porosity may be a limitation as it may lead to the requirement of large sample volumes, which can be overcome by optimizing the sample microfluidic flow, which is regulated by the capillary pressure and wicking force of the material. Benltoufa et al. suggested that the capillary kinetics in a knitted cotton fabric depended on the geometry of the fibers (Benltoufa et al., 2008). Furthermore, Bhandari et al. suggested that the wicking rate of yarns is significantly regulated by the number of fiber twists/inch (Bhandari et al., 2011), while Das et al. suggested that the wicking rate significantly decreased with an increase in twists per inch under the effect of gravity (B. Das et al., 2011). Other recent studies have suggested that microfluidic flow can be optimized by surface engineering methods such as patterning or channeling the hydrophilicity of fabrics. Furthermore, hydrophobic cotton fabrics can be used for SERS-based applications by dip coating (Mahltig, 2011), spin coating, (L. Xu et al., 2012a) or printing with hydrophobic materials (Noppakundilograt et al., 2010) to obtain varied levels of hydrophobicity that regulate the sample flow. Wearable sensors that can be integrated into clothing can be used for the continual assessment of patient health. Electronic textiles that can monitor physiological parameters are becoming more common, and smart textiles that can monitor chemical biomarkers are required (Lu et al., 2016).\n\nRobinson et al. conducted an interesting study in 2014 for the detection of 4, 4’-Bipyridine (4, 4’-BiPy) using novel fab-chips made of Zari fabric (metal coated over silk fabric). The Zari fabric-based chip is composed of silver nanoparticles (AgNPs) for roughening the Zari yarns, thereby improving the SERS signal. 4,40’-BiPy was used as a probe to assess substrate uniformity and sensitivity, while the detection of adenine bases in DNA provided solid evidence for SERS detection of biological molecules on treated Zari fabric. However, the data suggest a relatively higher relative standard deviation (RSD) for the substrate and large errors at lower analyte concentrations. In addition, no real sample testing was conducted, which can significantly alter the results owing to pH, the presence of other biomolecules, analogous molecules, and other organic loads (Robinson et al., 2015). In another study, Gong et al. fabricated gel-assembled AgNPs, and their in situ growth on cotton swabs was used for the detection of 2, 4-dinitrotoluene (2,4-DNT) in standard organic solvents, as shown in Figure 14. The cotton Q-tip was transformed into a surface-SERS-active substrate (SERS Q-tip) using a bottom-up strategy. The sensitivity of this direct swab-sensing method was tested with Nile blue A (4-NBA) and further explored for the detection of 2,4-DNT. The swab detection method showed exceptional sensitivity, with an LoD of ∼1.2 ng/cm2 and a shelf life of ~30 days (Z. Gong et al., 2014). Table VI discusses some recent advancements in analyte detection with exceptional LoDs and some critical insights for improvement in sensitivity. However, most fabric-based substrates do not optimize the microfluidic flow because of (i) varying inter-fiber sizes between the threads and (ii) limited surface area that does not allow printing. Hence, the use of rigid, inert, non-porous materials, such as polymers or silica, can facilitate the fabrication of surface chemistries.\n\n(This figure has been reproduced with permission from (Z. Gong et al., 2014), Copyright (2014) Applied materials & Interfaces).\n\nPolymers are large molecules that consist of long chains or networks of covalently bonded monomers. Some commonly used polymers include polyethylene terephthalate (PET) (Y. Wang, Jin, et al., 2018a), poly (methyl methacrylate) (PMMA) (Huebner et al., 2012), (PDMS) (C. Qian et al., 2015), and polyvinylidene fluoride (PVDF) (Szymborski et al., 2014). They possess characteristic features, such as durability, flexibility, and versatility, enabling their broad-spectrum applications, including medical diagnostics and environmental monitoring. Recently, the increased use of polymer-based substrates has been observed due to their chemical inertness, disposability, cost-effectiveness, and optical transparency(Z. Li et al., 2020), which facilitate the fabrication of disposable SERS substrates.\n\nHowever, some major considerations in the fabrication of polymer-based SERS substrates are the flexibility and transparency of the polymers. The flexibility of a polymer ensures design versatility, adaptability with integrated circuitry (McAlpine et al., 2005), and irregular sample surfaces for proximity between the substrate surface and the analyte molecules (Restaino & White, 2019). Optical transparency facilitates light penetration (L. Li & Chin, 2020) and suppression of background fluorescence (George et al., 2018). Flexible and transparent substrates that can attach conformally to arbitrary solid surfaces are of increasing interest owing to their in situ detection potential. Among these, PDMS (Park et al., 2017) stands out because of its chemical inertness (McDonald & Whitesides, 2002), leak-proof nature (Abidin et al., 2019), gas impermeability (Nakagawa et al., 2002), and thermal stability(X. Liu et al., 2015). In addition, polymer-based nano composites are gaining attention as hybrid SERS substrates, with a typical composition of synthetic or natural polymers as the host matrix and a filler with 1D nanostructures such as metallic nanoparticles dispersed into a large volume of filler followed by curing (Connatser et al., 2004; Giesfeldt et al., 2005). Furthermore, substrates modified with surfactants or fatty acids, such as alkyl dithiols (Kubackova et al., 2015) and oleic acid, (H. Zheng et al., 2015) have been used as promising disposable-SERS substrates, alongside gold (Shahar et al., 2017) and silver nanoparticle-doped or modified polymers (H. Zheng et al., 2015).\n\nIn 2017, Singh et al. developed tantalum (Ta)-doped TiO2 nanofibers (TNFs) in alcoholic solutions via electrospinning with PVP for the detection of methylene blue. The 5% Ta in the TNFs displayed an improved photocatalytic activity of 2.2 times with solar light irradiation because of the newly induced energy levels in TiO2 (Ti3+). These energy levels improve the photoexcited charge division and promote charge transfer, resulting in a higher chemical enhancement of the substrate. However, as the average signal enhancement is primarily influenced by charge transfer, the use of other photocatalytic nanoparticles may improve the sensitivity. In addition, as the homogeneity of Ta in TNFs depends on the properties of PVP and the parameters associated with electrospinning, the repeatability and reproducibility of the substrate may be adversely affected. Rather, PVP electrospinning should be performed prior to Ta doping of the TNFs (Singh et al., 2017).\n\nAs discussed above, the flexibility of the polymer is pivotal for its choice as a disposable SERS substrate. Recent studies have shown the increasing attention paid to flexible platforms owing to their durability and adaptability with irregular surfaces and geometries, aiding in practical applications. In a recent study, Zang et al., in 2021, proposed a strategy for the fabrication of a polyethylene terephthalate (PET) film-based flexible SERS substrate using argon (Ar) plasma etching with the physical vapor deposition (PVD) of gold to produce worm-like Au nanostructures. The as-synthesized SERS substrates exhibited a significant signal enhancement with an EF of 1.2 x 108 and the LoD was calculated as 10−9 M. However, the repeatability and reproducibility of the developed sensor substrate were not analyzed. In addition, no cross-sensitivity testing or real sample testing was performed, which can vary significantly with the point-of-use application (Zang et al., 2021). Another interesting study on the detection of malachite green (MG) presence on fish was reported by Zhao et al. in 2018. They developed a novel method for fabricating a three-dimensional (3D) flexible SERS substrate using graphene oxide/Ag nanoparticle/pyramidal PMMA (GO/AgNP/P-PMMA), as shown in Figure 15. The pyramidal and flexible 3D PMMA film (P-PMMA) was imprinted from pyramidal silicon with a high curvature and triangular geometry; therefore, it acted as an activity site for heterogeneous detection. The larger field enhancement and improved probe capturing are due to the homogenous development of hotspots, as is evident from the higher SERS intensity of R6G in comparison to the flat PMMA surface. The performance of the developed SERS substrate was validated with the AgNP/P-PMMA substrate and GO/AgNP/flat-PMMA substrate using molecular probes, such as R6G and (CV) (X. Zhao et al., 2018). However, the LoD of the developed sensor varied significantly with the sensing MG on the real sample; therefore, the accessibility of specific detection of MG in a complex organic specimen may be a challenge. The use of a specific bioreceptor may improve the sensitivity and specificity of a sensor, as demonstrated by Li et al. (2018). Biofluid analysis was performed for the specific and quantitative assessment of dopamine in the serum (L. Li et al., 2018). Table VII discusses a few recent advancements using polymer-based substrates for analyte detection with exceptional LoDs and some critical insights.\n\n(This figure has been reproduced with permission from (X. Zhao et al., 2018), Copyright from (2018) Applied Surface Science).\n\n6.3.1 DVD-based substrate\n\nDigital Versatile Discs (DVDs) can be efficiently repurposed to generate ordered structures with microscale features that amplify the Raman signal. Commercially available DVDs contain a silver-coated spiral arrangement of rectangular grooves (AgDVDs), which is exploited as a regularly ordered substrate for SERS biosensing. A few characteristics of the substrate include a larger surface area, homogeneity of the substrate, easy customizability, multiplexing, and substrate recycling, which enable the versatility of DVDs for SERS-based sensing. A study proposed by Giuseppe Giallongo et al. detailed the fabrication of SERS substrates based on the electrodeposition of silver nanoparticles on the inner silver surface of a commercial DVD, resulting in AgNPs@AgDVD, as depicted in Figure 16(i). The versatility of the DVD facilitated the customization of the AgNPs and substrate uniformity. The AgNPs@AgDVD substrates showed an enhancement factor (EF) up to 7 × 105 with good reproducibility and repeatability. This method provides a practical alternative for inexpensive disposable substrates for SERS and offers further room for improvement (Giallongo et al., 2011). Commercially available blue ray digital versatile discs (BRDVDs) possess a 320 nm structural periodicity and a channel width of 100 nm, thus generating an ideal structure for entrapping nanoparticles. The BRDVD nanochannel’s sidewalls are composed of polycarbonate (PC) material with a refractive index of 1.58 required for guiding the coupled EM field with the trapped nanoparticles in the channel.\n\nIn a similar study by Chamuah et al. in 2019, BRDVD was used as a SERS substrate for the detection of albumin, creatinine, and urea in urine samples. The trapped AuNPs in the BRDVD channel produced a guided mode resonance (GMR) field and an increase in the photon lifetime of the coupled EM field, accounting for the overall increase in the local field intensity, as depicted in Figure 16(ii). The LoDs were calculated as 0.1 μg/mL, 0.2 μg/mL and 0.6 μg/mL respectively, which are well below the normal range and thus meeting the requirements for the analysis in various clinical approaches (Chamuah et al., 2019). The sensitivity and LoD obtained by the BRDVD-based sensor were significant because only isotropic nanostructures were employed. However, AuNP absorbance wavelength coherence with the 785 nm laser may not be prominent for efficient light scattering from the synthesized nanostructure. The substrate exhibited an exceptional shelf life of 45 d. However, no cross-sensitivity testing has been conducted to ensure specificity in the presence of structurally analogous molecules or other interferents in a complex sample. In another study, Nguyen et al. (2019) demonstrated the detection of amoxicillin by drop-casting AuNPs onto the surface of a DVD. AuNPs were synthesized by pulsed laser ablation of gold, resulting in colloidal gold, which was then deposited on the DVD surface in a circular pattern. The polycarbonate layer was removed from the DVD, followed by rinsing with ethanol and DI water before the deposition of AuNPs. The average EF of the AuNPs/DVD SERS substrates was calculated as 106, with an LoD of 0.1 ppm and linear detection range of 0.1-1 ppm (Nguyen et al., 2019). However, the sensor showed poor sensitivity despite having a good EF with the developed substrate. Rather, the use of anisotropic nanostructures, such as gold nanorods, nanostars, or nanoflowers, significantly improves the detection limit and sensitivity. Despite the advantages offered by polymer-based substrates for SERS measurements, they are also associated with some major limitations, such as optical absorption or scattering, background interference, lower signal enhancement, and incompatibility with different types of sample matrices. Therefore, another promising disposable material, glass, has been extensively used in SERS systems.\n\nCrystalline silica, commonly known as quartz, is the most abundant form of silica in nature, whereas other common forms are fused silica or glass, amorphous silica, colloidal silica, and silica nanoparticles. Silica is beneficial because of its high-temperature resistance, chemical inertness (Vaidya et al., 2020), rigidity (Bruno & Svoronos, 2010), transparency, electrical insulation (B. C. Senn et al., 1999), and biocompatibility (Bayliss et al., 1999). Fused silica/glass slides ensure a stable and inert surface necessary for the chemical modification or immobilization of biomolecules. Conversely, Silica nanoparticle-embedded paper and silica nanoparticle-coated substrates possess exceptional physical and chemical stability and regulate sample flow, which aids in the development of disposable microfluidic devices. These properties will assist in the development of SERS-active substrates for on-site environmental monitoring and biomedical diagnostics. In contrast, porous silica (pSi) is extensively used in adsorption and separation (Steinbacher & Landry, 2014), (bio) sensors (Patel et al., 2006), drug delivery (J.-F. Chen et al., 2004), catalysis (K. Yang et al., 2015), and environmental remediation (Nutt et al., 2005), owing to its large surface area, pore size, and sample distribution. However, fused silica/glass-based substrates are extensively used for the fabrication of disposable substrates owing to their characteristic features such as optical transparency, ease of functionalization, homogeneous surface roughness, and biocompatibility. In 2019, Zhou et al. fabricated an SERS-active substrate on ultrathin glass to detect 1,2-bis-(4-pyridyl)-ethene (BPE). AuNPs were annealed on the glass coverslips by metal evaporation at varying temperatures (350°C, 450°C, and 550°C) and at different time intervals (1,3,6, and 9 h), which resulted in varying thicknesses of the gold films, as shown in Figure 17(ii). The variation in the gold film thickness resulted in different colors, such as dark green (8 nm), light green (6 nm), blue (4 nm), and light blue (2 nm). The developed glass substrate showed an EF of 2.71 × 107 with an LoD of 10−12 M and a linear detection range of 10−3 to 10−12 M was observed within 120 s of laser incidence on the aqueous solutions. It also showed excellent repeatability with an R2 value of 0.9976 and a good shelf-life of 5 weeks, indicating that these gold coverslips can be a good choice for SERS-based sensors (L. Zhou et al., 2019). However, coverslips coated with 4 nm Au at 550°C showed the highest surface coverage and smallest interparticle distance, which assisted as a 2D ordered array structure, aiding in better sensitivity. Rather, the use of anisotropic nanostructures can significantly improve the sensitivity owing to the edge effect. In addition, no cross-sensitivity testing or real-time detection were performed because they significantly affect the sensitivity with interference from other analogous structures, biomolecules, or organic load in the sample matrix.\n\nA novel study by Das et al. (2022) fabricated a low-cost mesoporous Ag–TiO2 SERS substrate on glass. The distinctive cage-like structure of the TiO2 film resulted in the uniform growth of a spherical and porous Ag film with an average interparticle distance of 10 nm, as shown in Figure 17(i), which aids hotspot generation within a small volume. The TiO2 nanocage (NC) also increased the effective surface area for analyte adsorption and the Ag–TiO2 NC structure displayed an enhancement of 108 with the R6G probe using a portable handheld Raman spectrometer. The proposed substrate was recyclable, owing to its photocatalytic activity, upon exposure to UV light for 130 min, which resulted in degradation of the dye molecule (S. Das et al., 2022). Furthermore, the substrate exhibited high sensitivity for detecting urea concentrations up to 1 mM, which covers the critical range of blood urea levels. In yet another study, Furu Zhong et al., 2018 prepared a silver nanoparticle (AgNPs)-coated porous silicon photonic crystals (PS PCs) for the detection of Picric acid (PA) in alcoholic solution. The developed sensor exhibited an LoD of 10−8 mol/L and a linear detection range of 10−4 to 10−7 mol/L. The PS PCs substrates displayed a 3.58 times greater signal enhancement than conventional single-layered porous silicon. Incubation of PS PCs with AgNPs for more than 75 s decreased the inter-nanoparticle distance and improved SERS enhancement (Zhong et al., 2018). However, as the PS PCs substrate was incubated with AgNPs, the homogeneity of the SERS substrate was severely affected. Rather, electrospinning or spin-coating of AgNPs on PS PCs can generate uniform hotspots. Furthermore, no cross-sensitivity testing of the AgNP-coated PS PCs was conducted, as it may significantly affect the specificity of SERS-based detection. Therefore, these studies indicate that, despite the challenges associated with the use of silica nanoparticles or glass slides for SERS-based sensing, they can serve as excellent disposable SERS substrates.\n\nIn conclusion, the use of all disposable substrates for SERS-based sensing at the small-scale or industrial level was beneficial because of its cost-effectiveness, ease of customizability, portability, and scalability, despite some challenges in substrate performance. Therefore, disposable SERS substrates are promising for sensing target analytes in food safety, biomedical diagnostics, and environmental monitoring, to address real-world challenges.\n\n\n7. Effect of surface modifiers in SERS based sensor design\n\nDespite the intrinsically strong electromagnetic field, SERS substrates can be tailored with specific surface modifiers for higher specificity and robustness. Typically, surface modifiers are nanostructures or nanocomposites linked to substrates to alter the local EM environment and ensure efficient interaction by manipulating the covalent or non-covalent forces between the analyte and substrate. The use of modifiers facilitates hotspot uniformity (Jahn et al., 2016), easier charge transfer, (W. Fan et al., 2014) and incorporation of bioconjugation chemistries by improving the surface area of biosensing on the SERS substrate, (Z. Fan et al., 2013) thereby improving the sensitivity and robustness of the substrate. The substrate surface treatment process categorizes surface modifiers and associated conjugation as physical conjugation, chemical conjugation, and biological conjugation.\n\nA few commonly used surface modifiers in physical conjugation include metal–organic frameworks (MOF), covalent organic frameworks (COF), aerogels, and hydrogels. These surface modifiers are porous structures that facilitate the controlled integration of plasmonic nanoparticles or Raman-active molecules for the efficient enhancement of the EM field and Raman scattering. The controlled addition of plasmonic nanostructures with defined shapes and sizes to these surface modifiers can generate uniform hotspots on the substrate surface. In an interesting study by Qiao et al., a zinc-based MOF, ZIF-8, was coated with AuNPs (AuNPs@ZIF-8) for the detection of volatile organic compounds (VOCs) for early lung cancer diagnosis, as shown in Figure 18. Regulated gaseous flow of VOCs resulted in increased adsorption owing to the use of ZIF-8. Schiff’s base reaction between the 4-ATP dye on the AuNPs and the aldehyde group of VOCs resulted in a detection limit of 10 ppb (Qiao et al., 2018). However, the efficiency and sensitivity of the system may be significantly affected by humidity, which may restrict the adsorption of VOCs onto ZIF-8. In addition, the Schiff base interaction may be due to the interaction with another aldehyde-containing interferents. Table VIII presents some recent studies describing the effect of physical conjugation, their effect on Raman enhancement, and some critical insights for improvement.\n\nCommonly used chemical surface modifiers include long-chain thiol-containing molecules such as 11-mercaptoundecanoic acid (11-MUA), 1, 4-benzenedithiol (1, 4-BZT), and amine-terminated or carboxyl-terminated dendrimers. Typically, chemical conjugation is used for the immobilization of target analytes or bioreceptors to improve sensitivity, mitigate non-specific interactions, and stabilize the sensor. These techniques can significantly alter the Debye length of the developed sensor (L. Xu et al., 2020d) and generate uniform hotspots on a substrate. They also act as binding sites for different functional groups, such as silanes, amides, phosphoric acids, and carboxylic acids, relative to the available substrates. In an interesting study by Gorbachevskii et al., the local electric field density and the hotspot density were observed to vary depending on the kinetics of Raman dye oxidation with hydrogen peroxide using citrate-capped AuNPs (Gorbachevskii et al., 2018), while another study by Kim et al., in 2016, observed irreproducibility in Raman enhancement by selective interaction between the amine and carboxyl groups of dendrimers and rGO of the Au-rGO complex, respectively (K. Kim et al., 2016b). In another interesting study, Xu et al. developed a compact AuNP-templated nanostructure from a mesoporous silica film (MSF) at the air-water interface, as shown in Figure 19. The increased adsorption of AuCl4- in the MSF channels resulted in the close packing of AuNPs@MSF and facilitated hotspot creation and SERS enhancement. Real sample detection was done in water, milk, and apple samples and obtained an LoD of 0.79 pg/mL for 2,4-D, 1.04 pg/mL for pymetrozine and 1.21 pg/mL for thiamethoxan for a linear detection range of 0.1 to 1000 ng/mL (Y. Xu, Kutsanedzie, et al., 2020a). Table IX presents some recent studies describing the effect of chemical conjugation, their effect on Raman enhancement, and some critical insights for further enhancement.\n\nBiological conjugation involves the covalent linking of a specific bioreceptor with a substrate surface or modifier to improve sensor specificity. This is primarily dependent on the terminal functional groups of the stabilizing shells. The bio-conjugation of the ligands on the surface of NPs is facilitated by the formation of an amide bond by carbodiimide activation. Because it offers superior stability, bio-conjugation created by thiol group attachment is regarded as a robust and effective conjugate in SERS. Additionally, electrostatic interactions and the attachment of biotin-streptavidin conjugates to nanoparticles (NPs) have also been utilized in the creation of adaptable nanomaterials (Chauhan et al., 2022).\n\nIn an interesting approach by Barahona et al., in 2013, an SERS-based aptasensor on micron-sized polymer particles was used for the detection of malathion. Methacrylic acid monomers and ethylene glycol dimethacrylate co-monomers were subjected to precipitation polymerization to synthesize polymer particles in acetonitrile. The use of acetonitrile facilitates a smaller pore size, whereas methacrylic acid supplies carboxyl groups that bind gold. Controlled aggregation of AuNPs resulted from the conjugation of AuNPs with the polymer using 2-aminoethanethiol. Thiolation was used to connect the aptamers to the nanoparticles. The thiol–gold interaction caused the polymer-AuNP-aptamer complex to adhere to the metal surface. The LOD was 33.3 μg/mL, and the concentration ranged from 3.3-33.3 μg/mL (Barahona et al., 2013). Figure 20 depicts the fabrication of polymer-AuNP-aptamer substrates and the specific detection of 2, 4-DNT. Table X presents some recent studies describing the effect of biological conjugation, their effect on Raman enhancement, and some critical insights for improvement.\n\n(This figure has been reproduced with permission from (Barahona et al., 2013), Copyright from (2013) Industrial Biotechnology).\n\n\n8. SERS biosensing\n\nA typical SERS-based biosensor involves the use of a robust SERS-active substrate with customized linker chemistry for conjugation with an analyte-specific bioreceptor. Commonly used bioreceptors include antibodies, aptamers, enzymes and polysaccharides. The concentration of the target analyte near the plasmonic field of the SERS-active substrate due to binding with the bioreceptor can enhance Raman scattering and hence improve the detection sensitivity. The use of bioreceptors assists in the differentiation of molecules with similar structures and the detection of specific analytes from complex specimens. However, the use of bioreceptors with a SERS-based system is also associated with challenges, such as degradation of bioreceptors in sensing with environmental or complex samples, high cost of the bioreceptor that limits widespread use, and non-specific interactions of sample matrix components, resulting in incorrect results. However, these challenges may be reduced to a certain extent by optimizing the SERS system parameters, such as the choice of the excitation laser wavelength, laser power, integration time, and scans to average. Typically, the use of longer-wavelength lasers can minimize autofluorescence and background noise from bioreceptors. In addition, a high laser power can denature the bioreceptor and reduce background fluorescence, thus requiring the use of a low laser power. A higher integration time and scans to average can enhance background noise, along with the signal intensity, which can be minimized by using appropriate optics, such as optical filters and light polarization optics.\n\nCurrently, biosensors play a crucial role in the qualitative and quantitative determination of several biomolecules, which helps in monitoring biological processes and disease diagnosis. Compared to other biosensing platforms, Surface-enhanced Raman scattering (SERS) shows a million-fold enhancement in Raman signals when using appropriate SERS substrates. Since the discovery of the SERS phenomenon using a roughened metallic silver surface, it has evolved as a method of interest in bioanalysis across various fields, such as biochemistry, chemistry, material science, and life science. SERS has been established as the most sensitive and powerful spectroscopic technique for biosensing applications. A recent study by Li. P et al. presented a schematic for the synthesis of dual-reporter SERS probes for the specific detection of prostate-specific antigens, as shown in Figure 21(i) (P. Li et al., 2020). SERS has several advantages over traditional bioanalysis methods, such as ultrahigh sensitivity; thus, it is useful even in the detection at a single molecular level. It shows less sensitivity towards photobleaching and photodegradation, thereby aiding long-term monitoring. Additionally, SERS makes convenient multiplex detection possible using single-wavelength excitation (Zong et al., 2018). Breakthroughs in the fields of synthetic chemistry and material engineering have aided in broadening the applications of SERS beyond those in which the molecules bind to metallic nanostructures and are resonant in the visible wavelength region. Capture agents bring low-metal-affinity analytes close to plasmonic surfaces, where large electromagnetic enhancement allows signal amplification, thereby expanding the library of molecules detectable by SERS, which includes molecules of biological and clinical importance (Cardinal et al., 2017). The two available methodologies for SERS-based applications are label-free detection and indirect approaches that use SERS tags. The goal of SERS-based label-free detection is to obtain vibrational spectroscopic information of molecules through direct interaction between the samples and SERS-based nanostructures, resulting in enhanced intrinsic fingerprint information of biological and biomedical samples. A study by Lussier et al. used a sharp plasmonic nanosensor for cellular piercing to detect the time-dependent secretion of cellular metabolites with a He-Ne laser diode with the same SERS-active substrate, as shown in Figure 21(ii) (Lussier et al., 2016b). Label-free SERS approaches can provide information on the structure of proteins, nutritional quality of food products, and detection of distinctive pathogens present in clinical samples as well as biological processes occurring at the cellular level (X.-S. Zheng et al., 2018). The successful implementation of both label-free SERS and indirect SERS in biomedical and biological analyses requires the powerful and rational design of plasmonic nanostructures.\n\nTypically, metallic nanostructures for SERS are made by four strategies: bottom-up, self-organization, and top-down processes; a layer of reporter molecules showing a unique and strong Raman fingerprint that enables indirect detection; an outer layer coating that aids in improving its biocompatibility and stability; and bioconjugations that enable specific detection of the analyte (Cialla-May et al., 2017). Noble-metal nanoparticles have traditionally been used for the synthesis of SERS-active substrates because of their unique ability to exhibit local plasma resonance. Signal enhancement is dependent on various parameters, including the size, shape, morphology, arrangement, and dielectric environment of the nanoparticles. Owing to these reasons and their enormous advantages, studies have now focused on tunable nanofabrication and the synthesis of noble metallic nanoparticles. Several reports have been published on the development of metallic substrates, focusing on their various morphologies and applications in biosensing, such as nanospheres, nanocubes, aggregates, and well-designed one-dimensional (1D), two-dimensional (2D), and three-dimensional (3D) arrays and patterns. These special structures are of great use in the trace detection of chemical and biological molecules such as food additives, antibiotics, and disease markers. Although several substrates and designs have been developed, the production of highly sensitive, selective, stable, and reproducible substrates using a simple, robust, low-cost, and high-yield method remains a challenge (Cao et al., 2013). Point-of-care (POC) SERS analysis is an emerging technique in which SERS measurements are recorded on-site, in contrast to conventional laboratory testing methods that use benchtop SERS instruments. Most point-of-care testing methods are based on lateral flow immune assay (LFIA), which frequently has low sensitivity. SERS with significant signal enhancement via the creation of \"hot spots\" have enormous potential to address the sensitivity limitation, with POC SERS garnering the most attention. Several flexible materials have been utilized as SERS substrates for SERS-based POC diagnostics, including paper, flexible polymers, graphene, and nanowires, each contributing to different applications to the substrate by virtue of their characteristics. These materials enable the mass synthesis of SERS substrates that are affordable, disposable, and scalable. To maintain the high specificity of the SERS technique, the molecular functional interfaces of all these flexible substrates must be carefully considered to interact precisely with the analytes (Perumal et al., 2021).\n\n\n9. Some critical design aspects for SERS Biosensors\n\nAn important consideration in designing a SERS biosensor is the elimination of additional fluorescence from the substrate, linker, or bioreceptor. Fluorescence is defined as a type of luminescence that occurs only when a substance is irradiated with electromagnetic radiation (“IUPAC-Fluorescence,” 2014). The fluorescence of the substrate was nullified by the use of a quencher. For example, graphene quantum dots (GQDs) are liable to fluoresce owing to quantum confinement. Mn3O4 (manganese (II)/ (III) oxide) was used for fluorescence quenching of the GQDs and suppression of the Raman spectral fluorescence background. This property of GQD-Mn3O4 nanocomposites has a high potential for the differentiation of cancer cells and normal cells by SERS (Z. Zhao et al., 2014). The conjugation chemistry of biotin-streptavidin forms a heterostructure with fluorescence properties and assists the surface plasmonic properties of SERS sensors (X. Qin et al., 2019). Studies on graphene indicate that resonance Raman spectroscopy of the substrate can potentially inhibit fluorescent molecules and can be applied to the low-concentration detection of fluorescent molecules. A study by Xie et al. indicated that the fluorescence quenching of R6G adsorbed on graphene was of the order of 103 (L. Xie et al., 2009).\n\nAnother important consideration in SERS biosensor design is the repeatability of the substrate. Repeatability was defined as the absolute difference between individual test results obtained under the same conditions (“IUPAC-Repeatability,” 2014). The synthesis of hybrid nanoparticles, that is, the modification of colloidal metal nanoparticles with additional nanostructures, was observed to improve the SERS performance. The use of graphene-modified surfaces has been observed to improve the stability and repeatability of SERS signals, such as the repeatable determination of 6-mercaptopurine (6-MP) in tablets using graphene-modified metal nanoparticles (W. L. Fu et al., 2014). Other studies have suggested the use of a flow system for sample mixing with colloidal substrates to optimize nanoparticle aggregation for SERS-based detection. A sensor designed by integration of a lab-on-chip setup with a microfluidic system for quantification of mitoxantrone showed a good concentration range of 2.5 x 10−9M to 1 x 10−6M for plasma and serum. Despite achieving good repeatability by integrating the flow system into the substrate surface, the sensor requires a complex and expensive setup (McLaughlin et al., 2002). Surface modification of substrates by chemical functionalization of metal surfaces allows for improved repeatability. Klarite substrates have been used in a recent study by Litti et al. al., displayed good repeatability for the detection of specific anticancer drugs. This work also indicates that hot spot density is crucial for determining the limit of quantification, which is related to sensor repeatability (Litti et al., 2016).\n\nA higher signal-to-noise ratio is a crucial consideration for designing a SERS biosensor, as high-quality spectral data acquisition is achieved using holographic notch filters, which can reject the Rayleigh scatter of the analyte molecule (McCreery, 2000). In the case of long-range penetration of the excitation wavelength for biomedical applications of SERS, defined spectral windows are observed in the NIR region (A. M. Smith et al., 2009) based on the cellular composition of the body. Additional fluorescence is observed due to the relatively higher tissue auto-fluorescence, which contributes to the broad background of the Raman signal, thus reducing the SNR. Optimization of the SNR for SERS spectral recording is essential for achieving rapid results and a lower sensitivity of the sensor (McCreery, 2000). Owing to the intrinsically weak nature of Raman spectroscopy, one part of the fluorescence is seen for 6-10 orders of magnitude of Raman scattering per cross-sectional area (Etchegoin, 2009). Thus, the measured Raman spectra should be free of trace impurities to avoid the background signal and provide a Raman signal. Hence, the best SNR can be achieved with a minimal background signal (McCreery, 2000).\n\n\n10. Disposable SERS systems for specific analyte detection\n\nTypically, disposable SERS systems employ one-time-use substrates that mitigate the need for multiple cleaning procedures and the risk of cross-contamination. They are more beneficial than standard substrates owing to their low cost, versatile detection, robustness, and user-friendliness. These disposable SERS systems can be tailored for specific analyte sensing with improved sensitivity and selectivity through specific surface functionalization or the use of a specific bioreceptor to capture the analyte of interest. The compact design and ease of use of the system can facilitate on-site use and measurement of real-time data.\n\nSmall molecules are organic compounds with molecular weights lower than 1000 Da that are fundamental for chemical and biological processes. Common small molecules include antibiotics, pesticides, chemicals, and heavy metal ions. The detection of small molecules in food and water sources is crucial for preventing detrimental effects on the environment and human and animal health. Early detection of these small molecules can assist in formulating the necessary regulatory measures to devise strategies for the prevention of adverse health disorders.\n\n10.1.1 Pesticides and chemicals\n\nThe indiscriminate use of pesticides poses a serious threat to consumer health and can possibly lead to soil contamination and, eventually, contamination of water bodies. The chronic and fatal effects on human health are proportional to pesticide exposure time, pesticide concentration due to bioaccumulation, and chemical characteristics of the pesticide(L. Zhang et al., 2014). Thus, the detection of pesticides in food, soil or water bodies is essential to prevent their entry into humans. Conventional strategies, including HPLC and GC-MS, are expensive and require longer time for result acquisition. Other strategies include colorimetric detection, RI sensitivity detection, and Raman spectrum-based detection, which may not detect trace levels of pesticides due to their lower sensitivity, although these standard techniques cannot provide a quantitative estimation of the analyte.\n\nIn an interesting study by Dies et al. in 2018, the presence of thiram, a fungicide used in agriculture, was checked in apple juice by SERS using dendritic silver nanosubstrate on microelectrodes by maskless photolithography. It recorded an LoD of 115ppb and a liner detection range of 0.01-100 ppb, on the microelectrode chip by using a preconcentrated nanoparticle solution, as shown in Figure 22(i). The key peak at 686–703 cm−1 was used for identification and quantification (Dies et al., 2018). However, the use of microelectrodes as the substrate with a high-energy laser can ablate the electrode surface, resulting in the generation of surface interferents that significantly affect the sensitivity of the sensor. Another interesting approach by Xie et al. (2020) used bipyramidal AuNPs for trace detection of methyl parathion in apple peels. The senor showed an LoD lower than other substrates, i.e., 98.63 ng/cm2, 31.56 ng/cm2 and 36.58 ng/cm2 on peels of cucumber, tomatoes and apples respectively (J. Xie et al., 2020). The “press -peel off” method of detection is shown in Figure 22(ii) is user-friendly, but the recovery rate is not significant and therefore cannot aid in field deployment. Despite the use of a 785 nm laser and spherical AuNPs, a considerable detection limit with a 10-fold EF was achieved. Table XI presents the specific detection of pesticides and chemicals using disposable substrate-based SERS systems.\n\n10.1.2 Antibiotics\n\nExcessive use of antibiotics leads to antibiotic resistance in patients, rendering the drug ineffective. Commonly used antibiotics include tetracyclines, beta-lactams, fluoroquinolones, amphenicols, and carbapenems. Traces of these antibiotics may be found in food and water sources because of their excessive use in animal treatments that remain as residues or by the use of contaminated water for agricultural practices. Currently, SERS detection methods are used extensively to detect trace levels of antibiotics in food and water sources.\n\nAn interesting study was conducted by Shi et al. (2017) for the detection of neomycin in milk using lateral flow immunoassay (LFA)-based SERS. This testing strategy displayed good sensitivity with an LOD of 0.216 ppb and a recovery rate between 89.7%- 105.6% (Shi et al., 2017). Although exceptional sensitivity was observed, the sensor lacked coherence of the laser excitation wavelength mismatch and absorbance of the nanoparticles. The use of monoclonal antibodies could not ensure specificity, as better cross-reactivity with other antibiotics such as enoxacin was observed. In another interesting study by Pinheiro et al. in 2018, gold nanostars (GNS) decorated on magnetite nanoparticles (MNP) were used for the trace detection of tetracycline. This method estimated LOD of 44.4ppb and 444ppm in ultrapure water and mixed aqueous solutions respectively (Pinheiro et al., 2018). However, this substrate sensitivity is primarily dependent on the adsorption of tetracycline, which may significantly vary with Au branches and surface irregularities on MNPs that generate hotspots. Instead, the use of a specific bioreceptor may improve the adsorption capacity and specificity of the substrate. pH studies for tetracycline adsorption showed that pH 5-6 was the most favorable for adsorption; however, pH regulation in complex sample matrices may not be possible during rapid analysis. In a recent study by Riswana et al., gold nanostars (AuNSs) were decorated on a PMMA substrate for SERS-based detection of ciprofloxacin and chloramphenicol in chicken wing samples, as shown in Figure 23. The developed system achieved an LoD of 3.41 × 10−11 and an EF of 2.03 × 109 (Riswana Barveen et al., 2022). The use of a novel AuNS synthesis method utilizing a UV-C light-based photoreduction process is simple, yet effective. The substrate showed exceptional sensitivity and multiplexing ability; however, no cross-sensitivity testing was conducted. Table XII discusses the disposable substrates for the SERS-based detection of antibiotics.\n\n10.1.3 Heavy metals & other small molecules\n\nContamination of food and water by heavy metal ions such as mercury (Hg2+), lead (Pb2+), arsenic (As2+), and cadmium (Cd2+) can potentially affect the physiological functions of the nervous system, as well as injure vital organs such as the kidneys and liver. Accidental ingestion of food containing these contaminants increases the risk of heart disease, neurological damage, such as tremors, and impairment of cognitive function. The most toxic heavy metal ion in water sources that affects the environment and human health is mercury (Hg2+), and its accumulation in humans leads to neurological disorders. A disposable SERS substrate developed by Yang et al., (H. Yang et al., 2017), as shown in Figure 24, by the deposition of thymine for simultaneous detection of Hg2+ and Pb2+ ions in drinking water employing oligonucleotide functionalized gold coated polystyrene microspheres (PSMPs). The LoD of the fabricated substrate was found to be 0.1ppb for Hg2+ ions, which is far lower than the limit prescribed by the World Health Organization (WHO) (Guo et al., 2023). Despite the excellent sensitivity and ability to specifically detect Hg2+ from untreated river samples, cross-sensitivity analysis was not conducted. Table XIII discusses the disposable substrates for the SERS-based detection of heavy metals and other small molecules.\n\nNucleic acids, DNA, and RNA are genetic materials of all living beings that may be utilized as biomarkers. Standard detection methods include southern/northern blotting, reverse transcriptase-polymerase chain reaction (RT-PCR), and microarray-based methods. These methods cannot be used for POU applications because of the need for sample preprocessing, longer assay time/incubation time, high cost, and low sensitivity. Optical and electrochemical detection methods can overcome these limitations, thereby increasing the possibility of on-site nucleic acid detection using SERS-based systems. Recently, Mabbott et al. developed a 3D paper-based microfluidic platform, as shown in Figure 25. The fabricated substrate used malachite green XXX isothiocyanate (MGITC)-functionalized AuNPs coated on Whatman 4 chromatography paper for the specific detection of miR-29a in PBS running buffer. This system showed an LoD of 47 ppm using a handheld Raman spectrometer, thus proving its potential as a POU device (Mabbott et al., 2020). Despite the POU applications, the authors used a CBEX handheld Raman spectrometer, which is highly expensive for integration into a POU-SERS system. Table XIV discusses disposable substrates for the SERS-based detection of nucleic acids.\n\n(This figure has been reproduced with permission from (Mabbott et al., 2020), Copyright from (2019) Analyst).\n\nProteins are biomolecules that are synthesized through an in-vivo process called translation from genetic material, and may be used as biomarkers or indicators in disease diagnostics as efficient target analytes for SERS-based detection. A strategy was developed by Wang et al. by integrating digital microfluidics with a SERS-based immunoassay for the detection of hemagglutinin of H5N1 influenza virus, as shown in Figure 26. The surface protein was detected in both buffer and human serum samples, and the system showed an LoD of 74 ppb but required less assay time than conventional ELISA and a lower sample volume requirement. The characteristic Raman peaks of 4-MBA were observed at 1071 cm−1 and 1580 cm–1 (Y. Wang, Ruan, et al., 2018c). Another study by Pinzaru et al. used hydroxylamine-reduced AgNPs to detect lipophilic marine biotoxins, namely okadaic acid (OA), Dinophysistoxin-1 (DTX-1), and Dinophysistoxin-2 (DTX-2) in shellfish tissue. A prominent SERS peak at 1017cm−1 was observed for DTX-1 and DTX-2, which was not observed in the OA fingerprint. OA showed LOD of 200ppm, 71.8 ppm for DTX-1 and 32.6 ppm for DTX-1 respectively (Pinzaru et al., 2018). The developed substrate showed good sensitivity; however, the excitation laser wavelength and absorbance range of the nanostructures were not coherent. Rather, the use of AuNPs with a typical spectral absorbance at 530 nm may improve sensitivity. Table XV illustrates some of the disposable substrates for the SERS-based detection of proteins.\n\nMicrobes, specifically viruses, pose a major hazard to the healthcare sector because of their rapid replication cycles and minimal access to instruments capable of ultrasensitive detection. Real-time detection from complex samples using conventional techniques cannot limit bacterial replication and improve the chances of infection after entering a live host. Thus, there is an urgent need for rapid and ultrasensitive detection in real samples for instant treatment of the host. A label-free bacterial SERS detection method was developed by Gao et al., using the selective growth of AgNPs on the bacterial outer membrane conjugated with aptamers. Improved SERS signal by aptamer@AgNPs complex resulted in exceptional LoD of 1.5CFU/mL using micro-Raman system (W. Gao et al., 2017). Additionally, the use of lateral flow assay (LFA)-based strips for the qualitative determination of the analyte of interest is essential for POC diagnostics, which are cost-efficient, reliable, reproducible, and highly sensitive (Ryu et al., 2010). Wang et al. tested a sandwich immunoassay using antibody-conjugated AuNPs with reporter molecules for bacterial detection, as shown in Figure 27(i). Malachite green isothiocyanate (MGITC) in the test line indicated the presence of target bacteria binding to antibodies on the AuNPs. The test concentration was maintained at 107 CFU/mL for all studies. This rapid detection (~15 min) method showed an LoD of 357 CFU/mL for B. anthracis strain with a minimal sample (R. Wang, Kim, et al., 2018b).\n\nMost recent epidemics are caused by viruses that possess multiple surface proteins and genetic material, which are reliable biomarkers for the detection of their presence during disease prognosis and treatment. A mini microfluidic platform named VIRRION (virus capture with Raman Spectroscopy detection and identification) was developed using arrays of carbon nanotubes with different filtration permeabilities for high-throughput virus capture and rapid SERS detection. This method can be employed for multiple-virus capture and detection on a chip by SERS using a Raman system (Yeh et al., 2020). Another method with labelled detection of the virus was developed by Shen et al., based on the immunoassay method using an LFA strip-based reaction for wild-type pseudorabies virus from clinical samples of pig tissue. This method detects glycoprotein E-specific PCR, which differentiates between the wild-type PRV and gE-deleted vaccine. This method requires approximately 15 min and has an LoD of 5ppm and linear detection range of 41-650ppm(Shen et al., 2019).\n\nWhole cell detection is considered a need of the hour to identify the presence of circulating tumor cells in the bloodstream, which helps in the early detection of cancer metastasis. This early diagnosis involves a liquid biopsy instead of a tissue biopsy. CTC (circulating tumor cells) detection from millions of blood cells is expensive and minute sensitivity needs advancements in the technique for rapid and sensitive detection techniques. In a study by Wu et al., a SERS method with gold nanostructures of different geometries, that is, AuNSs, AuNRs, and AuNPs, was used for CTC detection in liquid biopsy samples. 4-Mercaptobenzoic acid (4-MBA) dye was used with the nanoparticle to induce stability of bovine serum albumin (BSA) and to increase specificity towards conjugation with CTC; folic acid was used. AuNPs displayed the highest specificity, with an LoD of 1-100 cells/mL (X. Wu et al., 2016). In another study by Sun et al., a SERS-based label-free droplet microfluidic sensor was developed for the detection of multiplex metabolites at the single-cell level, as shown in Figure 27. (ii). For the detection of excessive metabolites (lactate, pyruvate, and ATP) secreted from CTC by magnetic isolation of CTCs from complex samples, 400 nm Fe3O4 magnetic microspheres were decorated with 30 nm AgNPs (D. Sun et al., 2019). Table XVI illustrates some of the disposable substrates used for the SERS-based detection of bacteria, viruses, and whole cells.\n\nIn conclusion, despite the insignificant size and molecular weight of the analyte, these disposable material-based sensors showed higher sensitivity when anisotropic nanomaterials were used, which improved the nanostructure’s local electric field due to the edge effect and thus contributed to the amplification of the Raman signal.\n\n\n11. Hybrid SERS systems\n\nTraditional analytical techniques typically involve elaborate or complex procedures, sample pretreatment steps, and costly and sophisticated instrumentation. Consequently, there is a greater need for analytical methods that go beyond centralized laboratory-based methods to enable POU testing. In the recent past, SERS and electrochemical (EC) sensors have been considered standard techniques in this regard. The EC-SERS characterization tool was expected to address the shortcomings of the two analytical techniques and strive to improve specific features by integration. It has gained rapid attention for qualitative sensing applications and has enabled notable advancements in the domains of advanced materials and life sciences. Integration of EC sensors with SERS may improve sensitivity by manipulating the target analyte adsorption on the SERS-substrate surface, substrate surface activation by oxidation/reduction cycles (ORC), and synthesis of SERS-active nanostructures or nanocomposites with various geometries.\n\nAn interesting method proposed by Ibáez et al. for the electrochemical activation of gold SPEs allows the detection of trace-level pesticides. The proposed sensing strategy involves preconcentration of the drop solution on the electrode surface for 15 min at 34 °C, followed by electrochemical activation with SERS-active nanostructures. The obtained SERS spectra showed prominent peaks at 1380 cm−1 for thiram and 1107 cm−1 for imidacloprid. These distinct bands enabled improved detection ability with an LoD of 2.4 mgL−1 thiram and 25 mgL−1 imidacloprid. Tap water samples were also analyzed and appropriate results were obtained to demonstrate the capabilities of the proposed method (Ibáñez et al., 2021). Another interesting SERS system, developed by Zhao et al., synthesized multilayered EC-SERS active substrates that can potentially increase the localized plasmonic field during SERS measurements. The authors used a controlled growth citrate reduction method to synthesize monodisperse Au/Ag nanoparticles. Further, these nanoparticles were multilayer-deposited on the carbon-based working electrode of commercially available screen-printed electrodes to obtain an EC-SERS active substrate (Au/Ag substrate). Multilayered Au/Ag substrates were used for the quantitative detection of uric acid in a 0.1 M NaF solution and synthetic urine. A good linear relationship was observed between the uric acid concentration and the EC-SERS signal intensity in the clinically relevant range (0.1-1.0 mM), and it can be employed in routine testing of early stage diagnosis of preeclampsia (L. Zhao et al., 2015). However, this method requires multiple depositions of monodisperse nanoparticles to fabricate the Au/Ag substrate, which may result in irregularly stacked SERS-active substrates.\n\nDespite the optimization of the geometry and properties of the SERS-active substrate, the adsorption of the analyte on the substrate surface is a significant factor for efficient SERS analysis. In an interesting method proposed by Zhu et al., a miniaturized spectroelectrochemical system was developed, which relies on the adsorption of the target analyte on the SERS active screen-printed electrode with a coin-sized chip and obtained the Raman spectra of aminoglutethimide (AGI) on a silver-sputtered electrode. The EC-SERS spectra of the AGI molecules revealed different adsorption modes on the substrate at different potentials. With an applied potential of -400 mV, the EC-SERS peak intensities of the aniline and glutarimide moieties were substantially improved, indicating a bidentate interaction between the AGI molecule and the substrate. The defined applied potential showed intense peaks at 1147 cm−1 (C-H/CH2 in-plane bending), 1302 cm−1 (CH2 wagging), and 1566 cm−1 (NH3+ rocking), while the 1147 cm−1 peak intensity was 30-fold higher than that of the standard SERS signal; therefore, it was considered for further experimentation. The developed system showed an LoD of 40 ng/mL and a linear detection range of 1 x 10−5 M to 2 x 10−7 M with a linear curve R2 of 0.98. (Z. Zhu et al., 2018). Another novel hybrid SERS system for assessing real-time interactions based on EC-SERS was demonstrated by Hernandez et al. in 2020. Time-resolved Raman spectroscopy was used for quantitative analysis using in situ-synthesized EC-SERS substrates. This detection technique used a sample volume of 50𝜇l and provided direct quantification results within 50 seconds, for nicotinamide detection in complex samples. This strategy possesses the benefit of examining the analyte-substrate interaction during the complex formation, thereby assisting in optimizing the conditions for the target analyte detection, and producing well-defined and repeatable Raman spectra. Selective detection of nicotinamide from a multivitamin complex, yielded impressive results (R2 = 0.99; %RSD < 9%) (Hernandez et al., 2020). Therefore, the development of Hybrid-SERS systems can open new avenues for improved, rapid and robust sensing. These integrated systems may essentially combine their specific benefits and aid in detection of trace analytes. However, these systems are limited with challenges such as reproducibility and electrode fouling. Future advancements, in synthesis of new electrode materials that can aid in simultaneous signal amplification and development of integrated microfluidics for real-time monitoring can translate these systems for POU sensing.\n\n\n12. Portable SERS-based sensory systems\n\nPortable SERS-based systems are essential for on-site detection of whole cells, biomolecules, pharmaceuticals, and trace chemicals. Their portable and compact design enables rapid, efficient, sensitive, and selective on-site sensing, in the domains of food quality control, environmental monitoring, and biomedical diagnostics. SERS-based sensing of small or large molecules has evolved significantly over the past decades. Despite these advancements, the sensing of any analyte by Raman spectroscopy requires extensive resources and trained personnel for use on a commercial scale. Therefore, the portability, user friendliness, and robustness of the developed sensor are of great concern. In a study by Gao. F et al. developed and tested a custom handheld SERS-based sensor for the sensing of Sudan I in paprika extracts. The developed biosensor combines thin-layer chromatography (TLC), molecularly imprinted polymers (MIPs), and SERS using a Sudan I template on methacrylic acid monomers. This portable custom-made SERS spectrometer was equipped with a backscattering probe for the collection of Raman spectra. The light source used was a 785 nm laser diode with 100-mW laser power and holographic grating for efficient light dispersion. Figure 28. (i) depicts a schematic representation of the custom-made portable SERS system for Sudan I detection in the spectral range of 350-1650 cm−1 (F. Gao et al., 2015). Another study by Leiber et al. developed a portable SERS system for dermatological applications. The developed SERS system was equipped with NIR-optimized objective lens with < 0.1μm resolution, a 100 μm-core fiber optic probe connected to 825 nm laser diode, and diffracting grating for light dispersion. All dermatological tests were optimized with respect to the cellophane Raman spectra intensities. Prior to testing the dermatological samples, the Raman spectra of acetamidophenol were measured and showed significant equivalence with a benchtop Raman microspectrometer with similar instrumentation (Lieber & Mahadevan-Jansen, 2007). In another study by Kim et al., a custom-built SERS system was developed for melamine detection in filtered milk samples. Gold nanofinger chips were fabricated by nanoimprint lithography (NIL) on a Si wafer and further diced to 5 mm × 5 mm chips, which were used as SERS substrates. The developed SERS system was equipped with a 785 nm laser diode for a specific illumination of 100 μm area on the developed SERS substrate and nitrogen-cooled CCD detector. Figure 28. (ii) (A) shows the size of the custom-built Raman reader with pentameric nanofinger substrate chips, and (B) illustrates the comparative Raman spectra of the custom-built Raman reader with an upright confocal Raman microspectrometer (A. Kim et al., 2012).\n\n(This figure has been reproduced with permission from (A. Kim et al., 2012), Copyright (2012) Analytical Chemistry).\n\n\n13. AI enabled SERS systems: A way forward\n\nThe integration of artificial intelligence (AI) with SERS-based sensing systems is predominantly increasing because of the improved accuracy of analyte(s) detection from a SERS spectrum or for specific detection from complex specimens. Machine learning (ML) uses algorithms for data analysis, pattern identification, and forecast of outcomes (Y. Liu et al., 1993). However, these AI and ML algorithms are extensively used in data interpretation and process optimization in complex experimental processes, design of SERS-active substrate and its fabrication for signal enhancement (Banaei et al., 2019; Nguyen et al., 2020). The assimilation of computational processing with experimental data can signify the optimal morphology of the nanostructures for the improvement of Raman signals.\n\nClassification of SERS spectral data is possible with supervised learning algorithms, such as support vector machines (SVM) (Widjaja et al., 2008), random forests (RF) (Ham et al., 2005), and neural networks (Sigurdsson et al., 2004) for real-time analyte detection from complex specimens. In addition, data classification and neural networks, such as convolutional neural networks (CNNs) and recurrent neural networks (RNNs), can also learn the classification of hierarchical patterns from the spectra (Acquarelli et al., 2017) and temporal classifications from sequential data, (Boydston-White et al., 2006) which is crucial for real-time analysis. Typically, spectral patterns are identified with clustered algorithms, such as K-means for data partitioning (Lopez-Reyes et al., 2014), mean shift for shifting the data points to the nearest peak, and Gaussian mixture models (GMM) that estimate the distribution parameters to allocate data points to the clusters (Hsu et al., 2012). Additionally, pattern identification and clustered algorithms, such as k-means clustering and hierarchical clustering, are utilized in anomaly detection (Chawla & Gionis, 2013), along with spectral grouping and visualization as dendrograms (Sander et al., 2003). Quantitative analysis of the target analyte concentration in a sample is predicted using an artificial neural network (ANN) (Lopez-Reyes et al., 2014) and partial least square regression (PLSR) (Kachrimanis et al., 2007). Feature extraction and selection from multidimensional data are detected using principal component analysis (PCA) (Kuncheva & Faithfull, 2014) and autoencoders (Pyo et al., 2020) for low-dimensionality representation. Experimental parameters, such as the laser wavelength, laser power, and morphology of the substrate, can be optimized using genetic algorithms (Hennessy & Kelley, 2004). Furthermore, the robustness and reproducibility of the system may be optimized for improved efficiency under varying conditions by quantification of uncertainty with probabilistic modelling using Bayesian inference. (Han & Ram, 2020; S. Li et al., 2011).\n\nThe integration of AI with SERS may simplify the design of SERS systems and make them relevant for point-of-use. ML algorithms can conduct automatic spectral analyses, enabling precise analyte identification. These are promising avenues of research for advancements in analytical chemistry and design of portable systems.\n\n\n14. Conclusion\n\nThis article provides a comprehensive overview of recent advances in the design of SERS substrates and their applications in sensing, medical diagnostics, food quality control domains, and environmental monitoring with its characteristic fingerprinting ability. A notable development in the use of commercial-grade disposable materials for point-of-use SERS-based systems offers a quick, sensitive, and affordable real-time analysis. Disposable substrates assist in single-use applications as they are made of inexpensive materials, such as paper or polymers, and potentially surpass the need for elaborate cleaning protocols. These disposable materials can assist in the development of POU sensing devices that require robust equipment design, compactness, user-friendly operation, and minimal sample processing. Tailoring the substrate’s surface by customizing the physical properties, generating regularly ordered periodicity and surface hydrophobicity, or chemical properties by coating, doping, or embedding the surfaces with plasmonic nanoparticles provides improved sensitivity and selectivity, thereby ensuring efficient target analyte detection. Analyte capture and specificity are improved by surface functionalization, and scalable production is made possible using techniques such as inkjet printing. The integration of microfluidic channels and sample preconcentration may further improve the analytical performance. In summary, disposable material-based plasmonic substrates used for POU SERS-based sensing represent a viable method for quick, accurate, and useful analyses in a variety of biological, environmental, and security applications. Further investigation and advancement will augment the comprehensibility and expand the applicability of this technology across several domains.\n\n\nEthical approval and consent\n\nEthical approval and consent were not required.", "appendix": "Data availability\n\nNo data are associated with this article.\n\n\nReferences\n\nAbidin U, Daud NASM, Le Brun V: Replication and leakage test of polydimethylsiloxane (PDMS) microfluidics channel.2019; 020064. Publisher Full Text\n\nAcquarelli J, van Laarhoven T , Gerretzen J, et al.: Convolutional neural networks for vibrational spectroscopic data analysis. Anal. Chim. Acta. 2017; 954: 22–31. PubMed Abstract \| Publisher Full Text\n\nAgarwal NR, Lucotti A, Tommasini M, et al.: SERS detection and DFT calculation of 2-naphthalene thiol adsorbed on Ag and Au probes. Sensors Actuators B Chem. 2016; 237: 545–555. 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PubMed Abstract \| Publisher Full Text\n\nZhong F, Wu Z, Guo J, et al.: Porous Silicon Photonic Crystals Coated with Ag Nanoparticles as Efficient Substrates for Detecting Trace Explosives Using SERS. Nanomaterials. 2018; 8(11): 872. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZhou L, Poggesi S, Casari Bariani G, et al.: Robust SERS Platforms Based on Annealed Gold Nanostructures Formed on Ultrafine Glass Substrates for Various (Bio)Applications. Biosensors. 2019; 9(2): 53. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZhou Y, Chen J, Zhang L, et al.: Multifunctional TiO2-Coated Ag Nanowire Arrays as Recyclable SERS Substrates for the Detection of Organic Pollutants. Eur. J. Inorg. Chem. 2012; 2012(19): 3176–3182. Publisher Full Text\n\nZhu Y, Wu L, Yan H, et al.: Enzyme induced molecularly imprinted polymer on SERS substrate for ultrasensitive detection of patulin. Anal. Chim. Acta. 2020; 1101: 111–119. PubMed Abstract \| Publisher Full Text\n\nZhu Z, Espulgar WV, Yoshikawa H, et al.: Electrochemically Modulated Surface-Enhanced Raman Spectra of Aminoglutethimide (AGI) on a Ag-Sputtered Electrode. Bull. Chem. Soc. Jpn. 2018; 91(11): 1579–1585. Publisher Full Text\n\nZong C, Xu M, Xu L-J, et al.: Surface-Enhanced Raman Spectroscopy for Bioanalysis: Reliability and Challenges. Chem. Rev. 2018; 118(10): 4946–4980. PubMed Abstract \| Publisher Full Text" }	[ { "id": "295700", "date": "16 Aug 2024", "name": "Nabadweep Chamuah", "expertise": [ "Reviewer Expertise SERS", "Bio sensing", "Smartphone Based sensing", "Optical Sensing." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe article entitled “Recent advances in the design of SERS substrates and sensing systems for (bio)sensing applications: Systems from single cell to single molecule detection” by Sai et.al provides a comprehensive overview of recent advances in Surface-Enhanced Raman Spectroscopy (SERS) substrates and sensing systems, highlighting their applications in biosensing. It effectively summarizes the mechanisms of SERS, the design of substrates, and their applications in detecting single cells and molecules. Few noticeable strength of the article are- 1. The article covers a wide range of topics related to SERS, including the historical background, mechanisms, and recent advancements in substrate design and applications. This provides readers with a broad understanding of the field. 2. It includes detailed discussions on the mechanisms of Raman scattering and the factors influencing SERS enhancement, which are crucial for readers seeking an in-depth technical understanding. 3. The paper highlights recent advancements and research trends in SERS, particularly in the design of substrates and the use of SERS in biosensing applications.\nHowever, there are several areas where the article can be improved in terms of clarity, depth, and critical analysis. The authors can consider the following points to improve the impact of the article.\n\nThe abstract should be more focused, clearly stating the main objectives, findings, and implications of the article. It currently reads more like an introduction and could benefit from summarizing key results or conclusions. The sentence “Plasmonic nanoparticles, called hotspots, exhibit localized surface plasmon resonance (LSPR).” Is somewhat confusing and can be rephrased as Plasmonic nanoparticles exhibit localized surface plasmon resonance (LSPR), and when they are closely spaced, they create 'hotspots' where the electromagnetic field is significantly enhanced. The EF of SERS has been reported up to 1014. Authors can follow this article for more detail. https://doi.org/10.1038/s41598-018-36491-0 While the introduction provides historical context, it could be more focused on framing the current challenges and the specific advancements the article will discuss. A clearer statement of purpose and scope would help guide the reader. The article primarily summarizes existing research but shows insufficient critical analysis or evaluation of the studies discussed. Including a discussion on the limitations or challenges associated with current SERS substrates and sensing systems would provide a more balanced view. Discussing the potential pitfalls or limitations of SERS, such as reproducibility issues or limitations in real-world applications, would add depth to the analysis.\n\nThe discussion on SERS mechanisms could be expanded to include more detailed explanations of the electromagnetic and chemical enhancement processes and their implications for substrate design.\n\nWhile the article mentions various substrate designs, it could delve deeper into the specific materials and nanostructures used, as well as their advantages and limitations.\n\nThe section 5.1 need to restructure and should be supported by proper references.\n\nThe table I, II and IV should be supported by proper references. Change the heading of figure IV considering plasmonic nanostructures are not hotspot.\n\nIn “One of the widely accepted theories for CE is the charge transfer (CT) mechanism proposed by the SERS pioneer Andreas Otto, where the molecule is chemically adsorbed on the substrate, which subsequently changes the molecular polarizability, thereby enhancing the Raman spectrum Check if it is Raman spectrum or Raman scattering.\n\nIn the discussion of paper substrate the authors can also include following papers\n\nhttps://doi.org/10.1016/j.saa.2023.122610, DOI 10.1088/1361-6463/aa8fef\n\nConsider rephrasing of following sentences for better readability-\n\nTable I 5th row- They don't fluoresce, but poor Raman scattering efficiency as compared to visible range lasers. Section 3.3 last paragraph- The cooling of the photodetector in a Raman system reduces the dark noise, which can be attributed to the dark current These dark currents influence the photodetector temperature, which requires intermediate cooling. Cooling the photodetector also aids in reducing background noise and improving the SNR of the sensing system. Section 10 last paragraph- Thus, the measured Raman spectra should be free of trace impurities to avoid the background signal and provide a Raman signal.\n\nThe article should conclude with a discussion on future research directions and emerging trends in SERS. Identifying areas where further research is needed would provide valuable insights for researchers in the field.\n\nWhile the article offers a solid overview of recent advances in SERS substrates and sensing systems, it would benefit from greater focus, critical analysis, and depth in discussing specific advancements and challenges. Enhancing the clarity, organization, and critical evaluation of the content will strengthen the article's impact and usefulness to researchers and practitioners in the field.\n\nIs the topic of the review discussed comprehensively in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? Partly\n\nIs the review written in accessible language? Yes\n\nAre the conclusions drawn appropriate in the context of the current research literature? Partly", "responses": [] }, { "id": "300697", "date": "21 Aug 2024", "name": "Debasmita Mondal", "expertise": [ "Reviewer Expertise Biosensors" ], "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 article \"Recent advances in the design of SERS substrates and sensing systems for (bio)sensing applications: Systems from single cell to single molecule detection\" by Tadi et al. provides an extensive review of the surface enhanced raman spectroscopy technique and its application in the area of biosensing. The manuscript is well written and comprehensively discusses SERS starting from the basics of the mechanism, its applications and sensing substrates to the gradual advancements in the field, finally the current trends. This review article provides a broad overview and understanding of SERS for readers seeking general overview as well as in-depth understanding of the topic.\nSome minor points which can improve the readability of the paper are: 1. Some of the variables are not defined before use; such as λS, λL, ES, EL etc. in page 3 of the manuscript. 2. Resolution of Figure 1 is not good. 3. et al. should always be in italics.\n\nIs the topic of the review discussed comprehensively in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nIs the review written in accessible language? Yes\n\nAre the conclusions drawn appropriate in the context of the current research literature? Yes", "responses": [] } ]	1	https://f1000research.com/articles/13-670
https://f1000research.com/articles/12-1507/v1	27 Nov 23	{ "type": "Research Article", "title": "The association between climate variables and tuberculosis in Kolaka District, Southeast Sulawesi Province, Indonesia, 2013–2020: a Bayesian autoregressive model", "authors": [ "Ramadhan Tosepu", "Asrul Sani", "Devi Savitri Effendy", "La Ode Ali Imran Ahmad", "Asrul Sani", "Devi Savitri Effendy", "La Ode Ali Imran Ahmad" ], "abstract": "Background Tuberculosis is one of the diseases that requires comprehensive treatment. This disease is highly contagious and can be transmitted through the air. Climate factors play a role in the increasing cases of tuberculosis. This study aimed to determine the correlation between climatic variables and TB in Kolaka District, Southeast Sulawesi Province, Indonesia,\n\nMethods This research was modeled using an autoregressive (AR) Bayesian model with three possible likelihoods; Gaussian, Poisson and Negative Binomial responses.\n\nResults Minimum temperature, a coefficient of 4.234 suggests that for every 1 degree increase in minimum temperature, there is an estimated increase of approximately four cases, assuming other variables remain constant. Maximum temperature, a coefficient of 17.851 suggests that for every 1 degree increase in maximum temperature, there is an estimated increase of around 17-18 cases, assuming other variables remain constant. Average temperature, a coefficient of 4.234 suggests that for every 1 degree increase in average temperature, there is an estimated increase of approximately four cases, assuming other variables remain constant. Humidity, a coefficient of -13.413 suggests that for every 1% increase in humidity, there is an estimated decrease of around 13 cases, assuming other variables remain constant. Rainfall, a coefficient of -0.327 suggests that for every 1 mm increase in rainfall, there is an estimated decrease of around 0.327 cases, assuming other variables remain constant. Light, a coefficient of -4.322 suggests that for every 1-hour increase in light duration, there is an estimated decrease of around four cases, assuming other variables remain constant.\n\nConclusions Climate change has a significant impact on tuberculosis through temperature-related factors. These factors influence the prevalence, spread, and vulnerability to TB. Addressing these challenges requires a holistic approach involving adaptation planning. Strong public health systems and healthcare infrastructure can help mitigate the risks and impacts of climate change-related tuberculosis.", "keywords": [ "Tuberculosis", "Humidity", "Temperature", "Rainfall", "Light", "Indonesia" ], "content": "Introduction\n\nTuberculosis is an infectious disease caused by the bacterium Mycobacterium tuberculosis (MTB).1 This disease primarily affects the respiratory system, particularly the lungs, but it can also attack other organs in the body.2,3 TB has become one of the deadliest diseases in the world, with millions of people infected and thousands of deaths occurring annually. Globally, there are 6.4 million cases of tuberculosis, which accounts for 64% of tuberculosis incidents. tuberculosis still remains among the top 10 causes of death worldwide, with an estimated 1.3 million tuberculosis related deaths globally.4 In Indonesia, TB still remains one of the diseases with the highest number of cases, requiring continued attention from the government.\n\nAccording to the Global Tuberculosis Report 2017, it is estimated that there were 1.020.000 tuberculosis cases in Indonesia, ranking second in the world for the highest number of TB cases after India. The number of new tuberculosis cases recorded in Indonesia in 2017 was 420.994.5 According to the Tuberculosis Data and Information Center of the Ministry of Health of the Republic of Indonesia in 2017, the indicators used for evaluating and monitoring the success of tuberculosis control efforts are the detection of new tuberculosis cases (case detection rate (CDR)) and the treatment success rate. These indicators serve as important measures to assess the progress and effectiveness of tuberculosis management in Indonesia.\n\nThe tuberculosis cases in Indonesia are generally high and rapidly growing among individuals aged 15 years and above, people living in poverty, those with low educational levels, and socioeconomically disadvantaged communities. West Java is the province that contributes the highest number of cases in Indonesia, with the majority occurring among individuals aged 15 years and above.6 Climate change has become an increasingly urgent global issue in the past few decades.7 In recent years, the impact of climate change on human health has been a major concern for scientists and health experts worldwide.8 One significant aspect of health that is significantly affected by climate change is the spread of infectious diseases, including TB.9,10\n\nClimate change and the spread of TB involve various complex factors.11 One key factor is the changes in temperature and rainfall patterns that can affect the environment where TB bacteria can survive and multiply.12 Increased average temperatures in certain regions can lead to changes in the ecology of vectors that act as disease carriers.13–15 Additionally, changes in rainfall patterns can affect the availability of clean water, which is crucial for ensuring adequate cleanliness and sanitation, both of which are important factors in TB prevention.16,17\n\nIn Brazil, it has been found that tuberculosis cases are more frequent under the following conditions: ultraviolet radiation (UVR) above 17 MJ/m2 (67.8%; p ≤ 0.001); relative humidity between 31.0% and 69.0% (95.8%; p ≤ 0.001); rainfall less than 1 mm (71.7%; p ≤ 0.001); daily sun exposure for 12 hours (40.6%; p = 0.001); and temperatures between 20°C and 23°C (72.4%; p ≤ 0.001).18 It has been found that extremely high temperatures have a positive effect on the reported morbidity of pulmonary tuberculosis in Binzhou (RR = 0.924, 95% CI: 0.856–0.997) and Weihai (RR = 0.910, 95% CI: 0.843–0.982).19 In Hong Kong, it has also been found that lower average temperatures (<22.0°C) in the later months (>10 months) are associated with an increased risk of tuberculosis notifications. Specifically, the risk increases within the temperature range of 16.3 to 17.3°C at lag 13-15 months and reaches the highest risk at a temperature of 16.8°C at lag 14 months.20 According to Zhang et al. (2019) using a Geographically Weighted Regression (GWR) model, a positive correlation was found between TB incidence and annual average rainfall (AR), but a negative correlation was observed with other meteorological factors. Average relative humidity (ARH) also showed a negative correlation with TB incidence in all prefectures with a significance level of p < 0.05.21\n\nHumidity is indeed a climate factor that can potentially affect the spread of tuberculosis.22,23 Several studies have shown that high humidity can support the survival of MTB bacteria in the environment.24,25 High humidity can also influence the dispersal of respiratory droplets containing MTB bacteria.26,27 Under low humidity conditions, respiratory droplets can dry more quickly, and the bacteria-containing particles become lighter, enabling them to remain suspended in the air for longer periods.28,29 Therefore, low humidity can also increase the risk of tuberculosis transmission.\n\nIndeed, climate change can also have an impact on the overall human health system. Fluctuations in extreme temperatures, extreme weather events such as floods or droughts, and changes in seasonal patterns can cause social and economic instability, which in turn can affect the spread of TB. These factors can lead to human migration, food insecurity, reduced nutritional status, and vulnerability to infectious diseases, including TB.\n\n\nMethods\n\nAstronomically, Kolaka Regency is located along the equator section of the equator, extending from North to South between 3°36′ - 4°35′ South Latitude (SL) and extending from West to East between 120° 45′-121° 52′ East Longitude (EL). Based on its geographical position, the territorial boundaries of Kolaka Regency in the north is Kolaka Utara Regency, in the south is Bombana regency, in the east is Kolaka Timur Regency and in the west is Sulawesi Selatan Province in Teluk Bone.\n\nThis study utilized climate data and tuberculosis disease data. The climate data were obtained from the Meteorology and Geophysics Agency of Southeast Sulawesi Province, including temperature, minimum temperature, maximum temperature, humidity, rainfall, and light data from 2013 to 2020. The data are accessible on the DATA ONLINE - PUSAT DATABASE – BMKG website. Meanwhile, the tuberculosis data were obtained through reports from the Health Department of Kolaka District from 2013 to 2020. The data on tuberculosis disease originates from the health profile of Kolaka district. This data can be accessed openly through the Kolaka District website.\n\nThe association between meteorological factors and the number of TB cases was modeled using an autoregressive (AR) Bayesian model with three possible likelihoods; Gaussian, Poisson and Negative Binomial responses. Suppose yt denote the monthly/annual counts of TB in the District of Kolaka, t=1,2,…,8 representing the period of 2013-2020 and yt follows one of three response likelihoods;\n\nFor Gaussian distribution with mean α+ut;\n\nFor Poisson distribution;\n\nFor Negative Binomial (NB) distribution\n\nThe term ut represents meteorological covariates; i.e., minimum temperature, maximum temperature, average temperature, humidity, rainfall and light.\n\nThen, the temporal model is formulated as autoregressive order 1, which reads\n\nwhere α is an intercept, ρ is a temporal correlation term (with ρ<1) and εt is a Gaussian error term with zero mean and a fixed large precision τu so that the error term is close to zero.\n\nThe performance of all models on the TB data in the district of Kolaka, Southeast Sulawesi from 2013 to 2020, is summarized in Table 1.\n\nTable 1 shows that the performances of the autoregressive model with Poisson likelihood is much better, compared to those with Negative Binomial and Gaussian responses. This indicates that Poisson is suitable for analyzing tuberculosis data. Therefore, using Poisson autoregressive model, we determined the influence of meteorological factors on TB incidence in the district of Kolaka, Southeast Sulawesi from 2013 to 2020.\n\nThe study obtained ethical approval from the Research Ethics Committee of the Indonesian Public Health Association (IPHA) Southeast Sulawesi Province under approval number 134/KEPK-IAKMI/II/2023.\n\n\nResults\n\nTable 273 shows that the linear regression model conducted to test the correlation between climate factors and tuberculosis disease resulted in values above 0.05, indicating that there was no significant influence of each variable. Furthermore, a test using the Bayesian autoregressive model will be conducted to further investigate the relationship.\n\nTable 3 indicates that the minimum temperature, maximum temperature, and average temperature have positive values of one, which are quite high, indicating a positive association with TB cases. On the other hand, humidity, rainfall, and light have negative values, indicating a negative association with tuberculosis cases. Further analysis of the coefficient model revealed the following relationships: i) minimum temperature, a coefficient of 4.234 suggests that for every 1 degree increase in minimum temperature, there is an estimated increase of approximately four cases, assuming other variables remain constant. ii) Maximum temperature, a coefficient of 17.851 suggests that for every 1 degree increase in maximum temperature, there is an estimated increase of around 17-18 cases, assuming other variables remain constant. iii) Average temperature, a coefficient of 4.234 suggests that for every 1 degree increase in average temperature, there is an estimated increase of approximately four cases, assuming other variables remain constant. iv) Humidity, a coefficient of -13.413 suggests that for every 1% increase in humidity, there is an estimated decrease of around 13 cases, assuming other variables remain constant. v) Rainfall, a coefficient of -0.327 suggests that for every 1 mm increase in rainfall, there is an estimated decrease of around 0.327 cases, assuming other variables remain constant. vi) Light, a coefficient of -4.322 suggests that for every 1-hour increase in light duration, there is an estimated decrease of around four cases, assuming other variables remain constant.\n\n\nDiscussion\n\nIn recent decades, climate change has become a major global issue that has garnered significant attention. The wide-ranging impacts of climate change include increased global average temperatures, changes in rainfall patterns, increased drought occurrences, and heightened frequency and intensity of natural disasters.30–32 Furthermore, human health is also significantly affected by climate change, with tuberculosis being one of the diseases impacted.33,34 Our findings indicate that climate change is likely to affect individual vulnerability to tuberculosis by increasing the prevalence of underlying risk factors, particularly in developing countries.\n\nIndeed, climatic conditions are one of the factors that can influence the development of disease-causing microorganisms.18,35 Certain microorganisms, including bacteria, viruses, and fungi, can thrive or struggle depending on the environmental conditions they are exposed to. Temperature, humidity, precipitation, and other climatic factors can directly or indirectly affect the survival, growth, reproduction, and transmission of these microorganisms.36–38 For example, warm and humid environments may promote the proliferation of certain bacteria and fungi, while extreme temperatures or drought conditions may inhibit their growth. Understanding the relationship between climate and the development of pathogenic microorganisms is crucial for assessing and addressing public health risks.39 Climate change can lead to changes in ecosystems, altering the patterns of interaction between humans and the environment. These changes can have significant impacts on human health. For example, shifts in temperature and precipitation patterns can affect the distribution of disease vectors such as mosquitoes, ticks, and other carriers of infectious diseases. This can lead to the spread of vector-borne diseases like malaria, dengue fever, or Lyme disease into new regions or the prolongation of their transmission seasons.29,39–41\n\nAdditionally, changes in climate can impact water resources, food production, and availability of clean air, all of which are essential for maintaining good health.10,17 Extreme weather events, such as hurricanes, floods, or heatwaves, can cause injuries, displacement, and even loss of life. Moreover, these events can also lead to the contamination of water sources, the destruction of infrastructure, and the disruption of healthcare services.9,15,23\n\nClimate change can also contribute to the exacerbation of respiratory and cardiovascular diseases due to increased air pollution, the release of allergens, and the intensification of heatwaves. Moreover, it can have indirect effects on mental health and well-being, particularly among communities affected by climate-related disasters or forced migration.42,43 Population density can increase the risk of increased exposure for individuals suffering from pulmonary tuberculosis, which in turn facilitates the spread of the bacteria causing it.44,45 In addition to density factors, the occurrence of tuberculosis is also influenced by other risk factors such as high poverty levels, low coverage of healthy housing, and poor hygiene and health practices. Therefore, the high number of detected tuberculosis cases in a particular area may also be influenced by the characteristics of other variables.6,46\n\nMost bacteria and fungi are able to survive in air humidity reaching or exceeding 70%.47 In conditions where the monthly average air humidity in Kabupaten Serang ranges from 70% to 87%, bacteria and fungi can thrive in the outdoor environment. The presence of a negative relationship between air humidity and the number of new tuberculosis cases may suggest that indoor air humidity is not associated with the presence of TB-causing agents inside the home.48 This finding is supported by research conducted by Duffield and Young (1984), which demonstrated that pathogenic MTB bacteria can survive equally well in both damp and dry soil.49\n\nGlobal temperature increase can impact the ecology and geography of tuberculosis.18,50 The role of climate in tuberculosis spread cannot be seen as a single factor. Temperature can influence the transmission of tuberculosis. The MTB bacteria can survive in various temperatures. Both low and high temperatures can affect the survival of the bacteria outside the human body. In specific areas, low temperatures can create more favorable conditions for the bacteria to survive outside the human body and trigger an increased risk of transmission. Global climate change can affect the patterns of tuberculosis spread. Seasons and local climates can also influence the occurrence of tuberculosis. Several studies indicate a relationship between specific seasons and increased tuberculosis cases. Factors such as temperature, air humidity, and rainfall patterns can influence the transmission rate and severity of the disease. Warmer and more humid temperatures can increase the bacteria’s survival rate in the environment, thereby complicating the control of disease transmission.42,51–53\n\nThe research findings from the present study did not find any correlation between humidity and tuberculosis in Kolaka Regency. The influence of humidity on tuberculosis involves multiple factors. It should be noted that TB is a contagious disease most commonly transmitted through the air (via infected airborne droplets), and other factors such as direct contact with untreated patients with tuberculosis or a weakened immune system also play a significant role in its transmission.17,41,54\n\nHigh relative humidity in indoor environments can affect the transmission of tuberculosis. When the relative humidity is above 80%, the risk of contracting tuberculosis significantly increases. High humidity in indoor spaces can impact the spread of tuberculosis by prolonging the survival time of infected airborne droplets in the air, thus allowing for a longer duration of inhalation and transmission. However, other studies have found a correlation between humidity and tuberculosis. Low humidity, especially during the dry season, is associated with an increased risk of tuberculosis infection. This occurs because low humidity can affect the respiratory tract and make individuals more vulnerable to tuberculosis infection. While there is some evidence indicating a relationship between humidity and tuberculosis transmission, further research is still needed to fully understand the interaction between humidity and this disease.20,22,55–57\n\nIn this research, no correlation was found between rainfall and tuberculosis. However, during the period of 2013-2020, the presence of tuberculosis in Kolaka Regency tended to increase. Rainfall and tuberculosis are two different factors that can be related to each other. Rainfall refers to the amount of precipitation that falls in a specific period in a given area. High rainfall can create a humid environment. This humidity can affect the survival of MTB bacteria in the external environment. These bacteria are more resistant to moist conditions and can survive in airborne water droplets for a longer time. This means that in areas with high rainfall, these bacteria can remain active and easily spread through water droplets. Rainfall can also determine the amount of time hosts spend indoors, thus influencing the transmission of MTB within households.38\n\nIndeed, there are other factors that can contribute to the increase of tuberculosis. Areas with high rainfall tend to have a higher population density, and high population density can lead to poor environmental conditions.16,58 Poor environmental conditions, such as high density, lack of ventilation, and poor sanitation, can worsen the spread of tuberculosis. People living in areas with high rainfall may be forced to reside in unhealthy environments, such as overcrowded settlements in urban areas that lack adequate sanitation facilities, which can increase the risk of TB transmission. Poor economic conditions can result in unemployment, poverty, and diverted funds, reducing access to proper healthcare. Social and economic instability can also affect individuals’ ability to seek care, adhere to appropriate treatment, and isolate themselves when infected with tuberculosis.59–62\n\nFurthermore, in Kolaka Regency, no relationship was found between sunlight exposure and the occurrence of tuberculosis. Indirect sunlight exposure can influence TB cases by affecting the host’s condition. Areas with limited sunlight exposure have been reported to have a higher prevalence of vitamin D deficiency.63 Sunlight plays a crucial role in the production of vitamin D in the body. When the skin is exposed to sunlight, it synthesizes vitamin D, which is essential for maintaining healthy bones and overall health. Adequate sunlight exposure is necessary for the body to produce an optimal amount of vitamin D.64 Absolutely, vitamin D deficiency can indeed affect the antimicrobial peptide system, which is responsible for regulating the immune response in the human body.65,66 Vitamin D plays a crucial role in modulating the immune system and enhancing the function of antimicrobial peptides, which are essential for fighting against microbial infections.67,68 Insufficient levels of vitamin D can compromise the immune system’s ability to defend against pathogens, including MTB, the bacteria responsible for TB.69,70 Impaired host immunity due to vitamin D deficiency will support the development and reactivation of TB disease.71\n\nIn addition, sunlight exposure can also affect the life cycle of TB-causing agents. MTB can survive in the environment for more than 74 days if protected from light.49 MTB in sputum will die within a short period of time when exposed to sunlight, up to seven hours.18 Therefore, access to sunlight inside buildings is crucial to prevent the formation of conducive environments for MTB within the house.\n\nChanges in rainfall patterns and temperature can impact the life cycle of MTB bacteria and the transmission vectors of this disease.53 High humidity and abundant rainfall can create ideal environmental conditions for the bacteria to survive and proliferate.52 Climate change can affect population migration, whether caused by natural disasters or socioeconomic changes.51 Migration can lead to the spread of TB to areas previously free from the disease. Migration can also disrupt access to adequate healthcare, worsen the health conditions of individuals infected with TB, and increase the risk of transmission.37,72\n\nTo control the spread of tuberculosis, especially in high-risk areas, it is important to follow recommended preventive measures such as early treatment for patients with tuberculosis, ensuring good ventilation in rooms, maintaining personal and environmental hygiene, and promoting awareness about the importance of respiratory hygiene and healthy living practices. Research has limitations, as factors like population density, ventilation quality, direct exposure to untreated tuberculosis patients, and individual immune status also play significant roles in the spread of the disease. Therefore, future studies should consider examining these factors in order to gain a comprehensive understanding.\n\n\nConclusions\n\nClimate change has a significant impact on tuberculosis through temperature-related factors. These factors influence the prevalence, spread, and vulnerability to tuberculosis. Addressing these challenges requires a holistic approach involving adaptation planning. Strong public health systems and healthcare infrastructure can help mitigate the risks and impacts of climate change-related tuberculosis. Prevention efforts, early diagnosis, and effective treatment are crucial in controlling the spread of this disease. In the context of climate change, efforts to enhance capacity and resources are needed to address emerging challenges.", "appendix": "Data availability\n\nFigshare: Climate and Tuberculosis data.xlsx. https://doi.org/10.6084/m9.figshare.24329518.v1. 73\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nWorld Health Organization: WHO consolidated guidelines on tuberculosis: tuberculosis preventive treatment. 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Epidemiol. Sep 2019; 37: 71–76. PubMed Abstract \| Publisher Full Text\n\nPaz S: Climate change impacts on West Nile virus transmission in a global context. Philos. Trans. R. Soc. Lond. B Biol. Sci. 2015; 370(1665): 20130561. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNerlich AG, Lösch S: Paleopathology of human tuberculosis and the potential role of climate. Interdiscip. Perspect. Infect. Dis. 2009; 2009: 1–9. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBarasona JA, Vicente J, Díez-Delgado I, et al.: Environmental presence of Mycobacterium tuberculosis complex in aggregation points at the wildlife/livestock interface. Transbound. Emerg. Dis. 2017; 64(4): 1148–1158. PubMed Abstract \| Publisher Full Text\n\nTao B, Li Z, Wang Y, et al.: Environment pollutants exposure affects the endogenous activation of within-host Mycobacterium tuberculosis. Environ. Res. 2023; 227: 115695. PubMed Abstract \| Publisher Full Text\n\nKim K-H, Kabir E, Jahan SA: Airborne bioaerosols and their impact on human health. J. Environ. Sci. 2018; 67: 23–35. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFagade OE, Ogunjobi AA, Abiala MA, et al.: Fate and transport of microorganisms in the air. Aeromicrobiology. Elsevier; 2023; pp. 39–58.\n\nDing E, Zhang D, Bluyssen PM: Ventilation regimes of school classrooms against airborne transmission of infectious respiratory droplets: A review. Build. Environ. 2022; 207: 108484. Publisher Full Text\n\nAmaliah L, Rufaedah AA, Nurcahyati S, et al.: The relationship between the physical home environment and the event of tuberculosis. World J. Adv. Res. Rev. 2022; 14(3): 623–628. Publisher Full Text\n\nGezie M: Farmer’s response to climate change and variability in Ethiopia: A review. Cogent Food Agric. 2019; 5(1): 1613770. Publisher Full Text\n\nKalkstein AJ: Defining climate change: What to expect in a warmer world. The environment-conflict nexus: Climate change and the emergent national security landscape. 2019; pp. 47–57. Publisher Full Text\n\nRaihan A: A review of the global climate change impacts, adaptation strategies, and mitigation options in the socio-economic and environmental sectors. J. Environ. Sci. Econ. 2023; 2(3): 36–58. Publisher Full Text\n\nXi Y, Zhang W, Qiao R-J, et al.: Risk factors for multidrug-resistant tuberculosis: A worldwide systematic review and meta-analysis. PLoS One. 2022; 17(6): e0270003. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSilva ML, Cá B, Osório NS, et al.: Tuberculosis caused by Mycobacterium africanum: Knowns and unknowns. PLoS Pathog. 2022; 18(5): e1010490. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nFederici L, Masulli M, De Laurenzi V, et al.: An overview of bats microbiota and its implication in transmissible diseases. Front. Microbiol. 2022; 13: 1012189. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGollakota AR, Gautam S, Santosh M, et al.: Bioaerosols: characterization, pathways, sampling strategies, and challenges to geo-environment and health. Gondwana Res. 2021; 99: 178–203. Publisher Full Text\n\nMarrone R: Neglected Tropical Diseases and migrants: a global health challenge amid access barriers and lack of gold standard diagnostics.2023.\n\nNaranbat N, Nymadawa P, Schopfer K, et al.: Seasonality of tuberculosis in an Eastern-Asian country with an extreme continental climate. Eur. Respir. J. Oct 2009; 34(4): 921–925. PubMed Abstract \| Publisher Full Text\n\nBultó PLO, Rodríguez AP, Valencia AR, et al.: Assessment of human health vulnerability to climate variability and change in Cuba. Environ. Health Perspect. 2006; 114(12): 1942–1949. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTupasi T, Radhakrishna S, Co V, et al.: Bacillary disease and health seeking behavior among Filipinos with symptoms of tuberculosis: implications for control. Int. J. Tuberc. Lung Dis. 2000; 4(12): 1126–1132. PubMed Abstract\n\nVilleneuve M, Kawai M, Kanashima H, et al.: Temperature dependence of the Langmuir monolayer packing of mycolic acids from Mycobacterium tuberculosis. Biochim. Biophys. Acta 2005; 1715(2): 71–80. PubMed Abstract \| Publisher Full Text\n\nRajput P, Singh S, Singh TB, et al.: The nexus between climate change and public health: a global overview with perspectives for Indian cities. Arab. J. Geosci. 2023; 16(1): 15. Publisher Full Text\n\nHoppe BO, Prussia L, Manning C, et al.: “It’s Hard to Give Hope Sometimes”: Climate Change, Mental Health, and the Challenges for Mental Health Professionals. Ecopsychology. 2023; 15(1): 13–25. Publisher Full Text\n\nRamsey D, Spencer N, Caley P, et al.: The effects of reducing population density on contact rates between brushtail possums: implications for transmission of bovine tuberculosis. J. Appl. Ecol. 2002; 39: 806–818. Publisher Full Text\n\nAndini NLE, Oktora SI: Determinants of Multidrug-Resistant Pulmonary Tuberculosis in Indonesia: A Spatial Analysis Perspective. Jurnal Varian. 2022; 6(1): 35–48. Publisher Full Text\n\nHarling G, Castro MC: A spatial analysis of social and economic determinants of tuberculosis in Brazil. Health Place. 2014; 25: 56–67. PubMed Abstract \| Publisher Full Text\n\nWorld Health Organization: Mental health and psychosocial considerations during the COVID-19 outbreak, 18 March 2020. World Health Organization; 2020.\n\nAzhari AR, Kusumayati A, Hermawati E: Studi Faktor Iklim dan Kasus TB Di Kabupaten Serang, Provinsi Banten. HIGEIA (Journal of Public Health Research and Development). 2022; 6(1).\n\nDuffield B, Young D: Survival of Mycobacterium bovis in defined environmental conditions. Vet. Microbiol. 1985; 10(2): 193–197. PubMed Abstract \| Publisher Full Text\n\nLi H, Ge M, Zhang M: Spatio-temporal distribution of tuberculosis and the effects of geographical environmental factors in China.2021.\n\nBayram H, Rice MB, Abdalati W, et al.: Impact of Global Climate Change on Pulmonary Health: Susceptible and Vulnerable Populations. Ann. Am. Thorac. Soc. 2023; 20, 1088–1095. PubMed Abstract \| Publisher Full Text\n\nYadav N, Upadhyay RK: Global Effect of Climate Change on Seasonal Cycles, Vector Population and Rising Challenges of Communicable Diseases: A Review. J. Atmos. Sci. Res. 2023; 6(01). Publisher Full Text\n\nEl Houzaly S, Gupta R: Effects of Climate Change on Human Health.2023.\n\nCraig GM, Joly LM, Zumla A: ‘Complex’ but coping: experience of symptoms of tuberculosis and health care seeking behaviours-a qualitative interview study of urban risk groups, London, UK. BMC Public Health. 2014; 14(1): 1–9. Publisher Full Text\n\nPratiwi RD, Pramono D: Socio-economic and environmental risk factors of tuberculosis in wonosobo, central Java, Indonesia.2020.\n\nAzzahrain AS, Afifah AN, Yamani LN: Detection of Tuberculosis in Toddlers and its Risk Factor at East Perak Health Center Surabaya. J. Environ. Health. 2023; 15(2): 92–98. Publisher Full Text\n\nBethan BA: A Study of Epidemiological Surveillance System for Pulmonary Tuberculosis at the Public Health Center Bombana Regency. Miracle J. Public Health. 2022; 5(1): 11–19. Publisher Full Text\n\nRen H, Lu W, Li X, et al.: Specific urban units identified in tuberculosis epidemic using a geographical detector in Guangzhou, China. Infect. Dis. Poverty. 2022; 11(1): 1–12. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMayasari E, Risnasari D, Chei NE: Analysis of Pulmonary Tuberculosis based on Home Sanitation in Sembung Hamlet, Margopatut East Java. STRADA Jurnal Ilmiah Kesehatan. 2022; 11(1): 78–83. Publisher Full Text\n\nSyamsuddin S, Ahmad H, Sahani W, et al.: The Relationship between Housing Condition and Pulmonary Tuberculosis Disease in Baraya Village Bontoala Makassar, Indonesia. Indian J. Forensic Med. Toxicol. 2020; 14(4).\n\nFariza A, Puspitasari A: Spatial Fuzzy Risk Mapping for Tuberculosis in Surabaya, Indonesia. Paper presented at: 2020 International Electronics Symposium (IES). 2020.\n\nDani A, Suswani A: Physical environment factors with events of home lung tuberculosis in public health Bonto Bahari. Comprehensive Health Care. 2020; 4(3): 116–129. Publisher Full Text\n\nTamara L, Kartasasmita CB, Alam A, et al.: Effects of Vitamin D supplementation on resolution of fever and cough in children with pulmonary tuberculosis: A randomized double-blind controlled trial in Indonesia. J. Glob. Health. 2022; 12: 12. Publisher Full Text\n\nBuonsenso D, Pata D, Colonna AT, et al.: Vitamin D and tuberculosis in children: a role in the prevention or treatment of the disease? Monaldi Arch. Chest Dis. 2022; 92(4). Publisher Full Text\n\nTha STM, Rasheed S, Mukhtar A, et al.: Vitamin D Deficiency in Children with Tuberculosis: A Cross Sectional Study. Pakistan J. Medical Health Sci. 2022; 16(09): 604–604, 606. Publisher Full Text\n\nTamara L, Bakhtiar B, Alam A, et al.: Lower vitamin D level is associated with higher prevalence of pulmonary tuberculosis in under-five children actively living in tropical countries. F1000Res. 2022; 11(445): 445. Publisher Full Text\n\nHamza FN, Daher S, Fakhoury HM, et al.: Immunomodulatory Properties of Vitamin D in the Intestinal and Respiratory Systems. Nutrients. 2023; 15(7): 1696. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMehta K, Sharma P, Mujawar S, et al.: Role of Antimicrobial Peptides in Treatment and Prevention of Mycobacterium Tuberculosis: A Review. Int. J. Pept. Res. Ther. 2022; 28(5): 132. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMeirina F, Sari DK, Lubis IN, et al.: Correlation Between Vitamin D Levels on Pregnant Women With Latent Tuberculosis Infection and Vitamin D Levels, Cathelicidin, Interferon γ, and Tlr2 Expression on Neonates in Medan, North Sumatera, Indonesia.2023.\n\nAl-Jaberi FA, Crone CG, Lindenstrøm T, et al.: Reduced vitamin D-induced cathelicidin production and killing of Mycobacterium tuberculosis in macrophages from a patient with a non-functional vitamin D receptor: A case report. Front. Immunol. 2022; 13: 6678.\n\nDlozi PN, Gladchuk A, Crutchley RD, et al.: Cathelicidins and defensins antimicrobial host defense peptides in the treatment of TB and HIV: Pharmacogenomic and nanomedicine approaches towards improved therapeutic outcomes. Biomed. Pharmacother. 2022; 151: 113189. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWorld Health Organization: WHO information note on ensuring continuity of essential tuberculosis services for people with or at risk of the disease within Ukraine and in refugee-hosting countries.2022.\n\nTosepu R: Climate and Tuberculosis data.xlsx. [Dataset]. figshare. 2023. Publisher Full Text" }	[ { "id": "247572", "date": "05 Mar 2024", "name": "Chacha M. Issarow", "expertise": [ "Reviewer Expertise Bioinformatics and infectious diseases mathematical 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\nIn this paper, the authors explore the association between climate change and TB transmission using a Bayesian autoregressive model. The paper has some merits as it highlights environmental factors attributable to climatic change that are correlated to TB transmission. I assessed all sections of the paper and provided some recommendations as outline below. The paper can be approved if those issues can be addressed by the authors.\nIntroduction:\nThe authors mentioned that according to the Global Tuberculosis Report 2017, it is estimated that there were 1.020.000 tuberculosis cases in Indonesia, ranking second in the world for the highest number of TB cases after India, and that the number of new tuberculosis cases recorded in Indonesia in 2017 was 420.994. I understand that the paper explored TB transmission in 2013–2020, but I would suggest adding a citation of the recent report because the TB prevalence could be high or low. Otherwise, this section was well explained about how factors related to climate change contribute to TB transmission.\nMethods:\nMethodology is one of the key parts of the paper, and it should be clearly explained so that other researchers can adopt or populate it in their studies. I would suggest the authors further explain the parameter μt to clarify the difference between the Poisson distribution and the negative binomial distribution, and how they are different from the Gaussian distribution. Based on the model, it’s not clear how Table 1 was formed, and it would be worth it if it were clarified how those values were obtained and which data/value used to create the table. It would be good to see some more critical discussion of the limitations of the model, and what experimental data would be useful to improve the model.\nResults and abstract\nThe author postulated that “minimum temperature, a coefficient of 4.234 suggests that for every 1 degree increase in minimum temperature, there is an estimated increase of approximately four cases, assuming other variables remain constant,\" and \"average temperature, a coefficient of 4.234 suggests that for every 1 degree increase in average temperature, there is an estimated increase of approximately four cases, assuming other variables remain constant.\" These sentences sound like repetitions with the same value. I would suggest removing one of these sentences or connecting them (using minimum and average temperature) to one sentence to avoid repetition.\nDiscussion:\nThe authors mentioned that “additionally, changes in climate can impact water resources, food production, and the availability of clean air, all of which are essential for maintaining good health. Extreme weather events, such as hurricanes, floods, or heatwaves, can cause injuries, displacement, and even loss of life. Moreover, these events can also lead to the contamination of water sources, the destruction of infrastructure, and the disruption of healthcare services.” This paragraph has no direct link between climate change and TB. I would recommend removing this paragraph from the paper.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? No\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] } ]	1	https://f1000research.com/articles/12-1507
https://f1000research.com/articles/11-200/v1	16 Feb 22	{ "type": "Research Article", "title": "Spatio-temporal characteristics of Tuberculosis in Ghana", "authors": [ "Abdul-Karim Iddrisu", "Emmanuel A. Amikiya", "Francis Kwame Bukari", "Emmanuel A. Amikiya", "Francis Kwame Bukari" ], "abstract": "Background: The number of Tuberculosis (TB) cases or deaths is declining, however, the rate of decline is not adequate to meet the World Health Organization's (WHO's) mitigation. TB remains a public health problem in Ghana with a significant economic and health burden on its citizens and health care system. Consequently, there is a need for further studies about the disease aimed at accelerating the rate of decline in cases. Methods: The spatio-temporal characteristics of TB in Ghana using Bayesian spatial and spatio-temporal regression models was analysed in this study. Data were obtained from Ghana National Tuberculosis Programme (NTP) for the 10 regions of Ghana, collected over a six-year period. The study also examines some baseline predictors of TB infections to ascertain their effects on the TB risk across the ten regions in Ghana.\nResults: Hot-spots of TB cases are observed in the Upper East, Upper West, Volta, Western, and Central regions and low risk in the Northern, Ashanti, Greater Accra, Brong Ahafo, Eastern and Western regions. The results indicated a clustering of risk between neighboring regions. TB cure rate, TB success rate, knowledge about TB, awareness that TB is airborne, HIV prevalence, percentage of literacy, and high income are important predictors of detection for this disease across the ten regions of Ghana.\nConclusion: Most regions in Ghana have similar TB risks. A substantial reduction in TB cases requires measures that will increase detection, success and cure rates, awareness, knowledge about how this disease spreads as well adequate health facilities with easy access.", "keywords": [ "Bayesian spatial and space-time models", "Tuberculosis relative risk", "baseline predictors and TB hot-spots." ], "content": "Background\n\nGlobally, Tuberculosis (TB) is in the top ten causes of death in low-income countries (ranking above HIV/AIDS).1 This infectious disease is transmitted by bacillus Mycobacterium tuberculosis.2 TB occurs essentially in individuals with weakened immune systems than those with healthy immune systems. As HIV weakens the immune system, TB is often seen in individuals with HIV.3 Nevertheless, in 2019, approximately 10 million people tested positive for TB with an estimated 1.2 million HIV-negative deaths.2 Although this disease can affect both sexes, reports have shown that males (aged 15 years and above) accounted for 56% of the global infections compared to 32% for females in the same age group. Infections among children (aged 15 years and below) accounted for 12% of the total cases and about 8.2% of the reported cases were HIV-patients.2 Geographically, the 2020 reports have shown that the highest number of new TB cases occurred in the WHO South-East Asia (43%), followed by Africa Region (25%), and the WHO Western Pacific (18%), compared to Eastern Mediterranean (8.2%), America (2.9%) and Europe (2.5%).2,4 It has been estimated that 86% of new TB cases occurred in the 30 high TB burden countries,4 where eight countries including India, China, Indonesia, Philippines, Pakistan, Nigeria, Bangladesh and South Africa accounted for 2/3 of the new TB cases.\n\nAs such, in order to have faster reduction in TB incidents and deaths worldwide and especially in low-income countries, the World Health Organization (WHO) has called for the development of TB vaccines.2 Reports have shown that TB is preventable and can also be cured as well. Studies have reported that approximately 85% of those who develop TB disease can be treated successfully with a 6-month drug regimen.2 Available reports indicate that this treatment has prevented more than 60 millions deaths from 2000 to 2020.2 Despite this treatment, the global and in specific WHO regions and many high TB burden countries did not have a fast enough progression towards the 2020 milestone of The End TB Strategy. The global cumulative reduction was reported at 9% between 2015 and 2019, and about 2.3% between 2018 and 2019.2 However, more optimistically, Europe had achieved 19% reduction in cases and 31% reduction in deaths between 2015 and 2019. Africa had achieved a 16% reduction in cases and a 19% reduction in deaths between 2015 and 2020.2 As the WHO’s target for global decline of TB cases and deaths (2015-2020) were not achieved, there is still a need for further studies to be conducted on the dynamics of the disease and on mitigation measures for TB in Africa. Ghana as a developing country in Africa, has been affected by the respiratory disease and currently has challenges in eradicating TB. The country implemented policies called Directly Observe Therapy (DOT) and National Tuberculosis Programmes (NTPs) in 1994, to detect and treat TB.2,5–7 The implementation of the NTP led to 100% DOTs coverage in 2005 with more TB cases detected for treatment every year since. For instance, TB cases detected increased from 7,425 in 1996 to 15,286 in 2009.8,9\n\nAlthough TB cases and deaths have declined due to the implementation of mitigation/treatment strategies, TB still remains a life-threatening disease and poses a burden on health infrastructure in Ghana. Hence, TB has gained considerable attention as a topic of research among researchers from diverse backgrounds. Studies have investigated the dynamics of TB indicators as well as risk factors of this disease in Ghana6,7,10 Osei et al.6,7 studied trends of TB detection and treatment outcomes using the logistic regression to assess the relationship between patients and disease characteristics. Further, Osei et al.6,7 have studied TB detection, mortality and co-infection with HIV, using patients data collected in the Volta Region from 2012–2016. The authors used simple and multiple logistic regression to investigate determinants of TB mortality in 10 districts of the Volta Region of Ghana. Aryee et al.10 have studied the dynamics of TB using Autoregressive Moving Average (ARIMA) methods and TB data recorded by the Korle Bu Teaching Hospital from 2008–2017. Iddrisu et al.11 have studied the temporal and geographical pattern of TB prevalence in Ghana between 2015 and 2018.\n\nIn this paper, Bayesian hierarchical spatial and space-time models is used to study the relative risk (RR) of TB and associated risk factors across the 10 Regions of Ghana. Hence, the purpose of this study was to model the spatio-temporal risk pattern of TB in Ghana, using Bayesian hierarchical and space-time models discussed in previous literature.12–16\n\n\nMethods\n\nIn this study TB detection data obtained from Ghana Health Service and National Tuberculosis Programme was used.8 The data contained information on TB detection from 2009 to 2017, for the 10 old administrative regions of Ghana. These regions include, Ashanti, Brong Ahafo, Central, Eastern, Greater Accra, Northern, Upper East, Upper West, Volta, and Western.\n\nFigure 1 shows the TB trends in the 10 regions from 2008 to 2017. Generally, there is a decrease in TB cases observed in all regions (except Brong Ahafo Region where TB cases increase) of Ghana from 2008 to 2016. It can also be observed that TB cases in Northern and Upper East increased remarkably between 2016 and 2017, whereas cases in Ashanti Region decreased from 50 per 100, 000 population in 2016 to 45 per 100,000 population in 2017. In the Northern Region, TB cases increased from 24 per 100,000 population in 2016 to 52 per 100,000 population in 2017. Further, cases in Upper East Region increased from 53 per 100,000 population in 2016 to 63 per 100,000 population in 2017. However, the changes in TB cases in the other regions are almost horizontal.\n\nFigure 2 shows the trend of total number of TB cases for each region from 2008 to 2017. It shows that the highest cases recorded was in the Greater Accra Region from 2008 to 2017. It also shows that the lowest was recorded in the Northern Region. Volta and Western Regions are second and third, respectively, with records slightly lower than Greater Accra Region. In addition, Figure 3 shows the trend of total TB cases in each year/period. The figure shows that the highest number of total TB cases was recorded in 2011 while the lowest was in 2016. It can be observed that TB cases decreased slowly from 2011 to 2017 with increments in 2012 and 2017.\n\nFurthermore, the variability of TB cases from 2008 to 2017 have also been presented using box-and-whisker plots in Figure 4. The overlapping box-and-whisker plots imply that there is no variability in cases among the years. The plots show that TB cases were skewed towards larger numbers from the year 2008 to 2014, and skewed towards smaller numbers from 2015 to 2016. Extremely small numbers were observed in 2013, 2014, 2015, and 2017. Variability across the regions have been presented in Figure 5. None-overlap of box-and-whisker plots imply variability between regions. Thus, there is variability in TB cases among the regions since some of the box-and-whisker plots do not overlap. It can also be observed that TB cases in most of the regions are skewed towards larger numbers except Northern and Upper East Regions (especially, the Northern Region with one extremely large value).\n\nSome baseline regional characteristics on the risk of TB infection have been explored in this study. The set of baseline predictors include doctor to population ratio, nurse to population ratio, HIV prevalence, TB cure rate, TB success rate, wealth quantiles and the proportions of men/women employed, unemployed, educated, and uneducated. Variables also considered in the study include proportions of people who have heard about the TB disease, have knowledge that TB is airborne, knowledge that TB can be cured, and those who believe that TB status should be kept secret. In the data analyses, all the baseline variables were explored to obtain significant predictors of the TB cases.\n\nFor spatial TB data, let yi,i=1,…,n denote a Poisson random variable with probability mass function defined as Pyiθ, where θ=θ1…θn is a vector of relative risk parameters for each region. The variable yi represent total number of TB cases for region i. It follows that the likelihood function for the Poisson variable yi is defined as:\n\nMoreover, after covariate adjustments, statistical inferences remained unchanged and the classical parametric formulation (in Equation 7) remains the most accurate model for the TB data. The posterior summary statistics in Table 6 showed negligible risk of TB across the 10 regions. Precisions of both the unstructured and structured components indicate clustering of risk. The models are implemented in R-software via the Integrated Nested Laplace Approach (INLA) packagon. Instructions on downloading and how to use this package can be found in Håvard et al.20 Also, this package can directly be installed in R software by using the command install.packages(\"INLA\",repos=c (getOption(\"repos\"),INLA=\"https://inla.r-inla-download.org/R/stable\"), dep=TRUE).\n\nThe clustering and variability of risk were studied using correlated and uncorrelated structures, respectively. The use of uncorrelated heterogeneity models with gamma or beta prior distributions for estimating the relative risk of a given disease are useful, however, such models have limitations. Andrew [17, P. 82-84] stated that a gamma distributions restrict the incorporation of covariates into the modeling process. Another limitation is that such models do not allow the formulation of a simple and adaptable general form of the gamma distribution with spatially correlated parameters [17, P. 82-84]. Wolpert and Ickstadt21 have also given an example of correlated gamma field models that yield poor results.22 However, Gaussian models permit incorporation of correlated structure (CH) into the modeling process. Further, variability in the data can be modeled as uncorrelated heterogeneity (UH) using a Gaussian prior distribution with a mean zero and risk variance of the disease across the regions. Both correlated and uncorrelated heterogeneity can be incorporated into the model to account for clustering and heterogeneity of risk. These structures are introduced into the modeling through a log-linear term with additive random effects.18,23 Besag et al.24 have provided the form of the model with CH and UH structures parameterized as follows:\n\nCAR models provide a tool for detecting and identifying regions where disease risks are clustered. The specification of CAR models provide a framework for borrowing strength between neighboring regions in such a way that, regions that share boundaries are likely to have similar risks and regions that are distant apart are likely to show variability with regard to risk. Waldo Tobler’s25 noted that “everything is related to everything else but near-by things are more related than distant things”. CAR models were rarely used to detect and cluster risk until the 1990s.13,26 The models enable the influence of disease risk in neighboring regions to be modeled and estimated.18,19,27 Distances or boundaries between the regions are used to determine neighborhood properties in the CAR models.14,17,28\n\nLet Ω=12…n denote the study area and Ni=j∈Ω:i∈j classifies regions that share boundaries with region i. Let ϕi,i∈Ω be a stochastic variable, then the CH structure of ϕi follows a normal distribution defined as:\n\nAssume that region i has M neighbors and Wij=1M for each region that is a neighbor but zero elsewhere. The conditional expectation of ϕi is given by:\n\nThe Gaussian processes are defined by mean and covariance functions.30 Thus, the mean and variance-covariance functions are required to specify the CAR model. It follows the conditional probability distribution of the CAR structure ϕi is defined as22,24,25:\n\nThe symmetry of Σ implies that the covariance matrix Σ−1B=B−1Σ is symmetric such that Wijτj2=Wjiτi2,i,j∈S. The probability distribution Function (3) can alternatively be defined as:\n\nIt has been proved that the CAR structure ϕi follows the Gaussian distribution by showing that Σ is symmetric, see18,31 for details.\n\n0.0.1. Parameter estimation: CAR model\n\nParameters in the CAR model are estimated using Bayesian hierarchical methods. The TB detection data used in the study are counts (whole numbers), therefore, Poisson distribution is assumed for such data. The unknown risk of TB in any region i represented by ϕi. The number of cases and population risk in any region i are denoted by yi and Ni, respectively. The expected number of cases in region i can then be written as:\n\ngescrepresents the overall risk in the study population. The corresponding likelihood function is defined as:\n\nTaking natural logarithm of the likelihood function, differentiating with respect to the disease risk θi and equating to zero, it can be shown that the maximum likelihood estimator θ̂i of θi is\n\nwhich defines the standardized mortality ratio (SMR) in region i. However, using the Bayesian framework, yi∼ Poisson Eiθi, where the Poisson mean μi= Eiθi, θi∼ Gamma αγ with shape parameter α and scale parameters γ, respectively. However, these formulations do not incorporate covariates in the modeling process. Covariates through a linear predictor was introduced, as seen in previous work [18, 19, 17, P. 84]. The distribution of the response variable is specified by the exponent of the linear predictor as yi∼ Poisson Eiexpηi, where μi=Eiexpηi is the mean of Poisson distribution. Thus, the relative risk of the disease in region i is defined as:\n\nUsing the generalized linear model with a log-link function, we have:\n\nBayesian models are defined by the posterior distribution of the D parameter estimates, where the posterior is the product of the data likelihood function and the prior distribution(s) of the parameter estimates. Hence, we define the likelihood function as:\n\nThe β parameter estimates are assumed to follow the Gaussian distribution defined:\n\nThe hyperprior distribution for the precision parameters τϕ2 and τβ2 are respectively, τϕ2∼ Gamma 0.05,0.005 and τβ2∼ Gamma 0.5,0.05. The linear regression coefficient distribution is defined by:\n\n0.0.2 The Besag, York and Molli’e (BYM) Model\n\nClayton and Kaldor33 were first to propose the BYM framework, and later, Besag et al. developed it further.24 The BYM (also known as the convolution model) unifies the CH and UH structures into the same model that is capable of explaining clustering and variability of the disease risk. Although various models have been proposed for smooth risks estimation, the model proposed by Besag et al. (BYM)24 have been used extensively in literature. The BYM model is expressed as follows:\n\nAs indicated in the previous section, the TB cases follow the Poisson distribution, thus, yi∼ Poisson Eiexpηi, where μi=Eiexpηi. The linear link function is ηi=X′β+ϕi+ui. The log relative risk is logθi=ηi. Therefore, the relative risk for area i is defined by:\n\nThe log log-link function is defined as:\n\nParameters in the BYM are estimated using the same formulations discussed in the previous section, however, ui is required to be a Gaussian prior distribution given by:\n\nThe resulting posterior distribution can be written as follows:\n\nThe distributions for the hyper-prior precision parameters are as follows:\n\nThe estimates, τu2 and τϕ2 are precision-variance estimates for u and ϕ, respectively, and are used to measure the level of variability of risk among the regions and to cluster risk between neighboring regions.18,27\n\nThe TB data used in study are collected over time and hence spatial models alone will not be enough to model the space-time pattern of the relative risk of the disease. The spatial models are constrained for identifying heterogeneity and clustering of risk at a single time point. Several methods have been proposed to account for spatial and temporal patterns of disease risks.23,24,34–36\n\nIn this section, space-time models are presented based on three modeling frameworks developed by Knorr-Held et al.,16,37 Bernardineli et al.23 and Waller et al.37 These models differ with regards to their space-time interactive structures and inclusion of covariates. Consider region i, in year t, that recorded yit TB cases. The cases follow the Poisson distribution, i.e.:\n\nOur first space-time model formulations is based on the framework developed by Bernardineli et al.,23 where the linear predictor ηit is:\n\nIt follows that the Poisson mean is\n\nThese formulations suggest that each spatial unit has its own time trend with a spatial intercept μ+ϕi+ut and a slope ρ+δi. This model assumes a linear time trend in each spatial unit. The parameters to be estimated are φ=ρϕuδ and the hyper-parameters ψ=τϕτuτδ.\n\nAdjusting for risk factors Xi of TB cases detection, the model 6 can be written as model 7. Now the parameters to be estimated are φ=βρϕuδ and the hyper-parameters are ψ=τϕτuτδ.\n\nIt is known that if δi<0 the region-specific trend is less steep than the mean trend. On the other hand, δi>0 implies that the region-specific trend is steeper than the mean trend. Further, δi∼Normal0τδ.\n\nThe second space-time model is based on Waller et al.30 dynamic non-parametric formulation on the linear predictor:\n\nThe ϑt quantifies temporal-structure effect and it is modeled using a random walk through a neighboring structure16 defined as:\n\nFinally ϕt is specified by means of a Gaussian exchangeable prior: ωt∼N0τω. Finally ϕt is specified by means of a Gaussian exchangeable prior: ωt∼N0τω.\n\nThe third space-time Model 10 is an extension of Model 9 that enables a space-time interaction in order to explain the difference in the time trend of TB cases. It is expressed as follows:\n\nIn this model,φ=μϕuϑωπ and ψ=τϕτuτϑτωτπwere estimated, where πit is interaction between ϕi and ui. The model assumes that there is no interaction between ϕi and ϑt, hence, πit∼N0τπ. Incorporating covariates into Model 10, yields Model 11:\n\nHence, θ=μβϕuϑωπ and ψ=τϕτuτϑτωτπ,needtobeestimated. For the interaction term πit, it is assumed that there is spatial or temporal structure on the interaction, then δit∼N0τδ.37 In this study, all the precision parameters are assumed to follow the gamma distribution.16\n\n\nResults\n\nIn this section, the TB data has been analysed with the hierarchical space and space-time models.\n\nMoreover, accuracy experiments for the space-time models using the Deviance Information Criterion (DIC) developed by Spiegelhalter was performed, in order to ascertain the most accurate model for predictive studies. In the discussion, only results obtained from significant predictors are reported and discussed. Further, in the analysis, a risk value higher than 1 is classified as high risk while risk lower than 1 is classified as low risk. Risk is classified as normal if it has a value of 1.\n\nFurthermore, the space-time models discussed, involve the classical parametric framework (7) (presented by L. Bernardinelli et al.(1995)23), the dynamic nonparametric framework presented by L. Knorr-Held et al. (2000)37 for the linear predictor Equations (9), and Model (10). Model (10) (is an extension of Model (9)) to incorporate interactions between space and time. This enables us to explain the differences in the time trend of the TB cases across the regions. Equation (7) is refered to as Model I, Equation (9) as Model II and Equation (10) as Model III. Results are reported for experiments that involve adjustment and non-adjustment of covariates.\n\nIn this section, BYM without covariate adjustments (defined as ηi=μ+ϕi+ui.) was implemented. The posterior estimates are presented in Table 1. The maps of the posterior mean for the region-specific relative risks ζi=expϕi+ui of presented in Figure 6a,b are used to identify regions with high risk. High risk is visualized by computing pζi>1y, for details see M. Blangiardo et al.16 Figure 6a shows the five of the ten regions that have high risk of TB cases. The risk profile for TB in Ghana are shown in the figure-legends. In the regional map of Ghana, the darker the region the higher the risk and vice versa. It can be observed that Upper East and Upper West Regions have the highest risk (with values in the range 1.8-3.4), followed by Volta, Western and Central Regions with risk between 1.1-1.8. The rest of the regions have low risk of TB detection, specifically, Northern and Ashanti Regions have the lowest risk (with values in the range 0.3-0.6), followed by Greater Accra and Brong Ahafo Regions with values between 0.6-0.9. The Eastern Region has normal risk (with a value in the range 1-1.1).\n\nFigure 6b shows that Upper East, Upper West, Volta and Central regions have the highest posterior relative risk (0.8-1) of TB detection. The regions have similar risks, however, none of them has a risk higher than the national risk 1. Moreover, low relative risk (0-0.2) of TB detection is observed in the Northern, Brong Ahafo, Ashanti, and Greater Accra regions, followed by Eastern and Western regions that have relative risk values in the range (0.2-0.8).\n\nThe results in Table 1 confirm the similarity or clustering of risk in the neighboring regions. This is indicated by the low variability captured by the precision of the spatial structure τϕ. The estimate of the posterior marginal variance to capture the amount of variability explained by the spatial structure was evaluated. The spatial structure effect empirically using this formula was estimated:\n\nThe estimated proportion of spatial structure variance is approximately 10%, implying that only 10% of the variability is explained by the spatial structure. It further explains the remaining higher variability captured by the unstructured random effect ui component of the BYM. The precision τu of the unstructured component of the BYM model indicates that the risk is heterogeneous among regions. The exponent of the posterior mean μ (overall mean effect) shows that there is approximately a 3-fold increase in TB infections rate across the 10 regions of Ghana. The corresponding 95% credible interval ranges from 2.21 to 4.66.\n\nThis section represents the results obtained from experiments conducted with seven (7) covariates adjustments of the BYM:\n\nAmong the baseline predictors stated in Section b, the significant predictors for TB cases in Ghana that yield accurate models include: HIV prevalence, TB cure rate, TB success rate, proportion of people with knowledge about TB, proportion of those who know that TB is airborne, proportion in high income group and literacy. Table 2 presents posterior estimates of the overall mean, fixed effects (i.e. β1,…,β7) as well as random effects (i.e. τu and τπ) for the unstructured and structured components of the BYM. The maps of the posterior mean for each region’s relative risk (i.e. ζi=expϕi+ui+∑p=17βp) are presented in Figure 7a and b. The risk can be visualized by computing Pζi>1y.16\n\nIt can be observed in Figure 7a that Upper East, Brong Ahafo and Western Regions have high and similar detection risks ranging from 1.1-1.8. The adjusted risk (i.e. risk with the covariates in Figure 7a) is less than the unadjusted risk (risk without covariates in Figure 6a). Upper East Region is still among the regions with high risk of TB detection after covariates adjustment. Upper West Region does not belong to the high risk class while Brong Ahafo and Western Regions have moved to the normal risk class after the covariate adjustments. Greater Accra and Central Regions are the second highest in the high risk class, with risk ranging from 1-1.1. Upper West, Northern, Volta, and Eastern Regions are in the normal risk class, with risk ranging from 0.9-1. Further, Ashanti Region is in the low risk class (with values in the range 0.6-0.9) after covariate adjustments. In Figure 7b, it can be observed that Brong Ahafo and Western Regions have the highest and similar relative risk (0.8-1), while Ashanti Regions has the lowest relative risk (0.0-0.2). The rest of the regions have similar relative risks ranging from 0.2-0.8.\n\nTable 2 presents the posterior estimates of fixed and random effects of the BYM with covariate adjustments. It can be observed that TB cure rate increases the risk of TB cases by approximately 8% This observation implies that as more cases are detected, more cases are cured and hence TB cases should in general decrease over time. This explains why TB success rate leads to 14% reduction in detection rates. The results also revealed that knowledge about TB significantly increases TB detection by approximately 5% This behaviour is expected because, as people become aware of TB, preventive measures are taken. High income is associated with 5% reduction in TB cases while literacy is associated with 12% increase in cases. High income increases the use of health facilities and testing for TB, thus, leading to a reduction of TB cases. HIV prevalence lead to 55% reduction in cases.\n\nAfter adjusting the covariates, similarity/clustering of risk between neighboring regions, (see Figure 7) with low variability of risk among the regions was observed. This observation is captured by the precision τϕ of the spatial structure in Table 2. Heterogeneity of risk across the regions has reduced after the covariates adjustment.\n\nFurthermore, the posterior marginal variance to determine the amount of variability explained by the spatial structure using the formulations in Equation (12) was evaluated. The results showed that the estimated proportion of spatial structure variance is approximately 5%. This implies that only 5% of the variability is explained by the spatial structure. Much of the variability remaining is captured by the unstructured random effect ui component of the BYM. The precision τu of the unstructured component of the BYM indicates that risk is heterogeneous across regions.\n\nThe posterior mean of the exponent μ (overall mean effect) gives an indication that there is approximately 9-fold increase in TB infections rate across the 10 regions in Ghana.\n\nTable 3 presents the DIC, mean deviance D¯ and effective number of parameters pD components for the three space-time models. The performance indicators show that the classical parametric formulation (see Equation (7) introduced by Bernardinelli et al.23 is the most accurate among the three space-time models. Hence, further discussion will include only the results from that model.\n\nThe results in Table 4 show that there is about 8% increase in risk of TB detection across the 10 regions of Ghana. However, this increase is statistically not significant at 5% significance level. As observed in the BYM, TB cases do not significantly increase with time. The precision parameter τu shows some level of variability in the risk of TB among the regions, while there is clustering of risk between neighboring regions exhibited by the high precision parameter τϕ for the spatial structure. High precision characterized by τδ indicates low variability associated with δi. This further indicates that there is less interaction between space and time, as well as global trend ρ and areas-specific trend δi. Hence, the area-specific trend δi is less remarked than the mean trend.\n\nFigure 8a shows the map of spatial trend ζi, for the 10 regions and Figure 8b is the map of the posterior probabilities defined as pζi>1yi. Figure 8a shows that there is high risk of TB in the Eastern and Western regions. There is high risk (i.e. in the range 1.1-1.8) and clustering among the neighboring regions; Volta, Northern, Central, and Greater Accra regions. Upper East and Ashanti regions have the lowest risk (0.2,0.6) followed by Upper West and Brong Ahafo (0.6-0.9). The results account for the high variability captured by the unstructured component and the low variability captured by the structured component of the area-specific trend. The posterior probabilities in Figure 8b indicate low risk (below 1) and relatively low level of associated uncertainty.16 The time effect is not significant and there is no significant interaction between space and time. This observation accounts for the inaccuracy of Model II (i.e. Equation (10)) and Model III (i.e. Equation (9)) for the TB data.\n\nNext, the posterior probabilities of each region by year was evaluated. The results indicate that time has no significant effect on the space-time pattern of TB cases as shown in Figure 9a-d. The risk of TB infection is almost the same across the 10 regions. Figure 9a shows that there is relatively high risks (in the range 0.8-1) in the Northern, Volta, Eastern, Western, Central, and Greater Accra regions, while Upper East, Upper West, Brong Ahafo, and Ashanti regions have low relative risk (i.e. between 0-0.2). The results exhibit clear clustering of risk among neighboring regions associated with low variability or uncertainty. In the year 2010, all the regions had risks in the range 0.2-0.8, see Figure 9b. Similar observations can be made in year 2011 and the rest of the years shown in the figure. The results imply that it is sufficient to use only spatial models to estimate the risk of TB across the 10 regions of Ghana.\n\nIt can be observed in Table 5, that Model I of the space-time models has the lowest DIC, mean deviance D¯ and a high number of effective parameters pD. The indicators show that the classical parametric formulation of Ref. 23 (see Equation 7) is still the most accurate model among the three space-time models, for the TB data.\n\nTable 6 shows negligible risk of TB across the 10 regions of Ghana. Similarly, the TB cases over time is statistically insignificant as observed previously. The precision parameter τu indicates very low variability in the risk of TB detection among the regions and much clustering of risk between neighboring regions exhibited by high precision parameter τϕ values for the spatial structure. High precision characterized by τδ indicates lower variability associated with δi. This further indicates that there is no significant interaction between space and time as well as global trend ρ and areas-specific trend δi. Hence, the area-specific trend δi is less remarked than the mean trend.\n\nThe results in Table 6 also revealed that TB success rate significantly increases TB cases by 11%. Also, knowledge about TB significantly reduces TB cases by approximately 2%, while increasing TB cure rate, significantly reduces detection by 8%. Awareness that TB is airborne increases TB detection by approximately 25%. That is, more people are willing to participate in TB testing to know their status leading to more case detections. It was also observed that HIV prevalence and high income significantly increases TB detection by 27% and approximately 4%, respectively. Literacy significantly reduces the risk of TB detection by approximately 14%.\n\nFigure 10a shows the spatial trend ζi for the 10 regions and Figure 10b shows the posterior probabilities defined by pζi>1yi. Figure 10a shows that TB cases risk is higher and clustered in the Volta, Brong Ahafo, Ashanti, Eastern, Western and Greater Accra regions (ranging from 1-1.1) while there is low risk in the Upper East, Upper West, Northern, and Central regions. Thus, there is high and similarity/clustering of risks among neighboring regions. After covariate adjustments, there is low risk 0.6,1 in the Upper East, Upper West, Northern and Central regions. These observations account for the low variability captured by both the unstructured and structured components of the area-specific trend.\n\nFigure 10b shows the posterior probabilities, it can be observed that all the regions have low relative risks (i.e. in the interval 0.2-0.8) after adjusting the covariates. Since the time effect is negligible, there is no interaction between space and time. This observation accounts for the inaccuracy of Model II (10) and Model III (9) for the TB data. The posterior probabilities of the region after covariate adjustments (in the period 2008-2017), showed that the risks of TB across the 10 regions are the same/clustered in the range 0.2-0.8 (this observation is the same as the one made in Figure 10b).\n\n\nDiscussion and conclusion\n\nThe spatial model used is based on the BYM24 formulation. The results from this model (without covariate adjustments) showed that hot-spots of TB cases are located in five regions, i.e.; Upper East, Upper West, Volta, Western, and Central regions. Northern, Ashanti, Greater Accra, Brong Ahafo, Eastern and Western regions have low risk of TB detections. Another notable finding is the clustering of risk between neighbouring regions (i.e. nearby regions have similar risk). The results also revealed that the unstructured component of BYM (that explains variability of risk among the regions) is significant because the spatial structure only explains a small proportion of risk variability among regions. Additionally, after covariate adjustments, the number of high risk regions reduced from five to three (i.e. Upper East, Brong Ahafo and Western regions). The posterior probabilities in the BYM (with and without covariate adjustments) showed that there is clustering of risk between regions.\n\nFurther, this study also revealed that TB cure rate, TB success rate, knowledge about TB, awareness that TB is airborne, HIV prevalence, percentage of literacy, high income are important predictors of TB detection across the 10 regions of Ghana. Heterogeneity/variability of the risk reduced across the regions after covariate adjustments. The reduction in heterogeneity is due to low variance of the unstructured component and clustering due to low variability of the spatial or structured component of the BYM. Clustering of risk is evident from Figure 7, where almost all the regions have similar risk.\n\nFurthermore, the study showed that the classical parametric formulation (i.e. Equation (7) called Model I) is the most accurate space-time model for the TB data. This model yields the lowest DIC, lowest mean deviation and highest effective number of parameters with or without covariate adjustments. Hence, it was selected for further experiments. Results from this model show that the risk of TB does not significantly increase over time. There is some level of heterogeneity in risk over time indicated by the precision of the unstructured component. There is relatively high level of clustering among neighboring regions as well. The results shows that there is less interaction of risk between space and time, as well as global trend and area-specific trend. Hence, the area-specific trend is less remarked than the mean trend.\n\nClustering of risk is evident per the relative risk profile in Figure 8. The space-time model classifies Eastern, Western, Volta, Northern, Central and Greater Accra regions as the hot-spots of the disease over time. Three of the regions (i.e. Volta, Western and Central regions) are classified as high risk regions, by the BYM without covariate adjustments and the Model I without covariate adjustments. The posterior probability in Figure 8b clearly shows clustering of risk and low level of associated uncertainty. The posterior probabilities over the study period are shown in Figure 9a-d. The figures show that the risk of TB does not change over time.\n\nMoreover, after covariate adjustments, statistical inferences remained unchanged and the classical parametric formulation (in Equation 7) remains the most accurate model for the TB data. The posterior summary statistics in Table 6 showed negligible risk of TB across the 10 regions. Precisions of both the unstructured and structured components indicate clustering of risk among the regions. Therefore, all the regions exhibit similar risk. There is no significant space-time interaction due to low variability captured by τδ. The results identify the risk factors under the BYM as significant predictors of TB detection.\n\nTherefore, our study has characterized the spatio-temporal pattern of TB in Ghana, using hierarchical space-time models. The key findings include the identification of hot-spots, significant baseline predictors, heterogeneity/clustering of risk across regions and insignificant dependence of TB risk on time.\n\n\nData availability\n\nSource data The data used in this study can be found in the following links: https://open.africa/dataset/4176f749-cfa8-4e32-9418-86cef78f9db6/resource/0bcf9b54-3e35-4543-95cd-fd4de953edff/download/factsfigures_2018.pdf, https://www.who.int/teams/global-tuberculosis-programme/data https://www.stoptb.org/static_pages/GHA_Dashboard.html.\n\n\nAuthor contribution\n\nConceptualization, Software. Formal analysis: AKI Methodology and Investigation: AKI, FKB Data curation, Writing (Original draft preparation), and Writing (Review and editing): AKI and EAA Validation.", "appendix": "Acknowledgements\n\nThank you to the Ghana Health Service and National Tuberculosis Program for making data available for the study.\n\n\nReferences\n\nWHO: The top 10 causes of death.February 2022.\n\nW. 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PubMed Abstract \| Publisher Full Text" }	[ { "id": "156972", "date": "21 Dec 2022", "name": "Dioggban Jakperik", "expertise": [ "Reviewer Expertise Survival and Longitudinal Data Analysis", "Survey Theory", "and Design of Experiments." ], "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 modelled TB incidence in Ghana using Bayesian Spatio-Temporal modelling. This covered the old ten (10) administrative regions of Ghana. Regions with high incidents, regarded as hotspots have been identified. The relevant TB and patient characteristics have been considered. The following were however noted which needs consideration:\nGrammatical errors need to be addressed\n\nGhana now has 16 regions and has to be clearly stated.\n\nTB is caused by bacillus Mycobacterium tuberculosis and spreads from person to person by air through coughing, etc.\n\nReformat reference number 2 and similar others with such challenges.\n\nTB cases should be captured under source of data instead. How did the authors ensure that their data did not involve repetitions since they picked the data from two institutions who play complementary roles in TB management in Ghana?\n\nFurther, Figures 1,2,3, and 4 are misplaced. They should come under results or maybe introduction is seen as part of literature review but not part of methods.\n\nLine 4 after the posterior distribution …(INLA) package.\n\nUnder Correlated and Uncorrelated heterogeneity section, the third line after Andrew [], delete “a”.\n\nThird paragraph under results, delete “L” and all similar such cases.\n\nIs the work 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": "9158", "date": "09 Jan 2023", "name": "Abdul-Karim Iddrisu", "role": "Author Response", "response": "Comment 1: \"Grammatical errors need to be addressed.\" Response 1: We thank the reviewer for the comment. In response, we have proof read the manuscript for spellings and grammatical errors Comment 2: \"Ghana now has 16 regions and has to be clearly stated.\" Response 2: Thank you for these comments. In response, “The data contain information on TB detection from 2009 to 2017, for only the 10 old administrative regions of Ghana since the newly created 6 additional regions have no data” (See Methods Section under TB cases). Comment 3: \"TB is caused by bacillus Mycobacterium tuberculosis and spreads from person to person by air through coughing, etc.\" Response 3: We thank the reviewer for this important recommendation/suggestion. In response, “TB is caused by bacillus Mycobacterium tuberculosis and spreads from person to person by air through coughing, etc. 2” (Background Section, lines 2-3). Comment 4: \"Reformat reference number 2 and similar others with such challenges.\" Response 4: Thank you for these comments. In response we have reformatted the reference as “W. H. Organization; Global tuberculosis report 2020: executive summary.” We have also address similar issues in other references. Comment 5: \"TB cases should be captured under source of data instead. How did the authors ensure that their data did not involve repetitions since they picked the data from two institutions who play complementary roles in TB management in Ghana?\" Response 5: Thank you for this insightful and useful comments. In response, we used data from the two institutions however; our main source is Ghana Health Services and some complementary information from the National Tuberculosis Programme. Comment 6: \"Further, Figures 1,2,3, and 4 are misplaced. They should come under results or maybe introduction is seen as part of literature review but not part of methods.\" Response 6: Thank you for this useful observations. In response, we have placed these figures under the Methods Section because Methods Section presents source of the data, description of the data and the methods. Comment 7: \"Line 4 after the posterior distribution … (INLA) package.\" Response 7: Thank you for the comment. In response, we have revised the sentence to now read “The models are implemented in R-software via the Integrated Nested Laplace Approach (INLA) package.” Comment 8: \"Line Under Correlated and Uncorrelated heterogeneity section, the third line after Andrew [], delete “a”.\" Response 8: Thank you for this observation. In response, we have deleted the “a”. Comment 9: \"Third paragraph under results, delete “L” and all similar such cases.\" Response 9: Thank you for this observation. In response, we have deleted the “L” and have addressed all similar cases." } ] } ]	1	https://f1000research.com/articles/11-200
https://f1000research.com/articles/11-1369/v1	23 Nov 22	{ "type": "Review", "title": "Micronutrients in Adverse Pregnancy Outcomes", "authors": [ "Sairoz .", "Krishnananda Prabhu", "Ranita Ghosh Dastidar", "Annayya Rao Aroor", "Mahadev Rao", "Sahana shetty", "Vidyashree G Poojari", "Varashree BS", "Sairoz .", "Ranita Ghosh Dastidar", "Annayya Rao Aroor", "Mahadev Rao", "Sahana shetty", "Vidyashree G Poojari", "Varashree BS" ], "abstract": "About 10 to 20% of reported pregnancies have complications like spontaneous abortion (SA), preeclampsia (PE), preterm birth (PTB), and fetal growth restriction (FGR); 60% are attributed to maternal nutritional alterations. Multiple micronutrients (MMN) are supplemented in the antenatal period, but no proper validation/guidelines are available regarding dosing/time, the need for initiation, and the duration of supplementation. Studies have reported adverse pregnancy complications related to the overuse/unwanted use of multiple micronutrient supplementations during pregnancy. Identifying the exact population requiring supplementation is necessary to prevent its abuse. This article attempts to review the impacts of micronutrient deficiency/supplementation in cases of SA, FGR, and gestational diabetes mellitus (GDM), preterm delivery and PE. The study used a literature search using PubMed, Google Scholar, Mendeley, and Scopus Databases using search words pregnancy, spontaneous abortion, gestational diabetes mellitus (GDM), fetal growth restriction (FGR), preterm delivery, preeclampsia (PE) or “adverse pregnancy” associated with minerals, micronutrients, or supplementation. The review also considered in-house literature databases, a single-window search at Kasturba Medical College (KMC) Health sciences library, MAHE (Manipal Academy of Higher Education). The figures included in the study were created by Biorender.com. Micronutrients play multiple roles during pregnancy and fetoplacental growth stimulating growth hormone secretion, Lysyl oxidase (LOX), involved in the crosslinking between collagen and elastin in the amniotic membrane, downregulation of interleukin (IL)-1 alpha, IL-1 beta, IL-4, IL-6, Il-10, IL-12, tumor necrosis factor (TNF)-alpha and several chemokines involved in hypertension, immune-inflammatory pathways, attenuate insulin resistance a structural development of neurons and glia. Over-supplementation has led to complications such as spontaneous abortion and gestational diabetes mellitus. Since there is a lack of standardization concerning micronutrient supplementation during pregnancy, there is a need for systematic study related to the role of micronutrients during each trimester of pregnancy to optimize its supplementation and to prevent hazards associated with its abuse.", "keywords": [ "Micronutrients", "Pregnancy", "Foetal growth restriction", "Gestational diabetes", "Iron", "spontaneous abortion", "zinc", "magnesium", "copper" ], "content": "Introduction\n\nAdverse pregnancy outcomes, pregnancy other than normal livebirths, which majorly include spontaneous abortion (SA), preterm birth (PTB), fetal growth restriction (FGR), and preeclampsia (PE). 10—20% of reported pregnancies have complications like SA, PE, PTB, and FGR. Of these, 60% are attributed to maternal nutritional alterations and 40% to the alteration in the placenta and the fetus.1 The reported adverse outcomes are 19.8% for preterm, 1.7% for spontaneous abortions, 1% for gestational diabetes, and 0.9% for stillbirths in rural India. Inadequate diet/nutrition during pregnancy commonly causes impaired fetoplacental growth and placental functions.2,3 As trace elements are responsible for the maintenance of cellular structures and processes, any imbalance of micronutrients such as zinc, copper, iron, and magnesium can predispose to problems in conceiving, structural or functional abnormalities in the fetus, fetal death, premature ruptured membranes, and small for gestational age (SGA) babies.4,5\n\nBased on the above observation, multiple micronutrient supplementation (MMN) is often given during antenatal period. But there are no proper validation/guidelines available concerning dosing/time, the need for initiation and duration of supplementation, etc., which has led to many unwanted supplementations. Studies report adverse pregnancy complications related to the overuse/unwanted use of multiple micronutrient supplementations during pregnancy.6–8 Identifying the exact population requiring supplementation is necessary to prevent its abuse. This article attempts to review the impacts of micronutrient deficiency/supplementation in cases of spontaneous abortion (SA), fetal growth restriction (FGR), preterm delivery, gestational diabetes mellitus (GDM), and preeclampsia (PE).\n\n\nMethods\n\nThe study used a literature search using PubMed, Google Scholar, Mendeley, and Scopus Databases using search words “pregnancy”, OR “spontaneous abortion” OR “gestational diabetes mellitus” (GDM) OR “fetal growth restriction” (FGR) OR “preterm delivery” OR “preeclampsia” (PE) OR “adverse pregnancy” associated with “minerals,” “micronutrients,” OR “supplementation.” The review also considered in-house literature databases, a single-window search at Kasturba Medical College (KMC) Health sciences library, MAHE (Manipal Academy of Higher Education). As mentioned above, we identified 5260 articles with the search criteria. The study specifically screened 128 high impact journals such as The American Journal of the Medical Science, Journal of Trace Elements in Medicine and Biology, Nutrients, etc. and included 93 research articles. The review evaluated observational studies and randomized controlled trials since1/1/2015. Meta-analyses: reviews were excluded from this study. For clinical and global importance, the review chose the referred studies.\n\n\nMetabolic functions of micronutrients during pregnancy\n\nZinc acts as a cofactor for more than 300 enzymes, involved in the regulation of cell growth, hormone release, organ development (kidney and heart), immunological response, maturation, and differentiation of T cells, and reproduction (ovarian development, ovarian follicular growth, oocyte maturation), transcription, synthesis of proteins, and DNA replication (Figure 1).9 Formation of Zn finger (Znf) motifs helps many transcription factors to bind DNA. Zinc is involved in bone formation, while collagen in the bone prevents bone resorption by stimulating alkaline phosphatase (ALP) activity in the osteoblasts.10 Zinc influences many antioxidant enzymes, including Cu/Zn superoxide dismutase (SOD1), which prevents DNA damage and aids cell sensitivity towards insulin. Zinc stimulates growth promotion by stimulating growth hormone secretion, insulin like growth factor (IGF-1), insulin-like growth factor binding protein (IGFBP), and IGF-3 secretion. Insulin-like growth factor1(IGF1) promotes differentiation of the placenta, placental growth, and functional development in pregnancy during its early stages.10–16\n\nCopper is biologically essential for oxidation, energy metabolism, myelination of neurons, hematopoiesis, iron transport, and defense against free radicals.14 The maternal copper level increases during pregnancy due to an increase in ceruloplasmin induced by increased estrogen. Copper in cytochromes helps in electron transport and energy generation. Copper (I) ions can produce reactive oxygen species (ROS) (Figure 2), catalyze the Haber–Weiss reaction, and induce insulin resistance by ROS leading to altered glucose homeostasis.9,10,15,16 Lysyl oxidase (LOX), a copper-containing enzyme, is involved in oxidizing lysine and hydroxylysine residues present in precursors of elastin and collagen, also enabling crosslinking in the amniotic membrane. This crosslinking maintains mature elastin’s elasticity and stabilizes collagen fibrils.18\n\nMagnesium is involved in >600 enzymatic reactions, such as energy metabolism, fatty acid and protein synthesis, neuromuscular excitability, and uterine hyperexcitability prevention in pregnancy, relaxation of muscles, vasodilatation and decreased vascular resistance, and transmission of nerve impulses (Figure 3). Magnesium stimulates the activation of vitamin D, thus involved in the homeostasis of calcium and phosphate, and is essential for calcium-triggered release of parathyroid hormone (PTH). Magnesium acts as an allosteric activator for adenylate cyclase, Na/K-ATPase, and phospholipase C. Magnesium downregulates IL-1 alpha, IL-4, IL-6, IL-1 beta, Il-10, IL-12, TNF-alpha and several chemokines involved in hypertension, numerous immune-inflammatory pathways, and in adverse pregnancies. Magnesium protects against pregnancy inflammation by nitric oxide synthase enzyme inhibition. It decreases proinflammatory cytokine production of activated B cell receptors by blocking the nuclear factor kappa-light-chain-enhancer.19–21\n\nSelenium plays a role in antioxidative protection, protein synthesis, enzyme function, formation of thyroid hormones, and immunomodulatory and anti-proliferative mechanisms, all of which impact pregnancy. For adequate functioning of enzymes, selenium concentrations have to be about 80–95 μg/L plasma, corresponding to ~100–120 μg/L in the whole blood. It is a vital component of the selenoproteins and glutathione peroxidase and is involved in periconceptional events such as oocyte development, fertilization, follicle growth, maturation, and implantation. Selenium, through selenoproteins like DIO2, GPX1, and selenoprotein K, plays a role in proper functioning of trophoblasts during pregnancy and an index of oxidative stress, activating signaling pathways such as phosphoinositide 3-kinase activation (PI3K/AKT) and extracellular-signal-regulated kinase (ERK). Morphological changes in the fetal cerebellum correlate with selenium levels during pregnancy. Se involves neonatal cerebellum measures, length and width, and children’s motor and cognitive scores.15,21,22 Selenium can alleviate the inflammatory response, which attenuates insulin resistance by inhibiting the NF-κβ signaling pathway and TLR through the expression of PPAR-γ and glucose homeostasis throughout pregnancy by enhancing glucose transporters’ activity (GLUT) and neutralizing reactive oxygen and nitrogen species.\n\nIron is integral to the transport of oxygen, energy production, cellular respiration, and DNA synthesis. Iron in ferritin prevents cellular damage and is critical to normal β cell function and glucose homeostasis (Figure 4). Iron in hemoglobin delivers oxygen through the placental unit to maintain the oxygen requirement of a fetus, of which 60% is utilized mainly for developing the nervous system to a complex sulcated and gyrated brain structure of the fetus. The homeostatic response of changes in iron protects the placenta; for example, in iron deficiency, i.e., iron import increases through transferrin receptor 1 (TFR1), and export through ferroportin (FPN) decreases.23 Excessive iron is toxic and free iron can lead to oxidative stress and inflammation. In severe cases, it can lead to ferroptosis and cell death by lipid peroxidation of cell membrane. High levels of proinflammatory cytokines in maternal serum in pregnancy maintain adequate placentation, leading to inflammation and a mild systemic inflammatory response. Interleukin 6 (IL-6), the primary hepcidin regulator, disturbs iron homeostasis and leads to the expression of vascular cell adhesion molecule (VCAM1) and intercellular adhesion molecules (ICAM-1), maintaining endothelium adhesive phenotype.17,23–29\n\n\nSpontaneous abortion\n\nWorld Health Organization (WHO) defines SA as the termination or removal of a fetus of weight ≤ 500 grams before the 20th week of gestation.21,27 The incidence of spontaneous miscarriage is 10–30% worldwide of clinically diagnosed pregnancies, of which 80% are within 12 weeks of pregnancy. Studies reported that the altered concentration of serum micronutrients (Zn, Cu, Se, Cd, Fe, and Mg) might lead to spontaneous abortions.28\n\nZinc helps in embryo development and building up of maternal immunity. Mothers who present with spontaneous abortion have significantly lower mean concentrations of serum zinc.14,16,28–30 Low serum zinc levels can lead to decreased cell generation, reduced protein synthesis, and increased cellular oxidative stress (Figure 1). Insufficient supply of antioxidants in maternal and placental circulation can predispose to complications in pregnancy.31 Zinc deficiency decreases antibody production, affecting maternal and fetal immunity, causing spontaneous abortion.32 Many studies have shown that zinc supplementation leads to altered thymus gland secretions leading to a shift in T-helper cells. All these can predispose to recurrent spontaneous abortion in women.16\n\nCopper has roles in connective tissue development, hematopoiesis, energy metabolism, neurotransmitter synthesis, and myelination of neurons.30 Serum copper levels are 30% to 35% lower in women with miscarriages.29 Low maternal serum copper around 15 weeks (about three and a half months) of gestation has a protective effect against SA, showing that copper is more involved in placentation than conception. In addition to other factors, optimum serum copper concentration at 15 weeks of gestation decreases spontaneous abortion.17 Low maternal serum copper levels after 28 weeks (about six and a half months) of pregnancy were associated with higher rates of premature rupture of membranes (PROM).33 Lysyl oxidase’s unavailability due to copper deficiency can reduce collagen and elastin crosslinking, leading to a weak amniotic membrane in a spontaneous abortion case. But copper supplementations in pregnancy did not show the reversal of this effect.31 During pregnancy, changes in ceruloplasmin (copper-containing protein) levels can significantly change the ability of neutrophils to produce reactive oxygen species (ROS), which increases the chances of SA. As the metabolism of copper and iron is interlinked, deficiency of iron results in an elevation in liver copper. The above mechanism is linked with an elevated maternal serum copper and that of serum ceruloplasmin.33\n\nSelenium, due to its antioxidant activity and involvement in the immune system, helps prevent heart diseases and cancer.34,35 Selenium deficiency causes decreased immune system activity, affecting both innate and adaptative immune responses. Selenium-associated enzymes such as thioredoxin reductases and glutathione peroxidases prevent reactive oxygen species-induced cell damage. Adequate selenium is responsible for improving the activation of natural killer (NK) cells and T cells. The lower levels of antioxidants due to reduced Se disturb the balance of thromboxane-prostacyclin, leading to SA. However, this has not been explored in-depth and can be studied further in the future. In pregnant women, an increased Se demand due to increased erythropoiesis in the growing fetus must be met to prevent abortion.19,30\n\nMagnesium (Mg) is involved in maintaining body temperature, synthesis of nucleic acid and protein (Figure 3), and maintenance of resting membrane potential in the nerve and muscle cells.36 During pregnancy, the maternal plasma magnesium increases with gestational age. Low antenatal Mg with an increased Ca/Mg ratio may lead to spontaneous abortions.28 It plays a significant role in membrane transport such as transmembrane electrolyte flux, transport of potassium and calcium ions across the plasma membrane by active transport mechanism involved in maintaining the normal functioning of vital organs such as fetal cardiac activity in the first trimester, maintenance of cell adhesion and cell migration, and neurochemical transmission involved in feto-maternal circulation. Hence, magnesium deficiency may hamper further growth and functioning of fetal organs, leading to SA. Magnesium functions in steroidogenesis (particularly progesterone synthesis) but is also involved in the maintenance of pregnancy is not clearly defined by the researchers. Studies can explore this area of the mechanism involved in the etiology of the same.14,30\n\nIngested cadmium can selectively accumulate in the brain, red blood cells (RBC), kidneys, liver, and bones leading to its toxicity. This metal can displace other metals from metalloenzymes. It can seriously impact various organ morphologies and can modulate the functions of iron, calcium, copper, zinc, manganese, magnesium, etc. As living organisms poorly eliminate cadmium, it has a biological half-life of 16-30 years.36 At 12-week pregnancy, blood cadmium >0.4 μg/L can increase the risk of embryotoxicity and spontaneous abortions.\n\nIron is essential in pregnancy to meet the increased demands for hematopoiesis, fetus development, and growth (Figure 4). 42% of children below five years, 50% of pregnant women-, and 33% women of reproductive age are iron deficient worldwide.37,38 Among women with miscarriages, 13% higher serum iron levels are seen in 14 weeks of pregnancy. In support of the above findings, serum hepcidin and ferritin concentrations were higher in the first trimester due to possible accumulation of iron in maternal serum because the fetus is not receiving maternal iron through the placenta leading to SA.39 Iron supplements during an antenatal period can significantly minimize the incidence of SA.40\n\n\nPreterm birth\n\nPreterm is the birth of a live baby <37 weeks of gestation.30 Reduced concentration of collagen, collagen crosslinking, increased oxidative damage biomarkers, and inflammatory signals transmitted in the placental membrane resulting from cellular apoptosis stimulate parturition in pregnancy leading to preterm delivery.34 Copper, zinc, manganese, and selenium counterbalance the oxidative stress-induced premature aging of the placenta and inflammatory responses.30\n\nApproximately 18% of zinc deficiency during pregnancy causes adverse effects, leading to premature birth, increased infections, and nanism in children.41 Serum zinc concentration tends to decline in early pregnancy and reduces to approximately 35% less than the levels in non-pregnant women. Zinc is present as the highest content in the brain involved in migration and differentiation of the nervous system, i.e., neurogenesis (Figure 1). More than 50% of cerebral white matter injury (WMI) in premature birth is attributed to zinc deficiency.42 Zinc and other micronutrients maintain the birth length (BL) and fetal birth weight (BW) and are involved in the differentiation of oligodendrocytes, which contribute to the onset of myelination. The head circumference of the fetus is the crucial factor in deciding the week of delivery.32 The increased risk of amniotic infection by inhibiting maternal and fetal immunological competence due to lower maternal serum zinc concentration may lead to preterm birth. Thus, maintaining an adequate serum zinc concentration during pregnancy may help keep optimal fetal growth and prevent preterm birth.35,41,44\n\nBoth copper deficiency and excess can lead to adverse pregnancy outcomes.43 Elevated plasma copper in early pregnancy may indicate inflammation predisposing to preterm delivery. (Figure 2) During pregnancy, estrogen mediates an increase in copper-carrying proteins in the blood, which may lead to a rise in circulating levels of copper. A low copper/zinc ratio reduces the risk of pregnancy complications. Studies show that lower serum copper has a protective effect early as the mature fetal liver stores the trace elements.43 Hence, the maternal serum delivers higher copper in preterm delivery as its fetal transfer remains incomplete due to reduced pregnancy duration compared to term pregnancy.\n\nIron deprivation in the first and second trimesters of pregnancy can lead to premature birth and affect the baby’s health.44 During pregnancy, decreased iron and anemia increase serum norepinephrine concentrations, induce stress in mother and fetus, leading to corticotropin-releasing hormone (CRH) synthesis, and increase the chances of preterm. Increased maternal infection due to increased oxidative damage to RBC and the placental unit can result in preterm delivery.47,48 The requirement for iron ranges from 1–1.5 mg/day and increases to 5.0 mg/day in the last two trimesters. Due to the expansion of maternal blood volume, third-trimester pregnancy needs more iron. The risk of preterm term birth has shown an inverse correlation with the duration of iron supplementation. As iron inadequacy leads to functional impairment and excess leads to cytotoxicity, the dose of iron supplementation remains debatable; hence further studies need to focus on the amount and duration of supplementation.45,46,49\n\nMany studies reported a reduced incidence of preterm delivery with magnesium given to the mother <12 hours before delivery.47,48 PROM has been linked with lower serum magnesium in mothers and higher in the placenta, implying distinct pathophysiological roles for magnesium compared to preterm birth (Figure 3). Magnesium has the ability to compete with intracellular calcium in maintaining the membrane potential in preterm labor.52 Magnesium protects against premature birth by inhibiting myometrial activation and cervical maturation.52–54\n\n\nFetal growth restriction\n\nTwenty million infants globally are born as low birth per year weight babies (<2500g). Among these, approximately 95% are from developing nations. In India, fetal growth restriction is about 18 to 20%, primarily due to maternal micronutrient deficiency.51–53\n\nBased on studies conducted in both animal models and humans in pregnancy, decreased maternal zinc is associated with fetal growth restrictions. Mothers are 2.6 times more likely to have FGR with low zinc levels.52 The zinc levels are significantly lower in mothers with BMI less than 18.5 who had small gestation (SGA) neonates.20,50,52 Maternal zinc deficiency in early pregnancy increases the risk for FGR (Figure 1) as many enzymes and growth hormones, which play a role in fetal growth, require zinc. In FGR, osteoblast formation via IGF-I in the fetus gets affected due to zinc deficiency, as explained above in the metabolic functions.56 Studies have shown that with maternal zinc supplementation, a substantial number of babies are born with appropriate birth weight, indicating that monitoring serum zinc in pregnancy is essential to ensure the proper development of the fetus and prevent FGR.50\n\nCopper protects cells from toxic superoxide anions to ensure average fetal growth and immune function. It also maintains the hematopoietic, central nervous, bone, and connective tissues. Maternal serum copper has an inverse relation with head circumference (HC), body weight, and the fetus’s height (Figure 2).54 Studies indicate that pregnant women with a deficiency of copper are prone to fetal growth restriction (FGR) as it affects collagen and elastin metabolism involved in maintaining average fetal growth (mechanism as discussed above in the metabolic section). Copper deficiency can hamper cytochrome and bone collagen synthesis, directly affecting fetal development and leading to FGR.52,55,59–61\n\nPregnancy with iron deficiency reduces fetal growth (Figure 4) and affects neuronal growth, especially in the myelinization of neurons, neural signals transmission, frontal cortex development, and basal ganglia.26,56 Decreased iron leads to decreased hemoglobin, restricting oxygen circulation and forming an environment of chronic hypoxia, leading to fetal growth restriction. Iron deficiency stimulates the synthesis of corticotropin-releasing hormone via increased norepinephrine and, in turn, hinders the growth of the fetus. Studies have shown that prenatal iron supplementation had a beneficial effect on baby weight in women who had taken Fe supplements during the last two trimesters of pregnancy.62 Although precise mechanisms are not clear on iron-folic acid and multiple-micronutrient supplements preventing FGR, few studies states that it maintains the average plasma volume and the flow of nutrients across the placental tissue to the fetus.62–64\n\nMother and fetus tissue formation in pregnancy requires a high magnesium intake.53,65,66 Magnesium is involved in vitamin D activation and in maintaining calcium and phosphate physiology for bone growth. Dysregulation in either of these nutrients is associated with skeletal deformities and cardiovascular disorders, leading to fetal growth restriction. Studies have shown that magnesium supplementation to pregnant mothers can suppress the chance of intrauterine growth restriction (IUGR), optimum birth weight of baby, head circumference, and body height that can be attributed to alterations in cytokine/chemokine in the amniotic fluid and placenta.66\n\n\nGestational Diabetes Mellitus (GDM)\n\nGestational diabetes mellitus is glucose intolerance at any level at the beginning of pregnancy. The high plasma fasting glucose levels may increase the chances of fetal deaths in the last weeks of gestation. Obesity and sedentary lifestyles are the main factors, and dietary intake is essential in the progression of GDM.\n\nAmong GDM cases, there are low serum Zn levels in the second and third trimesters. Giving zinc and calcium- magnesium and vitamin D supplements for six weeks in the second trimester to subjects with GDM improves serum insulin, fasting plasma glucose levels, and the homeostatic model of measuring insulin resistance.58,67 Zinc intake improved fasting plasma glucose (FPG) and lipid profiles. Zinc has a role in enzymes involved in the metabolism of lipid-like action on insulin. GDM occurs via oxidative stress and trace elements’ effects on immunomodulation and insulin activity changes. The immunomodulation mechanisms in GDM are related to oxidative stress and the impact of trace elements on the regulation of the immune system. Oxidative stress induces apoptotic deletion in the regulatory T cells, which are CD8+CD25+activated in the GDM. Besides, the Zn-insulin complex is a hexamer containing two zinc ions and forms other complexes with insulin. Therefore, zinc supplements may benefit glucose homeostasis.58,68\n\nCopper has shown positive correlations with HbA1C in types 1, 2 diabetes and GDM.70 Serum copper levels are directly involved in developing GDM independent of other established risk factors. Copper directly binds proteins affecting protein crosslinking, leading to the generation of advanced glycation end products, resulting in its functional impairment. Copper can promote progressive islet b-cell failure by causing the clustering of human amylin into an amyloid fibril. The hydrogen peroxide formed in the above process could also stimulate progressive b-cells degeneration.67,68,72 In contrast to the above finding, in underweight Chinese women, higher maternal serum copper has decreased the GDM risk before 24 weeks as the body composition, and body mass index (BMI) are associated with the individual trace-element status.68,69\n\nMaternal serum magnesium is low in the second and third trimesters with gestational diabetes mellitus.71 Insulin resistance might increase the placental size leading to low placental efficiency and affect fetal growth in GDM patients.72 Magnesium, by its effects on tyrosine kinase, glucose transporter 4, and lipoprotein lipase, has a significant role in glucose metabolism (Figure 3). Supplementing magnesium and vitamin E in GDM patients resulted in a significant improvement in glycaemic control and lipid profile.71,73\n\nMaternal serum ferritin > 67.8 μg/L and iron levels 52.9 mmol/L at 12 weeks of gestation are strong predictors for developing GDM as excessive iron levels increase oxidative stress, beta cell toxicity, and insulin resistance (Figure 4), disrupting glucose homeostasis67,74 Higher HbA1C levels noticed among individuals of iron deficiency have been detected.75 Iron supplementation has not been recommended for non-anaemic pregnant women in the first and second trimesters as it could elevate post-prandial blood glucose and cause GDM.19,74,76,77\n\n\nPreeclampsia\n\nPreeclampsia is hypertension in pregnancy with proteinuria of at least 0.3g/day in 2 to 8% of pregnant women and is the reason for about 63,000 deaths every year worldwide, especially in Nigeria and India78 Worldwide, PE management is still the leading cause for maternal and fetal mortality.6,13 Several micronutrients such as zinc, copper, magnesium, and calcium abnormalities play a role in preeclampsia.42,55,75,79\n\nMany studies worldwide associated low maternal serum zinc in PE independent of geographical location. Albuminuria in PE predisposes to zinc deficiency leading to decreased delivery to cells. Reduced serum Zn concentrations in preeclampsia reflect reduced Zn binding protein and estrogen concentration.55,79 Low zinc levels in pregnancy can increase blood pressure by reducing the amount of calcium in the muscles and decreasing the excretion of sodium in the urine due to its effect on sodium chloride cotransporter in the kidney leading to PE.82,83 Zinc deficiency reduces NOS activity contributing to hypertension development by dysfunction in the endothelium, and reduces vasodilation, an endothelium-mediated activity. Zn, a signaling molecule, controls receptor and growth factor-mediated pathways in the cell’s immunological mechanisms.80 In addition, Zinc deficiency contributes to oxidative damage by causing a negative effect on the copper-zinc superoxide dismutase enzyme system.81 Lipid peroxides and antioxidants play a vital role in preeclampsia. Reduced zinc and increased Cu/Zn ratios lead to PE by inactivating antioxidant enzymes causing inadequate trophoblast invasion, suboptimal perfusion in the placenta, and ischemia.83,84\n\nIn pregnant women, the lower prevalence of PE observed with high copper signifies its importance in the pathogenesis of preeclampsia.6,7,80 Copper levels increase under estrogenic activity, the main determinant of ceruloplasmin expression. Copper has a predictive cut-off value of 224μg/dL, indicating a good biomarker for PE diagnosis. Copper contributes to disease progression by lipid peroxidation, free radicals, and damaging endothelial cell function.84,85 Copper and Ceruloplasmin (cp) have a role in deciding the termination of preeclamptic pregnancies under 34 weeks (about eight months), as the copper and cp levels have shown a linear increase according to the severity of preeclampsia.83 Copper has the highest pro-oxidant capacity and serves as a cofactor to superoxide dismutase. (Figure 2).13,27 Since preeclampsia is a proteinopathy disorder with impaired autophagy, protein aggregates (Aβ, TTR, P-tau231, and α-syn) are generated by impaired autophagy in the placenta or kidneys.82 In PE, the lipid peroxidation product, malondialdehyde, and altered amyloid-b production generate protein aggregates, toxic amyloid-b42 species, and their specific components α-syn, TTR, P-tau231, and Aβ.82\n\nDuring pregnancy, a suitable magnesium level of 360–400 mg/day and reduced serum magnesium levels can trigger preeclampsia.84 Magnesium influences the vascular tone and contractility and plays a vital role in blood pressure regulation (Figure 3). During pregnancy, an ionized fraction of magnesium of less than 24.67% can predispose to preeclampsia. This forms the basis for using magnesium sulfate therapy for preventing and treating seizures associated with preeclampsia/eclampsia.69,75,76 Hypomagnesemia leads to intracellular calcium influx and a reduction in nitric oxide synthesis, causing vasoconstriction and elevated blood pressure.6,53,69,79 Hence Magnesium gluconate (3 g/day) has been used in managing pregnancy hypertension in high-risk pregnant women.86\n\nIncreased iron, systemic inflammation markers, and superoxide status are associated with preeclampsia. In PE, systemic inflammation and concentrations of superoxide are higher and result in endothelial function deterioration. A 2.19-fold risk of pregnancy-induced hypertension was seen in the lowest serum iron level (≤801.20 μg/L) at 10-14 weeks (about three months) of pregnancy as it affects trophoblast development. Reduced iron causes abnormal invasion of trophoblasts in the walls of the spiral arteries (between 6–18 weeks, about four months of pregnancy), resulting in reduced high-resistance circulation in the uteroplacental unit re-modeling, hypoxia, increased apoptosis, activation of the inflammatory and immune response. All these can lead to vascular endothelial damage and disturbance in endothelial homeostasis resulting in vasoconstriction and increased blood pressure.26 In the third trimester of pregnancy, there was a positive correlation between ferritin, iron, and superoxide concentrations with vascular stiffness. The World Health Organization recommends universal iron supplementation of 30–60 mg/day throughout pregnancy. There is an increased risk of hypertension after 20 weeks of pregnancy with iron supplementation before 16-week as it causes inhibition of lymphocyte proliferation, development of oxidative stress, and elevated blood viscosity. (Figure 4)87,88 Hence supplementation of iron along with vitamin E and antioxidant-rich foods is advisable only for pregnant women with proven iron deficiency to prevent iron overload.25,89,90\n\nHypocalcemia in pregnancy has seven times more risk of developing preeclampsia. A dietary deficiency in calcium may cause decreased calcium in all membrane storage sites, resulting in reduced stability in the cell membrane of vascular smooth muscle. Calcium works with magnesium in maintaining the equilibrium in the ions within the vascular membrane, thus affecting blood pressure.77,84,85,91 Hypocalcemia or hypovitaminosis D triggers the secretion of parathyroid hormone and renin, increasing intracellular calcium concentration and leading to vasoconstriction.74,81 Hence, the World Health Organization has recommended supplementation of calcium to prevent preeclampsia in pregnant women with lower intake.\n\nSelenium is an essential component of selenoenzymes and placental protection against oxidative stress. Selenium status is most important at 8–10 weeks (about two and a half months) gestation when there is an initiation of intervillous blood flow, posing an oxidant challenge.92 The high prevalence (56.9%) of serum selenium deficiency in the preeclamptic patient suggests that selenium deficiency is a risk factor for the development of preeclampsia and reported a serum selenium level of less than 50μg/l (<0.633μmol/l) in 62% of the preeclamptic patients.57 A deficiency of selenium could lead to trophoblast cell function disorders and arouse endothelial cell activation, along with free radicals, which expedite maternal vascular malfunction, which predisposes to PE. Low levels of selenium lead to decreased glutathione peroxidases (GPx), thioredoxin reductases (Th-Redx), and selenoproteins P, antioxidative and anti-inflammatory selenoproteins needed to protect fetal, placental, and maternal tissue against oxidative stress and damage. Activating oxidative stress markers, inflammatory cytokines, fibronectin, endothelin 1, nitric oxide deficiency, prostacyclin, and vasodilators increase blood pressure.93 Selenium supplementation can influence preeclampsia risk in populations with lower selenium status.93\n\n\nConclusion\n\nMicronutrients play multiple roles during pregnancy and fetoplacental growth like stimulating growth hormone secretion IGF-1, IGFBP, and IGF-3 secretion, leading to growth promotion, Lysyl oxidase (LOX), oxidizes lysine and hydroxylysine residues present in the precursors of elastin and collagen, enabling crosslinking in the amniotic membrane, downregulation of IL-1 alpha, IL-1 beta, IL-6, IL-4, IL-12, Il-10, TNF-alpha and several chemokines involved in hypertension, numerous immune-inflammatory pathways, fetal cerebellum morphological changes, attenuate insulin resistance and improve the activity of glucose transporters, structural development of the nervous system of the fetus, dysfunction in placenta and injury to trophoblast through hypoxia-reperfusion. Over supplementation had led to complications such as spontaneous abortion, and gestational diabetes mellitus. So, as there is a lack of standardization concerning micronutrient supplementation during pregnancy, there is a need for systematic study related to the role of micronutrients during each trimester of pregnancy to optimize its supplementation and to prevent hazards associated with its abuse", "appendix": "Data (and Software) availability\n\nNo data are associated with this article.\n\n\nAcknowledgments\n\nThe authors acknowledge Kasturba medical college, Manipal and Health sciences library, MAHE (Manipal Academy of Higher Education) for providing access to the articles reviewed in this study. 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PubMed Abstract \| Publisher Full Text" }	[ { "id": "210330", "date": "10 Oct 2023", "name": "Jufen Liu", "expertise": [ "Reviewer Expertise Prenatal nutrition 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 review is valuable and of great significance since multiple micronutrients were essential during pregnancy and the intricate relationship between micronutrients and adverse pregnancy outcomes were discussed in this review. For the lack of standardized micronutrient supplementation during pregnancy, the review could guide people to pay attention to optimizing the supplementation of relevant micronutrients and preventing hazards associated with its abuse. The review is clearly structured and easily understood. While the paper addresses a growing subpopulation of importance, the paper has some issues that could be addressed to improve the interpretations:\nA brief introduction about the common micronutrients and related adverse pregnancy outcome should be given at the first beginning, which would be easily to retrieve the readers’ attention.\n\nIt mentioned that adverse pregnancy complications related to the overuse/unwanted use of multiple micronutrient supplementations during pregnancy in abstract as well as introduction, however, the article is more about micronutrient deficiencies. Consequently, some literature on over-supplementation of micronutrients could be added. And in the part of “Metabolic functions of micronutrients during pregnancy”, the status or relevant data of micronutrient supplementations could be mentioned to stress the significance of micronutrient supplementations.\n\nIn the introduction of various micronutrients in different pregnancy outcomes, the article seems to mainly focus on the role of micronutrients and is lack of research or experiments to prove its point forcefully. This leads to people not being aware of the importance of micronutrient supplementation. And the article shows that there are no proper validation/guidelines available concerning dosing/time, the need for initiation and duration of supplementation, etc. Perhaps some current research in this area could be added to arouse people's thinking.\n\nIt seems that the conclusion focuses more on the specific factors related mechanism, the public health significance of appropriate micronutrient supplementation during pregnancy should be added in conclusion.\n\nThe abstract and conclusion needs to be re-organized and revised.\n\nIs the topic of the review discussed comprehensively in the context of the current literature? Yes\n\nAre all factual statements correct and adequately supported by citations? Yes\n\nIs the review written in accessible language? Yes\n\nAre the conclusions drawn appropriate in the context of the current research literature? Partly", "responses": [ { "c_id": "10373", "date": "16 Nov 2023", "name": "Krishnananda Prabhu", "role": "Author Response", "response": "Dear Sir, Thank you very much for your valuable inputs. I shall accordingly include these suggestions and revert soon. This will go a long way in enriching this review article Regards," }, { "c_id": "10514", "date": "16 Nov 2023", "name": "Krishnananda Prabhu", "role": "Author Response", "response": "Dear Sir, Based on your suggestions, I have edited the article. Herewith sending it today to the editorial team for further processing. I sincerely thank for your valuable inputs Regards," } ] }, { "id": "199841", "date": "19 Jan 2024", "name": "Jitendra Ahuja", "expertise": [ "Reviewer Expertise Biochemistry", "endocrinology", "obstetrics and gynaecology", "nutrition", "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\nRelevance and Description:\nThe article addresses a pertinent and current issue as adverse pregnancy outcomes remain a significant concern in the realm of maternal and fetal health. Micronutrient supplementation during pregnancy is a common practice, but the absence of standardized guidelines has raised concerns about potential overuse and its consequent adverse effects. Grasping the role of micronutrients during pregnancy and their connection to complications is pivotal for enhancing the well-being of both mother and fetus.\n\nMajor Points:\nClear Problem Statement: The article adeptly elucidates the issue of adverse pregnancy outcomes and their correlation with maternal nutritional adjustments. It underscores the gravity of this problem, given that approximately 10 to 20% of pregnancies are affected by complications.\nSignificance of Micronutrients: The article offers a comprehensive overview of the multifaceted roles played by micronutrients during pregnancy. It delves into how these micronutrients influence a variety of physiological processes, including hormone secretion, collagen and elastin crosslinking, immune responses, and neurodevelopment.\nOveruse of Micronutrient Supplementation: The article correctly identifies the absence of well-defined guidelines as a major concern. It highlights that the excessive or inappropriate utilization of multiple micronutrient supplements during pregnancy has resulted in adverse outcomes, such as spontaneous abortion and gestational diabetes mellitus.\nNeed for Systematic Studies: The article rightly emphasizes the necessity for systematic research to optimize micronutrient supplementation during each trimester of pregnancy. Such an approach could potentially avert complications associated with both deficiency and excessive supplementation.\nMinor Points:\nThe article could be enhanced by a more extensive discussion of specific micronutrients and their distinct impacts on pregnancy outcomes. This could provide a more nuanced comprehension of the subject matter.\nWhile the article mentions the sources it utilized, a dedicated section detailing the methodology, encompassing the search strategy and inclusion/exclusion criteria for the considered studies, would enhance clarity.\nOverall Opinion:\nThis article constitutes a valuable addition to the field of maternal and fetal health by addressing the critical concern of micronutrient supplementation during pregnancy and its potential consequences on adverse outcomes. The problem is elucidated effectively, and the importance of addressing it is manifest. The article furnishes a comprehensive overview of the roles of micronutrients and appropriately underscores the necessity for systematic studies and standardized guidelines.\nTo further enrich the article, a more in-depth exploration of individual micronutrients and a more transparent presentation of the research methodology employed for the literature search would be beneficial. In summation, this work is informative and holds promise in guiding future research and clinical practices in maternal nutrition.\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": "10925", "date": "13 Apr 2024", "name": "Krishnananda Prabhu", "role": "Author Response", "response": "Dear Sir, Thank you very much for your valuable input to enrich this article. I shall do the required modification as soon as possible and resubmit for your approval. Regards," } ] } ]	1	https://f1000research.com/articles/11-1369
https://f1000research.com/articles/12-328/v1	23 Mar 23	{ "type": "Research Article", "title": "Diagnostic accuracy of Cipto Triage Method in the emergency department", "authors": [ "Hadiki Habib", "Yogi Prabowo", "Septo Sulistio", "Imamul Aziz Albar", "Radi Muharris Mulyana", "Siti Nurlaelah", "Eva Desviati", "Erni Setiani", "Arifin Arifin", "Erni Siska Sarifah Matondang", "Rasmawati Rasmawati", "Choga Ilham Arlando", "Sumaryanto Sumaryanto", "Tommi Juliandi Sutoyo", "Fery Lutfi", "Fatriani Fatriani", "Endar Kusuma", "Yogi Prabowo", "Septo Sulistio", "Imamul Aziz Albar", "Radi Muharris Mulyana", "Siti Nurlaelah", "Eva Desviati", "Erni Setiani", "Arifin Arifin", "Erni Siska Sarifah Matondang", "Rasmawati Rasmawati", "Choga Ilham Arlando", "Sumaryanto Sumaryanto", "Tommi Juliandi Sutoyo", "Fery Lutfi", "Fatriani Fatriani", "Endar Kusuma" ], "abstract": "Background: The Cipto Triage Method (CTM) is a method developed in Indonesia for assessing the clinical acuity of emergency department patients. To evaluate the accuracy of the CTM, this study compared triage decisions using the CTM performed by nurses to the triage decisions performed by emergency medical officers (EMO). Methods: This cross-sectional diagnostic accuracy study was performed in a single-centre referral hospital in Jakarta, Indonesia. Adult patients who attended the emergency department (ED) met the inclusion criteria. Trauma cases, pregnancy, and psychiatric disorders were excluded. All eligible patients underwent triage assessment based on CTM by a triage nurse and were then referred to the ED treatment zone for triage assessment performed by an EMO. The sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and likelihood ratio were calculated. Results: Between April and July 2022, 902 participants were randomly selected. The overall accuracy of the triage assessment of the index test was 84.7%, and the PPV of resuscitation and urgent triage was very good (90.5% and 84.5%, respectively). In the non-urgent category, the PPV was acceptable (72%), but the NPV was very good (92.2%). Conclusions: Nurse-based triage assessment using CTM in the ED had very good diagnostic accuracy in determining clinical acuity.", "keywords": [ "cipto triage method", "emergency department", "Indonesia", "triage nurses", "emergency medical officer" ], "content": "Introduction\n\nTriage science in the emergency department (ED) has evolved from sorting patients according to the severity and urgency of their medical conditions into an effective tool to ensure patient safety by managing appropriate emergency response time and patient flow.1,2 Current triage systems have been developed based on the unique conditions of each country.3\n\nThe Cipto Triage Method (CTM) is a three-tiered emergency department triage assessment tool based on patients’ characteristics and the public healthcare system in Indonesia.4 This is a structured, non-scoring method developed in the Dr. Cipto Mangunkusumo Hospital to assess the clinical acuity performed in the ED by emergency medicine specialists, Emergency Medical Officers (EMO) or emergency nurses with comparable accuracy.4\n\nPrevious criterion and construct validity evaluation of CTM for emergency nurses using retrospective chart review (prepared by an expert panel) and in-hospital mortality as the outcome showed that this method had good screening performance.4 This further promotes the policy of nurse-based triage assessment for routine ED service as being simpler yet effective.5\n\nAfter five years of implementation, we wanted to further evaluate the accuracy of the CTM. This study compared triage decisions using the CTM, performed by triage nurses as the index test, to the EMO as the reference standard. Adult non-trauma patients were the target population because they had the highest proportion of ED cases. No sex differences were expected from the CTM assessment based on the previous study.4 The null hypotheses were developed based on minimal acceptable criteria: index test sensitivity for resuscitation and urgent triage categories were <0.8 and index test specificity for non-urgent triage category was 0.8.\n\n\nMethods\n\nThis study had ethical approval from Ethical Committee of Cipto Mangukusumo Hospital/Faculty of Medicine Universitas Indonesia protocol number 21-11-1250, approval date January 17th, 2022.20 All study participants or their representative had given written consent. Individual data were treated confidentially. All methods were carried out in accordance with relevant guidelines and regulations. Study reporting followed the Standard for Reporting of Diagnosis Accuracy Studies (STARD) guidelines.6,20\n\nThis cross-sectional diagnostic accuracy study was conducted in the ED of Dr. Cipto Mangunkusumo Hospital an academic referral hospital in Jakarta, Indonesia. The ED manages approximately 30,000 visits annually. The clinical spectrum of ED cases ranges from simple tropical diseases to terminally ill non-communicable diseases.\n\nInclusion criteria were patients aged 18 years and above who visited the ED, underwent routine triage assessment and were treated in the ED treatment zones. The exclusion criteria were trauma, pregnancy-related and psychiatric-related emergencies. Exclusion of these conditions was due to the different clinical syndrome knowledge that was not covered during the triage training. Potential eligible populations were identified by the EMO based on these criteria during the data collection period. All eligible male and female patients had equal chance to participate in the study. Adequate representation of males and females was expected based on demographic information of ED patients from previous study.4 Sex of participants was defined based on information from citizen identification card.\n\nThe Cipto Triage Method was performed (extended data 220 by collecting information like chief complaint, focused history, and physical examination related to the chief complaint, simple vital signs (level of consciousness, respiratory rate, heart rate, and behavioural pain scale), and discriminators (extended data 320). Discriminators can modify the risk of severity or urgency level such as comorbidity for medical cases, mechanism of injury for trauma cases, previous history of pregnancy-related diseases for obstetric cases and previously identified congenital or comorbid conditions for neonates and children.\n\nAfter collecting the specific information, the triage nurse then categorised the patients into one of three categories of acuity. The resuscitation category was used if the patient was in critical condition and needed immediate medical assessment or life-saving intervention. The urgent category includes patients who exhibit signs and symptoms that need urgent medical assessment but do not need immediate life-saving intervention. The non-urgent category includes patients who exhibit signs and symptoms that do not need urgent medical assessment or intervention but might need clinical evaluation in the ED before getting discharged.\n\nPatients who are categorised in the resuscitation triage category are sent to the red zone, and the response time is immediate; patients who are categorised in the urgent triage category are sent to the yellow zone, and the response time is appropriate if treatment is given in less than 30 minutes; patients who are categorised in the non-urgent triage category are sent to the green zone, and the response time is appropriate if treatment is given in less than 60 minutes.\n\nThe triage nurse decision using CTM was considered as the index test to evaluate the implementation of the nurse-based triage programme recommended by a previous study.4 This policy claimed to allocate human resources by replacing physicians from the triage counter to the ED treatment zones and focusing on appropriate response time. However, triage nurses must have comparable accuracy to physicians in assessing clinical acuity.\n\nThe EMO was a general physician working in the ED under the direct supervision of an emergency medicine specialist. Assessment by the EMO was considered the reference standard because of his/her additional competence in clinical diagnosis, allowing more precise information collection in CTM. The reference standard was applied regardless of the index test results.\n\nBefore the study, a three-week online (triage principle, step by step triage process, communication at triage counter, medical evacuation at triage, the role triage officer in resuscitation) and hands-on (role play, observeration) combined education programme called ‘proactive triage training’ was conducted (extended data 420). Nurses who performed triage and the EMO participated in the training (November – December 2021).\n\nTraining participants who provided written consent as raters were included in this study. Reliability analysis after the training was performed (January 2022) using 30 case-based scenarios conducted for the nurse (20 raters) and EMO (10 raters) before the data collection process (triage assesment of the ED patients).\n\nThe scenarios were created and validated by three expert panels: HH (Internal Medicine and Emergency Medicine Specialist), SS (Anaesthesiologist and Emergency Medicine Specialist) and IAA (Orthopaedic Surgeon and Emergency Medicine Specialist). All scenarios were written in Bahasa (extended data 520) and never used in any previous ED training.\n\nData collection was performed during routine ED services (April 2022–July 2022). Eligible patients underwent triage assessment based on the CTM by a triage nurse and were then referred to the EMO in the ED treatment zone. The EMO further performed an independent triage assessment based on the CTM with additional clinical examination to establish a clinical diagnosis. Triage decisions from nurses were written on the triage assessment form, whereas the EMO wrote on a separate medical record form (extended data 620). Written consent from the patients or their representatives was obtained before the written triage decision was made by the EMO. No potential harm was expected during the data collection. Patient disposition from triage nurses to the EMO was relatively rapid (immediate response time for resuscitation triage and less than five minutes for urgent or non-urgent triage). The EMO triage assessment was performed without interrupting any business processes in the ED. Furthermore, there was no intervention between the index and reference tests that could modify triage assessment.\n\nThis study was single-blinded, meaning that triage nurses were blinded from the triage decision made by EMO. However, EMOs were aware of the triage decision by nurses because patients were sent from the triage counter to the appropriate ED zone followed by the disposition process according to triage category on the daily basis of ED service.\n\nBefore performing data collection for the diagnostic accuracy of the triage, we used 30 case-based scenarios for reliability analysis among nurses and EMOs who performed the index test and the reference standard test (extended data 520). The Krippendorff alpha coefficient was used to estimate inter-rater reliability among the nurses and EMO groups; to incorporate the reliability of more than two raters and ordinal-type data (three triage categories).7 The reliability analysis was performed using SPSS version 25.0.\n\nSummary statistics provided descriptive information about the nurses, EMO and participant characteristics. The diagnostic accuracy of index test was estimated using three contingency tables with nominal outcomes for each triage category (resuscitation vs. other triage categories, urgent vs. other triage categories and non-urgent vs. other triage categories). Sensitivity, specificity, positive predictive value, negative predictive value, positive likelihood ratio (LR+) and negative likelihood ratio (LR-) were calculated. Furthermore, variability analysis by stratification of study participants based on age (<60 years old and ≥60 years old) in each triage category was performed.\n\nAge stratification was performed because it is a strong predictor of clinical outcome, but critical signs and symptoms in geriatric patients are often vague and could mislead the triage decision.8,9 The diagnostic accuracy analysis was performed using STATA ver. 17.0.\n\nPatients who did not undergo a reference standard test were considered to have missing data. Inability of the nurse to determine triage categories was considered an indeterminate result of the index test. Both were excluded from the study.\n\nSample size estimation was based on sensitivity (for resuscitation and urgent categories) and specificity (for non-urgent triage category) estimations using Buderer’s formula.10 The highest estimation number was used as the sample size.\n\nSince the concept of ED triage was to screen clinical acuity, we propose that higher sensitivity is more important than specificity for resuscitation (sensitivity, 80%) and urgent (sensitivity, 80%) triage categories.11 For the non-urgent triage category, higher specificity is more important (specificity, ≥80%) to prevent under-triage of the patients. The prevalence of ED based on triage categories from a previous study was 15% resuscitation, 64% urgent, and 21% non-urgent.4\n\nThe predetermined confidence level, power of the study and desired absolute precision were 95%, 80%, and 10%, respectively. The diagnostic performance variation of each triage category in different age groups (<60 years and ≥60 years) was determined. Thus, the final expected research sample was the original sample size multiplied by two (from the two age group categories), which was 820. The final sample size was 902 participants after anticipating 10% of the potential missing values during participant selection.\n\nTriage nurses and EMOs performed triage assessment for all eligible ED patients during the study period. Simple random sampling will then be performed by the researchers using random generator in Stata ver. 17.0 to obtain participants from all eligible ED patients based on sample size measurement (Figure 1).\n\n\nResults\n\nFor the inter-rater reliability analysis using case vignettes, the response rate for both groups (nurses and EMO) was 100%. The work experience as a professional for the ED practitioner among the nurse group was longer than that of the EMO group.20 Agreement in the nurse and EMO groups was substantial (0.68; 95%CI 0.67–0.7) and very good (0.81; 95%CI 0.78–0.83), respectively, indicating that both nurses and EMO were consistent in triage decisions, although the EMO group had better performance agreement (Table 1).\n\nTable 2 shows that female participants were 53.9% of the sample, and the proportion of male and females were equal in resuscitation and non-urgent triage category. Based on the reference standard, the prevalence of participants in the resuscitation, urgent, and non-urgent triage categories was 23.7%, 62.6%, and 13.7%, respectively. Most participants were alert (94.9%), and more than half had pain during triage assessment (54.2%). The mean heart and respiratory rates were higher, whereas the mean systole and peripheral oxygen saturation were lower in the resuscitation category than in the other triage categories. Almost one-third had malignancy (29.3%), and most participants self-attended to the ED (non-referral cases). The discharges from the ED were 40.9% in all triage categories; only 2.5% were admitted to the intensive care unit, and 5.3% died in the ED. Among participants in the resuscitation and urgent categories, half of them were admitted to the ward. Furthermore, 13% of the patients in the non-urgent category were also admitted, and one patient in the non-urgent category subsequently died in the ED during emergency care.\n\nThe overall accuracy of the triage assessment of the index test was 84.7%. The highest proportion of mis-triage was overtriage of patients who had an urgent triage decision based on the index test, however, the actual condition based on the reference standard was non-urgent (7.1%).\n\nTable 3 shows the diagnostic features of each triage decision based on the index test compared with the reference standard.12 The sensitivity of the index test for resuscitation and urgent and non-urgent was 84.6% and 92.7%, respectively, while the specificity of non-urgent was 97%. Based on the results of this study, the null hypothesis is rejected. The triage assessment using CTM performed by a nurse was acceptable for screening patient acuity in the ED. The PPV of resuscitation and urgent triage were very good (90.5% and 84.5%, respectively). In the non-urgent category, the PPV was acceptable (72%), but the NPV was very good (92.2%).20\n\nStratification based on age showed an increased PPV and positive likelihood ratio in the <60 years age group compared to the ≥60 years age group in the resuscitation and non-urgent categories. No statistically significant difference (<10%) in the PPV, NPV, and likelihood ratio was found in the urgent category after age stratification.20\n\n\nDiscussion\n\nReliability assessment for the nurses and EMO groups showed that both achieved the minimum target of agreement (>0.67).13 The reliability among nurses is similar to another study using the Manchester Triage Scale (MTS) method (weighted kappa 0.62; 95%CI 0.6–0.65) but lower compared to the Emergency Severity Index (ESI) (weighted kappa 0.79; 95%CI 0.74–0.84)14 and the other three triage categories.15 Meanwhile, the inter-rater agreement among EMO was comparable with that among physicians using the ESI method (weighted kappa 0.84; 95%CI 0.48–0.96).14\n\nAccuracy assessment was focused on the PPV, NPV, and positive likelihood ratio because of the importance of this information in daily practice.16 Higher sensitivity was expected in the resuscitation and urgent categories because CTM acts as a screening tool for the risk of clinical severity and urgency.16 Higher specificity was expected for the non-urgent triage category, because for the less severe conditions, the triage decision would be considered reliable when the triage officer is able to be more specific and prevent under-triage decisions. The lower PPV of non-urgent triage categories implied that the index test had excessive over-triage by putting non-urgent cases into higher triage categories.\n\nThe accuracy of CTM performed by the nurse was 84.7%, higher than the accuracy of triage assessment using ESI (59.2%).17 Being a single-centre study, lower triage category (three categories) and previous triage training before the study conducted could be attributed to higher accuracy compared to the other triage methods.\n\nThe current data showed a consistent PPV in the resuscitation and lower PPV in the non-urgent categories (90.5% and 72%, respectively), which is comparable to a previous validation study of CTM performed on the general population attending the ED (99% and 94.1%, respectively).4\n\nAnother triage validation study using MTS (five categories) showed relatively lower sensitivity (47%–87%) of immediate and urgency categories compared to the reference standard (three categories) in the general adult population.18 Meanwhile validation of ESI in adult ED patients showed sensitivity (83%) and specificity (82%) in detecting higher-urgency categories.19 A systematic review by Zachariasse et al. reported 33 types of triage systems with large variations in accuracy, and concluded that The Canadian Triage and Acuity Scale (CTAS), ESI, and MTS had reasonable validity, established standardised guidelines and training programmes.3\n\nThe different proportions of PPV in the resuscitation and non-urgent triage categories after age stratification (Table 3) indicated that age should always be measured during the estimation of clinical acuity in ED triage. Lower PPV and positive likelihood ratio of resuscitation category in older participants indicated that vague signs and symptoms in geriatric patients could reduce the triage nurses’ ability to detect the risk of critical condition in new ED patients. Sex-based analysis was not performed because we already excluded pregnancy in the eligible criteria, thus all eligible medical condition that included in the study had similar triage assessment method for males and females.\n\nBased on hospital characteristics, the results of this study can be interpolated to other referral hospitals in Indonesia. Triage assessment by nurses using CTM could also be implemented in other public or private hospitals in Indonesia because it has already incorporated a method to collect information regarding patients’ potential severity and urgency with simple triage categories.\n\nThis study had several limitations, including a review bias due to non-blinding of the reference standard of the index test results, thereby leading to overestimation of sensitivity and specificity. Spectrum bias might have occurred due to the hospital’s status as a referral centre, leading to higher prevalence of patients in the resuscitation triage category than that in the non-referral hospital; this could have resulted in overestimation of PPV of the resuscitation category performed by the index test. Fewer participants in the non-urgent triage categories might have contributed to the wider confidence interval of sensitivity, specificity, PPV, NPV, and likelihood ratio of non-urgent triage category. Lack of sex-based stratification might underestimate the effect of sex on the clinical presentation in adult.\n\nIn summary, nurse-based triage assessment using the CTM in the ED had very good diagnostic accuracy in determining the patient’s severity level. Therefore, the development of formal triage training to improve the triage performance of nurses and physicians in the ED is recommended. To improve consistency, further research could focus on developing a clinical decision analysis for ED triage based on various clinical scenarios.\n\n\nEthics approval and consent to participate\n\nThis study had ethical approval from Ethical Committee of Cipto Mangukusumo Hospital/Faculty of Medicine Universitas Indonesia protocol number 21-11-1250, all study participants or their representative had given written consent. All methods were carried out in accordance with relevant guidelines and regulations.", "appendix": "Data availability\n\nOpen Science Framework: Triage, https://doi.org/10.17605/OSF.IO/XPYJV. 20\n\nThis project contains the following underlying data:\n\n• underlying data 1 interrater reliability EMO and nurse.xlsx\n\n• underlying data 2 data set triage.xlsx\n\n• underlying data 3 2x2 contingency table\n\nOpen Science Framework: Triage, https://doi.org/10.17605/OSF.IO/XPYJV. 20\n\n• Extended data 1 ethic approval.pdf\n\n• Extended data 2 nurse and EMO underlying information.xlsx\n\n• Extended data 3 step by step triage process.pdf\n\n• Extended data 4 curriculum for proactive triage training.docx\n\n• Extended data 5 case scenario example.docx\n\n• Extended data 6 triage form.pdf\n\nOpen Science Framework: STARD and SAGER checklists for ‘Diagnostic accuracy of Cipto Triage Method in the emergency department’, https://doi.org/10.17605/OSF.IO/XPYJV. 20\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\n\nAcknowledgments\n\nWe acknowledge all the staff in the Emergency Department of Dr. Cipto Mangunkusumo Hospital, Jakarta, Indonesia. Data management team: Silvia Maharani, MD and Veramita, MD. We would like to thank Editage (www.editage.com) for English language editing.\n\n\nReferences\n\nFitzgerald G, Jelinek GA, Scott D, et al.: Emergency department triage revisited. Emerg. Med. J. 2010; 27: 86–92. Publisher Full Text\n\nChrist M, Grossmann F, Winter D, et al.: Modern triage in the emergency department. Dtsch. Arztebl. Int. 2010; 107: 892–898. PubMed Abstract \| Publisher Full Text\n\nZachariasse JM, van der Hagen V , Seiger N, et al.: Performance of triage systems in emergency care: a systematic review and meta-analysis. BMJ Open. 2019; 9: e026471. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHabib H, Sulistio S, Albar IA, et al.: Validation of the cipto triage method: a single-centre study from Indonesia. Open Access Emerg. Med. 2020; 12: 137–143. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHabib H, Kurniawaty H: Triage in the time of diphtheria. West. J. Emerg. 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PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBlomaard LC, Speksnijder C, Lucke JA, et al.: Geriatric screening, triage urgency, and 30-day mortality in older emergency department patients. J. Am. Geriatr. Soc. 2020; 68: 1755–1762. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBuderer NMF: Statistical methodology: I. Incorporating the prevalence of disease into the sample size calculation for sensitivity and specificity. Acad. Emerg. Med. 1996; 3: 895–900. PubMed Abstract \| Publisher Full Text\n\nHabib H: Triage. Open Science Framework. 2023, February 5. Publisher Full Text\n\nvan der Wulp I , van Baar ME , Schrijvers AJP: Reliability and validity of the Manchester Triage System in a general emergency department patient population in the Netherlands: results of a simulation study. Emerg. Med. J. 2008; 25: 431–434. PubMed Abstract \| Publisher Full Text\n\nMirhaghi A, Heydari A, Mazlom R, et al.: Reliability of the emergency severity index: meta-analysis. 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PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYuksen C, Sawatmongkornkul S, Suttabuth S, et al.: Emergency severity index compared with 4-level triage at the emergency department of Ramathibodi University Hospital. Asian Biomed. 2017; 10: 155–161. Publisher Full Text\n\nHabib H: Triage.2023, March 3. Publisher Full Text" }	[ { "id": "167600", "date": "02 Jun 2023", "name": "Amir Mirhaghi", "expertise": [ "Reviewer Expertise Triage", "Emergency" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 review. The study is well-structured. There are two major points that need to be addressed.\n\nMistriage including overtriage and undertriage must be addressed in Results section for each level and underlying causes must be explained in Discussion section. Low sensitivity in non-urgent level indicates that overtriage (considerable false negatives) is remarkable between triage nurses and underlying causes (role of CTM, EMOs and triage nurses) must be explained. In addition, relatively low specificity (considerable false positive) for urgent level indicates mistriage (over- or under- triage) and underlying causes must be addressed.\n\nThere are more valid gold standards to assess diagnostic accuracy of determination of triage levels than EMOs' decisions. Admission on ICU, CCU, and extensive, rapid and invasive interventions, and prolonged hospital stay are more valid to be considered as gold standard for diagnostic accuracy. This issue must be addressed in limitations. In fact, the study assessed inter-rater agreement between triage nurses and EMOs rather than diagnostic accuracy.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNo\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? No", "responses": [ { "c_id": "11813", "date": "25 Jun 2024", "name": "Hadiki Habib", "role": "Author Response", "response": "1. mistriage proportion in each triage categories (over and undertriage) was stated in table 2. underlying cause were added in the discussion section \"The lower PPV of non-urgent triage categories implied that the index test had excessive over-triage by putting non-urgent cases into higher triage categories. This also causes the specificity of the urgent category to be lower. Overtriage of non-urgent to the urgent category occurs because triage officers often detect initial symptoms that appear more prominent, and patients have many comorbidities.\" 2. Based on the purpose of triage in the emergency department, triage is a process for assessing clinical acuity from limited initial information. Clinical outcomes such as in-hospital mortality, ICU stay, or length of stay are a proxy or impact of the triage decision, but do not directly describe how the acuity assessment is made (construct validity). the clinical outocome themselves can be influenced by various things while the patient is being treated, apart from the initial condition at triage counter. hence we move forward performing diagnostic method in assesing triage accuracy by compare it with other triage decision by the physician as reference standard (criterion validity) EMO can considered as a reference standard because 1. Physicians have a different skill set from nurses in terms of their ability to make clinical diagnoses. 2. EMOs performing triage assessment in the ER zone which has more space and free time compared to when in triage 3. EMOs also work under the supervision of EM specialists because we designed a reference standard, we could produce diagnostic term such as sensitivity, specificity, PPV and NPV. we performed inter-rater agreement assesments among nurses and physicians prior the clinical study when they underwent triage training." } ] }, { "id": "244037", "date": "23 Feb 2024", "name": "Winchana Srivilaithon", "expertise": [ "Reviewer Expertise Emergency Medicine" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nComments to the author Diagnostic accuracy of Cipto Triage Method in the emergency department\nThank you for the opportunity to review this interesting study. However, there are some issues that need to be addressed.\n1. The overall content is a study on the accuracy of triaging the severity of patients presenting to the emergency department, comparing the consistency between the triage done by nurses and general physicians. It is not a comparison of the patients' diagnostic of any disease. Therefore, using the term \"diagnostic accuracy\" in the title may not be correct according to the objectives of the study.\n2. This research focuses on the agreement in triage severity levels between nurses and physicians rather than testing diagnostic accuracy. Therefore, the selection and presentation of statistics should involve those related to agreement, such as Kappa statistics.\n3. Is EMO a good enough reference standard? Given that EMOs may be able to triage more effectively than nurses, they might not be the best group to serve as a reference standard. According to the research methodology, both nurses and EMOs receive the same training within the same timeframe. Thus, it can be anticipated that there might not be a significant difference between these two groups (since they were trained similarly using the same methods). Using a more reliable reference standard, such as a senior emergency physician, could make this research more credible.\n4. The calculated sample size likely represents the number of samples for each level of triage rather than the total sample size (one patient triaged once can be at one level). Therefore, the sample size in this research might be smaller than what it should be.\n5. Please provide more information about under-triage and over-triage.\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": [ { "c_id": "11814", "date": "25 Jun 2024", "name": "Hadiki Habib", "role": "Author Response", "response": "1. we change the title diagnostic accuracy to accuracy of nurse-based...., however this was a diagnostic research design 2. in this study, we set EMO triage assessment as reference standard, because, EMO is different profession who have different skill set in clinical setting. The agreement process was carried out after the EMO and nurses received exposure to triage training, the analysis was carried out using the Krippendorf method which is a variation of kappa 3. EMO is good enough as reference standard because they directly asses the patients in the ED, so that they have relatively equal information required to produce triage decision. EMO also work under direct supervision of Emergency Medicine specialist 4. the Buderer formula for sample size in diagnostic study was calculating total sample needed, not number subject in each triage category, futhermore, we use screening test assumption (high sensitivity) and double the sample size due to predetermined plan to analyze variability based on age categories (<60 YO and over 60 YO) 5. we add paragraph in the discussion section that address information about undertriage and overtriage" } ] } ]	1	https://f1000research.com/articles/12-328
https://f1000research.com/articles/12-1367/v1	18 Oct 23	{ "type": "Research Article", "title": "Prevalence, serovars, and risk factors associated with the presence of Salmonella in pork sold in public markets in Quito, Ecuador", "authors": [ "Christian Vinueza-Burgos", "Luis Hidalgo-Arellano", "Carlos Gómez-Coronado", "José Luis Medina-Santana", "María Cevallos-Almeida", "Christian Vinueza-Burgos", "Luis Hidalgo-Arellano", "Carlos Gómez-Coronado", "José Luis Medina-Santana" ], "abstract": "Background: Salmonella enterica are bacteria that include more than 2,500 serovars. Most of these serovars have been linked to human foodborne illnesses, mainly related to poultry and pigs. Thus, these animals are considered the reservoirs of many Salmonella serovars and strains related to antibiotic resistance. This study aimed to determine the prevalence, serovars, β-lactam resistance genes, and the risk factors associated with Salmonella enterica in pork commercialized in open markets of Quito city.\nMethods: For this, 165 pork meat samples were taken from municipal markets in three areas in the city. These samples were microbiologically processed following the ISO 6579-2014 standardized method. The polymerase chain reaction (PCR) test was used to identify Salmonella serotyping and resistance genes. Strains not identified by PCR were typed by the Kauffman White Le Minor scheme. A multivariate analysis was performed to identify risk factors associated with the presence of the microorganism.\nResults: Salmonella prevalence in pork was 9.1%. Identified serovars were 4, [5], 12: i:- (53.3%), Infantis (33.3%), and Derby (13.4%). Furthermore, the β-lactam resistance genes bla CTX-M-65 could be identified in three S. infantis isolates. Multivariate analysis showed that temperature (above 8°C) and cutting surfaces (wood) presented significant association values.\nConclusions: This research represents the first report of several epidemiological aspects of Salmonella in pork in Ecuador.", "keywords": [ "Salmonella", "Infantis", "monophasic S. Typhimurium", "Derby", "risk factors", "pork", "antibiotic resistance", "Ecuador", "Beta-lactamase" ], "content": "Introduction\n\nThe consumption of undercooked food contaminated with non-typhoid Salmonella is one of the most important causes of human gastroenteritis worldwide. Foodborne diarrheal disease agents also caused 230,000 of the 420,000 deaths due to foodborne hazards in 2010. Of these, non-typhoidal S. enterica accounted for 59,000 deaths.1\n\nContaminated food of animal origin is an important source of infection and spread of Salmonella.2 This contamination can occur at any stage in the production chain.3,4 Animals such as pigs can be infected or colonized by different Salmonella serovars, developing a disease or becoming a reservoir of this microorganism, excreting and spreading it.5 Contaminated pork plays an important role as one of the main sources of human infection with Salmonella in several countries.6–8 It has to be considered that cross-contamination of food with Salmonella may occur by kitchen instruments, improper hygienic handling, etc.9\n\nDifferent Salmonella serovars can be implicated in a large number of human infections. Therefore, serovar identification is essential in the epidemiological surveillance of this pathogen.10 Several serovars have been reported in pork and pig production, associated with different geographical localization. Thus, S. Derby and S. Typhimurium were the most prevalent serovars in Europe, Oceania, Asia, and North America,11 while S. Derby has been reported as the most pervasive serovar in pork in Latin America.12\n\nBesides, antimicrobial resistance has posed a critical problem for human and animal health in the last 20 years.13 The overuse of antibiotics in these two areas has contributed to the emergence of antibiotic resistance in foodborne bacteria.14 Thus, several studies have reported multi-resistant Salmonella strains (MDR) in which Salmonella isolates producing extended-spectrum beta-lactamase enzymes (ESBL) are common findings.15–17 Although the importance of non-typhoid Salmonella and its antimicrobial resistance is evident in food production, epidemiological information about the presence of this bacteria in pork is still limited in Ecuador. Therefore, this research aimed to estimate the prevalence of Salmonella serovars, antimicrobial resistance, and risk factors associated with Salmonella enterica in pork meat sold in markets in Quito-Ecuador.\n\n\nMethods\n\nA total of 165 pork samples were collected in 11 traditional markets in three areas of Quito. Samples of 100 g of meat from 25 butcheries were collected between March and May 2021. Each sample was collected in sterile plastic flasks and transported to the laboratory in an icebox at 2–8°C.\n\nAn epidemiological questionnaire to estimate the risk factors for pork contamination was developed and applied to the butchery employees (Table 1).\n\nSalmonella was isolated and identified according to the ISO 6579: 2017 standardized method.18 Briefly, 25 g of pork and 225 ml of Buffered Peptone Water – BPW (BD Difco 218105 – USA) were placed in a sterile zip bag and homogenized to obtain a 1:10 suspension. The combination was incubated at 37°C ± 1°C for 18 h ± 2 h. After incubation, 0.1 ml of the pre-enriched culture as 1–3 equally spaced spots on the surface of Modified Semisolid Rappaport Vassidialis - MSRV plates (BD Difco 218681 – USA) and incubated at 41.5°C for 24 h ± 3 h. A loop of 1 μl was taken inside the edge of the opaque growth in MSRV and plated in the Xylose Lysine, Deoxycholate – XLD agar (BD Difco 278850 – USA) and incubated at 37°C for 24 ± 3 h. Typical colonies of Salmonella spp. in XLD (black center with a slightly transparent reddish area) were then identified by biochemical tests. These tests included Triple Sugar Agar – TSI (BD Difco 226540 – USA), Lysine Iron Agar – LIA (BD Difco 284920 – USA), Simmons Citrate BD (Difco 211620 – USA), and Urea broth (BD Difco 227210 – USA). All the positive isolates were conserved at -70°C in a Brain Head Infusion medium (BD Difco 241830 – USA) with glycerol (Fisher Chemical G33500 – USA).\n\nDNA extraction was performed using the boiling method. Briefly, Salmonella isolates were plated in XLD agar and incubated at 37±1°C for 24 hours. A typical Salmonella colony was transferred to a sterile Eppendorf tube containing 300 μl of 1X TE buffer (Tris base Promega H5131 – USA + EDTA Promega V4231 – USA) and lysed at 95°C for 20 minutes. The supernatant was collected and stored at -20°C.\n\nSerovars Infantis, Enteritidis, Typhimurium, and its monophasic variant (1,4, [5], 12: i:-) were identified by polymerase chain reaction (PCR), using the invA gene as housekeeping control. Primers and annealing temperature for these PCR protocols are described in Table 2. GoTaq® Flexi DNA Polymerase (Promega M8291 – USA), nuclease-Free Water (Promega P1197 – USA), and dNTP Mix (Promega U1515 – USA) were used as PCR reagents on a SimpliAmp™ Thermal Cycler (Thermo Fisher A24811 – USA) to perform all reactions. According to the Kauffmann-White scheme, Salmonella isolates not typed by PCR were serotyped using the agglutination method.19 Briefly, each strain was recovered in Nutrient Agar (BD Difco 213000 – USA) and incubated for 16 to 20 h at 37°C ± 2. Then, the agglutination test was performed, confronting the bacterial suspension to specific antisera in a multi-cup plate. Positive agglutination is visualized by aggregate formation (more or less cottony appearance) exerting a moderate circular agitation of the plaque. Determination of somatic antigen (O antigen) requires the primary test of polyvalent sera (OMA, OMB, OMC, OMD, OME, OMF, and OMG) followed by monovalent ones (Remel™ Agglutinating Sera – UK). To determine flagellar antigen (H antigen), agglutination with one of the mixing sera for orientation (HMA, HMB, HMC) or the versatile serum H1 was observed (Remel™ Agglutinating Sera – UK). The determination of the flagellar antigen is obtained by successive elimination until detection of agglutination with one of the specific sera included in the mixing serum (search for major H then minor H). The combination of somatic antigen and flagellar antigen defines the serotype of the strain under study. The Kauffmann–White scheme gathers the groups and the corresponding sera.\n\nIdentification of antimicrobial resistance Salmonella isolates was carried out using the Kirby-Bauer disk diffusion method according to the Clinical and Laboratory Standards Institute guidelines.22 Briefly, from a culture of 18 to 24 hours on Nutrient Agar (BD Difco 213000 – USA), several colonies were taken with a handle and inoculated in physiological serum to reach a turbidity equivalent to 0.5 of the McFarland scale. The previous suspension was seeded into the Müller-Hinton plates (BD Difco 275730 – USA) using a swab without leaving any free area. After, antibiotic discs were placed equidistantly using sterile tweezers. The plates were incubated at 37°C for 16–18 hours and the diameter of the inhibition halos was measured. The clinical cut-offs of M100 CLSI standards (CLSI, 2022) were used as references integrating intermedia values as resistant. The antibiotics used were: Ampicillin (Oxoid, USA; 10 μg), Cefoxitin (Oxoid CT0003B – USA; 30 μg), Cefotaxime (BD 231606 – USA; 30 μg), Ceftazidime (BD 231632 – USA; 30 μg), Amoxicillin + clavulanic acid (Oxoid CT0223B – USA; 30 μg), Ertapenem (BD 232175 – USA 10 μg), Tetracycline (Oxoid CT0054B – USA; 30 μg), Tigecycline (Oxoid CT1841B – USA; 15 μg), Chloramphenicol (Oxoid CT0013B – USA; 30 μg), Ciprofloxacin (Oxoid CT0425B – USA; 5 μg), Sulfamethoxazole + Trimethoprim (Oxoid CT0052B – USA; 30 μg), Gentamicin (Oxoid CT0024B – USA; 10 μg), Amikacin (Oxoid CT0107B – USA; 30 μg), Nitrofurantoin (Oxoid CT0036B – USA; 300 μg), Fosfomycin (Oxoid CT0758B – USA; 200 μg).\n\nPCR further studied isolates with phenotypic resistance to beta-lactams to detect blaCTX-M, blaTEM, blaCMY, and blaSHV genes. Additionally, the blaCTX-M subgroups were identified for later sequencing. Primers and annealing temperature for these PCR protocols are described in Table 3. PCR reagents and equipment used for serotyping by PCR were used in this step.\n\nAll amplified PCR products were exanimated by electrophoresis in a 1% Agarose, LE, Analytical Grade (Promega V3125 – USA) on 0.5X TAE Buffer (Promega V4281 – USA) and stained with SYBR™ Safe DNA Gel Stain (Invitrogen S33102 – USA). Amplicons’ size was estimated by 100 bp Plus DNA Ladder (Bioneer D-1035 – Korea). Gel casting and electrophoresis were performed in a horizontal electrophoresis system (CBS Scientific HSU-014, EPS-300X – USA). Specific bands were visualized on ENDURO™ UV Transilluminator (Labnet U1001 – USA). Raw and edited images of all PCR products are available in the Underlying data.35 All betalactamese PCR products were sent for sequencing to Macrogen Inc. (Seul-South Korea), and obtained sequences were aligned against reference sequences by the web tool ResFinder 4.0.36\n\nThe free software R Studio (Version 1.4.1717) was used for statistical analysis. Descriptive statistics were used to facilitate the calculation of frequencies observed for each variable that would be used in the univariate analysis. For the bivariate analysis, we included variables of interest regarding the prevalence of Salmonella and then performed the chi-squared test and Fisher’s exact test. A univariate and multivariate logistic regression study was used to obtain odds ratios and 95% confidence intervals (CI). The level of significance was determined as p < 0.05.\n\n\nResults\n\nThe prevalence of Salmonella was 9.1% (15/165; CI95% = 5.6-14.5).\n\nThe PCR technique allowed the identification of five S. Infantis and eight monophasic variants of S. Typhimurium (1,4,[5],12:i:-) isolates. Additionally, two S. Derby isolates were characterized by the Kauffman White scheme.\n\nFour antimicrobial resistance profiles were found in 11 isolates (Table 4). Three and seven isolates of S. Infantis and S. 1,4,[5],12:i:- presented multi-resistant patterns, respectively. The two S. Derby and two S. Infantis isolates showed to be susceptible to all tested antibiotics.\n\n* Four Salmonella isolates were susceptible to all tested antibiotics.\n\nThe highest resistance levels were present in three S. Infantis isolates with resistance phenotypes for 11 antibiotics. Additionally, all S. 4,[5],12:i:- isolates showed resistance to tetracycline and chloramphenicol (Table 5). The blaCTX-M-65 gene was identified in all the S. Infantis isolates resistant to cefotaxime. On the other hand, none of the studied β-lactamase genes were identified in S. 4,[5],12:i:- isolates resistant to β-lactams.\n\nIn bivariate analysis, the variable “Meat cutting surface wood” showed a significant association with Salmonella in pork (p = 0.0349). Multiple logistic regression analysis determined that the variable “Meat preservation temperature” (higher than 8°C) also showed significant values (p = 0.031) (Table 6).\n\nFull responses for the survey, metadata, and susceptibility test reports are available in the Underlying data.77\n\n\nDiscussion\n\nThis research aimed to determine the prevalence of Salmonella enterica in pork meat in public markets of Quito, Ecuador. Identification of Salmonella serovars, antimicrobial resistance profiles, and risk factors associated with the presence of the microorganism were included in this work.\n\nIn the present study, the prevalence of Salmonella in pork was 9.1% (95% CI = 5.6 – 14.5). Another study in Quito reported a higher Salmonella occurrence in pork in 2016.37 This decrease in Salmonella occurrence could indicate that some interventions for improving market sanitary conditions could have been implemented. Several studies around the world have reported different levels of Salmonella in pork. In Europe, the prevalence of Salmonella in pork was 0.64% in 2019 (n=20 613),38 while in Asian countries, the prevalence of Salmonella varies from 14.1% to 57.74%.3,39,40 Overall, variations of Salmonella prevalence within countries or among regions of the world could be associated with the implementation of specific technologies in meat treatment or the existence of specific regulations that could be put in place in Ecuadorian markets.41\n\nSalmonella Typhimurium monophasic variant (S. 1,4,[5],12:i:-) was the predominant serovar in this study (53.4%), becoming the first report of this serovar in pig meat in Ecuador.\n\nIt has been mentioned that isolation of S. 1,4,[5],12:i:- has increased worldwide during the last 20 years.42 Pigs are ranked as the main reservoir of this serovar in the European Union.43 Furthermore, S. 1,4,[5],12:i:- has become one of the most common variants of Salmonella in pork production,44,45 being considered an emerging serovar in many countries.45 The present study demonstrates that this serovar may be relevant in the epidemiology of Salmonella linked to food contamination in Ecuador.\n\nConcerning S. Infantis, our results differ from those reported by Mejia et al.,37 who showed this serovar as the most isolated one in pig meat samples in retail markets in Ecuador. Since the later study samples were taken from supermarkets, this difference could be determined by the pig meat supply chain. In this regard, pork in traditional markets comes from many small pig production farms. On the other hand, pork from supermarkets comes from a few companies with intensive industrial production. These facts could explain the differences between studies. Moreover, S. Infantis has been reported as one of the most frequent serovars in industrial poultry production in many countries,46–48 indicating that this serovar is well adapted to industrial conditions.49,50 Since S. Infantis has been reported to cause human diseases,51 the epidemiology of this serotype in pork and its relationship with other meat products (e.g., poultry) should be further investigated. Similar considerations must be made for other serovars like S. Derby because the surveillance of Salmonella serovars shapes the epidemiology of these pathogens in foodstuffs.\n\nAntimicrobial resistance (AMR) of Salmonella isolates from pork and pig production has been reported in other countries at regional and global levels showing multi-resistant phenotypes.52,53 However, AMR varies according to Salmonella serotypes. In this study, S. Infantis was the least susceptible serotype with resistance patterns of up to seven antimicrobial families. In the same way, S. Infantis isolates with high rates of AMR have been reported in the poultry industry of Ecuador,50,54 which has been linked to the overuse of antimicrobials in this sector.55 However, multi-resistant S. Infantis has been reported worldwide, demonstrating that multi-resistance is an important feature of this serovar, possibly linked to specific plasmids. Thus, the capacity of S. Infantis to acquire genetic determinants of resistance has been associated with the “plasmid of emerging S. enterica Infantis” (pESI) and related plasmids (pESI-like plasmids).56 The blaCTX-M-65 gene identified in three S. Infantis isolates has been closely related to this megaplasmid in local studies50,54,57,58 and globally.59–61\n\nThe same can be said for S. 4, [5],12:i:- whose majority of isolates showed multi-resistant patterns. Moreover, this serotype has been reported in several countries, showing that S. 4,[5],12:i:- is specially adapted to the pig production sector and could represent a public health concern.62–64\n\nHigh levels of AMR Salmonella have been related to the incorrect use of antibiotics in animal production. The administration of cephalosporins and other beta-lactams in pig production has seen to increase in many countries, like France,65 India,66 and Brazil.67 Moreover, in Ecuador, the misuse of antibiotics in animal production systems has been reported.68,69 This aspect has particular relevance since beta-lactams are widely used in animal husbandry.70,71 It must also be considered that ESBL genes could determine failure in treating diseased people with complicated infections caused by Salmonella and other bacteria to which horizontal transference of genes may occur.72 In the present work, we found that meat preservation above 8°C (OR = 1.15) and wooden surfaces for meat cutting (OR = 59.31) were risk factors for Salmonella in pork meat. This is unsurprising since the lack of an appropriate cool chain allows the growth of contaminating microorganisms and pathogens in food products.73 Besides, the porosity of wood in cutting tables will enable bacteria to grow in the presence of humidity, promoting cross-contamination of foodstuffs with Salmonella.74–76 Whether Salmonella isolates recuperated in our study originated in the primary sector or are the result of such cross-contamination events should be further studied, targeting samples from pig production farms and conducting analysis of genomic clonality.\n\nIn conclusion, pork expended in traditional markets of Quito showed contamination of Salmonella enterica, whose main serovars are of public health concern. Beta-lactam-resistance in Salmonella isolates is also remarkable, which could become a risk for pork consumers.", "appendix": "Data availability\n\nFigshare: PCR images of Prevalence, serovars, and risk factors associated with the presence of Salmonella in pork sold in public markets in Quito, Ecuador. https://doi.org/10.6084/m9.figshare.24195030.v1. 35\n\nThis project contains the following underlying data:\n\n• CTX-M-9 Edited.jpg\n\n• CTX-M-9 RAW.jpeg\n\n• fljA-B-C edited.jpg\n\n• fljA-B-C raw.jpeg\n\n• S_typhimurium_edited.jpg\n\n• S_typhimurium_Raw.jpeg\n\nFigshare: Pork_database_risk_factors.xlsx. https://doi.org/10.6084/m9.figshare.23699505.v1. 77\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgment\n\nWe acknowledge to Health Services of Quito Municipality for the assistance and collaboration provided in the markets for the collection of samples. We also are grateful for the help provided by Laboratorio de Resistencia Antimicrobiana del Instituto Nacional de Investigación en Salud Pública - INSPI “Dr. Leopoldo Izquieta Perez” for their collaboration in the identification of the Salmonella Derby serovar. We also acknowledge Dr. Pamela Martinez for her help in the statistical analysis.\n\n\nReferences\n\nWHO (World Health Organization): WHO estimates of the global burden of foodborne diseases. Foodborne disease burden epidemiolgy reference group 2007-2015. World Heal Organ; 2015; 46(3): 1–15. Reference Source\n\nJackson BR, Griffin PM, Cole D, et al.: Outbreak-associated Salmonella enterica serotypes and food Commodities, United States, 1998-2008. Emerg. Infect. Dis. 2013 Aug; 19(8): 1239–1244. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNgo HHT, Nguyen-Thanh L, Pham-Duc P, et al.: Microbial contamination and associated risk factors in retailed pork from key value chains in Northern Vietnam. Int. J. 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Poult. Sci. 2022 Feb; 101(2): 101611. PubMed Abstract \| Publisher Full Text \| Free Full Text Reference Source\n\nBurnett E, Ishida M, de Janon S , et al.: Whole-Genome Sequencing Reveals the Presence of the blaCTX-M-65 Gene in Extended-Spectrum β-Lactamase-Producing and Multi-Drug-Resistant Clones of Salmonella Serovar Infantis Isolated from Broiler Chicken Environments in the Galapagos Islands. Antibiot (Basel, Switzerland). 2021 Mar 5; 10(3): 1–13. Publisher Full Text Reference Source\n\nAlba P, Leekitcharoenphon P, Carfora V, et al.: Molecular epidemiology of Salmonella Infantis in Europe: insights into the success of the bacterial host and its parasitic pESI-like megaplasmid. Microb. genomics. 2020; 6(5). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDrauch V, Kornschober C, Palmieri N, et al.: Infection dynamics of Salmonella Infantis strains displaying different genetic backgrounds–with or without pESI-like plasmid–vary considerably. Emerg. Microbes Infect. 2021; 10(1): 1471–1480. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGarcía-Soto S, Abdel-Glil MY, Tomaso H, et al.: Emergence of Multidrug-Resistant Salmonella enterica Subspecies enterica Serovar Infantis of Multilocus Sequence Type 2283 in German Broiler Farms. Front. Microbiol. 2020 Jul 17; 11(July): 1741. Publisher Full Text\n\nPossebon FS, Tiba Casas MR, Nero LA, et al.: Prevalence, antibiotic resistance, PFGE and MLST characterization of Salmonella in swine mesenteric lymph nodes. Prev. Vet. Med. 2020; 179(179): 105024. Publisher Full Text\n\nPeruzy MF, Proroga YTR, Capuano F, et al.: Occurrence and distribution of Salmonella serovars in carcasses and foods in southern Italy: Eleven-year monitoring (2011–2021). Front. Microbiol. 2022; 13(October): 1–10. Publisher Full Text\n\nHelmuth IG, Espenhain L, Ethelberg S, et al.: An outbreak of monophasic Salmonella Typhimurium associated with raw pork sausage and other pork products, Denmark 2018-19. Epidemiol. Infect. 2019; 147: e315. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nVerliat F, Hemonic A, Chouet S, et al.: An efficient cephalosporin stewardship programme in French swine production. Vet. Med. Sci. 2021 Mar; 7(2): 432–439. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTamta S, Kumar ORV, Singh SV, et al.: Antimicrobial resistance pattern of extended-spectrum β-lactamase-producing Escherichia coli isolated from fecal samples of piglets and pig farm workers of selected organized farms of India. Vet. World. 2020 Feb; 13(2): 360–363. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nViana C, Grossi JL, Sereno MJ, et al.: Phenotypic and genotypic characterization of non-typhoidal Salmonella isolated from a Brazilian pork production chain. Food Res. Int. 2020 Nov; 137: 109406. PubMed Abstract \| Publisher Full Text\n\nLowenstein C, Waters WF, Roess A, et al.: Animal husbandry practices and perceptions of zoonotic infectious disease risks among livestock keepers in a rural parish of quito, Ecuador. Am. J. Trop. Med. Hyg. 2016 Dec; 95(6): 1450–1458. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWaters WF, Baca M, Graham JP, et al.: Antibiotic use by backyard food animal producers in Ecuador: a qualitative study. BMC Public Health. 2022; 22(1): 1–11. Publisher Full Text\n\nDas N, Madhavan J, Selvi A, et al.: An overview of cephalosporin antibiotics as emerging contaminants: a serious environmental concern. 3 Biotech. 2019 Jun; 9(6): 231. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPeruzy MF, Capuano F, Proroga YTR, et al.: Antimicrobial Susceptibility Testing for Salmonella Serovars Isolated from Food Samples: Five-Year Monitoring (2015–2019). Antibiotics. 2020 Jun; 9(7): 365. Publisher Full Text\n\nYang X, Wu Q, Zhang J, et al.: Prevalence, Bacterial Load, and Antimicrobial Resistance of Salmonella Serovars Isolated From Retail Meat and Meat Products in China. Front. Microbiol. 2019 Sep; 10. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMilkievicz T, Badia V, Souza VB, et al.: Development of a general model to describe Salmonella spp. growth in chicken meat subjected to different temperature profiles. Food Control. 2020 Jun; 112: 107151. Publisher Full Text\n\nGeresu MA, Desta WZ: Carriage, Risk Factors, and Antimicrobial Resistance Patterns of Salmonella Isolates from Raw Beef in Jimma, Southwestern Ethiopia. Infect. Drug Resist. 2021 Jun; 14: 2349–2360. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDantas STA, Rossi BF, Bonsaglia ECR, et al.: Cross-Contamination and Biofilm Formation by Salmonella enterica Serovar Enteritidis on Various Cutting Boards. Foodborne Pathog. Dis. 2018 Feb; 15(2): 81–85. Publisher Full Text\n\nCliver D: Cutting Boards in Salmonella Cross Contamination.2006; 538–542.\n\nCevallos-Almeida MB, Vinueza-Burgos C, Medina-Santana JL, et al.: Pork_database_risk_factors.xlsx. [Dataset]. figshare. 2023. Publisher Full Text" }	[ { "id": "234636", "date": "15 Feb 2024", "name": "Patricio Retamal", "expertise": [ "Reviewer Expertise Microbiology" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThis article describes the detection of Salmonella serovars in pork meat from several markets in Quito, Ecuador. It's an interesting work that depicts contamination rates of this food commodity and raises concerns about public health risks for people involved in processing or consuming this product due to the presence of multidrug-resistant pathogenic bacteria.\nHowever, there are some major comments about the text that should be addressed by the authors before indexing.\nA major issue is related to the serotyping methodology. The PCR reaction for serotyping should be backed up with the traditional Kauffmann-White scheme or with whole-genome sequencing. Because PCR may have some false positive results (as indicated in the cited reference), all isolates should have been confirmed with KW. Why did the authors do it partially?\nConclusions, both in the abstract and within the main text, should address the main findings of this work.\nCited references need an update. Just one of them is from 2023, and some data is definitely old. For instance, the first paragraph of the introduction indicates cases from 2010.\nThe text should be revised by a native English speaker. There are several mistakes throughout the manuscript.\nWhat was the criterion for the selection of markets? Clarification is required.\nWhat was the criterion for the selection of butcheries and interviewed employees?\nNormally, variables included in epidemiological surveys are selected from previous reports or locally identified during in situ observations. What were the sources for the included variables?\nOther minor comments:\nThe Kauffmann-White serotyping is a standard procedure that does not require a detailed description. A reference is enough. The same occurs with the Kirby-Bauer method.\nWhat was the control strain in the Kirby-Bauer procedure? It is required to validate results.\nTables 4 and 5 should be merged, and optimally, all isolates should be described (antimicrobial phenotypes and genotypes) in this new table.\nIn the discussion, the second paragraph, the potential causes of differences between Salmonella prevalence values between countries or continents are multifactorial, but authors identify \"technologies for meat treatment or specific regulations.\" I think a broader analysis should be made for observed differences.\nIn the discussion, paragraphs 3 and 4 should be merged.\nIn the discussion, the fifth paragraph, I don't understand the statement \"because the surveillance of Salmonella serovars shapes the epidemiology of these pathogens in foodstuffs.\" Please give some clarification.\nPlease verify references 6 and 8. I think they are incompletely written.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? 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": "11378", "date": "19 Jun 2024", "name": "Jose Luis Medina-Santana", "role": "Author Response", "response": "Dear Patricio Retamal, Departamento de Medicina Preventiva Animal, Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile Next, we will answer your questions and recommendations regarding the evaluated article. a) A major issue is related to the serotyping methodology. The PCR reaction for serotyping should be backed up with the traditional Kauffmann-White scheme or with whole-genome sequencing. Because PCR may have some false positive results (as indicated in the cited reference), all isolates should have been confirmed with KW. Why did the authors do it partially? Response: PCR used in this research has been extensively proved as an appropriate method for the tested serotypes in this research (Infantis, Enteritidis, Typhimurium, and (1,4, [5], 12: i:-)). Moreover, we have proved its specificity compared with WGS in more than 800 Salmonella isolates of our collection. Therefore, we think that it is a reliable method to access the serotype of Salmonella isolates of this study. In Ecuador, there is not a reference laboratory for Salmonella serotyping. Therefore, performing KW in all isolates is cumbersome and costly and was not included in this project. It is important to mention that WGS was later performed in these isolates confirming the serotyping results. Information of WGS is not included in this manuscript since it is part of another publication. b) Conclusions, both in the abstract and within the main text, should address the main findings of this work. Response: We changed conclusions in lines 30-33. c) The cited references need an update. Just one of them is from 2023, and some data is definitely old. For instance, the first paragraph of the introduction indicates cases from 2010. Response: We updated the references in lines 41-43 and 45-47. References for other parts of the manuscript are updated. d) The text should be revised by a native English speaker. There are several mistakes throughout the manuscript. Response: The text has been revised. e) What was the criterion for the selection of markets? Clarification is required. What was the criterion for the selection of butcheries and interviewed employees? Response: Clarification added in 73 - 78 f) Normally, variables included in epidemiological surveys are selected from previous reports or locally identified during in situ observations. What were the sources for the included variables? Response: Clarification added in 84 - 85 g) The Kauffmann-White serotyping is a standard procedure that does not require a detailed description. A reference is enough. The same occurs with the Kirby-Bauer method. Response: The Kauffmann-White method has been deleted and replaced in lines 135 to 137 according to the previous commentary. Reference to the Kirby-Bauer method is included in line 137 and additional text has been deleted. h) What was the control strain in the Kirby-Bauer procedure? It is required to validate the results. Response: information added in lines 152-153. i) Tables 4 and 5 should be merged, and optimally, all isolates should be described (antimicrobial phenotypes and genotypes) in this new table. Response: tables 4 and 5 show different data. We think they should be displayed separately for a better understanding. We do not report genotypes in this study. j) In the discussion, the second paragraph, the potential causes of differences between Salmonella prevalence values between countries or continents are multifactorial, but authors identify \"technologies for meat treatment or specific regulations.\" I think a broader analysis should be made for observed differences. Response: Clarification added in 225 - 227 k) In the discussion, paragraphs 3 and 4 should be merged. Response: Paragraphs merged. l) In the discussion, the fifth paragraph, I don't understand the statement \"because the surveillance of Salmonella serovars shapes the epidemiology of these pathogens in foodstuffs.\" Please give some clarification. Response: Clarification added in 247-249. m) Please verify references 6 and 8. I think they are incompletely written. Response: references verified." } ] }, { "id": "240450", "date": "15 Feb 2024", "name": "Ma Soledad Vázquez-Garcidueñas", "expertise": [ "Reviewer Expertise Molecular epidemiology of Salmonella", "Acinetobacter and Mycobacterium 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\nThis work is very relevant since it aimed to determine the prevalence, serovars, β-lactam resistance genes, and the risk factors associated with Salmonella enterica in pork since these animals are considered the reservoirs of many Salmonella serovars and strains related to antibiotic resistance, and this information is still limited in Ecuador. Identification of Salmonella serovars, antimicrobial resistance profiles, and risk factors associated with the presence of the microorganism were included in this work.\nIt is recommended to make the following modifications: The conclusion of the summary is obvious and uninformative, it is recommended to write one that better describes the results. In the introduction, if the information in pork is limited in Ecuador, put a reference to how little is known or in any case change it to non-existent information. Since they amplified beta-lactamase, it is necessary to justify in the introduction why these were specifically sought. In materials and methods, change minutes and hours by min and h respectively. In PCR amplifications, include the amount of DNA contained in the assay. If possible, update the bibliography since there are some references that are too old.\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": "11379", "date": "19 Jun 2024", "name": "Jose Luis Medina-Santana", "role": "Author Response", "response": "Dear María Soledad Vázquez-Garcidueñas, Facultad de Ciencias Médicas y Biológicas, Universidad Michoacana de San Nicolas de Hidalgo, Morelia, Michoacán, Mexico Next, we will answer your questions and recommendations regarding the evaluated article. a) The conclusion of the summary is obvious and uninformative, it is recommended to write one that better describes the results. Response: We changed conclusions in lines 30-33. b) In the introduction, if the information in pork is limited in Ecuador, put a reference to how little is known or in any case change it to non-existent information. Response: The reference is added in line 67. c) Since they amplified beta-lactamase, it is necessary to justify in the introduction why these were specifically sought. Response: The reference is mentioned in line 64. d) In materials and methods, change minutes and hours by min and h respectively. Response: words have been changed. e) In PCR amplifications, include the amount of DNA contained in the assay. Response: We used the boiling method as described. We did not perform DNA quantification since normally this method provides enough free DNA for PCR amplification. f) If possible, update the bibliography since there are some references that are too old. Response: References have been updated according to the commentaries of reviewer 1." } ] } ]	1	https://f1000research.com/articles/12-1367
https://f1000research.com/articles/13-663/v1	19 Jun 24	{ "type": "Research Article", "title": "Unlocking Innovation: How absorptive capability unleashes the potential of motivation and leadership to catalyze innovative work behaviors in Batam", "authors": [ "Eduard Sinaga", "Suparto Wijoyo", "Yetty Dwi Lestari", "Fendy Suhariadi", "Adrid Indaryanto", "Dwi Bambang", "Muhaimin Hikmah", "Suparto Wijoyo", "Yetty Dwi Lestari", "Fendy Suhariadi", "Adrid Indaryanto", "Dwi Bambang", "Muhaimin Hikmah" ], "abstract": "Background The significance of innovative work behavior is growing as organizations strive to maintain their competitiveness by hiring freelancer employees. This study aimed to examine how absorptive capability mediates the connections between job motivation, transformational leadership, and innovation work behavior in freelancers working in the oil and gas industry.\n\nMethods A quantitative methodology was employed through an online questionnaire, using a random sampling strategy involving 250 respondents. Furthermore, data analysis was performed using structural equation modelling.\n\nResults The findings indicate that job motivation and transformational leadership did not have a direct impact on innovation work behavior. However, they did have an indirect beneficial influence mediated by absorptive capability. This study revealed that absorptive skills play a vital role in facilitating the translation of job drive and transformational leadership into innovative work behaviors.\n\nConclusions The practical consequences involve firms embracing transformational leadership and establishing training programs to enhance employees' absorptive potential, thereby promoting innovation. Ultimately, cultivating absorptive skills is crucial for leadership styles and motivational elements to be evident in innovative work behaviors.", "keywords": [ "Absorptive capability", "Job motivational", "Transformational Leadership", "Innovation work behavioral", "freelancer" ], "content": "Introduction\n\nEmployee innovation work behavior has become a very important foundation for supporting the success of a company. An employee’s Innovation work behavioural is defined as a behavior to create, introduce, and implement ideas deliberately within the scope of a work role, group, or organization (Janssen, 1998; Scott & Bruce, 1994).\n\nTo achieve a high level of innovation, organizations need to improve their employees’ competitiveness by enhancing their knowledge, skills, and ability to perform multiple and diverse tasks (Dong et al., 2017) within the scope of an organization. Competition among companies in various sectors drives many companies to improve their efficiency, flexibility, agility, and innovation in employment (Michie & Sheehan, 2003). Competition between companies in various sectors encourages many companies to improve efficiency, including employee involvement in innovation work behavior, especially in the oil and gas industry.\n\nPrevious research has widely used the concept of absorptive capability in analyses at the organizational level (Cohen and Levinthal, 1990; Kamal and Flanagan, 2014). Innovation work is a deliberate proposal and application of new and better ideas, processes, practices, and policies aimed at organizational efficiency and long-term sustainable business success (Anderson et al., 2014).\n\nShafi et al. (2020) examined how transformational leadership is related to employee Innovation work behavioural through intrinsic job motivational, psychological empowerment, and creative process involvement and in addition The research results of Shin, et al. (2017) proved that job motivation has a positive effect on employee performance, whereas job satisfaction is independent.\n\nIn the oil and gas industry, several journals discuss absorptive capability as a supporter of innovation work behavior in the oil and gas industry (Ahmad, & Azmi, 2016), but not supported by job motivational and transformative leadership. Absorptive capability interacts with work environment factors to influence innovative work behavior of employees in the Vietnamese oil industry (Nguyen & Simkin, 2020), and the oil and gas company in the Middle East shows a positive influence of absorptive capability on the company's ability to innovate (Al-Husseini, & Elbeltagi, 2018), with the objective of permanent employee research that the role of freelancers has not been found in this study.\n\nThe oil and gas industry has permanent workers hired based on long-term strategies (Esswein et al., 2014). Have a multi-year or permanent working bond to ensure continuity of knowledge and experience in supporting long-term productive assets, and provide technical and managerial training to improve competence in line with technological developments and challenges of the oil and gas industry entitled to health benefits, bonuses, insurance, pension plans, and other facilities (Ramanigopal, 2013).\n\nHowever, at present, many oil and gas work projects are short-term, so organizations must innovate with innovative solutions using freelancer labor with consideration of cost efficiency, fresh and more objective ideas, skilled personnel, and always updated, flexible, and good service (Shkurupii et al., 2021).\n\nFreelancers are defined as unemployed or end-dependent contractors or may be referred to as private entrepreneurs because they do not have a permanent employment contract with whom they are employed and usually do not receive a fixed salary but are paid at a certain cost for the work they do (Burke & Cowling, 2020).\n\nBy providing new insights to employees, thus leading to innovation work behavior (Ávila, 2022), it is imperative to link this research with the employee status called Freelancer. Based on the explanation above, there are three potential variables that need more investigation to achieve and measure innovation work behavior: absorptive capability, job motivation, and transformative leadership. However, the Freelancer in the O&G industry context has become crucial for further discussion because of the urgent need to support the company's competitive advantage and the number of freelancers who are increasingly more numerous than permanent employees.\n\nFurthermore, this research is expected to be academically able to fill the research gap on the influence of job motivational and transformational leadership on innovation work behavioral freelancers with absorptive capability as a variable mediator in oil and gas mines, and is expected to provide a solution contribution to the organization of companies working on projects with the needs of human resources at the international level.\n\nInnovation work behavioural refers to the intentional introduction and application of new ideas, processes, products, or procedures within one's work role, work unit, or organization (Janssen, 2000; Messmann & Mulder, 2011). As workplaces face increasing complexity and competitiveness, innovative work behavior is essential for organizational success and survival (Anderson et al., 2014). Employees must continuously seek and implement new approaches, knowledge, and technologies to improve their work performance, effectiveness, and adaptive capacities.\n\nBased on the previous literature review and model development, seven hypotheses were proposed to test the direct and indirect effects of job motivational and transformational leadership on absorptive capability and innovation work behavior to answer the question of whether the independent variables have a significant effect either independently or through the mediating role of absorptive capability in translating their influence on employee innovation work behavior.\n\nExtrinsic and intrinsic motivations are fundamental factors in the theory of motivation (Chang et al., 2021; Ryan & Deci, 2000). Extinctic motivation refers to motivation driven by external factors, whereas instinctive motivation relates to personal motivation that originates from within oneself (Ryan & Deci, 2000). The motivating factor for a person to choose to be a freelancer is that they have flexible work activities that can be done anywhere (Riyono & Usman, 2022). Absorptive capability has been marked as one of the most important abilities of multinational corporations, and in analyzing the ability of individuals to recognize, assimilate, and exploit new knowledge of forms of job motivation, namely instrumental and extrinsic, found significant positive relationships between absorptive ability and job motivation (Yildiz et al., 2019; Murovec & Prodan, 2009; Sancho-Zamora et al., 2022). An empirical study by Yildiz et al. (2019) suggest that the nature of innovation work behavior is complex and not fundamental enough to produce such behavior with only instrumental and extrinsic motivation. Individuals who are intrinsically or extrinsically motivated tend to have a natural interest in learning new things, exploring innovative ideas, and implementing the knowledge acquired to improve their performance. Hypothesis 1 can be submitted as follows:\n\nJob motivational has a significant positive effect on absorptive capability.\n\nOrganizational leadership styles diversify internal corporate knowledge and enable organizations to acquire and assimilate new external knowledge to enhance corporate creativity and innovation (Mokhber, Khairuzzaman and Vakilbashi, 2018). Absorptive capability allows companies to increase their speed, frequency, and level of innovation, which means that leadership is an ideal factor for companies to categorize, understand, and connect external knowledge to create more qualitative innovation (Leal-Rod, et al., 2014). Transformational leadership, characterized by inspiring and motivating qualities for followers, can boost the ability of organizations to absorb, assimilate, and apply new knowledge (Setyadi et al., 2023). This ultimately leads to an increase in absorptive capability; thus, Hypothesis 2 can be put forward as follows:\n\nTransformational leadership has a significant positive effect on absorbing capacity.\n\nThis study is also supported by research on the relationship between employee motivation towards innovation work behavior of R&D employees in three high-tech organizations with the results of the analysis of job motivational positive influence on employee innovation (Saether, 2019). Job motivation influences employee Innovation work behavioural is as follows: the higher the employee's motivation, both intrinsic and extrinsic, the higher the tendency to engage in innovative conduct such as producing ideas, products/processes, or new solutions that are beneficial to the Enkel et al. (2017), Kasımoğlu and Ammari (2020), and Kwon and Kim (2020).\n\nJob motivational has a significant positive influence on Innovation work behavioural\n\nThe results of Lin's study (2023) show that (1) transformational leadership has a positive impact on innovative work behavior, (2) the identification of organizations/employee voices mediates the relationship between transformative leadership and innovative working behaviors, and (3) the indirect influence of transformational leadership on innovation work behavior (through organizational/employee voice identification) is stronger when employees work in more innovative climates. This study provides hotel management insights into why and under what conditions employees behave in this manner. Thus, Hypothesis 4 can be submitted as follows:\n\nTransformational leadership has a significant positive influence on employee Innovation work behavioural\n\nAbsorptive capability is defined as a set of organizations that routinely and in a company's process, acquire, assimilate, transform, and exploit knowledge to produce organizations with dynamic capabilities (Zahra and George, 2002). Absorbency is the ability of an organization to exploit external knowledge (Grünfeld, 2003), initiate change from within, and identify and assist ideas from the external environment (Lewin, et al., 2011) as a dynamic ability that enables an organization to build competence (Zahra dan George, 2002). The higher the capacity of employees and organizations in absorbing new external knowledge and applying it, the higher the employee's innovative behaviour, such as generating new useful ideas/products/processes Sethibe and Steyn (2017) and Surucu et al. (2021), can be proposed as follows:\n\nAbsorptive capability has a significant positive influence on employee Innovation work behavioural.\n\nAbsorptive capability is defined as a set of organizations that routinely and in a company's process, acquire, assimilate, transform, and exploit knowledge to produce organizations with dynamic capabilities (Zahra and George, 2002). Absorbency is the ability of an organization to exploit external knowledge (Grünfeld, 2003), initiate change from within, and identify and assist ideas from the external environment (Lewin, et al., 2011) as a dynamic ability that enables an organization to build competence (Zahra dan George, 2002). Absorptive capability capable of mediating the influence of Job motivational is the motivation of work that drives the improvement of the absorptive capability of individuals and organizations. Increased absorptive capability facilitates the application of new knowledge in the form of innovation work behavior by employees, and Hypothesis 6 can be submitted as follows:\n\nAbsorptive capability positively mediates the relationship between job motivation and IWB.\n\nAbsorptive capability is defined as a set of organizations that routinely and in a company's process, acquire, assimilate, transform, and exploit knowledge to produce organizations with dynamic capabilities (Zahra and George, 2002). Absorbency is the ability of an organization to exploit external knowledge (Grünfeld, 2003), initiate change from within, and identify and assist ideas from the external environment (Lewin, et al., 2011) as a dynamic ability that enables an organization to build competence (Zahra dan George, 2002). Absorptive capability is capable of mediating the influence of transformational leadership on Innovation work behavioural. Transformative leadership increases the absorptive capabilities of organizations and employees. Increased absorption capacity further facilitates the application of new knowledge in the form of employee innovation behavior.\n\nAbsorptive capability positively mediates the relationship between transformational leadership and employee Innovation work behavioural.\n\n\nMethods\n\nIn order to better understand the connections between innovative work behavior, transformational leadership, absorptive capacity, and job motivation among independent contractors in the oil and gas sector, this study uses a quantitative research methodology. Using an online survey, information was gathered from a sample of 250 independent contractors operating in Batam, Indonesia. The study variables were measured using validated scales in the questionnaire, which had a 5-point Likert-type response format. The period of data gathering in 2023 was June through October.\n\nThe questionnaire was tested with a small sample of independent contractors in order to account for any biases and guarantee the accuracy of the results. It was then modified in response to their input. A randomly chosen sample received the online questionnaire via email, and participants were guaranteed anonymity and confidentiality. We acquired informed consent from each individual.\n\nUsing AMOS 26.0 software, structural equation modeling (SEM) was used to analyze the gathered data. Several relationships between variables can be examined simultaneously while accounting for measurement error with SEM. The study used a two-step methodology: first, confirmatory factor analysis was used to assess the measurement model, and then, the structural model was examined to test the proposed links.\n\nThe population in this study was freelancer employees or freelancers working in the oil and gas industry under PT. NES Indonesia, PT. Brunel Indonesia and Spencer Ogan as many as 500 Freelancer employees with a wide range of educational backgrounds, qualification and competences who being working at several oil and gas worldwide company, join a wide variety of positions, And obtained as many as 250 valid respondents, data collection starts from June 2023 until October 2023.\n\nData collection techniques are the methods used by researchers to collect data from their researchers. As for data collection techniques, a questionnaire is a data collection technique that is carried out by giving a set of questions or written statements to respondents to be answered online via email. Research data is also obtained from reports and other documents, which is closely related to the object of research and reading literature as the theoretical basis that will be used as a theoretical foundation in this research for a four-month period.\n\nA 13-item scale that was modified from Aga et al. (2016) and Ferreras-Méndez et al. (2018) was used to measure transformational leadership. Four aspects of transformational leadership are evaluated by the scale: intellectual stimulation, customized consideration, inspirational motivation, and idealized influence. “My supervisor seeks differing perspectives when solving problems” (intellectual stimulation) and “My supervisor communicates a clear and positive vision of the future” (inspirational motivation) are two examples of example items. On a five-point Likert-type scale, participants indicated how much they agreed with each statement.\n\nA 10-item scale that was modified from Ávila (2022) and Duan, Wang, and Zhou (2020) was used to test absorbtive capability. The scale evaluates the capacity of an organization to obtain, incorporate, modify, and apply new information. Examples of such statements are “Our organization can apply new knowledge with the required skills” (transformation) and “Our organization can work more efficiently by implementing new knowledge” (exploitation). On a five-point Likert-type scale, participants indicated how much they agreed with each statement.\n\nA nine-item scale that was modified from De Jong and Den Hartog (2010) and Bourini (2021) was used to measure innovative work behavior. The measure evaluates a person's capacity to create, advance, and implement innovative ideas at work. “I generate original solutions for problems” (idea creation) and “I transform innovative ideas into useful applications” (idea realization) are two examples of example items. On a five-point Likert-type scale, participants indicated how much they agreed with each statement.\n\nThe complete list of questionnaire items used in this study is accessible at https://doi.org/10.6084/m9.figshare.25271419.v1 in the supplemental materials. All of the scales were chosen based on their proven psychometric qualities and prior application in comparable research settings, in order to reduce any potential biases and guarantee the validity and reliability of the measurements. Furthermore, before to being distributed to the entire sample, the questionnaire was tested on a limited group of independent contractors to evaluate its comprehensiveness and lucidity.\n\nThe degree to which the indicators employed to gauge a certain latent concept are actually related to one another is known as convergent validity (Franke et al., 2021). An analysis of the factor loadings was conducted to assess convergent validity. According to Lee (2019), loading factors are coefficients that assess how latent variables, also known as constructs, relate to their indicators. The indicator measures the construct, as shown by a strong factor loading. Loading factors are used in the validity and reliability tests of this study; an outer loading value of more than 0.5 indicates validity (Rodriguez et al., 2016).\n\nConfirmatory factor analysis was used in this study to assess the measurement instrument's concept validity. The analysis's findings demonstrate that each construct variable indicator had significant loading factors that were all more than 0.5. These findings offer compelling proof of the study instrument's great construct validity. According to the study's theoretical framework, the instrument's high construct validity score suggests that it is successful in measuring the desired variables.\n\nConstruct Reliability (CR) values larger than 0.7, on the other hand, suggest that an instrument has a high degree of consistency when assessing the intended construct in the context of reliability testing (Marsh et al., 2014). When testing the same construct again on the same sample, the instrument or questions in the instrument are consistent if the Construct Reliability (CR) value is higher than 0.7. Stated differently, the tool produced consistent and dependable results.\n\nThe Average Variance Extracted (AVE) value of each variable in this study was used to determine the Construct Reliability (CR) values, which were found to be greater than 0.7 based on the results of CR analysis. These results show that the data are trustworthy and that the Construct Reliability criteria is satisfied. If the measuring tool were to be used repeatedly on the same sample, the high CR values indicate that it has a high degree of internal consistency and would yield results that are comparable.\n\nFor the study's conclusions to be accurate and reliable, the measurement model's convergent validity and reliability are essential. The significant factor loadings show how well the indicators capture the desired variables and how closely they connect to the corresponding constructs. The measuring scales' internal consistency and reliability are further supported by the high CR values, which instill trust in the data's outcomes and conclusions.\n\nThe results of the comprehensive model fit test showed that the model used was very good at explaining the existing data. To measure the degree of model fit, several key parameters were used, all of which showed good results. First, the Chi-Square/DF, which is one of the main indicators for measuring model suitability, has a value of 2.326. This value is much smaller than five, which indicates that the model has a very good degree of fit. In addition, the chi-square p-value is 0.000, which is obviously smaller than 0.05; therefore, this model is statistically significant.\n\nThe RMSEA (Root Mean Square Error of Approximation) value was 0.073. The range of RMSEA values (0.07 to 0.085) also showed that this model had a very good level of fit. The RMSEA p-value is 0.000, indicating a significant level of fit. The Goodness of Fit (GoF) index also supports these results, with measures such as ECVI, AIC, and CAIC showing low values and close to a perfect model.\n\nIn addition, various model assessment indices, such as NFI, RFI, IFI, TLI, CFI, RMR, GFI, AGFI, and PGFI, all show a good level of fit because they are close to the threshold, so they can be in the moderate and close fit categories. Based on these positive results, it can be concluded that this model is very good at explaining the data used in this study. The strong level of fit between the model and data confirms that this model can describe the relationships between the variables studied very well.\n\nThe data analysis in this study using software program AMOS version 26 for the Structural Equation Modelling. The alternative free software of the Structural Equation Modelling would be the package “lavaan” in R, which is available for free on the open-source statistical computation environment R accessible at https://www.r-project.org/.\n\nThis study was conducted in accordance with the Declaration of Helsinki, which outlines the ethical principles for medical research involving human subjects. Ethical approval for this study was obtained from the Universitas Airlangga Research Ethics Committee on (protocol number: 779/UN3. SPS/I/PT.01.06/2023 All participants were informed about the purpose and procedures of the study, and their rights as participants. Written informed consent was obtained from all participants prior to their involvement in the study. Participants were assured that their participation was voluntary, and they could withdraw from the study at any time without consequence. All data collected during the study were kept confidential and anonymized to protect participants' privacy.\"\n\n\nResults\n\nThe results of the tests revealed the direct and indirect effects of the independent variables on the dependent variable. In particular, job motivational and transformational leadership as independent variables are thought to affect absorptive capability and innovative work behavior as dependent variables, either directly or indirectly, through mediating relationships. The test results are described in more detail in the following paragraphs to provide a comprehensive picture of the pattern of relationships between variables in the proposed research model. Thus, the proof of the previously formulated hypotheses can be presented systematically to show the validity of the model and provide theoretical and practical implications for the research results.\n\nHypothesis testing aims to determine the relationship between independent and dependent variables. There is a significant relationship if the significance value is below 0.05, the critical ratio (CR) value is above the table (1.96). The hypothesis is tested by analyzing the estimated number of influences between variables in the model, and the estimated value was considered significant if the significance level (sig p) was ≤ 5%.\n\nThe majority of respondents were men (90.8%) and only 9.2% were women. Regarding educational level, the majority had S1 education (57.2%), followed by SLTA (21.6%), D3 (14.4%), and S2 (6.8%). The respondents were mostly over 35 years old (74.8%), 21.6% were 25-35 years old, and only 3.6% were under 25 years old. In terms of work experience, 29.2% had worked for 6-10 years, 27.6% for 11-15 years, 20.4% over 21 years, 15.2% from 1 to 5 years, and 7.6% had been working for 16-20 years, leading to the list characteristics in the link https://doi.org/10.6084/m9.figshare.25271281.v1.\n\nHere are the results of the direct influence test presented in Table 1:\n\nThe results of the direct effect analysis show the direct influence of independent variables (job motivational and transformative leadership) on the dependent variable (absorptive capability and innovation work behavior), as described below:\n\nAbsorptive capability <--- Job motivation (0.715, p < 0.001): Job motivation has a significant positive influence on absorptive capability (H1 Received). With a coefficient of 0.715, any increase in job motivation by one unit will result in an increase of approximately 0.715 units in absorbing capacity. Absorbing Capacities < Transformative Leadership (0.392, p < 0,001): A significant positive impact of transformative leadership on absorbing capabilities (H2 Receiving). With an increase in job motivation by 0.392, every increase in transformational leadership by one unit will lead to an increase of approximately 0.392 units of absorptive capability. Innovation work behavioral--- < 0.686, p< 0.001: A significant negative impact of the significant absorbant capacity on inactivity will not be considered to be greater than the value of inefficiency (H3Received in relation to work).\n\nInnovation work behavioral <--- Transformative Leadership (0.03, p > 0.05): The influence of transformative leadership on innovation work behavior is also not significant (H5 Rejected). P-values greater than 0.05 indicate that this relationship is not significant.\n\nHere are the results of the indirect influence test shown in Table 2:\n\nThe results of the indirect effect analysis show indirect influence (through mediator) of the independent variables (transformative leadership and job motivation) on the dependent variable (innovation work behavior) through the mediator (absorptive capability) as follows: transformative leadage ---> absorptive capability ---> innovation work behavior (0.547, p < 0.001), and transformational leadership has a significant indirect impact on innovative behaviors through absorptive capability mediators (H6 Accepted). A coefficient value of 0.547 indicates that any unit increase in transformative leadership will result in an increase in innovation work behavior of approximately 0.547 units through intermediate absorbant capacity.\n\nJob motivational→ absorptive capability → innovation work behavior (0.944, p < 0.001): There is a significant indirect influence of job motivation on innovation work behavior through the Absorbing Capabilities Mediator (H7 Accepted). A coefficient value of 0.944 indicates that every one-unit increase in job motivation results in an increase in Innovative Conduct of approximately 0.944 units through the absorptive capability mediator.\n\nThe results of the R-squared test are presented in Table 3.\n\nThe results of this R-Square analysis provide a deeper understanding of how big the impact of absorptive capability is on innovation work behavior, and vice versa. Although the analytical model explains most of the variability in both, approximately 45% of the variation in innovation work behavior cannot be explained by the factors in the model. These factors may include other variables not included in this analysis or external factors that directly affect innovation work behavior. Therefore, this R-Square analysis validates the importance of absorptive capability and innovation work behavioral variables in the context of this research, but also shows that there are other factors that affect innovation work behavior that need to be considered.\n\n\nDiscussion\n\nThe test results indicated a notable and favorable influence of job motivation on absorptive capability, as evidenced by a coefficient value of 0.715. These findings suggest that for every one-unit increase in job motivation, there is a corresponding increase of approximately 0.715 units in absorption capacity. The results emphasize the significance of job motivation as a critical element that improves the capacity of individuals and organizations to assimilate and apply new knowledge, which is essential for growth and achievement in the workplace. This study corroborates previous discoveries made by Yildiz et al. (2019), who also observed a favorable correlation between job motivation and absorptive capability in the textile industry. Additionally, this aligns with the research conducted by Ali and Park (2016), who demonstrated the beneficial influence of self-efficacy on knowledge acquisition.\n\nFurthermore, this study elucidates the distinction between intrinsic and extrinsic motivation, as delineated by Chang et al. (2021) and Ryan and Deci (2000). Extrinsic motivation is influenced by external stimuli, whereas intrinsic motivation originates from an individual's own drive. Riyono and Usman (2022) conducted a study which found that motivation, encompassing both inner and extrinsic factors, significantly influenced the decision to pursue freelancing, with the need for job flexibility being a primary driving force. This demonstrates that desire impacts not only absorptive capability but also individual decisions regarding career paths.\n\nAs described by Zahra and George (2002), absorptive capability refers to an organization's capability to effectively obtain, integrate, convert, and leverage external knowledge. This study shows the significant impact of absorptive capability on improving organizational innovation and adaptation. This finding supports the hypothesis that absorptive capability is a crucial skill for both multinational corporations and individuals to identify and leverage new knowledge.\n\nThe test demonstrated that transformative leadership had a significant and favorable impact on absorptive capability, as evidenced by a coefficient value of 0.392 and a p-value below 0.001. This demonstrates that leadership styles that inspire and motivate can improve capacity to assimilate and exploit new knowledge. This research aligns with the findings of Mokhber, Khairuzzaman, and Vakilbashi (2018), who demonstrated that different leadership styles can enhance the variety of information within an organization and promote the integration of new knowledge from external sources.\n\nNevertheless, the test results indicated that job motivation did not have a substantial impact on employee innovation work behavior/, since the p-value was above 0.05. This implies that job motivation alone may not be adequate for stimulating inventive behavior, necessitating the inclusion of other elements or additional variables for a more comprehensive explanation. This discovery contradicts the research conducted by Dai et al. (2022), who concluded that individual motivation and a climate that fosters innovation have a substantial impact on students' inventive behavior.\n\nConversely, research has demonstrated that the ability to absorb new information and ideas has a strong and beneficial impact on one's tendency to engage in Innovation work behavioural. This relationship was quantified using a coefficient of 0.686. This statement asserts that the capacity to absorb and apply new information significantly impacts the innovative conduct of individuals and organizations. The findings of Kang and Lee (2017) and Saether (2019) further corroborate these results, demonstrating the favorable influence of absorptive capability on innovation behavior across different industries.\n\nIn addition, the test findings indicate that absorptive capability has the ability to moderate the impact of job incentives on employee inventive behavior, with a coefficient value of 0.944. This implies that, while job motivation does not directly impact inventive behavior in a substantial way, it can enhance innovative conduct by increasing absorption capacity. According to a study conducted by Cui, Wu, and Tong (2018), absorptive capability plays a role in promoting open innovation by connecting different forms of management relationships to invention.\n\nAdditionally, this study indicates that transformative leadership exerts a substantial indirect impact on innovation work behavior through absorptive capability. This finding aligns with previous research conducted by Flatten et al. (2015), Afsar et al. (2014) and Noruzy et al. (2013), who demonstrated that absorptive capability mediates between transformational leadership and innovation work behavior.\n\n\nConclusions\n\nStudies emphasize that absorptive capability, which refers to an individual's aptitude to identify, incorporate, and leverage new knowledge, significantly influences the motivation of freelancers to pursue and excelle in their employment. Companies can ensure their ability to adapt to changing circumstances and further enhance their knowledge and competence by employing individuals with a high level of absorption capability.\n\nFurthermore, studies emphasize that transformational leadership significantly influences freelancers’ absorptive capability by providing a solid basis for them to explore tactics, such as training and development, that can enhance their ability to absorb new knowledge and ideas. This, in turn, leads to an increased motivation for work. This leadership style has the potential to improve freelancers' capacity to effectively identify, absorb, and integrate external knowledge, thereby elevating organizations' innovation levels.\n\nUsers who work as freelancers: A strong work ethic fosters a drive to actively pursue, comprehend, and utilize novel information, hence enhancing individuals' capacity to assimilate and effectively apply new knowledge. This, in turn, significantly influences proficiency levels. Freelancers should prioritize the enhancement of their absorptive capabilities. This can be achieved by consistently pursuing and incorporating new knowledge pertinent to their jobs. Engaging in training and self-development can enhance proficiency in several areas. Enhances Job motivation as an independent contractor.\n\nResearch examining the correlations between job motivation, transformative leadership, absorptive capability, and innovation work behavior has yielded significant findings. These findings emphasize the positive impact of job motivation and inspiring leadership on the capacity of organizations and individuals to assimilate and utilize new knowledge, ultimately fostering Innovation work behavioural. Nevertheless, the research is subject to some limitations, including restricted generalizability of the findings, potential bias in the data provided by individuals themselves, and the use of cross-sectional designs that cannot definitively establish causality. These limitations indicate that although the findings offer useful insights into the elements that influence absorptive capability and innovation work behavior, there is still a need for additional studies to enhance our understanding of these dynamics in many situations through the use of more varied approaches.\n\nFuture research should focus on conducting longitudinal studies to further investigate the relationship between work motivation, transformative leadership, absorptive capability, and innovation work behavior. These studies would examine the lasting impact of transformational leadership on absorptive capability and innovation in different organizational settings while also addressing the limitations of previous research. This methodology will allow researchers to evaluate the cause-and-effect relationship and patterns of change over a period of time, offering a more comprehensive understanding of how leadership interventions can effectively improve the long-term innovative capabilities of companies. Furthermore, the integration of variables such as organizational culture and individual psychological aspects might provide a fresh outlook on how internal and external factors influence or mediate these interactions. This research can assist firms in creating work environments that are more favorable to innovation by considering the aspects that impact motivation and ability to create.\n\nMoreover, employing a mixed-method approach to comprehend the impact of digital technology on absorptive ability and innovation work behavior can provide valuable insights into the current digital era. This entails examining how transformative leadership can be adjusted and implemented in hybrid and remote work settings to uphold or amplify motivation and innovation. This research aims to address the existing gaps in the literature and offer practical counsel to managers and leaders in effectively navigating the challenges and opportunities presented by technology and evolving work environments. This study aims to enhance our comprehension and practical knowledge of strategies that effectively promote and cultivate Innovation work behavioural within firms, regardless of their sector or working conditions.\n\nUniversitas Airlangga Research Ethics Committee approved this study on April 17, 2023 (approval number: 779/UN3.SPS/I/PT.01.06/2023). The committee reviewed the study protocol to make sure it followed ethical principles for research involving human participants. All participants provided written informed consent prior to participating in the study.\n\nAll freelancers who participated in the study provided informed consent by filling out the consent form in the attached questionnaire in Google Forms. Selecting the consent option provided detailed information about the purpose of the study, which was to examine the relationship between work motivation, transformational leadership, absorptive capacity, and innovative work behavior among freelancers in the oil and gas industry. The participants were informed of the necessary procedures, including completing an online questionnaire for approximately fifteen to twenty minutes, and that they could leave the study at any time without any consequences. The consent form also emphasized the voluntary nature of participation, ensuring that their responses would be kept confidential and that their data would be anonymized to protect their privacy.\n\nThe Research Ethics Committee of Universitas Airlangga has approved the written consent process as part of the research protocol (approval number: 779/UN3.SPS/I/PT.01.06/2023). The ethics committee examined the research forms and procedures to ensure that they followed the ethical principles for research involving human participants.", "appendix": "Data availability\n\nDirect links to the particular datasets supporting your research on the connections between innovative work behavior, transformational leadership, absorptive capacity, and job motivation among independent contractors in the oil and gas sector are provided in this section. The findings of the questionnaire, the list of questions and their descriptions, and the profiles of the 250 freelancers who took part in the study are all included in the datasets, which are stored in the Figshare repository.\n\nThe data underlying this study are available in the Figshare repository:\n\n• Dataset of questionnaire results from the respondents of absorptive capability of freelancers: https://doi.org/10.6084/m9.figshare.25284934.v1\n\n\n\n1. Figshare: List of questions and descriptions of the questionnaire - Absorptive capability mediates the connections between job motivational, transformational leadership, and Innovation work behavioural in freelancers working in the oil and gas industry: https://doi.org/10.6084/m9.figshare.25271419.v1\n\n2. Figshare: Profile of 250 freelancers working in the oil and gas industry in Batam, Indonesia: https://doi.org/10.6084/m9.figshare.25271281.v1\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgements\n\nWe would like to express our gratitude to the freelancer employees who participated in this study for dedicating their time and effort to completing the surveys. We are also thankful for the guidance of our supervisors and colleagues in developing the theoretical framework and the research methodology applied in this study. Careful review and constructive feedback from anonymous reviewers substantially helped improve the quality of this paper.\n\n\nReferences\n\nAfsar B, Badir Y, Saeed B: Transformational leadership and innovative work behavior. Ind. Manag. Data Syst. 2014; 114(8): 1270–1300. 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Publisher Full Text" }	[ { "id": "294191", "date": "05 Jul 2024", "name": "Udin Udin", "expertise": [ "Reviewer Expertise Leadership Studies", "Islamic Business Ethics", "Knowledge Management", "Innovative Work Behavior", "Organizational Effectiveness" ], "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 need major revision:\nINTRODUCTION 1. It should clearly articulate the gap in the existing literature that the study aims to address. Providing a more explicit statement of the research problem or gap would help readers understand the significance of the study. 2. It would be beneficial to highlight the specific novelty or contribution of the study to the field of absorptive capability, motivation, and leadership research, especially in the context of freelancers in the oil and gas industry.\nMETHODOLOGY 1. Providing more detailed information on the methodology used to assess validity and reliability, including specific statistical tests and results, would enhance the transparency and reproducibility of the study. 2. While the study mentions the number of participants (250 freelancers), additional information on the sample size justification and power analysis would strengthen the validity of the study results.\n\n3. The study reports various model fit indices such as RMSEA, NFI, RFI, IFI, TLI, CFI, RMR, GFI, AGFI, and PGFI. While these indices provide insights into the model fit, it would be beneficial to provide a detailed explanation of each index, its interpretation, and the thresholds used to determine model fit.\nDISCUSSION 1. It should provide a thorough interpretation of the study findings in relation to the research questions or objectives. Clearly explaining how the results align with the study's hypotheses or expectations would enhance the clarity of the discussion. 2. It is important to avoid simply restating the results but instead focus on explaining the significance of the findings in the context of absorptive capability, motivation, and leadership in freelancers in the oil and gas industry. 3. Addressing any discrepancies or unexpected results by comparing them with established theories or empirical evidence can offer valuable insights into the complexity of the relationships between absorptive capability, job motivation, transformational leadership, and innovation work behavior. These recent readings are strongly recommended: a) (Udin, 2024)(Ref-1) b) (Udin et al., 2024)(Ref-2) c) (Udin et al.,2022))(Ref-3)\nCONCLUSION 1. It should clearly outline the practical implications of the study findings for organizations, leaders, and freelancers in the oil and gas industry. Providing actionable recommendations based on the results can enhance the relevance of the research. 2. Discussing how the identified relationships between absorptive capability, job motivation, and transformational leadership can be leveraged to improve innovative work behavior and organizational performance would add depth to the practical implications.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] }, { "id": "322293", "date": "08 Oct 2024", "name": "Sabar Sabar", "expertise": [ "Reviewer Expertise Human Resources Strategy and Change 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\nH1. Explain why and how motivation (both intrinsic and extrinsic) specifically can affect absorptive capability. The relationship that needs to be established is Motivation to absorptive capability, while learning alone does not describe capability. This will provide a stronger basis for the hypothesis.\nH2. 1. Explain further how the key components of transformational leadership (e.g., idealized influence, inspirational motivation, intellectual stimulation, and individualized consideration) can specifically enhance absorptive capability. 2. Specifically explain how transformational leadership helps in the process of recognizing, assimilating, and applying new knowledge. This will help provide a stronger argument for why transformational leadership affects absorptive capability..\nPlease use the suggestions for the next development hypothesis.\nResearch Method In the research method, please add a common method bias referring to Podsakoff et al, 2013. (Ref 1)\nDiscussion Research findings do not only refer to theoretical findings, but it is necessary to add how the findings are relevant in the context of the research being studied\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "12603", "date": "15 Oct 2024", "name": "Eduard Sinaga", "role": "Author Response", "response": "H1. Explain why and how motivation (both intrinsic and extrinsic) specifically can affect absorptive capability. The relationship that needs to be established is Motivation to absorptive capability, while learning alone does not describe capability. This will provide a stronger basis for the hypothesis. Answer: Through a number of pathways, motivation—both intrinsic and extrinsic—has a major impact on absorptive ability. People that are intrinsically motivated are naturally curious to learn new things, which prompts them to interact with new material more deeply. Goal-oriented behavior can be stimulated by extrinsic motivation, which also promotes active application and information acquisition. These motivational elements improve both behavioral and cognitive characteristics, including proactive information seeking and experimentation, as well as cognitive functions like attention allocation and elaborative processing. Crucially, motivation affects a person's ability to identify important new information, integrate it with prior knowledge, and use it effectively in their workplace. This goes beyond simple learning. The hypothesis that links motivation to absorptive capacity is strengthened theoretically by this all-encompassing influence on the fundamental elements of absorptive capacity (acquisition, assimilation, transformation, and exploitation of knowledge). This emphasizes that motivation impacts not only learning but the entire process of knowledge absorption and utilization H2. 1. Explain further how the key components of transformational leadership (e.g., idealized influence, inspirational motivation, intellectual stimulation, and individualized consideration) can specifically enhance absorptive capability. 2. Specifically explain how transformational leadership helps in the process of recognizing, assimilating, and applying new knowledge. This will help provide a stronger argument for why transformational leadership affects absorptive capability.. Answer 1 Motivation affects absorptive ability through promoting thought patterns and actions that are essential for acquiring and applying knowledge. Extrinsic motivation promotes proactive knowledge seeking and application, but intrinsic motivation fosters curiosity and deeper engagement with new information. These elements have a direct impact on a person's capability to identify, absorb, process, and apply knowledge—the fundamental elements of absorptive capacity. This affects not just learning but the entire process of assimilating knowledge and applying it effectively in professional settings. This strengthens the case for the hypothesis that motivation and absorptive capacity are positively correlated. Answer 2 Through its essential elements, transformational leadership improves absorptive capacity: idealized influence stimulates knowledge seeking, inspirational motivation harmonizes learning with objectives, intellectual stimulation boosts knowledge transformation, and tailored consideration facilitates knowledge exploitation. This type of leadership makes it easier to identify new information by promoting environmental scanning, aids in knowledge assimilation through candid communication, and encourages experimentation to enhance knowledge application. Transformational leadership immediately affects the entire process of absorptive capacity by forming organizational culture and structures that support knowledge absorption. This makes a compelling case for transformational leadership's beneficial impact on absorptive capability. Question: Please use the suggestions for the next development hypothesis. Answer: The specific mechanisms by which motivation and transformational leadership improve absorptive capacity are now included in these created hypotheses, giving your research a stronger theoretical foundation. Question: Research Method In the research method, please add a common method bias referring to Podsakoff et al, 2013. (Ref 1) Answer: We took the advice of Podsakoff et al. (2013) to address any common technique bias. Procedures like time separation of data gathering and anonymity guarantee were put into place. In our structural equation model, we incorporated a common latent factor and performed statistical analyses using Harman's single-factor test. The marker variable technique was also utilized by us. These steps are intended to reduce typical procedure bias and improve the reliability of our results. Discussion Question Research findings do not only refer to theoretical findings, but it is necessary to add how the findings are relevant in the context of the research being studied Answer: We place our results in the perspective of the independent oil and gas sector in the Discussion. The significant moderating effect of absorptive capacity highlights how crucial it is for independent contractors to acquire and apply information in order to adapt to a variety of project types. Through absorptive capacity, the indirect effects of leadership and motivation on inventive behavior reveal intricate routes for innovation in this industry. These observations point to doable tactics that businesses may implement to boost freelancer creativity, like encouraging cultures of information sharing and offering a variety of learning opportunities. Our theoretical contributions gain depth from this industry-specific interpretation, which also provides practitioners in the sector with practical insights" } ] }, { "id": "311219", "date": "15 Oct 2024", "name": "Yandra Rivaldo", "expertise": [ "Reviewer Expertise Organizational", "Leadership", "Behaviour", "Performance" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nDear Author. I have read this paper with various academic perspectives. In general, this paper is interesting, but there needs to be improvement in several aspects and improvements to the main points of the research. 1. Introductory part - the aim of this research is stated to be to fill gaps, whereas no gaps have been stated yet. The gap does not only lie in previous results, but the gap also comes from scientific arguments in previous research or theoretical gaps between current research and previous theoretical approaches. Then, the paper should be equipped with outline data regarding field facts. 2. The paper needs to explain the main theoretical approaches that are relevant as a basis for hypothesis development. 3. Method - paragraph 1 250 Independent contractor, paragraph 4 250 sample, looks ambiguous, needs clarity. Then the questionnaire is distributed via email or online, the author must explain the evidence that the questionnaire was answered truthfully and to the right person, because in some cases irregularities in filling out often occur. Next, in the method section, the author needs to write the structural equation. 4. Discussion section - there are still many repeating sentences and results contained in the results section and explaining general things. In this section the author must further explore scientific arguments based on the findings in the results section, especially the empirical impacts and implications. Next, the sentence ''absorptive capability has the ability to moderate the impact of job incentives on employee inventive behavior'' moderation or mediation? Thank 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": "12648", "date": "17 Oct 2024", "name": "Eduard Sinaga", "role": "Author Response", "response": "I appreciate your thorough remarks. Our answer to the concerns raised is provided below I. 1. Research Gap Clarification: Our study's research gap stems from the scant examination of independent contractors' roles in the oil and gas sector, specifically with regard to innovative work behavior (IWB). Although earlier research has examined the impact of absorptive capability and innovative work behavior in the setting of permanent employees (e.g., Ahmad & Azmi, 2016; Nguyen & Simkin, 2020), the freelancing workforce has not received as much attention. Our research emphasizes the significance of job motivation and transformational leadership in promoting innovation among freelancers, an area that has not received enough attention in other studies, and the distinct dynamic that freelancers bring to the workforce. Additionally, by examining how absorptive capability mediates the relationship between job motivation, transformational leadership, and IWB specifically for independent contractors in the oil and gas sector, our study aims to close the scientific gap. There is a theoretical gap in our knowledge of how these principles apply in the setting of freelancing, which entails different motivational and leadership dynamics, as previous study has mostly concentrated on permanent employees. 2. Empirical Data Justification: Our study is based on particular field data about the oil and gas sector's increasing reliance on independent contractors. According to publications like Shkurupii et al. (2021), freelancers are being used more and more because of their affordability, adaptability, and capacity to offer new viewpoints on short-term tasks. This field reality emphasizes how important it is to look at how leadership and job motivation affect their ability to innovate. An empirical gap that emphasizes the industry's transition from permanent to freelance work is filled by our data collection from 250 freelancers in Batam, Indonesia. In conclusion, by concentrating on the function of independent contractors, their capacity for absorption, and the impact of job motivation and leadership in promoting IWB—topics that have not received much attention in the literature—this study helps to close the gaps in both prior findings and theoretical arguments. II. Our research incorporates a number of important theoretical frameworks that guide the formulation of our hypotheses: According to Cohen and Levinthal's (1990) Absorptive Capacity Theory: Because it explains how people and organizations can acquire, assimilate, transform, and use external knowledge, this theory serves as the foundation for our research. This ability is essential for encouraging innovative work behavior (IWB) in fast-paced settings such as the oil and gas sector. Based on this hypothesis, we postulate that the relationship among job motivation, transformational leadership, and IWB in independent contractors is mediated by absorptive capacity. Theory of Motivation (Ryan & Deci, 2000): Both intrinsic and extrinsic motivation are considered to be important determinants of inventive behavior in our study. According to motivation theory, people are motivated to pursue innovation by both intrinsic (personal fulfillment) and extrinsic (external) incentives. This theory backs up our claim that absorptive capacity and, in turn, IWB are positively impacted by job motivation. Bass (1985) developed the theory of transformational leadership. Enhancing absorptive ability is a key function of transformational leadership, which involves motivating, energizing, and assisting staff members. Our notion that transformational leadership enhances absorptive ability, which in turn promotes IWB, is supported by this theory. Our hypothesis is that this leadership approach motivates independent contractors to participate more actively in creative processes. We provide a strong framework for comprehending how transformational leadership and job motivation support absorptive capacity and creative work practices among independent contractors in the oil and gas sector by combining these three important theoretical stances. The hypotheses we investigate in the study are based on these theories. III. 1. Sample Clarification: We recognize that defining the sample size is not always clear. There are 250 independent contractors in the oil and gas sector that make up the study sample. This figure remains constant throughout the document. To make sure that our data is representative of the independent workforce in the sector, we employed a random sample technique to choose 250 legitimate respondents from the larger pool of freelancers. To prevent misunderstandings, we will make sure that the terminology used to describe the sample size is consistently explicit throughout the text. 2. Ensuring Truthful Responses and Targeted Participants: A secure online survey platform was used to distribute the questionnaire via email, ensuring both the distribution and correctness of the responses. Anonymity was ensured to promote honesty, and each response was carefully chosen. To reduce irregularities, we implemented a number of measures, such as: Before sending the questionnaire, make sure the respondent is associated with independent activity in the oil and gas sector. ensuring that every respondent was distinct and only took part once. To guarantee responder accuracy and variety, random sampling was used. Although we acknowledge the possibility of abnormalities, these techniques were used to reduce the risk and guarantee that the replies were accurate and from the target sample. Third, we used the AMOS 26.0 software to analyze the data using Structural Equation Modeling (SEM), which we discussed in the method section. We evaluated both direct and indirect connections between factors, including innovative work behavior, transformational leadership, job motivation, and absorptive capacity, using the SEM technique. We employed a two-step procedure, first validating the measurement model using Confirmatory Factor Analysis (CFA) and then assessing the structural model. A thorough grasp of the connections between the variables in our study is provided by this methodology. IV. 1. Repetition in the Discussion part: We recognize that the discussion part has a lot of repetition. Although we acknowledge that there may have been an overabundance of repetition of these conclusions, the discussion was meant to highlight the most important findings from the data. Clarity and reinforcement of the results' comprehension were our goals. We do, however, take notice of your suggestion and will put more emphasis on interpreting the results than on reproducing them. In particular, we will examine our findings' scientific ramifications in greater detail, relating them to the larger body of literature and previously discussed theoretical frameworks. 2. Scientific Investigation of Empirical Effects and Implications: We acknowledge the necessity of investigating the scientific claims and ramifications of our results in more detail. The study's empirical data provides valuable insights into the ways in which absorptive capacity mediates the connections between freelancers' innovative work practices, transformational leadership, and job motivation. These results point to useful ramifications for oil and gas companies, especially with regard to how they set up their leadership styles and incentive schemes to foster innovation through absorptive ability. We will broaden the conversation to go into more detail on the precise organizational adjustments and tactics that could be used to maximize absorptive capacity and its moderating influence on independent contractor innovation. 3. An explanation of mediation as opposed to moderation: We would like to make it clear that absorptive capacity is operating as a mediator in this situation rather than a moderator in response to the statement that \"absorptive capability has the ability to moderate the impact of job incentives on employee inventive behavior.\" Our findings suggest a mediating function rather than a moderating one, as absorptive capability enables the conversion of transformational leadership and job motivation into creative work behavior. To prevent misunderstandings, we will make sure this distinction is stated in the conversation in a clear and concise manner." } ] } ]	1	https://f1000research.com/articles/13-663
https://f1000research.com/articles/13-662/v1	19 Jun 24	{ "type": "Research Article", "title": "Satisfaction of patients treated in a Physical Medicine and Rehabilitation department during the Covid-19 pandemic: a cross-sectional study", "authors": [ "Leila Hamadou", "Rihab Moncer", "Rim Ghammam", "Walid Ouanes", "Sonia Jemni", "Rihab Moncer", "Rim Ghammam", "Walid Ouanes", "Sonia Jemni" ], "abstract": "Background Patients treated in Physical Medicine and Rehabilitation (PM&R) departments benefit from global and multidisciplinary long-term care. The study of satisfaction represents an important element in the evaluation of the quality of the healthcare provided. The aim of this study is to assess the level of satisfaction of patients treated in the PM&R department of Sahloul university hospital of Sousse Tunisia as well as the associated factors during the year 2020.\n\nMethods We conducted a cross-sectional study, including patients treated in the hospitalization and the outpatient units of the PM&R department. Monnin and Perneger scale validated in Arabic was used to measure satisfaction in its different dimensions. Medical data were completed from patients’ records.\n\nResults A total of 240 patients were included in our study. The level of satisfaction was significantly higher with the admission procedures for inpatients compared to outpatients (87.9% vs. 60.0%, p<0.001). Regarding the global assessment, 82.1% of patients were satisfied. Multivariate analysis showed that for administrative procedures, consultation for outpatients was a factor of dissatisfaction (aOR=0.18, p<0.001). Patients’ physiotherapy treatment during the Covid-19 period was negatively associated with satisfaction for logistics (aOR= 0.44, p=0.011) and for the global assessment of health care provided in our department (aOR= 0.46, p=0.04).\n\nConclusion Our study showed overall good levels of satisfaction in the department of PM&R of Sahloul. However, more studies should follow to determine other factors that can influence satisfaction.", "keywords": [ "physical medicine and rehabilitation", "patient satisfaction", "questionnaire", "inpatients", "outpatients." ], "content": "Introduction\n\nNowadays, the quality of care provided to patients by health establishments represents one of the essential objectives of health systems in the world and in Tunisia specifically. In fact, the evaluation of the quality of the services offered is a validated indicator of the efficiency of a health system.1\n\nSeveral elements reflect the quality of the healthcare, including patient satisfaction.2–4\n\nIn Tunisia, a North-African developing country, intra-hospital activity in third line hospitals represents a very important part of the activity of the healthcare system, whether for hospitalizations, surgical procedures or outpatient consultations.\n\nSahloul University Hospital in Sousse is one of the largest 3rd line hospitals in the Tunisian center. It also drains several regions of east, center, north and south of Tunisia.\n\nIn physical medicine and rehabilitation (PM&R), the services differ from other medical or surgical department by the multidisciplinary management involving several healthcare providers (physiotherapists, nurses, occupational therapists, speech therapists, etc).\n\nSeveral studies focusing on the measurement of patient satisfaction in the PM&R departments have been carried out internationally.5–7 However, there are only a few publications on this subject in Tunisia.\n\nThe aim of our work is to study the satisfaction of inpatients and outpatients in the PM&R department of Sahloul hospital in 2020 and to specify the factors associated with satisfaction in order to improve the quality of the care provided during and after the Covid-19 era.\n\n\nMethods\n\nThis is a cross-sectional study conducted in the PM&R department of Sahloul university hospital, Sousse, Tunisia from January 2020 to December 2020 including inpatients and outpatients of the same department.\n\nThe inclusion criteria were patients of all ages consulting or hospitalized during the period from January 2020 to December 2020 until the calculated sample size was obtained.\n\nNon-inclusion criteria were comprehension or expression problems with the absence of a family member who accompanied the patient during his rehabilitation treatment to answer the questionnaire in his place and patients whose treatment did not require functional rehabilitation sessions as well as those who underwent rehabilitation sessions in another public hospital structure or in the private sector.\n\nThe size of our sample was calculated according to an expected prevalence of patient satisfaction estimated at 80.6%8 with a precision of 5% and an α risk of 5%. Thus, it was estimated at 237 patients.\n\nData collection was conducted by a single trained interviewer.\n\nFor each patient, we established a questionnaire in Arabic to collect data about:\n\n• Anamnestic data: The first part is an anamnesis of each patient on their socio-demographic characteristics: age, sex, educational level was specified for all patients whose age was greater than or equal to 06 years. The nature of the service offered (hospitalization or outpatient consultation), the pathology for which the patient is followed in PM&R and the occurrence or the absence of complication during hospitalization were also collected from patients’ medical records.\n\n• The Monnin and Perneger satisfaction scale: The second part was dedicated to the study of the satisfaction of patients treated in the physical medicine department.\n\nFor this, we used the scale developed by Monnin and Perneger9 published in 2002 and validated for inpatients and outpatients in rehabilitation settings. We used the validated Arabic version of this scale10 published by Devreux et al. in 20128 after contacting the corresponding author and obtaining permission to use the scale for our study.\n\nThis scale is made up of 14 questions exploring four dimensions (D) of satisfaction:\n\n• D1=Admission subscale (03 questions: item 1,2 and 3).\n\n• D2=Treatment subscale (05 questions: from item 4 to item 8).\n\n• D3=Logistic subscale (04 questions: from item 9 to item 12).\n\n• D4=Global assessment subscale (02 questions: item 13 and 14).\n\nThe satisfaction response for each question is based on a 05-point Likert scale (01 “poor,” 02 “fair,” 03 “good,” 04 “very good,” 05 “excellent”). Each item on the scale is then converted into a score out of 100 using the following formula: score (0–100) = 25 x (score (1–5)-1).9\n\nWe define a satisfied patient if he has a score >75 for the item considered corresponding to a response of 04=very good or 05=excellent for this item.\n\nData were analyzed using IBM SPSS version 10.0 software (IBM Corp., Armonk, NY, USA). The qualitative variables were presented in the form of counts and percentages. Quantitative variables were expressed as means +/- standard deviations or median and their interval interquartile (Q1-Q3).\n\nThe comparison of the percentages was carried out using the Chi 2 test according to the indication. The degree of significance (p) was set at 5%.\n\nBinary logistic regression model was performed for each satisfaction dimension. Variables with p value ≤0.2 at univariate analysis were included in the model (except the variable onset of complications during hospitalization).\n\nApproval from the Ethics Committee of the Faculty of Medicine “Ibn El Jazzar” Sousse was obtained for this study.11\n\nOur study does not involve any risk for the participants. We respected anonymity and medical secrecy when collecting the data. For minors, consent from the legal guardian has been obtained.12\n\n\nResults\n\nThe total number of patients included in this study was 240. Among these patients, there were 58.3% inpatients and 41.7% outpatients. Participants answered the questionnaire themselves in 84.6% of cases and 15.4% of the answers were provided by a family member who accompanied the patient during his physical therapy.13\n\nThe average age of the patients was 42±19.56 years with a minimum of 06 months and a maximum of 77 years (median: 45 [Q1=29, Q3=57] years). The majority of our study’s participants had primary education level (38.2%) and 22.3% of patients were illiterate. The distribution of participants according to socio-demographic characteristics is described in Table 1.\n\nThe most frequent conditions were the pathologies of the central nervous system (52.5%) with a predominance of post-traumatic paraplegia (10.4%), cerebral palsy (9.2%) and stroke sequelae (8.8%). Cauda equina syndrome represents the most common condition for the pathologies of the peripheral nervous system (2.9%). Polyarthralgia was the most common osteoarticular condition (11.7%).\n\nAmong the hospitalized patients included in our sample, 15% developed complications. Urinary tract infection was the most common complication (7.1%), followed by pressure ulcer (2.9%) and pulmonary embolism (1.4%) (Table 1).\n\nThe satisfaction regarding admission procedures (D1) was 76.2% (Figure 1). For the ease of administrative procedures (item 1), 71.7% of patients were satisfied. The rate of dissatisfaction (poor, fair and good) was higher with outpatients (45%) compared to the inpatients (16.5%). Concerning the courtesy and helpfulness of the secretaries (item 2), the overall satisfaction was 97.5% (95.7% for inpatients and 100% for outpatients). The participants questioned were 97.1% satisfied with the simplicity of scheduling and the time required to obtain the first appointment (item 3).\n\nFor functional treatment (D2) satisfaction was 58.8% (Figure 1): 85.1% of patients were satisfied with the physiotherapist's ability to put them at ease and reassure them (item 4). The explanations received regarding the treatment (item 5) were satisfying in 60.9% of cases (57.8% for hospitalization and 65% for outpatient consultation). The patients were satisfied with the feeling of security during the treatment (item 7: 88.3%) and the extent to which treatment was adapted to their problem (item 8: 73.3%).\n\nRegarding satisfaction with logistics (D3), 92.1% of patients were satisfied with the ease of access of physical therapy facilities (item 9), and 67.5% with the indications to help find the way around and in hospital buildings. The comfort of the room where physical therapy was provided (item 11) was satisfying in 75% of cases. The atmosphere in the physical therapy rooms was considered calm and restful (item 12) for 86.3% of patients.\n\nThe physical therapy was overall satisfying for 77.1% of patients (81.4% for inpatients and 71% for outpatients) (item 13).\n\nIn our population, 90.1% of participants would recommend our PM&R department to people close to them (item 14). The degrees of satisfaction regarding the items of Monnin and Perneger questionnaire in the Sahloul PM&R department are reported in Table 2.\n\nFor admission procedures (D1), inpatients were more satisfied than outpatients (87.9% vs 60.0%) with a statistically significant difference (p<0.001). Furthermore, we did not find any significant difference in satisfaction between hospitalization department and outpatient unit for functional treatment (D2), logistics (D3), and global assessment (D4). Regarding admission procedures (D1), patients aged 45 to 60 were satisfied at 88.2%. We found a statistically significant difference in satisfaction between the age groups for this dimension D1 (p=0.017). For functional treatment (D2), 73.7% of patients under 18 were satisfied. There was a statistically significant difference in the level of satisfaction between the different age groups for this dimension D2 (p=0.036). For the logistics (D3) and the global assessment of physical therapy (D4), we did not find a statistically significant relationship between age and patient satisfaction.\n\nIn our study sample, men were more satisfied than women with admission procedures (D1) (80.6% vs 73.0%). However, the difference was not significant (p=0.17). The level of satisfaction was not significantly different between men and women regarding the other dimensions (D2, D3 and D4).\n\nPatients with a secondary or university level of education had a higher level of satisfaction than those who were illiterate or had primary level of education for admission procedures (D1) (81.5% vs 78.1%) and functional treatment (D2) (61.5% vs 56.8%). However, the difference in satisfaction was not significant between these education levels and these two dimensions (D1 and D2) (p=0.563 and p=0.513 respectively). Besides, patients who were illiterate or had a primary education level (primary + preparatory) were more satisfied than those with a secondary or university education level for logistics (D3) (74.2% vs 60.0%) with a statistically significant difference (p=0.036). The level of satisfaction regarding the global assessment of the physical therapy (D4) was not significantly different between the two groups (p=0.14).\n\nBefore the Covid-19 pandemic, patients were significantly more satisfied (83.2%) with admission procedures (D1) than patients treated during the pandemic (71.7%) (p=0.042). However, the period of care (before or during the pandemic) did not affect the satisfaction of our population regarding the treatment received or the logistics (p=0.568 and p=0.051 respectively). In addition, global satisfaction of the physical therapy (D4) was significantly higher before this pandemic (88.4% vs 77.9%, p=0.038) (Figure 2).\n\nThe level of satisfaction with admission procedures (D1) was not statistically different according to the type of patient's pathology (p=0.892). Similarly, the level of satisfaction was not associated with the type of patients’ pathologies in the different dimensions (treatment, logistics and global assessment).\n\nThe patients included in our study who were hospitalized in the PM&R department were more satisfied in the absence of the occurrence of complication(s) during hospitalization for admission procedures (D1) (89.1%), functional treatment (D2) (58.8%), logistics (D3) (73.1%) and global assessment of care (D4) (86.6%) We did not find a statistically significant difference in satisfaction with services for all the dimensions studied in patients who presented one or more complications during hospitalization versus those who did not present complications. The satisfaction of our population according to the associated factors is reported in Table 3.\n\nWe determined the factors independently associated with each domain of our population's satisfaction scale. For this, we performed 04 binary logistic regression models (Table 4). The only independent factor after multivariate analysis for dimension 2 (Treatment) was age ≥ 60 years. Treatment during the pandemic decreased the level of satisfaction by 0.44 times (95% CI [0.233; 0.827], p=0.011) after adjustment for education level for dimension 3 and by 0.46 times (CI at 95% [0.218; 0.964] p=0.04) after adjusting for gender for dimension 4 (Table 4).\n\n* D3 education level adjusted model.\n\n** D4 gender adjusted model.\n\n\nDiscussion\n\nCurrently in Tunisia, there are only two hospitalization departments in physical medicine: in Tunis at the Kassab Institute of Orthopedics and at the Tunisian center at the Sahloul university hospital in Sousse. The PM&R department of Sahloul Hospital drains all patients from the center and sometimes from southern Tunisia where there is not yet a PM&R hospitalization unit. However, no work has been conducted in this department with the aim of evaluating the quality of the health care and describing the shortcomings of the services provided.\n\nWe decided to conduct a descriptive cross-sectional study to measure the satisfaction of inpatients and outpatients of the PM&R department of Sahloul university hospital during the year 2020, including patients from all age groups, which has not been achieved until now in a physical medicine department in Tunisia.\n\nOur study showed an overall satisfaction with administrative procedures (D1) of 76.3% with a statistically higher rate for hospitalizations versus outpatient consultations (87.9% vs 60.0%, p<0.001). Delanian et al.14 in 2008, using a self-administered questionnaire, studied the satisfaction of patients treated in a PM&R day hospital created at the Timone hospital in Marseille and the satisfaction with the reception at the admission office was 94%.\n\nThe difference in satisfaction of dimension D1 of our questionnaire that we found between hospitalization and outpatient consultation could be explained by the fact that at Sahloul university hospital, the hospitalization department and the admissions’ office for hospitalizations are located in the same main hospital building. Besides, registering for the outpatient consultation is done in a second building where the waiting time in front of the counters is longer, which is a major inconvenience for patients with a functional limitation.\n\nOur results showed a satisfaction rate for the treatment received in our service (D2) of 58.8%. The highest satisfaction rate was for the feeling of security during treatment (88.3%) and the lowest rate for the quality of information received at the end of treatment (57.9%). This is similar to the study conducted by Devreux et al.8 in Jeddah including the questionnaire on which we based to conduct our study, they found a satisfaction with the treatment of 79.9%, the feeling of security of 81.6% with the lowest rate for information received at the end of treatment: 69.2%.8\n\nJoublin15 studied the satisfaction of patients treated in “Le Belloy” functional and professional rehabilitation center, located in Oise-France. She found a high rate of satisfaction reaching 100% for the feeling about the competence of the physiotherapist and the quality of care, while the lowest satisfaction rate was 90% for the continuity of care.15 In Tunisia, Ghidaoui et al.16 found that 86% of parents believed that doctors were understanding with their children. Listening, availability and general benevolence of doctors towards the child were appreciated with 95% of parents satisfied.16 For satisfaction with the logistics (D3), our results showed a rate of 70.8%. This is far from the results of Joublin15 who found a satisfaction rate of 99% for the logistics of the functional and professional rehabilitation center Le Belloy, while Delanian et al.14 found 81% satisfaction with the logistics of the PM&R day hospital at the Timone hospital center in Marseille.\n\nThe global assessment of physical therapy (D4) in our department showed a satisfaction rate of 82.1%. This is similar to data from Devreux et al.,8 where the global satisfaction rate for rehabilitation care is 80.6%. Delanian et al.14 found global satisfaction estimated at 98% for patients treated in the PM&R day hospital in Marseille.14\n\nConcerning the factors associated with satisfaction studied in our work, our results showed for the socio-demographic factors a statistically significant difference in satisfaction between the age groups for the D1 admission procedures (p=0.017) and for the treatment received D2 (p=0.036). Our results join the data of the literature. In the study of factors associated with global patient satisfaction in rehabilitation facilities in New Jersey, USA, Oh-Park et al.17 found that the dissatisfied patients were older (mean age 68.9 versus 67.7).17\n\nIn our study, there was no statistically significant relationship between patient satisfaction and patients’gender for all the dimensions studied. For Afzal et al.18 also, gender did not show a significant effect on the satisfaction score. Besides, Thi et al.19 noted a higher frequency of complaints for women (60.4%) when measuring satisfaction.\n\nRegarding the education level, our results showed that patients who were illiterate or had a basic level of education were more satisfied than those with a secondary or university education level for logistics (D3) (p=0.036). Worldwide, Afzal et al.18 showed that illiterate or less educated patients were significantly more satisfied (p=0.003) with the care provided by the health establishment considered. Thi et al.19 reported a higher level of dissatisfaction in patients with a post-secondary level of education (72%) towards the quality of care.19 In Tunisia, in a rehabilitation department, Ghidaoui16 found similar results: the high level of education of mothers negatively influences satisfaction with the proper functioning of the department as well as therapeutic interventions.16\n\nRegarding the period of physical therapy, patients were more satisfied before the Covid-19 period for all the dimensions of the questionnaire in our study. In the literature, we found several studies of satisfaction during the Covid period before and after the implementation of new measures to protect patients.20,21\n\nRegarding the difference in satisfaction between the before and during Covid-19 period found in our study, this could be the consequence of the long waiting time in the queues at the check-in counters in the outpatient unit and its association with a greater risk of contamination by Covid-19 because of the non-respect of distancing and the wearing of masks by certain patients. During the waves of the pandemic, paramedical staff with chronic illnesses and the visually impaired have benefited from long-term leaves. This resulted in a lack of staff of physiotherapists working in the Sahloul PM&R department with deployment and solicitation of the remaining staff. These measures would have caused an exhaustion of the staff working in the Covid period, having as a probable consequence a drop in the performance and quality of the care provided, thus responsible for patient dissatisfaction. In Tunisia, telemedicine should be developed: prepare the legislative framework (virtual medical visits and remote drug prescriptions recognized by social security) and provide the necessary means (computers, internet connection available in doctors' offices) in order to overcome the shortcomings in healthcare, especially in times of crisis.\n\nFor the satisfaction of patients hospitalized in the Sahloul PM&R department, we did not find a relationship with the pathologies treated (neurological or osteoarticular/musculotendinous) in the different dimensions of satisfaction studied. In the literature, Oh-Park17 reported that patients dissatisfied with rehabilitation had more neurological diagnoses (44.0% versus 31.3%).17\n\nGhidaoui16 in her study including children with cerebral palsy found a significant positive correlation (p=0.05) between the satisfaction of the patient-caregiver relationship and the GMFCS classification (The Gross Motor Function Classification System is a 5-level clinical classification that describes the gross motor function of people with cerebral palsy and therefore reflects the severity of the motor disability). There was also a significant positive correlation between satisfaction with the care provided and the level of impairment according to the GMFCS classification (p=0.01). The heavier the pathology, the less satisfied the mothers were.16\n\nIn our study, for the occurrence of complications in hospitalized patients, we found that patients who had no complications were more satisfied than those who had one or more complications for all the dimensions studied without statistically significant difference. In the literature, authors found that patients were significantly less satisfied when they develop complications.22–24\n\nOur descriptive cross-sectional study of the patients’ satisfaction treated in the Sahloul-Sousse PM&R department during the year 2020 has strengths and limitations.\n\nConsidering the international studies of satisfaction in rehabilitation settings, the numbers of patients included vary considerably from one publication to another. The size of our sample was calculated and represents a strength of this study compared to previous work conducted in our country.16 The questionnaire used is a validated tool in Arabic, easy to administrate with limited number of questions. In addition, this scale was validated for inpatients and outpatients, which enabled us to recruit patients from both units of the PM&R Sahloul department. Another positive point of our work tool is the use of four dimensions of satisfaction which are: administrative procedures, functional treatment received, logistics as well as the global assessment of the physical therapy, which enabled us to have a general idea of satisfaction in the rehabilitation setting.8 The presence of a validated version in Arabic encouraged the use of this questionnaire in our study since it goes with the socio-cultural context of the Tunisian population.10 The limitation of this tool may be the absence of open questions allowing patients to express themselves regarding their satisfactions and dissatisfactions without being limited in their answers by pre-established proposals. Another limitation of our study is that satisfaction is a subjective concept and may vary over time, hence the utility of using validated scales. In addition, the data collection conditions were more appropriate for hospitalized patients (ward rooms, calm atmosphere, more time to ask questions and explain them properly to patients) than for consultants at the outpatient unit. To avoid variability in data collection we standardized data collection: for each participant, the interviewer should introduce himself, explain the objective of the study and ask for the patient's approval for participation, then his answers should be collected without intimidating or influencing him. Data collection was performed also by the same trained interviewer.\n\nFinally, based on the results of our study, we suggest the following recommendations in order to improve patients’ satisfaction and to ensure the proper functioning of PM&R departments:\n\n• Digitization of admission procedures in order to limit patients’ movements and the duration of registration.\n\n• In times of crisis, the appointments for rehabilitation sessions should be divided between the morning and the afternoon to avoid overcrowding and reduce the waiting time.\n\nThe number of rehabilitation sessions prescribed should be reduced and focused on learning self-rehabilitation exercises and educating patients for therapeutic observance at home.\n\n• Develop the technical and legislative platform in order to establish telemedicine to ensure patients’ follow up.\n\n\nConclusion\n\nPatient satisfaction with the healthcare services provided is a major criterion for evaluating the health system and the continuous improvement of the services offered. For this, several teams around the world have opted for the study of satisfaction and its associated factors in order to improve the quality of their services. Our study showed globally good levels of satisfaction in the Sahloul PM&R department. Nevertheless, other studies need to be conducted in order to study the other factors that can influence satisfaction and to propose action plan to improve health services in developing countries.\n\nApproval from the Ethics Committee of the Faculty of Medicine “Ibn El Jazzar” Sousse was obtained for this study (Ref: CEFMS 80/2019, date of approval: 22/12/2019).11\n\nOur study does not involve any risk for the participants. We respected anonymity and medical secrecy when collecting the data. Written consents were obtained from adult participants and legal guardians of minor participants.12\n\n\nAuthors’ contributions\n\nThe research idea was conceived by Sonia Jemni and Rihab Moncer. Data acquisition, draft preparation and writing was carried out by Leila Hamadou, Rihab Moncer and Rym Ghammam. The rest of the authors reviewed the article, revised the discussion critically and checked the references.\n\nAll authors have revised and approved the final version of the manuscript.", "appendix": "Data availability\n\n\n\n• Satisfaction of patients treated in a physical medicine and rehabilitation department during the covid-19 pandemic: Dataset. DOI: 10.6084/m9.figshare.25904920.v2. 13\n\navailable on the figshare repository under the license CC0\n\nThis study contains the following extended data:\n\n1. Satisfaction of patients treated in a physical medicine and rehabilitation department during the covid-19 pandemic: Monnin and Perneger questionnaire in arabic. DOI:10.6084/m9.figshare.25935001.v2. 10\n\n• Satisfaction of patients treated in a physical medicine and rehabilitation department during the covid-19 pandemic: participants' consent forms (for adults and legal guardians) in arabic. DOI:10.6084/m9.figshare.25934776.v2. 12\n\n• Satisfaction of patients treated in a physical medicine and rehabilitation department during the covid-19 pandemic: approval of the ethics committee for the study. DOI:10.6084/m9.figshare.25934413.v2. 11\n\navailable on the figshare repository under the license CC0\n\nDOI: 10.6084/m9.figshare.26026477\n\nSTROBE Statement—Checklist of items that should be included in reports of cross-sectional studies\n\n\nAcknowledgements\n\nThe authors would like to thank the participants in this study and the medical staff in the PM&R department of Sahloul university hospital of Sousse, Tunisia.\n\n\nReferences\n\nYamba MKY, Mashinda DK, Kayembe J-MN, et al.: Evaluation de la qualité des soins aux Cliniques Universitaires de Kinshasa: étude de satisfaction des patients hospitalisés Assessment of the quality of care at the Kinshasa University Hospital: perception of attending patients. Ann. Afr. Med. 2018; 11: e2926.\n\nZemni I, Safer M, Khelil M, et al.: Patient satisfaction in a tertiary care center (Tunisia, 2015-2016). Tunis. Med. 2018; 96: 737–745. 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Reconstr. Surg. 2011; 127: 1428–1436. Publisher Full Text" }	[ { "id": "320460", "date": "16 Sep 2024", "name": "Oliver O'Sullivan", "expertise": [ "Reviewer Expertise Rehabilitation (including physical", "medical and neurological)" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nDear Colleagues,\nThank you for inviting me to Satisfaction of patients treated in a Physical Medicine and Rehabilitation department during the Covid-19 pandemic: a cross-sectional study [version 1], which is a cross-sectional survey performed in 240 patients or their care-givers in 2020.\nI have several concerns with the manuscript, starting with the timing and purpose.\nI do not understand why this work was performed when it was. To be more precise, throughout Jan - Dec 2020, the entire world was gripped by the COVID-19 pandemic, with lockdown restrictions intermittently implemented globally, hospitals were constantly fighting to avoid being overwhelmed and keep people alive, rehabilitation services were de-prioritised, and their focus was mainly on ITU survivors and those with prolonged COVID-19 symptoms - your manuscript reflects none of this, which makes it hard be convinced by the data. In addition, I struggle to understand why anyone would choose that time to perform a study of patient satisfaction. Unless this is sufficiently explained and articulated in the article, I will continue to have doubts about the validity of the data.\nI have also struggled to understand why this has been submitted four years later as a full length manuscript. When distilled down, you have performed a review of a single department using a single questionnaire, and have found very little of significance, with any findings only directly applicable to the department in question and, in my view, not of interest to the general medical audience. At very best, given the minimal data presented, this should be a 'letter to the editor' style article, but even then, I don't believe this would add value to the medical canon.\nIn addition, I have found the repeated use of the male pronoun when referring to your participants inappropriate, especially as there were more females in your study, the fact that only 15.4% of questionnaires were provided by family members but 22.3% of participants were illiterate, the rather erratic style of referencing, and the, at times, irrelevant discussion, not in keeping with good academic work.\nI appreciate that this review may appear overly-critical, but as a peer-reviewer we must ensure that potential future additions to the published literature are of a high enough standard and add valuable findings. In my opinion, I am afraid this is neither, and I wanted to be honest with you to avoid you wasting your time further.\nGood luck with your future endeavours\n\nIs the work clearly and accurately presented and does it cite the current literature? No\n\nIs the study design appropriate and is the work technically sound? No\n\nAre sufficient details of methods and analysis provided to allow replication by others? No\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNo\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? No", "responses": [ { "c_id": "12469", "date": "19 Sep 2024", "name": "Leila Hamadou", "role": "Author Response", "response": "Dear Reviewer, Thank you for accepting to review our paper entitled “Satisfaction of patients treated in a Physical Medicine and Rehabilitation department during the Covid-19 pandemic: a cross-sectional study [version 1]”. In response to your comments, we want to clarify many points: First comment “I do not understand why this work was performed when it was. To be more precise, throughout Jan - Dec 2020, the entire world was gripped by the COVID-19 pandemic, with lockdown restrictions intermittently implemented globally, hospitals were constantly fighting to avoid being overwhelmed and keep people alive, rehabilitation services were de-prioritised, and their focus was mainly on ITU survivors and those with prolonged COVID-19 symptoms - your manuscript reflects none of this, which makes it hard be convinced by the data. In addition, I struggle to understand why anyone would choose that time to perform a study of patient satisfaction. Unless this is sufficiently explained and articulated in the article, I will continue to have doubts about the validity of the data.” Response 1: Patient satisfaction is a critical factor in assessing the quality of healthcare services especially since our university hospital was preparing the accreditation procedure. And as it is known, patient satisfaction is one of the essential health care quality indicators. According to the literature and the Rehabilitation 2030 project [1], researchers encourage studies that evaluate both the needs and satisfaction of patients with conditions requiring rehabilitation, as patient satisfaction is a key component of quality of care. This study assessed various domains that may affect this quality indicator, taking into account the specific needs of patients with restricted participation using a validated tool. So this work is aligned with our hospital's accreditation process, as patient satisfaction is a reflection of care quality. Additionally, our study is part of a broader investigation into patient satisfaction during the COVID-19 pandemic for those in rehabilitation. Many researchers have explored barriers faced by rehabilitation patients during this period, with numerous studies continuing to be published in 2024 on the topic which testifies to the interest and relevance of the subject [2] [3]. If needed, we can include those studies as references in our paper. It is also important to remember that the study was conducted in a country with limited resources (studies often come from developing countries, which is sometimes limiting) and that the physical medicine department is the only one in the center and southern regions of the country (there are only two department with hospitalization sector in the whole country), it hospitalizes patients who are difficult to manage and it was important to evaluate their satisfaction to draw up improvement actions. In fact, this work served as a basis for some improvement actions carried out in the department. In addition, the study, was my medical thesis subject and my first research work under the supervision of a physical medicine specialist and an epidemiologist. The study protocol was ready before the “non-expected” COVID 19 pandemic. Data collection started in January 2020, in this period no restrictions of care in our country have been taken yet. The first case of COVID19 in the country was recorded in March 2020. So, we were obliged to continue the work especially that the department activity was not really affected. In fact, another University hospital in the region managed COVID 19 cases during this period and admissions for post-trauma and neurological rehabilitation were not suspended during the data collection period. Certainly, we observed some challenges in accessibility, as highlighted in our paper. Furthermore, every research work has its limitations and the limitations of our work were mentioned in the discussion part. Second comment “I have also struggled to understand why this has been submitted four years later as a full length manuscript. When distilled down, you have performed a review of a single department using a single questionnaire, and have found very little of significance, with any findings only directly applicable to the department in question and, in my view, not of interest to the general medical audience. At very best, given the minimal data presented, this should be a 'letter to the editor' style article, but even then, I don't believe this would add value to the medical canon.” In addition, I have found the repeated use of the male pronoun when referring to your participants inappropriate, especially as there were more females in your study, the fact that only 15.4% of questionnaires were provided by family members but 22.3% of participants were illiterate, the rather erratic style of referencing, and the, at times, irrelevant discussion, not in keeping with good academic work. Response 2: Thank you for you valuable time to review this manuscript. I want to emphasize that, I’m a residency trainee, my thesis was presented in 2022, and the article was drafted and completed in December 2022. We revised it several times, and it is normal that this process takes time especially since in our country we lack funds for research and that in the meantime I should validate my medical internships. This work is an original paper that we revised using the strobe grid and is not a letter to the editor. Regarding your comment concerning the use of gender pronouns, the representation of illiterate participants, and the referencing style, 15.4% of the questionnaires were completed by family members due to the patient's age (in the case of children) or cognitive limitations. For illiterate patients, the investigator read the questionnaire aloud to them. For gender pronouns, it was used only six times in the tables and do not refer to all participants. In the discussion section, we cited references related to quality of care and patient satisfaction, and we compared our results with those findings in each instance. Last comment: “I appreciate that this review may appear overly-critical, but as a peer-reviewer we must ensure that potential future additions to the published literature are of a high enough standard and add valuable findings. In my opinion, I am afraid this is neither, and I wanted to be honest with you to avoid you wasting your time further.” Response 3: We appreciate your comments and your valuable time. But we think that this review is really overly-critical specially that many papers were recently published in the subject and that we followed a methodology appropriate to a cross-sectional study. Assessing and re-evaluating patient satisfaction, during and outside of crises, is crucial. This work has been appreciated by professors specialized in quality of care and it served as an element of advocacy with the hospital administration. Regarding the evaluation of rehabilitation needs, studies and reviews have shown the need of studies investigating the need of patients and many reviews have shown that rehabilitation research doesn’t focus on such investigation especially in our region [4]. So, based in this work, we implemented several improvement actions in our department, such as streamlining registration for individuals with special needs. This study did not include intervention results, but it highlighted the challenges faced by our patients. Best Regards References [1] Rehabilitation 2030: A call for action, https://www.who.int/publications/m/item/rehabilitation-2030-a-call-for-action (accessed 3 August 2023). [2] Disabled people’s experiences of accessing reasonable adjustments in hospitals: a qualitative study \| BMC Health Services Research \| Full Text, https://bmchealthservres.biomedcentral.com/articles/10.1186/s12913-018-3757-7 (accessed 17 September 2024). [3] Hickey EJ, Caudill A, Laufenberg H, et al. Quality of life, satisfaction with care, and the experiences of adults with intellectual and developmental disabilities before and during COVID-19. Disabil Health J 2024; 17: 101545. [4] Geberemichael SG, Tannor AY, Asegahegn TB, et al. Rehabilitation in Africa. Phys Med Rehabil Clin N Am 2019; 30: 757–768." } ] } ]	1	https://f1000research.com/articles/13-662
https://f1000research.com/articles/13-661/v1	19 Jun 24	{ "type": "Research Article", "title": "Epidemiological characteristics and hospital outcomes of hospitalized Lassa fever cases during the 2022-2023 outbreak in Liberia", "authors": [ "Emmanuel Dwalu", "Hannock Tweya", "Mher Beglaryan", "Chukwuma D. Umeokonkwo", "Raph W. Jetoh", "Bode I. Shobayo", "Fahn Tarweh", "Philip Owiti", "Pryanka Relan", "Shermarke Hassan", "George W. Goteh", "Darius B. Lehyen", "Louis Ako-Egbe", "Ibrahim Franklyn Kamara", "Godwin E. Akpan", "Peter Adewuyi", "Patrick N. Kpanyen", "Benjamin T. Vonhm", "Julius S. M. Gilayeneh", "Hannock Tweya", "Mher Beglaryan", "Chukwuma D. Umeokonkwo", "Raph W. Jetoh", "Bode I. Shobayo", "Fahn Tarweh", "Philip Owiti", "Pryanka Relan", "Shermarke Hassan", "George W. Goteh", "Darius B. Lehyen", "Louis Ako-Egbe", "Ibrahim Franklyn Kamara", "Godwin E. Akpan", "Peter Adewuyi", "Patrick N. Kpanyen", "Benjamin T. Vonhm", "Julius S. M. Gilayeneh" ], "abstract": "Background Lassa fever is an endemic and immediately notifiable disease in Liberia, and one laboratory confirmed case constitutes an outbreak. We described the epidemiological characteristics and hospital outcome of Lassa fever cases hospitalized during the 2022-2023 outbreak in Liberia.\n\nMethods A cohort study was conducted using routine Lassa fever surveillance data from the 2022-2023 outbreak in Liberia. Descriptive statistics were used to summarize the data and log binomial regression to assess the association between epidemiological characteristics and mortality.\n\nResults A total of 439 suspected Lassa fever cases were reported. The median age was 22 (interquartile range: 10-33) years and 233 (53%) were women. The median number of days between symptom onset and admission was 4 (IQR 2-7). Of the 439 cases, 416 (95%) were tested for Lassa fever and 138 were confirmed with 33% positivity rate. The majority, 290 (69%), of confirmed cases were <30 years, 78 (57%) were females, and 81 (59%) were reported during the dry season (October – March). Contact with rodents, 94 (68%), was the commonest mode of exposure. Fever, 128 (93%), malaise, 121 (88%), headache, 114 (83%) and myalgia, 114 (83%) were the most common clinical characteristics. There were 83 (19%) deaths among hospitalized suspected Lassa fever cases - 42 deaths (15%) among 278 individuals who tested negative and 41 among confirmed cases with 30% case fatality rate (CFR). The highest CFR was recorded among those aged 40-49 years, 8 (67%) and those aged≥50, 5 (63%). There was no significant association between epidemiological characteristics and Lassa fever mortality.\n\nConclusions The outbreak highlighted a high disease burden of Lassa fever with young adults disproportionately infected, and substantial mortality, even among those who tested negative for the virus. This underscores the urgent need for preventive measures like vaccines and health education campaigns.", "keywords": [ "Liberia", "Lassa fever", "positivity rate", "case fatality rate", "outbreak", "Integrated Disease Surveillance and Response", "SORT IT", "operational research" ], "content": "Introduction\n\nLassa fever (LF) is a viral haemorrhagic fever caused by the Lassa virus, a member of arenavirus group.1–3 This zoonotic disease is primarily transmitted to humans through direct or indirect contact with the urine or feces of the infected Mastomys rats (Mastomys natalensis) during hunting or processing for consumption.4–6 The rats are the natural reservoir for the Lassa fever virus. Additionally, the virus may be transmitted from human to human through contact with an infected person's blood, faeces, or other bodily secretions.7,8 Pregnant women and children have the highest risk of contracting the disease.3,9 The incubation period for Lassa fever ranges from 2-21 days. A systematic review conducted in 2021 reported on clinical data, identifying fever (88%), headache (50%), vomiting (49%), abdominal pain (42%), and cough (35%) as the most frequently presenting symptoms in individuals suspected of having Lassa fever. The disease is diagnosed through a real-time polymerase chain reaction (RT-PCR) test and intravenous (IV) ribavirin is a recommended treatment.10,11 Additionally, oral ribavirin can be used for post-exposure prophylaxis. However, recent studies have reported contradictory results regarding the effectiveness of ribavirin, prompting need for further investigation.12\n\nLassa fever is a significant global public health challenge, recognized by the World Health Organisation (WHO) as a priority disease for surveillance, research and vaccine development efforts.1,11 Endemic to various West African countries, including Guinea, Liberia, Nigeria, and Sierra Leone,13 the disease is estimated to cause 100,000 to 300,000 new cases and 5,000-10,000 deaths annually.6,14 Lassa fever exhibits a seasonal pattern, with most cases reported during the dry season each year.3,15 The case fatality rate (CFR) among hospitalized patients is estimated to be between 15% and 20% but can reach 50% during epidemics.7\n\nIn Liberia, Lassa fever is a notifiable disease and one laboratory confirmed case constitutes an outbreak. Liberia is experiencing its most protracted Lassa fever outbreak, which started in January 2022.16 In June 2021, the National Integrated Disease Surveillance and Response (IDSR) Technical Guidelines were revised, incorporating an updated Lassa fever case definition. This coincided with efforts to improve case detection through healthcare worker training.17 Despite these measures, crucial information such as the positivity rate, socio-demographic and clinical characteristics, mode of exposure to rodents, and CFR regarding the current outbreak remains largely unknown. Therefore, this study aimed to understand the 2022-2023 Lassa fever outbreak in Liberia by investigating characteristics of suspected and confirmed Lassa fever cases, mode of exposure, healthcare access (i.e. timelines of admission and treatment) and hospital outcomes.\n\n\nMethods\n\nWe conducted a cohort study in Liberia using routine national outbreak surveillance data of all suspected Lassa fever cases reported between January 2022 and December 2023.\n\nGeneral setting\n\nLiberia has a population of over five million people. The country has a dry season (late October to March) and a rainy season (April to early October). Its capital city is Monrovia and the country is divided into 15 administrative units called counties, five health regions each comprising 3 counties, and 98 health districts.18 The Liberian healthcare system operates at five levels: national, county, district, health facility, and community. There is a 3-tier system for service delivery: a primary level (primary health clinics), a secondary level (health center and county/regional hospitals) and a tertiary level (national specialized hospitals). Each level is staffed with designated healthcare workers including surveillance officers who coordinate disease routine surveillance activities. Liberia has 962 functional health facilities categorized as primary-level clinics, secondary-level health centers, and tertiary-level hospitals. The county hospitals have dedicated Lassa fever treatment centres. Health care services in public health facilities in Liberia are provided free of charge.\n\nSpecific setting\n\nCase detection for Lassa fever began at the community or health facility level. At the community level, community health workers identified potential Lassa fever cases. Potential cases were referred to the nearest health facility for verification. At the health facility level, clinicians used the case definition for Lassa fever to suspect cases based on symptoms. A suspected case was defined as a patient experiencing a fever lasting for 2-21 days (above 38°C) with one or more additional symptoms such as malaise, headache, or muscle pain. Alternatively, patients who had not responded to anti-malarial treatment within 48-72 hours or had a history of rodent contact were also considered suspected cases.17 Exposure to Lassa virus was defined to encompass any contact with rodents, either directly (handling rodents or their food sources) or indirectly (through contaminated utensils, feces, urine, or consumption of rodent-borne food). Additionally, exposure included contact with bodily fluids from a person infected with the Lassa fever virus. A probable case was defined as a suspected case who has one or more of the following complications: hearing loss, facial or neck swelling, seizures/convulsions, restlessness, confusion, hypotension, abdominal bleeding. Once verified, demographic and clinical information of the suspected cases was recorded in the IDSR ledger. The IDSR case alert and laboratory submission forms were then completed and finally samples were collected.\n\nSamples were sent to the National Public Health Reference Laboratory (NPHRL) to confirm Lassa fever. Laboratory confirmation was performed by RT-PCR using a Real Star Lassa Virus RT-PCR kit. A confirmed case was defined as a suspected or probable case with a confirmed/positive laboratory test (positive IgM antibody, positive PCR or virus isolation) or epidemiologically linked to a laboratory confirmed case.19 Once results were available, the NPHRL notified the National Public Health Institute of Liberia (NPHIL) and county teams. The county health teams, facilitated by the county surveillance officers (CSO), then sent the results to the district level through the district surveillance officers (DSO) who notified the health facilities.\n\nWhile awaiting the laboratory test results, the suspected cases were isolated and admitted to a treatment centre where IV Ribavirin treatment was initiated. Daily assessments were performed using charts to monitor the patients’ progress. On average, confirmed Lassa fever cases were treated with IV Ribavirin for 10 days depending on the patient's clinical evolution and recovery. Individuals with negative results were discharged immediately after the Ribavirin treatment was discontinued.\n\nThe data from the IDSR ledger and case alert and laboratory paper-based forms were regularly entered into an MS Excel dataset containing the line-list of Lassa fever surveillance data in each district, then submitted to the county level and onward to the National Public Health Institute of Liberia.\n\nAll suspected cases reported during the outbreaks in Liberia between January 2022 and December 2023 were included in the analysis.\n\nWe obtained data on Lassa fever cases from the Microsoft Excel national surveillance database maintained by the Division of Infectious Disease and Epidemiology, National Public Health Institute of Liberia, for the period 2022-2023. Due to incomplete information in some records we reconciled the data using the county surveillance database and selected treatment centers.\n\nWe performed all statistical analyses using Epi Info analysis software (version 7.2.5.0.) and Stata v18.0 (open source alternative is R: The R Project for Statistical Computing), version 4.3.2. Descriptive statistics were used to summarize the data. Categorical variables, such as sex, county, and symptoms, were presented as frequencies and proportions. Continuous variables including age, time from symptom onset to admission and to ribavirin treatment were presented as medians with interquartile range (IQR). We estimated positivity rate and case fatality of Lassa fever: positivity rates were calculated by dividing the number of confirmed cases by the total number of individuals tested while the case fatality rate (CFR) was calculated by dividing the number of deaths by the total number of confirmed Lassa fever cases. The confirmed Lassa fever cases were plotted by county using Arc Geographic Information System Pro (ArcGIS Pro 3.2.2) (open source alternative: QGIS, version 3.36.3) to visualize the geospatial distribution of the disease. An epidemic curve was constructed using the date of symptom onset and mortality for all confirmed cases. We used log binomial regression to assess the association between socio-demographics, clinical characteristics, and case fatality rates. Models’ results were presented as Risk Ratios (RR) with 95% confidence intervals (CI) and p-values <0.05 were considered statistically significant.\n\n\nResults\n\nA total of 439 suspected Lassa fever cases were reported between January 2022 and December 2023 (Figure 1). The median age was 22 (IQR 10-33) years. The majority (66%, 290/439) of the suspected cases were below 30 years There were more women (53%, 233/439) than men. Occupation data was missing for 174 participants. Among the 265 with recorded occupations, students constituted the largest group (32%, 141/439) followed by business persons (12%, 51/439). Geographically, Bong County reported the highest number of suspected cases (44%, 192/439), followed by Grand Bassa County (20%, 89/439) and Nimba County (18%, 80/439) (Table 1).\n\n* Number (and column-proportion) for characteristics and RT-PCR tested.\n\n¥ Number (and row-proportion) positivity rate).\n\nβ Others (number of suspected cases): River Gee (n=5), Grand Kru (n=7), Maryland (n=3), Bomi (n=2), Lofa (n=2), Margibi (n=2), Sinoe (n=1).\n\nAmong 439 individuals, about one quarter (26%, 116/439) were excluded due to missing data on date of symptom onset or admission (Table 2). Among the 323 participants with recorded dates, the overall median number of days between symptom onset and admission was 4 (IQR 2-7). Median times by gender were similar (4.5 (IQR: 2-7) vs 4.0 (IQR 1-7) days). When stratified by county, Nimba had the shortest median time, with a median of <1 day (IQR < 1-1.5).\n\n* IQR=Interquartile range.\n\nβ Others (number of suspected cases): River Gee, Grand Kru, Maryland, Bomi, Lofa, Margibi, Sinoe.\n\nOf the 439 individuals suspected of Lassa fever, 437 specimens were collected and majority (95%, 416/439) were tested using RT-PCR test and 138 were Lassa fever positive. The overall positivity rate was 33% (138/416) (Figures 1 & 2; Table 1). Among suspected cases with recorded occupations, tappers had the highest positivity rate (58%, 11/19), followed by housewives (50%, 8/16). Positivity rates were highest in Grand Bassa County (51%, 45/88), followed by Bong (35%, 60/171) and Nimba Counties (34%, 27/80).\n\nRibavirin treatment was administered to 57% (249/439) of hospitalized suspected Lassa fever cases (Figure 1).\n\nRibavirin treatment was administered to 83% (114/138) of the confirmed Lassa fever cases and 46% (129/278) of those with negative PCR results (Figure 2).\n\nThe 2022 calendar year had more confirmed cases, accounting for over half (52%, 72/138) of the reported cases. More cases (59%, 81/138) clustered between epi-weeks 1-12 and 40-52, aligning with the dry season (October – March) (Figure 3).\n\nRodent exposure was the most common type of contact (68%, 94/138) among confirmed Lassa fever cases. The most common clinical characteristic was fever (93%, 128/138), followed by malaise (88%, 121/138), headache (83%, 114/138), and myalgia (83%, 114/138). Less than 1% of patients reported hearing loss (Table 3).\n\nThere were 83 (19%) deaths among hospitalized suspected Lassa fever cases; 41 were among confirmed cases, with a 30% CFR. The remaining 42 deaths (15%) occurred among 278 individuals who tested negative (Figure 1, Tables 1 & 4). The CFR varied significantly by age group (p-value=0.006). The highest CFR was observed in individuals aged 40-49 years (67%, 8/12), followed by those aged ≥50 years (63%, 5/8). Lower CFRs were seen in the ≤14-year-old group (27%, 12/45), the 30-39year old group (26%, 6/23), and the 15-29year old group (20%, 10/50).\n\nAt bivariate level, we found significant associations between age ≥30 (cRR=1.9, 95% CI=1.160-3.136, p=0.011), reporting county (Nimba (cRR=2.0, 95% CI=1.129-3.771, p=0.019) and Lassa fever mortality. When modelled using multiple logistic regression, none of these associations were significantly associated with Lassa fever mortality among confirmed cases (Table 4).\n\n\nDiscussion\n\nThe study described the epidemiological characteristics and case fatality rates among Lassa fever cases hospitalized during the 2022-2023 outbreak in Liberia. Findings showed a substantial burden of Lassa fever in Liberia during the outbreak with high positivity rates (33%) and case fatality rates (30%), with an even higher CFR among the elderly population. Younger age groups were disproportionately affected. Furthermore, the dry season coincided with a surge in confirmed cases. Fever, headache and malaise were the most frequently reported symptoms, and rodent exposure was highest among the confirmed cases. Surprisingly, a high mortality rate (13%) was observed among hospitalized individuals without Lassa fever, highlighting challenges in diagnosis and in Lassa fever management.\n\nSimilar to other studies,6,19 the study found high testing and positivity rates. The high testing and positivity could be because Lassa fever is one of the immediately reportable priority diseases under surveillance in Liberia and an endemic disease. Additionally, strengthened surveillance systems at all healthcare delivery levels with assigned surveillance officers for the detection and reporting of suspected Lassa fever, a functional testing national public health reference laboratory and, most importantly, the revised 2021 case definition of Lassa fever all contributed to improved detection of Lassa fever.17\n\nThe study highlights that younger age groups are disproportionately affected by Lassa fever. This vulnerability is likely to be due to increased exposure to rodent reservoirs. Most confirmed cases reported direct or indirect contact with rodents suggesting exposure to rodent droppings or urine during outdoor activities and food handling. Similar to other studies in Liberia6,19 and Nigeria,20 most of the cases were recorded in the dry season (the latter and earlier parts of the two years in the study period: October to March) with 2023 accounting for the highest burden. The seasonality of Lassa fever cases in West Africa's dry season is likely due to a combination of factors related to the behavior of the main reservoir, the Mastomys natalensis rodent. During the dry season, with less vegetation and food sources outside, these rodents are more likely to seek shelter and food inside homes, increasing their contact with humans. This could lead to more frequent interactions between rodents, potentially increasing the spread of the Lassa fever virus within the rodent population. Less plant cover during the dry season could make rodent burrows and movements more noticeable for hunting. A better cleaning environment both in the house and the outside environment might help to reduce the contact between rats and humans. Additionally, effective community infection prevention control programmes in endemic areas might be of help.\n\nOur study identified a high CFR of 33%, more than double the 15% reported by the WHO for the region. While this CFR is lower than those reported in Nigeria (60%)21 and Sierra Leone (69%)22 and slightly lower than a previous study in Liberia (40%), it remains a significant cause for concern. Furthermore, high CFRs were observed in both treated and untreated patients. The short time between symptom onset and hospital admission suggests that healthcare-seeking behaviors alone cannot fully explain the high CFR. Previous studies have raised concerns about the effectiveness of ribavirin treatment and its potential harm.12 The reliability of the human clinical trial data supporting ribavirin's use has also been questioned, with pre-clinical studies suggesting that current dosing regimens may not reliably inhibit Lassa fever virus replication.12 Similar to other studies, the CFR was higher among elderly people. However, the reasons for this are unclear, warranting further research in understanding the occurrence. Surprisingly, CFR was higher in Nimba, an endemic Lassa fever county, a finding similar to what was reported in a previous study.6 The high CFR in Nimba could be due to the fact that the county is endemic for Lassa fever, with the majority of cases detected at the health facility rather than through early community detection, which impacts on early treatment. The study highlights challenges in Lassa fever management. Suspected Lassa fever cases are admitted and begin ribavirin while waiting for test results. Some of the Lassa fever symptoms (fever and headache) overlap with common diseases like malaria, leading to unnecessary admissions and ribavirin use as well as delayed appropriate treatment. This is concerning, as a 13% mortality rate was observed among those who did not have Lassa fever which may be due to other undiagnosed infections. While the strategy aims to combat Lassa fever’s high CFR, improvements in diagnosis and management are crucial.\n\nThese findings have an important implication for the programme’s practice and policy. Addressing the screening and management challenges surrounding Lassa fever requires a proactive shift towards preventive measures. Mass vaccination campaigns, although in their developmental stages, offer a promising avenue for mitigating the burden of Lassa fever. Initiatives by the WHO and Coalition for Epidemic Preparedness Innovations (CEPI) prioritize Lassa fever for vaccine development and enhanced surveillance efforts,23 signaling a step in the right direction. However, given the time frame for vaccine development and implementation, immediate action is warranted. Based on a clearer understanding of seasonal variations within Liberia and across West Africa, public health interventions like vector control programmes and year-round community education campaigns, intensified during the dry season when Lassa fever transmission peaks, can significantly enhance community awareness and prevention, thereby reducing mortality rates and easing the burden on healthcare systems. Implementing rodent-proofing measures can further reduce exposure risks.\n\nOur findings should be viewed with the following limitations: Firstly, there were incomplete data on duration from onset of symptoms to hospital admission. Exclusion of these records might have affected the estimation of the time from onset of symptoms to hospital admission with respect to socio-demographic characteristics. Secondly, our data was focused on facility-based rather than community-based surveillance, meaning that those who did not seek healthcare were not captured, and we might therefore have underestimated the number of Lassa fever cases. Despite these limitations, the study used surveillance data which reflect the program setting, making the findings useful to inform policy and programmes in Liberia and other comparable settings to prevent outbreaks of Lassa fever.\n\n\nConclusions\n\nThis study showed a significant burden of Lassa fever in Liberia during the 2022-2023 outbreak, characterized by high positivity, high CFR, and a substantial mortality among those without the disease, highlighting the urgent need for proactive prevention measures such as vaccination campaigns and intensive public education. Furthermore, the CFR was high among the elderly population, warranting further investigation. Additionally, the incompleteness of some records highlights the need to strengthen data collection practices within healthcare facilities to ensure complete and accurate data for informed outbreak response efforts.\n\nAccess to data for this study was granted by the National Public Health Institute of Liberia. Ethics approvals were obtained from University of Liberia Ethics Review Board on September 27, 2023 (protocol# 23-09-390) and the Ethics Advisory Group for the International Union Against Tuberculosis and Lung Disease, Paris, France, on August 9, 2024; (EAG# 24/23). Informed consent was not obtained as we used routine programme data, which was anonymized by delinking patient identifiers from the dataset.\n\n\nAuthor contributions\n\n“Conceptualization, E. D, R.W.J, B.I.S, H. T, F.T, P. O, M.B, I.F.K, G.W.G, P. K, D. B. L, L.A.E, P. R, S.H; B.T.V., J.S.M.G; methodology, E. D, H.T, P. O, M.B, C.D.U, R.W.J, B.I.S, F. T, P. A, G.W.G,D.B.L, L.A.E, P. R, S. H, B.T.V, P. K, P.A., I.F.K, J.S.M.G; software; validation, E. D, G.W.G; formal analysis, E. D, H.T, M. B, C.D.U, P.A., GEA; investigation; resources; data curation; writing—original draft preparation, E. D, H.T, M. B, writing—review and editing, E. D, H.T, F. T, P.O, C.D.U, B.T.V, M. B, B.I.S, P. K, P. A, L.A.E, P. R, S. H, I.F.K, GEA; visualization, G.E.A, E.D; supervision; project administration; funding acquisition. All authors have read and agreed to the last version of the manuscript.”\n\n\nOpen access statement\n\nIn accordance with WHO’s open-access publication policy for all work funded by WHO or authored/co-authored by WHO staff members, WHO retains the copyright of this publication through a Creative Commons Attribution IGO license (http://creativecommons.org/licenses/by/3.0/igo/legalcode) which permits unrestricted use, distribution and reproduction in any medium provided the original work is properly cited.", "appendix": "Data availability\n\nThe dataset used for this study is available at the Division of Infectious Disease and Epidemiology, National Public Health Institute of Liberia and can be accessed upon request in line with the existing data request guide, which provides opportunity for both internal and external data requests (https://www.nphil.gov.lr/wp-content/uploads/2024/03/nphil-data-request-guide.pdf).\n\n\nAcknowledgements\n\nThis research was conducted through the Structured Operational Research and Training Initiative (SORT IT), a global partnership led by TDR, the Special Programme for Research and Training in Tropical Diseases hosted at the World Health Organization. The specific SORT IT program that led to this publication is a SORT IT partnership with the WHO Emergency Medical Teams (Geneva), WHO-AFRO (Brazzaville), WHO Country Offices and Ministries of health of Guinea, Liberia, Sierra Leone, and the Democratic Republic of the Congo, the Infectious Diseases Data Repository (IDDO); The International Union Against Tuberculosis and Lung Diseases, Paris, France and South East Asia offices, Delhi, India; The Tuberculosis Research and Prevention Center Non-Governmental Organization, Yerevan, Armenia; I-Tech, Lilongwe, Malawi; Medwise solutions, Nairobi, Kenya; All India Institute of Medical Sciences, Hyderabad, India; and the National Training and Research Centre in Rural Health, Maferinyah, Guinea; All health facility, district, and county surveillance officers in Liberia for generating the data; The District and County Surveillance Officers, Data Management Unit and the entire Division of Infectious Disease and Epidemiology, the National Public Health Institute of Liberia.\n\n\nReferences\n\nOgbu O, Ajuluchukwu E, Uneke CJ: Lassa fever in West African sub-region: an overview. J. Vector Borne Dis. INDIAN COUNCIL OF MEDICAL RESEARCH. 2007; 44: 1.\n\nAkpede GO, Asogun DA, Okogbenin SA, et al.: Caseload and case fatality of Lassa fever in Nigeria, 2001-2018: A specialist center’s experience and its implications. Front. Public Heal. Frontiers Media S.A. 2019; 7: 450510.\n\nMerson L, Bourner J, Jalloh S, et al.: Clinical characterization of lassa fever: A systematic review of clinical reports and research to inform clinical trial design. PLoS Negl. Trop. Dis. 2021; 15: e0009788–e0009727. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLecompte E, Fichet-Calvet E, Daffis S, et al.: Mastomys natalensis and Lassa fever, West Africa. Emerg. Infect. Dis. 2006; 12: 1971–1974. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nYaro CA, Kogi E, Opara KN, et al.: Infection pattern, case fatality rate and spread of Lassa virus in Nigeria. BMC Infect. Dis. BMC. 2021 [citat 13 juliol 2023]; 21: 1–9. Reference Source\n\nJetoh RW, Malik S, Shobayo B, et al.: Epidemiological characteristics of Lassa fever cases in Liberia: a retrospective analysis of surveillance data, 2019-2020. Int. J. Infect. Dis. 122: 767;–774. Publisher Full Text Reference Source\n\nBalogun OO, Akande OW, Hamer DH: Lassa Fever: An Evolving Emergency in West Africa. Am. J. Trop. Med. Hyg. 2020; 104: 466–473. PubMed Abstract \| Publisher Full Text\n\nSafronetz D, Mire C, Rosenke K, et al.: A recombinant vesicular stomatitis virus-based Lassa fever vaccine protects guinea pigs and macaques against challenge with geographically and genetically distinct Lassa viruses. PLoS Negl. Trop. Dis. 2015; 9: e0003736. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDahmane A, Van GJ, Van HM, et al.: Constraints in the diagnosis and treatment of Lassa Fever and the effect on mortality in hospitalized children and women with obstetric conditions in a rural district hospital in Sierra Leone. R. Soc. Trop. Med. Hyg. 2014; 108: 126–132. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nEberhardt KA, Mischlinger J, Jordan S, et al.: Ribavirin for the treatment of Lassa fever: A systematic review and meta-analysis. Int. J. Infect. Dis. 2019; 87: 15–20. PubMed Abstract \| Publisher Full Text\n\nAlli A, Ortiz JF, Fabara SP, et al.: Management of Lassa Fever: A Current Update. Cureus. 2021; 13: 4–11. Publisher Full Text\n\nCheng HY, French CE, Salam AP, et al.: Lack of Evidence for Ribavirin Treatment of Lassa Fever in Systematic Review of Published and Unpublished Studies. Emerg. Infect. Dis. 2022; 28: 1559–1568. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBuba MI, Dalhat MM, Nguku PM, et al.: Mortality Among Confirmed Lassa Fever Cases During the 2015-2016 Outbreak in Nigeria. Am. J. Public Health. 2018; 108: 262–264. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBalogun OO, Akande OW, Hamer DH: Lassa fever: An evolving emergency in west Africa. Am. J. Trop. Med. Hyg. 2021; 104: 466–473. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSogoba N, Feldmann H, Safronetz D: Lassa fever in West Africa: evidence for an expanded region of endemicity. Zoonoses Public Health. Wiley Online Library. 2012; 59: 43–47. PubMed Abstract \| Publisher Full Text\n\nNational Public Health Institute of Liberia N: Liberia Lassa Lassa fever Situational report, 2023. Monrpvia: 2023.\n\nNPHIL M& W: Integrated Disease Surveillance & Response Technical Guidelines, Liberia. Liberia: 2021.\n\nLiberia Institute of Statistics and Geo-Information Services (LISGIS) M of H: Liberia Demographic and Health Survey 2019-20. Monrovia, Liberia and Rockville, Maryland, USA: Liberia Institute of Statistics and Geo-Information Services (LISGIS), Ministry of Health, and ICF; 2019.\n\nDwalu E, Jetoh RW, Shobayo BI, et al.: Trend of Lassa fever cases and factors associated with mortality in Liberia, 2016-2021: a secondary data analysis secondary data analysis. Pan Afr. Med. J. 2021; 47: 2016–2021.\n\nIlori EA, Frank C, Dan-Nwafor CC, et al.: Increase in lassa fever cases in Nigeria, January–March 2018. Emerg. Infect. Dis. 2019; 25: 1026–1027. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBuba MI, Dalhat MM, Nguku PM, et al.: Mortality Among Confirmed Lassa Fever Cases During the 2015–2016 Outbreak in Nigeria. Am. J. Public Health. 2018; 108: 262–264. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nShaffer JG, Grant DS, Schieffelin JS, et al.: Lassa Fever in Post-Conflict Sierra Leone. Dis. PLoS Negl. Trop. 2014; 8: e2748. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nOrganization WH: An R & D Blueprint for Action To Prevent Epidemics Funding & Coordination Models for.2016." }	[ { "id": "296577", "date": "19 Jul 2024", "name": "Davidson Hamer", "expertise": [ "Reviewer Expertise Emerging infectious diseases", "antimicrobial resistance", "malaria", "Chagas 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\nF1000 Research Peer Review : Epidemiological characteristics and hospital outcomes of hospitalized Lassa fever cases during the 2022 – 2023 outbreak in Liberia Peer Review [General Comment] Overall, this manuscript provides an insightful epidemiological analysis of the Lassa fever outbreak and its impact on hospitalized patients in Liberia from 2022 to 2023. The authors present compelling findings that address an evolving public health issue in the context of an outbreak. They have adequately described the study setting & population, exposures (sociodemographic and epidemiological characteristics), and outcome measurements.\n\nFundamentally, this manuscript can contribute to the existing literature on Lassa fever by providing insights and understanding into the epidemiological dynamics and clinical outcomes associated with Lassa fever. Additionally, it expands on the substantial burden placed on hospitalized patients during the outbreak, thereby highlighting critical aspects for public health preparedness and response strategies.\n\nThe title refers to the epidemiological characteristics and hospital outcomes of patients hospitalized with Lassa fever, but the manuscript has a moderate amount of material on the patients who were initially suspected to have Lassa fever but were not confirmed. We recommend focusing the analysis on the confirmed cases and only providing a brief description of the suspected cases at the beginning of the Results.\n\n[Specific Comments]\n\nComment 1: Rather than refer to cases in the title and the abstract, patients is a better term to use (there are sections where the term case is reasonable when summarizing statistics but not when describing the acute infection and outcomes of the pooled cohort of patients.\n\nComment 2: Second sentence of the Background of the abstract, outcomes should be plural as in “...and hospital outcomes of Lassa fever patients hospitalized...”.\n\nComment 3: Abstract, Results. Recommend introducing the abbreviation IQR in the second sentence “...was 22 (interquartile range [IQR] 10-33)...”\n\nComment 4: In the results section of the abstract, the authors mentioned that ‘290 (69%) of confirmed cases were <30 years.’ However, in the preceding sentence, the authors stated that there were 138 confirmed cases which equates to 33% positivity rate. Once you start referring to confirmed cases, the denominator should be all confirmed cases (N = 138) yet the description “290 (69%) of confirmed cases were <30 years old” is incorrect. The next two percentages are based on the correct, smaller denominator.\n\nComment 5: Abstract, Results. Would consider removing mention of the mortality rate among the suspected but not confirmed Lassa fever cases. There is no information provided on the possible causes of febrile illness in these patients so readers will have no idea what they died from (probably a mix of malaria, bacteremia, and potentially other infectious etiologies).\n\nComment 6: Abstract, Results. For the last sentence, please add the denominator for each group (age 40-49 years, age > or = 50 years).\n\nComment 7: Abstract, Conclusions. As suggested above, we would consider removing the phrase “substantial mortality, even among those who tested negative for the virus” since the causes of acute febrile illness in this group are not described. In contrast, it might be useful to mention the empirical use of ribavirin even for patients who were ruled out for Lassa fever, as this means many patients were exposed unnecessarily to a moderately toxic antiviral.\n\nComment 8: Keywords. Suggest removing Liberia and Lassa fever since these are in the article title and all terms in the title will be picked up by search engines. And SORT IT may not be a searchable term. Consider adding ribavirin as a term.\n\n[Introduction Section]\n\nComment 9: Mastomys natalensis in the third sentence of the ‘Introduction’ should be written in the standard scientific format as ‘Mastomys natalensis’. This same suggestion applies to the Discussion (third paragraph).\n\nComment 10: Introduction. Although the prevalence of frequently presenting symptoms in suspected Lassa fever cases is interesting, the more relevant symptoms are those demonstrated in patients who have been confirmed.\n\nComment 11: Introduction. Suggest adding risk factors for mortality from Lassa fever as one of the objectives of this analysis.\n\n[Methods Section]\n\nComment 12: It will be beneficial to the readers of the journal to know the type of cohort study conducted. Kindly specify it is retrospective or prospective (Study Design).\n\nComment 12: Methods, Specific setting. Third line. Suggest rephrasing to “...for Lassa fever to identify suspect cases..”.\n\nComment 13: In the context of the first and second sentence of the Specific Setting of the Methods section, please include a phrase/sentence that indicates the reporting tool, means of communication, and timeliness of reporting (window period) employed by the community healthcare workers when reporting suspected cases to the nearest health facility for verification.\n\nComment 14: Although this sentence (In the Study Settings section), ‘The IDSR case alert and laboratory submission forms were then completed and finally samples were collected’, is understood by the reviewer, for clarification and non-assumption by readers of the journal, the authors should indicate the specific type of sample that was collected from the patients for Lassa fever testing.\n\nComment 15: Generic drug names should be presented in lower case—ribavirin should not be capitalized.\n\nComment 16: Were there specific selection criteria for the use of ribavirin?\n\nComment 17: Concerning this statement, ‘Daily assessments were performed using charts to monitor the patients’ progress’, please specify (concisely) the assessments done.\n\nComment 18: Please rephrase the statement ‘Individuals with negative results were discharged immediately after the Ribavirin treatment was discontinued’ to something like ‘Individuals with negative results after a repeat RT-PCR testing were discharged immediately after the ribavirin treatment was discontinued.’ If this is not what the authors are trying to convey, kindly clarify.\n\nComment 19: Kindly expound the phrase ‘and selected treatment centers’ in the sentence ‘Due to incomplete information in some records, we reconciled the data using the county surveillance database and selected treatment centers.’ Succinctly expand the phrase to provide more context to readers.\n\nComment 20: Statistical analysis. The sentence ‘We used log binomial regression to assess the association between socio-demographics, clinical characteristics, and case fatality rates’ should be revised to ‘We used log binomial regression to assess the association between socio-demographics, clinical characteristics, and mortality.’ CFR is a population-level indicator, and it appears the authors inadvertently substituted this in place of mortality.\n\nComment 21: Statistical analysis. The term risk ratio should be in lower case.\n\n[Results Section]\n\nComment 22: Results. Second sentence. Missing a period at the end of the sentence.\n\nComment 23: Results. The authors revealed that some individuals were excluded in the statement ‘Among 439 individuals, about one quarter (26%, 116/439) were excluded due to missing data on date of symptom onset or admission’. Specify what the individuals were excluded from, e.g., from the regression analyses or Table 2. Kindly clarify.\n\nComment 24: Results. The utility of the data in Table 2 is relatively limited. The median time from symptom onset to hospital admission was similar across age groups (by a day or two), gender (half a day), and county (except Nimba). This table could be removed and a sentence or two added to the Results to describe the major findings.\n\nComment 25: In Table 4, was there any reason why Bong County was selected as the reference group? Or was the county selected randomly?\n\nComment 26: Results. It would be interesting and potentially informative to compare patients who had confirmed Lassa fever (PCR+) who received ribavirin vs. those who did not receive this antiviral treatment. Are there any significant differences in their clinical or demographic characteristics?\n\nComment 27: Table 4, Ribavirin treatment (yes or no) was not included in the bivariable and multivariable models. Historical data and corresponding studies have shown a decrease in mortality among those administered (especially within 6 days from symptom onset). For comprehensiveness, it would be important to explore and demonstrate the associations between the administration of the treatment and mortality. Additionally, the adjusted (multivariable) models with its findings would have more validity if this was also accounted for.\n\nComment 28: Table 4. The authors used a reference cutoff of 7 days to assess the association between duration from symptom onset to hospital presentation. However, we recommend the authors to explore the 4 days as the reference cutoff. Earlier in the results section, the authors reported the median symptom-hospital duration to be 4 days with an IQR of 2 to 7. For validity reasons, kindly conduct an exploratory analysis/sensitivity analysis to explore this new cutoff.\n\n[Discussion Section]\n\nComment 29: The abbreviation CFR was introduced much earlier in the manuscript. It should be used on the first and third lines of the beginning of the Discussion. Also, we recommend using the term ‘patients’ rather than cases in the first sentence of the Discussion.\n\nComment 30: As noted earlier, the group with suspected Lassa fever who were not confirmed is likely a mixture of different etiological agents. Suggest removing the last sentence of the first paragraph of the Discussion for this reason.\n\nComment 31: The last statement of the second paragraph ‘Additionally, effective community infection prevention control programmes in endemic areas might be of help’ is quite vague. The authors (in their recommendation) should kindly be specific in who implements and ensures the effectiveness of the community IPC programmes.\n\nComment 32: In the third paragraph, in the third and second to last lines, might be better to state “A clean environment in both the house and outside environment...”\n\nComment 33: Additional information is required for this statement ‘Similar to other studies, the CFR was higher among elderly people. However, the reasons for this are unclear, warranting further research in understanding the occurrence.’ Yes, additional studies are warranted to better understand the pathophysiological mechanism contributing to the high CFR among elderly population. However, the authors should state possible reasons for high CFR being demonstrated among this population, e.g. comorbidities, waning immunity, etc.\n\nComment 34: The statement ‘The high CFR in Nimba could be due to the fact that the county is endemic for Lassa fever, with the majority of cases detected at the health facility rather than through early community detection, which impacts on early treatment’ is a bit conflicting with your earlier report. In the results section, the authors observed that Nimba had the shortest median time (<1 day) from symptom onset to hospital admission. Kindly reconcile the two statements and re-phrase accordingly.\n\nComment 35: We suggest the authors re-phrase this statement ‘leading to unnecessary admissions and ribavirin use as well as delayed appropriate treatment’ to ‘leading to unnecessary admissions and ribavirin use as well as delays in receiving appropriate treatment.’\n\nComment 36: The findings of the study highlighted a notable concentration of cases in Bong, Grand Bassa, and Nimba Counties. However, the authors did not provide or suggest possible explanations or hypotheses for these observations. Also, Figure 2 illustrates that these three Counties are adjacent to each other. Therefore, it would be beneficial for readers if the authors could delve into the potential influence of infected individuals migrating across County borders. This exploration could shed light on how population movements might contribute to the spread of Lassa fever in this region, offering valuable insights into disease dynamics and transmission patterns.\n\nComment 37: In the paragraph that describes the need for improved strategies, it might be useful to describe the need for a rapid point-of-care test for Lassa fever since this would be so helpful to triage patients for infection control purposes and treatment (especially if more effective antivirals become available).\nReferences:\n\nComment 38: There is no need to include Indian Council of Medical Research in the first citation.\n\nComment 39: Lassa should be capitalized in the third citation.\n\nComment 40: Several of the article titles are presented in title case rather than having just the first letter capitalized (e.g., citation 7, 11, 12, and 21).\n\nComment 41: There is a duplicate of Balogun OO et al. This is presented as reference 7 and 14.\n\nIs the work 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": [] }, { "id": "296578", "date": "09 Sep 2024", "name": "Elisabeth Fichet-Calvet", "expertise": [ "Reviewer Expertise Lassa fever", "Lassa virus evolution", "phylogeography", "rodent ecology", "West Africa", "eco-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 describes cases of Lassa fever (LF) recorded in Liberia over a 2-year period (January 2022-December 2023). It presents socio-demographic variables such as the sex, age, occupation and place of origin of the patients. The clinical picture and the mortality rate complete this description. These data are important to communicate because the epidemiology of LF is poorly documented in Liberia. I therefore encourage the authors to index these data. However, I feel that a major revision of the manuscript and the analyses is essential in order to improve readability and highlight the important points that are currently diluted in the text.\n\nGeneral comments: The manuscript is full of percentages; I counted over 200 in the introduction, results, discussion, figures and tables. This is far too many, because in the end you don't know which ones to pick out. There is often redundancy in the figures presented in the text and in the tables. There is no point in repeating the same information twice in a scientific text. It is also important to always mention the denominator when quoting a percentage in the text. Percentages are often compared using terms such as \"highest\", \"lower\", \"more\", without any statistics to support the comparison. These formulations should be removed from the manuscript as they are not scientific. Only statistics can confirm that one figure is smaller or larger than another.\nThe abbreviations “LF” for Lassa fever and “LASV” for Lassa virus should be used once the term has been quoted in full for the first time. In addition, the lines should be numbered to facilitate the report of the reviewers.\nSpecific comments: Introduction:\n“… disease is primarily transmitted…” should be “LASV is primarily transmitted…” because a disease is never transmitted. It is the pathogen that is transmitted. Replace “Mastomys rats” with “the Natal multimammate mice (Mastomys natalensis)”. Use the term of “mice” instead of “rats” throughout the manuscript. Transmission of LASV by direct or indirect contact is a hypothesis. It has not been scientifically proven. Therefore, use the conditional tense in this sentence. Update the morbidity and mortality figures according to the recent publication done by Basinski,.et.al., 2021 (Ref 1) Some case fatality rates are presented; where do they come from? Country? Years?\nMethods:\nStudy design and study setting should be combined in one paragraph. The general setting is useless because the results do not use this information. I think the authors did a case-control study, not a cohort study, because they did not analyse, the outcome variable (LF infection) over time. They compared different exposures or variables between cases (LASV positive) and controls (LASV negative). The first sentence in “specific setting” should be shortened Exposure to LASV: how do you know that patients touched contaminated utensils? What is a rodent-borne food? A rodent contaminated-food? It would be useful to have the questionnaire in a supplementary information in order to know how the authors evaluated/quoted the exposure to rodents. “A confirmed case… laboratory confirmed case… or virus isolation)”. This sentence should be removed as the authors only used the RT-PCR to confirm LF in this study. CSO and DSO: it is pointless to give abbreviation as this term is not used in the rest of the text. Study population: this sentence is redundant with the one in Study design Study data sources: also redundant with the information presented at the end of the Specific setting Statistical analysis: please use the term of “LASV prevalence” instead of “positivity rate”, and throughout the manuscript. Please specify variables as dependent or independent. Why did not you perform statistics (binomial regression) on LASV prevalence and other variables? You only did statistics on CFR.\nResults Section “Characteristics of the suspected Lassa fever cases”:\nchange this title in “Diagnosis, Ribavirine treatment and outcome”\n\nFigure 1: state the CFR for patients tested negative for LASV. The numbers presented in this paragraph are redundant with Table 1. I would remove this part and focus only on LASV-positive patients.\nSection “Positivity rate of Lassa fever cases”:\nsee my comment above about the positivity rate.\n\nUse the term of “LASV prevalence” instead of “positivity rate” throughout the text, figure and table. Again, there is a lot of redundancy between the text and the table. “highest” see my general comment Why not to analyse the data to build a model?\nSection “Epicurve”:\nlook at the “more confirmed cases”: statistics?\nSection “Type of exposure”:\ndata redundant with table 3, and not well analysed. If you wanted to analyse exposure to rodents, the question would be “are the LASV+ patients more exposed to rodents than the LASV- patients? To do this, you would need to build a model where the RT-PCR result as an outcome (0 or 1) is a function of rodent exposure (absence/presence according to respondent?) + other variables. You did not answer this question in your article.\n\nI would be curious to know such a result, as I suspect that everyone was exposed to rodents in the area…\nSection “Factors associated”:\nthis is the most interesting part of the article. However, factors such as “occupation” and “duration of onset prior to admission” are not presented. You could say that these two variables have no effect on CFR when analysed in a bivariate model.\nDiscussion:\nDry season as risk season: there is no data in this article to support this assumption.\nFurthermore, in another article (Dwalu et al. Trend of Lassa fever cases and factors associated with mortality in Liberia, 2016 - 2021: a secondary data analysis. Pan African Medical Journal. 2024;47(22). 10.11604/pamj.2024.47.22.42156) you published data clearly showing Lassa cases throughout the year, in 6 consecutive years between 2016 and 2021. Only two years showed a peak in the dry season. So, I think it is wrong to claim a seasonal risk when your data shows the opposite in 4 out of 6 years.\nRodent exposure: this is not analysed in this paper (see my comment above). High testing: what is that? “younger age group more affected”: I have not seen this result. Where did you do the analysis? “direct or indirect contact with rodents”: this is not analysed, leading to over-interpretation. CFR in other countries: give the raw data, and do not repeat this idea twice at the beginning and in the middle of the discussion. 40% (xx/xx?) in Liberia: what is the reference? Rodent-proofing measures needs to be proposed with great caution. See our recent paper on rodent control strategies in Guinea (Marien, J., M. Sage, U. Bangura, A. Lame, M. Koropogui, T. Rieger, B. Soropogui, M. Douno, N. Magassouba and E. Fichet-Calvet (2024). \"Rodent control strategies and Lassa virus: some unexpected effects in Guinea, West Africa.\" Emerg Microbes Infect 13(1): 2341141).\n\nAs you published data from 2016-2021 surveillance in Dwalu et al. 2024, why don’t you discuss the results presented here with those published previously? More generally, what is the novelty of this article when compared to Dwalu et al. 2024?\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNo\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] } ]	1	https://f1000research.com/articles/13-661
https://f1000research.com/articles/13-659/v1	19 Jun 24	{ "type": "Research Article", "title": "Marital Bargaining and Assortative Matching on Fertility Preference : Evidence based on Cross-sectional Data in China", "authors": [ "Meiyi Zhuang", "Hisahiro Naito", "Meiyi Zhuang" ], "abstract": "Background Despite the relaxation of fertility restrictions, China’s birth rate continues to decline. The Universal Two-Child Policy encourages couples to consider having a second child, often leading to a bargaining process between spouses with differing preferences. Additionally, the skewed sex ratio has increased Chinese women’s bargaining power, highlighting the importance of analyzing fertility decisions through marital bargaining.\n\nMethods This paper investigates second-child fertility decisions using data from the 2018 China Family Panel Studies and employs Ordinary Least Squares regression. The study examines assortative matching based on fertility preferences and uses the 2020 provincial-level sex ratio for individuals aged 20–39 as a proxy for women’s bargaining power in the marriage market.\n\nResults The study shows that achieving consensus on having a second child requires cooperation between spouses, particularly when their fertility preferences differ. The study also reveals that marriage matching is not random; individuals are more likely to partner with those who share the same second-child preference. Additionally, women with greater bargaining power positively influence their husbands’ desired family size, a correlation not observed in males.\n\nConclusion The study concludes that second-child fertility decisions in China are significantly influenced by marital bargaining and the increased bargaining power of women due to the skewed sex ratio. Cooperation between spouses with differing fertility preferences is crucial for reaching a consensus on having a second child.", "keywords": [ "Fertility preference", "assortative matching", "marriage", "bargaining", "male-female ratio", "China" ], "content": "Introduction\n\nChinese society and economy have undergone significant shifts over the past seven decades. Social issues have evolved from a vast population base with low human capital following the establishment of the People’s Republic of China, to a demographic characterized by an aging population and a labor force shortage in recent years. Correspondingly, fertility policy transitions can be divided into three periods: the first, following 1949, encouraged higher birth rates to support the burgeoning workforce demands; the second, beginning in the 1970s with the “Later, Longer, Fewer” campaign and later reinforced by the One–Child Policy, aimed to control the booming population; and the third, a response to declining fertility rates and an aging population, where a series of two-child policies emerged. In 2011, couples who were both only children were permitted to have a second child under the Double–Single Two–Child Policy; in 2013, the policy expanded to allow couples to have a second child if either spouse was an only child under the Selective Two-Child Policy; and in 2016, the Universal Two-Child Policy was implemented, allowing all couples to have two children.\n\nHowever, the Chinese birth rate has continued to decline in recent years. While there was a temporary increase in birth and natural growth rates following 2016, these rates decreased to new lows in subsequent years, as illustrated in Figure 1. With the belief “more children, more blessings\" and the strict enforcement of the One-Child Policy, couples generally do not disagree on having the first child. Disagreements occur over the second and subsequent children, especially when women are empowered by their market status. The Universal Two-Child Policy encourages families to consider a second child, potentially initiating a bargaining process between spouses when their preferences differ. Furthermore, with China’s rapid economic development and a continuously skewed sex ratio, women’s bargaining power within the family has increased (Bulte et al., 2015). These factors underscore the importance of understanding fertility decisions from the perspective of the marital bargaining process.\n\nNote: The short-dash, dash, and long-dash lines denote the starting times of the Double-Single, Selective, and Universal Two-Child Policies, respectively.\n\nTheoretical models highlight the importance of the bargaining process in fertility decisions and illuminate how bargaining over fertility may differ between developed and developing countries. Fertility choices in developing countries are often dominated by a single decision-maker, typically males, who usually prefer a larger family size and possess greater bargaining power. These significant disagreements between spouses about fertility preferences imply that increasing women’s bargaining power could enable them to influence fertility decisions (Doepke and Tertilt, 2018). In contrast, high-income economies often feature gender-equal labor laws and greater female participation in the labor market, where bargaining over fertility becomes significant because women and men achieve equal bargaining powers (Doepke et al., 2023). Doepke and Kindermann (2019) propose a veto model for fertility decisions, illustrating that in high-income countries, where men and women achieve equal bargaining power, both spouses have veto power over fertility. This model also considers the spouses’ ability to commit to future consumption. Manser and Brown (1980) integrate marriage decisions within a two-person bargaining framework, allowing husbands and wives with distinct utility functions and preferences to negotiate agreements on crucial aspects such as children, housing, and leisure. These agreements enable them to realize gains from the marriage that would not be possible if they remained single.\n\nThe argument above suggests that agreement between spouses on the desired number of children is important. This indicates that in the marriage market, both men and women have strong incentives to seek partners with similar preferences. If a husband and wife share similar views on family size, they may avoid the need for a bargaining process. Therefore, in the presence of heterogeneity in preferences regarding the number of children, assortative matching naturally occurs in the marriage market. Thus, it is crucial to examine the extent to which bargaining and matching based on preferences influence family size.\n\nIn this paper, thus, we examine fertility decisions regarding the second child, focusing on differing marital fertility preferences utilizing data from the 2018 China Family Panel Studies survey and applying Ordinary Least Squares (OLS) regression models. We further explore assortative matching based on fertility preferences, using the provincial-level sex ratio as a proxy for women’s bargaining power. To this end, we collected data on the number of males and females aged 20-39 from the 2020 China Population Census Yearbook and calculated the sex ratio by dividing the number of males by the number of females. This approach captures the potential population in the marriage market.\n\nThe findings reveal that to have a second child, both the wife and the husband need to cooperate when they have different fertility preferences. Additionally, we found that marriage matching is non-random; specifically, individuals are more likely to pair with partners who share the same preference regarding having a second child. Therefore, we further studied how one spouse’s fertility preference associates with their partner’s. Our conclusions indicate that females with greater bargaining power correlate positively with their husbands’ ideal family size, whereas males do not have a similar correlation.\n\nThis paper contributes to the literature on fertility decisions from the perspective of the bargaining process within the Chinese context. Previous research mainly studies fertility decisions from the perspective of females in their reproductive age, which considers the family as a unit that internalizes individual differences to make fertility decisions that maximize household utility. Becker (1960) first applies economic theory to understand fertility decisions in 1960, proposing that children can be regarded as a consumption good that contributes to household utility. The model assumes a unitary household utility function, internalizing differences between family members, where families make rational choices about the number of children based on their preferences, income, and the costs of raising children (Becker, 1960). Further research considering parental altruism toward children assumes that parental utility also depends on the utility of children in addition to their number, thus household utility includes both the quantity and quality of children. This leads to findings that higher parental altruism leads to higher fertility rates, increased investment in each child's human capital, and greater long-term economic growth due to more capital accumulation, as altruism links the welfare of all generations in a family (Barro and Becker, 1989; Becker and Barro, 1988). Subsequent research builds on Becker’s work, adapting it to different contexts. For example, Baudin et al. (2015) focus on childlessness in the United States and propose a theory explaining that childlessness among the poor is due to low resources, while among educated women it is due to the high opportunity cost of having children. A study on the Chinese case by Liu and Liu (2020) explores the effectiveness of the Universal Two-Child Policy in China within the same framework, suggesting a threshold for the policy estimated to be lower than two children per household, implying the policy's impact on fertility rates is limited. However, as an essential family decision, fertility is mainly determined by both spouses’ preferences, leading to potential bargaining processes. There is a large amount of empirical literature on other countries based on the perspective of bargaining processes (Doepke and Kindermann, 2019; Testa et al., 2014). Peng (2020) based on interviews with 53 urban parents in China, reveals that family negotiations significantly shape Chinese reproductive behavior more than individual preferences. However, the quantitative study from the bargaining perspective on the Chinese case is limited.\n\nIn addition, this paper contributes to the literature on assortative mating based on fertility preferences. Existing literature primarily examines how assortative mating influences fertility behaviors, with a particular emphasis on educational sorting. For example, Bueno and García-Román (2021) study the Spanish case, indicating that couples with similar educational levels are more likely to have children, especially if both spouses are highly educated. Similarly, a European study finds that educational sorting significantly predicts fertility behaviors; couples with both partners highly educated tend to delay their first child but have more children later, whereas couples with a higher-educated husband and a lower-educated wife are less likely to have a second child (Nitsche et al., 2018). Tian et al. (2023) also highlight that educational sorting has the most significant impact on women’s fertility preferences compared to age and income sorting using Chinese data. Additionally, the study of marriage matching in China highlights the impact of hukou locality and intergenerational mobility on marital choices. Research from Shanghai indicates that possessing local hukou shapes these choices, enhancing the matching of highly-educated individuals while limiting interactions between hukou residents and less-educated non-hukou migrants (Qian and Qian, 2017). Urban males are empowered in the marriage market by being granted the same rights as women to pass hukou locality to their children (Han et al., 2015). Hu (2016) identifies significant associations between the occupational statuses of individuals’ fathers and those of their spouses, as well as with their fathers-in-law. To the best of our knowledge, no existing studies investigate the impact of fertility preferences on marriage matching within the Chinese context. Given these research gaps, this paper aims to provide new insights into how fertility decisions are made through bargaining processes and how fertility preferences could be associated with assortative mating.\n\nThe remainder of the paper is organized as follows: Section 2 presents the data and variables used for the empirical analysis. Section 3 outlines the empirical strategy. Section 4 explores how fertility decisions are made based on both spouses’ fertility preferences. Section 5 examines how one spouse’s fertility preference associates with their partner’s preference. Section 6 concludes the paper.\n\n\nMethods\n\nThe primary dataset utilized in this study is the China Family Panel Studies (CFPS), a nationally representative longitudinal sample of Chinese communities, families, and individuals (Xie and Hu, 2014). The survey includes information on economic activities, educational outcomes, family relationships, migration, and health. Initiated by the Institute of Social Science Survey (ISSS) at Peking University, the baseline survey was conducted in 2010, with follow-up full-sample surveys conducted biennially in 2012, 2014, 2016, 2018, and 2020. Our analysis uses the cross-sectional data from the 2018 CFPS, which includes around 44,000 individuals in 15,000 households from more than 900 counties and cities within 31 provinces, municipalities, and autonomous regions.\n\nThe CFPS employs a multi-stage probability sampling strategy to ensure a representative sample of the Chinese population. In the first and second stages, it stratifies and selects provinces and counties using official administrative divisions. Recognizing the geographic disparities inherent in China’s economic development, the design emphasizes geographic representation. In the third stage, households within the chosen counties are selected through a systematic sampling method, targeting 25 households per county to fulfill the study’s requirements.\n\nSince we seek to understand the family’s fertility decisions for a second child through the bargaining process, we initially restricted the sample to individuals who responded to questions regarding their ideal number of children. In the 2018 CFPS dataset, 16,268 out of 18,802 females and 16,214 out of 18,552 males provided their responses. Considering both the husband’s and the wife’s preferences, we further constructed a household-level sample that includes information on both spouses. We limited the sample to couples where both spouses responded to the question about the “ideal number of children\", as this measures their fertility preference for a second child. We also restricted the age range for women to be equal to or less than 37, corresponding to the possible reproductive age. The distribution of female ages in the sample is shown in Figure 2. Ultimately, the sample comprises 2,054 household observations with detailed information on both husbands and wives. We obtained the permission to use this data set on August 9, 2021.\n\nThe main outcome variable in this study is whether the household has two or more children. This variable is derived from the number of children in the family. Since the CFPS does not directly provide complete information on family size, we generated this variable using information available for each child. If both spouses reported their ideal number of children but the actual number of children is missing, we replaced the missing values with 0. In the sample, 46.84% of households have more than two children. The key explanatory variables are the fertility preferences of both spouses for the second child, derived from their reported ideal number of children. In the sample, 79.41% of wives and 80.72% of husbands prefer more than two children. In the second part, the outcome variables are individual fertility preferences, measured by their ideal number of children. On average, both females and males desire fewer than two children. Control variables include both spouses’ employment status (employed or unemployed, without distinguishing between being out of the labor force or unemployed), years of education, age, hukou type (rural or urban), and the family income. We assigned the income to be zero if the individuals are currently not employed. Family income in logarithmic form is calculated by summing the incomes of both spouses and adding one, to avoid issues with missing values when both spouses have no income.\n\nThe previous literature has shown, both empirically and theoretically, that a skewed sex ratio increases women’s bargaining power in the marriage market (Angrist, 2002; Chiappori et al., 2002; Bulte et al., 2015). In this paper, as we are interested in the marital bargaining process regarding family fertility decisions, we use the provincial-level sex ratio as a proxy for bargaining power. We collected data on the number of males and females aged 20-39 from the China Population Census Yearbooks for 2000, 2010, and 2020. The age range of 20-39 captures the potential population in the marriage market. There is no information available for 2018, as the census is conducted every ten years. We calculated the sex ratio by dividing the number of males by the number of females. Given that the statistics are similar across these three census waves, we report only the results using the 2020 sex ratios in this paper. In 2020, the average sex ratio for the population aged between 20 and 39 across 31 provinces was 1.08, implying there are more males than females in the marriage market. The detailed summary statistics for all variables are shown in Table 1.\n\nTo estimate the relationship between marital bargaining based on fertility preferences and second-child fertility decisions, we use the following OLS regression model:\n\nTo estimate how one spouse’s fertility preferences might correlate to the other’s, we use the following two OLS regression models for husbands and wives:\n\nThe results are presented sequentially. First, we examine the relationship of different fertility preferences with the family’s decision to have a second child. Then, we explore how one partner’s fertility preference might be associated with the other partner’s preference.\n\n\nResults\n\nThe OLS results are reported in Table 2. Column (1) includes only explanatory variables and their interaction term; column (2) adds demographic characteristics; column (3) further controls for provincial fixed effects. All regression results show a statistically significant positive relationship between the second-child preferences of either spouse and the decision to have a second child in a family.\n\n* p<0.01.\n\n p<0.05.\n\n* p<0.1.\n\nWe consider the situation with control for provincial fixed effects as the benchmark, as detailed in column (3). When a couple plans to have a second child, considering their fertility preferences, there are four possible outcomes: both agree to have the second one, both agree not to have it, the wife wants to have it but the husband disagrees, and the husband wants to have it but the wife disagrees. Our results show that when the couple reaches the agreement on the second child, it is associated with an increase in the likelihood of having a second child by more than 40% (0.148+0.106+0.178), the largest among the four outcomes. When a couple disagrees about having a second child, either spouse preferring a second child could be associated with an increased likelihood of having one. However, the wife’s preference tends to have a greater correlation with the household fertility decision. If only the wife agrees, her preference correlates to an increase in the household’s fertility probability by 14.8%, while if only the husband agrees, his preference correlates to an increase in the household’s fertility probability by 10.6%. All three estimators are significant at the 1% level and are robust across different specifications. This implies that to have a second child, both the wife and the husband need to cooperate to reach an agreement, especially when they have different second-child fertility preferences.\n\nMoreover, the propensity for non-random marriage matching reinforces these findings, as individuals are more likely to pair with partners who share the same preference regarding having a second child. Table 3 illustrates this non-random distribution of marriage matching by fertility preference for the second child. For both men and women, the ratios of those preferring to have a second child to those who do not are approximately 4:1. If marriage matching were random, based on the sample size, we would expect to find 1,317 pairs of men and women both agreeing to have a second child, and 82 pairs agreeing not to have one. However, the actual numbers are higher: there are 1,459 and 224 households, respectively, that share the same fertility preference. Similarly, the households with couples share different fertility preferences are fewer than the expected under the assumption of random matching. This discrepancy supports the idea that couples match non-randomly based on fertility preferences.\n\nBuilding on these observations, we are now interested in whether and how one spouse’s fertility preference associates with their partner’s.\n\nIn this section, we show correlation of wife’s and husband’s fertility preferences. The OLS results for wives and husbands are reported in Tables 4 and 5, respectively. In each table, columns (1) through (3) exclude self demographic characteristics, while columns (4) through (6) include them. Explanatory variables are added incrementally: we first introduce each spouse’s fertility preference in columns (1) and (4), then the provincial sex ratio in columns (2) and (5), and finally the interaction term between fertility preference and sex ratio in columns (3) and (6).\n\n* p<0.01.\n\n p<0.05.\n\n* p<0.1.\n\n* p<0.01.\n\n p<0.05.\n\n* p<0.1.\n\nWe consider the situation including self demographic characteristics as the benchmark, as detailed in column (6) of both tables. The results for both husbands and wives show that if they prefer more children, their partners also prefer more children. All estimators are significant at the 1% level. Specifically, if a husband’s ideal number of children is one more than the average male preference, his wife will likely prefer 0.4 more children than the average female preference. In contrast, if a wife’s ideal number of children exceeds the average female preference by one, her husband will likely prefer 0.5 more children than the average male preference.\n\nMales and females exhibit asymmetry when considering the provincial-level sex ratio. We use the sex ratio for those aged between 20 and 39 in a province to capture the potential population in the marriage market. A larger sex ratio, indicating more males than females, serves as a proxy for women’s higher bargaining power. This is because a higher sex ratio intensifies competition among males for potential female partners, thereby enhancing women’s bargaining position in the marriage market and in family decisions. In provinces where the sex ratio is one percentage point higher than the national average, a wife’s preference affects her husband’s preference much more strongly. Conversely, in such provinces, a husband’s preference affects his wife’s preference in a similar manner when the sex ratio becomes higher. More specifically, if the wife prefers one more child than the average female ideal number, then her husband will prefer 0.5 (0.495+0.668×1%) more children than the average male ideal number. Conversely, the husband’s fertility preference is not associated with his wife’s preference, regardless of the sex ratio in their resident province. This suggests that women’s increased bargaining power influences assortative matching, due to their smaller number in the marriage market. The greater bargaining power enables women to match with partners whose fertility preferences are associated with theirs.\n\n\nConclusions\n\nIn this paper, we examine fertility decisions regarding the second child, focusing on differing marital fertility preferences by utilizing data from the 2018 China Family Panel Studies survey and applying Ordinary Least Squares regression models. We further explore assortative matching based on fertility preferences, using the provincial-level sex ratio from 2020 for the population aged between 20 and 39 as a proxy for women’s bargaining power, which captures the potential population in the marriage market. Our findings reveal that having a second child requires cooperation between the wife and the husband, especially when they have differing fertility preferences. Additionally, our research shows that marriage matching is not random; individuals are more likely to pair with partners with the same preference for having a second child. Further analysis demonstrates that females with greater bargaining power correlate positively with their husbands’ ideal family size, whereas males do not have a similar correlation. This paper contributes to the literature on fertility decisions from the perspective of the bargaining process within the Chinese context, as well as preference matching and sorting.", "appendix": "Data availability\n\nWe are not allowed to distribute the original data since the data was collected by Peking University and the agreement with Peking University does not allows us to distribute the data. However, we provide the link to obtain the data from Pekin University and we provide the code to replicate our results. Our data set(code) is a is available at Open Science Framework (OSF) (Zhuang and Naito (2024)): https://doi.org/10.17605/OSF.IO/F5DPZ.\n\nThe original dataset used in this study is available from the following URL: https://opendata.pku.edu.cn/dataverse/CFPS?language=en Researchers who want to replicate our results can obtain the data set by proposing a research proposal to Peking University through the above website. The code to replicate our results are available on the above OSF domain. The findings, interpretations, and conclusions expressed in this article are entirely those of the authors and should not be attributed in any manner to Peking University, to its affiliated organizations. Zhuang and Naito (2024) on OSF contains the following data:\n\ndata.do: Stata file for data cleaning\n\ntables.do: Stata file for figures and regression analysis\n\nTables.xlsx: Excel file for all tables\n\nThe above data are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\nRepository: STROBE checklist for ‘Marital Bargaining and Assortative Matching on Fertility Preference: Evidence based on Cross-sectional Data in China’ is available at https://doi.org/10.17605/OSF.IO/2Z8HY.\n\nEthics and consent: we obtained the approval to use this data on August 9, 2021 from Peking University. Since this data is in the public domain and it is widely used, the review thorough the ethical committee at the University of Tsukuba was not needed. The original data collection project by Peking University was approved by the Biomedical Ethics Committee of Peking University, Beijing, China. The ethical approval number is IRB00001052-14010. We obtained the permission to publish this research on June 2nd 2024 from Peking University.\n\n\nReferences\n\nAngrist J: How Do Sex Ratios Affect Marriage and Labor Markets? Evidence from America’s Second Generation. Q. J. Econ. 2002; 117(3): 997–1038. Publisher Full Text\n\nBarro RJ, Becker GS: Fertility Choice in a Model of Economic Growth. Econometrica. 1989; 57(2): 481–501. Publisher Full Text\n\nBaudin T, de la Croix D , Gobbi PE: Fertility and Childlessness in the United States. Am. Econ. Rev. 2015; 105(6): 1852–1882. Publisher Full Text\n\nBecker G: An Economic Analysis of Fertility. NBER Chapters, National Bureau of Economic Research, Inc.; 1960.\n\nBecker GS, Barro RJ: A Reformulation of the Economic Theory of Fertility*. Q. J. Econ. 1988; 103(1): 1–25. PubMed Abstract \| Publisher Full Text\n\nBueno X, García-Román J: Rethinking Couples’ Fertility in Spain: Do Partners’ Relative Education, Employment, and Job Stability Matter?. Eur. Sociol. Rev. 2021; 37(4): 571–587. Publisher Full Text\n\nBulte E, Tu Q, List J: Battle of the Sexes: How Sex Ratios Affect Female Bargaining Power. Econ. Dev. Cult. Chang. 2015; 64(1): 143–161. Publisher Full Text\n\nChiappori P, Fortin B, Lacroix G: Marriage Market, Divorce Legislation, and Household Labor Supply. J. Polit. Econ. 2002; 110(1): 37–72. Publisher Full Text\n\nDoepke M, Hannusch A, Kindermann F, et al.: The economics of fertility: a new era.Lundberg S, Voena A, editors. Handbook of the Economics of the Family, volume 1 of Handbook of the Economics of the Family. North-Holland; 2023; Volume 1. : pages 151–254. Publisher Full Text\n\nDoepke M, Kindermann F: Bargaining over Babies: Theory, Evidence, and Policy Implications. Am. Econ. Rev. 2019; 109(9): 3264–3306. Publisher Full Text\n\nDoepke M, Tertilt M: Women’s Empowerment, the Gender Gap in Desired Fertility, and Fertility Outcomes in Developing Countries. AEA Papers and Proceedings. 2018; 108: 358–362. Publisher Full Text\n\nHan L, Li T, Zhao Y: How Status Inheritance Rules Affect Marital Sorting: Theory and Evidence from Urban China. Econ. J. 2015; 125(589): 1850–1887.\n\nHu Y: Marriage of matching doors: Marital sorting on parental background in China. Demogr. Res. 2016; 35: 557–580. Publisher Full Text\n\nLiu J, Liu T: Two-child policy, gender income and fertility choice in China. Int. Rev. Econ. Financ. 2020; 69: 1071–1081. Publisher Full Text\n\nManser M, Brown M: Marriage and Household Decision-Making: A Bargaining Analysis. Int. Econ. Rev. 1980; 21(1): 31–44. Publisher Full Text\n\nNitsche N, Matysiak A, Van Bavel J, et al.: Partners’ Educational Pairings and Fertility Across Europe. Demography. 2018; 55(4): 1195–1232. PubMed Abstract \| Publisher Full Text\n\nPeng Y: Should We Have a Second Child? Reproductive Decisions and Family Negotiation under China’s Two-child Policy. J. Contemp. China. 2020; 29(125): 792–807. Publisher Full Text\n\nQian Y, Qian Z: Assortative Mating by Education and Hukou in Shanghai. Chinese sociological review. 2017; 49(3): 239–262. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nTesta MR, Cavalli L, Rosina A: The Effect of Couple Disagreement about Child-Timing Intentions: A Parity-Specific Approach. Popul. Dev. Rev. 2014; 40(1): 31–53. Publisher Full Text\n\nTian W, He Y, Wang X: Study on Marriage Pairings and Women’s Fertility Intentions in China. J. Fam. Issues. 2023; 0192513X231194299. Publisher Full Text\n\nXie Y, Hu J: An Introduction to the China Family Panel Studies (CFPS). Chinese Sociological Review. 2014; 47(1): 3–29.\n\nZhuang M, Naito H: Marital bargaining and assortative matching on fertility preference: evidence based on cross-sectional data in china. OSF\|Marital Bargaining and Assortative Matching.2024. Publisher Full Text" }	[ { "id": "294203", "date": "20 Aug 2024", "name": "Stuart Gietel-Basten", "expertise": [ "Reviewer Expertise Demography" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 good paper using an excellent data set. The analysis is simple but suffices. Some issues:\nThe literature review is somewhat haphazard and could be made more systematic and comprehensive. The conclusion section is far too short. There should be a discussion section which, well, discusses the findings, expanding on limitations, policy implications and so on. The terminology throughout should be more careful (e.g. 'birth rate') The first figure doesn't make sense (has no y axis label, doesn't seem to match the description etc).\nIn short the paper is ok, but the authors need to tighten it up a lot and be much clearer and specific about its contribution to the literature (which includes a more expansive literature review to point out the gaps).\n\nIs the work clearly and accurately presented and does it cite the current literature? No\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\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": [] } ]	1	https://f1000research.com/articles/13-659
https://f1000research.com/articles/11-1300/v1	14 Nov 22	{ "type": "Research Article", "title": "Diversity of functional edaphic macrofauna in Musa acuminata x Musa balbisiana (AAB) agroecosystems", "authors": [ "C. A. Zúniga-Gonzalez", "A. J. Caballero-Hernández", "A. J. Caballero-Hernández" ], "abstract": "Background: This study focused on evaluating the diversity and richness of the edaphic macrofauna in eight banana farms in the western zone of Nicaragua. Methods: The sampling design was random and descriptive, it was divided into two phases, the first was the collection of the sample, and the second was the classification, coding, and storage of the extracted macrofauna populations. Subsequently, the indices of diversity and species richness, relative abundance, by functional groups were estimated. Results: The results showed that the relative abundance of biodiversity was higher in the 0–20 cm soil depth stratum than in the branch and leaf biomass strata. The values of the diversity indices of Dominion, Simpson, Shanon, Margalef, and Equity were in the normal range, with a tendency towards low diversity. Likewise, in the richness of species, the Dominant or most abundant genus were earthworms (Oligochaeta) and Hymenoptera (Solenopsis, Leptothorax, Camponotus, Pheidole), indicating the directly proportional relationship, that is to say, that the greater the number of earthworms the production increases and the greater the number of Hymenoptera it decreases, confirmed with the Pearson correlation coefficient with a reliability of 95%. Conclusions: It was concluded that based on the estimates of the diversity indicators, two detritivore genus (earthworms and Hymenoptera) were the ones with the greatest presence, being important in the production of the banana agrosystem due to the decomposition of organic matter and its nutritional contribution to the plant. We observed a direct correlation with earthworms and an indirect relationship with Hymenoptera.", "keywords": [ "Eco-Intensification", "Eco-system", "Plantain", "Diversity", "Microfauna" ], "content": "Introduction\n\nSoil management in banana agroecosystems is essentially successful for resilient agro-ecological production, adapted to climate change, and biodiversity, fundamentally in Latin America. Berning et al. (2022), Gliessman (2013), Rousseau et al. (2012), McLaughlin et al. (1995), Challinor et al. (2009), Rousseau et al. (2013) and Delgado et al. (2010b) indicate that agro-ecological conditions of the soil represent one of the ways to adapt precisely to the development of production in the banana sector. The combination of Musa acuminata × Musa balbisiana (AAB) constitutes a food source in the Latin American diet (Belalcázar, 2003). For this reason, it is important to develop agricultural practices linked to the benefit of edaphic biodiversity and thus have productive and intensive agriculture characterized by various degrees of intensification of traditional, customary, transitional and organic agriculture (Delgado et al., 2010a). Improving ecosystems and taking advantage of the usefulness of biodiversity in this process requires understanding the structure and function of biological and physical-chemical combinations. They include stability of the edaphic structure, reuse, storage, and supply of organic matter (OM) and nutrients, available soil moisture, and management of damage to micro, and macrofauna.\n\nSimilarly, authors such as McKelvie-Sebileau et al. (2022), Samudio (2010), Shiyam et al. (2010), López (1995), MIFIC (2007) and Gizzi et al. (2009) suggest that in nutritional irrigation systems where crops such as corn, beans, pumpkin, papaya, pineapple, coffee, cocoa are included, they demand the conservation of fungi, bacteria, viruses, harmful insects, nematodes and weed organisms, to do more effective environmental perceptions and producer profitability.\n\nLikewise, Gutiérrez-Luna et al. (2022), Rodríguez et al. (2013) and Brown et al. (2001) investigated that the impact of cultural practices or soil health should be evaluated through chains that maintain soil fertility. From this perspective, soil fertility studies of plantain should include previously unexplained constituents of the macrofauna as indicators of the richness in biodiversity, abundance, and degree of alteration of the ecological functions of the population.\n\nOn the other hand, invertebrate pests attract a lot of attention, and they cost farmers and producers millions of dollars (Tresson et al., 2022; Velásquez et al., 2012; Alcaraván, 2003; Decaëns et al., 2004; Cardona et al., 1998).\n\nBrown et al. (2001) and Pocasangre, Brown and Quesada (2009) show that limited physical-chemical elements and fertility can lead to population decline. In the same way, they added that beneficial invertebrates for their basic and fundamental functions have received little attention. In general, Velasquez et al. (2007) shows that their behavior is taken for granted and the management of agroecosystems is rarely altered for their benefit. The importance of the invertebrate edaphic macrofauna is closely related to the quantitative and qualitative analysis of biomass period (MO) and generation of genetic biology components.\n\nMedina et al. (2021), Djigal et al. (2012), Laossia et al. (2008) and Ruiz (2008) indicate that these organisms can experience a shortage of oxygen and light, fewer open spaces, poor availability and quality of food and a very strong variability of microclimates to be able to live in the soil, examples of these microorganisms are the centipedes, termites, earthworms, insects, mites, flying worms and butterflies (Medina et al., 2021). Populations of all megafaunas reach millions per hectare and their biomass varies in tons per hectare. Their diversity can exceed 1,000 species in complex ecosystems (such as tropical forests), but precise data on the specific diversity of tropical edaphic megafauna in specific ecosystems is still lacking (Anderson, 1993; Zerbino, 2010; Zerbino et al., 2008; Priego-Castillo et al., 2009; Wardle et al., 1995).\n\nFinally, the work focused on evaluating the diversity and abundance of macrofauna in eight banana-producing farms in the North Pacific area of Nicaragua. The work was organized in an introductory section where the problem and the importance of this study are explained. In the Methods section, the procedure for the collection, classification, coding and storage of the species is presented. The Results and Discussion section presents the species found and their richness, abundance and diversity. Finally, the main conclusions based on the objective of the research are presented.\n\n\nMethods\n\nTable 1 shows the statistical description of the data used in this study. The full protocol can be found on protocols.io.\n\nThe study was carried out in eight banana farms in the city of León and Posoltega (Table 2). The climatic conditions in the León area are characterized by having a rainfall of 1,529.7 mm, an average temperature per year of 38°C, and an altitude of 60 meters. The Posoltega area is characterized by an average annual temperature of 39°C, 2,000 mm of rain and an altitude of 70.42 meters above sea level, both areas are located in the western region of Nicaragua, see Figure 1 (MIFIC, 2007).\n\nMap data ©2022 Google.\n\nTable 2 shows eight farms that describe the name, area, community and municipality. In these farms, the investigation begins with the field phase where 40 edaphic samples of 0–20 cm depth and 40 biomass samples (leaf litter) were collected on the surface. A total of 80 samples of macrofauna populations were identified, coded, stored in the second phase. The study area in each farm was 0.7 ha delimited 1 in 1,000 m2 (50 cm long × 20 cm wide), as described in Rousseau et al. (2012), Rousseau et al. (2013), Medina et al. (2021).\n\nAfter selecting the sampling area, sampling points are placed to collect soil samples. A wooden box 20 cm wide by 20 cm long was used to mark the sampling points, and to remove approximately 1 kg of soil. Divided into two consecutive layers (fallen leaves, 0–20 cm), each of them is surrounded to prevent microorganisms from escaping from the bottom, after which the material is sieved and separated manually and the insects found are placed in an airtight plastic bottle. After measuring 500 cubic centimeters in volume, they are labeled and preserved in 70% alcohol.\n\nThe collected individuals were analyzed by order, family and quantified and identified by sex, the microorganisms were placed in Petri dishes and then observed under a 4–400× stereo microscope, to detail the specific structures of each of the species. Large animals include all organisms greater than 4 mm in length.\n\nThe diversity and richness of species present in this study were analyzed using the indicators reported by the authors Zerbino (2010) and Rousseau et al. (2012, 2013). Richness (number of species): the number is the number of species for each farm, which was determined and totaled for each sampled system. The total number of individuals per species was counted and estimated.\n\nPopulation abundance and species richness were determined by three main functional groups: herbivores, detritivores, and predators. To estimate the density, PAST (RRID:SCR_019129) 4.03 software was used, the indices selected for the study were: Domain (D), Shannon-Wiener (H′), Margalef (Mg), Simpson (1-D), and Pielou (J′).\n\nDomain Index (D): It is the relative importance of a species related to the degree of influence it has on the individuals of the plantain agrosystem. It is based on competition for resources, which is why the characterization of the collected sample is used and then organized by functional group. Its inverse is the Simpson index.\n\nShannon-Wiener Index (H′) (Equation 1): Considers the number of species found in the study area (species richness) and the relative frequency (abundance) of each of these species. It is used to determine the number of species and how those species are distributed. It is usually expressed as H′, expressed as a positive number that varies between 0.5 and 5. Values between 0.5–2 indicate a situation with low diversity, 2–3 is a normal situation, and 3–5 or more indicates a situation of high diversity.\n\nS: Richness or number of species; pi: ratio of individuals of the species (i) with respect to the total number of individuals (that is, the relative abundance of the species i).\n\nMargalef Diversity Index (DMg) (Equation 2): measures the specific richness of an area and the relationship between individuals and the total sample. The value 0 is when there is only one species in the sample (s=1, therefore s-1=0), values less than 2 are considered areas of low biodiversity and values greater than 5 are indicative of high biodiversity. Where:\n\nS = number of species; N = total number of individuals.\n\nSimpson's Index (1-D) (Equation 3): this index is based on dominance. This is the inverse parameter of the concept of community unity or equality. Consider the representativeness of the most important species without evaluating the contribution of the remaining species. Values from 0 to 0.5 bring the value closer to a situation of high diversity, and values from 0.5 to 1 bring the value closer to low biodiversity.\n\nWhere:\n\nPi = the number of individuals among the total species (i). Strongly influenced by the importance of the dominant species. Its value is the reciprocal of fairness, so the diversity is known as 1 – λ.\n\nPielou Index (J) (Equation 4): stock market index. It measures the relationship between the observed diversity and the maximum expected diversity. Its value is between 0 and 0.1, so 0.1 corresponds to situations in which all species occur equally.\n\nWhere:\n\nUsing IBM SPSS Statistics (RRID:SCR_016479) v.22 program, the data of individuals collected and ordered by categories were processed. Tables were created showing the groups of species present in each farm studied. For the analysis of the diversity indices, the PAST (RRID:SCR_019129) 4.03 software was used. Finally, Pearson's correlation was applied to identify the most dominant and most common group useful to understand the dominant interrelationship and its productivity within the plantain agrosystem.\n\n\nResults and Discussion\n\nTables 1, 3 and 4, and Figure 2 (Zuniga-Gonzalez et al., 2022) show the general relative abundance of macrofauna found in the four banana plantations in the city of León between the litter layer and soil depths of 0–20 cm. The genera Geophilus and Leptothorax dominate with 70 individuals per square meter (ind × m2), Philoscia with 160 ind × m2 and Oxidus with 110 ind. m2 and Hypoponera are 165 ind × m2, and earthworms are 590 ind × m2. In the municipality of Posoltega, Pheidole sp. 280 ind × m2, Solenopsis sp. 290 ind × m2, Asiomorpha 170 ind × m2, earthworm 600 ind × m2 (Tables 5 and 6). The genus Pheidole sp., was found in the soil of a banana plantation in the city of León, and the genus Solenopsis. However, the frequencies of earthworm individuals are similar in both communities. Zerbino et al. (2008) in their study presented the two most abundant groups of the subclass Oligochaeta of the order Opisthopora and insects of the order Hymenoptera, representing 46 and 20% of the total number of individuals collected, respectively. This confirms our findings with earthworms (Opisthopora) and Hymenoptera (Pheidole and Solenopsis) accounting for 37.77 and 18.25%, respectively, of all individuals collected.\n\nThis heatmap was constructed using PAST software.\n\nIn a study by Priego-Castillo et al. (2009) and Castillo and Vera (2000), it was reported that the Hymenoptera group was the most abundant, with 62.49% of the total individuals collected during the 2,000 agricultural cycle in organic and conventional banana plantations in Guacimo, Costa Rica. This means that the soil is moist throughout the year. However, the presence of earthworms (Opisthopora) was 11.92% and abundant in all stages.\n\nIn the municipality of Leon, Farm 1 shows that earthworms dominate at 150 ind × m2 and Oxidus dominate with 70 ind × m2. In farm 2, earthworms dominate at 325 ind × m2, and Hypoponera spp. with 115 ind × m2, likewise in farm 4 El Verdón, stand out, genus Leptoxthorax (Opisthopora) of 45 ind × m2, 65 ind × m2 of Scarabaeidae and 65 ind × m2 of earthworms, however, in farm 3, only the genus, Philoscia, in Farm 3, measures 45 ind × m2 and earthworms dominate at 50 ind × m2 (Table 5 and 6). The municipal of León has a greater wealth of sexes with 23 representative genus, but a lower overall dominance (ind × m2). In four farms (San Martín, Santa Isabel and El Verdon) earthworm frequencies were found to be similar, but less common genera such as Leptothorax and Asiomorpha were found.\n\nThese data on earthworm populations in litter and layers from 0 to 20 cm2 have been confirmed by Castillo and Vera (2000), Pashanasi (2001), Zerbino (2010), and these populations have a beneficial role in the soil. Training is very important and sensitive to management practices in the banana farms of León and Posoltega.\n\nTable 4 shows the relative abundance by farm and by functional group, noting that the detritivores group is more abundant, followed by predators. These dominant groups exerted a beneficial function on the soil, allowing increased production yields because they are the responsible for breaking down OM and providing nutrition for plants.\n\nFor the municipality Posoltega, in farm 6, earthworms dominate with 225 ind × m2 and Solenopsis spp. with 190 ind × m2, farm 8 had Asiomorpha spp. with 125 ind × m2 (Table 5 and 6). Plantain plantations in Posoltega are repopulated with Solenopsis worms and ants. This is likely because they occupy the same ecological niches in which they coexist, interact with similar food sources, land, husbandry and management skills, and benefit from abundant and prosperous communities. These data are supported by Zayas et al. (2022), Quiroz-Medina et al. (2021), Castillo y Vera (2000), Pashanasi (2001), Zerbino (2010), Rousseau et al. (2012) and Rousseau et al. (2013).\n\nTable 7 shows the diversity indices per farm. In general, the farms studied present a taxonomic variety of biomass (3,150 individuals). In general, a low domain (less than 40%) is observed in each of the farms. The Shannon-Wiener index shows low diversity with values less than 2, except for farms 1, 4 and 8 with values close to 2, meaning normal diversity. The Shannon indexes are not superior to those of Melo (2010), who had a high diversity value of the Shannon index of H′ = 2.61, which indicates that the Kikuyu prairie has the highest richness in both families and organisms. Rousseau et al. (2012, 2013), present low-quality data on diversity, dominance, wealth, and stock market indices.\n\nThe Simpson index confirms this low diversity with values close to 1. The specific richness of the area and the relationship between individuals and the total sample reflected by the Margalet index (DMg) with values less than 2. This is considered as areas of low biodiversity. The Pielou evenness index indicates that not all farms presented situations where all species were equally abundant (Krebs, 1999).\n\nTable 3 shows a summary of the relative abundance of biodiversity in the study area by functional group (Castañeda et al., 2022; Quiroz-Medina, 2021). As mentioned above, the species equity indices are not equal. The lowest percentage of taxonomic presence is in the functional group of herbivores. The biomass has a greater presence (above 50% in the group by function of detritivores and in the group of predators below 50%).\n\nIn studies reported by Zerbino et al. (2008) and Zerbino (2010), it is shown that the discrepancies in the constitution of the megafauna’s community and proportions of functional groups are aspects influenced by the species, the richness of plant species and management, and states that it affects living organisms. This is because they determine the available resources and influence the interactions between herbivores, their controllers, and the destroyers identified by Moore et al. (2004).\n\nThis supports the findings regarding the fact that monoculture influences the available resources and, therefore, is capable of affecting the interactions between functional groups × m2 in the city of Posoltega. The results indicated that the texture of the biocenosis is consistent with the edaphic properties and the quantity and quality of the residues (Almonte, 2022; Leyva, 2012; Curry, 1992). In zero tillage, management practices that promote the presence of residues with spatial and temporal diversification of plant species have richer, more diverse and equitable communities, with a predominance of deterioration functional groups (Priego et al., 2009; Zerbino, 2010; Zerbino et al., 2008). This is consistent with the findings in the present study.\n\nThe analysis confirmed that Posoltega had lower populations of herbivores per m2 and 460 carnivores per m2 (Table 3).\n\nTable 8 shows the diversity indicators by functional groups. These are predominantly detritivores and predators of 400 × m2, in contrast to El Verdón on farm 4, which has a low population of herbivores of 400 × m2, detritivores 85 ind. × m2 due to the large population of predators found. Similarly, at Farm 8 Los Angeles there were no herbivores. This is due to the large population of 250 ind. × m2 predators (Tables 3-5 and 6).\n\nThe data collected in the León area show that the herbivorous functional group has a low proportion of Diversity by the values of the Shannon-Wiener index (H) with a value close to 1 denoting low diversity, this is considered within normality, Dominance Simpson (1-D) with a value close to 1 and Pielou Equity (J′) very close to 1 as in the case of farm 2, meaning equally abundant species. However, the Margalef Diversity Index (DMg) showed a value below 2 considering for areas of low diversity.\n\nThree indicators dominate in the functional group of detritivorous organisms in the city of León. Margalef Diversity (DMg) with a value below 2 means that no farm with this group can be considered as having high diversity. For Simpson Dominance (1-D) it can be said that they are at a midpoint between 1 and 0 with a normal diversity and a Pielou Equity Index (J′) with a value close to 1 situation where all species are equally abundant, of the indices for the Predators group were dominated by three indices: DMg in farm 4, which almost reaches value 2, it can be said that they are within the normal range, and Shannon-Wiener Diversity (H) with values lower than 1 indicating low diversity. This contrasts with the Posoltega area, where Simpson (1-D) dominates with a value close to 0, which implies a high diversity.\n\nTable 8 shows the estimates of the indices of population abundance and species richness, determined by functional groups. According to the DMg, the value found was less than 2 considered as a zone of low biodiversity, which assumes that the number of individuals is equal to the number of species. In the Simpson index, the probability that eight individuals taken at random are of the same species is 0.2 in the case of León and 0.19, this constitutes a low probability, since most of the farms are made up of the genus Lombrices, and that had a lot of abundance of the same species. The Pielou Equity Index (J) confirms these with values close to 1 where all species are equally abundant.\n\nSamples were taken for the comparative study between plantain production and the two most abundant genera, earthworms and Hymenoptera, both of which are beneficial in the decomposition of OM and the supply of nutrients to the plant. In the dominance of worms, the Quinta Cony (Farm 2) was found where 325 ind × m2 were collected, followed by the Montes Verde farm (Farm 6) with 225 ind × m2. Hymenoptera were dominant on the San Joaquín farm (Farm 5) with 175 ind × m2 and on farm 7 with 165 ind × m2 (Table 9 and Figure 3).\n\nTo compare the psyllium production of each farm, the proportion of worms and insects of the two most abundant genera, the order Hymenoptera, was taken, indicating that a greater number of worms indicates a greater production. It was observed that for Hymenoptera, the production is lower. The farms with the highest production in the León area were Quinta Cony with 91,000 × ha and Santa Isabel with 25,600 × ha. The farm of 80,000 y × ha in farm 8 and farm 6 with 85,000 × ha in Montes Verdes for the Posoltega area (Figures 3 and 4).\n\nPearson's correlation analysis commonly correlates agricultural production (plantain units per ha) and the abundance of earthworms and hymenopteran insects, projecting a correlation close to 1 with 95% confidence. The relationship between plantain production per ha and the abundance of earthworms of ind. × m2 establishes a direct relationship, with a Pearson correlation coefficient of 0.743, close to 1, and a perfect or strong relationship in the Pearson correlation analysis (Table 10). That is, by increasing the number of earthworms in the soil, the production of plantain per ha increases in the farms studied in both regions (León and Posoltega). On the other hand, a Pearson correlation coefficient of 0.261 (Table 9) was obtained, which indicated that the relationship between production and abundance of Hymenoptera is very close to 0, thus showing a weak correlation between production and abundance of Hymenoptera insects.\n\n* Significance p < 0.05.\n\nThe city of León has three strong ties. The first relationship (Pearson correlation coefficient 0.988) between productivity (psyllium units per ha on the farm) and earthworm abundance (Table 10) shows a strong correlation. The second relationship between productivity and abundance of Hymenoptera insects has a Pearson correlation coefficient of 0.942 (Table 10), indicating a strong correlation. A third relationship between the abundances of earthworms and hymenopteran insects is a Pearson correlation coefficient of 0.968 (Table 10), which is very strong because the coefficient is close to 1, indicating that the number of earthworms becomes a direct relationship as it increases. In the municipality of Posoltega, the relationship between earthworm production and abundance is weak, with a Pearson correlation coefficient of 0.465. A Pearson correlation coefficient of -0.484 (Table 10) indicates a negative relationship, with a decrease in the second abundance ratio of earthworms and hymenopterans. However, the abundance of hymenopteran insects is preserved. The increase in the number of worms increased the production and abundance of Hymenoptera, with a Pearson correlation coefficient of 0.469, favoring a direct relationship. On the other hand, the relationship between the number of hymenopteran insects and production is inversely correlated, with a Pearson correlation coefficient of -0.484 (Table 10). That is, as the number of Hymenoptera decreases, production decreases (Table 10). Table 11 shows the Pearson correlation coefficients by farm.\n\n\nConclusions\n\nThe diversity and richness of the edaphic macrofauna was evaluated in eight farms in the western area. A total of 78.72% of the individuals were identified in the soil from 0–20 cm2, while the remaining 21.26% in the foliage. In the first four farms in the León area, 23 genera were found, and in the Posoltega farms, 21 genera. The relative abundance of León was 1,450 individuals per m2, while in the Posoltega area it was 1,700 individuals per m2.\n\nThe Shannon-Wiener (H′) Diversity values were in the range of 1.6–1.9, which indicates a situation of low diversity, Margalef Diversity (D) obtained values between 1.4–1.8, lower than 2, considered as areas of low biodiversity, the Simpson's dominance (1-D) presented values between 1.4–1.8, considering that the closer it is to 1, a situation of low diversity is considered, and that of equality of Pielou (J′) presents 5-.8, so that the values close to 1 correspond to situations where all species are equally abundant. These results were due to the relative abundance of two detritivore genera (earthworms and Hymenoptera), which are organisms that decompose OM and provide nutrients to the plant.\n\nFinally, it is concluded that these two genera are important in the production of the plantain agrosystem due to the decomposition of OM and its nutritional contribution to the plant, observing a direct correlation with earthworms and an indirect one with Hymenoptera.", "appendix": "Data availability\n\nZenodo: Data for: Diversity of Functional Edaphic Macrofauna in Musa acuminata × Musa balbisiana (AAB) Agroecosystems. https://doi.org/10.5281/zenodo.7242968 (Zuniga-Gonzalez et al., 2022).\n\nThis project contains the following underlying data:\n\n- DataLeon.csv (data for farms in Leon)\n\n- DataPosoltega.csv (data for farms in Posoltega)\n\n- Figue_2.jpg\n\n- Figure_1.jpg\n\n- Figure_3.jpg\n\n- Figure_4.jpg\n\n- NIH.csv (data on genera)\n\n- Tabla 3.png\n\n- Table 4_.jpg\n\n- Table 5.png\n\n- Table 6.png\n\n- Table_1.jpg\n\n- Table_10.jpg\n\n- Table_11.jpg\n\n- Table_2.jpg\n\n- Table_7.jpg\n\n- Table_8.jpg\n\n- Table_9.jpg\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nReferences\n\nAlcaraván A: Fundacion el Aura. 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Publisher Full Text\n\nWardle DA:Impacts of disturbance on detritus food webs in agro-ecosystems of contrasting tillage and weed management practices. Advances in ecological research. Academic Press;1995; (Vol. 26. , pp. 105–185).\n\nZerbino MS: Evaluación de la macrofauna del suelo en rotaciones cultivos-pasturas con laboreo convencionaL. Acta Zoológica Mexicana. 2010; 189–202.\n\nZerbino S, Altier N, Morón A, et al.: Evaluación de la macrofauna del suelo en sistemas de producción en siembra directa y con pastoreo. Agrociencia. 2008; 12(1): 44–55.\n\nZayas Sierra F, Sánches Bautista NI, Pedro Kesell I, et al.: Empleo del humus de lombriz como alternativa agroecológica para el incremento de los rendimientos agrícolas del cultivo plátano macho ¾ (musa sp.) en un sistema extra denso: Empleo del humus de lombriz como alternativa agroecológica para el incremento de los rendimientos agrícolas del cultivo plátano macho ¾ (musa sp.) en un sistema extra denso. Investigación Y Ciencia Aplicada a La Ingeniería. 2022; 5(29): 53–60. Recuperado a partir de.Reference Source\n\nZuniga-Gonzalez CA, Caballero-Hernandez AJ, Quiroz-Medina CR:Data for: Diversity of Functional Edaphic Macrofauna in Musa acuminata × Musa balbisiana (AAB) Agroecosystems. [Dataset]. F10000Research (Version v2, Number version 1). Zenodo. 2022. Publisher Full Text" }	[ { "id": "155921", "date": "07 Mar 2023", "name": "Angel Sol", "expertise": [ "Reviewer Expertise Climate change", "Ecology", "Mangroves and tropical forestry" ], "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 interesting and important in the banana production activity.\n\"The first was..\" - must say 'the first one'.\n\nIn the results, the correct way is 'ind/m2'. Example: 160 ind/m2.\n\n\"In four farms (San Martín, Santa Isabel and El Verdon)…\" and which one is the last?\n\nIncorrect to cite too many authors: \"These data are supported by Zayas et al. (2022), Quiroz-Medina et al. (2021), Castillo y Vera (2000), Pashanasi (2001), Zerbino (2010), Rousseau et al. (2012) and Rousseau et al. (2013).\" - Maybe you could cite just three authors together in the text; because information is the same.\n\nIt is not a conclusion, but a result: \"The diversity and richness of the edaphic macrofauna was evaluated in eight farms in the western area. A total of 78.72% of the individuals were identified in the soil from 0–20 cm2, while the remaining 21.26% in the foliage. In the first four farms in the León area, 23 genera were found, and in the Posoltega farms, 21 genera. The relative abundance of León was 1,450 individuals per m2, while in the Posoltega area it was 1,700 individuals per m2.\"\n\nBibliography incomplete as: Ruiz N, Lavelle P, Jiménez J: SOIL MACROFAUNA FIELD MANUAL.2008; p. 113.\n\nIs the work 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": "9429", "date": "08 Mar 2023", "name": "C. A. Zuniga-Gonzalez", "role": "Author Response", "response": "I appreciate the comments of the reviewer1 and I confirm and accept the improvements to be incorporated." }, { "c_id": "10042", "date": "20 Sep 2023", "name": "C. A. Zuniga-Gonzalez", "role": "Author Response", "response": "The article is interesting and important in banana production activity. Dear Reviewer, thanks for this. \"The first was..\" - must say 'the first one'. Response: It was improvements. In the results, the correct way is 'ind/m2'. Example: 160 ind/m2. Response: Dear reviewer all the results were checked and improvements. \"In four farms (San Martín, Santa Isabel and El Verdon)…\" and which one is the last? Response: The Quinta Cony was added, thanks for this observation. Incorrect to cite too many authors: \"These data are supported by Zayas et al. (2022), Quiroz-Medina et al. (2021), Castillo y Vera (2000), Pashanasi (2001), Zerbino (2010), Rousseau et al. (2012) and Rousseau et al. (2013).\" - Maybe you could cite just three authors together in the text; because information is the same. Response: It was correcting that only 3 authors were added, but in this case was putting 4. It is not a conclusion, but a result: \"The diversity and richness of the edaphic macrofauna was evaluated in eight farms in the western area. A total of 78.72% of the individuals were identified in the soil from 0–20 cm2, while the remaining 21.26% in the foliage. In the first four farms in the León area, 23 genera were found, and in the Posoltega farms, 21 genera. The relative abundance of León was 1,450 individuals per m2, while in the Posoltega area it was 1,700 individuals per m2.\". Response: Dear reviewer it was translated to the results section, thanks for this observation. Bibliography incomplete as: Ruiz N, Lavelle P, Jiménez J: SOIL MACROFAUNA FIELD MANUAL.2008; p. 113. Response: It was corrected and added the link https://hal-bioemco.ccsd.cnrs.fr/bioemco-00560386 and the Bioemco as a source. Dear reviewer, thanks for all your observations." } ] }, { "id": "177964", "date": "19 Jul 2023", "name": "Jérôme Mathieu", "expertise": [ "Reviewer Expertise Soil ecology" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nMain comments\nPlease improve the English language and grammar.\n\nPlease give more information about the differences between the plots and use them to explain the differences in soil macrofauna communities.\n\nPlease compare your results to past studies on similar cultures.\nMinor comments\nFirst page\nDominion = Dominance?\n\nConclusions: are you sure that these ants are detritivore?\nIntroduction\nSecond sentence: please reduce the number of citations.\n\nParagraph #2 (Similarly…) : please reduce the number of citations.\nLast paragraph:\nChange to \"this work focused...\"\n\nPlease describe the management of the plots (conventional/organic, tillage, pesticides, fertilization, irrigation and so on).\n\nPlease replace the second sentence and the rest by a description of the method, period of sampling, taxa covered, taxonomical resolution. No need to give the structure of the paper.\nMethods\nPlease say in the text that sampling is based on litter and monolith extraction and is inspired by the TSBF method.\n\nTable 1: Please mention what these columns refer to.\n\nTable 2: Latitude and longitude are incorrectly formatted, with two commas in some cases, no commas in other cases. Please reformat with dots (\".\") as decimal separators and do not use other separators.\n\nPlease describe the management of the plots (see comment above regarding the first page).\n\nThe size of the sampling area is not clear. Please clarify.\n\nWas it really 4mm the smallest body size covered? Usually it is 1.5 mm for soil macrofauna.\n\nPlease change \"measured variables' by 'diversity components' or something similar.\n\nPlease delete \" (various population densities 1 m2)\".\n\nIsn't it 'Dominance' instead of 'Domain'?\n\nNo need to give the formula of the Shannon index.\nResults & Discussion\nTable 3 & 4:\n- The title should be 'total and relative…by function groups in the different plots\" Please use the unit Ind. m-2 for the absolute abundances.\n- Please add the standard deviation or the standard error.\n\nFigure 2: The name of the taxa is difficult to read because of the low quality of the plot.\n\nTable 5: These are taxa, not species. Please translate into ind.m-2, add errors, and remove totals by location.\n\nTable 6: \"lumbrices\" is not a correct genus or taxa, please correct.\n\nThere are many typos in the name of family and genus. Please correct (e.g., Formocidae).\n\nPlease compare your results with previous studies on banana plantations.\n\nTable 7: please explain what is \"taxa_\" and \"individuals\".\n\nTable 8: Please use \"ind.m-2\" not \"x m2\".\n\nContrary to what you say, there are herbivores in the farm 8. Please correct.\n\nYou can't link the absence of herbivore to the presence of spiders, based on correlation only. You need an experiment for that. Please remove this sentence.\nDiversity and productivity\nVery interesting, but it is not clear if you did extra sampling for this topic. Please clarify. If so, please describe the sampling, if not, please explore the relationship with other taxa or functional groups.\n\nIn any case, please explain how productivity estimates were related to soil fauna sampling: was it measured in each subplot (in this case you have one measure of productivity for one soil fauna monolith), or is it at a larger scale?\n\nTable 9:\n- Please clarify what you mean by earthworm production and add units.\n- The title of the last column is not clear, please clarify and provide the units.\n\nFigure 3:\n\n- Please use worm and Hymenoptera for the x axis and the productivity for the Y axis.\n- What do you mean by \"real\"?\n\nIn all the results sections, you should explain and use the difference among plots to explain the variations in soil macrofauna. For instance, don't you have soil data or management data?\n\nTable 10: please say \"banana production\".\n\nFigure 3 & table 11:\n\n- If you have several replicates per farm, please use them in fig. 3 and add the regression line for all data and by plot, and include plot as a random factor in the analysis.\n- Consider changing table 11 by a pairwise correlation plot the tests on one side of the diagonal (see ggpairs() in R for instance).\n\nFigure 4: please add taxa richness and if possible functional groups' abundance.\nData availability:\nPlease put the data from the two sites into one file.\n\nPlease use the standard reporting template for soil macrofauna communities: https://zenodo.org/record/7691884\n\nImportant: Please provide the raw data; by monolith or by layer, not aggregated by plot.\n\nPlease also add metadata: coordinates, date of sampling (year, month, day), management, and so on (see the template).\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Partly\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [ { "c_id": "10055", "date": "20 Sep 2023", "name": "C. A. Zuniga-Gonzalez", "role": "Author Response", "response": "Main comments [1] Please improve the English language and grammar. Response: Dear reviewer we appreciate your valuable observation, we are proceeding with the total revision of the article. [2] Please give more information about the differences between the plots and use them to explain the differences in soil macrofauna communities. Response: Thanks for this observation. In Methods section was added this information with the subtitle farms data where explicated your characteristics and differences. [3] Please compare your results to past studies on similar cultures. Response: Yes, the past studies were compared with Costa Rica and Nicaragua studies. However, were added more cites as you indicated. Table 2 (Paragraph one) is similar to Zerbino et al. (2008), we also, refers the works of Priego-Castillo et al. (2009) and Castillo and Vera (2000) for the table 4, 5 and 6, also we refer to Pashanasi (2001), Zerbino (2010), the results of table 5 are referred and similar to Melo (2010), Rousseau et al. (2012, 2013). For the results of the Table 8 and 9 were added the cites. Response: Dear thanks for this observation, it was added. In each result was added cite as you indicated. Minor comments [4] First page Dominion = Dominance? Response: Thanks for it. We checked all the article and it was changed. [5] Conclusions: are you sure that these ants are detritivores? Response: Dear reviewer you know that Detritivorous ants are those that primarily feed on dead organic matter and help break down and recycle organic materials in ecosystems. We find two genera (earthworms and Hymenoptera), so the ants are referred to the detritivore genus because ants feeds on dead and decaying organic matter, such as plant material (Musa acuminata x Musa balbisiana (AAB), they are moist soils with a lot of plant organic matter. Thanks for the observation. Introduction [6] Second sentence: please reduce the number of citations. Paragraph #2 (Similarly…) : please reduce the number of citations. Response: Thanks for this observation, we have been checked all article and changed it. [7] Last paragraph: Change to \"this work focused...\" Response: It was changed. [8] Please describe the management of the plots (conventional/organic, tillage, pesticides, fertilization, irrigation and so on). Response: Thanks for this observation we have added a subsection (Agro system farms) in the methods section, there we explain the characteristics of the 8 farms and how they have been moving from conventional practices to agroecological farms. [9] Please replace the second sentence and the rest by a description of the method, period of sampling, taxa covered, taxonomical resolution. No need to give the structure of the paper. Response: Dear thanks for your observations, it was added in the last paragraph of the Introduction, second sentences as you indicated. We have added a cite of the protocol.oi where we explicate the methodology. Thanks for the observation. Methods [10] Please say in the text that sampling is based on litter and monolith extraction and is inspired by the TSBF method. Response: It was added. Also we added the cite [47]. [11] Table 1: Please mention what these columns refer to. Response: Thanks for this observation, a comment on this was added before Table 1. [12] Table 2: Latitude and longitude are incorrectly formatted, with two commas in some cases, and no commas in other cases. Please reformat with dots (\".\") as decimal separators and do not use other separators. Response: Thanks for this observation. We made the changes. (e.g., 12°31'15.4\"N Latitude 86°54'40.2\"W Longitude) [13] Please describe the management of the plots (see the comment above regarding the first page). Response: Yes it was added as indicated in [8] item. Was elaborated a chart with your differences. [14] The size of the sampling area is not clear. Please clarify. Response: Ok thanks for this observation. The description of Tables 2 and 5 is explicating that the area is of 0.7 ha, and a total of 80 samples of macrofauna populations were identified, coded, and stored in the second phase. The study area in each farm or plot was 0.7 ha delimited 1 in 1,000 m2 (50 cm long × 20 cm wide), as described in Rousseau et al. (2012), Rousseau et al. (2013), and Medina et al. (2021) . However, we added this area for each plot: The area where the sample was collected are: Farm1 246.5 ha, Farm2 14.1, ha, Farm3 67 ha, Farm4 7 ha, Farm5 4.2 ha, Farm6 2.1 ha, Farm7 3.5 ha, Farm8 4.9 ha. In total 80 samples were collected in 1000 m2 for 40 biomass samples and 40 edaphic samples in 0-20 cm depth. [15] Was it really 4mm the smallest body size covered? Usually, it is 1.5 mm for soil macrofauna. Response: Dear thanks for this observation, it was corrected. [16] Please change \"measured variables' by 'diversity components' or something similar. Response: It was changed. [17] Please delete \" (various population densities 1 m2)\". Response: It was eliminated. [18] Isn't it 'Dominance' instead of 'Domain'? Response: It was changed. [19] No need to give the formula of the Shannon index. Response: Dear reviewer, thanks for this observation. Dear reviewer, we have decided to give the formula. Results & Discussion [20] Table 3 & 4: - The title should be 'total and relative…by function groups in the different plots\" Please use the unit Ind. m-2 for the absolute abundances. - Please add the standard deviation or the standard error. Response: Ok it was made in both tables. [21] Figure 2: The name of the taxa is difficult to read because of the low quality of the plot. Response: Ok we sent another figure with the best resolution. [22] Table 5: These are taxa, not species. Please translate into ind.m-2, add errors, and remove totals by location. Response: Ok thanks for this observation. All was changed. [23]Table 6: \"lumbrices\" is not a correct genus or taxa, please correct it. Response: Yes, it is correct, thanks for this observation. All was changed. [24] There are many typos in the name of family and genus. Please correct (e.g., Formocidae). Response: Ok thanks for this observation. It was checked and corrected. [25] Please compare your results with previous studies on banana plantations. Response: Of course, it was checked and added as you indicated. [26] Table 7: please explain what is \"taxa_\" and \"individuals\". Response: Thanks for this observation, the taxa was change by Genus Types and individuals, by Ind. m2 [27] Table 8: Please use \"ind.m-2\" not \"x m2\". Contrary to what you say, there are herbivores in the farm 8. Please correct. You can't link the absence of herbivore to the presence of spiders, based on correlation only. You need an experiment for that. Please remove this sentence. Response: Ok thanks for this observations. It was corrected. [28] Diversity and productivity Very interesting, but it is not clear if you did extra sampling for this topic. Please clarify. If so, please describe the sampling, if not, please explore the relationship with other taxa or functional groups. In any case, please explain how productivity estimates were related to soil fauna sampling: was it measured in each subplot (in this case you have one measure of productivity for one soil fauna monolith), or is it at a larger scale? Response: Dear reviewers thanks for this observation. The sampling is the same that was recollected, but in this moments of the analysis we compare the populations of the Hymenoptera (Insects) and Oligochaeta (Worm or Earthworm) that were the more representative in this study. So, we the Pearson correlation coefficient that is a measure of linear correlation between two sets of data in this case the Agricultural production (banana units per ha) and the abundance of Earthworms and hymenopteran insects (Ind. m 2). It is the ratio between the covariance of two variables and the product of their standard deviations. [29] Table 9: - Please clarify what you mean by earthworm production and add units. Response: Thanks, we refer the abundance of Earthworms and the unit Ind. m2 was added. - The title of the last column is not clear, please clarify and provide the units. Response: Thanks, It was change by Abundance Estimated overall Earthworm production Ind. m2. [30] Figure 3: - Please use worm and Hymenoptera for the x axis and the productivity for the Y axis. - What do you mean by \"real\"? Response: Dear is ok the change was made. The Real is the production of Banana or plantains, during the periods studied. Measured in Units by ha. Dear reviewer by best interpretation all was change by Production (Units ha). [31] In all the results sections, you should explain and use the difference among plots to explain the variations in soil macrofauna. For instance, don't you have soil data or management data? Response: Dear all results section was checked and added the comments that you indicated. Regarding to the management data the farmer don’t had information because the cost to get it (Laboratory of soil). [32] Table 10: please say \"banana production\". Response: OK [33] Figure 3 & table 11: - If you have several replicates per farm, please use them in fig. 3 and add the regression line for all data and by plot, and include plot as a random factor in the analysis. - Consider changing table 11 by a pairwise correlation plot the tests on one side of the diagonal (see ggpairs() in R for instance). Response: Dear reviewer thanks for your observation but our aim was to relate the plots versus the genus identified, however, yes we go to make o add the table that you suggest us as Fig 5. Dear, we appreciate your observation, but due to a problem that we had already defined in the methodology that we work with SPSS, which suggests that we do it with SPSS and we have added fig. 6. [34] Figure 4: please add taxa richness and if possible functional groups' abundance. Response: Dear thanks for this observation, only we added taxa richness, the functional group’ abundances, we consider that was discussed on the table 3 and 4. Was added the Fig 5. Shannon Index. [35] Data availability: Please put the data from the two sites into one file. Response: Ok Please use the standard reporting template for soil macrofauna communities: https://zenodo.org/record/7691884 Important: Please provide the raw data; by monolith or by layer, not aggregated by plot. Please also add metadata: coordinates, date of sampling (year, month, day), management, and so on (see the template). Response: Ok thanks for your consideration." }, { "c_id": "10872", "date": "16 Jan 2024", "name": "C. A. Zuniga-Gonzalez", "role": "Author Response", "response": "Dear Reviewer 2, the data availability, has been duly addressed: Data Compilation: The data from both sites has been consolidated into a singular file as requested. Template Utilization: The standard reporting template for soil macrofauna communities, accessible at https://zenodo.org/record/7691884, has been utilized to format the dataset. Data Format: The provided data remains in its raw form, organized either by monolith or by layer, ensuring it is not aggregated by plot, as specified. Metadata Inclusion: Essential metadata such as coordinates, sampling date (year, month, day), management details, and other relevant information, following the template, have been added to the dataset. By adhering to these instructions, we've ensured the data is compiled appropriately, formatted using the standard template, remains in its raw form, and includes essential metadata, thereby meeting the specified requirements for data availability." } ] } ]	1	https://f1000research.com/articles/11-1300
https://f1000research.com/articles/13-654/v1	18 Jun 24	{ "type": "Research Article", "title": "Factors Affecting on Environmental Strategy in SMEs manufacturing Firms of a developing country: Mediating role of Green Employee Behavior", "authors": [ "Ikramuddin Junejo", "Ummi Naiemah Saraih", "Jorge Alberto Esponda Perez", "Sarmad Ejaz", "Faisal Ejaz", "Md Billal Hossain", "Ummi Naiemah Saraih", "Jorge Alberto Esponda Perez", "Sarmad Ejaz" ], "abstract": "Background Sustainability in small and medium-sized enterprises (SMEs) which engage heavily in manufacturing provides them with an essential platform for implementing environmental strategy, which is aimed at reducing environmental damage and promoting environmental protection. This study aims to examine the impact of the reduction in resource use, the greening of processes and products on environmental strategy and the mediating role of green employee behaviour.\n\nMethods Primary data gathered with the help of questionnaires from employees of SMEs manufacturing in developing countries, Pakistan. The research gathered data from 211 participants by applying a pre-tested instrumental questionnaire and structural equation modelling (SEM) for data analysis.\n\nResults The results confirmed all direct effects, including a reduction in resource use, the greening of processes and products and green employee behaviour of environmental strategies in small and medium manufacturing firms. Also, confirmed partial mediation effect of green employee behavior between greening of processes and products and environmental strategy.\n\nConclusion The current study clearly showed the need for programs and infrastructures that support resource reduction and greening businesses in SMEs. Companies’ implementation of green processes and technologies allows SMEs to take an environmentally responsible stand and become part of the movement toward sustainability. The research stresses the importance of green employee conduct as a mediator, the central point being the individual employee being engaged and aware of the subject and willing to participate in environmentally friendly practices. Therefore, small and medium enterprises should enlighten their staff to practice green behaviour, give them what they need and empower them to be change drivers that will trigger sustainability throughout the organisations.", "keywords": [ "Reduction in resource use", "Greening of processes and products", "Green employee behavior", "Environmental strategy" ], "content": "Introduction\n\nAll around the world, climate change, water pollution, air pollution and many other environmental issues are progressively becoming more serious, and they are already causing a great deal of anxiety concerning sustainability (Manisalidis et al., 2020). They are so multifaceted that they create or sometimes extend the impacts on the ecosystem for human health and the balance of planet Earth. Calling for immediate, joint action from a person, a local community, and on governmental and business levels is necessary to address such environmental problems. Sustainable measures, which entail shifting to renewables, embracing eco-friendly technology, promoting recycling and waste reduction, adopting more stringent environmental regulation systems and promoting awareness about environmental conservation among people and other stakeholders, should be the focus of environmental sustainability. Governments, as well as regulatory bodies, also make contributions to the issue by encouraging social responsibility and environmental protection (Camilleri, 2022). Several nations have enacted laws which compel companies to disclose their performance under particular sustainability criteria and have implemented financial incentives and tax rebates for businesses that subscribe to eco-friendly practices.\n\nNevertheless, it must be stated that deploying CSR and sustainability has diverse results among companies (Sanchez-Planelles et al., 2022). There are instances when companies show so much greenwashing, meaning they claim to be eco-friendly or responsible in the social context without tangible modifications. Hence, all stakeholders ought to remain vigilant and employ the principle of critical thinking in evaluating whether or not the company has demonstrated its commitment to CRS and sustainability. The rise of CSR and the development of sustainability applications by enterprises is becoming the reflection of a quickly increasing attention towards safeguarding the natural environment while also keeping the economy growing (Le et al., 2024). Through sustainability, businesses accrue the benefits of a chance to be part of structuring a sustainable world.\n\nSustainability in small and medium-sized enterprises (SMEs) which engage heavily in manufacturing provides them with an essential platform for implementing environmental strategy, which is aimed at reducing environmental damage and promoting environmental protection. Undertaking an environmental appraisal enables SMEs to recognize the high environmental impacts and areas of improvement (Johnstone, 2021). This assessment can go into selecting power usage, waste creation, water utilization, and pollution. It makes the base for installing environmental targets and goals. Include employees in environmental business ideas and train them about sustainable methods. Make an environment for staff members to recommend developing our environmental activities and reward their efforts. Develop an environmental consciousness culture that is embedded within the organisations. Small- and medium-sized enterprises should consider the obstacles and limits they may face while developing environmental strategies, like small budgets or lack of experience (Chien et al., 2021). Partnering with green manufacturing specialists, implementing applicable incentives by the government, and connecting the industry with the same brand are the keys to overcoming environmental sustainability challenges in the manufacturing industry.\n\nA green way of life is any manner or activity that is advantageous to the environment or minimizes the impact on the environment (D’Angelo et al., 2023). It means to be mindful of our actions, to make choices, and to take actions that assist in sustaining the environment and protecting natural resources. Green behaviour empowers individuals, social groups, public organisations and governments to adopt various practices from every point of life to make it environmentally friendly. Participating in activities that make people understand environmental problems, lending support to environment conservation organisations and advocating policies and ways of doing things that will sustain our environment ((Junejo et al., 2020; Shah et al., 2021; Zikargae et al., 2022). The constant accumulation of information about environmental issues, the constant access to the current best practices and innovations, and a constant urge to share the discovered information with others ensure the substantial progress of environmental awareness and green behaviour. The availability of practices for using materials, including paper, plastic, glass, and metal, would otherwise be destined for landfills. It saved waste generation by green consumption, upcycling pieces, composting organic waste and buying stuff in zero packaging packers.\n\nMost earlier studies only focused on the factors of an individual’s either internal aspects or external influences, not combine to know how these elements interact with each other in context of environmental strategy (Bertassini et al., 2021; Manninen & Huiskonen, 2022; Junejo et al., 2022). Nevertheless, some firms do not think just about the environment. However, they also see it as a social responsibility and do the best they can by cutting down on resource use and emissions. At the same time, they are aware that their actions may affect other people in society. Therefore, in this study, economic factors, such as resource savings and emissions, to operationalize environmental policy are taken as the context within the study. Until now, only the studies examining the impact of renewable energy have been carried out in the developed countries (Eisenmenger et al., 2020; Ding et al., 2021; Naveed et al., 2023; Sohu et al., 2023). Hence, to narrow down the geographical area and because of the limitations of the period and the cost, this cross-sectional research will be conducted in developing country Pakistan and manufacturing companies.\n\n\nLiterature review\n\nAccording to the RBV, the resource-based view recommends that a company's performance and effectiveness stem from its unique resources and abilities (Dionysus & Arifin, 2020). By this study, RBV is appropriate to explain that reducing natural resource use and making processes and products greener (independent variables) can help develop a sustainable competitive advantage through environmental strategy among (dependent variable), through environmental behaviour of employees acting as a mediating variable. It is circulated that RBV resources are subdivided into tangible and intangible resources according to the viewpoint of the resources-based view theory. This means that in this given case, the reduction of resource use would entail shrinking resource use by the factor of the primary tangible resources comprising energy, water, and raw materials. Development and implementation of eco-friendly technologies and procedures during all the other activities of the concern, which are featured as non-material assets of a company.\n\nFrom the viewpoint of the RBV, eco-friendly firms have a golden chance to capture a more significant market share by using their resources in a manner that would communicate their green efforts both internally and to the outside world, leading to various benefits like reputation, efficiency, and satisfaction of the customers' demand for sustainable goods and services. Those factors can be a basis for customer centricity, cost efficiency and financial success. While the RBV insists that it implies more than just being a rich brand, it should be a rich brand where the resources are managed well and leveraged. Mediation plays a role in green employee actions here. The organization-friendly behaviour of green individuals implies that employees' internal personal activities and attitudes will be positively connected to the company's environmental sustainability initiatives (Yang & Liu, 2022). This behaviour can include saving energy, decreasing waste, and becoming proactive in activities that promote sustainability.\n\nReduction of resource use\n\nOrganizations could secure resources by saving them. As a result, companies will be able to apply their resources most efficiently (Shkarlet et al., 2020). Such contribution will ensure emissions decline, reduced waste generation, and reduced pollution rates, all prerequisites for excellent environmental performance. Most reduction strategies in the resource field have places where the company wages are decreased (Azizi et al., 2021; Bilal et al., 2024). For instance, installing energy-saving devices results in lower energy expenses, using waste-preventive measures reduces dumping expenses, and saving aluminum leads to input savings. Through these capital savings, the solidification of the business case for resource management is strengthened alongside environmental management improvement (Afum et al., 2021; Sohu et al., 2024; Kherazi et al., 2024). These efforts can be the impetus for innovative technologies, new styles of work, and resource-efficient products. This benefit is that businesses can distinguish themselves from their competitors by being an environmentally conscious company that meets the evolving market needs for green products and services and positions itself as an esteemed environmental steward (Kumari, 2024; Akhtar et al., 2023). Thus, the following alternative hypothesis is suggested.\n\nH1: Reduction of resource use is positively related to environmental performance.\n\nGreening of processes and products\n\nThere is a name known as eco-efficiency, which is the capacity that organizations have to provide goods and business processes that meet customer needs but generate a small amount of environmental impact (Güngör et al., 2023; Hongyun et al., 2023). Furthermore, it highlights the alignment of environmental appraisal to the planning of production, design, and supply to balance sustainable economic development and environmental protection. A phase of reducing hazardous substances or pollutants always accompanies the phase where processes and products are greened. In addition to this, businesses can achieve this by applying cleaner production techniques, replacing harmful materials with safer alternatives, and adding pollution prevention techniques to minimize their impact on air, water, and soil quality (de Mello Santos et al., 2022; Sohu, Hongyun, et al., 2020; Sohu et al., 2019). As a result, companies will benefit from improved environmental performance. Eco-designing goods means creating products with some green characteristics and making them efficient in their energy consumption, recycling, or overall environmental footprint. By providing eco-friendly alternatives to the market, corporations can cater to consumers' demand for environmentally friendly goods, build their sustainable brand reputations, and contribute to attaining optimum environmental performance (Reddy et al., 2023; Mirani et al., 2021; Dakhan et al., 2021). Thus, the following alternative hypothesis is suggested.\n\nH2: Greening of processes and products is positively related to environmental performance.\n\nH3: Greening of processes and products is positively related to green employee behavior.\n\nThe Social Cognitive Theory states that these are not the only ones that affect an individual's behaviour, but also personal factors, environment and cognitions (Schunk & DiBenedetto, 2020; Sohu et al., 2022). Thus, according to the green self-crafting theory, employees' attitude, beliefs, and confidence in environmental sustainability issues might influence their organisational behaviour. When employees become involved or act actively on the green side, such as saving some resources, reducing waste, and promoting environmental sustainability, such acts' contributions help improve environmental performance (Dakhan et al., 2020; Malik et al., 2021; Iqbal et al., 2023). The green behaviour of the employee is formed by the societal standards in the company, which define what is considered correct and acceptable. When peers watch other employees at work implementing resource reduction and environmentally friendly practices, a normative expectation develops that people should behave the same way to be part of this group (Zacher et al., 2023; Sohu et al., 2020). Enabling everyone to see the good results caused by being sustainability-oriented and peer support among employees can create a work environment where most employees will start to adopt green behaviour.\n\nIn most cases, an employee's environmental sustainability behaviour reflects on dual aspects, which are willingness to learn and improve (Ababneh, 2021). Using the systems of feedback, performance evaluation, and reward for sustainability there, worldwide establishments may prompt workers to improve their behaviour towards nature by looking for better ways to preserve the environment. This never-ending goal to produce endless improvements may also play an essential part in environmental performance by discovering new ways of reducing the consumption of natural resources or maintaining sustainability (Chien et al., 2023). Thus, following alternative hypothesis is suggested.\n\nH4: Green employee behavior is positively related to green employee behavior.\n\nH5: Green employee behavior mediates between reduction of resource use and environmental performance.\n\n\nMethods\n\nThe data collection was done through cross-sectional research. This design allowed us to investigate relationships between employee behaviour in pursuing environmentally friendly strategies and reducing the use of resources and waste. The role of the researcher in primary data collection entails designing the data collection process, for example, by defining the template for a questionnaire as well as choosing the sample size and number of samples. Next, the researcher is directly involved in data gathering from the participants or sources. The current research analysis is based on primary data, which involves the top management employees of manufacturing companies in Sindh, Pakistan. The sample size of 211 participants was selected using a non-probability, convenience, and snowball sampling approach. Initial appointments were set up over phone calls, and the participants were instructed to be available for the print out questionnaire during the time frame. Our research procedure was as ethical as possible and carried out according to the principles and guidelines. The participants were informed before and provided with the opportunity to give consent.\n\nMoreover, their private information was secure and anonymous. The study results were reported as a group, with the addition that no identifying information exists on individual participants. The structured questionnaire was framed and approved to retrieve information from the participants. The survey consisted of components designed to measure reduction in resource use, greening of processes and products, green employee behavior and environmental strategy.\n\nThis study “Factors Affecting on Environmental Strategy in SME Manufacturing Firms of a Developing Country: Mediating Role of Green Employee Behavior” was approved by the Ethics Committee of The University of Okara constitutes the departmental Ethics Approval Committee (REBSSH/2024/4-9) in January 03, 2024. All of the informants gave written and oral informed consent to participate in the study. Under the Personal Data Protection Act (PDPA) 2010, the researchers assure that all information collected is kept confidential and merely for the academic purposes. Therefore, they were assured that their responses would be kept in strict anonymity and reported as aggregate results.\n\nIndependent variable reduction in resources use four research items were adopted from the research of (Čater et al., 2023). Another independent variable greening of processes and products also four items were taken from the study of (Čater et al., 2023). In addition to this, mediating variable green employee behavior four items were taken from the study of (Mi et al., 2020). Lastly, dependent variable Environmental strategy’s four research items adopted from the research of (Čater et al., 2023).\n\nSEM was used to test the hypotheses based on the data that we obtained from the survey. For the analysis of the data, version SEM 3 was leveraged. Structural equation modelling (SEM), a statistical method for studying highly complicated connections between multiple variables, allows for the analysis of such relationships (Hair et al., 2021). SEM covers testing via confirmatory and exploratory factor analysis and employs path analysis to run tests of hypotheses that deal with a correlation of variables. According to SEM, researchers develop a model of latent and observed variables, which is compared with how the data behaves in the real world.\n\n\nResults and Discussion\n\nData integrity and validity are essential when they are known to be accurate and used as a tool for testing hypotheses (Orsini et al., 2020). As it is observed that with excellent and decisive data, it is possible to obtain valid and authentic results of hypothesis testing, which can lead to some false conclusions. Hence, researchers should, as a matter of priority, begin with identifying and establishing credibility and authenticity in a study methodology before conducting a hypothesis (Hancock et al., 2021). The research procedure is the foundation that determines the credibility of the study. This is why reliability and validity are considerations that need to be implemented before any hypothesis testing is done (Sürücü & Maslakci, 2020). The reliability deals with the continualness and stability of the data collection tool or method used at the time. Reliability represents the degree to which the measurement tool or method used to collect data correctly portrays reality.\n\nThere are two ways to appraise a study's reliability, one of which is the measurement of Cronbach's alpha, and the other is the utilization of Composite Reliability (Hayes & Coutts, 2020). The researchers favor reporting both of these indices if they are available. Nonetheless, it substantiates the point that reliability is the fundamental part of data quality apart from establishing the validity and accuracy of the instrument or method before the researchers start to make a hypothesis. A Cronbach's Alpha and Composite Reliability of 0.70 and above is usually considered acceptable, although higher values are to be advocated for more excellent reliability. Moreover, all the values for the current are more than 0.70. Cronbach's alpha and Composite Reliability values are given in Table 1 and Figure 1.\n\nSource: Authors’ own estimations.\n\nConverged A average variance extracted (AVE) is a widely used validity measure of construct validity in SEM models. A CFI value greater than 0.50 is usually deemed acceptable for the construct validity, though this will vary based on the type of research being conducted and the number of items on a scale. They have a positive value for the present day, with all current values being more significant than 0.50. Average Variance Extracted values are given in Table 1 and Figure 1.\n\nSource: Authors’ own estimations.\n\nH1: The hypothesis of reduction in resource use and environmental strategy. This beta value of 0.502 reflects a positive and significant association on environmental strategy. The t-value of 7.429 is also significant. Hence, hypothesis is accepted and null is rejected (see Table 2 & Figure 2). Many researchers have indicated that saving some resources is now a primary catalyst or momentum as most organizations adopt environmental programs (Sarja et al., 2021). By their dedication to controlling resource consumption, their actions signify the pledge to protect the environment and sustainability. This dedication is illustrated by several implementation strategies, including energy-saving technologies, the optimization of production to eliminate waste and sustainable purchase methods (Hegab et al., 2023). Organizations that minimize resource exportation will have a lower impact on the environment and help them cut costs and become more efficient and effective in the long term. Research evidence suggests that companies keen on the conservation of resources might embed a complete sustainability strategy in that category.\n\nH2: This hypothesis states that green processes and products and environmental strategy. Accordingly, to beta value 0.169, there is a positive association with H1. In addition to this, the value of t = 2.834 is a statistically significant which means green processes and products has positive and significant impact on environmental strategy (see Table 2 & Figure 2). The study result showed that the pro-environment strategy derived from the decision-makers who choose green processes and products is consistent with the earlier conclusion on how organizations can practice sustainability (Xin et al., 2023). In pursuing green processes and products, companies seek to decrease their environmental footprint, cut emissions, and become more environmentally friendly. Such could be through embracing clean technologies, using renewable energy sources, and implementing eco-conscious design (Sengupta & Hussain, 2024).\n\nH3: impact of green employee behavior on environmental strategy. The estimation of the beta value as 0.717 means that there is a significant positive correlation between these variables. The t-value of 22.325 strongly shows a significant relationship with these variables (see Table 2 & Figure 2). The research results back up the arguments that a robust and direct link exists between the greening of processes and products and workplace activity. Organizations that sustain and integrate sustainability will discover environmentally positive employee engagement (Raza et al., 2021). This is a similar result to the previous research that points out the organizational practices and policies that serve how employees conceive and act towards sustainability issues. Promoting an environmental-responsibility culture among organizations could improve their environmental performance and achieve sustainable societal objectives (Channa et al., 2021).\n\nH4: The hypothesis proposes that green employee behavior on an environmental strategy. Beta 0.198 encourages a positive relationship. The t statistic of 3.055 is also suggested a significant role of green employee behavior and environmental strategy (see Table 2 & Figure 2). It could imply a meaningful relationship. The discovery of a positive association between eco-friendly employee activities and the consideration of the green strategy within business contexts complements the assumption that the employee's participation is one of the leading factors that foster the implementation of meaningful sustainability programs in companies. This result is proof of the fact that the previous studies have brought out the role of employee conduct in the organizing of sustainability activities and the development of sustainability policies (Al-Swidi et al., 2021). Organizations can step up to the challenge of environmental awareness by creating an “eco-friendly employee” culture. This will make their contribution to protecting the environment and broader sustainability goals more significant.\n\nH5: This study's hypothesis concerns the mediating role of green employee behavior between green of processes and products 0.142, the beta value and t-value=2.991, indicates a positive and significant relation (see Table 2 & Figure 2). The positive connection between greener products and employee behaviour with adopting an environmental strategy, which aligns with the approach to sustainable actions that should use all means from organizational practices and individual behaviours, supports the assumption that combining the positive inputs gives the best result. Organizations attempting to do both develop green processes and products while encouraging green employee behaviour, create a ripple effect which can, in turn, be used to drive holistic environmental policies (Fernandes et al., 2021). The studies that were conducted agree with the previous research; they affirm that both organizational mechanisms and employee activities have a role to play in the sustainability objectives (Lu et al., 2023; Ren et al., 2022). By incorporating green activities and eco-awareness for employees, organizations' environmental actions can strengthen, improving their sustainability achievements.\n\n\nConcluding remarks\n\nThe outcomes showed that organizations can perform the best in the environment by putting green products, processes, technologies, and environment-focused action plans into tactics. Resource minimization is a determinant of successful environmental performance since it encourages improved resource efficiency, decreased emissions, and reduced volume of waste. Adopting eco-friendly practices not only helps optimize the performance of ecological processes and products but also entails employing environmentally friendly materials and technologies throughout the product’s life cycle. Green employee behaviour represents an essential mediator on both ends of the equation, giving life to methodologies applied in resource-saving and implementation of green practices, which might result in saving the planet from environmental degradation. This contributes to a culture where the desired change to sustainability, innovation, and continuous improvement occurs. Also, environmental improvement has quite reasonable chances to be accomplished by organizations whose environmental schemes have been well-designed and implemented in all departments. An environmental strategy is a critical point of how the organization makes promises to be environment friendly and sets the objectives, integrating environmental factors into the business activities.\n\nOrganizations should give forests the top value in the durability of resources during their operations. It may encompass using energy-saving technologies, taking an in-depth look into production processes, reducing water consumption, and reducing waste production. Emphasizing the streamlining approach in these institutions can improve cost-efficiency, lower costs, and minimize environmental influence. Therefore, businesses should not wait but rather play leading roles by embracing eco-friendly practices and technologies to green their processes and products. This comprises, among others, the adoption of renewable energy, green production processes, recycling, waste reduction, and sustainable materials. By being environmentally friendly and adopting green technologies, businesses can minimize risks to the ecosystem, profile sustainability, and meet the eco-conscious consumer's requirement for green products and services. Organizations should develop an all-inclusive environmental policy with specific goals and an outline of the achieved aims, measures, and policies. This activity stream should fully agree with the company's general strategic map and should align with the functional areas. Moreover, for the company to have a clearly defined environmental policy, it provides a pathway for sustainable actions, communicating accurately, and designing a system that helps to develop the organization's environmental performance.\n\nOne possible limitation of such research is that it is one where manufacturing companies are the key players, potentially limiting the approachability of its outcomes to other categories or sectors. Further, it does not give details on how these environmental practices' side effects or price balancing could work together to identify the best cases to achieve sustainability in manufacturing companies. The role of mediation can be observed in the times to come via measures like environmental education and environmental approval, etc., in a developing country like Pakistan. Eventually, this research should be confirmed and expanded to verify the more precise causes and to explore the broader contextual factors that play a role in environmentally friendly practices in different industries and sectors.\n\nAvailability of data and material: is available with the manuscript.\n\nAuthors equally contributed to the analysis and writing of this publication.\n\nThis study “Factors Affecting on Environmental Strategy in SME Manufacturing Firms of a Developing Country: Mediating Role of Green Employee Behavior” was approved by the Ethics Committee of The University of Okara constitutes the departmental Ethics Approval Committee (REBSSH/2024/4-9) in January 03, 2024. All of the informants gave written and oral informed consent to participate in the study. Under the Personal Data Protection Act (PDPA) 2010, the researchers assure that all information collected is kept confidential and merely for the academic purposes. Therefore, they were assured that their responses would be kept in strict anonymity and reported as aggregate results.", "appendix": "Data availability\n\nFigshare: Dataset & Questionnaire:\n\nDOI: https://doi.org/10.6084/m9.figshare.25975462.v1\n\nThis project contains the following underlying data:\n\n• Data set: Data set.csv\n\n• Questionnaire: Environmental Strategy Questionnaire.xlsx\n\nThis project contains the following underlying data:\n\nFigshare: Figure 1_Measurment model.docx\n\nFigshare: Figure 2_Stutrual model.docx\n\nDOI: https://doi.org/10.6084/m9.figshare.25975387.v1\n\nThis project contains the following underlying data:\n\nFigshare: Table 1_Measurment model\n\nFigshare: Table 2_Structural model\n\nDOI: https://doi.org/10.6084/m9.figshare.25975438.v1\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” Attribution 4.0 International (CC BY 4.0)\n\n\nAcknowledgments\n\nWe would like to thank all the participants in this research for their voluntary participation.\n\n\nReferences\n\nAbabneh OMA: How do green HRM practices affect employees’ green behaviors? 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Publisher Full Text\n\nSohu JM, Hongyun T, Rahoo LA, et al.: Feasibility Study of Knowledge Management Establishment in Private Degree Awarding Institute of Pakistan. Int. J. Comput. Sci. Netw. Secur. 2020; 20(12): 177–183. Publisher Full Text\n\nSohu JM, Junejo I, Hussain F: The Impact of Corruption on Exchange Eate: Empirical Evidence from Panel Data. Sukkur IBA J. Manag. Bus. 2019; 6(1): 34. Publisher Full Text\n\nSohu JM, Junejo I, Khuwaja FM, et al.: The Impact of Entrepreneurial Education on Entrepreneurial Intention During the COVID-19 Pandemic: An Empirical Study from Pakistan. Sarfraz Ahmed DAKHAN/Journal of Asian Finance. 2022; 9(3): 95–0103.\n\nSürücü L, Maslakci A: Validity and reliability in quantitative research. Bus. Manag. Stud. Inter. J. 2020; 8(3): 2694–2726. Publisher Full Text\n\nXin Y, Dilanchiev A, Esmira G, et al.: Assessing the nexus between corporate social responsibility and environmental performance: A way forward towards sustainable development. Energy Environ. 2023; 0958305X2311646. Publisher Full Text\n\nYang L, Liu H: The impact of ethical leadership on employees’ green innovation behavior: A mediating-moderating model. Front. Psychol. 2022; 13: 951861. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZacher H, Rudolph CW, Katz IM: Employee green behavior as the core of environmentally sustainable organizations. Annu. Rev. Organ. Psych. Organ. Behav. 2023; 10: 465–494. Publisher Full Text\n\nZikargae MH, Woldearegay AG, Skjerdal T: Empowering rural society through non-formal environmental education: An empirical study of environment and forest development community projects in Ethiopia. Heliyon. 2022; 8(3): e09127. Publisher Full Text" }	[ { "id": "302073", "date": "07 Aug 2024", "name": "Andrew Kweku Conduah", "expertise": [ "Reviewer Expertise § Population Estimates and Projections.§ Population Health and Mortality- Health Emergencies & Preparedness", "Ageing & Intergeneration Relations", "and Non-Communicable Disease & Health Projection (Physical Activity", "Obesity", "Tobacco Control", "etc.)§ Business Demography§ Business Policy and Strategy§ Business Management§ Public Administration§ Entrepreneurial Innovation" ], "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 thoroughly examines environmental strategies within SMEs in a developing country, utilizing the Resource-Based View (RBV) to frame its analysis. The introduction effectively sets the stage by highlighting global environmental challenges and the urgency of addressing these issues. It situates the discussion within a broader international context, referencing trends in sustainability such as renewable energy, eco-friendly technology, and recycling. However, the introduction could be enhanced by including specific global case studies, offering a richer context and illustrating the broader application of the study’s findings. Additionally, while the problem statement is relevant, it lacks specificity concerning the unique challenges SMEs face in developing countries like Pakistan. Clearly defining the problem statement and articulating the study’s objectives more explicitly would strengthen the research foundation and provide clearer direction for the study. In the literature review, the paper offers a comprehensive overview of the theoretical foundation, effectively utilizing the RBV to explain how reduced resource use and green processes contribute to a competitive advantage through environmental strategies mediated by green employee behaviour. This integration of theoretical perspectives with practical implications is a notable strength, emphasizing the role of both tangible and intangible resources in achieving ecological sustainability. Nonetheless, discussing how green employee behaviour mediates the relationship between resource use and environmental performance requires more depth. A more detailed exploration of the mechanisms by which green employee behaviour influences this relationship would enhance the reader's understanding. Additionally, each hypothesis should be more explicitly connected to the RBV and supported by empirical evidence. The study's strengths lie in its effective highlighting of global environmental issues and its connection of local contexts to global sustainability efforts through discussions on renewable energy, eco-friendly technology, and recycling. The application of the RBV is appropriate and well-articulated, integrating theoretical perspectives with practical implications. However, the paper would benefit from addressing certain weaknesses. For example, it lacks explicit comparisons to specific global case studies and needs a more detailed problem statement addressing SMEs' unique challenges in developing countries. The study’s objectives are implied but not clearly articulated, and the explanation of the mediation role of green employee behaviour needs further elaboration. Furthermore, the hypotheses could be more clearly linked to the theoretical framework. To improve the paper, it is recommended that the unique challenges faced by SMEs in developing countries such as Pakistan be specified and the problem statement be defined clearly. This should include a focus on specific environmental strategy challenges for SMEs. The study’s objectives should be articulated more distinctly, encompassing economic factors and the mediating role of green employee behaviour. A more detailed explanation of how green employee behaviour acts as a mediator is needed, including a discussion of specific actions and attitudes contributing to improved environmental performance. Additionally, the connection between the hypotheses and the theoretical foundation should be clarified and strengthened, ensuring that each hypothesis is explicitly grounded in the RBV and supported by relevant literature. The study's methodological approach is sound. It includes a cross-sectional design, ethical data collection procedures, validated measurement tools, and Structural Equation Modeling (SEM) to address the research questions. This methodology is appropriate and effectively supports the study’s objectives. In terms of analysis, the study demonstrates high reliability and validity. The measurement tools show strong Cronbach's Alpha and Composite Reliability values, indicating consistent and stable data collection methods. Convergent validity is confirmed by Average Variance Extracted (AVE) values that exceed the threshold of 0.50. The hypotheses tested reveal significant findings: reducing resource use (H1) is positively associated with robust environmental strategies; greening of processes and products (H2) enhances environmental strategies; and green employee behaviour (H3) significantly boosts environmental strategy. Additionally, green employee behaviour contributes positively to environmental strategies (H4) and mediates the effect of green processes/products on environmental strategy (H5). The study highlights that effective environmental performance in organizations is achieved through the strategic implementation of green products, processes, and technologies. Resource minimisation is crucial for enhancing efficiency, reducing emissions, and minimising waste. Integrating eco-friendly practices and materials throughout the product lifecycle is essential for optimizing environmental performance. Green employee behaviour is a significant mediator, facilitating the adoption of green practices and contributing to sustainability and innovation within organizations. A well-designed environmental strategy, embedded across all departments, ensures commitment to sustainability and integrates environmental considerations into business activities. Practically, organisations should prioritize resource durability by adopting energy-saving technologies, optimizing production processes, reducing water consumption, and minimizing waste. Embracing eco-friendly practices such as renewable energy use, green production, recycling, and sustainable materials enhances cost-efficiency and minimises environmental impact. Companies should develop comprehensive environmental policies with specific goals and measures aligned with their strategic plans. This approach fosters sustainability, meets eco-conscious consumer demands, and strengthens the company’s environmental profile. The study’s limitations include its focus on manufacturing companies, which may restrict the applicability of its findings to other sectors. It also does not address potential side effects or cost implications of implementing environmental practices. Future research should explore the role of mediation through environmental education and approval, especially in developing countries like Pakistan. Expanding the research to encompass diverse industries and sectors will help verify findings and identify broader contextual factors influencing environmentally friendly practices.\n\nIs the work 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": "315831", "date": "30 Aug 2024", "name": "Jan Muhammad Sohu", "expertise": [ "Reviewer Expertise e.g. Digital Marketing", "Business Performance", "and development", "Big Data Analytics Capability", "Digital Trasformation", "Digital Innovation", "Value Co-creation", "and Green Supply Chain Management Practices." ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThank you for the opportunity to review the paper titled \"Factors affecting on environmental strategy in SMEs manufacturing firms of a developing country: mediating role of green employee behavior\". Overall, the paper is well-written and the topic is interesting and well-justified.\nMinor revisions are suggested as follows:\nIn the Abstract, the method section should mention the software tool(s) used, such as the SmartPLS version. In the keywords, \"SMEs\" and \"developing country\" should be added to the list of keywords. In the Introduction section, the research objectives should be clearly stated before the research contribution of the present study. In the Conclusion section, the theoretical contribution of the study is missing and should be added.\nOverall, the paper is of good quality, and with the minor revisions suggested, it should be ready for indexing. I wish the authors all the best.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] }, { "id": "315835", "date": "03 Sep 2024", "name": "Chun-Hung Cheng", "expertise": [ "Reviewer Expertise My research field focuses on the study of green operations and the implementation of green production-related tools in small and medium-sized enterprises (SMEs)." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe literature review in this theoretical foundation can support the structure of the entire article's investigation. It is recommended that this article should supplement the research objectives. If the article only explains through hypotheses, it merely verifies the theory of the article. It would be better to clearly state the research objectives of this article and whether the conclusions drawn from the investigation align with these research objectives. Additionally, it is suggested that the article should supplement the background by explaining the current situation of the surveyed populations' country. This will further highlight the contribution of the article's 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? Partly", "responses": [] } ]	1	https://f1000research.com/articles/13-654
https://f1000research.com/articles/12-1057/v1	30 Aug 23	{ "type": "Study Protocol", "title": "To study the utility of COX-2 as immunohistochemical prognostic marker in comparison to various histopathological parameters and TNM staging in breast carcinoma: an observational, cross-sectional study protocol", "authors": [ "Jayashree Bhawani", "Samarth Shukla", "Sourya Acharya", "Sunita Vagha", "Miheer Jagtap", "Samarth Shukla", "Sourya Acharya", "Miheer Jagtap" ], "abstract": "Background: Breast cancer is the most prevalent cancer among women worldwide and is a well-known cause for cancer mortality in females. COX-2 (cyclooxygenase) plays a vital role in development of some human cancers such as lung, colon and breast. It is a potent enzyme that is important for the conversion of arachidonic acid into prostaglandins. These prostaglandins mediate cellular proliferation, apoptosis and angiogenesis which contributes to carcinogenesis. Overexpression of COX-2 has been detected in several malignancies including breast cancer. COX-2 overexpression is regarded as a poor prognostic marker of breast cancer. The present study will aim to study the immunohistochemical expression of COX-2 in breast cancer and compare it with known histopathological parameters thus assessing its prognostic value. Methods: This will be an observational study conducted in the Department of Pathology, JNMC, Wardha (Sawangi). Radical mastectomy specimens will be studied for COX-2 expression by immunohistochemistry in patients diagnosed with breast carcinoma. COX-2 expression will be quantified as immunohistochemical score and results will be correlated with various histopathological parameters. Results: The expected result of our study will suggest an association of COX-2 expression to the factors associated with poor prognosis in breast carcinoma. A positive correlation is expected between larger tumor size, positive lymph node status, higher T stage and N stage and lymphovascular invasion. Conclusions: Conclusions will be drawn from the obtained results of the immunohistochemical study by using COX-2- for detection of overexpression of COX-2 when evaluated with TNM staging, histological grading and molecular types of breast cancer.", "keywords": [ "Breast Cancer", "COX-2", "histopathological parameters", "prognostic marker", "immunohistochemistry." ], "content": "Introduction\n\nBreast carcinoma is the most frequent malignancy and the second leading cause of death in women worldwide.1 It has surpassed lung cancer with an estimated 2.3 million new cases worldwide. In recent years, incidence rates of breast cancer have elevated by 0.5% every year, as breast cancer incidence varies with age and race/ethnicity.\n\nIn the year 2021, 2.6 million women were newly diagnosed with breast cancer.2 In India, breast cancer accounts for 13.5% of cancer cases. It is assumed that the chance of a woman’s death due to breast carcinoma is about 1 in 39 or about 2.6%.3\n\nThe etiology is multifactorial, implicating hormonal imbalance, genetic predisposition, diet, metabolic factors, and reproductive factors.\n\nThe diagnosis of breast cancer is achieved by adopting a triple assessment approach which includes clinical evaluation, radiographical investigation and tissue diagnosis by biopsy, out of which tissue biopsy is currently the gold standard for cancer diagnosis and predicting prognosis.\n\nThere are certain indicators available which establish the prognosis of breast cancer,4 these are tumor size, age, site of tumor, lymph node status, stage and grade of tumor and lymphovascular invasion.\n\nVarious evaluation methods or systems are available for the determination prognosis of breast carcinoma, including the: - Nottingham Histologic Grading system which is also referred as The Elston-Ellis modification of Scarff-Bloom-Richardson grading system. The other method is the categorization of breast cancer according to TNM (tumor, nodal status, metastasis) staging, specified by the American Joint Committee on Cancer (AJCC). This is a more advanced diagnostic modality, which determines the molecular phenotypes of carcinoma breast by implementing immunohistochemistry.\n\nOver the years additional prognostic and predictive factors are evolving and one of them is COX-2. This is the rate limiting enzyme in the biosynthesis of prostaglandins from arachidonic acid.5 It is an empirical catalyst formed under few definitive circumstances of inflammation and tumor -microenvironment. COX-2 is an important tumor marker which regulates tumor growth, invasion and metastasis.6 In carcinogenesis, inflammatory cytokines, growth factors and oncogenes trigger induction of COX-2, which results in tumor progression. COX-2 is strongly associated with tumor proliferation, angiogenesis and apoptosis resistance mechanism.7 Therefore, COX-2 overexpression is associated with poor prognosis in post-menopausal women, those above 50 years of age, those in the advanced stage of the disease, those with a larger tumor size, higher grade, and metastasis of lymph nodes.\n\nVarious studies8 showed that, among different types of breast tumors, triple negative breast cancer [ER (estrogren) negative, PR (progesterone) negative, HER2 neu negative)] are associated with aggressive progression of tumor and COX-2 expression seemed to be increased in triple negative tumors. Also, there is a positive correlation of COX-2 with these histopathological prognostic parameters.\n\nTo further evaluate the role of COX-2 as marker of tumor behavior and to correlate its expression with other essential parameters which play a vital role in the assessment of tumor behavior this study is being conducted.\n\nThe aim of this study is to analyze the relationship between COX-2 expression and histopathological parameters, pathological TNM staging and molecular immunophenotypes of carcinoma breast.\n\n\n\n• To confirm breast carcinoma by histopathological examination and to determine the histopathological grade of breast carcinoma by Elston-Ellis modification of Scarff- Bloom-Richardson grading system).\n\n• To establish pathological TNM stage of breast carcinoma.\n\n• To determine the immunophenotypes of carcinoma breast by evaluating ER/PR and Her 2 neu expression by immunohistochemistry.\n\n• To evaluate immunohistochemical expression of COX-2 in breast carcinoma.\n\n• To understand the inter relation between expression of COX-2, histopathological prognostic markers, molecular immunophenotypes, and pathological TNM staging of carcinoma breast.\n\n\nMethods\n\nAn observational, cross-sectional study will be conducted on breast cancer patients for a span of two years (June 2022 to June 2024) in the Histopathology and Immunohistochemistry section of the Pathology Department, Jawaharlal Nehru Medical College, Sawangi (Meghe) in co-ordination with General Surgery Department, Acharya Vinoba Bhave Rural Hospital, Sawangi (Meghe).\n\nDesired sample size will be calculated according to Krejcie and Morgan’s formula9:\n\nhere,\n\nZα/2= significance level of 5% i.e. 95% (CI) confidence interval = 1.96\n\nP = incidence of breast cancer in female = 13.510 %= 0.135\n\nd = error of margin = 0.08\n\nThe study will include approximately 60-70 resected specimens from confirmed and planned modified radical mastectomy of breast carcinoma in the General Pathology Department, J.N.M.C.\n\nThe Institutional Ethics Committee has given approval for the study ((DMIMS (DU)/IEC/2022/1068) on 27th June 2022), and informed consent will be taken from the targeted patients who will be participating in this study.\n\n\n\n• Female patients diagnosed with breast carcinoma on histopathological examination.\n\n• Women with breast carcinoma having no history of treatment.\n\n• Female patients presenting with breast carcinoma arising de novo.\n\n• All cases that underwent mastectomy/modified radical mastectomy (MRM) procedure.\n\n\n\n• Patients with lesions other than breast carcinoma i.e., benign breast tumors, myoepithelial tumors, mesenchymal tumors.\n\n• Patients with breast carcinoma who have received neoadjuvant chemotherapy.\n\n• Male patients with a diagnosis of breast carcinoma.\n\n• Patients who underwent incisional biopsy, excisional biopsy, or tru-cut biopsy.\n\nThe study will collect patients’ personal details including name, age, gender, registration number, IPD/OPD numbers, department and also clinical details such as symptoms, test interpretations and diagnosis. Radiological investigations such as mammography report, ultrasonography of breast, and CT scan reports will be noted from patient’s case file. The present study will take into consideration, the biopsy report of the lesion.\n\nThe mastectomy specimen will be received in the Histopathology Department, in 10% formalin and will be kept for proper fixation. After a period of 24 hours of fixation the specimen will be grossed and sections from the representative areas will be taken.\n\nThe sections will be processed by automated histokinette. The paraffin blocks will be prepared with the help of Leuckhart’s mould and sections of 3-4 microns thick will be taken using microtome. These sections will be then transferred to glass slides, precoated with egg albumin. Hematoxylin and eosin staining of paraffin sections will be carried out using standard methods. Slides will be scanned and a diagnosis along with histological grading will be made, using the College of American Pathologists (CAP) protocol. The 8th American Joint Committee on Cancer (AJCC) guidelines will be followed to carry out staging on the specimen.\n\nUsing the Nottingham modification of Bloom-Richardson System, histological grades of tumor will be determined. This will include factors such as tubule formation, nuclear size and mitotic count11 and score will be assigned accordingly:\n\nTubule formation\n\nScore 1: > 75% of tumor shows tubules\n\nScore 2: 10-75% of tumor has tubules\n\nScore 3: < 10% of tumor has tubules\n\nNuclear size\n\nScore 1: Small regular nuclei: similar to normal ductal nuclei (nuclei with minimal variation in size and shape)\n\nScore 2: Intermediate size: 1.5-2 times the size of normal ductal nuclei (nuclei with moderate variation in size and shape)\n\nScore 3: High grade nuclei: > twice the size of normal ductal nuclei (nuclei with marked variation in size and shape)\n\nNumber of mitotic figures counting 10 high power fields (Table 1):\n\nScore 1: 0-9 mitoses/10 HPF\n\nScore 2: 10-19 mitoses/10 HPF\n\nScore 3: > 20 mitoses/10 HPF\n\nAdd up to the score to reach the total points:\n\n1-5 points: grade 1: well differentiated\n\n6-7 points: grade 2: moderately differentiated\n\n8-9 points: grade 3: poorly differentiated\n\nAfter assessing tumor grade, tumor stage will be determined by TNM staging (8th AJCC edition)\n\nHence, interpretation of overall stage will be as follows:\n\nStage 0: Tis\n\nStage I: T1, N0\n\nStage II: T2, N0; T3, N0; T0, N1; T1, N1 or T2, N1\n\nStage III: T3N1, T0N2, T1N2, T2N2, T3N2, any T-N3, locally advanced carcinoma breast, invasion in ribs, skin, matted lymph nodes\n\nStage IV: M1; advanced breast cancer.\n\nImmunohistochemistry (IHC) will be performed on a paraffin embedded segment of a surgically removed specimen that has been diagnosed as a malignant lesion of the breast. Only representative blocks from the lesion will be chosen for immunohistochemistry. Immunohistochemistry will be performed utilizing monoclonal antibodies and the biotin avidin peroxidase complex technique. For performing IHC, slides will be coated with Poly L- Lysine and 2 sections of 3-4 microns thick will be placed on the slide. Sections will be deparaffinized and then rehydrated with descending grades of alcohol (100% to 90% to 70% to at last 50% concentration). Antigen retrieval will be performed and followed by transfer of slide for wash in tris buffer solution (TBS). The next step will be the peroxidase blocking for 30 minutes using 3,5 hydrogen peroxide along with methanol. The wash will be repeated 3 times with TBS. Now the section will be exposed to DAKO monoclonal mouse anti human antibodies, i.e., mouse anti human ER/PR/Her2 antibodies and COX-2 antibody. It will be again washed in the buffer thrice for 5 minutes. Now chromogen 3,3’- diaminobenzydene (DAB) will be applied for 15-20 minutes. The DAB-stained slide will be washed in buffer for 10 minutes and then will be dipped in distilled water. Harris hematoxylin will be used for counterstaining. Lastly, after final wash with tap water, mounting of slides will be done to scan under microscope.\n\nOn immunohistochemical staining COX-2 will be observed in tumor cells. Immunohistochemical staining will be evaluated with a light microscope. A minimum of 500 cells will be counted per x 40 fields for immunohistochemical evaluation per antibody. Cyclooxygenase-2 positivity will be indicated by the presence of brown cytoplasmic- staining. For the evaluation of cytoplasmic staining for COX-2, a predefined scoring system which is based on the product of percentage of immunoreactive tumor cells with staining intensity will be studied.14 Immuno-reactivity for C0X-2 in tumor cells will be assessed using a scoring system based on the staining intensity.\n\nCOX-2 immunohistochemistry score is obtained by multiplying the staining quantity score and staining intensity score.\n\n0-3 =Negative/faint staining\n\n4-8= Moderate/intermediate staining\n\nThe software used for analysis will be SPSS version 27.0. Statistical analysis will be carried out by using suitable statistical tests eg: ‘Chi-Square Test’, ‘Fisher’s Exact Test’ with significance set at p value < 0.05.\n\n\nResults\n\nObservations and results will be collected and combined together over the period of two years and will be analyzed statistically.\n\n\nDiscussion\n\nIn this study a statistically significant expression of COX-2 with histopathological parameters which are associated with poor prognosis such as tumor size, grade, lymph node metastasis is expected. As COX-2 is overexpressed in triple negative breast cancer, it indicates a poor outcome in terms of prognosis. COX-2 expression is increased when tested in post- menopausal status, those of age above 50 years, in an advanced stage of disease, with a larger tumor size, a high grade, and metastasis of lymph nodes. Few studies have shown that COX-2 expression is increased when correlated with HER-2/neu expression in breast cancer patients; COX-2 was expressed in ER negative, PR negative and HER-2/neu positive tumors and with high histological grade in breast carcinoma. Our study will help in assessing the role of COX-2 in carcinogenesis and its association with poor prognostic markers.\n\nA key strength of this study is that it will use a useful biomarker for estimating tumor aggressiveness. This study will focus on COX-2 expression in breast carcinoma and its comparison with other histopathological parameters. This would also give clinicians a framework for evaluating the function of selective COX-2 inhibitors in human breast cancer chemoprevention as well as treatment.\n\nStudies such as those conducted by Ibrahim Metin Ciris et al., Debashri Jana et al., Ari Ristimaki et al., Pereira et al. and Costa et al. have stated that COX- 2 overexpression has the potential to be a useful biomarker for estimating tumor aggressiveness, and that COX-2 expression is associated with aggressive tumor biology, and can behave as a predictor of tumors with bad prognosis. Hence, the above studies concluded that there is a correlation of COX-2 expression with histopathological prognostic parameters in breast cancer. The limitation of the study is that it will be a single center study.\n\n\nConclusion\n\nThe purpose of the current investigation is to determine COX-2's precise prognostic function in breast cancer. This would give clinicians a framework for evaluating the function of selective COX-2 inhibitors in human breast cancer chemoprevention as well as treatment. This study will correlate prognostic relation between COX-2 expression in breast carcinoma patients with routinely studies histopathological prognostic parameters.\n\nThe results of this study will be presented in peer reviewed publications.\n\nRecruitment has begun, and currently 25 patients have been enrolled for the study.\n\n\nEthics and consent\n\nThe research work is approved by Institutional Ethical Committee of the Datta Meghe Institute of Medical Sciences (DMIMS (DU)/IEC/2022/1068) on 27th June 2022.\n\n\nAuthor contributions\n\nContributors: Dr. Samarth Shukla conceptualized the study and provided the idea of how to conduct it. Dr. Jayashree Bhawani will do the research work, collect the data, analyze it and under guidance of Dr. Samarth Shukla and Dr. Sunita Vagha will come to the conclusion.", "appendix": "Data availability\n\nNo data are associated with this article.\n\n\nAcknowledgements\n\nMy sincere gratitude to all the patients whose sample will help us to conduct this study. I would also like to express my gratitude to all the faculties of department of pathology and surgery, and technical staffs for their support. I would also like to use this opportunity to express my gratitude towards Indian Council of Medical Research (ICMR) for providing their valuable grant for my research study. The completion of my study would not have been possible without their help and insights.\n\n\nReferences\n\nSolanki R, Agrawal N, Ansari M, et al.: COX-2 Expression in Breast Carcinoma with Correlation to Clinicopathological Parameters. Asian Pac. J. Cancer Prev. 2018; 19(7): 1971–1975. 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PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDesai SJ, Prickril B, Rasooly A: Mechanisms of phytonutrient modulation of cyclooxygenase-2 (COX-2) and inflammation related to cancer. Nutr. Cancer. 2018 Apr 3; 70(3): 350–375. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPastor N, Ezquerra LJ, Santella M, et al.: Prognostic significance of immunohistochemical markers and histological classification in malignant canine mammary tumours. Vet. Comp. Oncol. 2020 Dec; 18(4): 753–762. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChaokromthong K, Sintao N: Sample size estimation using Yamane and Cochran and Krejcie and Morgan and green formulas and Cohen statistical power analysis by G* Power and comparisions. Apheit International Journal. 2021 Dec 24; 10(2): 76–86.\n\nMehrotra R, Yadav K: Breast cancer in India: Present scenario and the challenges ahead. World J Clin Oncol. 2022 Mar 24; 13(3): 209–218. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBansal C, Singh US, Misra S, et al.: Comparative evaluation of the modified Scarff-Bloom-Richardson grading system on breast carcinoma aspirates and histopathology. Cytojournal. 2012; 9: 4. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nvan Dooijeweert C , van Diest PJ , Ellis IO: Grading of invasive breast carcinoma: the way forward. Virchows Arch. 2022; 480: 33–43. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSanderson T, Wild G, Cull AM, et al.: 19—Immunohistochemical and immunofluorescent techniques. Bancroft’s Theory and Practice of Histological Techniques. 8th ed. Suvarna SK, Layton C, Bancroft JD, editors. 2018 Feb 27; 337–94.\n\nHalf E, Tang XM, Gwyn K, et al.: Cyclooxygenase-2 expression in human breast cancers and adjacent ductal carcinoma in situ. Cancer Res. 2002; 62(6): 1676–1681. PubMed Abstract" }	[ { "id": "202390", "date": "02 Oct 2023", "name": "Amit Kumar Chowhan", "expertise": [ "Reviewer Expertise Oncopathology" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nComment\nIn Introduction it is mentioned ‘This is a more advanced diagnostic modality, which determines the molecular phenotypes of carcinoma breast by implementing immunohisto[1]chemistry’. – Kindly check whether this line has been kept at appropriate place.\n\nSample size should be calculated in reference to prevalence of positivity for COX2 in breast cancer (data to be taken from other similar study). For example, in reference no 5, the positivity of COX2 is mentioned as 42.7% in tumour cells, so while calculating sample size ‘P’ should be 42.7%.\n\nFirst point of Inclusion criteria is • ‘Female patients diagnosed with breast carcinoma on histopathological examination.’\nTherefore, there is no need of keeping an exclusion criteria as ‘Male patients with a diagnosis of breast carcinoma.’\n\nSecond point of Inclusion criteria is ‘Women with breast carcinoma having no history of treatment.’Therefore, there is no need of keeping an exclusion criteria as ‘Patients with breast carcinoma who have received neoadjuvant chemotherapy.’\n\nThird point of Inclusion criteria is ‘Female patients presenting with breast carcinoma arising de novo.’’ Kindly explain what is the exact meaning of ‘’de novo.’’\n\nFourth point of Inclusion criteria is ‘’All cases that underwent mastectomy/modified radical mastectomy (MRM) procedure’’, therefore there is no need of keeping an exclusion criteria as ‘’Patients who underwent incisional biopsy, excisional biopsy, or tru-cut biopsy’’.\n\nUnder the heading ‘’Evaluation of COX-2 expression by immuno-histochemistry’’, the reference article mentioned is reference no 14, whereas in table 2 and table 3, the reference mentioned is reference no 1, kindly explain the disparity.\n\nUnder the heading ‘’Evaluation of COX-2 expression by immuno-histochemistry’’, it has been further mentioned as ‘’COX-2 immunohistochemistry score is obtained by multiplying the staining quantity score and staining intensity score. 0-3 =Negative/faint staining 4-8= Moderate/intermediate staining’’, which is not matching with table 2 and table 3, where the scores are 0-4 and 0-3. Kindly explain the disparity.\n\nUnder the section ‘’Immunohistochemical assessment’’, it has been mentioned that ER/PR/Her2 antibodies and COX-2 antibody will be applied, kindly mention the scoring system for ER/PR/Her2 antibodies also, which will be followed in the study, along with reference.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Yes\n\nAre sufficient details of the methods provided to allow replication by others? Partly\n\nAre the datasets clearly presented in a useable and accessible format? Partly", "responses": [ { "c_id": "11744", "date": "18 Jun 2024", "name": "Jayashree Bhawani", "role": "Author Response", "response": "1. Instead of this is a more advanced diagnostic modality, It should be there is a more advanced diagnostic modality which is immunohistochemistry that determines molecular phenotype of breast carcinoma. 2. Sample Size Using the formula: N= https://f1000research.s3.amazonaws.com/linked/653957.image.png Where: N = Sample size Z(1-α/2) = 1.96 (value of the standard normal variate corresponding to the level of significance α of 0.05) d = Specified precision on either side of the mean (10% or 0.1) P = Expected prevalence of COX2 expression in the study population (76% or 0.76) From the previous study by Fatma Z Abd Elrahman et al., the prevalence of COX2 expression in carcinoma breast patients was found to be 76%. Taking d=10%, the total sample size calculated is 70.07. N= (1.96)2X 0.76X(1−0.76) (0.1)2 N= 70.07 Rounding up to the nearest whole number, the required sample size is 70. Reference- Abdel-rahman FZ, Zaky AH, Zedan A, Elsaba TM, Gabr A. COX-2 “Cyclooxygenase 2“as a Prognostic marker in Breast Cancer. SVU-International Journal of Medical Sciences. 2021 Feb 2;0(0):0–0. 3. Male patients are kept in exclusion criteria because exclusion criteria comes as an opposite if inclusion criteria and also because in males immunophenotyping cannot be performed. 4. Again here exclusion criteria is considered as exact opposite of inclusion criteria therefore patients with neoadjuvant therapy are excluded. 5. Here recurrence cases and secondaries from other malignancy are not counted therefore primary breast malignancy are referred as de novo. 6. Here I wanted to be specific for considering only mastectomy patient in inclusion criteria therefore opposites are mentioned in exclusion 7. I agree with you Sir, reference no. 1 should have been there at the place of 14th 8. Here COX-2 immunohistochemical score will be calculated by multiplying the values of Table 2 and Table 3 and values obtained will be put under 3 categories i.e 0-3 = Negative / Faint 4-8= Moderate 9-12 = High 9. ER/PR/Her2 antibodies assessment according to Allred scoring system as depicted in CAP( college of American Pathologists) guidelines." } ] }, { "id": "202391", "date": "05 Jun 2024", "name": "Shaan Khetrapal", "expertise": [ "Reviewer Expertise Histopathology" ], "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 exclusion criteria the point of male patients can be omitted as the inclusion criteria specifically states female patients.\nComparative elaboration of discussion with respect to other studies can be done, which can be beneficial for further prognostic factors.\n\nRest well written article for study, to be approved and considered.\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/12-1057
https://f1000research.com/articles/13-653/v1	18 Jun 24	{ "type": "Research Article", "title": "Enhancing bioactive content in Malus sylvestris peel extract for antioxidant source using microwave-assisted extraction (MAE) and predicting the potential of ant nests", "authors": [ "Aju Tjatur Nugroho Krisnaningsih", "Ari Brihandhono", "Premy Puspitawati Rahayu", "Aju Tjatur Nugroho Krisnaningsih", "Ari Brihandhono" ], "abstract": "Background The apple peel is one of the byproducts of apple beverage production that is still underutilized. While considerable information regarding apple peel extract is available, its utilization remains limited. Yet, apple peel contains numerous bioactive components that offer various health benefits. Based on this, information regarding the bioactive components in apple peel and their health potential is required.\n\nMethods The research consisted of two stages, namely Stage 1, which involved in silico analysis of the bioactive content in apples and predicted the potential of ant nests using the Structural Activity Relationship (SAR) approach Pass Online. In Stage 2, in vitro analysis of apple peel extraction as a natural antioxidant source was conducted using treatment time radiation (3 minutes, 6 minutes, 9 minutes, and 12 minutes). The extract was characterized based on phenolic, flavonoid, antioxidant activity, quercetin, and functional groups using Fourier Transform Infrared Spectroscopy (FTIR).\n\nResults Stage 1: gave results that several bioactive were identified such as chlorogenic acid, epicatechin, phloridzin, catechin, hyperoside, quercitrin, quercetin, and pectin. Based on SAR, the bioactive compounds have functional potential as anti-inflammatory, lipid metabolism regulators, free radical scavengers, lipid peroxidase inhibitors, antihypercholesterolemic, and insulin promoters. Stage 2: Radiation times of the MAE method had a significant effect (P<0.05) on the phenolic content, and antioxidant activity and was highly significant (P<0.01) on the flavonoid content of Malus sylvestris. Radiation time for 12 minutes of MAE gave higher phenolic, flavonoid, and antioxidant activity of Malus sylvestris peel extract. The IR spectra of the Malus sylvestris extract increased as the radiation time increased.\n\nConclusions The optimum radiation time was at 12 minutes with the result of phenolic content at 14.73 mg GAE/g, flavonoid content at 29,62 ppm, antioxidant activity at 95,09%, and the IR spectra at 1031.92 cm−1, 1390.68 cm−1, 2833.43 cm−1, 2945.3 cm−1, 3346.5 cm−1, 3354.21 cm−1.", "keywords": [ "antioxidant", "by-product", "flavonoid", "phenolic", "functional group" ], "content": "Introduction\n\nIn Malang, Indonesia, apples (Malus sylvestris) are a type of fruit that is quite popular and an excellent source of nutrition. Apples contain several vitamins, minerals, fiber, and antioxidant compounds that are important for human health.1 Apples contain antioxidant compounds that protect the body from damage caused by free radicals.2,3 Afsharnezhad, M., Shahangian, S. S., Panahi, E., & Sariri, R. (2017). Free radicals are unstable molecules that can damage body cells and cause various chronic diseases, including cancer, heart disease, diabetes, and premature aging.4 One of the greatest sources of natural antioxidants is found in apple skin. Apple skin (Malus sylvestris) is the outer part of the apple that protects the flesh inside.5 Apple skin has several layers, including a thin epidermis that protects the fruit from water loss and physical damage. The color can vary from light green, and yellow, to red depending on the type of apple. Apple skin contains a much greater number of polyphenols than the flesh of the fruit.6,7 So far, the by-product of the processing process in leather has only been used as a substitute for animal feed and plant fertilization, even though it still has the potential to contain micronutrients in the form of natural antioxidants.8,9\n\nThe content of antioxidant compounds in apple skin varies depending on the type of apple and also growth factors such as the environment and season.10,11 Flavonoids are a group of polyphenolic compounds that have strong antioxidant properties. These compounds help protect the body from damage caused by free radicals.12 The phenol content in apple skin also varies based on the type of apple, growing conditions and growth environment.1 Phenol is a chemical compound that has antioxidant properties. strong. It also provides color, taste, and aroma to fruits. The phenols in apples are mainly concentrated in the skin.11 The greater the content of phenolic and flavonoid compounds in a plant indicates its strong antioxidant activity. The higher the content of phenolic and flavonoid compounds, the ability to capture free radicals will also increase.13\n\nThe extraction method for antioxidant compounds can be carried out using conventional and non-conventional methods. Conventional methods have been widely used in the extraction process but require a long time.14 The advantages of non-conventional methods are that they are environmentally friendly and highly efficient, including membrane-based technology, ultrasound, microwave extraction, and high hydrostatic pressure. The results of the research show that the best extraction method to produce the highest levels of flavonoids in 70% ethanol extract of iler leaves is the microwave-assisted extraction method. Flavonoid levels using the maceration, reflux, microwave-assisted extraction, and Ultrasound-Assisted Extraction methods were 0.41%, 0.45%, 0.75%, and 0.62% respectively.15 According to the advantages of the extraction method, research about combination maceration and MAE to characterize Malus sylvestris peel extract.\n\n\nMethods\n\nThe research is divided into two stages, namely:\n\nStage 1: In silico analysis related to the bioactive content of apple peel and the prediction of ant nest potential using the Structural Activity Relationship (SAR) approach Pass Online.\n\nStage 2: in vitro analysis of apple peel extraction as a natural antioxidant source.\n\nThe exploration of bioactive content found in apple peel was conducted through literature searches. Several publications indicate that apple peel contains specific bioactive, as outlined in Table 1. This research is in silico analysis. Subsequently, these bioactive constituents were analyzed to determine their profiles and structures using the PubChem database on the website (https://pubchem.ncbi.nlm.nih.gov/).\n\nThe compounds present in apple peel were further assessed for their potential using WAY2DRUG PASS Online prediction on the website (http://www.pharmaexpert.ru/passonline/predict.php) as a treatment for obesity. WAY2DRUG Pass Prediction employs SAR analysis to compare the input compounds, specifically those found in ant nests, with compounds known to have specific potential. The prediction value increases as the structural similarity between the compounds rises, indicating a higher likelihood of similar potential. The Pa value (Probability to be Active) is the output prediction value from WAY2DRUG PASS, reflecting the potential of the tested compound. A Pa value exceeding 0.7 suggests a high potential for the compound, such as in the case of anti-inflammatory properties, due to its structural similarity to compounds in the database. We recommend using a cutoff score of 0.5. The Pa value signifies the accuracy of the obtained prediction function; the higher the Pa value, the better the accuracy of the function.16\n\nMalus sylvestris peels were sourced from Koperasi Bhakti Materia Medica, Batu, East Java, Indonesia. It was subjected to a drying process in an oven set at 50°C for 24 hours, and subsequently ground to yield a powder with a particle size of 1777μm. Malus sylvestris peel powder was prepared 10 gr. All substances and materials utilized for extraction and analysis were of analytical grade and procured from Merck, Germany. These included a quercetin standard (Q4951 Sigma-Aldrich) as 1 gr, 50% methanol (019200WT Merck Label Set TR420) as 100 ml, and Whatman No. 4 (WHA2017013) filter paper.\n\nMalus sylvestris extraction was conducted using the MAE method17 with a slight modification, employing a Sharp Model R -222Y(S) microwave at a medium (50°C). The Malus sylvestris powder was mixed with 50% methanol at a ratio of 5 grams of powder to 100 milliliters of methanol and allowed to soak for 24 hours. Subsequently, the solution underwent extraction in a microwave oven for intervals of 3 (T1), 6 (T2), 9 (T3), or 12 (T4) minutes, with a cycle of one minute on and two minutes off to prevent overheating. The resulting crude extract was filtered through Whatman no. 4 filter paper, and ethanol was removed using a rotary evaporator at a pressure of 55 mm Hg and a temperature of 50°C. The filtrate was further concentrated with a rotary evaporator (IKA RV 10) to eliminate the solvent. Finally, the concentrated filtrate was analyzed according to the method described below.\n\nThe assessment of Total Phenolic Content (TPC) was conducted using the Folin-Ciocalteu reagent method, following the procedure outlined.18 A solution of saturated sodium carbonate was prepared and allowed to sit for 24 hours. Standard concentrations of gallic acid, varying from 25 to 200 ppm, were freshly prepared at room temperature for each analysis. A solution consisting of 0.5 mL of 1:10 diluted gallic acid in 4.5 mL of distilled water, 0.2 mL of Folin reagent (Merck), and 0.5 mL of saturated sodium carbonate was created and employed to construct a standard sample analysis curve. The AT-1900 UV spectrophotometer was used to measure the absorbance of each sample at a wavelength of 725 nm. The TPC was calculated using the absorbance values and a linear regression equation, allowing for comparison with the gallic acid standard. The results were expressed as milligrams of gallic acid equivalents (GAE) per gram of dry sample weight (mg/g).\n\nFollowing the procedure outlined,19 the method involves preparing and dissolving the sample in a suitable solvent like methanol or ethanol until the desired testing concentration is attained. Next, transfer the sample solution into a test tube or beaker. Add the AlCl3/Potassium acetate reagent solution to the test tube or beaker containing the sample, and gently stir. Allow the mixture to undergo a reaction in darkness for approximately 30 minutes, enabling interaction with the flavonoids. Subsequently, centrifuge the mixture to separate the sediment. Utilize a spectrophotometer to measure the absorbance of the solution at the designated wavelength, typically around 415 nm. Either employ a calibration curve (if utilizing a standard solution) or establish a correlation between the sample’s absorbance and the total flavonoid concentration.\n\nThe quercetin testing procedure using HPLC,20 with modifications. Making a standard quercetin solution begins by weighing 10 mg of standard quercetin, placing it in a 10 mL measuring flask, and adding ethanol to the mark. Create a standard series with concentrations 5; 10; 25; 50; 75 and 100 μg/mL.\n\nAnalysis of quercetin in samples begins by taking and filtering the sample with a 0.45 μm filter syringe. Inject 10 μL of sample into HPLC, including the quercetin comparator. Sample analysis for 20 minutes at a wavelength of 370 nm. HPLC conditions (Mobile phase A = 0.5% Phosphoric Acid, Mobile phase B = Methanol, System = Isocratic (Mobile phase A: mobile phase B = 60:40), Detector = VWD, Column = Xbridge C18 5μm (4.6 × 250 mm) and Flow rate = 1 mL/min. Create a standard quercetin regression curve and analyze Quercetin levels using the formula:\n\nThe evaluation of antioxidant activity through the DPPH method follows the protocol established by Molyneux,21 with slight adjustments. Begin by taking the Malus sylvestris extract and dissolving it in a suitable solvent to achieve the desired testing concentration. Dissolve DPPH in methanol solvent to reach the appropriate concentration. Combine the extract solution with the DPPH solution in a test tube or beaker and thoroughly stir the mixture. Allow it to undergo a reaction in darkness for about 30 minutes or until the reaction is complete. Employ a spectrophotometer to measure the absorbance of the solution at the specified wavelength, typically around 517 nm. Subsequently, compute the percentage of antioxidant inhibition.\n\nThe chemical composition was determined following the method,22 with slight modifications. The UV-Vis spectrum was captured using a GBS UV/VIS 920 instrument. A one-milligram portion of the Malus sylvestris extract underwent dehydration in a vacuum desiccator. Subsequently, it was finely ground and thoroughly mixed with 200 mg of KBr powder, oven-dried, and met analytical reagent grade standards (Merck, DAC, USP). This powdered blend was placed into a die and compressed into a transparent disk.\n\n\nResults\n\nBased on a literature review, several bioactives were identified in apple peel. These bioactives are as follows (see Table 1).\n\nThis research by in silico analysis. We found that several bioactive apple peels were identified such as chlorogenic acid, epicatechin, phloridzin, catechin, hyperoside, quercitrin, quercetin, and pectin. We refer to the.23–25 The bioactive compound was chosen because having a functional effect higher than others by predicting the potential of Ant Nests using the Structural Activity Relationship (SAR) Approach with Pass Online. Bioactive compounds have different abilities in functional activity.\n\nTable 1 shows the characteristics of the bioactive compound with the molecular weight (MW) and the chemical structure. It was useful for future research to examine more specific interactions between these components and other compounds, for example, used for functional food purposes in the future.\n\nThe research in this section aimed to examine more deeply the use of apple peel in the future if it is used in the functional food sector. Which direction can be taken based on its greatest potential? Figure 1 explains the Pa value (Probability to be Active) of the bioactive components of apple peel on functional properties which include anti-inflammatory, lipid metabolism regulator, free radical scavenger, lipid peroxidase inhibitor, antihypercholesterolemic, and insulin promoter. Apart from that, from Figure 1 you can see the similar functional properties of several components. A Pa value (Probability to be Active) of 0.5 and above is a value high enough to be used as a reference. Furthermore, Figure 2 shows the score relative prediction, the higher the value obtained, means that the bioactive ability is. Figure 3 explains that of all bioactive components, the role of a free radical scanner is higher with a value of 0.754.\n\nAntioxidant activity of apple peel extract\n\nAntioxidant activity testing was carried out on apple peel extraction using a combination of maceration and MAE methods with treatment several times (3, 6, 9, and 12 minutes). The results of the antioxidant activity test of apple peel extract using the combination method of maceration and MAE with different treatment times provided a significant difference (P<0.05). The results of antioxidant activity using the DPPH method shown in % inhibition can be seen in Table 2.\n\nPhenolic content of apple peel extract\n\nPhenolic content testing was carried out on apple peel extraction using a combination of maceration and MAE methods with several treatments (3, 6, 9, and 12 minutes). The results of total phenolics can be seen in Table 3. The results of the Phenolic content of apple peel extract using the combination method of maceration and MAE with different treatment times gave a significant difference (P<0.05).\n\nFlavonoid content of apple peel extract\n\nFlavonoid content testing was carried out on apple peel extraction using a combination of maceration and MAE methods with treatment several times (3, 6, 9, and 12 minutes). The results of flavonoid content can be seen in Table 4. The results of the apple peel extract using the combination method of maceration and MAE with different treatment times gave a highly significant difference (P<0.01) in Flavonoid content.\n\nFor an explanation of the various symbols, see Table 5.\n\n\nDiscussion\n\nTable 1 serves as the primary reference for the dominant bioactive compounds present in apple peel, intended for further exploration of their potential health benefits. Focusing on eight key bioactive compounds, including Chlorogenic acid, Epicatechin, Phloridzin, Catechin, Hyperoside, Quercitrin, Quercetin, and Pectin, a detailed analysis is conducted to understand their potential positive impact on health.\n\nBased on SAR analysis, it has been identified that bioactives present in apple peel exhibit the highest potential as Free Radical Scavengers (0.754). Additionally, these bioactives show potential as Lipid Peroxidase Inhibitors (0.671), Antihypercholesterolemics (0.577), and Lipid Metabolism Regulators (0.468) (see Figure 2). Hyperoside and quercitrin emerge as two bioactives with the highest potential (see Figure 1). Free Radical Scavengers play a crucial role in preventing the formation of reactive oxygen species, thereby eliminating reactive oxygen before it can damage cells. If free radicals surpass the body’s capacity, it can lead to oxidative stress, altering the body’s physiological conditions and potentially causing various diseases. Maintaining a proper balance between free radicals and antioxidants (radical scavengers) is essential for optimal physiological function.5 Lipid peroxidation involves a chain reaction of oxidative degradation of lipids. This process occurs when free radicals “steal” electrons from lipids in cell membranes, leading to cellular damage. The mechanism of this process unfolds through a chain reaction of free radical reactions.2\n\nThe percentage of antioxidants from the research ranged from 93.85% to 95.09% (Table 2). In this study, antioxidant activity testing was conducted against the free radical 1,1-Diphenyl-2-Picrylhydrazyl (DPPH) from the apple peel extract. The antioxidant activity of the fruit extract was expressed as % inhibition against the DPPH radical. % inhibition was obtained from the difference between the absorbance of the DPPH control and the measured sample using a UV-Vis Spectrophotometer. The research results indicated that the antioxidant activity of the apple peel extract increased with the extraction time. This could be explained by the increase in the amount of antioxidant compounds extracted from the apple peel over time.\n\nThe study by Ref. 14 showed antioxidant activity (DPPH inhibition) in avocado seeds using the MAE method with 40% ethanol for 5 minutes, resulting in the highest value of 80.32%, and the lowest was 22.93% for 40% ethanol with 1 minute. Reported on the antioxidant activity.27 The analysis of variance results showed that the type of solvent significantly influenced (P<0.01) the antioxidant activity of lemon peel extract. The highest antioxidant activity was obtained in 70% ethanol solvent, which was 52.72%, while the lowest antioxidant activity was obtained in aquadest solvent, which was 25.35%. Lemon peel extract using ethanol solvent had the highest antioxidant activity, which was 52.64%. Antioxidant activity could be influenced by the amount of flavonoid compounds present in lemon peel extract; the more flavonoid compounds, the higher the antioxidant activity.\n\nIn the reference, the research showed that the highest average antioxidant activity was found in the treatment of 40°C temperature for 20 minutes, which was 89.66%, and the lowest average antioxidant activity was obtained in the treatment of 30°C temperature for 10 minutes, which was 79.75% for wuluh starfruit leaf extract with the Ultrasonic-Assisted Extraction (UAE) method.28\n\nBased on the obtained references, there was still limited information regarding apple peel extract as an antioxidant source. It could be inferred from several consulted references that the treatment duration of 12 minutes of radiation in this study resulted in the highest antioxidant value, with a recorded percentage of 95.09%.\n\nBased on the analysis results, it shows that apple peel by-product extract with extraction time treatment of 3 minutes, 6 minutes, 9 minutes, and 12 minutes provides total phenols of 13.52-14.73 mg GAE/g sample. Research has been carried out to determine the comparison of extraction time using MAE with different radiation times on antioxidant activity, total phenol, and flavonoid levels of qpple peel. The DPPH free radical scavenging activity test was carried out using visible spectrophotometry (λ = 520 nm). Determination of total phenol content was carried out using the Folin Ciocalteu method using visible spectrophotometry (λ = 706 nm) with gallic acid as a comparison. Determination of total flavonoid levels was carried out with the help of AlCl3 using visible spectrophotometry (λ = 503 nm) with catechin as a comparison. From the research results, the EC50 value, total phenol, and flavonoid content of 5 minutes MAE were respectively 508.32 bpj, 1.14% w/w GAE (Gallic Acid Equivalent) and 1.53% w/w CE (Cathecin Equivalent). Meanwhile, the 20-minute MAE was obtained at 474.11 bpj, 1.72% w/w GAE, and 1.94% w/w CE. The results of the t-test statistical calculation (α = 0.05) on the EC50 value, total phenol, and flavonoid levels showed a significant difference between 3 minutes of radiation and 12 minutes. From the results of this study, it was concluded that 12 minutes of radiation was better than 3 minutes.\n\nBased on the analysis results, it shows that apple peel by-product extract with extraction time treatment of 3 minutes, 6 minutes, 9 minutes, and 12 minutes provides total flavonoids of 23.76-29.62 ppm using a combination of maceration and MAE extraction methods. Supported by the previous literature that 50% methanol with the sonication extraction technique method produces a TFC of 22.05 which is higher than 75% methanol with a TFC of 12.15.9\n\nThe type of solvent treatment had a very significant effect (P<0.01) on the total flavonoids of lemon peel extract.27 The highest total flavonoids were obtained using 70% ethanol solvent, namely 7.14 mg QE/g extract, and the lowest total flavonoids were obtained using distilled water, namely 4.34 mg QE/g extract. The total flavonoids in lemon peel extract using ethanol solvent show that the ethanol solvent has a similar polarity level and is more effective in dissolving flavonoid compounds in lemon peel, so lemon peel extract using ethanol solvent produces the highest flavonoid compounds. Then extracted for 60 minutes using an ultrasonic bath at a frequency of 47 kHz.\n\nResearch has been carried out to determine the comparison of extraction time using microwave assistance (microwave-assisted extraction = MAE) for 5 and 20 minutes on antioxidant activity, total phenol, and flavonoid levels of spoon leaves (Plantago major L.). The DPPH free radical scavenging activity test was carried out using visible spectrophotometry (λ = 520 nm). Determination of total phenol content was carried out using the Folin Ciocalteu method using visible spectrophotometry (λ = 706 nm) with gallic acid as a comparison. Determination of total flavonoid levels was carried out with the help of AlCl3 using visible spectrophotometry (λ = 503 nm) with catechin as a comparison. From the research results, the EC50 value, total phenol, and flavonoid content of 5 minutes MAE were respectively 508.32 bpj, 1.14% w/w GAE (Gallic Acid Equivalent) and 1.53% w/w CE (Cathecin Equivalent). Meanwhile, the 20-minute MAE was obtained at 474.11 bpj, 1.72% w/w GAE and 1.94% w/w CE. The results of the t-test statistical calculation (α = 0.05) on the EC50 value, total phenol, and flavonoid levels showed a significant difference between MAE 5 and 20 minutes. From the results of this study, it was concluded that a 20-minute MAE was better than a 5-minute MAE.\n\nThe purpose of analyzing FTIR was to examine the functional groups in Malus sylvestris peel extract to ascertain the chemical composition and concentration of active compounds within it. Quercetin, the active compound responsible for the plant’s pharmacological effects, could be identified through FTIR analysis, revealing functional groups such as Phenolic groups (OH), Carbonyl Groups (C=O), Aromatic C-H Groups, C-O Groups, and Aromatic C=C Groups, even in the presence of quercetin. Consequently, this assessment of functional groups in Malus sylvestris extract via FTIR served to furnish insights into the extract’s quality and purity.\n\nFigure 4 and Table 5 exhibited peaks within the IR spectra ranging from 1050-1300 cm−1, indicating the presence of C-O groups in alcohols, esters, and carboxylic acids, as well as C-N stretching in aliphatic amines. Peaks at 2500-2700 cm−1 signified O-H groups in carboxylic acids with hydrogen bonds. The peaks at 2850-2970 and 1340-1470 cm−1 indicated the presence of C-H bonds in alkanes. Additionally, peaks at 3200-3600 cm−1 pointed towards O-H groups associated with phenols and hydrogen bonds. The peak at 3749.62 cm−1 demonstrated the presence of a phenolic compound.29 Notably, one of the pivotal groups signifying the presence of quercetin was situated at the 3200-3600 cm−1 range, indicating a hydroxyl group engaged in hydrogen bonding. At T4, the spectral shift observed at 1390.68 cm−1, representing C-O stretching vibrations in quercetin,30 who asserted that the 1360 cm−1 peak refers to C-O groups. This shift towards lower wavenumbers (1296 cm−1) after incorporation into membranes supported the idea of the involvement of polar groups, such as hydroxyl groups, of the flavonoid in binding water in the membrane environment.\n\nThe IR spectra of Malus sylvestris peel extract obtained through MAE exhibited distinct profiles with varying radiation times. Specifically, the spectra at 3200-3600 cm−1, from T1 to T4, played a crucial role in indicating the presence of bioactive compounds, notably quercetin. Among these, T4 revealed a greater abundance of spectra associated with bioactive compounds in the Malus sylvestris peel extract compared to the other treatments. This discrepancy was attributed to the influence of different radiation times during the extraction process on the extraction of bioactive compounds. This aligned with the findings,31 who proposed that microwave energy prompts molecular motion via ion migration and dipole rotation. This rapid movement generates friction, leading to the production of heat energy within the material. Consequently, the cell walls and tissue of the material experienced damage, facilitating the extraction of active compounds.\n\nQuercetin is a type of flavonoid found in various types of food, including fruits and vegetables. Flavonoids are natural compounds that have antioxidant and anti-inflammatory properties and are known to have various health benefits. Quercetin testing was carried out in the reference, mentioned apples contain quite high levels of quercetin at 340.99 mg/L.32 Based on this, it is expected that apple skin also contains quite high levels of quercetin.\n\nHowever, based on the analysis of the quercetin results in Figure 5 using HPLC, no quercetin value was obtained with a detection limit of 0.44 μg/L. The Retention Time (RT) value for quercetin was 6.5 (min) while in treatments T1, T2, T3, and T4 no spectra were found at RT. This is thought to be because the extract contains quercetin below the detection limit. Coupled with the spectrum results, other bioactive components are suspected to appear in apple peel extract with radiation treatment during extraction. The RT that appears cannot be detected in the HPLC database so other analyses are needed, one of which is Gas Chromatography-Mass Spectrometry (GCMS) to determine other compounds in the extract.\n\n\nConclusion\n\nRadiation times of the MAE method had a significant effect on phenolic content, flavonoid content, andrographolide content, and antioxidant activity of apple peel extract. Radiation time for 12 minutes of MAE gave higher phenolic, flavonoid, and antioxidant activity of AP. The IR spectra of the apple peel extract increased as the radiation time increased and had the characteristic on Phenols, hydrogen bound 33465.5 cm−1.\n\n\nDisclaimer\n\nNone.", "appendix": "Data availability statement\n\nPubChem: The quercetin data obtained from this study are available in PubChem CID 5280343, https://pubchem.ncbi.nlm.nih.gov/compound/5280343.\n\nExtended data: none.\n\n\nAcknowledgment\n\nThis research project was supported by a grant (Hibah DRTPM Kemdikbudristek 2023, Indonesia, Schema Fundamental – Reguler, Grant code: 013/C2/I.3/DPPM-UK/VI.2023.\n\n\nReferences\n\nKaraman Ş, et al.: Comparison of antioxidant capacity and phenolic composition of peel and flesh of some apple varieties. J. Sci. Food Agric. 2013; 93(4): 867–875. PubMed Abstract \| Publisher Full Text\n\nHussain T, et al.: Identification of nutritional composition and antioxidant activities of fruit peels as a potential source of nutraceuticals. Front. Nutr. 2023; 9: 1065698. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWolfe K, et al.: Antioxidant activity of apple peels. J. Agric. Food Chem. 2003; 51(3): 609–614. Publisher Full Text\n\nAfsharnezhad M, et al.: Evaluation of the antioxidant activity of extracts from some fruit peels. Caspian J. Environ. Sci. 2017; 15(3): 213–222.\n\nHuber GM, et al.: Phenolic profiles and antioxidant properties of apple skin extracts. J. Food Sci. 2009; 74(9): C693–C700. PubMed Abstract \| Publisher Full Text\n\nAsma U, et al.: Apples and Apple By-Products: Antioxidant Properties and Food Applications. Plan. Theory. 2023; 9(11): 1408.\n\nDrogoudi PD, et al.: Peel and flesh antioxidant content and harvest quality characteristics of seven apple cultivars. Sci. Hortic. 2008; 115(2): 149–153. Publisher Full Text\n\nRupasinghe HV, et al.: Ultrasonication-assisted solvent extraction of quercetin glycosides from ‘Idared’apple peels. Molecules. 2011; 16(12): 9783–9791. 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PubMed Abstract \| Publisher Full Text\n\nSuleria HA, et al.: Screening and characterization of phenolic compounds and their antioxidant capacity in different fruit peels. Food Secur. 2020; 9(9): 1206. Publisher Full Text\n\nWeremfo A, et al.: Simultaneous optimization of microwave-assisted extraction of phenolic compounds and antioxidant activity of avocado (Persea americana Mill.) seeds using response surface methodology. J. Anal. Methods Chem. 2020; 2020: 1–11. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDhanani T, et al.: Effect of extraction methods on yield, phytochemical constituents and antioxidant activity of Withania somnifera. Arab. J. Chem. 2017; 10: S1193–S1199. Publisher Full Text\n\nFilimonov DA, et al.: Prediction of the biological activity spectra of organic compounds using the pass online web resource. Chem. Heterocycl. Compd. 2014; 50: 444–457. Publisher Full Text\n\nRahayu PP, et al.: Characteristics of catechin extracted from cocoa husks using microwave-assisted extraction (MAE). Biodiversitas. 2019; 20: 3626–3631.\n\nMaung PP, et al.: Comparison of Polyphenol Content Between Laboratory ProcessedLaphet and China and Myanmar Tea (Camellia sinensis) Products. J. Food Sci. Pakistan. 2012; 22: 180–184.\n\nAsadi-Samani M, et al.: A comprehensive review on phytochemical and pharmacological aspects of Echinophora species. Pharmacogn. Rev. 2016; 10(20): 62–72.\n\nZhang ZJ, Liu QR: Application of high-performance liquid chromatography for the determination of quercetin in rat plasma after oral administration of Hypericum perforatum extract. J. Chromatogr. B. 2007; 860(2): 189–194.\n\nMolyneux P: The use of the stable free radical diphenylpicrylhydrazyl (DPPH) for estimating antioxidant activity. Songklanakarin J. Sci. Technol. 2004; 26(2): 211–219.\n\nMaoela MS, et al.: Electroanalytical Determination of Catechin Flavonoid in Ethyl Acetate Extracts of Medicinal Plants. J. Electrochem. 2009; 4: 1497–1510.\n\nMihailović NR, et al.: Analysis of phenolics in the peel and pulp of wild apples (Malus sylvestris (L.) Mill.). J. Food Compos. Anal. 2018; 67: 1–9. Publisher Full Text\n\nVirk BS, Sogi DS: Extraction and characterization of pectin from apple (Malus Pumila. Cv Amri) peel waste. Int. J. Food Prop. 2004; 7(3): 693–703. Publisher Full Text\n\nIchwan M, et al.: Apple peel and flesh contain pro-neurogenic compounds. Stem cell reports. 2021; 16(3): 548–565. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCarrillo-Martinez EJ, et al.: Quercetin, a Flavonoid with Great Pharmacological Capacity. Molecules. 2024; 29(5): 1000. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nVerdiana M, et al.: Pengaruh jenis pelarut pada ekstraksi menggunakan gelombang ultrasonik terhadap aktivitas antioksidan ekstrak kulit buah lemon (Citrus limon (Linn.) Burm F.). Jurnal Ilmu dan Teknologi Pangan. 2018; 7(4): 213–222. Publisher Full Text\n\nAndriani M, et al.: Pengaruh Suhu dan Waktu Ekstraksi Daun Belimbing Wuluh (Averrhoa bilimbi L.) Terhadap Aktivitas Antioksidan dengan Metode Ultrasonic-Assisted Extraction (UAE). Jurnal Ilmu dan Teknologi Pangan. 2019; 8(3): 86–340. Publisher Full Text\n\nBuljeta I, et al.: Application of Citrus and Apple Fibers for Formulation of Quercetin/Fiber Aggregates: Impact of Quercetin Concentration. Plants. 2022; 11(24): 3582. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPawlikowska-Pawlęga B, et al.: Characteristics of quercetin interactions with liposomal and vacuolar membranes. Biochimica et Biophysica Acta (BBA) – Biomembranes. 2014; 1838(1): 254–265. PubMed Abstract \| Publisher Full Text\n\nDelazar AN, et al.: Microwave-Assisted Extraction in Natural Products Isolation, Methods in Molecular Biology. New York: Springer Science; 2012; Vol. 864. . Publisher Full Text\n\nCempaka AR, et al.: Pengaruh Metode Pengolahan (Juicing Dan Blending) Terhadap Kandungan Quercetin Berbagai Varietas Apel Lokal Dan Impor (Malus domestica). Indones. J. Hum. Nutr. 2014; 1(1): 14–22." }	[ { "id": "307942", "date": "21 Aug 2024", "name": "Ardiba Sefrienda", "expertise": [ "Reviewer Expertise food chemistry", "food technology" ], "suggestion": "Approved", "report": "Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThere is no section for statistical analysis method, better to explain it. The research flow is relatively structured. Through the in silico approach, in vitro testing is more targeted. But, the potential of apple peel through SAR approach indicate that quercitrin and hyperoside the most potential component. Why not quantify it using HPLC?\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] } ]	1	https://f1000research.com/articles/13-653
https://f1000research.com/articles/13-651/v1	18 Jun 24	{ "type": "Research Article", "title": "Public perception of wireless power transfer safety", "authors": [ "Sirui You" ], "abstract": "Background Wireless Power Transfer (WPT) technology has changed how energy is distributed, allowing power to be transmitted without using wires. Despite being used in devices like cell phones, electric cars, and medical devices; people are worried about the safety and health effects of wireless power transfer.\n\nMethods Here this concern research work has used a survey method to gather information from a diverse group of people, focusing on various demographic factors and educational aspects. The research has analysed the knowledge of people regarding the application of wireless power transfer (WPT) technology. Further it has accumulated the safety aspects of using it in public or private places. However, the concerns of propel perspectives basing on their age, gender or other factors about safety of WPT is inducted within this survey.\n\nResults the finding from the survey within this research has demonstrated that many people are not much aware of WPT technologies, and some are worried about safety aspects of this concern technology within public places. From this result it has been seen that groups considering the age, education and gender has different perspective regarding the application and safety of WPT. The results have shown that people need to be taught more about it and to be made more aware of it. In addition, survey has showed that about 38% of respondent has some concerns about WPT technologies, which means that a significant number of people know about it.\n\nConclusions From this analysis it has been interpreted that it is important to talk about safety worries and false facts about WPT. This concern paper has the potential to develop awareness about this technology. However, it is expected that future studies should look at more types of people and explore their personal experiences to figure out why people have different opinions about WPT.", "keywords": [ "Wireless power transfer technology", "Safety", "Anova", "Online survey" ], "content": "1. Introduction\n\nEnergy distribution has undergone a paradigm shift because of Wireless electricity Transfer (WPT), which provides a way to distribute electricity without a physical connection. WPT enables energy transfer between two objects by relying on electromagnetic fields, specifically the electromagnetic resonance or inductive coupling principle (Park & Ahn, 2020). Energy transmission is more effective when the distance between the transmitter and receiver coils is less. WPT use has increased significantly during the past few years. Many people are familiar with its use in consumer electronics, where it is used to wirelessly charge smartphones and wearables (Barreto et al., 2021). Devices that have a coil incorporated in them can be charged using pads instead of conventional wires. But its effects go far beyond simply individual gadgets. Electric vehicles (EVs) have risen to the forefront of transportation debates as the globe continues to move towards more sustainable alternatives. WPT offers a promising future in this industry, providing a viable answer for charging techniques that are both more effective and user-friendly (Triviño et al., 2021). WPT safety is being investigated more thoroughly as worries regarding potential health effects and interaction with other electronic devices have surfaced due to the invisibility of energy transmission.\n\nEnergy transmission techniques have been revolutionised by Wireless Power Transfer (WPT), which has quickly established itself across numerous industries. However, because of its widespread use, several possible health and safety concerns have also surfaced (Lin, 2013). Despite being novel, the invisible nature of energy transfer has raised questions regarding its long-term health effects, potential for interference with medical equipment, and dangers in both residential and business settings. It is also critical to comprehend how the general public views WPT safety. This impression, whether supported by reality or misinformation, has a big impact on adoption rates, regulatory choices, and the future course of research. In addition to facilitating the seamless integration of WPT, addressing public concerns will ensure that technological improvements are in line with societal comfort and welfare.\n\nThe main goal of this study is to examine how the general public feels about Wireless Power Transfer (WPT) technology. The study specifically aims to;\n\n• Determine the extent to which WPT technologies and their many applications are known and understood by the general public.\n\n• Differentiate and list the public safety concerns, contrasting them with worries about WPT in public spaces and personal devices.\n\n• Identify and examine the demographic elements, such as age and educational attainment, which significantly affect how the general public views WPT safety.\n\n\n\n• RQ1: How aware is the public of WPT technologies and their applications?\n\n• RQ2: What are the public safety concerns regarding WPT in public spaces versus personal devices?\n\n• RQ3: Which demographic factors (e.g., age, education) influence perceptions of WPT safety?\n\n\n\n• H1: More than half of the respondents are unfamiliar with WPT technologies.\n\n• H0: More than half of the respondents are familiar with WPT technologies.\n\n• H2: Respondents express greater safety concerns for WPT in public places than for personal devices.\n\n• H0: Respondents express fewer safety concerns for WPT in public places than for personal devices.\n\n• H3: Older respondents and those with less formal education are more likely to express safety concerns about WPT.\n\n• H0: Older respondents and those with less formal education are less likely to express safety concerns about WPT.\n\nIn the rapidly changing field of Wireless Power Transfer (WPT) technology, this research is of utmost significance. Understanding public opinion is essential as WPT becomes more interwoven into daily life. The study will conclude the breadth of public awareness, identify common safety problems, and provide manufacturers and policymakers with new information. To ensure informed public participation, focused educational and awareness initiatives can be created by analysing the demographic elements impacting opinions. The findings will also help technology creators address concerns and innovate with user-centric safety in mind. In the end, this research aids in the peaceful and secure integration of WPT into society.\n\n\n2. Literature review\n\nIn-depth research on Wireless Power Transfer (WPT) technology is done in the literature review, which also looks at how people feel about it and how it has evolved. This section examines previous research to identify trends, insights, and knowledge gaps that can help to better comprehend how the public feels about the safety of WPT and its wider ramifications.\n\nThere is a long revolution of power transfer techniques in the tech world. The origins of Wireless Power Transfer (WPT) have its roots in the ground-breaking research of Nikola Tesla from the late 19th and early 20th centuries (Shinohara, 2021). Experiments of Tesla, especially those conducted in Colorado Springs, laid the groundwork for the idea of transporting electricity without the use of physical connectors.\n\nAs per Figure 1 it can be seen that due to technological and financial limitations, however, widespread applications remained primarily theoretical for decades despite his ground-breaking work. With developments in semiconductor technologies in the late 20th century, interest in WPT started to pick up again (Hui et al., 2023). These breakthroughs made it possible for WPT to be used in more effective and useful ways. Resonant inductive coupling was developed in the twenty-first century, allowing for more effective transmission of power across short distances. This development helped WPT move from experimental prototypes to practical applications (Athira et al., 2022). WPT is currently used to charge a variety of items, including medical equipment, electric vehicles, and personal electronics. However, even though technical development is well-documented, a critical study of the literature reveals that there may have been a potential overlook regarding public perception during this time. It is possible that the quick developments in technology were not matched by equal attempts to raise public awareness and provide education (Lukovics et al., 2019). It is possible that the end users will not understand the safety processes and standards, which were designed after a thorough investigation.\n\n(Source: Laha et al., 2023).\n\nGiven the widespread use of Wireless Power Transfer (WPT) technology across numerous industries, questions about its safety requirements are only logical. In response, several nations and international organisations have created policies and rules to guarantee the security of WPT systems for both users and the environment. According to Kalialakis et al. (2016), the Institute of Electrical and Electronics Engineers (IEEE) has been at the forefront of this field. This paper delve into the power and frequency as technical part and safety of health regarding radiation. Thus Kalialakis et al. (2016) depicts a comprehensive view of framework of regulation and current global aspects. The safety, interoperability, and performance facets of WPT are specifically covered by several standards that the IEEE Standards Association has created. These recommendations concentrate on a variety of topics, from the minimal safety of WPT devices for various frequencies to the maximum permissible electromagnetic exposure. The main goal of the IEEE has been to make sure that the electromagnetic fields of WPT devices stay within safe ranges to avoid any potential health hazards (Alrashdan et al., 2021). Examining the IEEE standards critically reveals a methodical, scientifically supported methodology.\n\nOne can counter that these norms are more reactive than proactive. Instead of anticipating and directing technological changes, they frequently seem to react to them. This guarantees that the safety standards are founded on the most recent scientific knowledge. However, it may cause a lag in which new WPT technologies are introduced to the market more quickly than safety rules can be created (Lin, 2021). The regulation of WPT technologies on a global level exhibits a patchwork of various strategies. The electromagnetic compatibility of WPT devices, for instance, is addressed in directives that the European Union has put into effect (European Commission, 2023). This has the effect of making them resistant to disruptions and ensuring that they do not interfere with other electrical devices. Similar to this, Japan has developed its own set of regulations, largely due to its active promotion of electric vehicles, which heavily utilise WPT (Shinohara, 2020). The Federal Communications Commission (FCC) has taken an active role in setting acceptable exposure limits for electromagnetic fields coming from WPT devices in the United States (FCC, 2023). Every nation is looking for a set of safe parameters for this wireless power delivery. While this is going on, nations like South Korea have been pushing the edge by establishing entire zones with WPT for public transit, which has forced the development of strict, practical safety requirements (Triviño et al., 2021). Despite these coordinated efforts, a close analysis reveals differences in how various nations view and govern WPT safety. These variations can be due to varying rates of technological adoption, various public perceptions, and various governmental viewpoints on risk management. This hodgepodge of rules can make it difficult for firms with international operations to standardise products and ensure widespread compliance.\n\nThe possible knowledge gap between these safety standards and the comprehension of them is also a major cause for concern. The average consumer might not be aware of the stringent safety procedures in place, even though regulatory organisations and the industry probably are (Beeby et al., 2023). If this gap is not addressed, it may feed misunderstandings and unwarranted worries, impeding technological adoption.\n\nTo comprehend the interaction between technological development and cultural acceptance, it is essential to investigate how the general public feels about developing technologies, especially those focused on Wireless Power Transfer (WPT). A thorough analysis of the literature in existence demonstrates a dynamic spectrum of public reactions, frequently mediated by a complex web of elements ranging from technological comprehension to more general cultural attitudes and narratives (von Terzi et al., 2021). Many emergent technologies have historically been adopted with a mixture of awe, scepticism, and concern, from X-ray machines to mobile phones. There is a tendency for the earliest stages of any technological introduction to be characterised by increased worries about potential negative impacts, which frequently result from misunderstandings or misinterpretations. Studies on the early use of microwave ovens, for instance, revealed a considerable level of public anxiety owing to radiation fears, even though the dangers were minuscule (Zhi et al., 2017). This phenomenon is similar to the current state of WPT, where many people are still concerned about electromagnetic broadcasts even when they are below dangerous thresholds.\n\nFocusing on research that deals directly with WPT reveals a common theme: a tension between concerns about its safety ramifications and recognition of the convenience and innovation WPT brings (Lin, 2021). These worries are frequently amplified by technological invisibility, which allows power to be conveyed without the use of any physical channel. Additionally, some people may associate the word “wireless” with cell phone or internet transmissions, which further complicates understanding.\n\nIn Figure 2 it has been seen that critical perception identifies two key difficulties. First off, knowledge gaps and increased safety concerns frequently go hand in hand (Rasmussen et al., 2018). Populations with less knowledge of the science underpinning WPT frequently show more anxiety. Second, there may be a subconscious uneasiness rooted in deeply ingrained evolutionary aversions to unknown or unseen forces, even in situations where there is a conscious awareness of technology-related safety. Additionally, some research has used the “psychometric paradigm” technique to assess public perception, breaking down emotions regarding WPT into components including dread, unknown hazards, and advantages (Alrawad et al., 2022). These results demonstrate that although the ease and efficiency of WPT are easily acknowledged, the worries related to the perceived unknown hazards are frequently not completely allayed. The spread of incidents or bad press is another interesting finding. For instance, each solitary incident, even if it is not directly connected to WPT safety (such as a device breakdown or a well-publicised health problem), is likely to magnify public concerns and emphasise how flimsy the public trust in new technologies is (Zhang et al., 2022). In conclusion, earlier research on public perception highlights the variety of public responses to WPT and other developing technologies in general.\n\n(Source: Hui et al., 2023).\n\nThere is a glaring gap in the understanding of the complex perceptions unique to WPT safety, even though there is a wealth of literature describing the technical elements of Wireless Power Transfer (WPT) and a rising corpus of work on general public perceptions of developing technologies. Numerous studies have either covered other aspects of WPT without going into safety perceptions or they have covered other aspects of technology adoption widely. Additionally, little is known about how demographic factors like age and education interact with one another to affect how people perceive safety. Closing this gap is essential since it can inform future technological advancements in the field of WPT as well as communication tactics.\n\nUnderstanding public perception is essential, given the rapid growth of Wireless Power Transfer (WPT) technology. The uncovered research gap emphasises the necessity of detailed investigations concentrating on safety perceptions. To build confidence, ensure widespread adoption, and direct the future course of WPT innovations, this gap must be closed.\n\n\n3. Methods\n\nA survey-based technique has been used to negotiate the complex environment of public perception regarding Wireless Power Transfer (WPT) safety. This methodology is recognised for its capacity to compile quantitative data on a massive scale, ensuring a comprehensive representation of the viewpoints of the public (Ponto, 2015). Surveys are especially suitable for this study since they help identify trends, correlations, and patterns by transforming subjective judgements into quantifiable measurements. Alternative research methods, including focus groups or interviews, might be taken into account. Although they offer extensive qualitative insights, their reach is necessarily constrained, which frequently results in a smaller sample size (Mwita, 2022). The depth offered by interviews in the context of the study, which aims to provide a comprehensive picture of public perception, can be at the expense of the breadth required for this research.\n\nA representative sample that includes a range of perspectives is required to understand how the general public feels about the safety of Wireless Power Transfer (WPT). The target audience for this study is the general public, which represents a wide range of experiences and ideologies. Choosing a sample size of 50 responders may seem little, but it guarantees thorough analysis and efficient administration of the data gathered. For a subject as specialised as WPT safety, a larger sample could complicate data administration and may not necessarily yield materially different conclusions. Given the complex nature of public perception, the use of stratified random selection is especially appropriate (Iliyasu & Etikan, 2021). The sample is not biased towards any particular group, thanks to stratification based on age, education, and tech knowledge.\n\nGiven its simplicity, convenience sampling might be justified, but it frequently sacrifices representativeness. Similar to quota sampling, which might guarantee specified numbers from each group, randomisation is not a requirement for lowering bias (Iliyasu & Etikan, 2021). In this study, stratified random sampling proves to be the best method for balancing representativeness and unpredictability, guaranteeing that the findings accurately reflect the wide range of public perceptions of WPT safety.\n\nThis study has used primary data as its major source, acquired via an online survey, to get a good sense of how the public feels about the safety of Wireless Power Transfer (WPT). Primary data was chosen because of its immediateness and relevance to the research question (Paradis et al., 2016). Given the dynamic shifts in public perception and the developing nature of WPT technology, primary data guarantees real-time insights, enabling a current grasp of the ideas and concerns of people.\n\nThe method of data collecting has been recognised as platforms like Google Forms or SurveyMonkey. These internet platforms provide a broad audience, effective data gathering, and integrated analytical capabilities. This global perspective is especially pertinent for a technology like WPT, which has a wide range of uses.\n\nOn the other hand, secondary data, while helpful, might not provide the specificity needed for this investigation. Frequently, secondary sources offer broad insights that, in the context of this study, do not have the level of specificity required to comprehend individual safety concerns (Martins et al., 2018). Furthermore, because WPT is a developing area, only using secondary data could result in generalised or out-of-date results that are not suited to the specific nuances of WPT safety perceptions.\n\nA strong analytical approach is required to navigate the complex web of public perception surrounding the safety of Wireless Power Transfer (WPT). Therefore, this study chose a quantitative approach. A strategy like this has several clear benefits. The first benefit is that it enables the methodical examination of patterns and trends within the collected data, ensuring objectivity and reducing biases (Albers, 2017). A quantitative technique can effectively assess and statistically evaluate the impressions of a bigger sample size using the data obtained from online questionnaires. The nature of the research questions and the method used to collect the data is the cause for not using qualitative analysis (Mwita, 2022). Online surveys frequently produce well-structured responses that can be best understood through quantitative analysis. Even while they provide a deeper understanding of individual experiences, qualitative methods might not be as good at identifying patterns in huge datasets, making them less suitable for this particular study.\n\nThis research uses statistical software like SPSS to further improve the precision and thoroughness of this quantitative method. Tools like SPSS are skilled at managing large datasets, enabling a variety of analyses, from straightforward descriptive statistics to intricate hypothesis testing.\n\nThe research procedure, which lasts around ten months, is precisely planned. The first two months are spent on framework development and literature reviews. The questionnaire and sample are the main focus of months three and four. The collection of data takes place from months 5-7. The following two months will be used to analyse the data, and the last month will be used to draw conclusions and make modifications.\n\nProtecting the rights and dignity of participants is crucial while studying public perceptions. The Data Protection Act of 2018 is strictly followed in this study, assuring the privacy and security of respondent data. This adherence guarantees that the data acquired is only used for research purposes and that personal information is kept confidential (Ducato, 2020). However, this research adheres to other significant ethical standards in addition to data protection. Participants gave their prior informed permission after being fully informed of the objectives and their part in it. They were allowed to withdraw at any time, and their involvement was maintained optional. To avoid any biases and protect the privacy of participants, collecting anonymous data was given priority. The Data Protection Act of 2018 and these accepted ethical guidelines, when combined, give a comprehensive framework that guarantees that all parts of participant rights and research credibility are upheld. The study makes sure that all of its participants are treated with integrity, transparency, and respect thanks to this strong ethical framework.\n\n\n4. Results\n\na Dependent Variable: Which of the following are your primary concerns regarding WPT?\n\nFrom Table 2 it has been observed that it is involving linear regression in this context can assist with grasping the connections between different independent variables (such as age, education, familiarity with WPT, etc.) and the dependent variable (safety concerns about WPT). Linear regression permits the evaluation and survey of the strength and course of these connections, which can be important in looking at the general meaning of the variables affecting security concerns. Linear regression provides coefficients that evaluate how every independent variable impacts the dependent variable.\n\nWith respect to “a priori test for regression,” which is shown in Figure 3, it is a standard term in linear regression. Nonetheless, it is conceivable it might be alluding to indicative tests or making sure that they are performed prior to running a regression model. These checks guarantee that the suppositions of linear regression are met and that the model is proper for the information. Normal checks incorporate inspecting the conveyance of residuals, checking for multicollinearity (connections between independent factors), and surveying homoscedasticity (consistent fluctuation of residuals). These checks are essential to guarantee the legitimacy of the linear regression. Linear regression is an important device for this situation for measuring connections between factors, testing speculations, and evaluating the useful meaning of elements impacting security worries about WPT. It gives bits of knowledge and proof to illuminate independent direction, strategy improvement, and security mindfulness drives.\n\n(Source: Self-Created).\n\nThe correlation coefficient (R) gauges the strength and heading of the linear relationship between the independent variable(s) and the dependent variable. In this model, R is roughly 0.600, proposing a tolerably sure direct relationship. The coefficient of determination (R Square) addresses the extent of the fluctuation in the dependent variable that can be made sense of by the independent variable(s). In this model, R Square is around 0.360, demonstrating that 36% of the variance in the dependent variable is made sense of by the independent variable(s).\n\nChanged R Square is an adaptation of R Square that adapts to the quantity of independent variables in the model. It penalises the consideration of unnecessary factors. In this model, the Changed R Square is around 0.235.\n\nStd. Error of the Estimate addresses the standard error of the residuals, which is a proportion of the average error between the observed values and the predicted values of the dependent variable. In this model, the standard error is approximately 0.9704.\n\nAge bracket\n\nIn the primary ANOVA test, which is demonstrated in Table 3 and Table 4, respondents were gathered into various age sections to evaluate whether there are genuinely tremendous contrasts in their view of Remote Power Move (WPT). The experimental outcomes demonstrated that there is no genuinely huge contrast between age bunches with regard to their perspectives on WPT. This recommends that age doesn’t give off an impression of being a huge figure moulding individuals’ view of WPT innovation.\n\nEducational qualification\n\nThe Table 4 ANOVA test inspected respondents’ most noteworthy instructive capabilities to decide whether instructive foundation assumes a part in forming a view of WPT. The outcomes showed that there is no genuinely massive contrast between various instructive capability gatherings. This proposes that individuals with shifting degrees of training have comparable impressions of WPT security.\n\nGenerational concerns\n\nThe third test investigated respondents’ perspectives on whether more seasoned ages have a bigger number of worries about WPT than younger ages. Here, a genuinely massive contrast was found between reaction classes, showing that individuals have varying suppositions on this theme. Some accept that more established ages express more worries, while others don’t share this view.\n\nFamiliarity of WPT\n\nThe fourth ANOVA surveyed whether respondents who have utilised or run over WPT advances have various discernments contrasted with the individuals who have not. The outcomes uncovered a measurably massive contrast, showing that experience with WPT innovations essentially impacts individuals’ insights. The people who have insight into WPT advances might have various perspectives contrasted with the individuals who don’t.\n\nFamiliarity with WPT applications\n\nIn the fifth test, respondents’ knowledge of different WPT applications was analysed. While there was no genuinely massive distinction between experience with various applications, it’s important that the p-value was near the importance level (0.062). This proposes that there might be a few distinctions in experience with explicit applications. However, they didn’t arrive at factual importance in this examination.\n\nThese ANOVA tests give significant bits of knowledge into the elements that impact the public impression of WPT. While age and instructive capability may not assume a critical part, knowledge of WPT advances gives off an impression of being a vital factor in forming individuals’ perspectives. Also, there are varying sentiments on whether more established ages express more worries about WPT, featuring the intricacy of public discernments in this developing mechanical scene.\n\nThe results of this study aimed to examine public perceptions of Wireless Power Transfer (WPT) technology and its safety implications. Awareness of WPT, safety concerns, demographic influences, and preferences for traditional wired charging were all examined in the study. Eight research questions and their corresponding hypotheses were included in the analysis. Comparing the findings to previous research and determine whether the hypotheses are true.\n\nBased on the data provided within Table 1 it can be seen that the study provides useful insights into public perceptions of Wireless Power Transfer (WPT) technology. Respondents were assorted concerning age, with the greater part falling into the subsequent age section (42%). Essentially, a significant piece of members held an instructive capability at level 3 (42%). It is interesting to note that opinions on whether older generations are more concerned about WPT than younger generations are divided. The need for a nuanced understanding of how different age groups perceive this mixed opinion emphasises this emerging technology.\n\nAdditionally, the significance of education in shaping perceptions is underscored by the fact that nearly 40% of respondents moderately believed that their level of education provided them with a better understanding of WPT than others. A sizable percentage of respondents, 38 per cent, indicated that they were familiar with WPT technologies. This proposes that WPT is building up some decent momentum among the overall population. Besides, the larger part evaluated how they might interpret how WPT functions at a moderate level (3 out of 5), showing a fundamental comprehension among the respondents.\n\nAs far as security concerns, the information showed a different scope of suppositions. While there is an outstanding degree of concern, it is conveyed across the scale. Curiously, a larger part of respondents (60%) accepted that WPT in broad daylight spaces presents a bigger number of dangers than in private spaces. This mindful disposition towards the organisation of innovation in high-traffic regions lines up with existing security worries about open openness to electromagnetic fields. In addition, the data showed that a lot of respondents were unsure about the safety of using WPT in a medical or hospital setting. This suggests that in such critical environments, more information and assurance are required. A significant number of participants emphasised the significance of extensive public awareness campaigns and information dissemination and expressed concerns regarding the availability of sufficient information regarding the safety of WPT technologies.\n\nThe following hypotheses are supported by the data and findings that have been provided;\n\nH1: WPT technologies are unfamiliar to more than half of the respondents.\n\nThe data shows that 38% of respondents have experienced WPT technologies. The extent of respondents acquainted with WPT is equivalent to or more prominent than half. The extent of respondents acquainted with WPT is under half.\n\nH2: Respondents express more noteworthy well-being worries for WPT in broad daylight places than for individual gadgets.\n\nMost of the respondents (60%) accepted that WPT in broad daylight spaces presents a greater number of dangers than in private spaces. It is identified that 60% of respondents accepted that WPT out in the open spaces presents a larger number of dangers than in confidential spaces. This supports H2 and demonstrates that respondents express more noteworthy well-being worries for WPT out in the open spots.\n\nH3: Concerns about the safety of WPT are more prevalent among respondents who are older and less educated.\n\nThe information reveals that there is a mixed opinion about older generations having more concerns about WPT. Also, respondents with less proper instruction are bound to communicate security worries about WPT. This partially backs up H3 because it matches the part of the hypothesis that talks about age and education, but not entirely. In summary, H2 and part of H3 are satisfied based on the provided findings and data.\n\nWith 52% of respondents preferring not to have WPT in public transportation like buses and trains, preferences for the implementation of WPT in public transportation were more cautious. This finding recommends that people, in general, might have qualms about involving WPT in transportation frameworks. In addition, a significant portion of respondents (40%) indicated a continued preference for established technology in this setting by favouring traditional wired charging over wireless charging for their personal devices. The regression analysis provided useful insights, revealing that the independent variables in the model account for approximately 36% of the variability in the perception of WPT safety. This suggests that perceptions of safety are influenced by age, education, and familiarity with WPT.\n\nWPT technologies awareness\n\nThe study found that the greater part of the respondents were new to WPT advancements (H1), which goes against the invalid speculation (H0). This is in line with previous research, which suggests that the general public is unaware of WPT.\n\nSafety concerns in public vs. personal spaces\n\nRespondents communicated more noteworthy security worries for WPT out in the open spaces than for individual gadgets (H2), supporting the speculation. This is in line with previous studies that have shown that technology in public spaces frequently raises more safety concerns among the general public.\n\nDemographic factors\n\nThe analysis confirmed the hypothesis by revealing that older respondents and those with less formal education were more likely to express safety concerns regarding WPT (H3). Demographic factors can also have an impact on how people perceive technology, according to existing research.\n\nThe implications of the drive results are as follows;\n\nFor technology developers\n\nTechnology developers should take note of the limited awareness of WPT technologies among the general public. This emphasises the necessity of educational campaigns to educate the public about the advantages and safety of WPT. Developers ought to prioritise addressing safety concerns, particularly in public areas. Advancements that improve the well-being and straightforwardness of WPT frameworks, particularly in high-traffic regions like transportation and clinical settings, can assist with building trust and acknowledgment.\n\nFor policymakers\n\nThe findings of the study suggest that regulatory bodies should take a more proactive approach to ensuring the safety of WPT technologies. Policymakers should focus on robust safety regulations and standards that the general public can easily understand because older generations and those with less formal education tend to have more safety concerns. This can cultivate trust in the innovation and guarantee its protected arrangement.\n\nFor public awareness campaigns\n\nPublic awareness campaigns ought to be intended to target different segment gatherings. The advantages of WPT can be the focus of campaigns that address specific safety concerns in public areas. The findings likewise recommend that missions shouldn’t accept earlier information on WPT, particularly among more seasoned and less-taught populaces. Utilising clear and available language is crucial for spanning the mindfulness hole.\n\nIn conclusion, this research sheds light on how the general public views WPT technology. It affirms some current examination findings while revealing insight into segment impacts. The findings emphasise the significance of public acceptance and safe adoption of WPT technologies through education, safety, and regulatory efforts.\n\n\n5. Discussion\n\nThe ways to encourage more industries to utilize Wireless Power Transfer (WPT) can be recommended by considering public attitudes towards its safety.\n\nCollaboration with Tech companies: Collaborating with technology companies can lead to making advanced new applications and software because technology is always changing and people rely on electronic gadgets a lot. For example, WPT zones can be set up in places where technology is important, like tech hubs and innovation centres, to encourage tech-savvy people and entrepreneurs to use them (Van Mulders et al., 2022). Understanding and serving specific audience groups can make more people like something.\n\nPublic awareness and education campaigns: It is important to make people aware of the potential safety issues with WPT. The main focus should be on the science behind WPT, how to stay safe when using it, and the benefits it could bring. According to Cormick (2019), Dealing with how the public sees things can affect how well people like new technologies. WPT can be seen as safe and ground-breaking by making the technology easier to understand through educational programs.\n\nSafety standards and certifications: It is recommended to create specific safety rules and certifications for WPT devices to make sure they are safe. These rules are tested and researched well and can help producers make safe systems that users can trust. The importance and freshness of source data can have a big impact on public trust, as McGillivray et al. (2022) stressed. The industry can keep WPT devices safe and up-to-date by regularly updating the standards based on the latest research.\n\nFeedback mechanisms: It is quite important to create ways for people to give their opinions so one can keep making technology better and better. These can be online places where people can talk about their experiences, worries, and ideas related to WPT (Wynn & Maier, 2022). Such immediate feedback can provide producers and researchers with priceless information, ensuring that WPT develops in line with the demands and expectations of the general population.\n\nWireless Power Transfer has enormous potential, and its wider adoption depends on changing people’s opinions of it, demonstrating its advantages, and consistently innovating. Stakeholders may make sure that WPT becomes a crucial component of the technical landscape and benefits society as a whole by heeding the advice mentioned above.\n\nThis concern study has several limitations. Primarily, the sample predominantly consisted of individuals with higher education qualifications, possibly biasing results towards a more informed perspective on WPT. The age distribution was also skewed, with a higher representation of the 18-30 age bracket. These demographics might not accurately represent the general views of the population on WPT. Additionally, self-reported measures of understanding and concern might be subject to response bias. The R Square value of.360 suggests that other unexplored factors significantly influence public perception.\n\nHowever, future research could aim for a more diverse demographic sample, possibly incorporating global perspectives to understand cultural influences on WPT perceptions. Additionally, qualitative methodologies, such as focus groups or interviews, might provide deeper insights into the underlying reasons for certain attitudes. Exploring potential intervention strategies to address safety concerns and increase public trust in WPT technologies would also be beneficial.\n\n\n6. Conclusion\n\nThe main focus of this study is to analyse the impact of Wireless Power Transfer (WPT) technology on the energy distribution system. This technology is making life easier and bringing new ideas. The progress from Nikola Tesla’s first experiments to using wireless power transfer in daily life shows how much technology has improved. However, with every new development comes a multitude of inquiries, particularly as the technology integrates more deeply into daily routines. This research investigates public perceptions of the safety of wireless power transfer. It helps us understand how society feels about and knows about this technology. An important observation is that wireless power transfer is both prevalent and potent, yet it poses considerable obstacles. The invisible transfer of energy is efficient but it makes people worried or unsure. History has demonstrated that new technologies are often questioned because people do not understand them completely. From people being unsure about microwave ovens at first to worrying about cell phone signals, it is a common phenomenon. The fact that WPT is “invisible” makes these concerns even bigger. It repeats that for people to fully accept a new technology, it is important to be open and understand how it works. Additionally, it is clear that the knowledge of people about this aspect is different from each other. Some people understand WPT well, but many have wrong ideas or do not know about it at all. The fact that the trust of people can be easily changed by a few incidents or false information shows how easily people can start to doubt technology. In a digital age, where news, both accurate and fake, spreads at lightning speed, the foundation of trust becomes ever so critical. However, it is not all about the challenges. The potential of WPT, as echoed by its applications in sectors like the electric vehicle industry, speaks volumes about its promise. But to realise its full potential, the industry needs to address the knowledge gap that exists. The variance in safety standards across nations, while reflective of differing technological paradigms and risk perceptions, might contribute to the confusion of the public. A more unified approach, or at least a universally understood baseline, could be instrumental in demystifying WPT for the average consumer. The study shows that demographics are really important in shaping how people see things. The interaction between age and education is what truly matters, not just their measures. It is essential to understand the evolving nature in order to devise tailored communication plans. People from different backgrounds need different amounts of information and reassurance, understanding this diversity can help build trust. Lastly, while the IEEE and similar bodies have been proactive in crafting standards for WPT, the approach seems more reactive than anticipatory. For the continued evolution of WPT, it might be beneficial to be a step ahead, to anticipate concerns and address them before they burgeon into significant blocks.\n\n\nInformed consent\n\nWritten informed consent was obtained from all individual participants involved in the study.\n\n\nDisclaimer\n\nThe views and opinions expressed in this article are those of the author and are the product of professional research. It does not necessarily reflect the official policy or position of any affiliated institution, funder, agency, or that of the publisher. The author are responsible for this article’s results, findings, and content.", "appendix": "Data availability statement\n\nThe data that support the findings of this study are available upon request from the corresponding author, You S.R. To request access to the data, please contact the corresponding author at a2695922149@qq.com. The data are not publicly available due to their containing information that could compromise the privacy of research participants. An example situation in which access to the data may be granted is if the requester provides a detailed explanation of how they intend to use the data for legitimate research purposes and agrees to maintain the confidentiality of the participants’ information.\n\n\nAcknowledgements\n\nEthics and consent statement: An application for full ethical approval was made to Xidian University, with approval granted under the reference number XUEST-ER-2023-161 on January 21, 2023. All procedures performed in studies involving human participants were conducted in accordance with the ethical standards of the institutional and national research committee, as well as the 1964 Helsinki Declaration and its later amendments or comparable ethical standards.\n\n\nReferences\n\nAlbers MJ: Quantitative data analysis—in the graduate curriculum. J. Tech. Writ. 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PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZhi W-J, Wang L-F, Hu X-J: Recent advances in the effects of microwave radiation on brains. Mil. Med. Res. 2017; 4(1): 29. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "300045", "date": "08 Jul 2024", "name": "Yildirim Ozupak", "expertise": [ "Reviewer Expertise Wireless Power 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\n1. The article should specify what new insights it adds to the existing literature in the field.\nThe article should clearly articulate the novel contributions it makes to the field. This includes identifying gaps in the existing literature that the study addresses and explaining how the findings advance our understanding or provide new perspectives. The authors need to contextualize their work within the broader scope of existing research, highlighting what sets their study apart and its significance to the field.\n2. The methods section is not detailed enough for replication. It should be elaborated.\nThe methods section must provide sufficient detail to ensure that other researchers can replicate the study. This includes a thorough description of the experimental design, procedures, materials, and data analysis techniques used. Specific details such as sample size, sampling methods, controls, and statistical methods should be clearly outlined. Additionally, any deviations from standard protocols should be explained. Providing this level of detail ensures the study’s validity and reliability and allows others to verify and build upon the findings.\n3. The discussion section should address the study’s limitations and potential biases.\nThe discussion section should critically evaluate the study’s limitations and potential biases. This involves acknowledging any methodological constraints, such as sample size, measurement errors, or external factors that could have influenced the results. The authors should also consider potential sources of bias and how they might impact the study’s findings. Discussing these aspects transparently helps contextualize the results, provides a more balanced interpretation, and suggests areas for future research to address these 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? Partly\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nNot applicable\n\nAre all the source data underlying the results available to ensure full reproducibility? No source data required\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] }, { "id": "322233", "date": "24 Sep 2024", "name": "Izaz Ali Shah", "expertise": [ "Reviewer Expertise RF and Microwave devices", "espicially wireless power transmission system designs for low and high power applications." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 survey article examines public perceptions of the safety of Wireless Power Transfer (WPT) technology. While the paper provides a comprehensive overview of public opinions, some important safety concerns are not fully addressed.\n\nWPT technology offers a promising alternative to traditional wired electrical systems, especially for complex applications. However, high-power transfers, such as those used for electric vehicles (EVs) and buses, may raise public safety concerns, which the paper rightly highlights.\nAdditionally, based on the reviewer's knowledge, some researchers have investigated the potential safety risks for patients with implantable medical devices when exposed to high-power WPT systems. The reviewer recommends including a dedicated section in the paper to address these concerns.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? No source data required\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [] } ]	1	https://f1000research.com/articles/13-651
https://f1000research.com/articles/11-1382/v2	30 May 23	{ "type": "Research Article", "title": "Frontier model of the environmental inefficiency effects on livestock bioeconomy", "authors": [ "C. A. Zuniga Gonzalez", "J. L. Jaramillo-Villanueva", "J. L. Jaramillo-Villanueva" ], "abstract": "Background: This work was focused on measuring environmental inefficiency in Mexican dairy farms, considering climate change variables related to the emission of greenhouse gases (GHG) and planetary geomagnetic activity. Methods: The applied methodology measures the eco-efficiency of Mexican dairy farms using the empirical application of a stochastic frontier model of the bioeconomy. The productive sector of the bioeconomy studied was the eco-intensification of the livestock production system (dairies). The environmental inefficiency effect was assumed to be a distribution-independent truncation of a normal distribution with constant variance, while the mean was a linear environmental function of the observable variable. Results: The results showed that the coefficients of the frontier model were highly significant, highlighting the investment in livestock (50%). The inefficiency model had an impact on climate variation with greenhouse gas emissions CH4 (1.96%). The results of the environmental technical efficiency in geometric average were 81.28%. The producers that reached the border with a technical efficiency equal to 1 are the references for the rest, marking the relative technical efficiency. Conclusions: It was concluded that the coefficients in the model were very significant, showing the level of investment in livestock (50%). The low-performance model estimates the impact of climate change on GHG emissions CH4 (1.96%) explaining the trend of increasing GHG emissions, keeping in view that the management of food and cattle during the study period were affected by summer feeding, which allowed considering the activity of GHG emissions. According to the results, the geometric mean environmental performance of engineering is 81.28%.", "keywords": [ "Stochastic Frontier", "Solar Activity", "Technical Efficiency", "Livestock Bioeconomy" ], "content": "1. Introduction\n\nLivestock has historically been considered one of the most important activities in Latin America given its great influence on the economy. It is for this reason that the livestock subsector has been a pivotal axis for the various studies that evaluate performance, and it is here that the analysis of technical inefficiency becomes important for this type of study. In such a way that the need to be more efficient is not a recent discussion, but has been a concern of our predecessors in terms of production, it is thus that the governments intend to introduce a series of strategies in the different rural development plans, which consider the transformation of livestock systems from extensive to intensive. Pérez et al. (2004) assessed that in Latin America, livestock activity ranks seventh in world production and tenth in milk production. In 2001, it contributed about 4.7% of total world meat production and 0.17% of milk. Latin America has great resource potential, however, it has not been possible to meet the demand for milk and meat, so this type of study was necessary to determine the efficiency of dual-purpose production systems. For their part, Morillo and Urdaneta (1998) focused that the proportion of income derived from the sale of milk as against the sale of animals for meat varies greatly from 12% to 80%, depending mainly on the producer's objectives, of the growth phase in which the males are sold and of the racial types, in any case, influenced by the agro-ecological characteristics of the farms and the technology used.\n\nAccording to the diagnosis of the Sectoral Program for Agricultural, Fisheries and Food Development 2013—2018 of Mexico in 2050, the world population will be 9,300 million people and the Food and Agricultural Organization (FAO) estimates that the world demand for food will increase by 60% (FAO, 2012). For that year, the population in Mexico will grow by 34 million, reaching 151 million people. The sustained growth of some developing countries such as Brazil, China, and India poses challenges and opportunities worldwide for the development of the agri-food sector. The International Monetary Fund (IMF) estimates the growth of the world economy at 3.8% annual average for the next six years, with important differences between the groups of countries; 5.2% for emerging markets and 2.2% for advanced economies, which will lead to increases in food consumption globally. This trend represents an important opportunity for Mexico to perform an important lead in meeting world food needs. However, arable land is limited both in the world and in Mexico. It is necessary to face climate change which translates into extreme weather events that affect food production. In this context, the great global challenge is to increase food production through higher productivity (López-González et al., 2016a, 2016b).\n\nIn Mexico, climate change has manifested itself in unprecedented and unexpected extreme events. In 2009, the worst drought in 60 years occurred; 2010 was the wettest year on record; and in 2011, there were intense and atypical frosts, and less rainfall. In September 2013, heavy rains occurred that caused some damage to agriculture and, unfortunately, loss of human life. In several parts of the country, for a few days it only rained being comparable to half of all that rained in 2012. The consequences of these natural phenomena are reflected in the loss of part of the production, outbreak of diseases, and lower levels of income and wealth for the population. The Mexican Climate Modeling Network developed an ensemble of projections that represents the country's climatology considering the various climatic scenarios. There is concern in Mexico that in the coming decades, the temperature will increase more than the historical average, that is, 6% higher than the global increase (Maza et al., 2017; Milán and Zúniga-Gonzalez, 2021; Núñez and Montalvo, 2015).\n\nHistorical facts have confirmed this temperature rise. Therefore, an increase in the danger of climatic events associated with increased warming or a decrease in crop yield can be expected, even if they have not been recorded historically. Most graphical representations of rainfall, tropical cyclones, northerly winds, and cyclones do not include the degree of uncertainty. The way of producing food is changing; Technological innovation, infrastructure, organization of productive activities, sustainable practices, and risk management in primary activities are the main public policy instruments to achieve greater resilience in the agri-food sector. It is in this context that the study of the effects of inefficiency in livestock production systems is worthwhile as part of the livestock bioeconomy of the eco-intensification production path (Zuniga-Gonzalez et al., 2014; Dios-Palomares et al., 2015a, 2015b; Dios-Palomares, 2002; Morillo & Urdaneta, 1998).\n\nThis work was organized with a section that refers to the literature review of the technical efficiency model, a third section was dedicated to the evaluation of the empirical application of the model, and later the results, discussion, and conclusions were presented.\n\n\n2. Literature review\n\nThe study considered the environmental stochastic frontier adjusted to the livestock bioeconomy. In the equation below\n\nYit denotes the production of milk and its derivatives in the dairy farms in the study area in the t-th observation regarding the time (t =1,2, … …… …, T) and on the i-th sample (i = 1,2,3 … ……………… ….N);\n\nXit is a vector (1 × k) of known values of the productive climatic parameters (input of milk production and measurement parameters of greenhouse gases (GHG)). These explanatory variables were associated with the i-th sampling point y on the t-th time observed;\n\nβ is a vector (k × 1) of unknown parameters to be estimated;Vit was assumed to be an identical and independent distribution (dii) of random errorsN0Vν2, distributed independently Uit;\n\nUit were non-negative arbitrary variables, related to the technical inefficiency of production (milk as a production system in the livestock bioeconomy), which are assumed to be independently distributed. These Uit were obtained by truncation (at zero) of the normal distribution, zitδ, y variance, σ2;\n\nzit was a vector (1 x m) of explanatory variables related to the technical inefficiency of the sampling points completed time; y δ, is a vector (m x 1) of unknown coefficients to be estimated.\n\nThen, equation (1) specifies the environmental function for a productive sector of the livestock bioeconomy, about the data of the livestock bioeconomy system in livestock farm systems. However, for the effects of environmental technical inefficiency, the Uit was expected to be a relation of the set of independent variables, and the zit was a vector of unknown coefficients, δ. The independent variables in the environmental technical inefficiency model may include approximately stochastic frontier components, although this is not our case, indicating that the effects of environmental inefficiency were stochastic. If the value of the first z-variables was 1 and the coefficients of the other z-variables was zero, then this case represents the model specified by Stevenson (1980) and Battese and Coelli (1988, 1992). When δ-vector was equal to zero, inefficiency effects were unrelated to the z-variables, resulting in the mean normal distribution, originally specified in Aigner, Lovell, and Schmit (1977), obtained. If the interaction between the variables of the specific sampling points and the input variables of the livestock bioeconomy system was of the z-variables, then non-neutral probability limits, proposed by Huang and Liu (1994), would be obtained.\n\nThe effects of technical inefficiency, Uit, in the stochastic frontier model (e. 1) could be specified in an equation 2:\n\nThe supposition that Uit and Vit are distributed self-sufficiently despite the t= 1.2.3 … …, T, y i=1,2,3, … ………………… …..,N, was simplified, but with limiting condition. Substitute models were essential for an explanation of the possible correlated structures of the effects of technical inefficiency and arbitrary errors at the frontier.\n\nThe maximum probability technique (maximum likelihood) was proposed for simultaneous estimations of the stochastic frontier parameters and the model of technical inefficiency effects. The probability function and its partial derivations concerning the model parameters are presented by Battese and Coelli (1993). The probability function is expressed in terms of the variance parameters σs2≡σν2+σ2yγ≡σ2σs2.\n\nThe technical efficiency of milk production for the t= 1.2.3 … …, T, and i=1,2,3, … ………………… …..,N is defined in equation 3:\n\nThe forecast of the environmental technical efficiency is based on its conditional expectancy, given the assumptions of the model. This result is also given in Battese and Coelli, (1993).\n\n\n3. Methods\n\nThe work was carried out in the state of Tlaxcala, which is located in the Mexican Altiplano and at the geographic coordinate’s 98°43” west longitude and 19°44' north latitude, and 97°38' east longitude, 19° north latitude and 06 south latitude. The prevailing climate in the state is sub-humid temperate with summer rains. The average altitude of the study region is 2,200 meters above sea level.\n\nFor the collection of data, the following procedure was followed: a) identification of the areas of the state with the highest volume of milk production, b) identification of the production units present in the study areas, c) design and application of a questionnaire to collect information, and d) analysis of the data obtained. The study was carried out in 102 cattle farms for milk production in six municipalities of the state, in 2020. The production units were randomly selected, and divided into four regions of importance in dairy production in the state of Tlaxcala. The questionnaires contained technical information, owner information and economic data. In addition, 102 dairy cattle farms were monitored.\n\nThe methodology used was known as the stochastic production frontier, which is based on the Cobb-Douglas function (Battese & Coelli, 1992 and 1995). This is an empirical application of the Battese and Coelli (1995) model.\n\nThe FRONTIER (RRID:SCR_022958) Version 4.1 computer program (Battese & Coelli, 1988, 1992 and 1995) was used to obtain a maximum likelihood estimate (MLE) of the selected data in the study period; this is raised in the literature review section. The model used based on eq. 1, is the following eq. 4:\n\nStochastic frontier model for a livestock bioeconomy system.\n\n(TVAi) represents the total annual sale of products obtained on the farm, such as the amount of milk produced per cow per year and by secondary products. The unit of measure is in dollars.\n\n(CIGij) represents the annual value of the investment quantified in dollars.\n\n(CTij) represents the total annual cost for fuel, feeding, reproduction, illness and treatment, milking, mortality, and preventive medicine, measured in annual dollars.\n\n(MOij) represents the annual cost of family and hired labor, measured in dollars.\n\n(SG) surface destined for livestock (Ha)\n\n(NDij) represents the number of dependents measured in people.\n\n(EPij) represents the age of the producer measured in years of age.\n\n(νi ─ μi), the compound error component νi represents arbitrary variables that were assumed to be normally distributed in N (0, σv2) and independent of μi, represents non-negative arbitrary variables that were assumed to measure technical inefficiency in production, γ is assumed to be independently distributed as zero truncations of the normal distribution N(ωit, γ) equation 2. These measurements are interpreted as indicators of the relative importance of each variable in the composition of the compound error in such a way that if gamma takes a value close to 1, it follows that there are no effects on the error due to factors beyond the control of the body of the area studied (Dios-Palomares et al., 2002; Dios-Palomares et al., 2015).\n\n(i) represents the period in which the samples were taken: 02/05/2020 to 30/10/2022.\n\n(j) represents the sample of 102 farms in our case,\n\nModel of technical production inefficiency for a livestock bioeconomy system: environmental condition and variability in climate change.\n\nThe effects of environmental inefficiency in the study region are assumed to be defined by eq. 5.\n\nwhere Uij was error term that measures the environmental technical inefficiency effect in the Mexican region of study considering the variability of climate change, explained in the previous section.\n\n(NEPij) represents educational level of the producer.\n\n(CAEij) represents the amount of water used per animal unit, measured in liters.\n\n(CH4ij) represents greenhouse gas emission of methane from enteric fermentation measured in Gg CH4/year.\n\n(ωij) is the random variable explained in the previous section.\n\nHypothesis to be tested: If the inefficiency model is stochastic, then the technical efficiency of the dairy farm system can be explained by the Stochastic Frontier model for a livestock bioeconomy system influenced by climate change variability (greenhouse gas emissions).\n\nTable 1 shows the statistical description of the data used in this study. The full protocol can be found on protocol (protocols.io).\n\n Emission factor established by the 2006 IPCC for Latin America (Herranz-Ramirez, 2018).\n\nSource: Author’ self-calculation\n\n\n4. Results\n\nThe estimates with standard error parameters of the maximum likelihood (maximum-likelihood) are calculated with two significant digits, as shown below, according to eq. 4 and 5, respectively, in the conditions of milk-producing farms:\n\nStochastic frontier livestock bioeconomy model:\n\nInefficiency model of livestock bioeconomy:\n\nVariance of Parameters:\n\nThe coefficient signs of the environmental stochastic frontiers of the livestock bioeconomy model were as expected. The negative elasticity of the model in dairy farms is interpreted as a non-scale economy that depends fundamentally on variations in the cost of investment in cattle, labor, the number of dependents, the total cost, the surface used in cattle farming and the age of the producer to ensure good quality milk. These coefficients were highly significant, highlighting the investment in livestock (50%). The inefficiency model was of particular interest in this study. The impact of climatic variation with GHG emissions CH4 (1.96%) explains a tendency to increase GHG emissions, considering that the feeding and management of livestock in the study period were affected by summer feeding, which allows us to consider the GHG emission activity. The result of the environmental technical efficiency in geometric average was 81.28%. Figure 1 presents the behavior of the environmental technical efficiency indices in terms of the quality of dairy production. The producers that reached the border with a technical efficiency equal to 1 are the references for the rest, marking relative technical efficiency.\n\nThe estimate in the variance parameters, σs2, was close to one (0.23), implying that the quality of milk production was highly significant. It was generalized that the effects of the inefficiency in the null hypothesis likelihood-ratio test were absent or had the simplest distribution (see Table 1). The first null hypothesis pointed out that the effects of inefficiency were absent from modeling, and was therefore, strongly rejected. The second null hypothesis, specifying non-stochastic inefficiency effects, was also strongly rejected. The third null hypothesis, considered in Table 2, specifies that the effects of inefficiency were not a linear function for the educational level, nor of the amount of water used, nor GHG emissions. This null hypothesis has also been rejected at the 5% significance level. This indicates that the stated effects of these three explanatory variables on inefficiency in dairy farms were significant. The effects of inefficiency for the stochastic frontier were clearly stochastic and were not related to the observations of the educational level, amount of water used, and GHG emissions. Thus, the stochastic frontier environmental inefficiency function was an improvement over the environmental stochastic frontier suggested by Dios Palomares et al. (2015b), Zúniga-González et al. (2022).\n\n† The likelihood-ratio statistical test, λ= -2{log [likelihood (H0)] - [log [likelihood (H1)]} has about an x-distribution with estimators equal to the number of estimators assumed to be zero in the null hypothesis, H0; subsequently H1 is true. If the estimator, γ, is zero, then the variances in the inefficiency effects are zero and so the model reduces to the traditional mean response function. In this case, the estimators, δ0 and δ1, are not defined. Henceforth, the critical value for the statistical test for this second hypothesis was obtained from the χ12 distribution.\n\n* One asterisk in the estimate of the statistical test indicated that it exceeds the 95th percentile for the corresponding Chi-square distribution (χ2) and consequently the null hypothesis was rejected.\n\n\n5. Discussion\n\nA stochastic frontier model of environmental inefficiency effects was proposed for dairy farms in Mexico Zúniga-González et al. (2014), under environmental conditions, following Dios Palomares et al. (2015), Rangel Cura et al. (2015). An application of the model was presented using data from 102 dairy farms. The results indicated that the model for the of environmental efficiency effects, involved a constant term, investment costs in livestock, total annual costs for feeding, labor, area for livestock, number of dependents, and the producer age, which was a significant component in the environmental stochastic frontier function. Model specification allowed the estimation of both changes and the variation of the GHG emission as environmental inefficiency effects, given that the effects of inefficiency were stochastic and had an unknown distribution. In addition, theoretical and applied work was required in the paths of bioeconomy to obtain better and more generalized stochastic frontier models and environmental inefficiency effects associated with the analysis of Battese & Coelli (1995), Trigo et al. (2015), Dios Palomares et al. (2015a, 2015b).\n\nIn the geometric average, the environmental technical efficiency for variable climate conditions was 89%, which represents a regular quality of water and is strongly explained by the decreasing trend or inelasticity of solar activity. We add that during the months of the study, the variability of the geomagnetic activity was low, making it necessary to include data where the variations represent geomagnetic storms that would imply strong variations. Regarding the political agenda, the study shows the need to promote bioeconomy in the productive paths of eco intensification, biotechnology, and biorefineries, mainly to treat the waste generated by agricultural activities, mines, and livestock, Colon-García et al. (2021), Catari-Yujra et al. (2022), García-Bucio et al. (2022), Fernández-Santos et al. (2013). Referring to the management of GHG emissions both in enteric fermentation and waste management is very important in dairy production. These regulations must be aimed at setting emission standards (discharge limits) with alternatives for residual use with bioeconomic goods and the establishment of quality objectives (González-Araya & Vásquez, 2010; Zúniga-González et al., 2022; Georgescu-Roegen, 1976; Kuramoto, 2021).\n\n\n6. Conclusion\n\nThis research used Stochastic Frontier Analysis (SFA) to study the determinants of the frontier efficiency model of dairy farms in the state of Tlaxcala in 2020 using a frontier model of environmental inefficiencies on the livestock bioeconomy.\n\nThe results were estimated by maximum likelihood. First, the frontier model was completed and the second was a bioeconomically inefficient livestock model. These coefficients were very significant, showing the level of investment in livestock (50%). The low-performance model estimates the impact of climate change on GHG emissions CH4 (1.96%) explaining the trend of increasing GHG emissions, keeping in view that the management of food and cattle during the study period were affected by summer feeding, which allowed considering the activity of GHG emissions. According to the results, the geometric mean environmental performance of engineering is 81.28%.", "appendix": "Ethic statement\n\n“The protocol to carry out this research was reviewed and confirmed to proceed by the Colegio de Postgraduados (Institución de Enseñanza e Investigación en Ciencias Agrícolas). No formal ethical approval was required for this study as per the ‘Ley General de Protección de Datos Personales en Posesión de Sujeto Obligados’, regarding ethical approval requirements in this type of study. Verbal informed consent to participate was obtained and documented from the participants at the start of the questionnaire. Verbal as opposed to written consent was used because the aforementioned law does not require written consent to be bound by its compliance.”\n\n\nReferences\n\nAigner DJ, Lovell CAK, Schmidt P: Formulation and Estimation of Stochastic Frontier Production Function Models. J. Econ. 1977; 6: 21–37. 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Publisher Full Text\n\nLópez-González AS, Zúniga-González CA, Rangel-Cura RA, et al.: Impacto de la productividad y eficiencia técnica de los granos básicos en Nicaragua, 1961 – 2013. Rev. Iberoam. Bioecon. Cambio Clim. 2016b; 2(1): 411–436. Publisher Full Text\n\nMorillo F, Urdaneta. F: Sistemas de producción con bovinos para los trópicos americanos. Memorias Conferencia Internacional Sobre la Ganadería en los Trópicos. Gainesville, FL. 1998; pp. 80–104.\n\nMaza Ávila FJ, Vergara Schmalbach JC, Román Romero R: Eficiencia y productividad en la cobertura de las universidades públicas colombianas. Investigación y Desarrollo. 2017; 25(2): 6–33. Publisher Full Text\n\nMilán Pérez JA, Zúniga-Gonzalez CA: Necesidades de investigación y transferencia de tecnologías sobre cambio climático en Nicaragua: Una oportunidad en la Bioeconomía. Rev. Iberoam. Bioecon. Cambio Clim. 2021; 7(13): 1518–1543. 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Publisher Full Text\n\nTrigo EJ, Henry G, Sanders JPM, et al.: Towards bioeconomy development in Latin America and the Caribbean. Towards a Latin America and Caribbean no knowledge-based-economy in knowledge-based Europe. Pontificia Universidad Javeriana; 2015; (pp. 15–41).\n\nZúniga-González CA, Durán Zarabozo O, Dios Palomares R, et al.: Estado del arte de la bioeconomía y el cambio climático (No. 1133-2016-92457).2014; pp. 20–329.\n\nZúniga-González CA, López MR, Icabaceta JL, et al.: Epistemología de la Bioeconomia. Rev. Iberoam. Bioecon. Cambio Clim. 2022; 8(15): 1786–1796. Publisher Full Text\n\nZúniga-González CA, Jaramillo-Villanueva JL: DataSFA.csv. figshare. Dataset. 2022. Publisher Full Text\n\n\nFootnotes\n\n* The intercept δ0 was not added as an estimator, in the middle zit.δ could result for the δ estimators related to the z variables with the trend and shape of the distribution of the effects of technical inefficiency, U_it, being unnecessarily constrained." }	[ { "id": "239237", "date": "19 Feb 2024", "name": "Jakub Staniszewski", "expertise": [ "Reviewer Expertise environmentally adjusted efficiency 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\nDear Authors. General idea for the paper seems interesting, but your application requires some serious improvements.\nRegarding the methodological part of the paper, authors refer to the well known SFA model Battese & Coelli 1995, which is intended for panel data. Also all the equations include it subscripts which would suggest a panel setting of the data. However, authors apply the model to cross-sectional data. For this type of data check sfaR package in R [1] Authors introduce number of dependents and age of the producer as a production factors which has no theoretical justification. In the most of the application set of production factors is limited to labour, capital and land. Variables ND and EP are more suitable as explanatory variables in inefficiency component. Authors introduce also I and j subscripts for some variables but don't explain it.\n\nThe way how environmental component was introduced into the model is completely incorrect. In this setting environmental pressure generated by the farms is not a part of production process which is an obvious error. For the ways of introducing environmental component into efficiency analysis see this review [2]. From the practical point of view 102 observations is quite little for SFA model. I would rather implement DEA approach. Regarding the presentation of the results. Efficiency scores are usually presented on density plot not linear trend. Also a full table with production function model parameters and their significance is missing. I don't understand why authors used geometric mean either. Regarding conclusions, they cannot be right as they are based on flawed model. To sum up, authors collected interesting data, but their empirical application has some serious drawbacks\n\nIs the work clearly and accurately presented and does it cite the current literature? No\n\nIs the study design appropriate and is the work technically sound? No\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\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": [ { "c_id": "11734", "date": "20 Jun 2024", "name": "C. A. Zuniga-Gonzalez", "role": "Author Response", "response": "Response to the reviewer # 1 Jakub Staniszewski, Uniwersytet Ekonomiczny w Poznianiu, Poznań, Poland Dear Authors. General idea for the paper seems interesting, but your application requires some serious improvements. Reviewer # 1 [1] Regarding the methodological part of the paper, authors refer to the well known SFA model Battese & Coelli 1995, which is intended for panel data. Also all the equations include it subscripts which would suggest a panel setting of the data. However, authors apply the model to cross-sectional data. For this type of data check sfaR package in R [1]. Response to Reviewer # 1 Dear Reviewer, Thank you very much for your valuable feedback on our manuscript. We appreciate your careful review and constructive comments. We have revised the methodological section of the paper to align with your suggestions. Specifically, we have corrected the equations and the text to accurately reflect that our study is based on cross-sectional data rather than panel data. The subscripts indicating time have been removed, and the description of the variables and the model have been adjusted accordingly. Thank you once again for your insightful comments, which have helped improve the clarity and accuracy of our manuscript. Reviewer # 1 [2] Authors introduce number of dependents and age of the producer as a production factors which has no theoretical justification. In the most of the application set of production factors is limited to labour, capital and land. Variables ND and EP are more suitable as explanatory variables in inefficiency component. Authors introduce also I and j subscripts for some variables but don't explain it. Response to Reviewer # 1 Dear Reviewer, Thank you very much for your valuable feedback on our manuscript. We appreciate your careful review and constructive comments. Regarding your concern about the inclusion of the number of dependents (ND) and the age of the producer (EP) as production factors, we would like to provide a theoretical justification for their inclusion in the production function (equation 4). Age of the Producer (EP): The age of the producer is considered a proxy for the experience and accumulated knowledge that can enhance management practices and decision-making in dairy farming. Experienced producers are likely to be more efficient in utilizing resources and implementing effective production techniques, which can directly impact productivity. Number of Dependents (ND): In the context of family-run dairy farms, the number of dependents often correlates with the availability of additional family labor. This labor can be crucial in small-scale operations where family members contribute significantly to farm activities, thereby influencing overall productivity. We have clarified this theoretical justification in the revised manuscript to reflect the rationale behind including these variables as part of the production function. Additionally, we have corrected the subscripts and ensured that the methodological section accurately reflects the cross-sectional nature of our data. Thank you once again for your insightful comments, which have significantly contributed to improving the quality of our manuscript. Here is the theoretical justification: Reviewer # 1 [3]The way how environmental component was introduced into the model is completely incorrect. In this setting environmental pressure generated by the farms is not a part of production process which is an obvious error. For the ways of introducing environmental component into efficiency analysis see this review. Response to Reviewer # 1 Thank you for your thorough review and valuable feedback on our manuscript. We appreciate your insights and the opportunity to clarify our methodology. Response to the Comment on Environmental Component Integration Regarding your concern about the integration of the environmental component into our model, we respectfully disagree with your assertion that the environmental pressure generated by the farms is not a part of the production process. In our study, we aimed to capture the comprehensive impact of dairy farming, which includes both economic production and environmental consequences. The variables related to environmental pressure, such as greenhouse gas emissions (CH4) and water use per animal unit (CAE), are critical to understanding the overall efficiency and sustainability of the dairy production process. Theoretical Justification for Environmental Variables Greenhouse Gas Emissions (CH4): Methane emissions from enteric fermentation represent a significant environmental impact of dairy farming. Including CH4 in the inefficiency model allows us to account for the environmental pressures and their influence on production efficiency. By doing so, we acknowledge that environmental factors are intertwined with the production process and can affect the overall performance of the farm. Amount of Water Used per Animal Unit (CAE): Efficient water use is vital in dairy farming, particularly in areas where water scarcity can limit production. The amount of water used per animal unit reflects the farm's resource efficiency and can significantly impact productivity and environmental sustainability. Incorporating CAE in the inefficiency model aligns with our objective to evaluate how environmental resource management affects production efficiency. Our approach is supported by the literature, which emphasizes the importance of considering environmental factors in efficiency analysis. For instance, several studies have integrated environmental variables into stochastic frontier analysis to assess their impact on technical efficiency. Clarification of the Model To further clarify, our model does not treat environmental pressures as direct inputs in the production function but rather as factors influencing the inefficiency component. This distinction is crucial, as it allows us to evaluate how well farms manage both their production and their environmental impacts. Reviewer # 1 [4] From the practical point of view 102 observations is quite little for SFA model. I would rather implement DEA approach. Response to Reviewer # 1 Dear Reviewer, Thank you for your thorough review and valuable feedback on our manuscript. We appreciate your insights and the opportunity to address your concerns. Response to the Comment on the Sample Size and Methodology Regarding your comment on the sample size and the suggestion to use the DEA approach instead of the SFA model, we would like to provide the following clarifications and justifications: Sample Size Consideration While it is true that a larger sample size is generally preferred for robust statistical analysis, the application of the Stochastic Frontier Analysis (SFA) with 102 observations is still valid and has been documented in the literature. Several studies have successfully applied SFA with relatively small sample sizes, demonstrating its flexibility and applicability in various contexts. Justification for Using SFA Over DEA Statistical Noise Handling: One of the primary advantages of SFA over DEA is its ability to separate inefficiency from statistical noise. SFA incorporates a stochastic error term, which allows it to account for random shocks and measurement errors that may affect the production process. This is particularly important in our study, where environmental factors such as weather conditions can introduce variability that is beyond the control of the farmers. Parametric Nature: SFA is a parametric approach, which means it specifies a functional form for the production frontier. This allows us to make more precise inferences about the production technology and the relationship between inputs and outputs. In contrast, DEA is a non-parametric method and does not impose a specific functional form, which can lead to less precise efficiency estimates in the presence of noise. Integration of Environmental Variables: Our study aims to incorporate environmental variables such as greenhouse gas emissions (CH4) and water use per animal unit (CAE) into the efficiency analysis. SFA is well-suited for this purpose because it allows for the inclusion of these variables in the inefficiency model, providing insights into how environmental pressures impact production efficiency. DEA, while useful for certain applications, does not easily accommodate the integration of such explanatory variables in the same comprehensive manner. Literature Support: The use of SFA with smaller sample sizes is supported by several studies in agricultural economics and related fields. These studies demonstrate that SFA can yield meaningful and reliable results, even with a limited number of observations, provided the model is appropriately specified and the assumptions are met. Conclusion In conclusion, while we acknowledge the importance of sample size in statistical analysis, we believe that the application of the SFA model in our study is justified and appropriate given the context and objectives of our research. The SFA model's ability to handle statistical noise and incorporate environmental variables makes it a suitable choice for analyzing the efficiency of dairy farms in our dataset. We appreciate your suggestion to consider DEA, but we believe that SFA offers a more robust and insightful framework for our specific research goals. Reviewer # 1 [5]Regarding the presentation of the results. Efficiency scores are usually presented on density plot not linear trend. Also a full table with production function model parameters and their significance is missing. Response to Reviewer # 1 Dear Reviewer, Thank you for your insightful comments and suggestions regarding the presentation of our results. We appreciate your feedback and have taken steps to address the points you raised. Presentation of Efficiency Scores We agree that a density plot is more appropriate for presenting efficiency scores. We have replaced the linear trend plot with a density plot to better illustrate the distribution of the efficiency scores. This change provides a clearer visualization of the data. Inclusion of Model Parameters Table We acknowledge the importance of providing a full table with the production function model parameters and their significance. We have now included a comprehensive table in the manuscript, detailing the estimated coefficients, standard errors, t-values, and p-values for the model parameters. This addition enhances the transparency and interpretability of our results. The revised manuscript with these updates is attached for your review. We believe these changes address your concerns and improve the overall presentation of our findings. Reviewer # 1 [6] I don't understand why authors used geometric mean either. Response to Reviewer # 1 Dear Reviewer, Thank you for your continued feedback and for giving us the opportunity to clarify our methodology. Regarding your concern about the use of the geometric mean, we would like to explain the rationale behind this choice. In efficiency analysis, it is standard practice to use the geometric mean rather than the arithmetic mean to calculate average efficiency scores. This is because efficiency scores are typically multiplicative rather than additive, and the geometric mean provides a more accurate measure of central tendency for these types of data. Geometric Mean Justification: Nature of Efficiency Scores: Efficiency scores, by their nature, are ratios and often exhibit a skewed distribution. The geometric mean is more appropriate for such data because it minimizes the impact of extreme values, providing a more robust measure of central tendency. Multiplicative Data: In contexts where data are multiplicative, as is the case with efficiency scores, the geometric mean is more meaningful. It accurately reflects the central tendency of ratios and percentages, which are inherently multiplicative. Precedent in Literature: The use of geometric mean in efficiency analysis is well-documented and widely accepted in the literature. It ensures that the aggregated efficiency measure remains within the feasible range (i.e., between 0 and 1 for efficiency scores). By using the geometric mean, we aim to present a more reliable and interpretable measure of average efficiency, which aligns with best practices in the field of efficiency and productivity analysis. We hope this clarifies our approach. We appreciate your insights and are open to further discussion to improve our work. Reviewer # 1 [7] Regarding conclusions, they cannot be right as they are based on flawed model. Response to Reviewer # 1 Regarding the concern that our conclusions might be flawed due to an allegedly defective model, we respectfully disagree. We have thoroughly justified our model choice and the inclusion of environmental variables, as explained in our previous responses. The use of the geometric mean for efficiency scores and the integration of environmental factors into the inefficiency model are well-supported by existing literature and best practices in efficiency analysis. Our conclusions are based on robust statistical methods and significant results, demonstrating the reliability and relevance of our findings. We are confident that our model accurately captures the complexities of dairy farm efficiency and the impact of environmental factors. We appreciate your insights and hope that our explanations clarify the robustness of our model and the validity of our conclusions. Reviewer # 1 [8] To sum up, authors collected interesting data, but their empirical application has some serious drawbacks Response to Reviewer # 1 Dear Reviewer, Thank you for your thorough review and for recognizing the value of the data we collected. We appreciate your feedback and the opportunity to address your concerns. Response to the Comment on Empirical Application We acknowledge that the empirical application of our study has some limitations, as you have pointed out. However, we believe that the methodology we employed—Stochastic Frontier Analysis (SFA)—is appropriate for the objectives of our research. We have carefully considered the integration of environmental factors into the inefficiency model and provided a detailed justification for our approach. Addressing Specific Drawbacks Model Selection: We chose SFA over DEA because SFA allows us to incorporate statistical noise and provides a way to separate inefficiency from random error. This is particularly important in agricultural studies where external factors such as weather conditions can significantly affect production. Geometric Mean: The use of the geometric mean to report efficiency scores is a standard practice in efficiency analysis. It provides a more accurate representation of central tendency when dealing with ratio data, such as efficiency scores, which are bound between 0 and 1. Environmental Variables: Incorporating environmental variables like methane emissions (CH4) and water usage (CAE) into the inefficiency model is critical for understanding the broader impacts of dairy farming. These variables are not just peripheral but integral to assessing the sustainability and overall efficiency of agricultural practices. Moving Forward We are committed to further refining our empirical approach in future research. Your insights have been invaluable in highlighting areas for potential improvement. Specifically, we will consider exploring additional methodologies and robustness checks to enhance the reliability of our findings. Conclusion In conclusion, while there are always areas for improvement, we believe that our study provides significant insights into the efficiency and sustainability of dairy farming in Tlaxcala. We appreciate your constructive feedback, which will help us to strengthen our research and its contributions to the field. Finally, Dear Reviewer, Thank you for your valuable feedback and for providing the references to enhance our manuscript. We appreciate your insights and the opportunity to improve our work. Acknowledgment of References We have carefully reviewed the references you suggested: [1] Staniszewski J, Matuszczak A: \"Environmentally Adjusted Analysis of Agricultural Efficiency: A Systematic Literature Review of Frontier Approaches.\" Zagadnienia Ekonomiki Rolnej / Problems of Agricultural Economics. 2023; 374 (1): 20-41. [2] Dakpo, H., Desjeux, Y., Henningsen, A., Latruffe, L. : \"Stochastic Frontier Analysis Routines.\" 2023. https://cran.r-project.org/web/packages/sfaR/sfaR.pdf These references have been incorporated and cited in our revised manuscript. Their insights have helped us to better frame our methodology and contextualize our findings within the broader literature on agricultural efficiency and environmental impacts. Confirmation of Inclusion The references have been added to both the introduction and the methodology sections of our paper. They provide a robust foundation for our approach and support the integration of environmental factors into our efficiency analysis. Thank you once again for your constructive suggestions and for pointing us toward these valuable resources. We believe that their inclusion significantly strengthens our study." } ] } ]	2	https://f1000research.com/articles/11-1382
https://f1000research.com/articles/13-211/v1	21 Mar 24	{ "type": "Clinical Practice Article", "title": "Bilateral congenital muscular torticollis in infants, report of two cases", "authors": [ "Anna Öhman" ], "abstract": "Background Congenital muscular torticollis (CMT) is a well-known diagnosis among physiotherapists specializing in pediatric care, especially when working with infants. However, knowledge of bilateral torticollis is limited. The purpose of this article was to describe how bilateral torticollis can appear in infants.\n\nCase One infant with CMT with sternocleidomastoid tumor (SMT) on the right side, and some limitation in rotation towards the right side and in lateral flexion towards the left side, that is, the muscle on the right side was shortened. While sitting with support, he tilted the head to the left and was stronger in the lateral flexors on the left side which fit well with a postural left-sided torticollis (PT). The other infant had bilateral muscular torticollis (MT), the sternocleidomastoid muscle thickened bilaterally, and both active and passive rotations were affected. The head was held in flexion, and active rotation was severely limited to both sides. For both cases the therapeutic interventions were to gain a normal range of motion (ROM) and a good posture of the head.\n\nConclusions CMT can appear in different ways and may be bilateral. Both infants gained good ROM and better head position, however case I still needs some training. To gain more knowledge about bilateral CMT, we should follow these cases over a longer period of time. It is important to communicate and discuss our experiences with each other to understand rare cases of CMT.", "keywords": [ "Torticollis", "bilateral", "infant", "physiotherapy" ], "content": "Introduction\n\nCongenital muscular torticollis (CMT) is a common congenital musculoskeletal anomaly among infants. CMT results from shortening or excessive contraction of the sternocleidomastoid (SCM) muscle. A sternocleidomastoid tumor (SMT) may be visible one to four weeks after birth, which consists of fibrous tissue and disappears within a few months (Cheng, Tang and Chen, 1999; Kurtycz, Logrono, Hoerl and Heatley, 2000; Tang et al., 2002; Wei, Schwartz, Weaver and Orvidas, 2001; Ohman and Beckung, 2008). The head is typically tilted towards the affected muscle, and the chin is rotated towards the other side. The true etiology of CMT have been discussed; one hypothesis is that the condition could be the sequel of an intrauterine or perinatal compartment syndrome (Davis, Wenger, Mubarak, 1993), several studies are pointing in that direction (Bielski et al., 2006; Hardgrib, Rahbek, Möller-Madse and Maimburg, 2017; Lee et al., 2011a, 2011b; Pazonyi, Kun and Czeizel, 1982; Xiong et al., 2019). CMT can be divided into three groups: I SMT group with a clinically palpable sternomastoid tumor; II muscular torticollis group (MT) with tightness of the SCM muscle; and III postural torticollis group (PT) with all the clinical features of torticollis, but without the tightness or tumor of the SCM muscle (Cheng et al., 2001). Treatment for CMT is aimed to prevent facial and skull asymmetry, neck movement limitation, and long-term posture change. Treatment includes active positioning, active range of motion (ROM), stretching of the shortened muscle, strengthening of the contralateral muscle, and surgery.\n\nBilateral torticollis is rare and not often reported, Matuszewski, Pietrzyk, Kandzierski and Wilczynsk (2017) reported a case of a child with bilateral torticollis, referred to the orthopedic department at the age of 12 years. The first symptoms appeared at preschool age. This child had severe limitations in range of motion and required bilateral surgery (Matuszewski, Pietrzyk, Kandzierski and Wilczynsk, 2017). Babu et al., presented a case report of a 19-year-old girl with congenital bilateral sternocleidomastoid contracture (Babu, Lee, Mahadev and Lee, 2009).\n\nA few articles describing case reports of bilateral torticollis have not been published in English (Chiari, 1952; Kustos and Magdics, 1993; Shi et al., 2016; Shinoda and Yamada, 1969).\n\n\nCase I\n\nCase I was a Caucasian boy (3.5 months of age) who came to Friskispraktiken, a physiotherapy clinic, in Gothenburg, Sweden for a second opinion since the first examiner found it confusing, when the motion, muscle function/strength, and tilting of the head did not clearly fit left- or right-sided torticollis. I met this boy in October 2020. When he was 3.5 months of age, he had bilateral torticollis. On the right side, the patient had a sternocleidomastoid tumor and some limitation in rotation towards the right side and in lateral flexion towards the left side, that is, the muscle on the right side was shortened. When lying in the supine or prone position, he tilted the head to the right side and rotated to the left (Figure 1), which fit well with right-sided torticollis, SMT. While sitting with support, he tilted the head to the left (Figure 2) and was stronger in the lateral flexors on the left side (Figures 3 and 4), which fit well with a postural left-sided torticollis (PT). Muscle function and strength were measured using the Muscle Function Scale (MFS) (Figure 5) (Ohman and Beckung, 2008; Ohman, Nilsson and Beckung, 2009).\n\nThis is in agreement with right-sided torticollis. I confirm that I have obtained permission to use this image from the parents of the patient included in this presentation.\n\nThis is agreeable with left-sided torticollis. I confirm that I have obtained permission to use this image from the parents of the patient included in this presentation.\n\nThis is agreeable with left-sided torticollis. I confirm that I have obtained permission to use this image from the parents of the patient included in this presentation.\n\nThis is agreeable with left-sided torticollis. I confirm that I have obtained permission to use this image from the parents of the patient included in this presentation.\n\nWhen the Muscle Function Scale (MFS) is used, the infant is held in a vertical position and then lowered to the horizontal position in front of a mirror. The head position is observed and both sides are tested. Scores are given according to the head position in relation to the horizontal line. The infant must be observed with the head held in the same position for five seconds to obtain the score at that level. This figure has been reproduced/adapted from Ohman et al. (2009). Reprinted by permission of Informa UK Limited, trading as Taylor & Francis Group, www.tandfonline.com.\n\nTreatment involved stretching of the muscle on the right side, strength training on the right side as the left side was stronger, and tilting the head to the left in a vertical position. The treatment at that time gave quick results, equal strength in the lateral flexors of the neck, motion in lateral flexion, and rotation only a marginal difference.\n\nAt the follow-up at two years of age, he had relatively good motion and no head tilt, but he had an indication of a discreet muscular string on the right side. At the next follow-up at two and a half years of age, he had a discreet tendency to tilt the head to the right and was slightly stronger on the right side. The muscular string is still rather discreet and felt only when stretching the muscle. He has started treatment again, and the muscular string may worsen as he grows in height. The SCM muscle grows from about 4 cm in infants to 14 cm at 13 years of age, according to measures made by Jones (1968). Case I must be followed-up for a longer time, as there is a risk that he will need surgery later in life.\n\n\nCase II\n\nCase II was admitted to Friskispraktiken, Gothenburg, Sweden was a Caucasian girl (2.5 months of age), who was prenatally in breech presentation, and was turned by the healthcare provider some weeks before delivery. At the time of delivery, she was in a cephalic presentation and was fixed in the birth canal. In August 2020 at 2.5 months of age, she visited the clinic and was referred for moderate brachycephaly. It was also obvious that the neck was affected, the sternocleidomastoid muscle was thickened bilaterally, and both active and passive rotations were affected. The head was held in flexion (Figure 6), and active rotation was severely limited to both sides, less than 45° bilaterally (Figure 7). Passive rotation was close to 90°, but with a clear stop, the mean normal range of rotation for infants is 110° (19). Kinesiology taping was used as a complement, relaxing technique on both sides (Figure 8), and tape was applied across the sternocleidomastoid muscle on both sides. The parents worked with head control and stimulated motion in all the directions. They worked hard to stimulate rotation on both the left and right side. When taped, it was easier for her to move the head with a greater range of motion. When she was about five months old, the problem was solved, and she had a good head position and active rotation of approximately 80° bilaterally and passive rotation >90° bilaterally. However, after reading the case reported by Matuszewski et al. (2017) I decided to check her again.\n\nI confirm that I have obtained permission to use this image from the parents of the patient included in this presentation.\n\nI confirm that I have obtained permission to use this image from the parents of the patient included in this presentation.\n\nI confirm that I have obtained permission to use this image from the parents of the patient included in this presentation.\n\nAt the age of nearly three years, she had an active rotation of 70° bilaterally and passive rotation of 90° bilaterally. Passive lateral flexion was full (i.e., ear to shoulder bilateral). Muscle function and strength were assessed bilaterally according to the MFS scale she scored 4 bilaterally. The marginal flexion of the head might be within the normal span. I have decided to follow her once a year for at least some years to ensure that it stays good.\n\n\nDiscussion\n\nThe combination of SMT and PT on different sides is, to my knowledge, not reported; there are probably more cases even though it might be rare. There may also be more cases than expected, but it is easy to miss if they are very mild. The current described case first met a less experienced physiotherapist, and it is understandable that she became confused. Torticollis is usually on one side, right- or left-sided. It is important to have good documentation, and if the examiner feels unsure, ask for a second opinion from a more experienced colleague. The examiner must follow the progress attentive and carefully adjust the treatment.\n\nAs the muscle grows to about 10 cm during the child’s skeletal growth, in the first 13 years, it may be important to follow up during childhood. This will ensure that skeletal growth problems will eventually be discovered early. In my experience, adults with neglected CMT have difficulty finding physicians or physiotherapists who understand that they have experienced CMT. Even with a clear muscular string and a typical head position, some adults do not receive a correct diagnosis and treatment. For a clinician with experience in children who need surgery for CMT, an adult with the same problem is easy to recognize. However, bilateral torticollis is more confusing, and more knowledge of its long-term effects is needed.\n\nBilateral sternocleidomastoid tumors have been reported, with or without torticollis (Dangi and Gwasikoti, 2020; Kumar, Prabhu, Chattopadhayay and Nagendhar, 2003; Tufano, Tom and Austin, 1999). However, not much information is available on long-term results. Neck problems are not uncommon among adults, and we should be aware that there could have been an earlier bilateral torticollis that contributed to this problem.\n\n\nConclusions\n\nCMT can appear in different ways and may be bilateral. To gain more knowledge about bilateral CMT, we should follow these cases over a longer period of time. It is important to communicate and discuss our experiences with each other to understand rare cases of CMT.\n\n\nConsent\n\nWritten informed consent for publication of their clinical details and clinical images was obtained from the parents of the patients.", "appendix": "Data availability\n\nAll data underlying the results are available as part of the article and no additional source data are required.\n\n\nAcknowledgements\n\nMany thanks to the parents for allowing me to use their infants’ information and photos.\n\n\nReferences\n\nBabu MK, Lee P, Mahadev A, et al.: Congenital bilateral sternocleidomastoid contracture: a case report. J. Pediatr. Orthop. B. 2009; 18(3): 145–147. PubMed Abstract \| Publisher Full Text\n\nBielski RJ, Gesell MW, Teng AL, et al.: Orthopaedic implications of multiple gestation pregnancy with triplets. J. Pediatr. Orthop. 2006; 26(1): 129–131. PubMed Abstract \| Publisher Full Text\n\nCheng JCY, Wong MWN, Tang SP, et al.: Clinical determinants of the outcome of manual stretching in the treatment of congenital muscular torticollis in infants. J. Bone Joint Surg. Am. 2001; 83: 679–687. PubMed Abstract \| Publisher Full Text\n\nCheng JCY, Tang SP, Chen TMK: Sternocleidomastoid pseudotumor and congenital muscular torticollis in infants: A prospective study of 510 cases. Pediatrics. 1999; 134(6): 712–716. PubMed Abstract \| Publisher Full Text\n\nChiari K: Bilateral torticollis. Z. Orthop. Ihre Grenzgeb. 1952; 83(1): 151–153. Undetermined Language. PubMed Abstract\n\nDangi S, Gwasikoti N: A Case of Bilateral Sternocleidomastoid Tumor in a Neonate: Case Report. Clin. Pediatr. (Phila). 2020; 59(7): 723–724. PubMed Abstract \| Publisher Full Text\n\nDavis J, Wenger D, Mubarak S: Congenital muscular torticollis: Sequela of intrauterine or perinatal compartment syndrome. J. Pediatr. Orthop. 1993; 13: 141–147.\n\nHardgrib N, Rahbek O, Möller-Madse, et al.: Do obstetric risk factors truly influence the etiopathogenesis of congenital muscular torticollis. J. Orthop. Traumatol. 2017; 18(4): 359–364. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJones P: Torticollis in infancy and Childhood. Springfield, Illinois: Charles C Thomas; 1968.\n\nKumar V, Prabhu BV, Chattopadhayay A, et al.: Bilateral sternocleidomastoid tumor of infancy. Int. J. Pediatr. Otorhinolaryngol. 2003; 67(6): 673–675. PubMed Abstract \| Publisher Full Text\n\nKurtycz DF, Logrono R, Hoerl HD, et al.: Diagnosis of fibromatosis colli by fine-needle aspiration. Diagn Cyto-pathol. 2000; 23: 338–342. PubMed Abstract \| Publisher Full Text\n\nKustos T, Magdics M: Bilateral torticollis. Orv. Hetil. 1993 Dec 19; 134(51): 2817–2820. Hungarian. PubMed Abstract\n\nLee SJ, Han JD, Lee HB, et al.: Comparison of Clinical Severity of Congenital Muscular Torticollis Based on the Method of Childbirth. Ann. Rehabil. Med. 2011a; 35: 641–647. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLee YT, Cho SK, Yoon K, et al.: Risk factors for intrauterine constraint are associated with ultrasonographically detected severe fibrosis in early congenital muscular torticollis. J. Pediatr. Surg. 2011b; 46(3): 514–519. PubMed Abstract \| Publisher Full Text\n\nMatuszewski L, Pietrzyk D, Kandzierski G, et al.: Bilateral congenital torticollis: a case report with 25 years of follow-up. J. Pediatr. Orthop. B. 2017; 26(6): 585–588. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nOhman A, Beckung E: Reference values for range of motion and muscle function in the neck - in infants. Pediatr. Phys. Ther. 2008; 20: 53–58. PubMed Abstract \| Publisher Full Text\n\nOhman A, Nilsson S, Beckung E: Validity and reliability of the Muscle Function Scale, aimed to assess the lateral flexors of the neck in infants. Physiother. Theory Pract. 2009; 25(2): 129–137. PubMed Abstract \| Publisher Full Text\n\nÖhman A, Beckung E: Functional and cosmetic status in children treated for congenital muscular torticollis as infants. Adv. Physiother. 2005; 7(3): 135–140. Publisher Full Text\n\nPazonyi I, Kun A, Czeizel A: Congenital postural deformity association. Acta Paediatr. Acad. Sci. Hung. 1982; 23(4): 431–445. PubMed Abstract\n\nShi XL, Li CS, Zhou KP, et al.: Congenital bilateral sternocleidomastoid contracture: a case report. Zhongguo Gu Shang. 2016; 29(1): 86–88. Article in Chinese. PubMed Abstract\n\nShinoda T, Yamada E: Bilateral torticollis muscularis. Seikei Geka. 1969 Jul; 20(9): 985–990. Japanese. PubMed Abstract\n\nTang SF, Hsu KH, Wong AM, et al.: Longitudinal followup study of ultrasonography in congenital muscular torticollis. Clin. Orthop. 2002; 403: 179–185. PubMed Abstract \| Publisher Full Text\n\nTufano RP, Tom LW, Austin MB: Bilateral sternocleidomastoid tumors of infancy. Int. J. Pediatr. Otorhinolaryngol. 1999 15; 51(1): 41–5. PubMed Abstract \| Publisher Full Text\n\nWei JJ, Schwartz KM, Weaver AL, et al.: Pseudotumor of infancy and congenital muscular torticollis: 170 cases. Lanryngoscope. 2001; 111: 688–695. PubMed Abstract \| Publisher Full Text\n\nXiong Z, Zeng S, Chen H, et al.: Unique finding in congenital muscular torticollis. Clinic screening on the neck of one day old neonate and ultrasonographic imaging from birth through 3 years of follow-up. Medicine (Baltimore). 2019; 98(11): e14794. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "264886", "date": "02 May 2024", "name": "Kimberly B. Castle", "expertise": [ "Reviewer Expertise Pediatric physiotherapy with specific emphasis on core trunk and neck control including torticollis" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 topic of interest to many pediatric physiotherapists and pediatricians. There is benefit in disseminating the information from these cases.\nDetails of the second case are much more specific than those of the first case. It is difficult to understand the exact extent of the first infant's passive limitation even with the photographs as there are no measures or estimates of limitations beyond the Muscle Function Scale.\n\nAs Dr. Ohman is the creator of the MFS, the evaluations using the tool are deemed to be accurate. However, the photos appear to show a difference in the trunk alignment of the infant when held to each side. Is the reader to assume that the infant is righting the trunk to some extent in addition to righting the head to the left (first MFS photo)? If not, is there a photo in which the therapist's hands support the trunk similarly that would allow comparison? Perhaps a brief explanation of the difference would be helpful for interpretation.\nIn the second case, was the flexed neck posture true neck flexion or rather a forward head posture with cervical flexion & capital extension? It is difficult to assess from the lateral photo and would be interesting to know if SCM were the only muscles that were tight or if there was increased tension in posterior neck musculature as well.\nFinally, the discussion including typical growth in the muscular and skeletal growth throughout childhood was helpful. It would also be helpful to include a synopsis of how passive and active components impacted these children's posture and active movement depending on posture, position and the effects of gravity.\n\nIs the background of the cases’ 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 conclusion balanced and justified on the basis of the findings? Yes", "responses": [ { "c_id": "11626", "date": "28 Jun 2024", "name": "Anna Öhman", "role": "Author Response", "response": "Author response: Thanks for all valuable comments, there are a lot more to discuss about CMT, Your review add some new thoughts." } ] }, { "id": "264882", "date": "09 May 2024", "name": "Lucie Pelland", "expertise": [ "Reviewer Expertise Biomechanics", "neuroscience", "pediatrics" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe topic is relevant to practice as bilateral torticollis is a rare clinical presentation. As stated by the author, a bilateral presentation can lead to uncertainty in diagnosis.\n\nThe Introduction could be improved in terms of the logical flow of information provided. As an example, possible causes of CMT are presented, including SCM tumor and intra-uterine or perinatal compartment syndrome. I suggest that these possible causes be related to the three clinical CMT groups presented. This would tie in how compartment syndrome relates to this classification. The author should also consider introducing the MFS in the introduction and present a rationale on how the MFS, within a standardized clinical assessment, could provide an approach to avoid a missed diagnosis of bilateral CMT. The introduction should end with the statement of aim provided in the abstract - which could be modified as follows: Our purpose was to describe the clinical presentation of bilateral CMT to improve diagnosis.\n\nIn the cases, there is no need to include the clinic where the clinical evaluation was performed. This information is provided in the author's contact. The language used should be formalized for scientific writing (e.g., 'I met this boy in October 2020' should be stated as 'On clinical examination in October 2020'). It might be clearer to align the figures for the two cases with the MFS and to provide the score for each Figure. For Case I, I would place Figures 3 and 4 side by side to more clearly show that the left SCM is stronger than the right. As well, in Figure 1, it is not clear if the head position may have been influenced by the asymmetric positioning of the upper limbs in prone support. In case II, the HEP for parents is not clear - as well, was kinesiotaping applied at home? This would be important information for clinicians treating infants with bilateral CMT. For Case II, the figures do clearly show the forward head flexion. For clarity, I would suggest, again, that all positions in the MFS should be shown. This would help to problem solve the clinical presentation (which is the aim of the paper). The quality of the images in Figure 5 needs to be improved.\n\nThe discussion repeats information that has been presented in the cases and in the introduction. I suggest that the discussion should focus on providing the structured approach, including the MFS, that should be used to avoid 'missing the diagnosis' of bilateral CMT. Treatment could be summarized in alignment with the clinical findings, providing a translation of findings to practice to improve patient outcomes.\n\nGeneral Comments: 1. There is a need for improving grammar and sentence structure throughout. 2. In the abstract, avoid using abbreviations that are only used once. 3. Specificity of terminology needs to be verified (e.g., in the abstract, 'how bilateral torticollis can appear in infants' would be better stated as 'how bilateral torticollis may present clinically'. 4. Once a term is abbreviated (e.g., SCM for sternocleidomastoid) it should then be used consistently.\n\nOverall, this is a clinically relevant paper which focuses on an area of pediatric practice which requires further evidence.\n\nIs the background of the cases’ history and progression described in sufficient detail? Partly\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? No\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? No\n\nIs the conclusion balanced and justified on the basis of the findings? No", "responses": [ { "c_id": "11627", "date": "28 Jun 2024", "name": "Anna Öhman", "role": "Author Response", "response": "Thanks for all valuable comments made changes and added information, hopefully made the manuscript better. New grammar check was also done" } ] } ]	1	https://f1000research.com/articles/13-211
https://f1000research.com/articles/13-648/v1	17 Jun 24	{ "type": "Research Article", "title": "RNA-sequencing Reveals Altered Gene Expression in the Ventromedial Hypothalamus Following Predator Odor Exposure", "authors": [ "Ashely Shemery", "Megan Gibson", "Erin Gorrell", "Diamond Daniel", "Helen Piontkivska", "Colleen M Novak", "Ashely Shemery", "Megan Gibson", "Erin Gorrell", "Diamond Daniel", "Helen Piontkivska" ], "abstract": "Background Physical activity is the second largest contributor to our total daily energy expenditure (EE). Uncovering ways to increase EE during activity could yield new approaches to treat obesity. The ventromedial hypothalamus (VMH) regulates body weight by modulating muscle metabolism and sympathetic nervous system (SNS) activity. The VMH also mediates behavioral responses to predator threat. While the VMH is a potential mediator of metabolic responses to predator threat, the mechanisms are unknown.\n\nMethods and Results Exposing rats to predator odor (PO) exposure causes a rapid increase in skeletal muscle thermogenesis that peaks between 20-30 min and dissipates to baseline by 4 hr. This thermogenic response is associated with weight loss and increased EE even when controlling for physical activity. To probe potential targets of PO-induced metabolic responses in the VMH, we first performed qPCR for genes known to be involved in brain regulation of muscle metabolism using VMH samples from rats exposed to PO or control odor for either 30 min or 4 hr. Next, to uncover novel, relevant genes, we performed RNA-sequencing on VMH samples of rats exposed to either PO or control odor for 20 min. qPCR results show that after 4 hr of PO exposure, Bdnf and Sirt1 expression were increased. RNA-sequencing analyses further identified 245 differentially expressed genes (DEGs) that showed at least 1.5-fold change in expression due to PO exposure. Functional and Gene Ontology annotation showed that pathways related to immune response, oxidative stress, and synaptic plasticity were overrepresented among these DEGs.\n\nDiscussion Taken together, these findings suggest that acute PO exposure induces both rapid and delayed changes in VMH gene expression that likely have downstream metabolic consequences.", "keywords": [ "Predator threat", "skeletal muscle", "thermogenesis", "corticosterone", "sirtuin", "BDNF", "SF-1" ], "content": "1. Introduction\n\nNon-exercise activity thermogenesis (NEAT) is the strongest predictor of resistance to weight gain with overfeeding, making it a promising target for obesity treatments (Levine et al., 1999). Understanding the cellular and molecular mechanisms underlying brain regulation of energy expenditure (EE) is critical when exploring ways to manipulate NEAT. The ventromedial hypothalamus (VMH) plays a necessary role in energy homeostasis through its regulation of autonomic nervous system activity and its complex connections with other brain regions involved in feeding and thermoregulation (King, 2006). Activation of the VMH induces sympathetic nervous system (SNS) drive to white adipose tissue (WAT), brown adipose tissue (BAT), and skeletal muscle, which was associated with increased thermogenesis in BAT and skeletal muscle (Gavini et al., 2016). Additionally, the VMH mediates multiple behavioral responses including aggression (Falkner et al., 2016; Hashikawa et al., 2017), fear responses and memories (Silva et al., 2016), and aversion to predator odor (Perez-Gomez et al., 2015). Though not fully understood, the processing of both metabolic signals and predator threat by the VMH reflects the shared importance of SNS outflow in both systems.\n\nCentral regulation of BAT thermogenesis and WAT browning have been heavily investigated for their potential to increase EE in small rodents (Morrison et al., 2014). Though far less investigated, skeletal muscle has a substantial capacity for increasing EE and is clinically relevant as it makes up 40% of total human body mass and accounts for 20-30% of total resting oxygen uptake (Zurlo et al., 1990; Janssen et al., 2000; van den Berg et al., 2011). Ferret predator odor (PO) exposure to rats causes a rapid increase in skeletal muscle thermogenesis, likely due to SNS activation, that peaks between 20-30 min and dissipates over the course of a few hours (Gorrell et al., 2020). Chronic PO exposure for 3 weeks decreases body weight without changing food intake, physical activity, or BAT thermogenesis in mice (Genne-Bacon et al., 2016), suggesting potential involvement of skeletal muscle. As a dual processor of metabolic and predator threat responses, the VMH is a likely mediator of PO-induced skeletal muscle thermogenesis, though the underlying cellular and molecular mechanisms have remained unexplored.\n\nIn the brain, expression of the transcription factor steroidogenic factor 1 (SF-1) is restricted to the VMH, where it is required for VMH development and vitality as well as normal energy balance and response to predator threat (Ikeda et al., 1995; Shinoda et al., 1995; Kunwar et al., 2015). The VMH, including the SF-1 cell population found there, regulates energy balance by engaging SNS outflow to regulate peripheral tissue metabolism and counteract hypoglycemia (King, 2006). Importantly, increased VMH SF-1 expression improves skeletal muscle metabolism and is associated with increased SNS activation (Kim et al., 2012). In addition to SF-1, at least two other genes in the VMH may be critical in SNS-driven skeletal muscle metabolism, namely Bdnf and sirtuin 1 (Sirt1). Within the VMH, BDNF is positively associated with and is a downstream target of SF-1 (Tran et al., 2006). VMH BDNF microinjections activate the SNS and amplify EE by increasing physical activity and resting metabolic rate in the absence of BAT activation (Wang et al., 2010), suggesting potential contribution from skeletal muscle. SIRT1 is a metabolic sensor protein expressed in many tissues where it regulates metabolism in response in nutrient availability (Imai et al., 2000; Ramadori et al., 2008). Over- and under-expression of SIRT1 in VMH SF-1 neurons reveals that SIRT1 protects against dietary obesity by regulating EE as well as skeletal muscle glucose uptake (Ramadori et al., 2011). Moreover, SF-1, BDNF, and SIRT1 expression levels in the brain are all associated with psychological stressors, making these genes possible candidates involved in VMH regulation of skeletal muscle thermogenesis following PO exposure (Rage et al., 2002; Kunwar et al., 2015; Yu et al., 2018). However, although PO induces c-fos in the VMH (Masini et al., 2005), there is virtually no information regarding the cellular and molecular alterations that follow. Here, we explored changes in VMH expression of Sf-1, Bdnf, and Sirt1 in response to PO exposure at time points with thermogenic relevance to the predator-threat response. Additionally, we performed RNA-sequencing to explore transcriptome-wide changes in VMH gene expression after acute PO exposure. Collectively, our results suggest PO causes rapid and delayed transcriptional changes in the VMH that are associated with inflammation, oxidative stress, and synaptic plasticity.\n\n\n2. Methods\n\nAll experiments used Sprague-Dawley rats (Envigo) individually housed in a temperature-controlled room (24°C ± 1°C) on a 12/12 hr light/dark cycle with lights on at 7:00AM and light off at 7:00PM EST. Rats were given free access to both water and standard laboratory chow (5P00 Prolab RMH 3000, LabDiet, St. Louis, MO, USA). To verify the time-course of the muscle thermogenic response, we used 7 rats (3 female, 4 male). For RNA-sequencing, we used 6 male rats. For qPCR and corticosterone assays, we used 24 male rats. All procedures were approved by Kent State University Institutional Animal Care and Use Committee; sample sizes were determined based on prior effect sizes (Gorrell et al., 2020), with random assignment to experimental condition. Exposure to odor precluded blinding to experimental group or condition. Efforts were made to ameliorate suffering and minimize distress of animals using analgesics before and after surgical procedures, anesthesia, and habituation prior to exposure to potentially stressful contexts.\n\nChanges in skeletal muscle temperature in response to predator-odor or control-odor stimuli were measured using surgically implanted temperature transponders (implantable programmable temperature transponder-300; IPTT-300, BioMedic Data Systems, Seaford, DE; calibrated range 32°-43°C); transponders were used that had showed high correlation compared with water-bath temperature (R2 ≥ 0.97) as well as in vivo with rectal temperature in the physiological range (R2 ≥ 0.97) (Wacker et al., 2012). Transponders are 14 mm long and 2 mm in diameter, sufficiently small to surgically implant into the gastrocnemius muscle group bilaterally in rats. Transponders were implanted under surgical anesthesia, with 5% isoflurane for induction followed by 2-3% for maintenance. Animals were given 1 week to recover.\n\nControl odor or predator odor exposure was achieved by dropping a fragment (1-2” × 2”) of a clean towel or an identical towel that had been used as bedding for ferrets (Mustela putorius furo) for 2 weeks (Marshall BioResources, North Rose, NY) into the rat’s home cage. All animals were habituated to handling as well as daily exposure to control odor in their home cages for 2 weeks prior to experimental odor exposure. For the thermogenic time course experiment, animals were exposed to both PO and control odor (identical towels without contact with ferrets; Marshall BioResources), each on separate experimental days separated by 1 week. Due to potential odor contamination, we declined to counterbalance odor exposure, though order effects have previously been ruled out as a contributor to PO-induced thermogenesis (Gorrell et al., 2020). Thus, to remain consistent with habituation, all animals were exposed to control odor first. At 3 hrs after lights-on, baseline temperatures were measured using a transponder reader (DAS-7007S; IPTT-300, BioMedic Data Systems, Seaford, DE) to manually retrieve transponder temperature data. To minimize human interference during measurements, animal cages are placed on PVC stands (122 cm × 30 cm × 30 cm) that expose the underside of the cage. The transponder reader can rapidly, accurately, and reliably measure temperature through the cage bottom. Following odor exposure, temperatures were measured at defined timepoints for 4 hr following odor exposure.\n\nFor RNA-sequencing, animals were exposed to either control odor (n = 3) or predator odor (n = 3), as described above, for 20 minutes. Animals were then anesthetized via 5% isoflurane inhalation and rapidly decapitated using a guillotine. Brains were dissected out then flash frozen in 10-20 ml isopentane (2-methylbutane; MilliporeSigma #320404) chilled on dry ice. Bilateral micropunches of the VMH were collected. Briefly, brains were coronally sectioned using a cryostat up to the start of the VMH. A micropunching tool 1mm in diameter and 1.5mm in length was inserted into the VMH and samples were ejected into microcentrifuge tubes. Samples were stored in a freezer at -80°C until processing.\n\nFor qPCR and corticosterone assays, animals were exposed, as described above, to either control odor for 30 minutes (n = 6) or 4 hours (n = 6), or predator odor for 30 minutes (n = 6) or 4 hours (n = 6). Animals were then anesthetized via isoflurane inhalation and rapidly decapitated using a guillotine. Brains were dissected out and flash frozen in isopentane chilled on dry ice. Trunk blood was collected in 4mL BD Vacutainer™ Plastic Blood Collection Tubes with K2 EDTA using a freshly cleaned plastic funnel. Tubes were inverted to mix then centrifuged at 2,000 × g for 15 minutes at 4°C to separate plasma. Plasma was pipetted into 1.5mL microtubes and stored in the -80 until needed.\n\n2.4.1 RNA isolation, purification and quality check\n\nTo isolate and purify high quality RNA from small VMH micropunches, we performed a technique combining the use of TRIzol and silica-based columns. Micropunches were sonicated in 250 uL of TRIzol™ Reagent (Thermofisher Scientific, Waltham, MA). 50 uL of chloroform was added to homogenate and incubated at room temperature for 5 minutes to facilitate phase separation. Samples were centrifuged at 12,000 × g for 15 minutes at 10°C. The aqueous layer (~100 uL) was pipetted into a fresh microcentrifuge tube and mixed with an equal volume of ice-cold 70% ethanol to precipitate mRNA. The mixture was then pipetted onto a silica-based column membrane (Invitrogen™ PureLink™ RNA Mini Kit, Thermofisher Scientific, Waltham, MA). Samples were centrifuged at 12,000 × g for 30 seconds at 10°C and the supernatant was discarded. Samples were washed as directed by kit instructions. RNA was eluted into a fresh collection tube with 30 uL of nuclease-free water. RNA concentration and quality were assessed using a spectrophotometer. All samples had 80-110 ng/uL, a 260/280 ratio of 2.0-2.1, and a 260/230 ratio of 1.8-2.0. Samples were stored in a freezer at -80°C until processing.\n\n2.4.2 RNA library preparation\n\nRNA samples were shipped to Novogene Bioinformatics Technology Company, Ltd. (Sacramento, CA) for sequencing. Before processing, RNA samples passed an integrity and purity assessment via the Qubit® Fluorometer (Invitrogen, ThermoFisher, Waltham, MA) and Agilent Bioanalyzer® RNA 6000 Nano/Pico Chip (Agilent Technologies, Santa Clara, CA) with an RNA Integrity Number of ≥ 7. RNA sample libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA). Briefly, poly-A mRNA was isolated and purified from total RNA before being fragmented and primed with random primers. Following double-stranded cDNA synthesis, ends were repaired and tagged for adaptor ligation. Finally, 250-300bp fragments were isolated and enriched by PCR.\n\n2.4.3 RNA library quality check\n\nHigh-quality RNA library yield and quality were assessed and confirmed using a Bioanalyzer Agilent DNA 1000 Chip (Agilent Technologies, Santa Clara, CA). Sample libraries were sequenced by the Illumina HiSeq 4000 system using CASAVA v1.8 software (Illumina Biotechnology Co., San Diego, CA) with a paired-end 150bp sequencing strategy and sequencing depth of ~5 million reads. An extensive data quality assessment confirmed all sample libraries yielded between 4.6-5.8 million clean reads, 6.9-8.8G clean reads, a base calling error rate of 0.03%, a Q30 score of >93%, and a GC content of 50%.\n\n2.4.4 Mapping reads to rat genome\n\nRaw reads were filtered to remove reads containing adapters, reads containing poly-N, and low quality reads. Clean reads were mapped to the Ensembl Rattus norvegicus Rnor_5.0 version 79 reference genome using the hierarchical indexing for spliced alignment of transcripts 2 (HISAT2) algorithm v2.1.0-beta (Kim et al., 2014; Kim et al., 2015; Cunningham et al., 2019). Briefly, the algorithm identifies all represented splice sites. Then, it aligns reads to a single exon of the genome. These reads are segmented and mapped to the adjacent exons. Reads are further segmented and mapped to several exons. A quality assessment revealed that all sample libraries achieved a mapping rate of ~95%, with approximately ~6% of reads mapping to multiple areas of the genome.\n\n2.4.5 Gene expression quantification and quality check\n\nHTSeq v0.6.1 was used to count reads mapped to each gene or exon using union mode where each gene is the union of all its exons (Anders et al., 2015). To normalize mapped read counts, gene expression quantification is expressed in fragments per kilobase of transcript sequence per million base pairs sequenced (FPKM) (Mortazavi et al., 2008). RNA-sequencing requires biological replicates to ensure accuracy (Liu et al., 2014). Here, we have 3 replicates per group. Pearson’s correlation coefficient analysis confirms that the genes expressed in each of the control group replicates (r2 = 0.98) as well as the experimental group replicates (r2 = 0.98) are highly correlated indicating minimal intragroup variance.\n\n2.4.6 Differential gene expression analysis\n\nDifferentially expressed genes were analyzed for statistical significance using DESeq2 v1.38.3 (Love et al., 2014) using HTSeq counts. The Benjamini-Hochberg procedure was used to control the false discovery rate (FDR) (Benjamini and Hochberg, 1995). Adjusted p value (padj) cut-off of 0.05 and a fold change of 1.5 were used to identify 245 differentially expressed genes (Table S1). A relatively relaxed fold-change cut-off was used to ensure the capture of a broader set of potentially relevant DEGs.\n\n2.4.7 Functional annotation, pathway and gene ontology (GO) enrichment analysis\n\nWe further focused on 186 out of 245 DEGs that corresponded to protein-coding genes (Table S1). Functional annotation and protein-protein interaction analysis was performed using STRING ver. 12.0 (Szklarczyk et al., 2023), followed by annotation and pathway enrichment analysis using ClueGO plug-in v2.5.9 (Bindea et al., 2009) for Cytoscape (Shannon et al., 2003). We focused on KEGG, Molecular Function and Immune System Process ontologies in ClueGO, using two-sided hypergeometric test with Benjamini-Hochkins correction for multiple tests. To be considered a cluster, the cut-off of at least 3 genes representing at least 4% of all genes in that category must be present. The leading group terms (shown with the largest circles) are based on the largest number of genes in that category (see also Table S2). Additional Gene Ontology annotations and enrichment analyses were performed using DAVID (The Database for Annotation, Visualization and Integrated Discovery, ver. v2023q3) (Sherman et al., 2022) and ShinyGO 0.77 (Ge et al., 2020), with respective FDR cut-offs of 0.05.\n\n2.4.9 Accession to RNA-seq data\n\nData are deposited in NCBI GEO with accession number GSE142617. To review the GEO accession, see https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE142617.\n\nPlasma corticosterone was assayed using the Enzo corticosterone ELISA kit (#AD1-900-097, Enzo Life Sciences, Farmingdale, NY). Thawed plasma samples were diluted 1:25 by pipetting 10 uL of plasma sample into microtubes containing 240 uL of nuclease-free water and mixing. To dissociate corticosterone from carrier proteins, samples were incubated in a water bath at 70°C for 1 hr; we found this to be more effective than the steroid displacement technique recommended in the kit instructions. With this exception, the rest of the assay was carried out following kit instructions.\n\nApproximately 160 ng of isolated RNA was reversed transcribed using the High-Capacity cDNA Reverse Transcription Kit (Applied Biosystems, Cheshire, UK). The target cDNA was amplified by PCR. All qPCR assays were carried out in triplicate using the Brilliant III Ultra-Fast QPCR Master Mix (Agilent Technologies; Santa Clara, CA) and using PrimeTime Gene Expression Probes (IDT DNA Technologies). The assay identification numbers for each gene are: Nr5a1 (Rn.PT.58.33726779), Sirt1 (Rn.PT.58.44487135), Bdnf (Rn.PT.58.13660615), Gapdh (Rn.PT.39a.11180736.g). The cDNA quantities were normalized by using the housekeeping gene Gapdh as a reference and the Δct method (Schmittgen and Livak, 2008) was used to analyze relative gene expression. Results are displayed as a percentage of baseline.\n\nAll data are expressed as the mean ± SEM. Statistical analyses were performed using IBM® SPSS® Statistics software version 26 (https://www.ibm.com/support/pages/spss-statistics-v26-now-available). Figures were created using Systat Software Inc. SigmaPlot version 14.0 (https://grafiti.com/download-sigmaplot-software/). When applicable, normality distribution was tested with the Shapiro-Wilk normality test. For the thermogenic time course following odor exposure experiment, differences between PO and control odor exposure were analyzed using a 2-way repeated measures ANOVA (odor: PO or control odor; time: 15 time points) followed by Bonferroni post-hoc tests (Table 1). Post-hoc paired samples t-tests were performed following significant main effects and interactions. Differences in plasma corticosterone levels and VMH expression of Sirt1, Bdnf, and Sf1 were analyzed using 2-way ANOVAs (odor, PO or control odor; time, 30 min or 4 hr). RNA-sequencing data were performed as described above. The level of significance was set at p ≤ 0.05.\n\n\n3. Results\n\nGorrell et al. (2020) reported that PO exposure increased muscle thermogenesis, peaking between 15-30 min, but did not observe its full time-scale capacity. Our goals here were to (1) isolate the thermogenic contribution of skeletal muscle from other potential thermogenic tissues following PO, and (2) capture the full length of the PO-induced thermogenesis. To achieve this, we measured gastrocnemius temperature via surgically implanted transponders at regular intervals until temperatures returned to baseline.\n\nFigure 1 shows that PO exposure rapidly increased gastrocnemius muscle thermogenesis, peaking at 20 min (X¯ = 1.60°C) and dissipating near baseline by 4 hr (X¯ = 0.06°C). A two-way repeated-measures ANOVA of raw temperature change showed a main effect of odor, F(1, 6) = 107.76, p < 0.001, where PO exposure resulted in higher muscle temperatures (X¯ = 36.84°C, SEM = 0.15°C) compared to exposure to control odor (X¯ = 35.86°C, SEM = 0.13°C). Follow-up t-tests indicated that PO significantly increased thermogenesis from baseline beginning 5 min after PO exposure and persisting for 3.5 h. There was also a significant interaction between odor and time, F(14, 84) = 11.99, p < 0.001, where PO increased thermogenesis more than control odor and the magnitude of this difference changed with time.\n\nGastrocnemius muscle temperature (A) and temperature (temp) change from baseline (B) across time following odor (PO) exposure. Significant difference between baseline temperature and timepoint temperature within PO condition, p < 0.05; ϮSignificant difference between PO and control odor, p < 0.05; PO, predator odor; CTL, control odor.\n\nTo control for individual differences in muscle temperature, we performed a two-way repeated measures ANOVA on temperature change from baseline which revealed the same pattern as raw temperature change with a main effect of odor, F(1, 6) = 93.08, p < 0.001, where PO (X¯ = 1.09°C, SEM = 0.10°C) increased muscle thermogenesis more than control odor (X¯ = 0.98°C, SEM = 0.05°C). Follow up t-tests indicated that PO significantly increased thermogenesis from baseline beginning 5 min after PO exposure and persisting for 3.5 h. There was also a significant interaction between odor and time, F(14, 84) = 11.99, p < 0.001, where PO increased thermogenesis more than control odor and the magnitude of this difference changed with time.\n\nSkeletal muscle is a major target of corticosterone where it can cause proteolysis to rapidly increase energy availability during psychologically stressful events (Bodine and Furlow, 2015). Acute increases in corticosterone are beneficial, but chronic increases can cause muscle atrophy (Tomas et al., 1979). Just 10 min of ferret exposure significantly increases plasma corticosterone levels which dissipate near control levels after 1 hr in rats (Roseboom et al., 2007). However, it is unknown if corticosterone levels remain elevated following 4 hr of constant PO exposure. We found that PO exposure significantly increased plasma corticosterone after 30 min but not 4 hr (Figure 2). A two-way ANOVA showed a significant interaction between time and odor, F(1, 20) = 11.55, p = 0.003, where PO (X¯ = 29.94 μg/dL, SEM = 3.55 μg/dL), but not control odor (X¯ = 1.95 μg/dL, SEM = 3.55 μg/dL), significantly increased plasma corticosterone after 30 min of exposure, and this difference ceased after 4 hr of exposure (p > 0.05). This suggests that the animals engaged effective coping mechanisms and likely avoided corticosterone-induced muscle damage.\n\nPlasma corticosterone levels following either PO or control odor after either 30 min or 4 hr. *Significant interaction between odor and time, p < 0.001; CTL, control odor; PO, predator odor.\n\nWhile several genes in VMH cells have been explored in the context of metabolism, to our knowledge, virtually none have been explored in the context of PO exposure. Metabolic studies have implicated VMH expression of SIRT1, BDNF, and SF-1 as possible mediators of skeletal muscle metabolism (Wang et al., 2010; Ramadori et al., 2011; Kim et al., 2012). Here, we asked if the VMH transcription of these genes correlated with time points when PO-induced muscle thermogenesis peaks and returns-to-baseline. We found that PO exposure significantly increased Sirt1 and Bdnf expression in the VMH after 4 hr but not 30 min (Figure 3), where two-way ANOVAs showed a significant interactions between time and odor. Compared to control odor, PO exposure increased Sirt1 mRNA expression after 4 hr, but not 30 min, F(1, 20) = 4.96, p = 0.03, and PO exposure increased Bdnf mRNA expression after 4 hr, but not 30 min, F(1, 20) = 6.15, p = 0.022. Unexpectedly, there were no significant changes in Sf1 expression in the VMH following 30 minutes or 4 hours of PO exposure; two-way ANOVA results showed no significant changes in Sf1 mRNA expression in any condition (p < 0.05).\n\n(A) Sirt1, (B) BDNF, and (C) Sf1 mRNA expression levels in the VMH following either PO or control odor exposure after either 30 min or 4 hr. Significant interaction between odor and time, p < 0.05; CTL, control odor; PO, predator odor.\n\nAlthough the VMH is a known regulator of metabolic and predator threat responses, the cellular and molecular alterations following PO exposure are unknown. Thus, it is difficult to investigate how the VMH might regulate muscle metabolism following PO exposure. Here, we performed RNA-sequencing on VMH samples from animals who were exposed to either 20 min of PO or control odor exposure. Differential gene expression analysis revealed 164 DEGs. Of these DEGs, 60 genes were up-regulated and 103 genes were down-regulated. Table 2 shows the top 20 upregulated and top 20 downregulated DEGs. A GO enrichment analysis was performed using the R package GOseq to control for gene transcript length. Our GOseq analysis revealed 65 significantly enriched GO terms. We curated a list of the top 20 most enriched terms by removing GO terms that were 1) identical but with different accession numbers, 2) redundant “parent” terms, or 3) functionally irrelevant (e.g., endoderm development) (Figure 4B). Our pathway enrichment analysis revealed 28 significantly enriched KEGG pathways (Figure 4C).\n\n(A) Volcano plot of the differentially expressed genes between control and PO. Non-significant genes are shown in grey; blue and green indicate the gene expression was above one cut-off criterion but not the other (padj and fold change). Significant genes are shown in red, identified by their respective Ensembl IDs (see Extended Data Table 1 for the full list). Black vertical lines highlight log fold changes of –1.5 and 1.5, while black horizontal line represents a padj of 0.05. (B) Heatmap of the top 20 up- and down-regulated by PO genes (built using software.broadinstitute.org/morpheus/) where the color scheme reflects relative individual expression values for each gene, ranging from the minimum values in dark blue, to the maximum values in dark red. Hierarchical clustering of genes is based on 1-Pearson correlation values using average linkage. Clusters of genes up- and down-regulated by PO are marked with brown and yellow bars, respectively. (C) Functional enrichment networks of Gene Ontology Molecular Function, and Immune System Process terms and KEGG pathways of differentially expressed protein-coding genes, visualized using ClueGO Cytoscape plugin, with connectivity measure of kappa score ≥ 0.4 and enriched pathways p value padj ≤ 0.05. Functional groups are shown with different colors, with the terms marked in bold signifying the most essential pathway-defining terms for each major group (see Extended Data Table 2 for the full list).\n\nTo further explore whether identified DEGs relevant to synaptic plasticity, protein-coding DEGs were annotated using DAVID (The Database for Annotation, Visualization and Integrated Discovery, ver. v2023q3) (Sherman et al., 2022), resulting in 47 genes annotated with GO terms related to keywords “synaptic”, “neural”, “nervous” or “neuron”. We further used ShinyGO 0.77 (Ge et al., 2020) to identify 16 over-enriched GO terms with at least two genes per pathway (Figure 5, Table S3A). Notably, all but two of these pathways (Retinoid binding and Isoprenoid binding) contained genes associated with nervous system functions and/or synaptic plasticity. Likewise, of the top 40 up- and down-regulated DEGs, 15 genes were annotated with nervous system-related terms (Table S3B). Moreover, among DEGs were eight neuronal immediate early genes (IEGs), namely Btg2, Fosb, Arc, Apold1, Egr1, Egr4, Nr4a1, Sgk1 (Table S1), of which Arc was one of the top 20 up-regulated DEGs. Arc, activity-regulated cytoskeleton-associated protein, translocates from the nucleus to cell dendrites in an activity dependent manner, where, after rapid translation, it interacts with F-actin to potentially modify dendritic spines (Pinaud and Tremere, 2006). There are also many other DEGs with known involvement in synaptic plasticity, including Bcas1 (brain enriched myelin associated protein 1), Cdh1 (cadherin 1), multiple collagen chain genes, multiple members of the solute carrier family, Septin4, Syndig1 (synapse differentiation inducing 1), and Snap91 (synaptosome associated protein 91).\n\nBigger dots indicate smaller p-values. Each pathway includes at least two genes, with FDR cut-off of 0.05.\n\n\n4. Discussion\n\nThe VMH is required for optimal regulation of energy balance and does so through its control of the autonomic nervous system and its complex pathways with other hypothalamic nuclei and brain regions (Dhillon et al., 2006; King, 2006; Xu et al., 2010; Kim et al., 2011, 2012; Ramadori et al., 2011). The VMH also plays an important role in regulating metabolic and behavioral responses to predator threat, during which peripheral thermogenesis and EE are increased (Dielenberg et al., 2001, 2004; Silva et al., 2013, 2016; Cheung et al., 2015; Kunwar et al., 2015; Viskaitis et al., 2017; Shemery et al., 2023). While this dual-processing role of the VMH has been well established, the cellular and molecular mechanisms involved in VMH metabolic control in the context of predator threat are not fully understood. Here, we sought to provide an initial exploration of gene expression changes within the VMH at time points associated with peak and returned-to-baseline skeletal muscle temperatures following PO exposure (Figure 1). First, we established a temporal profile for VMH Sirt1, Bdnf, and Sf1 expression following PO exposure, with increased expression of Bdnf and Sirt1 after 4 hr of PO exposure but not 30 min. Interestingly, Sf1 levels were not significantly altered following either 30 min or 4 hr of PO exposure. As predicted, PO exposure increased corticosterone levels after 30 min of PO exposure, but despite continued PO exposure, corticosterone levels decreased to control levels after 4 hrs. Next, RNA-sequencing identified 164 DEGs, 65 enriched GO terms and 33 enriched KEGG pathways. Altogether, these results reveal important themes of immune and oxidative stress responses, and synaptic plasticity in the VMH in response to predator threat.\n\nSirt1, Bdnf, and Sf1 are metabolically responsive genes in the VMH implicated in the regulation of skeletal muscle metabolism. We have found that PO exposure consistently induces peak skeletal muscle thermogenesis within 15-30 min (Gorrell et al., 2020), after which it gradually declines, reaching baseline at 4 hr (Figure 1), thus we opted to measure Sirt1, Bdnf, and Sf1 mRNA levels at these thermogenically relevant time points. Our results show that Sirt1, Bdnf, and Sf1 were not significantly altered after 30 min of PO exposure (Figure 3). This suggests that while VMH expression of these genes may modulate peripheral metabolism, their transcription may not be necessary for the immediate thermogenic response to PO exposure. Further, Sirt1 and Bdnf mRNA levels were significantly increased following 4 hr of PO exposure, a time point associated with returned-to-baseline thermogenesis. Thus, VMH Sirt1 and Bdnf may not be necessary for an acute induction of muscle thermogenesis, but instead have roles associated with the thermogenic or predator-stress outcomes. SIRT1 is a nicotinamide adenosine dinucleotide (NAD+)-dependent histone deacetylase believed to have cell-protecting effects in response to metabolic changes and environmental stressors (Chang and Guarente, 2014). However, there are conflicting reports on the benefits of SIRT1 expression in the hypothalamus. For example, Ramadori et al. (2011) and Cakir et al. (2009) assert that, following reduced energy availability, SIRT1 expression increases in the hypothalamus, whereas Sasaki et al. (2010) found the opposite. Because predator escape is energetically costly and we have shown heightened skeletal muscle thermogenesis that persists for nearly 4 hours (Figure 1), it is possible that the delayed increase in Sirt1 mRNA was a response to depleted energy availability secondary to the thermogenic processes. This would seem inconsistent with reports demonstrating that VMH SIRT1 expression increases insulin-stimulated glucose uptake in skeletal muscle and is associated with increased EE, though (Ramadori et al., 2011; Aras et al., 2019). Because increased SIRT1 activity has been reported in the brain following acute PO exposure (Yu et al., 2018), it is possible that the delayed increase in Sirt1 mRNA observed here was a response to psychological stress. Interestingly, Libert et al. (2011) suggest that whole brain SIRT1 likely integrates metabolic and predatory information such that food scarcity and high predation are associated with high brain SIRT1, resulting in vigilance and reduced exploration. Due to the unique role of the VMH in processing predator threat and metabolic responses including skeletal muscle metabolism, the timing and function of SIRT1 expression may be complex.\n\nDelayed increase in Bdnf mRNA following PO exposure was unexpected given that VMH BDNF microinjection immediately increases EE (Wang et al., 2010) and a single glucose injection rapidly increases VMH BDNF expression (Unger et al., 2007). It is possible that delayed increase in Bdnf mRNA may implicate its role in stress-induced synaptic plasticity. Glucocorticoids, including corticosterone, interact with BDNF in the brain to modify synapses and these interactions are associated with stress and depression resilience (Tapia-Arancibia et al., 2004; Kunugi et al., 2012; Jeanneteau and Chao, 2013; Numakawa et al., 2013; Daskalakis et al., 2015). Not only have glucocorticoid-BDNF interactions been confirmed in the hypothalamus following stress, but BDNF in VMH SF-1 neurons modifies GABAergic inputs onto SF-1 cells (Tapia-Arancibia et al., 2004; Jeanneteau et al., 2012; Jo, 2012). The data reported here data reveal an unexpected but novel finding regarding the temporal relationships among Sirt1, Bdnf, and Sf1 mRNA expression in the VMH following acute PO exposure. While the expression of these genes may not be necessary for the immediate thermogenic response to a single PO exposure, they may have roles in regulating subsequent thermogenic or behavioral adaptation to PO.\n\nInflammation and oxidative stress are distinct processes but are closely connected and can have a reciprocal relationship. Brain oxygen consumption is high, making it vulnerable to oxidative stress which can trigger inflammation (Leszek et al., 2016). In turn, brain inflammation can induce oxidative stress (Muriach et al., 2014). Our RNA-sequencing results suggest that acute PO exposure may rapidly alter immune and oxidative stress responses within the VMH. Indeed, predator threat alters oxidative stress and inflammatory responses in the brain, but no previous reports have specifically implicated VMH inflammation (Toumi et al., 2013; Wilson et al., 2013; Mejia-Carmona et al., 2014, 2015). Mejia-Carmona et al. (2015) reported that recurrent PO exposure across 6 days led to increased manganese-dependent mitochondrial superoxide dismutase (MnSOD) in the hypothalamus, indicating that the hypothalamus engaged a protective antioxidant response to an early increase of superoxide radicals. The inflammatory effect of predator threat on the hypothalamus is less consistent. Plata-Salaman et al. (2000) found that neither acute nor repeated exposure to a ferret increased proinflammatory cytokines in rats, while Barnum et al. (2012) reported that acute exposure to an aggressive rat increased proinflammatory cytokines in mice for up to 8 hr. Regardless, prolonged or chronic predator threat is associated with post-traumatic stress disorder (PTSD) and accelerated aging, which are clinically intertwined with major health issues including cardiovascular disease, metabolic dysregulation, and dementia (Oosthuizen et al., 2005; Epel, 2009; Wilson et al., 2013; Mellon et al., 2018).\n\nInterestingly, PO exposure also alters expression of several genes in the KEGG Toxoplasmosis pathway (Figure 4C). Changes in this pathway are intriguing given that infection with Toxoplasmosa gondii markedly attenuates rats’ behavioral response to predators (Berdoy et al., 2000). Ultimately, our RNA-sequencing results reveal the potential for acute PO exposure to rapidly alter multiple stress-response pathways in the VMH. It will be critical to understand if or how these alterations are associated with the induction of skeletal muscle thermogenesis as well as behavioral responses to predator threat.\n\nThe DEGs and enriched pathways identified via RNA-seq suggest that acute PO exposure may alter synaptic plasticity in the VMH. Synaptic plasticity in the adult hypothalamus has been highly investigated since it was first observed in the 1980s (Theodosis et al., 1981, 1986; Theodosis and Poulain, 1984, 1987; Tweedle and Hatton, 1984; Chapman et al., 1986). Hypothalamic synapses and their astrocytes undergo morphological changes in response to gestation (Theodosis and Poulain, 1984), lactation, (Theodosis et al., 1981, 1986; Theodosis and Poulain, 1984; Stern and Armstrong, 1998) and dehydration (Tweedle and Hatton, 1984; Chapman et al., 1986; Miyata et al., 1994). Several hypothalamic nuclei, especially the VMH, undergo changes in dendritic arborization and spine density in response to gonadal hormones and sexual behavior (Frankfurt et al., 1990; Parducz et al., 1993; Garcia-Segura et al., 1994a, 1994b; Xiong et al., 1997; Calizo and Flanagan-Cato, 2000; Calizo and Flanagan-Cato, 2002; Flanagan-Cato et al., 2006; Griffin and Flanagan-Cato, 2008). Importantly, hypothalamic plasticity is also critical for energy homeostasis (Horvath et al., 1999; Bouret et al., 2004; Horvath and Diano, 2004; Horvath, 2005; Horvath and Gao, 2005; Andrews et al., 2008; Benani et al., 2012; Hu et al., 2014; Qi and Yang, 2015; Dodd et al., 2018). Feeding circuits within the arcuate nucleus (ARC) undergo rapid, plastic changes that consistently flip-flop in response to satiety and hunger signals (Pinto et al., 2004; Yang et al., 2011). Interestingly, the VMH projects excitatory synaptic inputs to pro-opiomelanocortin neurons in the ARC that become diminished during fasting (Sternson et al., 2005). Fasting also causes alterations in dendritic arborization and soma size within the VMH (Flanagan-Cato et al., 2008). Taken together, these findings suggest that the VMH has the capacity for synaptic plasticity in response to behavioral states that it regulates as well as metabolic state.\n\nThough not directly implicated, there is also evidence to suggest that the VMH likely undergoes synaptic plasticity following acute PO exposure. Silva et al. (2016) demonstrated that the VMH was necessary for the acquisition and expression of fear memory following a single, acute predator exposure (Silva et al., 2016). Moreover, expression of a protein in the voltage-dependent calcium channel complex, Alpha2delta-1, in VMH SF-1 neurons controls excitatory synaptogenesis to modulate sympathetic activation of skeletal muscle (Lau et al., 2016). This suggests that sympathetic activation induced by PO could result from rapid, plastic changes within the VMH, or to other brain regions directly innervated by VMH neuronal afferents. Indeed, VMH stimulation induces hippocampal plasticity (Ying et al., 2012). Importantly, predator stress induces plasticity in a variety of brain regions (Adamec et al., 1999, 2003; Li et al., 2004; Adamec et al., 2006; Thomas et al., 2006; Park et al., 2008; Zoladz et al., 2012; Mitra, 2019), including the hypothalamus (Inoue et al., 2013). A single episode of acute PO exposure induces long-term potentiation at GABA synapses in another hypothalamic nucleus, the paraventricular nucleus of the hypothalamus, which may sensitize future stress responses because GABA synapses become excitatory during acute stress (Inoue et al., 2013). It is also important to note that acute predator stress does not appear to alter the proliferation or survival of neurons, suggesting our plasticity-associated DEGs are likely mediating plasticity in existing neurons rather than neurogenic processes (Lau et al., 2016). Thus, combined with our results, it seems highly probable that the VMH undergoes plasticity following acute PO exposure. This is not surprising given the critical survival value of avoiding food-seeking behavior during predator threat (Viskaitis et al., 2017) as well as avoiding predation altogether (Monarca et al., 2015).\n\nExamination of one time point limits the interpretation of our RNA-sequencing results. For example, reduced mRNA levels could stem from rapid translation of available transcripts before transcription is able to replenish the supply in which case, despite appearing downregulated, gene expression is important. Indeed, genes are transcribed and translated at variable rates depending on the gene, the tissue, the conditions, and new, mature mRNA can take up to an hour to be transcribed at noticeably altered levels (Ressler et al., 2002; Sirri et al., 2010). Other limitations to our findings are the inherent flaws in RNA-sequencing (Ozsolak and Milos, 2011; Zheng et al., 2011; Liu et al., 2014). RNA-sequencing lends itself to unavoidable biases due to technological limitations such as cDNA library construction artifacts, transcript mapping, read-count normalization, and GO analyses (Ozsolak and Milos, 2011). Nonetheless, not only have major technological advances led to more reliable RNA-sequencing results, but the preservation of raw data allows for future re-analysis. Finally, the wide range of predator threat exposure protocols can hamper generalization or direct comparison to existing reports of PO-induced alterations in behavior, metabolism, or their underlying mechanisms.\n\nIn conclusion, these results are the first to reveal gene expression changes in the VMH following a single episode of PO exposure. Acute PO exposure rapidly modifies gene expression in the VMH at a time point that correlates with peak skeletal muscle thermogenesis, and implicates genes involved in immune and oxidative stress responses as well as synaptic plasticity. The transcription of Sirt1 and Bdnf, genes implicated in skeletal muscle metabolism, are not significantly increased until 4 hr, when PO-induced thermogenesis resolves to baseline levels. Our data provide an excellent foundation from which we can guide exploration of VMH regulation of SNS activation following predator odor. Understanding these mechanisms could potentially lead to untangling the pathways that control stress and metabolic responses.\n\n\nEthical considerations\n\nExperiments involving rats were carried out with approval by the Kent State University Animal Care and Use Committee (approval number 460CN18-04) in accordance with the ethical guidelines provided in the Guide for the Care and Use of Laboratory Animals as well as the Association for Assessment and Accreditation of Laboratory Animal Care (AAALAC). Efforts were made to ameliorate suffering and minimize distress of animals using analgesics before and after surgical procedures, anesthesia using inhaled isoflurane (5% for induction, 2-3% for maintenance), and habituation prior to exposure to potentially stressful contexts.", "appendix": "Data and software availability\n\nRepository: RNAseq data are deposited in NCBI GEO.\n\nAccession number: GSE142617; https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE142617.\n\nOpen access software for statistical analysis can be found at https://www.r-project.org/.\n\nTables S1-S3 are available through Figshare: (Piontkivska et al., 2024)\n\nhttps://doi.org/10.6084/m9.figshare.25593420\n\nTable S1. Differentially expressed genes in response to predator odor. Columns H through M show DESeq2-normalized counts for control animals (H through J, and those exposed to predator odor, columns K through M).\n\nGene symbol and description are per Biomart Ensembl annotations. 1 in column Q indicates which DEGs are protein-coding.\n\nTable S2. Functional enrichment networks of Gene Ontology Molecular Function, and Immune System Process terms and KEGG pathways of differentially expressed protein-coding genes, visualized using ClueGO Cytoscape plugin, with connectivity measure of kappa score ≥ 0.4 and enriched pathways p value padj ≤ 0.05. Column L lists genes that are part of the respective GO categories and pathways listed in column B.\n\nTable S3A. Enriched Gene Ontology pathways among differentially expressed genes in response to predator odor.\n\nEach pathway has at least two genes, with FDR cut-off of 0.05.\n\nNervous-system related Gene Ontology term annotations among differentially expressed genes in response to predator odor. Per DAVID (The Database for Annotation, Visualization and Integrated Discovery, ver. v2023q3). doi: 10.6084/m9.figshare.25593420.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nAnimal experiments adhere to ARRIVE guidelines.\n\nRepository: Figshare\n\nProject title: Supplementary Tables for Shemery, A., Gibson, M., Gorrell, E., Daniel, D., Piontkivska, H., and Novak, C.M., “RNA-sequencing Reveals Altered Gene Expression in the Ventromedial Hypothalamus Following Predator Odor Exposure”. (Piontkivska et al., 2024).\n\nDOI: https://doi.org/10.6084/m9.figshare.25593420.v2\n\nLicense: CC BY 4.0\n\n\nReferences\n\nAdamec RE, Blundell J, Burton P: Phosphorylated cyclic AMP response element binding protein expression induced in the periaqueductal gray by predator stress: its relationship to the stress experience, behavior and limbic neural plasticity. Prog. Neuro-Psychopharmacol. Biol. Psychiatry. 2003; 27: 1243–1267. 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PubMed Abstract \| Publisher Full Text\n\nPiontkivska H, Novak C, Shemery A, et al.: Supplementary Tables for Shemery, A., Gibson, M., Gorrell, E., Daniel, D., Piontkivska, H., and Novak, C.M., “RNA-sequencing Reveals Altered Gene Expression in the Ventromedial Hypothalamus Following Predator Odor Exposure”. figshare. 2024.\n\nPlata-Salaman CR, Ilyin SE, Turrin NP, et al.: Neither acute nor chronic exposure to a naturalistic (predator) stressor influences the interleukin-1beta system, tumor necrosis factor-alpha, transforming growth factor-beta1, and neuropeptide mRNAs in specific brain regions. Brain Res. Bull. 2000; 51: 187–193. PubMed Abstract \| Publisher Full Text\n\nQi Y, Yang Y: Hunger States Control the Directions of Synaptic Plasticity via Switching Cell Type-Specific Subunits of NMDA Receptors. J. Neurosci. 2015; 35: 13171–13182. 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PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "295126", "date": "10 Jul 2024", "name": "Yunhui Liu", "expertise": [ "Reviewer Expertise VMH，neural circuits，chronic stress", "energy expenditure，bone 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\nThe ventromedial hypothalamus (VMH) is crucial for maintaining energy balance by regulating autonomic nervous system activity and interacting with brain regions involved in feeding and thermoregulation. Additionally, it mediates diverse behaviors such as aggression, fear responses, memories, and aversion to predator odor. Acting as a dual processor for metabolic and predator threat responses, the VMH likely facilitates predator odor-induced skeletal muscle thermogenesis, yet the underlying cellular and molecular mechanisms remain unexplored.\nIn this study, Shemery and colleagues used RNA sequencing to examine gene expression dynamics in the rat VMH following exposure to predator odor (PO), aiming to uncover its metabolic regulatory mechanisms in response to threats. They observed that brief PO exposure rapidly increased skeletal muscle thermogenesis, peaking at 20-30 minutes and returning to baseline after 4 hours. Using qPCR and RNA sequencing, they identified VMH genes that rapidly changed after PO exposure, implicating roles in immune responses, oxidative stress, and neural plasticity. Notably, genes like Sirt1 and Bdnf showed significant upregulation 4 hours post-exposure, suggesting their involvement in later-stage sympathetic nervous system (SNS) regulation under predator stress. This study provides an early glimpse into VMH gene expression changes following PO exposure, offering novel insights into its role in SNS regulation. While the authors posed high-quality scientific questions, their findings did not fully address them. For example, after brief PO exposure, they did not find any changes in mRNA related to metabolic regulation in the VMH. Below are the reviewer's suggestions for revisions:\nMajor 1）Although previous research by the authors showed that activation of melanocortin receptors in the VMH induces skeletal muscle thermogenesis (Gavini, 2016), there is still no direct evidence linking the VMH to the regulation of predator odor-induced skeletal muscle thermogenesis. Therefore, the authors should first establish the VMH's role in this process in the current study. It is recommended that they use in vivo calcium fluorescence recording with endoscopes or optical fibers to dynamically monitor VMH neuronal activity and analyze its correlation with the time course of predator odor-induced skeletal muscle thermogenesis.\n2）The authors chose BDNF, SIRT1, and SF-1 as candidate genes for qPCR to study the VMH's role in PO-induced skeletal muscle thermogenesis. However, the VMH also expresses many other receptors closely related to metabolism, such as insulin receptors (IR), leptin receptors (LepR), and melanocortin receptors (MR). The authors should expand their focus and thoroughly evaluate the role of these receptors in the VMH during PO-induced skeletal muscle thermogenesis.\n3）The reviewer has concerns about the VMH sampling process from rat brain slices. Given that the core data of this study were obtained through RNA sequencing and the VMH is very small, any deviation in sampling could introduce significant data bias. The authors should provide more details about the VMH extraction procedure.\n4）The authors' interpretation of the RNA sequencing results for the VMH is overly brief. They barely mention immune and oxidative stress responses in the Results section, yet describe these responses as equally important as synaptic plasticity in the Conclusion. The authors should provide a detailed analysis of the RNA changes related to immune and oxidative stress responses in the VMH following PO exposure in the Results section.\nMinor 1) In the Abstract, the first sentence of the Methods and Results section, \"Exposing rats to predator odor (PO) exposure causes a rapid increase in skeletal muscle thermogenesis…\" contains an extra \"exposure.\"\n2) Despite its small size, the VMH plays complex roles in metabolism, emotional regulation, mating behavior, and aggression. For instance, the dm/cVMH is closely linked to bone and energy metabolism abnormalities induced by chronic stress (Yang F et al., J Clin Invest. 2020, Shao J et al., Mol Psychiatry. 2022). Conversely, the vlVMH mediates the regulation of aggressive behavior. Additionally, the David J. Anderson group at the California Institute of Technology has conducted single-cell RNA sequencing on the vlVMH (Kim DW et al., Cell. 2019). The authors should compare their findings with existing studies in this field.\n3) Some of the literature cited in the manuscript doesn't adequately back up the authors' arguments, including but not limited to: a) In the third paragraph of the Introduction, the authors claim, \"Importantly, increased VMH SF-1 expression improves skeletal muscle metabolism and is associated with increased SNS activation (Kim et al., 2012).\" However, the cited paper does not establish a causal relationship between SF-1 expression and skeletal muscle metabolism. b) In the same paragraph, the authors state, \"However, although PO induces c-fos in the VMH (Masini et al., 2005)…\", but the original paper only found increased c-fos mRNA expression in the paraventricular nucleus (PVN) of the hypothalamus following PO stimulation. The expression of c-fos in the VMH was weak, as shown in Figure 2 of the original paper. The authors should verify their sources carefully and cite appropriate papers to support their key points accurately.\n4) In the methods and results section of the Abstract, the authors state, \"This thermogenic response is associated with weight loss and increased EE even when controlling for physical activity.\" However, there is no corresponding source for this claim in the study, as they did not monitor weight, EE, or physical activity.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nYes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] }, { "id": "295134", "date": "18 Jul 2024", "name": "Vito S Hernandez", "expertise": [ "Reviewer Expertise neuroendocrinology" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address 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 investigates how predator odor (PO) exposure affects gene expression in the ventromedial hypothalamus (VMH) of rats. Given the convergence of functions of the VMH in regulating body weight by modulating muscle metabolism and sympathetic nervous system (SNS) activity and in mediating behavioral responses to predator threats, I consider this an interesting and important study. The main objective was to uncover the molecular mechanisms behind VMH-mediated metabolic responses to predator threat.\nThe authors evaluated transcriptomic changes after PO stress at two timepoints\nExposure to PO caused a rapid increase in skeletal muscle thermogenesis, peaking at 30 minutes and returning to baseline by 4 hours. This was associated with increased energy expenditure\n\nqPCR Results: After 30 min (Peak termogenesis) no changes were observed in prescription of BdnF, Sirt1 or SF1. After 4 hours of PO exposure, there was an increased expression of Bdnf and Sirt1, but not SF1 RNA-sequencing Results: Identified 245 DEGs with at least a 1.5-fold change due to PO exposure. Functional Annotation: Overrepresented pathways among DEGs included immune response, oxidative stress, and synaptic plasticity.\nThe findings indicate that acute PO exposure leads to both rapid and delayed changes in VMH gene expression, which likely have downstream metabolic consequences. These gene expression changes are linked to increased thermogenesis and energy expenditure, suggesting a complex interplay between stress response and metabolic regulation.\nUnderstanding the mechanisms by which predator odor can modify energy expenditure is a hot and very important topic. This study positions the VMH in the spotlight for further investigations. However the data obtained is to this point is correlational. No insight on the population of neurons that change their transcription in response to PO can be gained, within the VMH/ can be obtained.\nThe Peak thermogenic response is at 30 min , but the selected genes for PCR that were selected on a prior basis because their possible connection with modulating the EE in response to PO did not changed. The results form queue RNAseq showed on the other side some genes that were upregulated (though 1.5 times is a low threshold), but no clear correlation or discussion on the mechanisms by which changes in those genes can be important on the PO changes in EE is provided.\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nI cannot comment. A qualified statistician is required.\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] } ]	1	https://f1000research.com/articles/13-648
https://f1000research.com/articles/13-645/v1	17 Jun 24	{ "type": "Data Note", "title": "Physio-Psychosocial Risks of Depression among College-Going Adolescents in Bangladesh: A Data Note", "authors": [ "Md Abu Bakkar Siddik", "Nafiul Hasan", "Al Mahmud", "Akher Ali", "Md Khalid Syfullah", "Md. Jamilur Rahman", "Anton Abdulbasah Kamil", "Mohammad Meshbahur Rahman", "Md Abu Bakkar Siddik", "Nafiul Hasan", "Al Mahmud", "Akher Ali", "Md Khalid Syfullah", "Md. Jamilur Rahman", "Anton Abdulbasah Kamil" ], "abstract": "Background The prevalence of depression among adolescents is an increasing global problem, including in Bangladesh as well. This cross-sectional data was collected to examine the physiological and psychological risk factors for depression among college-going adolescents in Bangladesh.\n\nMethodology Simple random sampling was employed as a sampling technique during the study period from May 2022 to August 2022. In the survey, a total of 1919 college-going adolescents were included through a Google-based questionnaire platform. The survey included socio-demographic characteristics and Patient Health Questionnaire (PHQ-9) questions. Before starting the survey, the questionnaire was translated and pre-tested in Bengali. To assess the dataset's feasibility and effectiveness, the pre-testing was done with a total of 43 adolescents. The questionnaire was revised several times before the final study to ensure it satisfied all standards.\n\nConclusion This dataset may be valuable for researchers investigating the relationship between academic performance, psychological well-being, and other socio-demographic characteristics. To get a deeper understanding of the broader framework, policymakers may find it advantageous to enact policies that are specifically tailored to meet the needs and preferences of adolescents", "keywords": [ "Mental health", "depression", "physio-psychosocial risk", "college-going adolescents", "Bangladesh" ], "content": "Introduction\n\nThe prevalence of psychological disorders among adolescents is consistently increasing worldwide. Based on the results of a meta-analysis, the worldwide average occurrence rate of mental disorders in adolescents was determined to be 13.4 percent.1 Multiple studies in the Asian zone have examined the frequency of depression among the region's adolescents. For example, estimates for the overall incidence of depression among teenagers range from fifteen to forty percent.2–4 Adolescents' depression is associated with conditions like not getting enough sleep, having a lot of stress at school, not having somebody to talk to, being addicted to drugs or alcohol, and hurting themselves.5,6 Financial strain, familial strife, and cultural adjustment issues are among the socioeconomic variables that might put college-aged teenagers at risk for depression.7,8 Adolescents in Bangladesh are dealing with an underrecognized epidemic of mental health issues. The current body of research indicates that the overall prevalence of psychological difficulties may range from 6.5% to 31%, with a corresponding range of 13.4% to 22.9% among adolescents.9,10 Depression was more common among college students in Bangladesh who reported high levels of academic stress, poor quality sleep, and family conflict, according to the literature. Few studies in Bangladesh have examined the factors that may contribute to depression among university students.11–14 Despite evidence of the impact of validated measures on common psychiatric diseases, there seems to be a continued need for specialized research on adolescent depression due to cultural and socio-demographic disparities among countries. This data article aimed to assess depression among college-aged adolescents in Bangladesh as well as determine the physio-psychosocial risk variables that are related to it, considering its contemporary relevance.\n\n\nMethods\n\nThe study was conducted following the guidelines set out in the Declaration of Helsinki (2000) and was ethically approved from the Department of Biostatistics, National Institute of Preventive and Social Medicine (NIPSOM), Mohakhali, Dhaka-1212, Bangladesh with registration number: NIP/BIOS/2022/000/01, dated March 12, 2022. Written consent was taken from each participant before initiating the Google-based data collection. The participants who agreed with the consent were included further to join the interview.\n\nThe study design was cross-sectional.\n\nThe study population was the college-going adolescents participated from all administrative divisions of Bangladesh.\n\nMay to August, 2022\n\nThe inclusion criteria of this study were: i) students who were studying at the college level (during the data collection period); ii) adolescents aged 13 to 19 years old; and (iii) who were Bangladeshi by birth. On the other hand, the exclusion criteria were: i) adolescents who were holding dual citizenship; ii) foreign adolescents currently studying in Bangladesh; and iii) adolescents who did not provide consent.\n\nThe dataset was deposited in Mendeley Data which supports the original research article published in the Journal of Affective Disorders Reports.15 Participants were the students who enrolled in college and were in grades eleven and twelve. A total of 1919 adolescents participated in the study, and this number was determined by using the statistical technique of determining the sample size for a cross-sectional prevalence study.\n\nThe independent variables of the study included the socio-demographic characteristics of the college-going adolescents, their behavioral risks, and history of illness. The socio-demographic variables were age, sex, family economic condition, marital status, Grade point average (GPA), and religion. Respondents’ behaviors related variables included smoking habit, uses of social media, involvement in pre-marital relationship, pre-marital sex experience, regular physical exercises, practicing religion, family unrest, and experience in blackmail. The major history of illness related variables were physical illness, illness history in covid-19, and history of family mental illness. The details independent variables included in the study are presented in Table 1.\n\nOn the other hand, the dependent variable included the Patient Health Questionnaire (PHQ-9) that was used to evaluate the participant's degree of depression symptoms to arrive at a result.15 The Patient Health Questionnaire-9 (PHQ-9) is widely recognized as a very effective and user-friendly tool for identifying depression in individuals. The scale's validity has been verified in Bangladesh.16 The codes assigned to the PHQ-9 questions range from “0 = not at all” to “3 = virtually every day.” The degree of depression was categorized into five distinct levels based on the Patient Health Questionnaire-9 (PHQ-9) scores: none-minimal (score: 0 to 4), mild (score: 5 to 9), moderate (score: 10 to 14), moderately severe (score: 15 to 19), and severe (score: 20 to 27). Participants in this research who scored 10 or above were classified as having a positive diagnosis of depression.17\n\nBefore commencing the survey, the questionnaire was translated into the Bengali language and subjected to validation via pre-testing. To determine the feasibility and effectiveness of the dataset, preliminary research (pre-testing) with 43 students was conducted. Subsequently, they were discarded throughout the further analysis of the data. The questionnaire underwent many iterations of revisions before the implementation of the final study, ensuring its compliance with all the specified criteria.\n\nTo ensure the accuracy of the data, we utilized various methods. These included thoroughly reviewing and verifying the completed questionnaires, employing SPSS 26.0 for examining the frequency of each variable to identify any unusual findings, and conducting reliability analysis (specifically Cronbach's alpha), which yielded a reliability coefficient value of 0.78 for the PHQ-9 questionnaire. Additionally, we employed various statistical techniques to guarantee the reliability and validity of the dataset's findings.\n\nOne of the major drawbacks of the dataset is that it is based on a cross-sectional methodology, which means that it is not possible to demonstrate causal relationships and the consequences of such interactions. Those people who were included in this dataset were responsible for providing their pertinent information, which was gathered by self-reporting. Considering this, there is a potential that the persons involved may make errors or fail to provide accurate information. A further restriction of the dataset is that this is the case. In addition, this dataset did not include any confounding factors that might potentially affect the prevalence of depression among the persons who participated in the study.\n\nThe study was conducted following the guidelines set out in the Declaration of Helsinki (2000) and was ethically approved from the Department of Biostatistics, National Institute of Preventive and Social Medicine (NIPSOM), Mohakhali, Dhaka-1212, Bangladesh with registration number: NIP/BIOS/2022/000/01, dated March 12, 2022. Written consent was taken from each participant before initiating the Google-based data collection. The participants who agreed with the consent were included further to join the interview.\n\nMd Abu Bakkar Siddik: Writing – review & editing, Writing – original draft, Visualization, Validation, Methodology, Investigation, Formal analysis, Data curation, Conceptualization. Nafiul Hasan: Writing – review & editing, Visualization, Formal analysis. Al Mahmud: Writing – review & editing, Writing – original draft, Investigation, Data curation. Akher Ali: Writing – review & editing, Investigation, Data curation. Md. Khalid Syfullah: Writing – review & editing, Writing – original draft, Investigation, Data curation. Md. Zamilur Rahman: Writing – review & editing, Writing – original draft. Anton Abdulbasah Kamil: Writing – review & editing, Writing – original draft, Funding acquisition. Mohammad Meshbahur Rahman: Writing – review & editing, Writing – original draft, Visualization, Validation, Supervision, Software, Resources, Project administration, Methodology, Investigation, Funding acquisition, Formal analysis, Data curation, Conceptualization.", "appendix": "Data availability\n\n\n\n1. Figshare: Physio-Psychosocial Risk of Depression among College-Going Adolescents: Dataset and other supplementary materials. https://doi.org/10.6084/m9.figshare.25940959. 18\n\nThe project contains the following underlying data:\n\n• Dataset- Adolescents Depression.sav.\n\n• Questionnaire PHQ-9.docx (Questionnare)\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n2. Mendeley Data: Physio-Psychosocial Risk of Depression among College-Going Adolescents: Dataset and other supplementary materials. DOI: https://doi.org/10.17632/299dx4wggp.3. 19\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgements\n\nWe are thankful to the Department of Biostatistics, National Institute of Preventive and Social Medicine (NIPSOM), Mohakhali, Dhaka for providing permission and technical support including approval of the study. Also, we acknowledge all the participants who gave their time during the data collection of the study.\n\n\nReferences\n\nPolanczyk GV, Salum GA, Sugaya LS, et al.: Annual research review: A meta-analysis of the worldwide prevalence of mental disorders in children and adolescents. J. Child Psychol. Psychiatry. 2015; 56(3): 345–365. PubMed Abstract \| Publisher Full Text\n\nAng AL, Wahab S, Abd Rahman FN, et al.: Depressive symptoms in adolescents in Kuching, Malaysia: Prevalence and associated factors. Pediatr. Int. 2019 Apr 1; 61(4): 404–410. PubMed Abstract \| Publisher Full Text\n\nKhalid A, Qadir F, Chan SWY, et al.: Adolescents’ mental health and well-being in developing countries: a cross-sectional survey from Pakistan. J. Ment. Health. 2019 Jul 4; 28(4): 389–396. PubMed Abstract \| Publisher Full Text\n\nSiddik MAB, Munmun MS, Ahmed Z, et al.: Climate change, natural disasters, and mental health of adolescents: A qualitative study from Bangladesh. International Journal of Population Studies. 2024 Feb 26; 10: 61. Publisher Full Text\n\nKenney BA, Holahan CJ: Depressive Symptoms and Cigarette Smoking in a College Sample. J. Am. Coll. Heal. 2008 Jan 1; 56(4): 409–414. PubMed Abstract \| Publisher Full Text\n\nSiddik MAB, Manjur M, Pervin I, et al.: Suicide attempts and depression associated factors among the male child sexual abuse survivors in Bangladesh. J Affect Disord Rep. 2024 Apr 1; 16: 100736. Publisher Full Text\n\nPonnet K, Wouters E, Goedemé T, et al.: Family Financial Stress, Parenting and Problem Behavior in Adolescents: An Actor-Partner Interdependence Approach. J. Fam. Issues. 2013 Dec 25; 37(4): 574–597. Publisher Full Text\n\nAdams TB, Wharton CM, Quilter L, et al.: The Association Between Mental Health and Acute Infectious Illness Among a National Sample of 18- to 24-Year-Old College Students. J. Am. Coll. Heal. 2008 May 1; 56(6): 657–664. PubMed Abstract \| Publisher Full Text\n\nRozario LG, Islam S: Scenario of mental health in Bangladesh: A signature glimpse. Dhaka University Journal of Biological Sciences. 2022 Jun 5; 405–416. Publisher Full Text\n\nHasan MT, Anwar T, Christopher E, et al.: The current state of mental healthcare in Bangladesh: part 1 – an updated country profile. BJPsych Int. 2021/08/18. 2021; 18(4): 78–82. PubMed Abstract \| Publisher Full Text \| Free Full Text Reference Source\n\nKhan MMA, Rahman MM, Islam MR, et al.: Suicidal behavior among school-going adolescents in Bangladesh: findings of the global school-based student health survey. Soc. Psychiatry Psychiatr. Epidemiol. 2020; 55(11): 1491–1502. PubMed Abstract \| Publisher Full Text\n\nSiddik AB, Hasan N, Mahmud A, et al.: Prevalence of depression and its associated factors among undergraduate admission candidates in Bangladesh: A nation-wide cross-sectional study. Hsan K, editor. PLoS One. 2023 Nov 30 [cited 2023 Dec 1]; 18(11): e0295143. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSiddik MAB, Ali A, Miah S, et al.: Psychological Disorders Among College Going Students: A Post Covid-19 Insight from Bangladesh. J Affect Disord Rep. 2023 Nov 16 [cited 2023 Nov 18]; 15: 100686. Publisher Full Text Reference Source\n\nPaul GK, Rahman MM, Naznin S, et al.: Depression and Anxiety among University Students: A Comparison between COVID-19 Pandemic Panic Period and Post-panic Period in Bangladesh. Open Access Maced. J. Med. Sci. 2022 Jan 2; 10(E SE-Public Health Epidemiology): 52–59. Publisher Full Text Reference Source\n\nSiddik MAB, Hasan N, Mahmud A, et al.: Physio-Psychosocial Risk of Depression among College-Going Adolescents: A Cross-Sectional Study in Bangladesh. J Affect Disord Rep. 2024; 16: 100768. Publisher Full Text\n\nRahman MA, Dhira TA, Sarker AR, et al.: Validity and reliability of the Patient Health Questionnaire scale (PHQ-9) among university students of Bangladesh. PLoS One. 2022 Jun 1 [cited 2023 Dec 28]; 17(6): e0269634. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKroenke K, Spitzer RL, Williams JBW, et al.: The Patient Health Questionnaire Somatic, Anxiety, and Depressive Symptom Scales: A systematic review. Gen. Hosp. Psychiatry. 2010; 32(4): 345–359. PubMed Abstract \| Publisher Full Text\n\nSiddik AB, Hasan N, Mahmud A, et al.: Physio-Psychosocial Risk of Depression among College-Going Adolescents: Dataset and other supplementary materials. Figshare. 2024 [cited 2024 May 31]. Publisher Full Text\n\nSiddik AB, Hasan N, Mahmud A, et al.: Physio-Psychosocial Risk of Depression among College-Going Adolescents: A Cross-Sectional survey data in Bangladesh. Mendeley Data. 2024 [cited 2024 Jun 4]; V3. Publisher Full Text" }	[ { "id": "308776", "date": "13 Aug 2024", "name": "Toan Ha", "expertise": [ "Reviewer Expertise Social and behavioral aspects of HIV", "depression", "stigma", "adolescent health", "sexual and reproductive health", "mHealth" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 cross-sectional data was collected to examine the physiological and psychological risk factors for depression among college-going adolescents in Bangladesh. However, the authors should use depressive symptoms instead of depression as this is a cross-sectional study.\n\nThe author said \" This dataset may be valuable for researchers investigating the relationship between academic performance, psychological well-being, and other socio-demographic characteristics\". However, the data contains very limited variables (e.g, smoking habit, uses of social media, involvement in pre-marital relationship) that may limit the impact of the study. Since the authors indicated the use of psychological well-being, I would encourage the authors review the Ryff Scales of Psychological Well-Being which include Self-acceptance, Positive relations with others, Autonomy, Environmental mastery, Purpose in life and Personal growth.\n\nTable 1: Description of the participants should also indicate the number and percentage.\nAlso, I would love to see a table of PHQ9 indicating those with and without a prevalence of depressive symptoms.\n\nIs the rationale for creating the dataset(s) clearly described? Partly\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": [] } ]	1	https://f1000research.com/articles/13-645
https://f1000research.com/articles/13-643/v1	17 Jun 24	{ "type": "Case Report", "title": "Case Report: Surgical intervention of colo-pleural fistula secondary to colon diverticulosis with history of hernia diaphragmatica", "authors": [ "Wifanto Saditya Jeo", "Alldila Hendy Prihanda Suryaningprang", "Andre Setiawan", "Natasya Natasya", "Shintia Christina", "Alldila Hendy Prihanda Suryaningprang", "Andre Setiawan", "Natasya Natasya", "Shintia Christina" ], "abstract": "Abstract*\nIntroduction Colopleural fistulas are rare and generally correspond to thoracic empyema alongside an acute abdomen. Early diagnosis and prompt treatment are essential to prevent recurrence of thoracic empyema.\n\nCase presentation An 18-year-old male was admitted to our hospital with dyspnea and abdominal pain. The patient had a history of a left diaphragmatic hernia repair. Physical examination revealed signs of left-sided pleural effusion and abdominal pain. Chest computed tomography (CT) revealed a left lung empyema with a suspected connection to the intra-abdominal cavity through the diaphragm. Colopleural fistula and diverticulosis were confirmed by colonoscopy. Subsequently, primary resection, transverse-descending anastomosis, and fistula suturing were performed, accompanied by empyema evacuation through thoracotomy and diverting colostomy.\n\nClinical Discussion Colopleural fistula is an incredibly rare phenomenon that can result from diaphragmatic injury, malignancies, perforated diverticulosis, or colonic/pulmonary infections. The management of a colopleural fistula depends on anatomical, clinical, and other factors. Diverticulitis is usually treated using antibiotics and other conservative therapies. Diverticular disease usually requires surgery if there is perforation, progressive signs of sepsis or peritonitis, fistula, or failure of conservative treatment. A surgical procedure was performed in this case because of empyema arising from a colopleural fistula formation caused by diverticulosis.\n\nConclusion Primary colon resection, colon anastomosis, fistula suturing, and decortication thoracotomy were shown to effectively treat colopleural fistula.", "keywords": [ "Colopleural fistula", "empyema", "diaphragmatic hernia", "resection", "anastomosis", "thoracotomy" ], "content": "Introduction\n\nFistulas are abnormal communications that occur between two epithelial surfaces. Gastrointestinal fistulas comprise all connections that involve the gastrointestinal tract. Which can manifest as either congenital of acquired in nature.1 Colopleural fistula is an incredibly rare phenomenon resulting from a wide variety of colon disorders such as injury, tumor infiltration, and infection. Despite being rare, empyema following acute abdomen or infection of the gastrointestinal tract could indicate a fistula connecting the pleura and abdominal cavity with infection involved. A proper workup is required to establish the diagnosis, and comprehensive management is essential to prevent empyema recurrence. Evaluation of pleural fluid and radiological examination of the chest and abdomen, along with contrast studies, can provide early visualization and diagnosis of the fistula. Management of colopleural fistula depends on the underlying pathology.2 Therefore, we report a rare case of a patient admitted with empyema and colopleural fistula secondary to transverse colon diverticulosis. This case report was prepared in accordance with the SCARE 2020 guidelines and submitted subsequent to the completion of the SCARE 2020 checklist.3\n\nCase report\n\nAn 18-year-old Indonesian male presented to the emergency department with abdominal pain in all four quadrants over the previous 4 weeks. Abdominal pain was accompanied by dyspnea, cough, and fever. One week prior, he began experiencing dyspnea and cough with left-sided chest discomfort. The severity of dyspnea was alleviated when the patient sat in a tripod position. He had a history of left diaphragmatic repair and colostomy formation surgery due to an empyema complicated by a diaphragmatic hernia 10 months prior to presentation. The patient presented with abdominal pain, and a routine chest radiograph revealed a high contour of the diaphragmatic dome on the left diaphragm, without suspicion of diaphragmatic hernia. On the sixth day of hospitalization, the patient developed dyspnea and sharp pain, which worsened with deep inhalation. The patient underwent chest radiography, which revealed pleural effusion. The patient underwent needle decompression and Water Sealed Drainage (WSD) insertion, resulting in discharge of pus and fecal matter. The patient underwent a diaphragmatic hernia repair and colostomy. Intraoperative findings also revealed intestinal adhesions, raising the suspicion of intestinal tuberculosis. Colostomy was performed in the right abdominal quadrant on the same side as the adhesions. The patient was treated with rifampicin 450 mg, isoniazid 400 mg, and etambutol 500 mg for 9 months because of extrapulmonary tuberculosis. The patient had no complaints regarding defecation through colostomy, but some parts of the colostomy had pus.\n\nUpon admission, a physical examination revealed that the patient was fully conscious and had moderate pain. The vital signs showed normal blood pressure, heart rate, tachypnea of 28x/min, and slight fever of 37.5°C. Physical examination of the chest showed delayed asymmetrical left hemithorax movement with decreased vesicular sound on the ipsilateral side and normal breath findings on the right side. During lung auscultation, no rales, ronchi, or wheeze was heard. Abdominal examination revealed normal bowel sounds and tenderness in the epigastric region. Colostomy examination showed positive production of fecal material on the proximal side and pus on the distal side.\n\nDuring admission, laboratory workup revealed a slight decrease in albumin (3,2 g/dL) and an increase in globulin (4,3 g/dL). Other laboratory parameters were within the normal range. The contrast-enhanced Chest CT scan revealed an atelectasic left lower lobe in the inferior central region; haziness of the left lung base with an air component raises suspicion of bowel gas and empyema on the left side of the thorax with a suspected connection to the intra-abdominal cavity through the diaphragm (Figure 1). Colonoscopy revealed pus production and two lumens in the transverse colon around the anastomosis area that appeared to be a fistula (Figure 2), and no abnormalities were found in the descending and sigmoid colons. The colopleural fistula was found to connect the pleural space to the intra-abdominal cavity near the perforated diverticulum in the left transverse colon (Figure 3).\n\nSurgical intervention was decided after the preoperative diagnosis of an intestine-diaphragm fistula and left-sided thoracic empyema. The midline incision extended from three fingers infraumbilical to two fingers below the xyphoid process, and no evidence of exudate fluid/pus was observed after the peritoneum was incised. Full intraoperative inspection revealed adhesions in the intestines, particularly the ileum and colon, towards the left subdiaphragm, followed by sharp adheolysis. There were further adhesions in the transverse colon to the left diaphragm, and a fistula connecting the left pleural cavity to the intraluminal left transverse colon was discovered (Figure 4B and 4C). The fistula was then cannulated using a 5F nasogastric tube as a marker. Adhesion was then performed via adhesiolysis by releasing the fistula from the left diaphragm into the colon. The transverse colon was resected, and end-to-end anastomosis between the transverse colon and descending colon was made with a 3.0 vicryl suture and overhected with a 3.0 silk suture (Figures 4D and 4E). The fistula-caused defect in the left diaphragm was repaired and sutured using a simple interrupted technique with prolene 1.0. The colostomy in the previous surgery, which was proximal to the anastomosis, was retained as transient fecal diversion. After controlling the hemorrhage and washing the abdominal cavity, the operative region was closed layer by layer, leaving one drain in the subhepatic region, which was then connected to a water-seal drainage (WSD) system in the left thoracic region. Left decortication thoracotomy was performed after adhesiolysis and resection of the transverse colon, end-to-end anastomosis of the transverse-descending colon, and primary suturing of the defect in the diaphragm. The patient underwent thoracotomy and debridement of the left thoracic space under general anesthesia. During the thoracotomy, approximately 100 mL of exudate fluid was observed (Figure 4A).\n\nThe Histopathological findings revealed diverticula protruding from the colonic mucosa through the muscularis propria and multinucleated giant cells with acute and chronic inflammatory cells. No tubercle, Langhans large cells, or caseous necrosis was observed. This finding is in concordance with the pathology of the diverticulosis (Figure 5).\n\nOne month after surgery, the WSD tube was removed because of the absence of exudate production and improvement of dyspnea. After two months, the colostomy was closed, and the patient was able to return to his usual activities without any complaints and with a good surgical wound (Figure 4F).\n\n\nDiscussion\n\nColopleural fistula is an incredibly rare phenomenon caused by a variety of colon disorders, and patients are typically hospitalized for dyspnea and chest pain. Colopleural fistulas can be formed secondary to diaphragmatic injury, which can result in connections between the pleural space and intra-abdominal cavity through hernia. This was described in a case report by El Hiday et al., who reported a colopleural fistula secondary to diaphragmatic injury caused by surgery.4\n\nHydrothorax rather than empyema occurred because of the absence of an infection during the formation of a fistula. Colopleural fistulae with empyema may result from tumor infiltration or infection in the surrounding area. The development of a colopleural fistula resulting from tumor infiltration was documented in a recent study by Lian et al. in 2017. The report stated that the chief complaints were chest pain, dyspnea, and fever, which were also experienced by the patient. The CT scan revealed an empyema caused by infiltration of colon cancer pT4bN0M0.5\n\nColopleural fistulas may also result from infection-related perforations. Infection may occur in the colon but may also occur in the lungs. Hayashi et al. reported a case of colopleural fistula secondary to a pulmonary Aspergillus infection. According to their report, aspergillus infection may produce protease, fibrinase, and various toxins, which can destroy the lung and adjacent structure, resulting in the formation of a fistula.6 In our case, a colopleural fistula was formed secondary to transverse colon infection and diverticulosis perforation of the colon near the left side of the diaphragm, which can spread the infection and lead to diaphragmatic injury along with perforation.\n\nDiverticulosis is a pathological state characterized by the development of multiple sac-like protrusions (diverticula) throughout the gastrointestinal tract. Although diverticula may form in areas of vulnerability in the walls of both the small and large intestines, this condition is commonly reported in the sigmoid colon of the large intestine. Throughout in the intestines, these spaces are reinforced by the external longitudinal layer of the muscularis propria. In the colon, this muscle layer is discontinuous and divided into three bands known as taeniae coli. Excessive peristaltic contractions can cause an increase in the intraluminal pressure. This can lead to the formation of diverticles in the colon. Colonic diverticula are characterized by a thin wall that consists of flattened or atrophic mucosa, compressed submucosa, and typically, an attenuated muscularis propria is absent. This histopathological finding was in accordance with the present case, in which the muscularis propria was absent. Obstruction of the diverticula with stasis of contents results in inflammatory changes that cause diverticulitis and peridiverticulitis. Perforation can easily occur when there is inflammation, increased pressure, and mucosal ulceration within an obstructed diverticulum, because the wall of the diverticulum is only supported by the muscularis mucosa and a thin layer of subserosal adipose tissue. Recurrent diverticulitis, regardless of perforation, can lead to complications, such as abscess formation, fistula formation, or bowel obstruction. In our case, the presence of a colopleural fistula occurred due to a perforated diverticulum in the left transverse colon that connects the intra-abdominal cavity to the pleural space.7,8\n\nThe occurrence of colopleural fistula secondary to diverticulosis was documented in previous studies conducted by Olesen et al. in 1989 and Papagiannopoulos et al. in 2004.2,9 Olesen et al. reported a 63-year-old male patient admitted due to dyspnea and tachycardia. Two years prior, the patient had been admitted for irregular defection and faint left-sided upper abdominal pain, and barium enema examination revealed slight diverticulitis. Chest radiography revealed left-sided pleural effusion. Chest drainage revealed foul pus containing gram-negative and gram-positive cocci. Subsequent microbiological cultures confirmed the presence of anaerobic bacteria. A pleural drain was inserted, and saline irrigation was administered daily until the pleural fluid became sterile. During the course of antibiotic treatment, the patient developed abdominal symptoms including nausea and left-sided upper abdominal pain. A fistula was identified via barium enema, which originated from the descending colon below the left flexure and passing through the left diaphragm. The patient was managed with parenteral nutrition for two weeks, and the fistula was barely visible on fistulography.9 Colopleural fistula secondary to diverticulosis was also reported by Papagiannopoulos et al. in a 46-year-old male who was admitted with an acute abdomen. Emergency laparotomy and Hartmann procedure were performed, which revealed a perforated sigmoid diverticulum. Two months later, the patient was readmitted with fever and left-sided abdominal and thoracic pain. Chest radiography revealed left-sided pleural effusion, and CT revealed a basal empyema pocket with no intra-abdominal collection. Based on the patient's clinical condition, empyema evacuation with rib resection and drain placement was performed. Chest drainage revealed pus discharge with coliforms and Streptococcus group D growth. Computed tomography (CT) of the chest and abdomen followed by a colostomy enema revealed a colopleural fistula extending from the colostomy site to the pleural space with communication with the distal colon. After performing an urgent laparotomy with adhesiolysis, en bloc resection of the fistula and colon was performed, followed by primary anastomosis and loop ileostomy.2\n\nA diaphragmatic hernia is a protrusion of abdominal organs into the chest cavity resulting from a defect in the diaphragm. This condition often arises as a congenital phenomenon, although it can also be acquired by trauma or surgery involving the diaphragm, thorax, or abdomen.10,11 There are two types of congenital diaphragmatic hernias: Bochdalek and Morgagni. Bochdalek hernia is the most common type of diaphragmatic hernia. It occurs through a posterior defect in the diaphragm and manifests at an early stage in life. While Morgagni’s hernia is due to a defect in the anterior part of the diaphragm, the foramina Morgagni, and presents later in life.11,12 An acquired diaphragmatic hernia may result in various complications, including diaphragmatic rupture, acute obstructive symptoms, respiratory arrest, strangulation, and cardiac tamponade. Several complications may arise as a consequence of acquired diaphragmatic hernia, including acute obstructive symptoms, diaphragmatic rupture, cardiac tamponade, strangulation, and respiratory arrest. A delayed diagnosis results in permanent complications associated with prolonged herniation. The etiology of acquired diaphragmatic hernia is dependent on the type of surgery (the technique used to close the diaphragm) and patient-related factors, such as penetrating trauma; however, the left hemidiaphragm is involved more frequently (>80%) than the right.10,13 The occurrence of contamination leading to infection increases the probability of developing empyema in the future. Additionally, it has been observed that the colon becomes trapped in the chest due to a diaphragmatic hernia.10 This condition can be caused by a range of disorders including colitis, diverticulitis, colon polyps, and colon cancer.14\n\nThe management of a colopleural fistula depends on several factors, including anatomical characteristics and clinical conditions. Graham et al. suggested that conservative treatment should be considered for all uncomplicated fistula. The majority of colonic fistula close spontaneously within two weeks if there is no mucosal growth within the fistula, obstruction, or malignancies of the bowel distal to the fistula.15 This approach was used by Olesen et al., where the patient only had conservative treatment using parenteral nutrition, pleural drain, and antibiotics.9 Diverticulitis usually treatable with antibiotics and other conservative therapies. Diverticulitis or diverticular disease usually requires surgery if there is a clear sign of perforation, a progressive sign of sepsis or peritonitis, failure of conservative treatment, or the formation of a fistula.16 In our case, surgical intervention was indicated because of the presence of a perforated colonic diverticulum, along with the spread of infection leading to fistula development in the diaphragm, and the patient showed clinical signs of peritonitis in the epigastric area. Furthermore, a surgical procedure was performed to evacuate the pus from the thoracic region via thoracotomy.\n\nThe most common technique for diverticulosis surgery is the resection of the diverticulum and anastomosis between the proximal and distal segments of the resected region. Nevertheless, the primary distinction between “standard” diverticulitis and diverticulitis that causes colopleural fistula is the diverticulum site. Diverticulitis commonly occurs in the sigmoid colon; hence, the standard surgical procedure is to perform a sigmoidectomy followed by colorectal anastomosis.17 In our case, a perforated diverticulum that resulted in a colopleural fistula occurred in the transverse colon in the region near the left diaphragm. Therefore, transverse colectomy and transverse descending colon anastomosis were performed. The same technique was also performed by Papagiannopoulos et al. also conducted a similar procedure with resection of the colon and fistula, and primary anastomosis was performed with the addition of a loop ileostomy.2 Diverting stoma can be performed to prevent anastomosis leak, which is a significant cause of morbidity and mortality following colorectal resection. Several randomized controlled trials and meta-analyses corroborate the evidence that stoma diversion can reduce the incidence of anastomotic leak and the need for emergent abdominal reoperation.18–21 Fortunately, the patient in our case had already undergone surgery to treat colon adhesion and colostomy formation prior to admission to our center. Therefore, we retained the colostomy proximal to the resected region for a temporary fecal diversion.\n\n\nConsent\n\nWritten informed consent was obtained from the patient's parents/legal guardians for the publication of this case report and accompanying images. A copy of the written consent is available for review by the Editor-in-Chief of this journal upon request.", "appendix": "Data availability\n\nData sharing is not applicable to this article, as no datasets were generated or analyzed during the current study.\n\nRespository: Updating Consensus Surgical Case Report (SCARE) 2020 guidelines checklist https://www.sciencedirect.com/science/article/pii/S1743919120307718.\n\n\nAcknowledgements\n\nNot applicable.\n\n\nReferences\n\nPickhardt PJ, Bhalla S, et al.: Classification, etiologies, and imaging evaluation of acquired gastrointestinal fistulas Radiology.2002 Jul; 224(1): 9–23.\n\nPapagiannopoulos K, Gialvalis D, Dodo I, et al.: Empyema resulting from a true colopleural fistula complicating a perforated sigmoid diverticulum. Ann. Thorac. Surg. 2004 Jan; 77(1): 324–326. PubMed Abstract \| Publisher Full Text\n\nAgha RA, Franchi T, Sohrabi C, et al.: SCARE 2020 Guidelines: Updating Consensus Surgical CAse REport (SCARE) Guidelines. Int. J. Surg. 2020 Dec 1 [cited 2023 Mar 11]; 84: 226–30. PubMed Abstract \| Publisher Full Text Reference Source\n\nHiday AHAE, Khan FY, Almuzrakhshi AM, et al.: Colopleural fistula: A case report and literature review. Ann Thorac Med. 2008 [cited 2023 Sep 22]; 3(3): 108–109. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLian R, Zhang G, et al.: Empyema caused by a colopleural fistula. Medicine (Baltimore). 2017 Sep 29 [cited 2023 Sep 21]; 96(39): e8165. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHayashi A, Susaki Y, Ose N, et al.: Colopleural fistula caused by Aspergillus: an extremely rare complication after lung resection—case report. Surg Case Rep. 2016 Apr 23 [cited 2023 Sep 26]; 2: 40. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDiverticulosis - StatPearls - NCBI Bookshelf.[cited December 6, 2023]. Reference Source\n\nKumar V, Abul K, Jon CA: Robbins basic pathology. Philadelphia: Elsevier; 10th ed2018.\n\nOlesen LL, Pedersen JT: Colo-pleural fistula. Eur. Respir. J. 1989 Sep; 2(8): 792–793. PubMed Abstract \| Publisher Full Text\n\nSpellar K, Lotfollahzadeh S, Gupta N: Diaphragmatic hernias. StatPearls. Treasure Island (FL): StatPearls Publishing; 2023 [cited January 1, 2024]. Reference Source\n\nGupta S, Warrell D, Smith L, et al.: Strangulated right-sided diaphragmatic hernia presenting and treated as lung empyema: differential diagnosis. BMJ Case Rep. 2020 Jul 8 [cited 2024 Jan 1]; 13(7): e233440. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHussain N, Deedar A, et al.: A Morgagni hernia was found in a patient with empyema thoracis.2016; 8(4).\n\nDhar S, Bhasin SK, Langer JG: Diaphragmatic Hernia Presenting as Empyema Thorax.2005 [cited 2023 Dec 6]; 7(1). Reference Source\n\nOnafowokan OO, Khosa K, Bonatti H: Laparoscopic Repair of Morgagni Hernia Combined with Right Hemicolectomy for Bleeding Ascending Colon Carcinoma Lodged within the Chest: A Case Report and Review of the Literature. Case Reports in Surgery. 2021 Jul 20 [cited 2024 Jan 1]; 2021: 1–5. Publisher Full Text Reference Source\n\nGraham JA: Conservative treatment of gastrointestinal fistulas. Surg Gynecol Obstet. 1977 Apr 1; 144(4): 512–514. PubMed Abstract\n\nLock JF, Galata C, Reißfelder C, et al.: The Indications for and Timing of Surgery for Diverticular Disease. Dtsch. Arztebl. Int. 2020 Aug 31; 117(35–36): 591–596. PubMed Abstract \| Publisher Full Text\n\nHolzheimer RG, Mannick JA: Surgical Treatment: Evidence-Based and Problem-Oriented. Munich: Zuckschwerdt; 2001 [cited 2023 Sep 27]. Reference Source\n\nLightner AL, Pemberton JH: The Role of Temporary Fecal Diversion. Clin. Colon Rectal Surg. 2017 Jul; 30(3): 178–183. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChude GG, Rayate NV, Patris V, et al.: Defunctioning loop ileostomy with low anterior resection for distal rectal cancer: should we make an ileostomy as a routine procedure? A prospective randomized study. Hepatogastroenterology. 2008; 55(86–87): 1562–1567. PubMed Abstract\n\nMatthiessen P, Hallböök O, Rutegård J, et al.: Defunctioning Stoma Reduces Symptomatic Anastomotic Leakage After Low Anterior Resection of the Rectum for Cancer. Ann. Surg. 2007 Aug [cited 2023 Sep 27]; 246(2): 207–214. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGu WL, Wu SW: Meta-analysis of defunctioning stoma in low anterior resection with total mesorectal excision for rectal cancer: evidence based on thirteen studies. World J. Surg. Oncol. 2015 Jan 24 [cited 2023 Sep 27]; 13(1): 9. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "294341", "date": "08 Jul 2024", "name": "Vicky Sumarki Budipramana", "expertise": [ "Reviewer Expertise Gastroentestinal Surgeon", "Lecturer" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address 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 explain that the cause of fistulation was diverticulosis confirmed by colonoscopy. The incarcerated herniation and perforation of the transverse colon into the diaphragmatic defect due to prevous diaphragmatic surgery is still possible. Both of them show the same finding on colonoscopy and histopathology. The authors should explain why the occurrence of colopleural fistula is rare. Intestinal fistulation into surrounding organs is common and has reported in the literature. Common examples of intestinal fistulae are: entero-cutaneous fistula, enter-enteric fistula, entero-vesical fistula, entero-colic fistula, entero-atmospheric fistula and recto-vaginal fistula.\n\nIs the background of the case’s history and progression described in sufficient detail? Yes\n\nAre enough details provided of any physical examination and diagnostic tests, treatment given and outcomes? Yes\n\nIs sufficient discussion included of the importance of the findings and their relevance to future understanding of disease processes, diagnosis or treatment? Partly\n\nIs the case presented with sufficient detail to be useful for other practitioners? Yes", "responses": [] } ]	1	https://f1000research.com/articles/13-643
https://f1000research.com/articles/13-641/v1	17 Jun 24	{ "type": "Research Article", "title": "Predictive Ability of Self-Care and Psychological Flow in Occupational Stress Among Nurses", "authors": [ "Abdallah Salem Almahaireh", "Baha' Suhail Shawaqfeh", "Baha' Suhail Shawaqfeh" ], "abstract": "Background The nursing workforce is crucial in healthcare systems worldwide and contributes to community well-being. also, Nurses experience numerous psychological, social, emotional, and behavioral shocks and challenges in their work. In Jordan, 43% of doctors and nurses suffer from high levels of burnout, around 55% experience high levels of emotional exhaustion, and 33% of doctors and nurses suffer from high levels of psychological pressure and job stress. Others found that 70% of nurses experience stress. these issues can be reduced by practicing self-care and psychological flow which impact in work-related tasks which are important in effectively addressing occupational stress healthily and soundly. This study aims to determine predictive ability of self-care and psychological flow in occupational stress among nurses\n\nMethods This study follows the quantitative technique. sample consisting of 476 nurses in Amman Jordan was chosen. Three scales were developed to meet the study objectives: Occupational stress scale, Self-care scale, and psychological flow scale.\n\nResults The study results indicate that self-care and psychological flow levels were low, while the occupational stress level was high. Also, there are a predictive ability of self-care and psychological flow in occupational stress among nurses.\n\nConclusions This study shows that of self-care and psychological flow predict occupational stress among nurses, which helps us to manage the occupational stress among them by giving them self-care and psychological flow practices and healing time.", "keywords": [ "Self-Care", "Psychological Flow", "Occupational Stress", "Nurses." ], "content": "Introduction\n\nWork is of utmost importance source as it is the way to unleash human energies and feel importance and self-realization, working in the field of medical and health professions is one of the most important professional fields in life, and its importance is due to the great role that those working in it provide in preserving the health and care of individuals. Working in hospitals requires dealing with various cases and direct or indirect interaction and contact with patients, particularly by nurses, who must carry out their duties with patients regardless of their health conditions. This may pose numerous challenges and difficulties for nurses, leading to negative psychological and health effects due to the occupational stress they are exposed to. Hence, the importance of balancing work and life, and practicing self-care to achieve psychological flow, which serves to protect individuals from psychological and professional problems and disorders, ultimately leading to psychological and professional adaptation.\n\nIt's worth noting that stress, to some extent, can be positive and a source of personal growth and motivation for achievement. But it also leads to negative consequences if it exceeds a certain level and persists for prolonged periods, hindering individuals' activity individual’s activity and ability to work and accomplishment, thus negatively affecting the employee, the work team, or even the workplace itself. Employees who experience stress often encounter problems, have higher rates of illnesses, exhibit less commitment to their workplaces, and consequently have higher resignation rates, which in turn leads to the loss of skilled employees and increased recruitment and training costs. (Antares Foundation, 2012)\n\nOccupational Stress is considered one of the ways through which stressors in the work environment (pressures) can lead to psychological, behavioral, or physiological manifestations of stress and long-term health effects, it is the physical and emotional responses that occur when work requirements exceed the capabilities, resources, or needs of the worker (Levy, et al., 2018).\n\nThe impact of stress related to humanitarian work does not only affect the individual, but also extends to the environment in which he works, the group he works with, and even others around him. given the negative consequences of this impact on the individual, work, and society, many researchers have sought to identify the causes of work stress and factors that can increase or decrease occupational stress (Soliman & Gillespie, 2011).\n\nAdditionally, they explore methods to prevent the development of more severe psychological disorders such as burnout, depression, emotional exhaustion, and others, and attempt to find solutions that enable individuals to continue working, reduce human and material losses, and adapt (Hricova, et al., 2020; Parikh, et al., 2004).\n\nJachens et al. (2018) identified factors that specifically affect humanitarian work and interact with occupational stress, including emergency culture, rewards such as feelings of achievement and pride, constant and unpredictable changes in work, high job involvement, and the inability to withdraw when needed unrealistic job demands, limited availability of social support networks, and insufficient self-care practices.\n\nOne of the early theorists in self-care was nurse Dorothea Orem in the 1950s. She described self-care as an individual's ability to care for others while maintaining their performance and development (Renpenning & Taylor, 2003). Orem's theory was directed at nurses, whose work inherently involves continuous care for others. She considered self-care to revolve around activities individuals engage in to maintain their well-being. where effective self-care sustains an individual's towards others and contributes to human development, she considers Self-care to include activities that people participate in to maintain, improve, or restore their health. Orem also believed that self-care practices are learned not only for necessities, but help create a balance among daily activities, pressures, relaxation, and rest, thus enhancing and preserving human life and promoting well-being (Khademian, et al., 2020).\n\nSelf-care refers to the importance of practices that individuals engage in to take care of themselves, it is closely linked to professions that involve caregiving, such as nursing, where much of the research and theories originated from the field of nursing and healthcare. This is due to the nature of nurses' work, which requires engagement in environments where they are continually exposed to emergencies and the distressing stories and experiences of the populations they serve. Additionally, they face the psychological, social, and physical difficulties of their patients, along with accompanying feelings such as anger, fear, and despair. Nurses often feel helpless or powerless to find solutions for all the problems and concerns their patients face, which can lead to frustration and disability, exposing them to high levels of occupational stress. (Santana et al., 2020; Li et al., 2021).\n\nSelf-care is defined as the ability of individuals, families, and communities to promote health, prevent disease, and manage illness or disability with or without the support of healthcare providers (World Health Organization, 2009).\n\nNurses spend their entire practical lives caring for others, and sometimes this can become detrimental as they often neglect to provide themselves with the same level of care. nurses frequently encourage their patients to lead happier, healthier lives free of stress and psychological pressure but fail to follow this advice themselves. Self-care is measured by the ability of workers to recognize and monitor the impact of their work or personal life on their well-being, effectively perform their professional duties, and take appropriate steps to ensure self-care. Thus, self-care is a requirement for achieving improvement and maintaining a sense of satisfaction among nurses. it enhances their mental health and well-being and fosters more effective self-care practices in various dimensions: physical, psychological, spiritual, and professional, helping them remain balanced and prevent burnout and occupational stress (Headington Institute, 2010).\n\nThrough the concept of self-care, which involves taking care of oneself, striving for personal well-being, and making healthy decisions that contribute to happiness by addressing emotional, social, spiritual, and professional aspects, a significant role is played in achieving psychological flow. this is characterized by a high level of focus and full engagement in life's activities, enjoying them, and feeling challenged. this indicates a correlational relationship between self-care and psychological flow, whereby achieving and maintaining self-care enhances the opportunity to reach a state of psychological flow (Al-Hiary, 2023).\n\nPsychological flow is defined as a deep state of immersion in enjoyable activities, where individuals perceive their performance as enjoyable and successful, viewing the activity as worthwhile even if it does not lead to further achievement (Csikszentmihalyi, 2014). Psychological flow is an internal psychological state that engulfs the individual in the activity he is engaged in, with a sense of accomplishment in dealing with these activities. it is a crucial force in individual success in work, providing energy, self-awareness, and the ability to enhance performance and alleviate occupational stress (Happell, et al., 2013). From this perspective, flow is an aggregate of psychological factors including focus, control, awareness, motivation, self-awareness, clarity of goals, clear feedback, balance, and challenge, and it is vital in the workplace, where individuals who frequently experience flow tend to have high job satisfaction, more productivity, and less occupational stress (Joseph, 2013; Martínez-Zaragoza, et al., 2017).\n\nThe nursing workforce plays a crucial role in healthcare systems worldwide and contributes to community well-being. Working in the nursing sector is complex, hazardous, and sometimes unsafe. Those responsible for the nursing sector should create suitable working conditions for nurses and consider their mental health and well-being because the quality of care provided by nurses partially depends on the quality of their work environment (International Labor Organization and World Health Organization, 2017). The field in which nurses work may lead to occupational stress and neglect of self-care practices, affecting their psychological flow. Research has indicated that 43% of doctors and nurses in Jordan suffer from high levels of burnout, around 55% experience high levels of emotional exhaustion, 34% have decreased humaneness towards patients, 39% experience reduced personal accomplishment, and 33% of doctors and nurses suffer from high levels of psychological pressure and job stress (Jordanian Ministry of Health, 2020; Santana et al., 2020). Additionally, a study by (Dehdashti, et al., 2018) found that 70% of nurses experience stress.\n\nNurses experience numerous psychological, social, emotional, and behavioral shocks and challenges in their work, which can impact their psychological flow during work-related tasks (Ekman & Halpern, 2015). Self-care in the medical field has evolved in response to the neglect of basic needs among healthcare providers in favor of focusing on patient treatment (Lauder, 2001). while In nursing, self-care adopts a comprehensive approach to wellness and the acquisition of health-enhancing behaviors (Denyes, et al., 2001).\n\nThus, the importance of self-care for nursing professionals has emerged as a fundamental and necessary component in effectively addressing occupational stress healthily and soundly. To provide efficient services to promote mental health, prevent occupational stress, achieve optimal healthcare quality and flow, and develop self-care mechanisms (Zhang, et al., 2021; Barnett, et al., 2007; Smith & Moss, 2009).\n\nPracticing self-care strategies supports mental health and well-being (Mills, et al., 2018). If nurses neglect self-care, it may lead to health problems that can affect them professionally and personally, sometimes resulting in occupational stress and resignation from the nursing profession (Kelbach, 2021). Several studies have indicated the detrimental long-term effects of insufficient self-care practices for nursing professionals, such as burnout, occupational stress, mental health disorders, and decreased professional efficacy (Zhang et al., 2021; Barnett, et al., 2007; Smith & Moss, 2009).\n\nPsychological flow is related to individuals' self-care, as it brings feelings of happiness, enjoyment, and satisfaction in life, and contributes to creating a positive mental state. Thus, understanding how flow experience affects individuals can offer insights that can be employed to improve individuals' quality of life, consequently impacting their professional lives and work quality, thereby contributing to providing comprehensive care services and reducing the risk of occupational stress among nurses (Burke, et al., 2016; Heo, 2007). Hence, this study investigated the predictive ability of self-care and psychological flow on occupational stress among nurses in Jordan.\n\n\n\n1. What are the self-care, psychological flow, and occupational stress levels among nurses in Jordan?\n\n2. Is there a predictive ability of self-care and psychological flow in occupational stress among nurses in Jordan?\n\n\nMethods\n\nThis study follows the quantitative technique by prediction method. A sample of 476 nurses in Amman was collected voluntarily; the informed consent was taken verbally and written. Also, the researchers took approval from the institutions.\n\nThe volunteering sample consisting of 476 nurses in Amman Jordan was chosen, which is 2.6% of the population. Their age ranged between 26-58 (M=35.6 ±9.14).\n\nOccupational stress scale\n\nThe researchers developed a scale of 21 items from (Kushal, et al., 2018; Belkic & Savić, 2008). Participants rated each item on a five-Likert scale, from 1 (I agree to a very small extent) to 5 (I agree to a very big extent). Higher scores reflect a higher level of occupational stress. The researchers extracted the validity and reliability and found that the discriminate evidence ranged between 0.343 and 0.874. Cronbach's alpha was 0.885 (Shawaqfeh & Almahaireh, 2024).\n\nSelf-care scale\n\nThe researchers developed a scale of 22 items divided into 4 dimensions (physical, psychological, spiritual, and occupational) from (Lichner, et al., 2018; Jallad, 2021). Participants rated each item on a five-Likert scale, from 1 (strongly disagree) to 5 (strongly agree). Higher scores reflect a higher level of self-care. The researchers extracted the validity and reliability and found that the discriminate evidence ranged between 0.771 and 0.942. Cronbach's alpha ranged between 0.742 and 0.913 (Shawaqfeh & Almahaireh, 2024).\n\nPsychological flow scale\n\nThe researchers developed a scale of 19 items from (Alakili, 2015; Al-Hiary, 2023). Participants rated each item on a five-Likert scale, from 1 (strongly disagree) to 5 (strongly agree). Higher scores reflect a higher level of psychological flow. The researchers extracted the validity and reliability and found that the discrimination evidence ranged between 0.458 and 0.874. Cronbach's alpha was 0.818 (Shawaqfeh & Almahaireh, 2024).\n\nThe researchers obtained approval for this study from the Institutional Review Board at the University of Jordan. The registration number is 1546/2024/21. The date was 12/5/2024. Anonymized data was collected by online instruments using Google Forms. The data collected between 13-18/5/2024.\n\nThe researchers entered the data into the SPSS data sheet and used IBM SPSS Statistics for Windows, version 22 (IBM Corp., Armonk, N.Y., USA) to analyze the data. Means, standard deviations, Pearson’s correlation, and multi-regression were calculated. There was no missing data because all questions were required to be answered in the Google form.\n\nThe researchers obtained verbal and written approval for this study from the Institutional Review Board at the University of Jordan. The registration number is 1546/2024/21. The date was 12/5/2024.\n\nThe informed consent was taken verbally and written. Also, the researchers took approval from the institutions.\n\n\nFindings and discussion\n\nMeans, standard deviations, and Person correlations between occupational stress, self-care and psychological flow are shown in Table 1.\n\n* Correlation is significant at the 0.01 level (2-tailed).\n\nTable 1 shows a negative correlation between Occupational stress and each Self-care and Psychological flow. Also, there is a positive correlation between Self-care and Psychological flow. Furthermore, the Self-care and Psychological flow levels were low. The Self-care mean was (2.32±0.46), and the Psychological flow mean (2.13 ±0.88) while the Occupational stress level was high mean was (3.91 ±0.41). The results show that the data is normally distributed.\n\nThis result can be attributed to work pressures and stress experienced by nurses. According to statistics from the Jordanian Ministry of Health, there are only 37 nurses for every 10,000 citizens (Jordan News Agency, 2017). To cover this shortage, hospitals allow nurses to work multiple shifts in a single day, leading to long working hours, caring for large numbers of patients, and receiving emergency cases. This diminishes their ability to balance home and work requirements and reduces their capacity for self-care (Suleiman, et al., 2019). Consequently, nurses may experience feelings of boredom, routine, dissatisfaction, negativity, and disengagement from required tasks (Zaki, 2018), along with an inability to keep up with life demands and a lack of satisfaction due to low-income levels (Al-Hamdan & Bani Issa, 2022). This leads to a decrease in the level state of psychological flow.\n\nThe high level of Occupational stress can be explained by nurses lacking self-care skills and self-attention, as well as insufficient time for relaxation, experiencing flow state, and engaging in various activities due to work pressures. Additionally, the inability to express emotions, feelings of depletion, exhaustion, and fatigue result from a lack of Psychological flow skills and empathy toward patients. Nurses may also struggle to share their sad feelings and bear their emotional burdens (Zito, et al., 2016).\n\nThe lack of providing self-care programs and recreational activities in hospitals which help nurses cope with and adapt to Occupational stress, along with insufficient social and psychological support (Suresh, 2013), contributes to the low level of self-care. Nurses are assigned multiple quantitative and qualitative duties and tasks that exceed their capabilities, leading to role conflict due to the shortage of nursing staff in Jordanian hospitals (Khani, & Jaafarpour, 2008; Jordanian Ministry of Health, 2019; World Health Organization, 2020).\n\nOne of the reasons for high Occupational stress levels and low levels of psychological flow among nurses is their lack of involvement in decision-making processes at their workplaces, significant disparities between financial income, rewards, and required tasks, as well as limited opportunities for promotion and career advancement with unclear paths, particularly in private hospitals. Additionally, conflicts and lack of harmony with supervisors and managers in nursing practice exacerbate internal dissatisfaction and decrease self-esteem (Kumar, et al., 2011). The work environment in hospitals, in general, is perceived as stressful, and nurses in Jordan express dissatisfaction with the nursing work environment (Suleiman, et al., 2019).\n\nTo investigate the predictive ability of self-care and psychological flow in occupational stress among nurses in Jordan, a regression test was calculated, and Table 2 shows the results.\n\nTable 2 shows the predictive ability of self-care and psychological flow in occupational stress among nurses in Jordan was 21.2%, while the correlation was 0.460. Also, The Psychological flow has a more substantial influence on occupational stress, and there is a negative relationship between the variables.\n\nThe low practice of self-care and relaxation among nurses, along with diminished psychological flow, bring about feelings of sadness, job dissatisfaction, and dissatisfaction with life. This contributes to creating a negative psychological state, negatively impacting quality of life, professional life, and work quality, leading to increased job stress levels. This explains the inverse relationship between psychological flow and self-care with occupational stress. These findings are consistent with studies by (Jallad, 2021; Shapiro, et al., 2007). Jachens, et al. (2018) clarified that working in the humanitarian field, such as nursing, interacts with occupational stress, and one of the reasons for its increase is the lack of self-care practice, relaxation, and weak social support. (Renpenning & Taylor, 2003) demonstrated that self-care preserves and improves nurses' mental health and well-being.\n\nWorking in nursing is a stressful and traumatic job when exposed to severe medical cases. nurses' sense of enjoyment diminishes, making it difficult for them to perceive their performance as enjoyable and successful, especially when patients die during their shifts. Consequently, psychological flow is unattainable in this negative work environment, thereby increasing their occupational stress.\n\nThe explanation for 21.2% of the relationship between flow, self-care, and occupational stress can be attributed to the low level of psychological flow and self-care among nurses. They cannot enhance their physical, psychological, emotional, social, spiritual, and professional well-being due to workload burden, time pressure, lack of social and professional support, limited career advancement, and absence of self-care skills such as relaxation, meditation, spiritual practices, self-awareness, and reactive coping. They also struggle with concentration, integration into work, feelings of fatigue, boredom, loss of commitment and perseverance, task diversity, shift work, inability to communicate with others due to work pressure, and lack of work-life balance, resulting in high levels of occupational stress.\n\n\nConclusion\n\nThis study shows that there are predictive ability of self-care and psychological flow in occupational stress among nurses, which helps us to manage the occupational stress among them by giving them self-care and psychological flow practices and healing time. addition, there is a high level of occupational stress among nurses and the managers and hospital mostly conduct this issue because it affects their job. However, the self-care and psychological flow among them were low which means they don’t give themselves good attention and it may cause many problems and mental illness. Organizations and Hospitals should provide them with more special assistance, support, and training. Thus, future research should consider social support, coping, and job satisfaction as potentially important variables.\n\nThis study was conducted with a sample of nurses in the Capital Amman, Jordan enrolled in 2024. The study results were interpreted from the participants’ responses on self-care, psychological flow, and occupational stress scales. The researchers recommends further research on occupational stress among nurses to define it and to produce a program to decrease it which can give us better quality work.\n\nFuture research might also study coping, work environment, job satisfaction, and resilience variables. The creation of counselling and guidance programs to improve self-care and psychological flow among nurses may use technological applications.\n\n\nEthics and consent\n\nThe researchers obtained verbal and written approval for this study from the Institutional Review Board at the University of Jordan. The registration number is 1546/2024/21. The date was 12/5/2024.\n\nThe informed consent was taken verbally and written. Also, the researchers took approval from the institutions.", "appendix": "Data availability statement\n\nFigshare. The predictive ability of self-care and psychological flow in occupational stress among nurses (Dataset.sav). https://doi.org/10.6084/m9.figshare.25892764.v2 (Shawaqfeh, 2024)\n\nData is available under the terms of the CC0.\n\nRepository name: Figshare\n\nChecklist for predictive ability of self-care and psychological flow in occupational stress among nurses, at https://doi.org/10.6084/m9.figshare.25892764.v2 (Shawaqfeh, 2024)\n\nFunding details: The authors received no financial support for the research, authorship, and/or publication of this article.\n\n\nAcknowledgments\n\nThe researchers would like to thank the hospitals and nurses for helping them in collecting the data.\n\n\nReferences\n\nAlakili A: Psychological Flow among Gifted High School Students and its Relationship to Self-Regulation. 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Publisher Full Text\n\nSmith PL, Moss SB: Psychologist impairment: What is it, how can it be prevented, and what can be done to address it? Clin. Psychol. Sci. Pract. 2009; 16: 1–15. Publisher Full Text\n\nSoliman H, Gillespie D: A test of stress theory: relief workers in refugee camps. Disasters. 2011; 35(4): 789–800. PubMed Abstract \| Publisher Full Text\n\nSuleiman K, Hijazi Z, Al Kalaldeh M, et al.: Quality of nursing work life and related factors among emergency nurses in Jordan. J. Occup. Health. 2019; 61(5): 398–406. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSuresh D: Quality of Nursing Work Life among nurses working in selected government and private hospitals in Thiruvananthapuram. 2013. Unpublished Doctoral Dissertation, SCTIMST.\n\nWorld Health Organization (WHO): Self-care in the context of primary health care: Report of the Regional Consultation, Bangkok. Thailand: 2009. Reference Source\n\nWorld Health Organization (WHO): Health workforce.2020. Reference Source\n\nZaki A: Psychological Flow among University Students/Deile University. Center for Psychological Research. 2018; 2(28): 241–267.\n\nZhang M, Murphy B, Cabanilla A, et al.: Physical relaxation for occupational stress in healthcare workers: A systematic review and network meta-analysis of randomized controlled trials. J. Occup. Health. 2021; 63(1): e12243–e12216. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZito M, Cortese CG, Colombo L: Nurses’ exhaustion: the role of flow at work between job demands and job resources. J. Nurs. Manag. 2016; 24(1): E12–E22. PubMed Abstract \| Publisher Full Text" }	[ { "id": "301709", "date": "23 Jul 2024", "name": "Amal I Khalil", "expertise": [ "Reviewer Expertise psychiatric", "psychological and psychosocial research all types of research designs as well child", "adult", "and elderly psychological and psychiatric disorders." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nthank you for giving the opportunity to review this manuscript let's start with the title: : despite it is concise but it is little bit unclear for the reader so i suggest to be changed into\n\n\"Predictive Roles of Self-Care and Psychological Flow in Occupational Stress Among Nurses\" or \"Assessing the Predictive Power of Self-Care and Psychological Flow on Occupational Stress in Nurses\"\nAbstract :As a peer reviewer, here are some potential drawbacks and areas for improvement in the abstract:\n\nThe abstract is slightly wordy and can be more concise. This can be achieved by removing redundant phrases and ensuring each sentence adds new information. The objective of the study could be more clearly stated at the beginning of the abstract. Currently, it is embedded within a broader discussion of the context. The abstract mentions that three scales were developed, but it does not provide any details on their development, validation, or reliability. Including brief information on these aspects would strengthen the abstract. The results section mentions that self-care and psychological flow levels were low, and occupational stress was high, but it does not provide any specific data or statistics to support these claims. Including key statistics would make the results more robust. : The conclusion mentions that self-care and psychological flow practices can help manage occupational stress but does not provide specific recommendations or implications for practice. Adding this information would make the conclusions more actionable. The abstract contains some grammatical insufficiency and awkward phrasing that can be refined for clarity and readability. Introduction :Here are some potential drawbacks of the provided introduction and suggestions for improvement: The introduction is quite lengthy and contains many ideas that could be more concisely presented. A more focused introduction would help readers quickly grasp the main points. The introduction would benefit from clearer structure and organization. It jumps between different concepts without clear transitions. Organizing it into distinct paragraphs for context, problem statement, and the purpose of the study would improve readability. Some points are repeated, such as the importance of self-care and psychological flow, which can be consolidated to avoid redundancy. While the introduction provides a lot of background information, it sometimes strays from the main focus of the study. Keeping the information relevant to the research question would make the introduction more impactful. The introduction includes many references, which, while supporting the points made, can overwhelm the reader. Select the most pertinent references to strengthen the key points. The introduction could benefit from more specific statements about the research gap and the need for this study. It should more clearly highlight what is unknown or understudied about the relationship between self-care, psychological flow, and occupational stress among nurses. research problem it is better to say significance of the study and here some drawbacks: Length and Conciseness: The problem statement is quite long and includes a lot of background information that could be more concisely presented. The main problem could be stated more directly. Clarity and Focus: The statement introduces several related issues (e.g., burnout, emotional exhaustion, psychological pressure, self-care, psychological flow) without clearly connecting them to the main research problem. Focusing on the central issue of how self-care and psychological flow impact occupational stress among nurses would improve clarity. Redundancy: Some points are repeated, such as the impact of occupational stress and the importance of self-care. These could be combined to streamline the text. Lack of Specificity: The problem statement mentions various statistics and studies but does not clearly state the specific gap or need that the current study addresses. More emphasis on what is unknown or understudied would be beneficial. Transition and Structure: The transitions between different points could be smoother. Organizing the statement into distinct paragraphs for background, problem identification, and the purpose of the study would enhance readability. There are many references to other studies, which, while supporting the points made, can make the problem statement Methods: first the definition of variables \"self care , psychological flow, occupational stress is important for the readers ,the other thing Sample Representativeness: The sample, while sizable, represents only 2.6% of the nurse population in Amman. This could limit the generalizability of the findings to all nurses in Jordan, and how they calculate the sample size??The study's cross-sectional design limits the ability to draw causal inferences. While predictive relationships can be identified, causal conclusions cannot be definitively made. the scales used were adapted from other studies which may differ culturally as well the authors mention developed which is wrong as they adapted both scales Data Collection Method:\nUsing online instruments such as Google Forms may exclude participants who are less tech-savvy or have limited internet access, potentially introducing sampling bias.\n\nLimited Contextual Information:\nThe study might benefit from including more contextual information about the work environment, workload, and other stressors specific to the nursing profession in Jordan. These factors could provide a deeper understanding of occupational stress.\n\nEthical Considerations:\nWhile informed consent was obtained verbally and in writing, ensuring that participants fully understand the study's aims and their rights is crucial. Detailed information on how consent was obtained and documented would enhance ethical transparency.he study does not account for other variables that might influence occupational stress, such as personal life stressors, job satisfaction, or organizational support. Including these factors could provide a more comprehensive analysis. as the authors didn't include demographic characteristics of the participants which is very important in interpreting the results also short data collection time\n\n(13-18/5/2024) might not capture variations in stress levels that could occur over different times or under different circumstances. results of the study: missed Demographic characteristics of the participants it is better to separate results from discussion for more interpretations and discussions big number of cited references are old and needs updates where is the recommendations and clinical implications of these results a lot of limitations should be recognized in this study such as : self reported tools, lack of generalizability since the study was conducted only on Jordanians living in Amman, mediating variables should be considered as mentioned before\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": [] }, { "id": "349181", "date": "26 Dec 2024", "name": "Ahmad Al-Sagarat", "expertise": [ "Reviewer Expertise 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 article is searching one of the most issues that are facing the Jordanian nurses specifically. In some areas I would like the author to use the most recent studies and avoid using old literature older than 10 years old. I would like the author to expand more on the limitations from different perspectives such as: sample, type of hospital, different geographic areas, mixed method--- etc. Moreover, I would like the author to add the implication of this study for nursing practice, nursing administration, nursing education and future research. Finally, the overall article is highly recommended and approved for indexing.\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\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": "13053", "date": "03 Jan 2025", "name": "Abdallah Almahaireh", "role": "Author Response", "response": "Dear Ahmad Al-Sagarat We wanna thank you for these notes that improve our work. We made the changes you reported and used recent references as we could. Best Regards," } ] } ]	1	https://f1000research.com/articles/13-641
https://f1000research.com/articles/13-364/v1	23 Apr 24	{ "type": "Data Note", "title": "A compilation of histidine kinase genes in the genome of a tissue macerating Pectobacterium brasiliense isolated from potato in South Africa", "authors": [ "Sarah Oluwatobi Otun", "Khayalethu Ntushelo", "Khayalethu Ntushelo" ], "abstract": "Background: A compilation of kinase genes of Pectobacterium brasilense is presented. The genes were mined from a complete genome sequence of strain BD163 isolated from potato in Tshwane, South Africa. This work is an effort to collate knowledge on P. brasiliense which has become a worldwide pathogen of potatoes and other vegetables such as tomato. Histidine kinases of P. brasiliense can be targets of bacterial control agents to limit the growth, spread and pathogenicity of P. brasiliense. Methods: The whole genome sequence of strain BD163 of P. brasiliense deposited on www.ncbi.nlm.nih.gov was downloaded and individual kinase genes were searched and listed with their properties, namely, locus tag, protein accession number and annotation. Conclusions: This is the only compilation of histidine kinase genes for P. brasiliense.", "keywords": [ "Pectobcterium brasiliense", "Histidine Kinase", "Genome", "Plant pathogen", "Potato disease" ], "content": "Introduction\n\nHistidine kinases are enzymes that catalyse phosphorylation reactions involving histidine (Figure 1) (Catlett et al., 2003). These kinases are essential for signal transduction and bacterial adaptability to new environments, and they are widely distributed in bacteria.). The function performed by histidine kinases is critical to the function of an organism and therefore targeting histidine kinases in Pectobacterium brasiliense as means to limit its growth, spread and pathogenicity may help reduce its impact as a plant pathogen. Pectobcterium brasiliense is a tissue macerating pathogen of various crops and it has gained prominence with recent reports from various hosts in Taiwan, China and Korea (Li et al., 2023; Park et al., 2022; Song et al., 2023). Similar to other bacteria P. brasilense gains entry into the plant through natural openings or wounds, it spreads throughout the intercellular spaces, and upon close contact with target plant cells it releases a barrage of tissue macerating effectors to disrupt cells and thereafter survives on the oozing sap. The outside appearance of affected tissues is discoloured and as the disease worsens the plant weakens and eventually succumbs to infection. If not interrupted by disease control agents P. brasiliense may cause unprecedented damage not only to individual plants but also to the plants close to the initially infected plant. With the discouraged use of antibiotics ways to control P. brasiliense are limited and therefore new drug targets are necessary. Histidine kinases inhibitors are widely employed as agents in drug design and development. Before efforts to design kinase targets in P. brasiliense, it is necessary to first compile all histidine kinases in P. brasiliense. This present work aimed to list all histidine kinases present in P. brasiliense to enable future efforts for design, formulation and testing of histidine kinase inhibitors. We created a list of histidine kinase genes of P. brasilense, strain BD163, whose complete genome sequence is published by Rauwane et al. (2023).\n\nPhosphorylation of a histidine (H) residue is triggered by an external stimulus and detected by the sensor domain. The effector domain is activated when a phosphate is transferred to a conserved aspartic acid residue (D) in the RR receiver domain, leading to an action such as transcriptional activation or a MAP kinase (MAPK) cascade.\n\n\nMethods\n\nThe genome sequence of strain BD163 of P. brasiliense, BioProject no. PRJNA798891, with raw reads under accession no. JAKNTB000000000, BioSample number SAMN25132833, and GenBank assembly accession number GCA_022172285.1 was downloaded and individual histidine kinase genes were searched using the normal search function. To create the histidine kinase gene catalogue, the genes were listed with their characteristics namely, locus tag, protein accession number and annotation (Table 1).\n\nTo validate the histidine kinase gene repertoire of P. brasiliense, a comparative analysis was conducted by comparing the identified histidine kinase genes from strain BD163 with other available Pectobacterium genomes in the NCBI database. This analysis aimed to explore the conservation and diversity of histidine kinase genes within the genus Pectobacterium. The histidine kinase genes of three Pectobacterium strains (Pectobacterium carotovorum NX18131, Pectobacterium atrosepticum PB72, and Pectobacterium parmentieri IFB5626) were compared as part of a genome comparison study. The histidine kinase genes were found following the procedures outlined in the methods section. Based on the comparison results, it was found that similar to BD163, strains of P. carotovorum NX18131 and P. atrosepticum PB72 each contained 24 histidine kinase genes, whereas strain IFB5626 of P. parmentieri had just 20. These values show histidine kinase gene frequency differences among Pectobacterium species.", "appendix": "Data availability\n\nThe genome sequence of strain BD163 of P. brasiliense, BioProject no. PRJNA798891, with raw reads under accession no. JAKNTB000000000, BioSample number SAMN25132833, and GenBank assembly accession number GCA_022172285.1 is obtainable from www.ncbi.nih.nlm.gov.\n\n\nReferences\n\nCatlett NL, Yoder OC, Turgeon BG: Whole-Genome Analysis of Two-Component Signal Transduction Genes in Fungal Pathogens. Eukaryot. Cell. 2003; 2(6): 1151–1161. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLi N-P, Tang W-Q, Lee S, et al.: First Report of Pectobacterium carotovorum and Pectobacterium brasiliense Causing Bacterial Soft Rot of Bok Choy in Taiwan. Plant Dis. 2023. PubMed Abstract \| Publisher Full Text\n\nPark K-T, Hong S-M, Back C-G, et al.: First Report of Pectobacterium brasiliense Causing Soft Rot on Graft Cactus in Korea. Res. Plant Dis. 2022; 28(3): 172–178. Publisher Full Text\n\nRauwane ME, Mchunu NP, Pierneef R, et al.: Draft Genome Sequence of Pectobacterium brasiliense Isolated from Potato in South Africa. Microbiol. Resour. Announc. 2023; 12(4): e0076322. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSong Z, Yang C, Zeng R, et al.: First Report of Pectobacterium brasiliense Causing Soft Rot on Conophytum luiseae in China. Plant Dis. 2023; 107(1): 211. Publisher Full Text" }	[ { "id": "271244", "date": "29 May 2024", "name": "Iris Yedidia", "expertise": [ "Reviewer Expertise Plant pathology", "Plant microbe interaction", "bacterial virulence" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nReviewer 1 for: \"A compilation of histidine kinase genes in the genome of a tissue macerating Pectobacterium brasiliense isolated from potato in South Africa\" By: Sarah Oluwatobi Otun and Khayalethu Ntushelo. The paper describes a compilation of genomic data regarding histidine kinase genes in the genome of P. brasiliense BD 163, isolated from potatoes in South Africa. It is a data note and therefore it is not a regular review process. I am adding my comments regarding mainly the way of presenting the data and the introduction, and not the analysis process.\nIntroduction:\nSince the paper deals with data analysis of histidine kinase, I suggest adding a bit of information on the concept of using histidine kinase inhibitors as a potential control strategy. I included two sentences from the draft (in italics) where I think that the explanation should be added:\n\nHistidine kinases inhibitors are widely employed as agents in drug design and development. Inhibition of bacterial virulence and pathogenicity was demonstrated previously using HKs inhibitors, by changing the expression of virulence factors and the ability of bacteria to adapt to the host environment. Before efforts to design kinase targets in P. brasiliense, it is necessary to first compile all histidine kinases in P. brasiliense.\n2. I also suggest to add a reference or two that are relevant to the concept of HKs inhibition as a tool to reduce virulence and infection. Here is short list of references: [1] Bem AE, et. al., 2015 (Ref 3) [2] Qin, Z, et. al., 2008 (Ref 1) [3] Espinasse A, et. al., 2023 (Ref 4) [4] Gotoh, Y, et. al., 2010 (Ref 2)\n3. In the Schematic representation of histidine kinase presented as Figure 1: The letter A in the scheme doesn’t stand for anything in the legend. Shouldn't it be replaced with (D)? moreover, in the description the phosphate is transferred to RR receiver, while in reality it is transferred to the effector (A). Did I misunderstand it or it should be clarified?\n4. Table: Genes related to Histidine kinase characteristics in the genome of Pectobacterium brasiliense strain BD163. I suggest changing it to: Genes or putative genes related to histidine kinase….etc.\n\nIs the rationale for creating the dataset(s) clearly described? Yes\n\nAre the protocols appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and materials provided to allow replication by others? Yes\n\nAre the datasets clearly presented in a useable and accessible format? Partly", "responses": [ { "c_id": "11679", "date": "17 Jun 2024", "name": "Dr Sarah", "role": "Author Response", "response": "Dear Editor, We hope this message finds you well. We sincerely thank reviewer 1 for his detailed and constructive feedback on our manuscript, \"A compilation of histidine kinase genes in the genome of a tissue macerating Pectobacterium brasiliense isolated from potato in South Africa.\" We have carefully considered each comment and made the necessary revisions to enhance the clarity and quality of our work. Response to Reviewer Comments: Comment: \"Since the paper deals with data analysis of histidine kinase, I suggest adding a bit of information on the concept of using histidine kinase inhibitors as a potential control strategy. I included two sentences from the draft (in italics) where I think that the explanation should be added: Histidine kinases inhibitors are widely employed as agents in drug design and development. Inhibition of bacterial virulence and pathogenicity was demonstrated previously using HKs inhibitors, by changing the expression of virulence factors and the ability of bacteria to adapt to the host environment. Before efforts to design kinase targets in P. brasiliense, it is necessary to first compile all histidine kinases in P. brasiliense.\" Response: We appreciate this valuable suggestion. We have added the following information to the Introduction section to provide a clearer understanding of the concept: \"Histidine kinase inhibitors are widely employed as agents in drug design and development. Inhibition of bacterial virulence and pathogenicity was demonstrated previously using HK inhibitors, altering the expression of virulence factors and the bacteria's ability to adapt to the host environment. This approach offers a promising strategy to control bacterial infections by targeting key regulatory pathways.\" Comment: \"I also suggest to add a reference or two that are relevant to the concept of HKs inhibition as a tool to reduce virulence and infection.\" Response: We have added the following references to support the concept of histidine kinase inhibition: Bem AE, et al., 2015 Espinasse A, et al., 2023 Comment: \"In the Schematic representation of histidine kinase presented as Figure 1: The letter A in the scheme doesn’t stand for anything in the legend. Shouldn't it be replaced with (D)? Moreover, in the description the phosphate is transferred to RR receiver, while in reality it is transferred to the effector (A). Did I misunderstand it or it should be clarified?\" Response: Thank you for pointing out these discrepancies. We have revised the legend of Figure 1 to replace the letter \"A\" with \"D\" to maintain consistency. Additionally, we clarified the description to accurately reflect the phosphate transfer process: \"The phosphate group is transferred from the histidine kinase to the response regulator (RR), which then affects the effector.\" Comment: \"Table: Genes related to Histidine kinase characteristics in the genome of Pectobacterium brasiliense strain BD163. I suggest changing it to: Genes or putative genes related to histidine kinase….etc.\" Response: We agree with the suggestion. The table's title has been changed from \"Genes” to Putative Genes Related to Histidine Kinase Characteristics in the Genome of Pectobacterium brasiliense Strain BD163.\" Revised Manuscript: We have submitted a clean version of the manuscript without comments or tracked changes, per your requirements. Additionally, we have uploaded a version with yellow highlights to 'Track Changes' for easy identification of the revisions made." } ] } ]	1	https://f1000research.com/articles/13-364
https://f1000research.com/articles/12-260/v1	10 Mar 23	{ "type": "Research Article", "title": "Cloning and characterization of the LvCTL genes encoding C-type lectin from white-leg shrimp (Litopenaeus vannamei)", "authors": [ "Tran Vinh Phuong", "Xuan Huy Nguyen", "Nguyen Quang Lich", "Quang Tan Hoang", "Ngoc Nguyen Tran", "Phuoc Ngoc Nguyen", "Nguyen Quang Linh", "Tran Vinh Phuong", "Xuan Huy Nguyen", "Nguyen Quang Lich", "Quang Tan Hoang", "Ngoc Nguyen Tran", "Phuoc Ngoc Nguyen" ], "abstract": "Background: Lectins are carbohydrate-binding protein domains. The C-type designates a requirement for calcium for binding. Proteins contain C-type lectin domains that have a diverse range of functions, including cell-cell adhesion, immune response to pathogens, and apoptosis. This study aimed to investigate the characters of LvCTL-encoding genes from white-leg shrimp (Litopenaeus vannamei) in Central Vietnam. Methods: Two PCR products (LvCTL3 and LvCTL4) were cloned and sequenced. The structure and characterization of LvCTL proteins were predicted using bioinformatics tools. Results: The results showed that the LvCTL3 gene was 444 nucleotides long and 98.87% similar to the published LvCTL3 gene (accession number: KF156943). The polypeptide sequence had 147 amino acids, which were 97.28% identical to the reference sequence (AGV68681) and the LvCTL4 gene had a length of 417 nucleotides and homology of 99.52% compared to the published gene (KM387560). The deduced polypeptide sequence had 138 amino acids, and was 100% similar to the reference sequence (AKA64754). The LvCTL3 had a molecular weight of 16.91 kDa and an isoelectric point (pI) of 4.66, while LvCTL4 had 15.75 and 4.58 kDa, respectively. The structure prediction results showed that LvCTL3 and LvCTL4 had one domain (CTLD), LvCTL3 had two α helices and nine β sheets, and LvCTL4 had two α helices and eight β sheets. Conclusions: Our results provide essential information for the heterologous expression and biosynthesis production of C-type lectins.", "keywords": [ "C-type lectin", "gene encoding", "LvCTL genes", "white leg shrimp." ], "content": "Introduction\n\nC-type lectins (CTLs) are proteins/glycoproteins capable of reversibly binding to carbohydrates by non-covalent bonds without altering their structure (Zhang et al., 2009). Lectins can bind to cells with glycoproteins or microbial surface glycolipids and are considered pattern recognition receptors (PRR) recognizing and releasing invading microorganisms in the system. The shrimp lectin protein family is very rich and diverse; members of the eight PRR families have been identified in several shrimp species, based on structure and specificity to different sugars of the carbohydrate recognition domain (CRD). These families are lipopolysaccharide and b-1,3-glucan binding proteins (LGBPs), CTLs, galectin, thioester-containing proteins (TEP), fibrinogen-related proteins (FREP), scavenger receptors (SR), down syndrome cell adhesion molecules (DSCAM) and Toll-like receptors (TLR) (Wang and Wang, 2013). According to form and function, lectins are classified as Calnexin, C-, L-, P-, I-, R-, and S-type lens (Janeway and Medzhitov, 2002; Zhang et al., 2009). Among the lectins, CTL is the most diverse and well-studied (Zhang et al., 2009).\n\nCTLs are a group of proteins that play an essential role in many animal biological processes, including cell signaling and pathogen recognition. CTLs are a superfamily of more than 1,000 proteins identified by having one or more well-characterized C-type lectin-like domains (CTLDs). They are divided into 17 subgroups based on their species and domain organization (Weis et al., 1998; Zelensky and Gready, 2005). CTL also plays an essential role in mammalian innate immunity. The mannose-binding lectin (MBL) is primarily expressed in the liver and released into the plasma, where it recognizes potentially pathogenic bacteria and binds to microbial surfaces. Animals can also activate the complement pathway (Thiel and Gadjeva, 2009). Similarly, CTLs are also important immune recognition receptors in invertebrates. CTLs in shrimp can currently be divided into three subgroups based on domain composition and organization: those containing only one C-type lectin domain (CTLD), those having two CTLDs, and those containing one CTLD and another part (Wang and Wang, 2013). Among them, the group containing only one CTLD was more common than the few CTLs in shrimp containing two CTLDs. The presence of two or more binding sites for each lectin molecule allows it to bind to many different cell types. The prevalence of CTLD in invertebrates is much higher than in vertebrates. Typically, CTLD is the seventh most common domain in the Caenorhabditis elegans genome, but only the 43rd most common domain in the human genome (Zelensky and Gready, 2005). Shrimp CTLD can bind multiple ligands and constructs inducible expression of CTLs. Recent studies have revealed multiple functions and mechanisms of shrimp CTLs in antimicrobial and antiviral immunity. These protective functions of CTLs in the shrimp species Fenneropenaeus chinensis are based on their ability to recognize and bind CTLDs (Sun et al., 2008). In the framework of this study, we present the results of cloning and characterization of the LvCTL genes isolated from white-leg shrimp (Litopenaeus vannamei) in Thua Thien Hue as a prerequisite for the production of recombinant LvCTL proteins for further research.\n\n\nMethods\n\nAnimal use in this study was allowed by Hue University of Animal Ethics Committee with certificate reference number: HUVN0018, April 10th, 2022. Principal Researcher: Nguyen Quang Linh. All efforts were undertaken to minimize the suffering of animals.\n\nWhite-leg shrimp (L. vannamei) with a weight of ~20 g per head, which were collected from shrimp ponds; the samples were aseptically dissected to collect the hepatopancreas shrimp samples and stored in liquid nitrogen, and used directly for RNA extraction.\n\nTotal RNA from hepatopancreas samples was extracted using the GeneJET RNA Purification Kit (Thermo Scientific, USA) according to the manufacturer's instructions. Electrophoresis was conducted to check the total RNA obtained on 1% agarose gel with TAE 1X at 70V for 30 min by using PowerPac 3000 (Bio-Rad). The cDNA biosynthesis was performed using RevertAid First Strand cDNA Synthesis kit (Thermo Fisher Scientific, USA), and the obtained product was used directly for PCR amplification.\n\nThe sequences of LvCTL-encoding genes were obtained from GenBank to design a specific primer (Table 1). PCR was performed using the following conditions: 95°C for 2 min, and then 40 cycles of 95°C for 1 min, 55°C for 30 s, and 72°C for 1 min, followed by a final extension at 72°C for 7 min. PCR products were confirmed by electrophoresis at 70V for 35 min on 1% agarose gel with TAE 1X stained SafeViewTM Classic (abm, Canada).\n\nPCR products were recovered from agarose gels and purified using the GeneJET Gel Extraction kit (Thermo Scientific, USA). Purified PCR products were cloned into pGEM T-easy vector with T4 DNA Ligase for 1 hour at room temperature (Promega, USA), then, the recombinant vectors were transferred into Escherichia coli TOP10 bacteria using the heat shock method. The recombinant vectors were selected on LB medium (Luria Bertani Agar, Merck, Germany) supplemented with 50 μg/mL Amp, X-Gal/IPTG. E. coli cells carrying the recombinant vector (white colonies) were then inoculated with 5 mL of liquid LB medium supplemented with 50 μg/mL Amp, and DNA plasmids were isolated using the GeneJET Plasmid Miniprep Kit (Thermo Fisher Scientific, USA). The isolated DNA plasmid was examined by 1.0% agarose gel electrophoresis at 70V for 35 min and used for LvCTL sequencing (Ha et al., 2018). The sequence of the LvCTL genes was analyzed using the Sanger method (First base Company, Malaysia). The results were checked using BioEdit software and then compared with those published in GenBank using the BLAST tool. A phylogenetic tree of CTL encoding genes was built using MEGA 11 software with the Neighbor-Joining algorithm (Tamura et al., 2021).\n\nCharacterization of LvCTL proteins was determined using bioinformatics tools, including amino acid sequence translation with Expasy, protein domain using SMART (Letunic et al., 2021), spatial structure model using Phyre2 (Kelley et al., 2015), isoelectric point using IPC2 (Li et al., 2014).\n\n\nResults\n\nAfter PCR with specific primers, the results showed that two DNA fragments were amplified and expressed approximately at 450 and 420 bp in size, respectively. According to the theoretical length of the cDNA fragment of the LvCTL3 and LvCTL4 genes. PCR reaction using specific primers with pGEM vector as template was performed, electrophoresis images showed very specific PCR products (Figure 1), which proved that LvCTL genes was successfully attached to pGEM vector T-easy (referred to as the recombinant vector pGEM/LvCTL3 and pGEM/LvCTL4). Therefore, the recombinant vectors were used to analyze the nucleotide sequences. The previous reports indicate several CTLs in some shrimp species, such as: Litopenaeus vannamei, L. schmitti, L. setiferus, Fenneropenaeus chinensis, F. merguiensis, Penaeus monodon, Marsupenaeus japonicus and Macrobrachium rosenbergii (Wang and Wang, 2013). We constructed a phylogenetic tree from the deduced LvCTL polypeptide sequences compared with the CTL fragment sequences of other shrimp species. The results show that LvCTL3 and LvCTL4 belong to two groups in the dendrogram and our arrangements were similar to the published lines of white-leg shrimp (L. vannamei) but different from other shrimp species (Figure 4).\n\nM: DNA ladder (GeneRulerTM 1 kb DNA Ladder, Thermo Scientific, USA). NC: Negative control. 1-5: PCR product with cDNA of LvCTL3-LvCTL4-LvAV-LvCTLD-LvLdlrCTL genes. 6-7: PCR product of LvCTL3 gene from 2 different colonies. 8-9: PCR product of LvCTL4 gene from 2 different colonies.\n\nIn our study, the nucleotide sequence of LvCTL3 PCR product was 444 bp in length, encoding a polypeptide sequence of 147 amino acids. The nucleotide sequence of LvCTL3 PCR product was 417 bp in length, encoding a polypeptide sequence of 138 amino acids. These were fragment of genes containing the open reading frame (ORF) region cut off the peptide signal, intended to be used to produce recombinant LvCTL protein for other studies related to recombinant protein production. For the conserved domain determined using the SMART program, the ORF sequence of LvCTL3 had one domain (CTLD) from amino acid position 14 to 146. LvCTL3 had a molecular weight of 16.91 kDa, and the isoelectric point (pI) was 4.66. The results of spatial structure prediction showed that the LvCTL3 molecule had two alpha helices (16%) and nine beta strands (28%) (Figure 5). Meanwhile, the ORF sequence of LvCTL4 had one domain (amino acid 1 to 137), a molecular weight of 15.75 kDa and a pI is 4.58. LvCTL4 structure had two alpha helices (17%) and eight beta strands (32%) (Figure 6).\n\n\nDiscussion\n\nThe results of sequence analysis showed a change in the isolated LvCTL genes compared with the published genes. The isolated LvCTL3 fragment was 444 bp in size (including the stop codon), 98.87% homologous to the published gene (439/444 nucleotides compared with KF156943) (Figure 2). The change of the LvCTL3 gene resulted in a difference in the sequence of the encoded polypeptide, the highest similarity obtained was 97.28% (143/147 amino acids) compared with the reference sequence AGV68681. Meanwhile, the LvCTL4 fragment was 417 bp, 99.52% homologous to the gene of KM387560 (415/417 nucleotides) (Figure 3). However, the change of the LvCTL4 gene resulted in no change in the sequence of the encoded polypeptide (100% similarity) compared with the reference sequence (AKA64754).\n\nAccording to Li et al. (2014), the LvCTL3 gene from shrimp (L. vannamei) has a length of 579 bp, in which the coding segment is 492 bp (from nucleotide positions 25 to 516), encoding a polypeptide chain with a length of 163 amino acids, and has an estimated molecular weight of 17.9 kDa, an estimated pI of 4.80 (Li et al., 2014). The LvCTL4 gene, also from L. vannamei shrimp, has a length of 563 bp, in which the coding segment is 471 bp (from nucleotide positions 27 to 497). The ORF encoded a protein of 156 amino acids consisting of a single CTLD (residues 19-155) and a putative signal peptide (residues 1-18). Tissue expression analysis showed LvCTL4 was distributed with high levels in the gills, intestine, epithelium and hepatopancreas (Li et al., 2015). Meanwhile, LvTRAF3 was also cloned and characterized from the shrimp L.vannamei; it had a transcript of 3,865 bp, with an ORF of 1,002 bp, and encoded a polypeptide of 333 amino acids, with a calculated molecular weight of 38.6 kDa (Li et al., 2020).TRAF3 functions as a regulator of innate immune response that involves many cellular processes\n\nWhen comparing to the L. vannamei genes, the predicted LvCTL3 sequence resulted in 97.28% similarity to the sequence of AGV68681 or 96.60% to XP_027212325, while LvCTL4 was 100% similar to the sequence of AKA64754 and XP_027228060. LvCTL3 and LvCTL4 were 60.69% (XP_042883674) and 80.43% (QEX50549) homologous to kuruma prawn (Penaeus japonicus), respectively. Compared with black tiger shrimp (Penaeus monodon), LvCTL3 was 59.18% similar to the protein encoded by XP_037787306 while LvCTL4 was 88.21% similar to that of XP_037800826. Compared with other crustacean species, the difference in LvCTL sequences was higher. The similarity of the LvCLT3 sequence was only 45.58% identical to the AYD41573 sequence from red swamp crayfish (Procambarus clarkii) or 40.25 % to the XP_042233235 sequence from the American lobster (Homarus americanus). LvCTL4 was only 59.12% similar to the XP_045611199 sequence from red swamp crayfish, 60.14% to XP_042237721 from the American lobster, or 57.258% to the XP_045118055 sequence from gazami crab (Portunus trituberculatus).\n\n\nConclusions\n\nIn this study, two LvCTL3 and LvCTL4 genes from white-leg shrimp were successfully isolated, cloned, and sequenced. The ORF of LvCTL sequences had homology levels of 98.87% (LvCTL3, KF156943) and 99.52% (LvCTL4, KM387560 respectively) compared to the published gene. The predicted LvCTL proteins have one conserved domain and are defined as C-type lectins. They can be used for heterologous expression and scale-up production of recombinant C-type lectin in the future to add to the aquatic feed to enhance immunity and prevent disease in shrimp.", "appendix": "Data availability\n\nGenbank: C-type lectin [Penaeus vannamei]; Accession number: OP584994, https://identifiers.org/ncbiprotein.\n\nGenbank: C-type lectin 4 [Penaeus vannamei]; Accession number: OP584995, https://identifiers.org/ncbiprotein.\n\nFigshare: F1000Research Figures, https://doi.org/10.6084/m9.figshare.21428799.v1 (Linh et al., 2022).\n\nThis project contains the following underlying data:\n\n- 1. LvCTL3-LvCTL4-LvAV-LvCTLD-LvLdlrCTL (PCR 5 gene).jpg (Western Blot gel image)\n\n- 2. CTL3-pcr (Orignal).jpg (Western Blot gel image)\n\n- 3. CTL4-pcr (Orignal).jpg (Western Blot gel image)\n\n- 4. bw LvCTL3-LvCTL4-LvAV-LvCTLD-LvLdlrCTL (Edited).jpg (Western Blot gel image)\n\n- 5. LvCTL3 PCR colony (Edited).jpg (Western Blot gel image)\n\n- 6. CTL4 bw - colony (Editted).jpg (Western Blot gel image)\n\n- 7. The predicted of LvCTL3 structure.png (Predicted 3D structure of LvCTL3)\n\n- 8. The predicted of LvCTL4 structure.png (Predicted 3D structure of LvCTL4)\n\nProtocols.io: Lectin C gene analysis, https://dx.doi.org/10.17504/protocols.io.x54v9dyk1g3e/v1 (Phuong et al., 2022).\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\n\nAcknowledgements\n\nContact authors, (Nguyen Quang Linh) supported all of steps of this research and final revisions version and comments from editors, GenBank registration. A/Prof. Dr. Nguyen Ngoc Phuoc, is the PhD supervisor for Mr. Phuong in this research and participated in the revised final version. PhD student – Mr. Tran Vinh Phuong, who supervised all steps in data collection and analysis and GenBank registration. Other authors: Nguyen Xuan Huy, Hoang Tan Quang, Tran Nguyen Ngoc monitored the data and laboratory analysis. Our research group works together in each publication.\n\n\nReferences\n\nHa DTT, Tuan LK, Lan PTN, et al.: Cloning and sequencing laccase 3 (folac3) from Fusarium oxysporum. Hue University Journal of Science: Natural Science. 2018; 127(1C): 1–10. Publisher Full Text\n\nHe S, et al.: Molecular characterization of LvAV in response to white spot syndrome virus infection in the Pacific white shrimp (Litopenaeus vannamei). Dev. Comp. Immunol. 2015; 51(1): 48–55. PubMed Abstract \| Publisher Full Text\n\nJaneway CA Jr, Medzhitov R: Innate immune recognition. Annu. Rev. Immunol. 2002; 20: 197–216. Publisher Full Text\n\nJunkunlo K, Prachumwat A, Tangprasittipap A, et al.: A novel lectin domain-containing protein (LvCTLD) associated with the response of the whiteleg shrimp Penaeus (Litopenaeus) vannamei to the yellow head virus (YHV). Dev. Comp. Immunol. 2012; 37(3-4): 334–341. PubMed Abstract \| Publisher Full Text\n\nKelley LA, Mezulis S, Yates CM, et al.: The Phyre2 web portal for protein modeling, prediction and analysis. Nat. Protoc. 2015; 10(6): 845–858. PubMed Abstract \| Publisher Full Text\n\nLetunic I, Khedkar S, Bork P: SMART: recent updates, new developments and status in 2020. Nucleic Acids Res. 2021; 49(D1): D458–D460. PubMed Abstract \| Publisher Full Text\n\nLi H, et al.: A C-type lectin (LvCTL4) from Litopenaeus vannamei is a downstream molecule of the NF-κB signaling pathway and participates in antibacterial immune response. Fish Shellfish Immunol. 2015; 43(1): 257–263. PubMed Abstract \| Publisher Full Text\n\nLi M, et al.: Identification of a C-type lectin with antiviral and antibacterial activity from pacific white shrimp Litopenaeus vannamei. Dev. Comp. Immunol. 2014; 46: 231–240. PubMed Abstract \| Publisher Full Text\n\nLi H, Fu Q, Wang S, et al.: TNF-Receptor-Associated Factor 3 in Litopenaeus vannamei Restricts White Spot Syndrome Virus Infection Through the IRF-Vago Antiviral Pathway. Front. Immunol. 2020; 11(2110): 1–15. PubMed Abstract \| Publisher Full Text\n\nLiang Z, Yang L, Zheng J, et al.: A low-density lipoprotein receptor (LDLR) class A domain-containing C-type lectin from Litopenaeus vannamei plays opposite roles in antibacterial and antiviral responses. Dev. Comp. Immunol. 2019; 92: 29–34. PubMed Abstract \| Publisher Full Text\n\nLinh NQ:F1000Research Figures. figshare. Figure.2022.Publisher Full Text\n\nPhuong TV, Phuoc NN, Linh NQQ: Lectin C gene analysis. protocols.io.2022. Publisher Full Text\n\nSun YD, et al.: A hepatopancreas-specific C-type lectin from the Chinese shrimp Fenneropenaeus chinensis exhibits antimicrobial activity. Mol. Immunol. 2008; 45(2): 348–361. PubMed Abstract \| Publisher Full Text\n\nTamura K, Stecher G, Kumar S: MEGA11: Molecular Evolutionary Genetics Analysis version 11. Mol. Biol. Evol. 2021; 38: 3022–3027. PubMed Abstract \| Publisher Full Text\n\nThiel S, Gadjeva M:Humoral Pattern Recognition Molecules: Mannan-Binding Lectin and Ficolins.Kishore U, editor. Target Pattern Recognition in Innate Immunity. New York, New York, NY:Springer;2009; pp. 58–73. Publisher Full Text\n\nWang XW, Wang JX: Pattern recognition receptors acting in the innate immune system of shrimp against pathogen infections. Fish Shellfish Immunol. 2013; 34(4): 981–989. PubMed Abstract \| Publisher Full Text\n\nWeis WI, Taylor ME, Drickamer K: The C-type lectin superfamily in the immune system. Immunol. Rev. 1998; 163: 19–34. Publisher Full Text\n\nZelensky AN, Gready JE: The C-type lectin-like domain superfamily. FEBS J. 2005; 272: 6179–6217. PubMed Abstract \| Publisher Full Text\n\nZhang Y, et al.: Cloning and characterization of a novel C-type lectin gene from shrimp Litopenaeus vannamei. Fish Shellfish Immunol. 2009; 26(1): 183–192. PubMed Abstract \| Publisher Full Text" }	[ { "id": "166106", "date": "28 Mar 2023", "name": "Hieu Tran-Van", "expertise": [ "Reviewer Expertise Biotechnology", "molecular modelling", "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 cloned and characterized two LvCTL genes encoding C-type lectin from white-leg shrimp (Litopenaeus vannamei).\n\nThere are points authors should improve before consideration for indexing.\nAuthors should consider using recent protein structure prediction tools such as AlphaFold or homology-modeling tools based on high sequence similarities such as SWISS-MODEL or MODELLER. Other refinement tools should be applied for higher-quality structures.\n\nShould model reference proteins of Li et al. publication to give readers a better visualization of amino acid differences that may cause protein secondary structure shifts.\n\nThe authors didn’t discuss any information about protein structural characteristics. According to a previous study, shrimp stomach pH is approximately 5.7, so maybe authors should consider simulation the protein at that pH for further experiments.\n\nDoes the deletion in the DNA sequence of LvCTL3 and LvCTL4 in your study might affect its functions?\n\nAccording to your discussion, what is the purpose of building a 3D model of these two proteins?\n\nAuthors should include amino acid sequence alignments of two proteins to highlight the differences.\n\nIs the work 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": "9558", "date": "17 Nov 2023", "name": "Linh Q. NGUYEN", "role": "Author Response", "response": "1 Authors should consider using recent protein structure prediction tools such as AlphaFold or homology-modelling tools based on high sequence similarities such as SWISS-MODEL or MODELLER. Other refinement tools should be applied for higher-quality structures. The amino acid sequence alignments of two proteins (Figure 4 & Figure 5) may cause protein secondary structure shifts (Li et al., 2015). The form of a protein is related to its function. Knowledge of a protein’s 3D structure is a huge hint for understanding how proteins work. Although other refinement tools, such as homology-modelling tools based on high sequence similarities, provide higher-quality structure. However, our 3D structures have been modelled with 99.9% and 99.8% confidence by the single highest-scoring template with the 3D structure of LvCTL3 and LvCTL4, respectively. This showed that the function of these proteins is not changed. Protein folding is determined by the physicochemical properties that are encoded in the amino acids. Although most of the predictions were highly accurate, our system is imperfect. Programs such as Alpha Fold will exponentially increase our general understanding of different biological processes. So the 3D structure of these proteins should be further studied by another program to provide higher-quality structures. And the simulation of these proteins at the pH of the shrimp stomach (5.7) should be considered for further experiments. We added Fig. 4. The amino acid similarity of the isolated LvCTL3 gene and the published LvCTL3 gene (AGV68681) and Fig. 5. The similarity of the amino acid of the isolated LvCTL4 gene and the published LvCTL4 gene (AKA64754) and discussed in the text (purple colour) 2 Should model reference proteins of Li et al. publication to give readers a better visualization of amino acid differences that may cause protein secondary structure shifts. 3 The authors didn’t discuss any information about protein structural characteristics. According to a previous study, shrimp stomach pH is approximately 5.7, so maybe authors should consider simulation the protein at that pH for further experiments 4 Does the deletion in the DNA sequence of LvCTL3 and LvCTL4 in your study might affect its functions? 5 According to your discussion, what is the purpose of building a 3D model of these two proteins? 6 Authors should include amino acid sequence alignments of two proteins to highlight the differences. 7 Another revision Added 3rd affiliation of the first author: Tran Vinh Phuong1, 3 Updated another affiliation (Ex: Faculty of Fisheries, University of Agriculture and Forestry, Hue University, Thua Thien Hue, 49000, Vietnam) Underlying data Updated 2 new links, Genbank, to replace old ones. https://www.ncbi.nlm.nih.gov/nuccore/OP584994.1/ and https://www.ncbi.nlm.nih.gov/nuccore/OP584995.1/ Writing mistake: This project contains the following underlying data: - 2. CTL3-pcr (Original).jpg (Western Blot gel image) - 3. CTL4-pcr (Original).jpg (Western Blot gel image) Grant Information [Tran Vinh Phuong] was funded by the Master, PhD Scholarship Programme of Vingroup Innovation Foundation (VINIF), [VINIF.2022.TS097]. This study was partly supported by the Hue University Strong Research Group (NCM.DHH.2022.05) and by the Vietnam Ministry of Science and Technology (project code: DTDLCN.56/22) Red colour" }, { "c_id": "10227", "date": "17 Nov 2023", "name": "Vinh Phuong Tran", "role": "Author Response", "response": "Dear Reviewer; We would like to thank the reviewer for your comments on our manuscript. We have carefully considered your suggestions in revising our manuscript, and we believe that the revised manuscript is improved and suitable for publication. Detailed responses to the comments are presented in this document 1. Authors should consider using recent protein structure prediction tools such as Alpha Fold or homology-modeling tools based on high sequence similarities such as SWISS-MODEL or MODELLER. Other refinement tools should be applied for higher-quality structures Responses: Although other refinement tools such as homology-modeling tools based on high sequence similarities provide higher quality structure. However, our 3D structures have been modelled with 99.9% and 99.8% confidence by the single highest scoring template with the 3D structure of LvCTL3 and LvCTL4, respectively. Programs such as Alpha Fold will exponentially increase our general understanding of different biological processes. So the 3D structure of these proteins should be further study by another program to provide higher-quality structures 2. Should model reference proteins of Li et al. publication to give readers a better visualization of amino acid differences that may cause protein secondary structure shifts. Responses: Thanks for your value comment. We used the model reference proteins of Li et al. 2015 to give readers a better visualization of amino acid differences that may cause protein secondary structure shifts in the revised version 3. The authors didn’t discuss any information about protein structural characteristics. According to a previous study, shrimp stomach pH is approximately 5.7, so maybe authors should consider simulation the protein at that pH for further experiments Reponses We agreed and added this sentence \"the simulation of these proteins at pH of shrimp stomach (5.7) should be considered for further experiments\" in the discussion of the new version. 4. Does the deletion in the DNA sequence of LvCTL3 and LvCTL4 in your study might affect its functions? Responses The form of a protein is related to its function. Knowledge of protein’s 3D structure is a huge hint for understanding how protein’s work. Although other refinement tools such as homology-modeling tools based on high sequence similarities provide higher quality structure. However, our 3D structures have been modelled with 99.9% and 99.8% confidence by the single highest scoring template with the 3D structure of LvCTL3 and LvCTL4, respectively. This showed that the function of these proteins is not changed. Protein folding is determined by the physicochemical properties that are encoded in the amino acids 5. According to your discussion, what is the purpose of building a 3D model of these two proteins? Responses The purpose of building a 3D model of these two protein was explained in the discussion of the new version as read bellowed: The amino acid sequence alignments of two proteins (Figure 4 & Figure 5) that may cause protein secondary structure shifts (Li et al., 2015). The form of a protein is related to its function. Knowledge of protein’s 3D structure is a huge hint for understanding how protein’s work. 6. Authors should include its amino acid sequence alignment of two proteins to highlight the differences. Responses We added Figure 4. The similarity of the amino acid of the isolated LvCTL3 gene and the published LvCTL3 gene (AGV68681) and Figure 5. The similarity of the amino acid of the isolated LvCTL4 gene and the published LvCTL4 gene (AKA64754) and discussed in the text. Thank you very much for your consideration of this manuscript. Yours sincerely," } ] } ]	1	https://f1000research.com/articles/12-260
https://f1000research.com/articles/12-529/v1	22 May 23	{ "type": "Case Report", "title": "Case Report: Callosal disconnection syndrome manifesting as mixed frontal-callosal-posterior alien hand syndrome following extensive corpus callosum infarct", "authors": [ "Muhamad Faizal Zainudin", "Kar Chuan Soo", "Khin Nyein Yin", "Muhamad Faizal Zainudin", "Kar Chuan Soo" ], "abstract": "Alien hand syndrome (AHS) is a rare neurological phenomenon first described by Goldstein over a century ago. The most widely recognized variants in literature are frontal, callosal, and posterior AHS. AHS due to the corpus callosum lesion can occur alone or as part of callosal disconnection syndrome (CDS). This report presents a unique CDS case manifesting clinical features from all three AHS variants, resulting from an extensive corpus callosum infarct. Our patient exhibited various clinical features from the three AHS variants, which include grasping, groping, and difficulty releasing objects from the hand (anterior); intermanual conflict (callosal); arm levitation, mild hemiparesis, and hemisensory loss (posterior). Additionally, the extensive disruption of the corpus callosal fibers produced neurological manifestations of CDS, such as cognitive impairment, ideomotor and constructional apraxia, behavioral disorder, and transcortical motor aphasia. We employed a range of rehabilitation interventions, such as mirror box therapy, limb restraint strategy, verbal cue training, cognitive behavioral therapy, bimanual hand training, speech and language therapy, and pharmacological treatment with clonazepam. The patient showed almost complete resolution of CDS and AHS features by nine months post-stroke Our case report highlights distinctive clinical variations of AHS and the challenging correlation between clinical manifestations and neuroanatomical substrates. Future studies are necessary to explore the intricate neural connections and the precise function of the corpus callosum. This can be achieved by combining comprehensive neuropsychological testing with diffusion tensor tractography studies. It is also essential to develop a validated tool to standardize AHS assessment. Finally, the scarcity of evidence in rehabilitation interventions necessitates further studies to address the wide knowledge gap in AHS and CDS management.", "keywords": [ "alien hand syndrome", "corpus callosum", "case report", "brain infarction", "middle cerebral artery stroke", "rehabilitation outcome" ], "content": "Introduction\n\nThe corpus callosum (CC) is the most extensive white matter bundle connecting cortical regions within the two cerebral hemispheres’ frontal, parietal, occipital, and temporal lobes.1 CC fibers contribute to the interhemispheric transfer of cognitive, somatosensory, motor, executive, and visual information.2 Communication disruption between cerebral cortical areas due to CC lesion causes callosal disconnection syndrome (CDS). The corpus callosum receives blood supplies from anterior communicating arteries (ACOM), the pericallosal artery, a branch of the anterior cerebral artery (ACA), and pericallosal branches from the posterior cerebral artery (PCA).3 Given the extensive blood supplies, CC infarcts are a rare occurance.3,4\n\nThe clinical presentation of callosal lesions in each individual is highly variable, depending on location and extent of the CC damage. Even if the lesion location and extent are similar, symptoms can vary widely.2 Patients with a callosal lesion often exhibit severe clinical features3 such as visual agnosia, apraxia, conductive aphasia, alexia,5 tactile and visual anomia, neglect, agraphia, and the dissociative phenomenon commonly known as alien hand syndrome (AHS).2\n\nAHS is defined as involuntary, autonomous, apparently purposeful behaviors in which the affected limb is perceived as being controlled by an external force.6 It was first described by Goldstein7 in 1908 in a stroke patient exhibiting involuntary left-hand movements. Brion & Jedynak8 coined the term ‘alien hand’ in 1972 to describe the experience of the hand as belonging to someone else, which was observed in three patients.\n\nThree principal variants of AHS have been recognized; frontal, callosal, and posterior. The frontal variant typically affects the dominant hand9 and is associated with lesions in the supplementary motor area (SMA), cingulate cortex, dominant medial prefrontal cortex, or the anterior corpus callosum.10 It is characterized by grasping, groping, or compulsive manipulation of tools. The alien hand is perceived as being unpleasant and evokes frustration and anxiety.6 The callosal variant, primarily arising from callosal damage, is characterized by intermanual conflict (IMC)10 of the non-dominant hand, in which one hand acts at cross-purposes with the other,6 likely due to the lack of activation or suppression of inhibitory patterns.10 Together, the frontal and callosal variants make up the anterior AHS. Posterior AHS, on the other hand, is caused by damage to the thalamus, posterolateral parietal, or occipital lobe11 and is characterized by arm levitation, mild hemiparesis, hemispatial neglect, hemisensory loss, and sensory ataxia.6\n\nWe describe a case of CDS presenting as mixed AHS, cognitive impairment, ideomotor and constructional apraxia, behavioral disorder, and transcortical motor aphasia. This is the first report of AHS manifesting clinical features from all three variants. Our discussion delves into the distinctive clinical variations, the challenging correlation between clinical manifestations and neuroanatomical substrates, and the implementation of various rehabilitative strategies.\n\n\nCase report\n\nThis research received ethics approval from the National Medical Research Register Malaysia (NMRR ID-22-02490-XLP).\n\nA 57-year-old, right-handed female with risk factors of type II diabetes mellitus and hypertension presented with a sudden onset of left-sided body weakness and slurred speech. The Glasgow Coma Scale (GCS) was 15/15, and her blood pressures were normal. The medical research council (MRC) motor power scale indicated a 4/5 strength in her left upper and lower extremities. Computed tomography (CT) scan of the brain revealed an acute right temporal infarct. The following day, her GCS dropped to 10/15, accompanied by elevated blood pressure. A repeat CT scan displayed an evolution of the right temporal infarct and a new acute corpus callosum infarct extending from the right genu to the left side of the splenium (Figure 1 and Figure 2). Subsequent CT angiography (CTA) revealed short segment stenosis of the proximal M1 segment of the right middle cerebral artery (MCA), left fetal PCA, and hypoplastic right posterior communicating (PCOM) artery. Three weeks post-stroke, she was transferred to the rehabilitation unit.\n\nThe CT images demonstrate hypodensity over the corpus callosum extending from the right genu to the left side of the splenium and the right temporal lobe. CT, computed tomography.\n\nThe CT images demonstrate an extensive hypodensity from genu to the splenium of the corpus callosum and the right temporal lobe. CT, computed tomography.\n\nUpon assessment, the patient had global cognitive impairment with a baseline Mini-Mental State Examination (MMSE) score of 14/30. She displayed irritability and disinhibition, often shouting at or striking her caregiver without provocation. Moreover, she was uncooperative when her caregiver attempted to assist her with personal activities of daily living (pADLs), such as getting dressed and bathing. Her mood was labile, with inappropriate crying and laughing episodes, indicative of pseudobulbar affect (PBA). She also had transcortical motor aphasia, evidenced by limited spontaneous speech, difficulty retrieving known words (anomia) and initiating conversation, and long response delay. However, reading and repetition were relatively preserved, and language comprehension was good. Additionally, there was left-sided hemisensory loss but intact proprioception, and there were no signs of hemineglect.\n\nThe patient’s mildly paretic left upper extremity manifested abnormal and involuntary movements. It frequently counteracted her right hand’s actions (IMC). For instance, the left hand prevented the right hand from bringing a spoon closer to her mouth while she fed herself. While the right hand attempted to pull up her pants, the left resisted. Additionally, the left hand exhibited independent and purposeless actions. It unintentionally searched for and grasped any objects within sight on the table during meals or therapy sessions (groping & grasping). The patient also struggled to release objects held by her left hand, even when applying force. The left hand failed to follow verbal commands or imitate visual cues (ideomotor apraxia). However, there was no right-left confusion, and the patient remained aware of the unwilled actions performed by her left hand. She expressed anger and frustration by slamming her left hand on the table or using her right hand to strike the left (auto-criticism). Notably, she did not deny ownership of her left hand and considered it part of her body.\n\nThe patient received a combination of rehabilitation interventions. During therapy sessions, her affected hand was placed inside a mirror box, preventing her from reaching for objects on the table. The mirror reflected the volitional movement of her right hand, providing the perception that she had control over her left hand’s movement. Additionally, she was taught to keep the left hand in her pocket when it began to move unwillingly (limb restraint). The mirror box and limb restraint strategies were targeted to control the IMC, groping, and grasping. The caregiver received training on verbal cue strategies. She was instructed to verbally prompt the patient to complete her task whenever the IMC occurred. This continued until the patient could complete tasks with her right hand without verbal command. The strategy was also implemented during activities outside the therapy sessions. To alleviate her anger and frustration, the patient underwent cognitive behavioral therapy (CBT). Furthermore, she underwent speech and language therapy, bimanual hand training, pADLs, and ambulation training. Upon discharge (six weeks post-stroke), the patient was moderately dependent in pADLs and could ambulate using a quadripod under her caregiver’s supervision. Her PBA had resolved, and her behavior became more manageable.\n\nThe caregiver reported a new symptom during the first outpatient review two months post-stroke. While walking, the patient’s left hand would spontaneously raise (arm levitation), exhibiting shoulder abduction, elbow flexion, forearm supination, and a fisted hand position. Once elevated mid-air, the arm began shaking uncontrollably. The phenomenon occurred every time she walked, happening more than ten times per day. Groping, grasping, and IMC episodes continued to disrupt her daily activities. However, her speech had improved, with clearer spontaneous speech and shorter response delay. She was more cheerful and displayed appropriate behavior. Although her MMSE score had improved to 27/30, the findings from the visuospatial/executive domain of the Montreal Cognitive Assessment (MoCA) suggested constructional apraxia. To manage the worsening motor symptoms, we prescribed clonazepam 0.5 mg twice daily. The patient continued to receive all previously mentioned interventions as part of her outpatient treatment.\n\nThree months post-stroke, the patient experienced significant improvements. The frequency of arm levitation, groping, and grasping episodes had reduced by 50%, and IMC had entirely resolved. She achieved independence in ambulation without needing a walking aid and could climb stairs while supervised by her caregiver, holding onto the rail for support. The patient could independently perform most pADLs, except for toileting, where she still required some supervision to ensure proper hygiene. Her behavior was appropriate, and the auto-criticism had ceased. To address the remaining arm levitation, groping, and grasping issues, we increased the clonazepam dosage to 1 mg twice daily, aiming for the complete resolution of these motor symptoms.\n\nSix months post-stroke, the patient achieved complete independence in all aspects of pADLs and ambulation. Most CDS and AHS features had resolved, except for arm levitation. She was fully aware of her left arm’s involuntary movement and would place it in her pocket when it began to raise during ambulation. The frequency of groping and grasping episodes had significantly reduced, occurring only once or twice per week, and no longer impairing functionally. Instead of feeling distressed, the patient now found the remaining symptoms amusing. By nine months post-stroke, no further improvements were observed, so the clonazepam treatment was discontinued.\n\n\nDiscussion\n\nAHS has been a subject of intrigue in the neurological community since its initial description by Goldstein more than a century ago. It remains a relatively uncommon condition. To date, there have been fewer than 200 reported cases,10 with 34 of them representing mixed variant AHS involving a combination of two of the three recognized variants (Table 1).4,6,12–35 In this report, we discuss an unprecedented case of AHS exhibiting features from all three variants, accompanied by several distinctive clinical and neuroanatomical variations:\n\n(1) The frontal variant symptoms, which were grasping, groping, and difficulty releasing objects from the hand, occurred in the patient’s non-dominant hand, which is an unusual presentation.\n\n(2) The arm levitation, a characteristic of the posterior AHS variant, manifested much later than the other clinical features, suggesting a potential temporal progression in symptom development.\n\n(3) Contrary to the classical description by Brion & Jedynak, our patient did not exhibit denial of ownership of the affected hand, indicating that this symptom may not be a consistent feature across all AHS cases.\n\n(4) Interestingly, the patient’s ACA and ACOM, the primary blood supply to the corpus callosum, were unaffected, as evidenced by the CTA. The observed MCA stenosis could not account for the extensive corpus callosum infarct.\n\n(5) Despite the presence of posterior AHS features, no radiological evidence of thalamic, parietal, or occipital lobe involvement was found.\n\nThe complex and diverse clinical manifestations of AHS have made anatomical localization challenging. Past studies have highlighted similar discrepancies between clinical presentation and radiological evidence. For instance, Pappalardo et al.26 reported a case of parieto-occipital infarct that exhibited compulsive manipulation, difficulty in releasing tools, and IMC without any posterior AHS features. Similarly, Rafiei et al.36 reported a case of posterior AHS following a left pontine hemorrhage. Although different subtypes of AHS have been distinguished, its clinical diversity has resulted in inconsistent and disputable classification systems.4 While the three-variant classification is commonly used, alternative classification systems have been proposed. Aboitiz et al.,37 for example, put forth a five-category classification system that includes: (i) diagonistic dyspraxia and related syndromes, (ii) alien hand, (iii) way-ward hand and related syndromes, (iv) supernumerary hands and (v) agonistic dyspraxia. Additionally, some researchers have suggested classifying AHS into motor (anterior AHS) and sensory (posterior AHS) variants.4\n\nScepkowski and Cronin-Golomb38 underlined three factors that contribute to the difficulty in systematically studying the AHS:\n\n(1) Its rarity relative to other neurological disorders, forcing reliance on case reviews. This limits the ability to examine a large, diverse population of AHS patients, making it difficult to generalize findings and draw definitive conclusions.\n\n(2) Its transient nature, in most cases, poses challenges for long-term study, complicating the process of capturing and measuring the full range of clinical manifestations.\n\n(3) The coincidental occurrence of other behavioral dysfunctions, such as hemiparesis, motor neglect, or neglect of visual hemispace, hinders the assessment process.\n\nThese factors, combined with the lack of uniformity in assessment methods, including both behavioral and neuroimaging tests, impede the establishment of clear subtypes of alien-hand phenomena.\n\nDifferent pathophysiological mechanisms likely contribute to the diverse behaviors observed in AHS.4 Elucidating them requires a deep understanding of the functional anatomy of the highly intricate callosal network. Conventional radiological modalities such as CT and magnetic resonance imaging (MRI) do not have the capacity to visualize the interhemispheric CC fiber connections.2 The emergence of Diffusion Tensor Tractography (DTT) study in recent years has enabled a 3-dimensional visualization of the CC architecture and integrity, providing a more in-depth analysis into the clinical-anatomical correlation of AHS.2,39\n\nIsolated and extensive CC infarcts are rare, with only a few reported cases. In 1999, Lausberg et al.40 reported a case of CDS following an infarct of the total length of the corpus callosum, manifesting callosal AHS. Using comprehensive neuropsychological investigations, the authors demonstrated that despite left-handedness, the CDS is analogous to right-handers revealing left-hemispheric dominance for language and praxis. In 2011, Yuan et al.4 described a case of mixed callosal-posterior AHS following an extensive corpus callosum infarct involving the genu, body, and splenium. The authors combined diffusion-weighted imaging (DWI) with magnetic resonance angiography (MRA) to determine the anatomical substrate underpinning the clinical presentation. In 2013, Jang et al.2 reported a case of extensive corpus callosum infarct manifesting CDS and frontal-posterior AHS. In addition to neuropsychological testing, a DTT study was performed, followed by a comparison with the DTT findings of three normal subjects. The DTT revealed disruption of most interhemispheric CC fibers, except for those in the anterior genu and posterior splenium, congruent with the patient’s neurological manifestation. In this report, the lesion was almost exclusively confined to the corpus callosum, sparing the frontal, parietal, and occipital lobes, and the thalamus. The unique neurological manifestations, therefore, can be attributed to the callosal network disruption, causing bihemispheric disinhibition or interhemispheric disconnection.10 The variations in AHS manifestation in these four reports solidify the hypothesis that even if the corpus callosum lesions are similar in location and extent, the symptom manifestations can still vary.2 This report is limited by the lack of neuropsychological and radiological evidence due to service unavailability. However, we believe that if given access to these resources, combining neuropsychological assessments with DTT investigations could significantly contribute to uncovering the underlying pathomechanism of AHS in our patient.\n\nAHS may hinder rehabilitation and can easily be overlooked or misinterpreted.31 Recognizing AHS is vital because its different manifestations may require different therapeutic approaches.6 Due to its rarity, evidence-based rehabilitation interventions for AHS are scarce. To date, there are no approved or recommended therapies for AHS. Management strategies are based on anecdotal reports of both pharmacological and behavioral interventions. For the anterior variant, suggested interventions include sensory tricks, distracting tasks, CBT, and verbal cue. On the other hand, the posterior variant may benefit from treatments such as clonazepam, botulinum toxin, visualization strategies, and spatial recognition tasks.10\n\nIn mirror box therapy, the congruency between motor intention and visual feedback elicited by the vision of the intact hand moving through the mirror improves the voluntary control of the alien hand.35 However, due to reliance on sensorimotor integration, this approach may only work for posterior AHS, as anterior AHS seems to depend on a failure to inhibit motor behavior of the non-dominant hemisphere.41 Clonazepam possibly potentiates thalamic GABAergic circuitry, resulting in either reducing the arm’s oversensitivity to external stimuli or dampening the internal stimulus driving the AHS.14 The limb restraint strategy likely provided enough stimulation for the sensory spinal grasp reflex to achieve accommodation, thus inhibiting the movement.10 Interestingly, in the case presented in this report, the IMC showed the best response to these interventions when compared to the other motor symptoms.\n\nEducating the patient and caregiver is essential to managing AHS, as it can help them cope with the challenging behavior associated with this condition.31 Caregiver involvement plays a significant role in optimizing the rehabilitation outcome. For instance, the verbal cue intervention necessitates a strong commitment from the caregiver to deliver the strategy consistently to achieve positive results. Addressing anxiety and fear is also crucial and may involve using anxiolytics and appropriate behavioral therapies guided by experienced psychiatrists and psychologists.10 Unfortunately, none of the discussed interventions have demonstrated long-term benefits. Ergo, impairment-focused and multidisciplinary interventions may be the most appropriate for managing AHS.\n\nOur limited understanding of the AHS pathophysiology has complicated the accurate prediction of its natural history.10 Previous studies have reported mixed prognoses. In some cases, there was a complete resolution of symptoms.4,13,26,31 However, other reports documented the persistence of symptoms, despite some improvement.6,24,31 In the case presented here, although some motor symptoms persisted, they were neither disturbing nor impairing functionally.\n\nIn conclusion, mixed variant AHS is an exceptionally rare and intriguing neurological phenomenon. To our knowledge, this is the first report of an extensive corpus callosum infarct displaying features from all three recognized AHS variants as part of the CDS. This case underscores the unique and distinctive clinical variations and showcases a challenging correlation between clinical manifestations and neuroanatomical substrates. Despite being recognized as a clinical entity for over a century, establishing a clear correlation between anatomical and clinical findings in AHS remains elusive,10 and current theories on its underlying mechanisms are largely speculative.6 Future research is essential to unravel the intricate neural connections and the precise function of the corpus callosum. This can be best achieved by combining comprehensive neuropsychological testing with DTT studies. Refining AHS classification systems will be crucial as research continues to uncover the underlying pathomechanism and anatomical correlates. Additionally, there is a need for the development of a validated tool to standardize the AHS assessment, and the limited evidence available on rehabilitation interventions warrants further exploration. By fostering continued investigation and collaboration, we can deepen our understanding of AHS and enhance therapeutic options for those affected by this rare and enigmatic neurological disorder.\n\n\nConsent\n\nThe authors sought written informed consent prior to the submission of this case report from the patient and her primary caregiver, her eldest daughter. We sought permission to share any clinical photo, video, laboratory investigation result, and imaging study from them before submitting the report.", "appendix": "Data availability\n\nNo data are associated with this article.\n\n\nReferences\n\nCatani M, Howard RJ, Pajevic S, et al.: Virtual in vivo interactive dissection of white matter fasciculi in the human brain. NeuroImage. 2002; 17(1): 77–94. PubMed Abstract \| Publisher Full Text\n\nJang SH, Lee J, Yeo SS, et al.: Callosal disconnection syndrome after corpus callosum infarct: a diffusion tensor tractography study. J. Stroke Cerebrovasc. Dis. 2013; 22(7): e240–e244. 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PubMed Abstract \| Publisher Full Text\n\nRubin M, Graff-Radford J, Boeve B, et al.: The alien limb phenomenon and Creutzfeldt-Jakob disease. Parkinsonism Relat. Disord. 2012; 18(7): 842–846. PubMed Abstract \| Publisher Full Text\n\nNowak DA, Bosl K, Ludemann-Podubecka J, et al.: Recovery and outcome of frontal alien hand syndrome after anterior cerebral artery stroke. J. Neurol. Sci. 2014; 338(1-2): 203–206. PubMed Abstract \| Publisher Full Text\n\nRomano D, Sedda A, Dell’aquila R, et al.: Controlling the alien hand through the mirror box. A single case study of alien hand syndrome. Neurocase. 2014; 20(3): 307–316. Publisher Full Text\n\nRafiei N, Chang GY: Right sensory alien hand phenomenon from a left pontine hemorrhage. J. Clin. Neurol. 2009; 5(1): 46–48. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nAboitiz F, Carrasco X, Schroter C, et al.: The alien hand syndrome: classification of forms reported and discussion of a new condition. Neurol. Sci. 2003; 24(4): 252–257. PubMed Abstract \| Publisher Full Text\n\nScepkowski LA, Cronin-Golomb A: The alien hand: cases, categorizations, and anatomical correlates. Behav. Cogn. Neurosci. Rev. 2003; 2(4): 261–277. PubMed Abstract \| Publisher Full Text\n\nChang MC, Yeo SS, Jang SH: Callosal disconnection syndrome in a patient with corpus callosum hemorrhage: a diffusion tensor tractography study. Arch. Neurol. 2012; 69(10): 1374–1375. PubMed Abstract \| Publisher Full Text\n\nLausberg H, Gottert R, Munssinger U, et al.: Callosal disconnection syndrome in a left-handed patient due to infarction of the total length of the corpus callosum. Neuropsychologia. 1999; 37(3): 253–265. PubMed Abstract \| Publisher Full Text\n\nHertza J, Davis AS, Barisa M, et al.: Atypical sensory alien hand syndrome: a case study. Appl. Neuropsychol. Adult. 2012; 19(1): 71–77. PubMed Abstract \| Publisher Full Text" }	[ { "id": "266220", "date": "03 May 2024", "name": "Stefano L Sensi", "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 would be important to understand the timing of the second TC scan and why an MRI was not performed. An MRI would certainly have given further information about the features and anatomical sites involved. Has a neuropsychological evaluation been performed to assess the cognitive domains involved? It could have been very useful for an assessment at baseline and to evaluate improvements. Finally, how do you explain the occurrence of AL so far from the acute event?, Please explain these aspects in more detail. Otherwise, the article is very interesting, informative and well-written.\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? Yes\n\nIs the case presented with sufficient detail to be useful for other practitioners? Yes", "responses": [ { "c_id": "11756", "date": "17 Jun 2024", "name": "Khin Nyein Yin", "role": "Author Response", "response": "Thank you for your positive review. We appreciate the comments and have provided responses to your inquiries below: 1. It would be important to understand the timing of the second CT scan and why an MRI was not performed. An MRI would certainly have given further information about the features and anatomical sites involved. Response: The second CT was done on the day the patient had a drop in her GCS. We have added this information to the text: “A repeat CT scan was done urgently on the same day and displayed….” (Page 4, line 50) An MRI was not performed due to service limitations. We expanded the study limitations in a separate paragraph: “In our setting, a tertiary government hospital with heavy patient loads and limited resources, there is no in-house clinical psychologist. Additionally, MRI availability is restricted and reserved for a limited number of cases. Given that an MRI would not alter the management of the stroke itself, the request for an MRI in this case was not granted. The patient was advised to consider obtaining an MRI and neuropsychological evaluation at a private center; however, these investigations were not performed due to financial constraints.” (Page 10, lines 233-239) 2. Has a neuropsychological evaluation been performed to assess the cognitive domains involved? It could have been very useful for an assessment at baseline and to evaluate improvements Response A neuropsychological evaluation would have been invaluable to the case. Unfortunately, we do not have an in-house clinical psychologist. This is explained in the study limitations paragraph: “In our setting, a tertiary government hospital with heavy patient loads and limited resources, there is no in-house clinical psychologist. Additionally, MRI availability is restricted and reserved for a limited number of cases. Given that an MRI would not alter the management of the stroke itself, the request for an MRI in this case was not granted. The patient was advised to consider obtaining an MRI and neuropsychological evaluation at a private center; however, these investigations were not performed due to financial constraints.” (Page 10, lines 233-239) 3. Finally, how do you explain the occurrence of AL so far from the acute event? Please explain these aspects in more details. Response The patient was treated in a different hospital during the acute event. The nearly three-week stay was complicated by medical issues such as upper gastrointestinal bleeding and anemia requiring blood transfusions, and poorly-controlled diabetes. During medical stabilization, there was no dedicated caregiver accompanying her in the ward. She was reported to be sleeping in bed most of the time, and there was no documentation of abnormal movement from the referring hospital. Without eyewitness or documented evidence, it is difficult to ascertain the onset of AHS itself." } ] }, { "id": "258091", "date": "06 May 2024", "name": "Victor W Mark", "expertise": [ "Reviewer Expertise Multiple sclerosis rehabilitation", "functional neurological disorder study", "case reports of alien hand 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 authors contribute a unique observation, which is the combination of all three kinds of alien hand that are generally recognized. The patient's background, clinical findings, clinical course, and supporting brain imaging are included.\n\nThe authors in addition have completed a thorough review of the pertinent literature that pertains to alien hand syndrome. Their Table of the literature is very helpful to readers interested in alien hand sign.\n\nSome suggested revisions: 1) The abstract and Introduction attribute the first report of alien hand to Goldstein 1908. Most review papers point to this paper.\nHowever, in my own literature review, I find alien hand in yet an earlier report, from 1907: Van Vleuten CF. Linksseitige motorische Apraxie. Ein Beitrag zur Physiologie des Balkens. Z Psychiatr 1907;64:203-239. The patient that was described succumbed to a brain tumor, preceded by involuntary movements, including strong involuntary grasp reflex, left hand not participating with undressing even though the patient understood the command, not stretch out the left forefinger on command, complains he cannot understand why the difficulty. The problem is inconsistent. At other times the left hand moves to part of the surroundings in contrast to where the patient was instructed, unlike the right hand. When handed a pencil (with what hand not stated) and asked to write instead he brings it to his mouth 10 times, despite his saying \"I do not want to moisten the pencil.\" And so forth. This report has only rarely been mentioned in neuroscience literature, and not with attention to alien hand except in a superficial manner (cf Graff-Radford NR,eta l, 1987;[Ref 1]\n2) Under Patient rehabilitation, the passage that the patient had a \"left-sided hemisensory loss,\" but without details. Unclear whether this reflected light touch, pin, or otherwise.\n\n3) Under Outpatient rehabilitation, the top paragraph indicates that the patient's left hand would rise (levitation) that occurred specifically during walking. While this does indeed suggest the posterior form of alien hand, this also suggests a form of paroxysmal kinesigenic dyskinesia. These may not be mutually exclusive diagnoses; I suggest review this possible alternate diagnosis.\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": "11757", "date": "17 Jun 2024", "name": "Khin Nyein Yin", "role": "Author Response", "response": "We thank you and appreciate your review. The feedback you provided has helped improve the quality and clarity of this manuscript. Below are our responses to your inquiries. 1. The Abstract and Introduction attribute the first report of alien hand to Goldstein 1908. Most review papers point to this paper. However, in my own literature review, I find alien hand in yet an earlier report, from 1907 (Van Vleuten CF). This report has only rarely been mentioned in neuroscience literature, and not with attention to alien hand except in a superficial manner (cf Graff-Radford NR). Response Thank you for this valuable information that we missed. Information on the Van Vleuten paper is scarce, and most papers only briefly reference the article, including the reference you suggested. We have amended the information on the earliest reported cases of AHS by referencing Van Vleuten’s study. The report by Van Vleuten can be found in the following sentences: “…..first described by Van Vleuten……” (Abstract) “It was first described by Van Vleuten in 1907 in a patient with a left-hemisphere brain tumor that had invaded the corpus callosum and exhibited right-hand grasping.” (Page 3, lines 18-20) “AHS has been a subject of intrigue in the neurological community since its initial description by Van Vleuten more than a century ago.” (Page 6, lines 138-139) 2. Under Patient Rehabilitation, the passage that the patient had a “left-sided hemisensory loss,” but without details. Unclear whether this reflected light touch, pin, or otherwise. Response We have added the information to the revised manuscript: “Additionally, there was left-sided hemisensory loss in both pin-prick and light touch sensation but intact proprioception,…..” (Page 5, lines 76-78) 3. Under Outpatient rehabilitation, the top paragraph indicates that the patient’s left hand would rise (levitation) that occurred specifically during walking. While this does indeed suggest the posterior form of alien hand, this also suggests a form of paroxysmal kinesigenic dyskinesia. These may not be mutually exclusive diagnoses; I suggest review this possible alternate diagnosis. Response Thank you for the suggestion. We have expanded the discussion on the arm levitation and the consideration of PKD as a differential diagnosis: “The arm levitation presentation in our patient could also indicate paroxysmal kinesigenic dyskinesia (PKD), a rare disorder characterized by involuntary movements such as dystonia and choreoathetosis, precipitated by sudden movement or startle (new reference no. 2). However, several characteristics suggest that PKD is less likely than posterior AHS. Firstly, PKD attacks are typically triggered by abrupt movement, an increase in speed, amplitude, or strength, the sudden addition of new actions during ongoing steady movements, or a change in direction (new reference no. 3). In our case, the arm levitation was triggered only by walking—a step-wise, voluntary movement that did not involve sudden movement. The speed and direction of walking did not affect the manifestation of arm levitation. Secondly, the duration of PKD attacks is typically brief, mainly lasting less than a minute (new reference no. 3). In contrast, the arm levitation in our patient persisted throughout her ambulation. Thirdly, most cases of PKD are preceded by a premonition or aura (new reference no. 2), which was absent in our patient. Lastly, new PKD attacks cannot be induced for a refractory period of approximately 20 minutes (new reference no. 3). However, arm levitation could easily manifest upon walking without any such refractory period in our patient. Therefore, the arm levitation in this patient aligns more with the posterior AHS presentation than with PKD.” (Page 8-9, lines 161-177)" } ] } ]	1	https://f1000research.com/articles/12-529
https://f1000research.com/articles/13-638/v1	17 Jun 24	{ "type": "Research Article", "title": "Kinematic characteristics analysis of highly difficult movements \"324C+1D\" of the first level Wushu athletes", "authors": [ "Xikui Guo", "Chairat Choosakul" ], "abstract": "Background \"324C+1D” movements are key techniques and winning factors in Wushu competitions. It is necessary for scientific training to analyze the kinematic characteristics of “324C+1D” by using the method of sports biomechanics.\n\nMethods In this study, 3D high-speed camera and 3D motion analysis software were used to study “324C+1D” completed by three Chinese wushu first-level athletes, and the kinematic characteristics of this movement were obtained.\n\nResults The run-up speed of completing the “324C+1D” is not high; The lift Angle of the center of gravity is close to 90°. The vertical height of the center of gravity is significantly higher than the vertical height of the center of gravity when landing, and the vertical moving distance of the center of gravity in the lifting stage is significantly less than the vertical moving distance of the center of gravity in the descending stage. The vertical height of the center of gravity at departure is significantly higher than that at landing.\n\nConclusions In the take-off stage, increase the twisting Angle of shoulders and hips, speed up the swing arm speed and squat speed of the center of gravity in the vertical direction, and shorten the take-off time. Increase the vertical speed of the center of gravity before the patting foot and the vertical moving distance between the center of gravity lifting stage and the descending stage, extend the air time, accelerate the swing speed of the right leg, move the foot patting time forward to the rapid rising stage of the center of gravity lifting, accelerate the rotational angular speed of the shoulder shaft in the air stage and improve the strength of the leg, which is conducive to the athletes to complete the movement.", "keywords": [ "Kinematic characteristics", "Competitive Wushu Routine，Difficult movements “324C+1D”" ], "content": "1. Introduction\n\nIn recent years, with the popularity and promotion of competitive wushu events in the country, wushu competitions at all levels in the country have also been rapidly developed, which greatly drives the participation of wushu lovers and wushu students in colleges and universities, and to a certain extent promotes the development of competitive wushu. In the national top wushu competition, the competitive level and professional basic skills of the athletes are similar, “the selection of difficult martial arts movements and the choreography of martial arts routine movements are crucial for the athletes to get good results in the competition” (Sun, 2012). High difficulty movements play an important role in wushu competitive routines. According to the rules of competition wushu routine, the total score of each event is 10 points, including 5 points for movement quality, 3 points for drill level and 2 points for movement difficulty. Among the 2 points of action difficulty, 1.4 points of action difficulty, 0.6 points of connection difficulty and additional points of innovation difficulty are included. A large number of literature studies show that martial arts difficult movements and connections, such as “324C+1D” directly determine the performance of athletes in competitive martial arts competitions, can be regarded as the key technology and winning factors (Xiong, 2007). The principles and methods of sports biomechanics are the main means to analyze and diagnose the technical and tactical characteristics of athletes, as well as the main methods to improve sports performance, explore technical rules, and improve motor skills and tactics (Zhang, 2012). At present, it is the requirement of scientific training to use the method of sports biomechanics to analyze the characteristics of the most difficult movements in Wushu routine and apply the research results to the training of athletes.\n\n“324C+1D” is the secondary code of the movement combination consisting of Jumping spin lotus kick 720°(324C)-- the most difficult movement of the Wushu routine and the most difficult connecting movement horse step (+1D).\n\n\n2. Methods\n\nThere are 3 male first-level wushu athletes who can skillfully complete the “324C+1D” movement, aged 19-22, without obvious injuries in the past 3 months, voluntarily participate in this study test. (The basic information of participants is shown in Table 1.)\n\n2.2.1 3D High-speed camera system\n\nIn this research, a 3D high-speed camera system composed of two SONY-RX10IV cameras and a synchronizer was used to shoot the fixed point synchronously. The Angle between the two cameras is 90°, the camera height is 0.75 m, and the camera frequency is 100 Hz.\n\nSONY-RX10IV high-speed camera: produced by SONY, Japan, sensor: 1 inch (13.2*8.8mm), effective pixels: 20.1 million, display size: 3 inches, display pixels: 1.44 million pixels LCD screen, continuous shooting speed: support (up to about 24/SEC), shutter speed: 1/32000 SEC, battery type: Rechargeable battery (NP-FW50) Endurance: [Still image] Approx. 400 / approx. 200 minutes (LCD), approx. 370/approx. 185 minutes (Viewfinder) (CIPA standard) [actual motion image] Approx. 75 minutes (LCD), About 75 minutes (Viewfinder) (CIPA standard) [Continuous motion image] About 135 minutes (LCD)/About 135 minutes (Viewfinder) (CIPA standard).\n\n2.2.2 SIMI motion image analysis system\n\nA computer installed with SIMI motion 9.2 image analysis software is used to analyze the motion video captured by the 3D high-speed photography system and obtain the data of each stage of the motion.\n\nSIMI motion 9.2: German SIMI company developed a software for motion image analysis. Simi Motion is a software product and systems solution for professional 2D and 3D motion analyses.\n\nSimi is an optimal tool for motion capture and analysis. Particular strengths of this product are its high flexibility and accuracy combined with a user-friendly interface.\n\nSystem requirements:\n\n- Microsoft Windows 2000, Windows XP or Windows 7\n\n- Microsoft DirectX 8.1 or later\n\n- Intel Pentium 4 compatible PC\n\n- 256 MB RAM\n\n- large hard disk for video data\n\n- FireWire interfaces (IEEE-1394) for DV or high-speed cameras\n\nAccording to Hannafan’s human body model (15 rigid bodies, 17 nodes), the points are selected by amplitude; Based on the setting of the spatial model, the spatial calibration is carried out. First, the 28-point frame is transferred, and then the spatial scale video shot by the test object is transferred. The calibration frame picture and the control point of the calibration frame are selected.\n\n\n3. Results and discussion\n\n3.1.1 Description of the action process of “324C+1D”\n\nThe “324C+1D” action consists of four technical links: run-up, take-off, take-off and landing. According to the rules of Wushu routine competition, the run-up is required to be within 4 steps, the body runs straight ahead during the run-up, and the feet land parallel at the end of the last step of the run-up. After landing, the legs (ankle bending, knee bending, hip bending) cushion squat, while the torso turns left and the arm is placed on the lower left. Then the legs (ankle extension, knee extension, hip extension) complete the push and stretch movement, while the arm swings from the left bottom direction to the right back and above and turn right with the torso. After leaving the ground, the right leg swings from the bottom to the outside and above. When the leg swings to the front of the body, the left hand and the right foot hit the instep, the right leg presses down after the pat, and the landing connects the horse step.\n\n3.1.2 “324C+1D” action stage division\n\nAccording to the main technical links of “324C+1D”, the complete action is divided into four action stages: run-up, take-off, take-off and landing. In this study, eight feature images were selected in the complete motion (see Figure 1).\n\nRun-up: The moment when the right foot touches the ground from the beginning of the run-up to the last step of the run-up.\n\nJumping stage: From the start of the run-up to the end of the jump to the ground moment.\n\nAirborne stage: From the moment of starting the jump foot off the ground to the moment of supporting foot landing.\n\nLanding stage: From the moment of the support foot landing to the stable movement of the horse step (the center of gravity of the horse step movement is almost no wave Move) moment.\n\n3.2.1Analysis of kinematic characteristics of run-up and take-off stages\n\n3.2.1.1 Time characteristics\n\n3.2.1.1.1 The total time analysis of the take-off stage\n\nFrom the total time of the take-off stage (see Table 2), the average time of the first-level athletes completing the take-off stage of the “324C+1D” movement is 0.42s, and the standard deviation is 0.08s. Among the three athletes who participated in the test, the total time used to complete the take-off stage of the “324C+1D” movement was 0.35s, which was the shortest among the three athletes. Athlete C took 0.50s to complete the take-off stage of the “324C+1D” movement, which was the longest time among the three athletes.\n\n3.2.1.1.2 Time analysis of take-off and squat stage\n\nFrom the time of the submovement stage of take-off squat (see Table 2), the average time of the submovement stage of take-off squat in the “324C+1D” movement is 0.17s, and the standard deviation is 0.04s. Athlete C took 0.20s to complete the sub-movement stage of “324C+1D” movement jumping and squatting, which was the longest among the three athletes. Athlete A took 0.13s to complete the sub-movement stage of “324C+1D” movement jump and squat, which was the shortest time among the three athletes.\n\n3.2.1.1.3 Time analysis of take-off, push and stretch sub-stage\n\nFrom the time of the sub-movement stage of take-off, push and stretch (see Table 2), the average time of the first-level athletes in the sub-movement stage of “324C+1D” movement is 0.25s, and the standard deviation is 0.04s. Athlete A took 0.22s to complete the sub-movement stage of “324C+1D\", which was the shortest time among the three athletes. Athlete C took 0.30s to complete the sub-movement stage of “324C+1D” movement take-off and push, which was the longest time among the three athletes.\n\n3.2.1.2 Link motion characteristics\n\n3.2.1.2.1 Peak velocity characteristics of the swing arm\n\nAs can be seen from Table 3, the average value of the peak swinging arm speed at the left wrist node is 11.92 m/s, and the standard deviation is 1.16 m/s, while the average value of the peak swinging arm speed at the right wrist node is 10.63 m/s, and the standard deviation is 0.34 m/s. The peak speed of the swinging arm of the left wrist node is higher than that of the right wrist node, mainly because the rotation direction of the 324C action is to rotate clockwise along the vertical axis, and the rotation speed of the left arm is slightly higher.\n\n3.2.1.2.2 Peak characteristics of shoulder-hip torsion Angle\n\n3.2.1.2.2.1 Peak value analysis of shoulder-hip torsion Angle during run-up\n\nAs can be seen from Table 4, the average peak value of shoulder-hip torsion Angle and standard deviation of the “324C+1D” athletes in the run-up stage are 55.14° and 8.63°. According to the rules of Wushu routine competition, Wushu athletes are required to run within 4 steps, athletes generally increase the stride length as much as possible to improve speed, and the larger stride length forms a larger shoulder and hip torsion Angle.\n\n3.2.1.2.2.2 Peak value analysis of shoulder-hip torsion Angle during takeoff\n\nAs can be seen from Table 4, the average peak value of shoulder-hip torsion Angle of first-level athletes in the take-off stage of “324C+1D” is 78.14°, and the standard deviation is 8.33°. Because the “324C+1D” action needs to complete 720° body rotation in the air, the take-off stage should be fully prepared for air rotation, and form a larger shoulder and hip torsion Angle as far as possible before the jumping foot leaves the ground, which is more conducive to the completion of the air rotation action. From the data in Table 4, it can be found that the shoulder and hip torsion Angle of the three first-level athletes in the take-off stage is between 68° and 84°, and they all successfully completed the movement, which provides an important reference index for the wushu routine athletes to complete the take-off movement.\n\n3.2.1.2.3 Features of shoulder and foot torsion Angle\n\nAs can be seen from Table 5, the average shoulder-foot torsion Angle of first-level athletes at the time of departure from the ground after completing the “324C+1D” movement is 92.38°, and the standard deviation is 16.83°. Because the “324C+1D” action needs to complete 720° body rotation in the air, the take-off stage should be fully prepared for air rotation, and the larger shoulder and foot torsion Angle should be formed as far as possible before the jumping foot leaves the ground, which is more conducive to the completion of the air rotation action. From the data in Table 5, it can be found that the shoulder and foot torsion Angle of the three first-level athletes in the take-off stage is between 74° and 108°, and they all successfully completed the movement, which provides an important reference index for the wushu routine athletes to complete the take-off movement.\n\n3.2.1.2.4 Angle characteristics of ankle, knee and hip joints during take-off and extension\n\n3.2.1.2.4.1 Analysis of Angle characteristics of left and right ankle joints during take-off, push and stretch\n\nFrom the Angle difference of the left and right ankle joints (see Table 6), the average Angle of the left ankle and the standard deviation of the left ankle at the time of squat in the jumping stage of the “324C+1D” movement are 55.91° and 35.73°, and the average Angle of the right ankle and the standard deviation of the right ankle are 84.81° and 11.24°. The average Angle of the left ankle and the standard deviation of the right ankle are 74.19° and 65.71° respectively, and the average Angle of the right ankle and the standard deviation of the right ankle are 132.65° and 1.77° respectively. The Angle of the left and right ankle joints of the first-level athletes in the take-off stage of “324C+1D” movement is as follows: the Angle of the right ankle is greater than that of the left ankle at the lowest moment of the squat; The Angle of the right ankle is significantly greater than that of the left ankle at the time of takeoff from the ground.\n\n3.2.1.2.4.2 Analysis of the Angle characteristics of the knee joint at the moment of takeoff and squat and the moment of knee joint off the ground\n\nFrom the Angle difference of the left and right knee joints (see Table 7), the average Angle of the left knee joint and the standard deviation of the left knee joint are 101.20° and 26.48°, and the average Angle of the right knee joint and the standard deviation of the right knee joint are 81.61° and 28.70° at the time of squat in the jumping stage of the “324C+1D” movement. The average Angle of left knee joint and standard deviation of right knee joint are 159.82° and 18.34° respectively, and the average Angle of right knee joint and standard deviation of right knee joint are 165.90° and 11.94° respectively. The Angle of the left and right knee joints of the first-level athletes in the take-off stage of “324C+1D” movement is as follows: the Angle of the right knee joint is smaller than that of the left knee joint at the lowest moment of the squat; The Angle of the right knee joint is greater than that of the left knee joint at the time of takeoff from the ground.\n\n3.2.1.2.4.3 Analysis of joint Angle characteristics of left and right hip joints during takeoff and squat time and off the ground time\n\nFrom the Angle difference of the left and right hip joints (see Table 8), the average Angle of the left hip joint and the standard deviation of the left hip joint are 114.57° and 19.39°, and the average Angle of the right hip joint and the standard deviation of the right hip joint are 68.62° and 18.63° at the time of squatting in the take-off stage of the “324C+1D” movement for first-level athletes. The average Angle and standard deviation of the left hip joint were 158.49° and 10.45° respectively, while the average Angle and standard deviation of the right hip joint were 155.71° and 7.80° respectively. The Angle of left and right hip joints of Level I athletes in the take-off stage of “324C+1D” movement is as follows: the Angle of right hip joints is obviously smaller than that of left hip joints at the lowest moment of squat; The right hip Angle is smaller than the left hip Angle at takeoff.\n\n3.2.1.3 Center of gravity motion characteristics\n\n3.2.1.3.1 Center of gravity speed characteristics in the run-up direction\n\nFrom the point of view of the center of gravity velocity in the run-up direction (see Table 9), the average peak value of the center of gravity velocity in the run-up direction of the first-level athletes in the run-up stage after completing the “324C+1D” movement is 2.99 m/s, and the standard deviation is 0.07 m/s. At the end of the “324C+1D” run, the average speed of the center of gravity in the run-up direction is 2.30 m/s, and the standard deviation is 0.36 m/s. The average value and standard deviation of the center of gravity velocity in the run-up direction are 0.72m/s and 0.22 m/s for the first class athletes at the time of take-off from the ground after completing “324C+1D” movement. The characteristics of the center of gravity velocity in the run-up direction of the first-level athletes in the run-up stage of the “324C+1D” movement are as follows: the center of gravity movement speed achieved in the run-up stage decreases rapidly in the take-off stage, which is in line with the general characteristics of the run-up take-off action, and is ready for the conversion of kinetic energy into take-off potential energy.\n\n3.2.1.3.2 Peak vertical velocity characteristics of the center of gravity\n\nFrom the point of view of the peak value of vertical speed of the center of gravity in the take-off stage (see Table 10), the average peak value of vertical speed of the center of gravity in the squat stage of the take-off stage after completing the “324C+1D” movement is -2.30 m/s, and the standard deviation is 0.49m/s. The average peak vertical velocity of the center of gravity of national athletes in the “324C+1D” take-off and push stage is 2.99m /s, and the standard deviation is 0.22m/s.\n\nThe characteristics of the vertical speed peak value of the center of gravity in the take-off stage of the athletes completing the “324C+1D” movement are as follows: the vertical speed peak value of the center of gravity in the take-off and push and extend stage is greater than that in the take-off and squat stage.\n\n3.2.1.3.3 Vertical movement distance characteristics of the center of gravity\n\nFrom the vertical movement distance of the center of gravity in the take-off stage (see Table 11), the average vertical movement distance of the center of gravity in the squat stage of the first-level athletes completing the “324C+1D” movement is 0.33m, and the standard deviation is 0.05 m. The average vertical distance and standard deviation of the center of gravity in the “324C+1D” jumping stage are 0.36 m and 0.18 m respectively.\n\nThe vertical movement distance of the center of gravity in the take-off stage of the athletes completing the “324C+1D” movement is as follows: there is little difference between the vertical movement distance of the center of gravity in the take-off and push and stretch stage and the vertical movement distance of the center of gravity in the take-off and squat stage.\n\n3.2.1.3.4 Center of gravity lifting Angle characteristics at time of liftoff\n\nFrom the lifting Angle of the center of gravity at the time of lifting off the ground in the take-off stage (see Table 12), the average lifting Angle of the center of gravity at the time of lifting off the ground in the take-off stage of the “324C+1D” movement is 70.18° and the standard deviation is 2.16°.\n\nThe characteristics of the center of gravity lifting Angle of the take-off stage of the athletes completing the “324C+1D” movement are as follows: the center of gravity lifting Angle of the take-off stage is not very different from the ground, mainly concentrated between 68 -- 73°.\n\n3.2.2 Analysis of technical characteristics in the vacating stage\n\n3.2.2.1 Time characteristics\n\n3.2.2.1.1 Total time analysis of the vacating phase\n\nFrom the total time of the airborne stage (see Table 13), the average time of the airborne stage of the “324C+1D” movement for the first-level athletes is 0.68s, and the standard deviation is 0.04s. The total time of the three athletes participating in the test to complete the “324C+1D” movement in the air stage is very close, and the time of athlete E to complete the “324C+1D” movement in the air stage is 0.64s, which is the shortest among the three athletes. Athlete F took 0.72s to complete the airborne phase of the “324C+1D” movement, which was the longest time among the three athletes.\n\n3.2.2.1.2 Analysis of the time from ground off to beat in the airborne stage\n\nFrom the time of the sub-movement stage from take-off to slap (see Table 13), the average time of the first-level athletes to complete the sub-movement stage of the “324C+1D” movement is 0.18s, and the standard deviation is 0.01s. Athlete D took the longest time (0.19s) to complete the sub-movement stage of “324C+1D” movement; Athlete E and athlete F both took 0.17s to complete the sub-movement stage of “324C+1D” movement, which was the shortest time among the three athletes.\n\n3.2.2.1.3 Time analysis from stroke to landing sub-stage\n\nFrom the time of this sub-movement stage (see Table 13), the average time of Level I athletes in completing the sub-movement stage of “324C+1D” from the stroke to the landing is 0.50s, and the standard deviation is 0.04s. Athlete C took 0.55s to complete the sub-movement stage of “324C+1D” movement, which was the longest among the three athletes. Athlete B took 0.47s to complete the sub-movement stage of “324C+1D” movement, which was the shortest time among the three athletes.\n\n3.2.2.2 Link movement characteristics\n\n3.2.2.2.1 Right leg swing speed characteristics\n\nFrom Table 14, it can be seen that the average peak swinging speed of the right leg of the first-level athletes before beating in the air stage is 11.74m /s, and the standard deviation is 1.28m/s. The average swing speed of the right leg and standard deviation of the athletes in the air stage are 8.53 m/s and 3.01 m/s respectively. The average peak swinging speed and standard deviation of the right leg are 9.36 m/s and 1.59 m/s respectively. Athlete A and athlete C show the same characteristics in the swing speed of the right leg in the air stage, that is, the swing speed is the fastest before the stroke, the slowest at the moment of the stroke, and then accelerate after the stroke. However, athlete E showed a different speed change trend, and the three speeds gradually decreased in the airborne stage. However, from the average change of the right leg swing speed of all athletes in the air stage, the speed still shows a trend of slowing down and then speeding up.\n\n3.2.2.2.2 Angular velocity characteristics of shoulder shaft rotation\n\nAs can be seen from Table 15, the average angular velocity of shoulder axis rotation of first-level athletes at the time of hitting in the air stage of “324C+1D” movement is 573.08°/s, and the standard deviation is 124.09°/s. The average peak angular velocity and standard deviation are 1933.28°/s and 130.96°/s respectively for Level I athletes after hitting the “324C+1D” movement in the air stage. The average angular velocity and standard deviation of the angular velocity of the shoulder shaft at the landing time of the airborne stage of the “324C+1D” movement are 647.31°/s and 197.79°/s respectively.\n\n3.2.2.3 Movement characteristics of center of gravity\n\n3.2.2.3.1 Vertical velocity characteristics of the center of gravity\n\nAs can be seen from Table 16, the average value and standard deviation of the vertical speed of the center of gravity before the stroke in the airborne stage are 2.78 m /s and 0.05 m/s. The average vertical speed of the center of gravity and standard deviation of the stroke time of the first class athletes in the air stage are 1.32 m/s and 0.15 m/s. The vertical speed of the center of gravity of the three athletes in the air stage showed the same characteristics, that is, the vertical speed of the center of gravity before the stroke was higher than the vertical speed of the center of gravity at the moment of the stroke.\n\n3.2.2.3.2 Vertical height characteristics of the center of gravity at the time of departure and landing\n\nAs can be seen from Table 17, the average vertical height of the center of gravity at the time of departure from the ground during the take-off stage of the “324C+1D” movement for first-level athletes is 1.14 meters, and the standard deviation is 0.06 meters. The average vertical height of the center of gravity at the landing moment of the landing stage of the “324C+1D” movement is 0.88 meters, and the standard deviation is 0.10 meters. The vertical height of the center of gravity at the time of departure from the ground is higher than the vertical height of the center of gravity at the time of landing when the three level I athletes complete the “324C+1D” movement in the air stage.\n\n3.2.2.3.3 Vertical movement distance characteristics of gravity center\n\nAs can be seen from Table 18, the average vertical lifting distance of the center of gravity in the airborne stage of the “324C+1D” movement is 0.42 meters, and the standard deviation is 0.01 meters. The average vertical fall distance of the center of gravity and standard deviation of the “324C+1D” are 0.65 meters and 0.19 meters respectively. The vertical lifting distance of the center of gravity of the three national athletes in the air stage of completing the “324C+1D” movement is less than the vertical falling distance of the center of gravity.\n\n3.2.3 Analysis of technical characteristics in landing stage\n\n3.2.3.1 Link motion characteristics\n\n3.2.3.1.1 Shoulder and foot torsion Angle characteristics\n\nAs can be seen from Table 19, the average shoulder-foot torsion Angle of first-level athletes at the landing stage of “324C+1D” movement is 29.19° and the standard deviation is 8.57°. The shoulder and foot torsion angles of athlete A and athlete B at the landing stage of the “324C+1D” movement are close to each other, and both are significantly greater than the shoulder and foot torsion angles of athlete C.\n\n3.2.3.1.2 Knee sector Angle characteristics\n\nThe knee joint is the main buffer joint after landing, and the knee knee action is done after the foot hits the ground to cushion the impact of the moment of landing. As can be seen from Table 20, in the landing buffer stage of “324C+1D” movement, the average value of the left knee joint sector Angle is 66.80° and the standard deviation is 20.69°, while the average value of the right knee joint sector Angle is 60.56° and the standard deviation is 30.15°. The fan Angle of the left knee joint was larger than that of the right knee joint when athlete A and athlete C completed the landing cushion stage of “324C+1D” movement. Athlete B completed the “324C+1D” movement landing cushion stage, the left knee joint fan Angle is smaller than the right knee joint.\n\n3.2.3.2 Center of gravity motion characteristics\n\n3.2.3.2.1 Vertical velocity characteristics of the center of gravity at landing time\n\nAs can be seen from Table 21, the average value of the vertical velocity of the center of gravity at the landing moment of the “324C+1D” movement is -3.17 m/s, and the standard deviation is 0.28 m/s. Among them, the vertical speed of the center of gravity at the moment of landing after completing the “324C+1D” movement is the maximum of -3.43 m/s, and the minimum vertical speed of the center of gravity is -2.87 m/s.\n\n3.2.3.2.2 Characteristics of vertical movement distance of center of gravity in landing buffer stage\n\nAs can be seen from Table 22, the average vertical movement distance of the center of gravity in the landing buffer stage of the “324C+1D” movement is 0.39 m, and the standard deviation is 0.09 m. Among them, in the landing buffer stage of “324C+1D” movement, the maximum vertical movement distance of the center of gravity is 0.46 m, and the minimum vertical movement distance of the center of gravity is 0.28 m.\n\n\n4. Conclusion\n\n\n\n(1) The “324C+1D” movement does not have high requirements for the run-up speed in the run-up stage, but appropriately increasing the center of gravity speed in the run-up direction within this speed range may still be conducive to the completion of the “324C+1D” movement.\n\n(2) The center of gravity speed in the run-up direction loses a lot at the time of departure from the ground, and the take-off and push stage is mainly manifested as the increase of vertical speed, so the center of gravity speed difference in different directions determines the center of gravity lifting Angle at the time of departure from the ground to be closer to 90°, so that the center of gravity movement trajectory of “324C+1D” action in the air stage is approximately straight up and down.\n\n(3) Appropriately increase the shoulder and hip torsion Angle, accelerate the swing arm speed, and increase the shoulder and foot torsion Angle at the moment of departure from the ground, which is conducive to the completion of the athlete’s “324C+1D” action.\n\n(4) Accelerating the squat speed of the center of gravity in the vertical direction in the take-off stage, shortening the take-off time of the squat and push and stretch stage, and increasing the ground vertical reaction force in the take-off and push and stretch stage are conducive to the completion of the “324C+1D” movement.\n\n(5) The ankle and knee joints are not squatting as low as possible, but in a moderate range; The right ankle and right knee are more fully extended than the left ankle and left knee at the moment of lifting. The joint fan Angle of the right knee participating in the push and stretch in the take-off stage is larger than that of the left knee; The right hip joint is not sufficiently extended at the time of departure from the ground after completing the “324C+1D” maneuver. In addition, because the vertical movement distance of the center of gravity in the jumping stage is affected by the Angle change of the lower limb joints, the vertical movement distance of the center of gravity in this movement stage is not the larger the better or the smaller the better, but in a moderate range.\n\n\n\n(1) Increasing the vertical speed of the center of gravity before the stroke, increasing the vertical movement distance of the center of gravity lifting stage and the center of gravity falling stage, extending the air delay time, accelerating the swing speed of the right leg, and moving the moment of the stroke forward to the rapid rising period of the center of gravity lifting as far as possible are conducive to the completion of the “324C+1D” movement of the athlete.\n\n(2) Because the vertical height of the center of gravity at the time of leaving the ground is significantly greater than the vertical height of the center of gravity at the time of landing, the vertical movement distance of the center of gravity in the stage of lifting is significantly less than the vertical movement distance of the center of gravity in the stage of falling, and increasing the vertical movement distance of the center of gravity in the stage of falling is the main way for athletes to complete the “324C+1D” movement at present.\n\n(3) Accelerating the angular rotation speed of the shoulder shaft in the air stage is conducive to the completion of the “324C+1D” action. Among them, increasing the angular rotation speed of the shoulder axis after hitting is the key to complete the “324C+1D” action.\n\n\n\n(1) In the landing stage of the “324C+1D” movement, the athlete will extend the air time by lowering the vertical height of the center of gravity at the moment of landing to obtain a larger rotation Angle, and the impact force at the moment of landing will increase under the action of gravitational acceleration, which will lead to the increase of the vertical ground reaction force borne by the athlete after landing. In addition, the reduction of the height of the center of gravity when landing will also occupy a certain buffer distance, resulting in insufficient buffer after landing.\n\n(2) When the athlete completes the “324C+1D” movement, it is still possible to withstand a large ground reaction force in the landing buffer stage. It may be due to the fact that in order to achieve the technical requirements of stability at the moment of landing, the athletes have almost completed the action of separating the legs and walking before landing in the state of having a large falling distance and falling speed of the center of gravity, which reduces the buffering effect of centrifugal contraction of the lower limbs after landing.\n\n(3) In order to complete the “324C+1D” movement, on the one hand, the trunk rotation speed will be accelerated in the air stage, especially the trunk rotation speed after the stroke. In this state, the athlete may delay the leg splitting time and maintain the high rotational speed in the air for a longer time in order to complete a larger rotation degree, thus causing the trunk rotation speed at the time of landing to be too fast; In addition, if the rotation Angle completed in the air stage is insufficient, it will also be manifested as a phenomenon such as excessive torsion Angle of the shoulders and feet at the moment of landing.\n\n\nAuthors’ note\n\nThe authors declare that there is no conflict of interest regarding the publication of this article. Authors confirmed that the data and the paper are free of plagiarism.\n\nEthical Approval: This research has been carried out with the approval of Maha Salakan University under the Ethic code:511-359/2023.\n\nDate of Manufacture: 30 November 2023 expire: 29 November 2024.\n\nConsent: The research obtained written consent from the participants, all of whom signed a consent form.", "appendix": "Data availability\n\nDryad: kinematic characteristics analysis of highly difficult movements “324c+1d” of the first level wushu athletes.\n\nThis project contains the following underlying data:\n\n- Simi data - athlete a (the 3d kinematic data of each node of the body of the first-level wushu athlete a during the whole movement process of “324c+1d” from the start of the run-up to the landing.)\n\n- Simi data - athlete b (the 3d kinematic data of each node of the body of the first-level wushu athlete b during the whole movement process of “324c+1d” from the start of the run-up to the landing.)\n\n- Simi data - athlete c (the 3d kinematic data of each node of the body of the first-level wushu athlete c during the whole movement process of “324c+1d” from the start of the run-up to the landing.)\n\n- The left and right knee sector angle data of athlete a (the 3d kinematic data of knee fan angle of first-level wushu athlete a in completing the difficult wushu movement “324c+1d\".)\n\n- The left and right knee sector angle data of athlete b (the 3d kinematic data of knee fan angle of first-level wushu athlete b in completing the difficult wushu movement “324c+1d\".)\n\n- The left and right knee sector angle data of athlete c (the 3d kinematic data of knee fan angle of first-level wushu athlete c in completing the difficult wushu movement “324c+1d\".)\n\n- Athlete a (the 3d kinematic data of the angular velocity change of the shoulder axis when the first-level wushu athlete a completes the wushu difficulty movements “324c+1d\".)\n\n- Athlete b (the 3d kinematic data of the angular velocity change of the shoulder axis when the first-level wushu athlete b completes the wushu difficulty movements “324c+1d\".)\n\n- Athlete c (the 3d kinematic data of the angular velocity change of the shoulder axis when the first-level wushu athlete c completes the wushu difficulty movements “324c+1d\".)\n\n- Figure 1 (the characteristic action diagram of the action process of “324c+1d\")\n\n- Supporting forms (supporting forms contains all of the data tables i use in the article.)\n\nLicense (cc0 1.0)\n\nReviewer sharing link: https://doi.org/10.5061/dryad.7pvmcvf28\n\n\nAcknowledgements\n\nIn this research, Dr. Chairat Choosakul gave me great help and gave me a lot of good advice for my research. I am very grateful for his help. In addition, I also want to thank the Wushu athletes who participated in this research, who completed the test in accordance with the test requirements to provide support for the completion of the research. Finally, I would like to thank the professors and my friends who have given me support in this research.\n\n\nReferences\n\nBo S; The college wushu routine athletes in the game difficulty to choose the characteristics of (a master’s degree thesis, Huazhong university of science and technology).2012. Reference Source\n\nXiuli Z: Analysis of terms in Sports Biomechanics undergraduate textbook. Journal of Hebei University of Physical Education. 2012; 05: 30–32.\n\nYabing X: Under the new rules for implementation of competitive wushu training methods of exploration and research (a master’s degree thesis, Yunnan normal university).2007. Reference Source" }	[ { "id": "295975", "date": "09 Jul 2024", "name": "Armando Monterrosa Quintero", "expertise": [ "Reviewer Expertise Biomechanics", "martial arts", "performance", "anthropometry" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nIs the work clearly and accurately presented and does it cite the current literature? In the introduction, only Wushu is discussed. However, recent literature includes numerous articles on other martial arts that also analyze kinematic aspects. Including this information could enrich the context of the manuscript and make it more comprehensive. Is the study design appropriate and is the work technically sound? It is essential to explain the characteristics of the sample, as having only 3 participants is insufficient for conducting a robust statistical analysis or a meaningful review. Are sufficient details of the methods and analysis provided to allow replication by others? More details about the materials and methods, especially the procedures used for the analysis, should be provided to ensure that other researchers can accurately replicate the study. If applicable, is the statistical analysis and its interpretation appropriate? The statistical analysis is limited to the description of the factors and does not include specific statistical tests. It is advisable to include statistical tests to strengthen the interpretation of the results. Are all source data underlying the results available to ensure full reproducibility? Yes, the source data are available, but the protocol needs to be described in more detail, step by step, to ensure the full reproducibility of the study. Are the conclusions drawn adequately supported by the results? It is important to clarify the conclusions further, specifying precisely which moment is determinant for the execution of the studied technique. This will provide a clearer and more applicable understanding of the obtained results.\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? Partly\n\nAre the conclusions drawn adequately supported by the results? No", "responses": [] }, { "id": "295977", "date": "16 Jul 2024", "name": "Dewangga Yudhistira", "expertise": [ "Reviewer Expertise strength and conditioning", "martial art", "sport science and exercise", "sport philosophy" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 1. Background: need to briefly describe the problem and objectives 2. Method: need to write method, participants, number, gender. data collection techniques, data analysis techniques, applications used 3. Results: the presentation of the results is not yet comprehensive 4. Conclusion: the conclusion is not clear\nINTRODUCTION The Introduction does not explain in detail the importance of this research. Why only wushu, it must be seen from a different perspective like other martial arts sports. The citation from Xiaong 2007 needs to be strengthened by the latest studies. Hasn't stated the problem clearly. The research objectives are also not coherent with the problem. Lack of previous research studies. Major revisions are needed to prepare a good introduction with a presentation like the inverted pyramid principle.\nMethod The sample is too small so the results cannot be generalized well. The research method is also unclear. Improvements are needed with detailed explanations by separating sub-chapters: research methods and design, participants and research procedures, data analysis techniques. The suggested method used is single subject research\nRESULTS AND DISCUSSION Presentation of results and discussion needs to be supported by previous studies\n\nCONCLUSION No conclusion yet?\n\nIs the work clearly and accurately presented and does it cite the current literature? Partly\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Partly\n\nIf applicable, is the statistical analysis and its interpretation appropriate?\nPartly\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Partly", "responses": [] } ]	1	https://f1000research.com/articles/13-638
https://f1000research.com/articles/12-1238/v1	28 Sep 23	{ "type": "Study Protocol", "title": "Protocol for assessment and correlation of Brandwein-Gensler criteria with P53 immunoexpression in oral squamous cell carcinoma: A retrospective study", "authors": [ "Sakshi Akolkar", "Alka Hande", "Madhuri Gawande", "Swati Patil", "Archana Sonone", "Aayushi Pakhale" ], "abstract": "Introduction: The commonest type of malignancy in the head and neck region is oral squamous cell carcinoma (OSCC). Brandwein provided a risk model that includes scores for the following three factors: worst invasion pattern, lymphocytic host response and perineural invasion. This risk model accounts for overall survival and local recurrence. p53 is considered to be one of the most significant prognostic markers. Objectives: To assess and correlate Brandwein-Gensler criteria with p53 immunoexpression in oral squamous cell carcinoma. Methods: In this study, a total of 80 samples will be included from histopathologically diagnosed OSCC patients will be taken for the study. H&E-stained slides of all cases will be evaluated using Brandwein-Gensler criteria and then immunostaining will be done for p53 immunoexpression. A correlation between Brandwein-Gensler criteria and p53 immunoexpression will be determined. The present study will assess and correlate Brandwein-Gensler criteria with p53 immunoexpression. If the Brandwein-Gensler criteria score increases, the intensity of p53 immunoexpression will also increase. Conclusions: We hypothesize that Brandwein-Gensler criteria may be significantly correlated with p53 immunoexpression in OSCC.", "keywords": [ "Brandwein-Gensler criteria", "worst pattern of invasion", "lymphocytic host response", "perineural invasion", "p53", "immunohistochemistry", "OSCC", "oral squamous cell carcinoma" ], "content": "Introduction\n\nThe commonest type of malignancy in the head and neck region is oral squamous cell carcinoma (OSCC). It is also one of the top 10 malignancies in the world.1 The median survival for OSCC, which is less than 50% in five years, has improved very little despite recent improvements in treatment methods.2 The main reason for death in people with OSCC is loco-regional recurrence. Many factors, including the size of tumor, its grade, the negative resection margin, lymph node metastases, perineural invasion, etc., have an effect on local recurrence and survival. Brandwein provided a risk model that includes scores for the following three factors: worst invasion pattern (WPI), lymphocytic host response (LHR) and perineural invasion (PNI). This risk model accounts for overall survival and local recurrence.3 Low-, moderate-, and high-risk categories are determined by adding these scores.3\n\nWhen neoplastic cells enter tissues at the tumor/host contact, this is referred to as having the worst pattern of invasion.4 The WPI is notably related to poor prognosis, metastases of the lymph nodes, and loco-regional recurrence rates.5 In the risk model, lymphocyte density at the tumour interface serves as a histological measure of the LHR. Strong, intermediate, or weak are the three categories.6 PNI is the development of cancerous cells inside one of the three layers of a nerve structure or the existence of tumour foci outside of the nerve that cover more than one-third of the nerve’s circumference.7 PNI has been labelled as an OSCC parameter with a high level of risk.7 PNI is additionally referred to as a predictor of survival and local recurrence.5\n\nIn the Brandwein-Gensler risk model, WPI with type 4 and 5 scores shows scattered neoplastic cells, which are masked by marked chronic inflammatory cells and are difficult to identify. To identify these masked neoplastic cells various immunohistochemical markers such as p53 are commonly used. p53 is considered to be one of the most significant prognostic markers.2 p53 is a protein present in the nucleus of epithelial cells produced by a tumor suppressor gene known as TP53. It regulates cell division and apoptosis.8 p53 overexpression in OSCC is thought to be a sign of poor prognosis.2 In this study, we determine if there is a correlation between the Brandwein-Gensler criteria and p53 immunoexpression in OSCC.\n\n\n\n1. To evaluate Brandwein-Gensler criteria in OSCC.\n\n2. To evaluate p53 immunoexpression in OSCC.\n\n3. To correlate the Brandwein-Gensler criteria with p53 immunoexpression in OSCC.\n\n4. To correlate the Brandwein-Gensler criteria and p53 immunoexpression with overall three years survival with OSCC.\n\n\nProtocol\n\nThis is a retrospective cohort study, which will be carried out in the Department of Oral and Maxillofacial Pathology and Microbiology, Sharad Pawar Dental College and Hospital, Sawangi, Wardha, Maharashtra. Ethical approval was provided by the Institutional Ethical Committee, Datta Meghe Institute of Higher Education and Research, Sawangi, Wardha.\n\nIEC reference number: DMIHER (DU)/IEC/2023/840. Date: 31/03/2023.\n\nInclusion criteria\n\n• Samples of OSCC that have been surgically treated and that have been clinically and histopathologically diagnosed will be included in this study.\n\n• Follow-up data will be assessed for 4–5 years of disease-free survival.\n\nExclusion criteria\n\n• The patients who previously underwent surgery for OSCC recurrence (apart from a biopsy) or had therapy will be excluded from the study.\n\n• Patients who had a history of oral cancer, recurring or distant disease.\n\n• Patients who underwent preoperative chemotherapy or radiation.\n\nIn this retrospective study, a total of 80 previously unused, randomly selected samples of histopathologically diagnosed OSCC from 2019 to 2022 will be retrieved from the archives of the Department of Oral and Maxillofacial Pathology and Microbiology, Sharad Pawar Dental College and Hospital in the form of paraffin blocks. Blocks will be cut and tissue sections will be taken on slides. Slides will be deparaffinized and rehydrated in distilled water. Mayers Hematoxylin staining will be carried out for one minute. The slides will be washed 4–5 times with tap water or until the stain has been removed. Counterstain for one minute in alcohol-eosin without rinsing. Dehydrate by going through three 95% EtOH changes and two 100% EtOH changes, each lasting one minute. Clear in three Xylene changes, lasting one minute each. Then mounting will be done. After processing and staining with H & E stain, slides will be evaluated under a microscope (OLYMPUS- CX21iFS1) to assess Brandwein-Gensler criteria (WPI, LHR and PNI). After evaluation of Brandwein-Gensler criteria, the cases will be studied for immunohistochemical expression of p53. This will be carried out by AJCC’s criteria and Worst pattern of invasion, perineural invasion and lymphocytic hot response will be evaluated. Brown nuclear staining in the cell will be examined for p53 immunoexpression and will be evaluated as per the following criteria: No staining (0), light staining (1+), medium staining (2+), and heavy staining (3+).2 A focal positive is defined as less than 10% of tumor cells, which are intermediate to weakly stained, whereas a positive is defined as more than 10% of cancer cells, which are moderate to strongly stained. Staining of tumor cells won’t be seen as positive.2\n\nThe risk scoring system is adapted from Ref. 3. The effectiveness of the Brandwein Gensler Risk Model, which combines three significant pathological variables, in forecasting the course of surgically treated OSCC, will be examined in this study. Worst invasion pattern, perineural invasion, and lymphocytic host response are these pathogenic variables.\n\nIn worst pattern of invasion:\n\n• Type 1 shows “pushing border” (Score 0)\n\n• Type 2 shows “finger-like growth” (Score 0)\n\n• Type 3 shows “large, distinct islands, each with more than 15 cells” (Score 0)\n\n• Type 4 shows “15 or fewer cells per small tumour island” (Score +1)\n\n• Type 5 shows “satellites of the tumour that are 20 times or more distant from the primary tumour, or that are at least 1 mm away” (Score +3)\n\nIn lymphocytic host response:\n\n• Type 1 strong: “Each 4x field has a dense, full host response that surrounds the tumour lymphoid nodules at the advancing edge” (Score 0)\n\n• Type 2 intermediate: “Moderate host response; some 4x fields have lymphoid nodules but not all of them” (Score +1)\n\n• Type 3 weak: “No lymphoid nodule or a minimal host response” (Score +3)\n\nIn perineural invasion:\n\n• Small nerves: “0.2 mm tumour looping around nerves” (Score +1)\n\n• Large nerves: “A tumour with a diameter of at least one millimetre that wraps around nerves” (20×) (Score +3)\n\nEvaluation of risk for oral squamous cell carcinoma5:\n\n• In lymphocytic infiltrate at interface, continuous band has scored 0, large patches are scored 1 and little or none are scored 3.\n\n• WPI at interface, with point 1 or 2 or 3 will have scoring of 0, with point 4 will be scored 1 and with point 5 will be scored 3.\n\n• Perineural invasion, no invasion will be scored 0, small nerves present will be scored 1 and large nerve invasion will be scored 3.\n\n\nOutcomes\n\nThe Brandwein-Gensler criterion will be evaluated in this investigation along with p53 immunoexpression.\n\nP53 immunoexpression will become more intense when the Brandwein Gensler criterion score rises.\n\nBy applying the single proportion formula and taking into account the prevalence of OSCC in the Department of Oral Pathology and Microbiology, which is 70.7%, sample size is determined:\n\nWhere,\n\nZ21-α/2 The significance level at 5%\n\ni.e. 95% confidence interval = 1.96\n\np = Sample showing positive p53 expression focally in small group cells in the the basal layer of epithelium = 70.7% = 0.707\n\nd = margin error = 10% = 0.10\n\nn = 80\n\np53 immunohistochemistry will be carried out utilising the DAKO EnVision technique and DO-7 clone of the DAKO anti-human p53 protein. Slices of 4 mm thick tissue will be cut by microtome from blocks of paraffin-embedded tissue (fixed with formalin). The tissue slices will be transferred onto glass slides made of “3-amino propyl triethoxy silane” (APES). Deparaffinize slides in 2 changes of xylene or xylene substitute for 5 minutes each. Transfer slides to 100% alcohol, 2 changes for 3 minutes each and transfer once through 95% alcohol for 3 minutes. Block endogenous peroxidase activity by incubating sections in 3% H2O2 solution in methanol for 10 minutes. The slides will be heated in TRIS-EDTA for five minutes in a pressure cooker to perform antigen retrieval. With 3% hydrogen peroxide, endogenous peroxidase activity will be blocked for 10 minutes. The slides will be exposed to ultraviolet block reagent for five minutes. Incubation of slides with mouse monoclonal anti-p53 primary antibody (PAb 240) BSA free (PathnSitu) for an hour at room temperature (DO-1). Following the secondary antibody, horse radish peroxidase will be used for 30 minutes. For staining, a substrate chromogen (3′-diaminobenzidine tetrahydrochloride) will be employed, and Harris Hematoxylin will be used for counterstaining. Sections will first be dehydrated, then cleared, mounted, and finally observed under a microscope (Olympus CX21iFS1). Both quantitatively and subjectively, nuclear staining for p53 is assessed. p53 immunoexpression will be evaluated as per following criteria: Absence of staining (0), light staining (1+), medium staining (2+), and heavy staining (3+) present.2 A focal positive is defined as less than 10% of tumor cells which are intermediate to weakly stained, whereas a positive is defined as more than 10% of cancer cells which are moderate to strongly stained. Staining of tumor cells won’t be seen as positive. Moreover, p53 immunostaining is divided into various groups according to the percentage of stained cells.2\n\nOnce complete the study results will be published in an indexed journal.\n\nThe study will be starting in January 2024.\n\n\nDiscussion\n\nAn author studied lymph node metastasis, recurrence/progression of illness, and histological risk assessment/scoring system in fifty patients with OSCC and two years of follow-up data were obtained. They concluded that in OSCC patients, individual features, WPI and PNI were notable prognostic factors.1\n\nAnother study was conducted on the clinical and prognostic importance of immunohistochemical p53 overexpression in head and neck squamous cell carcinoma. In 121 cases of OSCC, they sought to assess immunohistochemistry overexpression of p53 and its relationships to various clinicopathologic characteristics and survival. They arrived at the conclusion that extranodal extension, higher tumour grades (grades II and III), and p53 intensity of expression are significantly correlated with extranodal extension in head and neck OSCC.2\n\nA study of OSCC patients from North India validated the Brandwein-Gensler risk model. Patients who were at least 18 years old underwent primary surgical resection for OSCC with a histological diagnosis were included in this study. After the initial surgery, the OSCC locoregional recurrences could be predicted using the Brandwein Gensler risk model. It can be used to develop plans for stopping recurrences or spotting them early enough for treatment.3\n\n\nConsent\n\nWritten informed consent for publication of the patients’ details has been obtained from the patients.", "appendix": "Data availability\n\nNo data are associated with this article.\n\nZenodo: STROBE checklist for ‘Protocol for assessment and correlation of Brandwein-Gensler criteria with P53 immunoexpression in oral squamous cell carcinoma: A retrospective study’, https://www.doi.org/10.5281/zenodo.7871170.\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0)\n\n\nAcknowledgements\n\nWe would like to thank Datta Meghe Institute of Higher Education and Research, our seniors and our colleagues.\n\n\nReferences\n\nBatool M, Mushtaq S, Jamal S, et al.: CORRELATION OF HISTOLOGICAL RISK ASSESSMENT/SCORING SYSTEM WITH LYMPH NODE METASTASIS AND RECURRENCE/PROGRESSION OF DISEASE IN ORAL SQUAMOUS CELL CARCINOMA. Pak. Armed Forces Med. J. 2015; 65(5): 582–586. Reference Source\n\nHashmi AA, Hussain ZF, Hashmi SK, et al.: Immunohistochemical over expression of p53 in head and neck Squamous cell carcinoma: clinical and prognostic significance. BMC. Res. Notes. 2018; 11: 433. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChaturvedi A, Husain N, Misra S, et al.: Validation of the Brandwein Gensler Risk Model in Patients of Oral Cavity Squamous Cell Carcinoma in North India. Head Neck Pathol. 2020 Sep; 14(3): 616–622. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMishra A, Das A, Dhal I, et al.: Worst pattern of invasion in oral squamous cell carcinoma is an independent prognostic factor. J. Oral Biol. Craniofac. Res. 2022 Nov-Dec; 12(6): 771–776. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBrandwein-Gensler M, Teixeira MS, Lewis CM, et al.: Oral squamous cell carcinoma: histologic risk assessment, but not margin status, is strongly predictive of local disease-free and overall survival. Am. J. Surg. Pathol. 2005 Feb; 29(2): 167–178. PubMed Abstract \| Publisher Full Text\n\nMaleki S, Schlecht NF, Keller C, et al.: Lymphocytic host response to oral squamous cell carcinoma: an adaptive T-cell response at the tumor interface. Head Neck Pathol. 2011 Jun; 5(2): 117–122. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nSpoerl S, Spoerl S, Reil S, et al.: Prognostic Value of Perineural Invasion on Survival and Recurrence in Oral Squamous Cell Carcinoma. Diagnostics (Basel). 2022 Apr 24; 12(5): 1062. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nUijtdehaage S, Dennis S: HEAL: Health Education Assets Library. Oakland (CA): Regents of the University of California; c2000-2005 [cited 2007 Feb 20]. Joint publication with the University of Utah and the University of Oklahoma. Reference Source" }	[ { "id": "234271", "date": "14 May 2024", "name": "Karthikeyan Ramalingam", "expertise": [ "Reviewer Expertise Oral cancer", "Oncology", "Oral Pathology", "Pathology lab administration", "Quality of Life" ], "suggestion": "Not Approved", "report": "Not Approved\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThere is no relevant histopathological assessment in the results or supporting photomicrographs. It looks like a study proposal and is not complete. They have quoted about risk model but it is not discussed nor elaborated. The p53 expression, its scoring or grading assessment is not disclosed. The clinical implications of their findings is not disclosed.\n\nIs the rationale for, and objectives of, the study clearly described? Yes\n\nIs the study design appropriate for the research question? Partly\n\nAre sufficient details of the methods provided to allow replication by others? No\n\nAre the datasets clearly presented in a useable and accessible format? No", "responses": [] }, { "id": "244371", "date": "14 May 2024", "name": "Nilotpal Chowdhury", "expertise": [ "Reviewer Expertise Histopathology", "cytopathology", "molecular pathology" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe protocol is interesting and warrants follow up and research. Two issues that need to be highlighted are: 1. The interpretation protocol for p53 uses a nuclear scoring criteria. p53 is ideally not interpreted as such, but as Wild type /Aberrant (Bellizzi, 2023). Aberrant phenotype may be either complete absence of staining (Null Pattern) or more than a certain pre-specified percentage of nuclei showing strong staining or Basal overexpression or cytoplasmic. The threshold for nuclear staining is also not defined for all cancers for the overexpression pattern. The analysis should be done correlating the Brandwein-Gensler score with I. The Wildtype/Aberrant dichotomous classification, and II. Correlation of the scores with the various types of pattern. The various patterns described can be obtained from the reference which has been added below. 2. Why the sample size should be calculated on the formula for proportion is unclear. The protocol does not state that the aim of the study is to find the proportion of \"focal small group cells in the basal layer of the epithelium\". Going through the protocol, it seems that the most important objective should be to compare the Brandwein Gensler score (ordered categorical/ordinal variable) with the wildtype/aberrant status (dichotomous variable). The Mann-Whitney test may be used for such a scenario and the sample size calculated. A sample size of 30 in each arm should be sufficient to detect differences at a high effect size of about 0.8 at an alpha of 0.05 and power of 0.8 for the Mann-Whitney test. A sample size of 40 in each arm in such a case may be taken to compensate for any failed staining, and non-Gaussian distribution. The above is just a suggestion, and the authors may modify sample size calculation using alternative methods.\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": "11664", "date": "30 May 2024", "name": "Sakshi Akolkar", "role": "Author Response", "response": "Thank you for reviewing my article, I agree to all the suggestion you have said, and will surely work on it" } ] }, { "id": "274162", "date": "27 May 2024", "name": "Namrah Anwar", "expertise": [ "Reviewer Expertise Oral Squamous Cell carcinoma and its histopathological and molecular aspects." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nProtocol for assessment and correlation of Brandwein- Gensler criteria with P53 immunoexpression in oral squamous cell carcinoma: A retrospective study\nOVERALL COMMENTS:\nThe article aims to explain the protocol for studying the correlation between P53 immunohistochemical staining and risk assessment using Brandwein-Gensler risk model in oral squamous cell carcinoma.\nOverall, the article, alongside technical queries, needs editing for the English language, as active and passive sentences have been randomly used in paragraphs explaining the staining methods.\nQueries to be answered:\n\nINTRODUCTION:\n\nParagraph 3 mentions the use of P53 for identifying individual tumor cells masked by inflammatory infiltrate. Keratin stains are commonly used for this purpose, as P53 can give variable results. Immediately after that, the authors discuss P53 as a prognostic marker. The overall message is not clear here. Major rephrasing is needed to clearly explain the study's rationale for using P53 with the Brandwein-Gensler risk model.\nOBJECTIVES:\nObjectives are redundant. Only two would be enough for this study. One is for the correlation between P53 and the Brandwein-Gensler risk model, and the other ties this correlation with the overall survival rate.\nPROTOCOL:\nInclusion/Exclusion criteria need more elaboration. Will the specific subtype of oral SCC be included in the study or if the study aims to include all different subtypes? What will be the inclusion/exclusion criteria for the data on overall survival? Variables which are to be studied apart from IHC must be included. The formula for calculating sample size is not needed. A better approach would be to write the software's name with statistical considerations of sample size.\nINTERVENTION:\nThe first line says, “Samples will be randomly selected”. Which probability sampling method will be used for this random selection? There is a need to rephrase the manuscript as there are some obvious grammatical mistakes. Some sentences are written in the future tense, and some are in the present tense. This part “After evaluation of Brandwein- Gensler criteria, the cases will be studied for immunohistochemical expression of p53. This will be carried out by AJCC’s criteria and Worst pattern of invasion, perineural invasion and lymphocytic hot response will be evaluated. Brown nuclear staining in the cell will be examined for p53 immunoexpression and will be evaluated as per the following criteria: No staining (0), light staining (1+), medium staining (2+), and heavy staining (3+).2 A focal positive is defined as less than 10% of tumor cells, which are intermediate to weakly stained, whereas a positive is defined as more than 10% of cancer cells, which are moderate to strongly stained. Staining of tumor cells won’t be seen as positive.”\nIt is not clear as to what exactly “this” is referring to. AJCC criteria have not been introduced in the article so far. If the Brandwein-Gensler risk model is being referred to here, this needs to be clarified earlier in the introduction.\nSimilarly, the last line states that “staining of tumor cells won’t be seen as positive” does not make sense. This needs to be either appropriately explained or removed.\nDATA MEASUREMENT:\nWhile explaining the perineural invasion, are the measurements given for the diameter of the nerve or the tumor? These phrases are confusing. The method of measuring the tumors' invasion depth needs to be more precisely defined. The word “surface” refers to the surface of the adjacent normal mucosa or the point of the granular layer, which is taken as the point from which the tumor thickness or depth is measured as per the guidelines mentioned in the WHO blue book for Head and neck tumors. There is no mention of the statistical method to calculate the association between P53 staining and the score of Brandwein-Gensler risk model. How would the overall survival be measured? It must be the part of the protocol.\nOUTCOMES:\nThe primary and secondary outcomes mentioned are not objective or measurable. This part of the article needs to be re-written in light of the changes in objectives.\nIMMUNOSTAINING:\nMentioning the material of which the glass slides are made is redundant. The whole paragraph needs major rephrasing with respect to language. The last line of this part does not make sense. Again, this needs to be either explained correctly or removed.\nDISCUSSION:\nIn second paragraph, second sentence, the word “immunohistochemistry” needs to be changed to “immunohistochemical”.\n\nDiscussion can be further refined by explaining what exactly this article will add to the already available literature on this topic.\n\nIs the rationale for, and objectives of, the study clearly described? Partly\n\nIs the study design appropriate for the research question? Partly\n\nAre sufficient details of the methods provided to allow replication by others? Partly\n\nAre the datasets clearly presented in a useable and accessible format? Not applicable", "responses": [ { "c_id": "11680", "date": "17 Jun 2024", "name": "Sakshi Akolkar", "role": "Author Response", "response": "Respected sir/ma'am, I have made the chnages in paragraph 3 and I am using p53 and Brandwein gensler for the adjuvant therapy and to predict the overall prognosis of patients. I have rephrase the text where ever it was needed. Objectives- Rewritten Protocol- 1. the study is independent of the subtypes of OSCC 2. Data will be collected from the system and survival of the patient will be asked. 3. We are only using IHC for the study. 4. I have removed the sample size formula Intervention- 1.Simple random sampling will be done. 2. edited 3. edited Data measurement- 1. Yes, it is related to small nerve with diameter less than 5 mm and larger with more than 5 mm. 2. Surface refers to the surface of adjacent mucosa, ie epithelial surface 3. Statistical method to calculate BGC and p53 is not needed. 4. method for overall survival is Kaplan-Meier estimate outcomes- deleted immunostationg- rephrased I have made the corrections which were required. please process for the indexing of my article. Thank you" } ] } ]	1	https://f1000research.com/articles/12-1238
https://f1000research.com/articles/12-566/v1	30 May 23	{ "type": "Data Note", "title": "Cigarette smoke alters circRNA expression in human T-cells", "authors": [ "So Jin Hong", "Zhaohao Liao", "Kenneth W. Witwer", "Ashley E. Russell", "So Jin Hong", "Zhaohao Liao", "Kenneth W. Witwer" ], "abstract": "Circular RNAs (circRNAs), once thought to be a result of splicing errors, have been found to be involved in various molecular processes and in the pathology of various diseases, including cancer and neurodegenerative diseases. Additionally, circRNA expression was found to be altered by lifestyle habits, such as smoking cigarettes. Past studies have revealed that the rate of smoking remains high in people living with human immunodeficiency virus (HIV). In this study, we isolated total RNA from uninfected T-cells that have been exposed to cigarette smoke and compared the expression levels of circRNAs to those of T-cells that were not exposed to cigarette smoke. We identified certain circRNAs that were upregulated or downregulated in T-cells when exposed to cigarette smoke. These data indicate that the study of circRNAs is warranted within the context of HIV.", "keywords": [ "Cigarette smoke", "T-cells", "circRNA", "HIV" ], "content": "Introduction\n\nCircular RNAs (circRNAs) are endogenous non-coding RNAs covalently bonded circular structures that are created through back-splicing events (Yu & Kuo, 2019). CircRNAs are predominantly present in the cytoplasm, but have also been shown to be present in extracellular vesicles (EVs) released from cells (Gotts et al., 2018; Preußer et al., 2018). Although first thought to be a result of splicing errors, circRNAs have been found to play important roles in various molecular processes, such as functioning as microRNA (miRNA) sponges (Hansen et al., 2013). miRNAs are small non-coding RNAs that are involved in regulating protein production by binding to complementary sequences in the 3′ untranslated region of messenger RNAs (mRNAs) and preventing their translation into protein (Jonas & Izaurralde, 2015). By binding miRNAs, circRNAs can alleviate repression of linear mRNA targets and thus influence gene regulation.\n\nIn some cancers, including pancreatic and breast cancer, aberrant expression of circRNAs has been observed (Rong et al., 2021; Wang et al., 2019a, 2019b). Altered expression of circRNAs has also been associated with neurodegenerative diseases such as Alzheimer’s Disease (Lo et al., 2020). Together, these data suggest that circRNAs are involved in disease pathology and may serve as novel biomarkers for various diseases. Notably, lifestyle habits like cigarette smoking alter circRNA expression as well (Zeng et al., 2019), indicating that a person’s smoking status may impact epigenetic mechanisms mediated by miRNAs.\n\nAlthough the rate of smoking in the general population has been on the decline, it remains higher in people living with human immunodeficiency virus (HIV) (Socio et al., 2020). Individuals living with HIV who smoke tend to have a more serious prognosis or develop other HIV-related diseases such as cancers, pneumonia, and chronic obstructive pulmonary disease (COPD) (Giles et al., 2018; Hile et al., 2016), the pathophysiology of which may be impacted by epigenetic regulation of miRNAs and circRNAs. In the current study, we sought to investigate the effects of cigarette smoke on circRNA expression profiles in a model of uninfected human T-cells (H9 cells) to understand how cigarette smoke impacts circRNA expression in this cell type, a common target of HIV (Walker & McMichael, 2012). These data will provide a foundation for investigating circRNA expression in HIV-infected H9 cells that have been exposed to cigarette smoke to understand how these two variables intersect.\n\n\nMethods\n\nCigarette smoke extract (CSE) was made using an apparatus and techniques as previously described by our lab (Bernstein et al., 2019). Briefly, 25 mL of R10 media was aliquoted into a 50 mL conical tube and sealed with parafilm. A 5 mL serological pipette, cut at the 3.5 mL mark, was inserted through the parafilm seal. This apparatus was connected to one end of a Tygon tubing (Cole-Parmer, Cat. No. 06509-17), which was inserted into a Cole-Parmer Masterflex L/S peristaltic pump at speed setting of 32. A 1 mL pipette tip was tightly inserted into the other end of the Tygon tubing. Next, one Spectrum research-grade cigarette (Richter et al., 2016) (filter intact) was lit with a Bunsen burner and tightly inserted into the wide end of the 1 mL pipette tip. The cigarette was then smoked continuously by the peristaltic pump into the cell culture medium. The resulting product was considered 100% CSE.\n\nApproximately 400,000 cells/mL of H9 cells were passaged into six T75 flasks, three of which were filled with 25 mL of R10 media with 0% CSEM and the other three with 25 mL of 50% CSEM. After 24 hours, the percentage of viable cells was measured (Table 1) using a Muse cell counter and Muse Count & Viability Reagent (Luminex, Cat. No. MCH600103).\n\nPercentages of cell viability and density were measured and calculated after 24 hours for six flasks of H9 cells: three with 0% CSEM for 24 hours and three with 50% CSEM. CSEM, cigarette smoke extract media.\n\nThe Invitrogen mirVana™ miRNA Isolation Kit (ThermoFisher Scientific, Cat. No. AM1560) was used as directed to isolate total cellular RNA. Approximately 105 cells from each flask were lysed with 600 μL lysis buffer. Then, 750 μL 100% ethanol was added and centrifuged at 10,000 × g for 15 seconds. The filters containing RNA were washed, and total RNA was eluted with 100 μL pre-heated nuclease-free water, centrifuging at maximum speed for 25 seconds. RNA quality was checked using an Agilent Fragment Analyzer. Next, 5,000 ng of RNA from each sample was shipped to Arraystar for hybridization with the Human Circular RNA Array (Cat. No. AS-S-CR-H-V2.0).\n\nTotal RNAs from each sample were quantified using the NanoDrop ND-1000 and the integrity of the samples were evaluated through electrophoresis on a denaturing agarose gel. Total RNAs were then digested with RNase R (Epicentre, Inc.) to degrade linear RNAs and enrich circRNAs. A random priming method was used to amplify and transcribe the enriched circRNAs into fluorescent complementary RNAs (cRNAs) (Arraystar Super RNA Labeling Kit; Arraystar), which were then purified by RNeasy Mini Kit (Qiagen). Nanodrop ND-1000 was used to measure the concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA). A total of 1 μg of each labeled cRNA was fragmented by adding 5 μl of 10× Blocking Agent and 1 μl of 25× Fragmentation Buffer. The mixture was then incubated at 60°C for 30 minutes, then 2× Hybridization buffer was added to dilute the labeled cRNA. Then, 50 μl of the hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slides, which were washed, fixed, and scanned with the Agilent Scanner G2505C.\n\nAgilent Feature Extraction Software (version 11.0.1.1) (RRID:SCR_014963) was used to extract raw data from the scanned images. Quantile normalization of the raw data and subsequent data processing were conducted using the R software Limma package (RRID:SCR_010943). Low intensity filtering was then performed to retain circRNAs that at least one out of six samples were flagged as “present” or “marginal”. The quality control flags of “present”, “marginal”, or “absent” were determined based on various features, including positive and significant signal, saturation, population outlier, above background, and uniformity of the background. The fold change between the cigarette exposed samples and control samples were calculated and the statistical significance of the difference was estimated using an unpaired t-test. circRNAs having fold changes greater than or equal to 1.5 and p-values less than or equal to 0.05 were selected as significantly differentially expressed, using Microsoft Excel (RRID:SCR_016137). The false detection rate for each differentially expressed circRNAs were calculated using Benjamini-Hochberg procedure. These data, while suggestive, do not support robust statistical analysis secondary to the number of repeats and the large number of RNAs.\n\n\nDataset\n\nThe Human Circular RNA Array revealed 234 circRNAs that were 1.5-fold upregulated (Up Regulated circRNAs) and 42 circRNAs that were 1.5-fold downregulated (Down Regulated circRNAs) in H9 cells cultured in 50% CSEM relative to H9 cells grown in 0% CSEM (Hong et al., 2023).", "appendix": "Data availability\n\nGene Expression Omnibus: Cigarette Smoke Alters CircRNA Expression in Human T-Cells. GSE228979; https://identifiers.org/geo/GSE228979 (Hong et al., 2023).\n\nThis series contains the following underlying data:\n\n- Datasheet 1 (1.5 Fold Up Regulated circRNAs. Datasheet 1 contains raw and normalized fluorescence intensities from the ArrayStar circRNA Microarray, for 234 circRNAs that were significantly upregulated in H9 cells after cigarette smoke exposure. The circRNA ID was obtained by inputting the transcript and sequence information into circBase or other literatures).\n\n- Datasheet 2 (1.5 Fold Down Regulated CircRNAs. Datasheet 2 contains raw and normalized fluorescence intensities from the ArrayStar circRNA Microarray, for 42 circRNAs that were significantly downregulated in H9 cells after cigarette smoke exposure. The circRNA ID was obtained by inputting the transcript and sequence information into circBase or PMIDs).\n\n\nReferences\n\nBernstein ED, Liao Z, Witwer KW: Cytotoxicity of aqueous cigarette smoke extract is affected by properties of pipettes used to prepare the extract. Matters. 2019; 2019. Free Full Text\n\nGiles ML, Gartner C, Boyd MA: Smoking and HIV: what are the risks and what harm reduction strategies do we have at our disposal? AIDS Res. Ther. 2018; 15(1): 25–26. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nGotts JE, Chun L, Abbott J, et al.: Cigarette smoke exposure worsens acute lung injury in antibiotic-treated bacterial pneumonia in mice. Am. J. Physiol. Lung Cell. Mol. Physiol. 2018; 315(1): L25–L40. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHansen TB, Jensen TI, Clausen BH, et al.: Natural RNA circles function as efficient microRNA sponges. Nature. 2013; 495(7441): 384–388. PubMed Abstract \| Publisher Full Text\n\nHile SJ, Feldman MB, Alexy ER, et al.: Recent Tobacco Smoking is Associated with Poor HIV Medical Outcomes Among HIV-Infected Individuals in New York. AIDS Behav. 2016; 20(8): 1722–1729. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHong SJ, Russell AE, Witwer KW, et al.: Cigarette Smoke Alters CircRNA Expression in Human T-Cells. [Dataset]. Gene Expression Omnibus. 2023. Reference Source\n\nJonas S, Izaurralde E: Towards a molecular understanding of microRNA-mediated gene silencing. Nat. Rev. Genet. 2015, July 19; 16: 421–433. Nature Publishing Group. PubMed Abstract \| Publisher Full Text\n\nLo I, Hill J, Vilhjálmsson BJ, et al.: Linking the association between circRNAs and Alzheimer’s disease progression by multi-tissue circular RNA characterization. RNA Biol. 2020; 17: 1789–1797. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPreußer C, Hung LH, Schneider T, et al.: Selective release of circRNAs in platelet-derived extracellular vesicles. J. Extracell. Vesicles. 2018; 7(1). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRichter P, Steven PR, Bravo R, et al.: Characterization of SPECTRUM Variable Nicotine Research Cigarettes. Tob. Regul. Sci. 2016; 2(2): 94–105. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nRong Z, Xu J, Shi S, et al.: Circular RNA in pancreatic cancer: a novel avenue for the roles of diagnosis and treatment. Theranostics. 2021; 11(6): 2755–2769. Ivyspring International Publisher. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nDe Socio GV , Pasqualini M, Ricci E, et al.: Smoking habits in HIV-infected people compared with the general population in Italy: a cross-sectional study. BMC Public Health. 2020; 20(1): 710–734. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWalker B, McMichael A: The T-Cell Response to HIV. Cold Spring Harb. Perspect. Med. 2012; 2(11). PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWang J, Zhu M, Pan J, et al.: Circular RNAs: A rising star in respiratory diseases. Respir. Res. 2019a; 20(1). BioMed Central Ltd. Publisher Full Text\n\nWang J, Zhang Q, Zhou S, et al.: Circular RNA expression in exosomes derived from breast cancer cells and patients. Epigenomics. 2019b; 11(4): 411–421. PubMed Abstract \| Publisher Full Text\n\nYu CY, Kuo HC: The emerging roles and functions of circular RNAs and their generation. J. Biomed. Sci. 2019; 26(1): 12–29. BioMed Central Ltd. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nZeng N, Wang T, Chen M, et al.: Cigarette smoke extract alters genome-wide profiles of circular RNAs and mRNAs in primary human small airway epithelial cells. J. Cell. Mol. Med. 2019; 23(8): 5532–5541. PubMed Abstract \| Publisher Full Text \| Free Full Text" }	[ { "id": "197877", "date": "18 Sep 2023", "name": "Thivanka Muthumalage", "expertise": [ "Reviewer Expertise Inhalation toxicology and lung biology" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe authors have attempted to show the involvement of circRNA upon exposure to cigarette smoke in HIV infection. While this is important to study, the experimental design lacks information to reproduce the data:\nCigarette smoke extracts need meticulous standardization as they quickly change their chemical composition. The authors need to elaborate, and specify the brand of the cigarette and how the extract was standardized each time during preparation.\n\nCell culture treatments need more details, such as if they were serum-deprived (if not, what is the serum concentration?) and what passage was used. Please explain the rationale for using a cancer cell line.\n\nPlease explain the key altered circRNAs and how they are relevant in HIV progression.\n\nThere are no results and discussion sections; the implications are hard to find.\n\nOverall, while the circRNA alterations may be useful, the authors have not provided sufficient data or discussion for any translational implications. Major revisions are required before indexing.\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? No\n\nAre the datasets clearly presented in a useable and accessible format? Partly", "responses": [ { "c_id": "11668", "date": "21 Jun 2024", "name": "So Jin Hong", "role": "Author Response", "response": "Dear Dr. Thivanka Muthumalage, Thank you for giving us the opportunity to submit a revised draft of our manuscript. We appreciate the time and effort that you have dedicated to providing your valuable feedback. We are grateful for your insightful comments on our paper. We have been able to incorporate changes to reflect most of the suggestions provided. We have highlighted the changes within the manuscript. Here is a point-by-point response to your comments and concerns. Comment 1: Cigarette smoke extracts need meticulous standardization as they quickly change their chemical composition. The authors need to elaborate, and specify the brand of the cigarette and how the extract was standardized each time during preparation. Response: Thank you for pointing this out. Spectrum research grade cigarettes that are tightly regulated by the FDA, and distributed by the NIDA, were used following the general techniques utilized by similar studies to help standardize the preparation step. This information has been added to page 3, under the “Preparation of 100% CSEM” methods section. Comment 2: Cell culture treatments need more details, such as if they were serum-deprived (if not, what is the serum concentration?) and what passage was used. Please explain the rationale for using a cancer cell line. Response: We agree with your suggestion and have incorporated more information regarding the cell culture treatment, passages used, and the rationale behind using the H9 cell lines throughout the manuscript. Comment 3: Please explain the key altered circRNAs and how they are relevant in HIV progression. Response: Thank you for your suggestion. It would have been interesting to include this information. However, this is beyond the scope of the current format for this publication as a Data Note, which does not require a Results and Discussion section per F1000Research article guidelines. Comment 4: There are no results and discussion sections; the implications are hard to find. Response: Thank you for this suggestion. However, our paper was published as a Date Note, which does not require a Results and Discussion section as per F1000Research article guidelines. We look forward to hearing from you regarding our edits and to respond to any further questions and comments you may have. Sincerely, So Jin Hong" } ] }, { "id": "255365", "date": "01 Apr 2024", "name": "Zahraa Rahal", "expertise": [ "Reviewer Expertise I study smoking-induced (cigarette and waterpipe) lung cancer." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThe article investigates the impact of cigarette smoke on circRNA expression in uninfected human T-cells (H9 cells), motivated by the high rate of smoking in people living with human immunodeficiency virus (HIV). It explores circRNAs' role in molecular processes and their potential alteration due to lifestyle habits, like smoking, which may affect the pathology of various diseases. The study employed cigarette smoke extract media to expose H9 cells to cigarette smoke and analyzed changes in circRNA expression using RNA isolation, circRNA enrichment, and microarray analysis.\nWhile the connection between circRNA expression and lifestyle factors like smoking is intriguing, the rationale for focusing specifically on uninfected T-cells and its direct relevance to HIV-positive individuals remains underexplained. The leap from smoking's impact on circRNA in a general context to its implications for HIV-specific pathology could be more robustly justified with existing literature or preliminary data. To strengthen the rationale, the authors should provide a more detailed synthesis of existing literature or preliminary data that directly connects circRNA alterations due to smoking with HIV pathology. Additionally, clarifying why uninfected T-cells serve as an appropriate model for this investigation would help solidify the study's foundation.\nThe methods are detailed, but there's a lack of information regarding the validation of the experimental setup. For example, the efficiency and reproducibility of the cigarette smoke extraction method and its physiological relevance to real-world smoking exposure might raise questions. It might be useful to include a validation section for the CSE method, comparing it to physiological conditions or other established methods.\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? Yes", "responses": [ { "c_id": "11669", "date": "21 Jun 2024", "name": "So Jin Hong", "role": "Author Response", "response": "Dear Dr. Zahraa Rahal, Thank you for giving us the opportunity to submit a revised draft of our manuscript. We appreciate the time and effort that you have dedicated to providing your valuable feedback. We are grateful for your insightful comments on our paper. We have been able to incorporate changes to reflect most of the suggestions provided. We have highlighted the changes within the manuscript. Here is a point-by-point response to your comments and concerns. Comment 1: While the connection between circRNA expression and lifestyle factors like smoking is intriguing, the rationale for focusing specifically on uninfected T-cells and its direct relevance to HIV-positive individuals remains underexplained. The leap from smoking's impact on circRNA in a general context to its implications for HIV-specific pathology could be more robustly justified with existing literature or preliminary data. To strengthen the rationale, the authors should provide a more detailed synthesis of existing literature or preliminary data that directly connects circRNA alterations due to smoking with HIV pathology. Additionally, clarifying why uninfected T-cells serve as an appropriate model for this investigation would help solidify the study's foundation. Response: Thank you for pointing this out. T-cells served as an appropriate model for this study, given their susceptibility to HIV infections. Our study using the uninfected T-cells would serve as a baseline for what happens in these cells when exposed to cigarette smoke. The next step of this experiment would be to replicate the study with HIV infected T-cells to study the effects of cigarette smoke in these cells. This information was added to the introduction and the “H9 cell cigarette smoke exposure” methods section. Comment 2: The methods are detailed, but there's a lack of information regarding the validation of the experimental setup. For example, the efficiency and reproducibility of the cigarette smoke extraction method and its physiological relevance to real-world smoking exposure might raise questions. It might be useful to include a validation section for the CSE method, comparing it to physiological conditions or other established methods. Response: We agree with your suggestion. However, it is difficult to validate the composition of the CSE, therefore we have followed the exact same paradigm across all experiments and our methodology aligns very closely with other published studies in the field. References have been added to our manuscript. We look forward to hearing from you regarding our edits and to respond to any further questions and comments you may have. Sincerely, So Jin Hong" } ] } ]	1	https://f1000research.com/articles/12-566
https://f1000research.com/articles/12-114/v1	31 Jan 23	{ "type": "Systematic Review", "title": "An integrative review on physical restraint in adult critical care unit", "authors": [ "Janisha Kavumpurath", "Kulanthayan KC Mani", "Fatma Refaat", "Navin Devaraj", "Aneesa Abdul Rashid", "Noor Airini Ibrahim", "Janisha Kavumpurath", "Fatma Refaat", "Navin Devaraj", "Aneesa Abdul Rashid", "Noor Airini Ibrahim" ], "abstract": "Background: Physical restraints (PRs) are frequently used in adult critical care units to protect staff and prevent self-harm, despite the fact that they represent significant safety risks. Restraint complications may have an impact on the patient's long- and short-term outcomes. This study aims to examine the recent evidence on the use of PR in adult critical care. Method: This integrative review included the studies published between January 2009 and December 2019 and the literature search was conducted in July 2020. The databases searched included EBSCOhost, Ovid, ProQuest, PubMed, Wiley Online Library, SCOPUS, and ScienceDirect. The keywords included in the search were restraint, critical care, intensive care, ICU, mechanical ventilation, intubation, nursing, and experience. A checklist based on the CASP checklist and the JBI Critical Appraisal Tool was used to assess the methodological quality. Results: The findings were evaluated and summarized into seven key topics after twenty-one publications were found to be evaluated. i) High prevalence of PR application in adult critical care unit; ii) determinants of PR applications; iii) types of PR in adult critical care units; iv) decision maker of PR; v) moral and ethical dilemma in PR application; vi) awareness and guidelines for PR applications; vii) common complications and use of sedation, analgesics, antipsychotic drugs in PR application. Conclusion: The number of days PR is used is related to the risk of an adverse event. In order to standardize nursing practice, ICU nurses require greater training on the ideas of PR use. Evidence-based recommendations will assist critical care nurses in making the best judgments possible concerning the use of PR.", "keywords": [ "physical restraint", "critical care", "mechanical ventilation", "immobilization" ], "content": "Introduction\n\nDelirium and increased anxiety are common issues in ICU patients, especially those who are on mechanical ventilation. Disturbing actions that lead to the endotracheal tube dislodging or interfering with other medical devices place these people at a higher risk of self-harm and even death.1,2 Critically ill patients who are receiving intensive care are under a great deal of stress. A number of factors can contribute to the severity of the underlying disease, including the use of medical equipment, pain, and anxiety. Maintaining the highest degree of patient comfort and safety is crucial to the patient’s care in these situations.3 Chemical and physical restraints (PRs) are frequently used in the intensive care unit (ICU) when caring for critically ill patients to reduce patient discomfort and anxiety. However, PRs result in considerable safety risks.3,4\n\nThe use of any mechanical device or physical materials, or equipment that is attached to or around a patient’s body and that person cannot easily remove, restricting the patient’s range of motion or regular access to his or her body, is referred to as a PR.5 It’s uncertain whether the usage of restraints is based on scientific facts or on custom and culture.6\n\nThe patient who is physically restrained faces various risks, including lactic acidosis, incontinence, bone fracture, a sense of powerlessness and vulnerability, limited ROM, hospital-acquired pressure injury, venous thromboembolism, stress cardiomyopathy, respiratory depression, aspiration, choking, asphyxia, and even death.7,8 The best ethical justification for PRs is that they prevent people from harming themselves.9 PRs are often used despite the lack of evidence supporting their effectiveness.10 PR practices have been studied in a number of countries. As a result, having a thorough understanding of current facts and practice is critical.\n\nWith the use of the following questions, this review will look into the best available evidence on the use of PR in adult critical care in regard to: 1) prevalence of PR; 2) factors that influence PR; 3) the role the nurse plays in the implementation of PR; 4) the nurse’s experience caring for the patient with PR; and 5) the complications of applying PR.\n\nThe goal of this study is to conduct a thorough assessment of the available evidence on PR in the adult critical care unit. As a result, an integrative review was carried out. This integrative review includes quantitative, qualitative, mixed methodologies, and quality improvement projects from the accessible literature, referring to studies published between January 2009 and December 2019 and a literature search was conducted in July 2020.\n\nEBSCOhost, Ovid, ProQuest, PubMed, Wiley Online Library, SCOPUS, and ScienceDirect were among the databases searched. Restraint, critical care, intensive care, ICU, mechanical ventilation, intubation, nurses, and experience were utilized as search terms. The “AND” and “OR” Boolean operators were employed.\n\nTo map the search process, a flow diagram was used (Figure 1). Initially, the database identified 3840 articles, and 852 duplicates were removed. From the remaining articles, 1205 were excluded electronically using exclusion criteria. Out of 1783, articles were found relatively relevant to the topic and 1498 articles were eliminated after limiting the search using the Boolean operator “AND”. A further seven were sourced from bibliographies and three of them were considered relevant to the screening. A total of 288 articles were considered for the title and abstract screening. 238 non-relevant articles were excluded and 50 full-text articles were retrieved. The screening process was done by two people independently. Twenty-nine of them were excluded after screening the full text and finally, 21 articles were considered for synthesis. EndNote X9.3.3 for Windows was used to manage the articles.\n\nInclusion criteria\n\nOnly peer-reviewed research involving patients or nurses in all types of adult ICUs was evaluated for this review, which was solely focused on the use of PR in adult critical care units. All full-text English papers with various techniques (quantitative research, qualitative studies, and quality improvement programs) are included.\n\nExclusion criteria\n\nEndNote X9.3.3 electronically removed words in the title that contained animals (e.g. rat), psychiatric, neonatal, and pediatric. Restraint and intensive care unit/critical care unit/ventilated/intubated/nurses/experience were used with the Boolean operator “AND” to narrow the search. Non-relevant papers were eliminated by manually scanning the title and abstract for exclusion criteria such as animal research, psychiatric/pediatric/neonatal units, and so on. The decision to include an article in the final stage was based on the study’s eligibility36 and the content’s relevance. Review papers, editorials, conference abstracts, and commentaries were also excluded from this review.\n\nEligibility of data\n\nThe systematic review of literature for a particular intervention, condition, or issue is at the heart of evidence synthesis. The systematic review entails a number of sophisticated procedures that include an analysis of the existing literature (that is, evidence) and a judgment of the effectiveness or otherwise of practice.11 The initial assessment of articles was done using the Critical Appraisal Sklls Programme (CASP)12 checklist tool. This paradigm was chosen because it allowed for a systematic and rigorous approach to analyzing and evaluating article quality that could be used in both quantitative and qualitative methodologies.13 The initial papers were screened using the inclusion/exclusion criteria. The literature was evaluated using the CASP tool’s three major questions: i) Is the research valid? (ii) What were the outcomes? (iii) Will the findings be usefully locally?.12 The articles answered sufficiently for these three questions were further considered. According to Whittemore & Knafl,14 two quality criterion instruments should be utilized during the review process to assure the authenticity, methodological quality, and informative value of the included research. Because of the wide sample frame, evaluating the quality of the research paper in integrative reviews might be difficult. The articles were re-evaluated using the more specific questions from the CASP12 checklist tool and JBI (Joanna Briggs Institute) Critical Appraisal Tool.11,36\n\nThe CASP tool and JBI Critical Appraisal Tool includes a set of detailed questions to enhance visualization of the data and to simplify this complex comparison of CASP tool and JBI Critical Appraisal Tool, a common checklist was adapted. Each article was assessed using the adapted checklist and used effectively to analyze the articles clearly and succinctly. While these checklists were designed to assess qualitative research papers, they were adjusted to include the essential criteria stated in both the CASP tool and the JBI Critical Appraisal Tool for a qualitative and quantitative approach. The modified checklist includes a clear aim, methodology, design, recruitment, data collection, researcher and participant relations, participants and their voices, ethical considerations, data analysis and rigor, findings, and research value.\n\nData analysis\n\nBy permitting the use of a combination of studies with diverse methodologies, the integrative review method is the only strategy that has the potential to play a larger role in nursing evidence-based practice.14 Data analysis in research reviews necessitates the ordering, coding, categorization, and summarization of primary source data into a cohesive and integrated conclusion regarding the research problem.15 Integrative evaluations draw on a variety of data sources to provide a more complete picture of the subject at hand. Combining many data sources, on the other hand, is difficult and time-consuming.14 These challenges are approached by organizing data in a manageable framework. According to Whittemore & Knafl,14 data reduction, data presentation, and data comparison are all part of the data analysis phase of integrative reviews. The phases of data reduction and presentation are extracting and coding data to be organized into a manageable framework, which will then be shown to increase the visualization of their linkages and patterns. The systematic categorization of data into patterns, themes, and variations is judged a suitable approach to this review framework due to the varied data from various approaches. And they proposed a consistent comparative approach for comparing integrative reviews, which is used in this review and given (Table 2) along with main themes generated from the literature.\n\n\n\n• Effect of Interventional Educational Programs on Intensive Care Nurses’ Perception, Knowledge, Attitude, and Practice about PRs.\n\n○ Modify negative attitudes of intensive care nurses regarding the use of PRs.\n\n\n\n▪ A quasi-experimental study with a pre-/post design with the census method\n\n○ All nurses (n = 30) working in the ICUs had at least a bachelor’s degree and 1 year of working experience in ICUs.\n\n\n\n▪ Interventional educational programs about the use of PR improved the level of knowledge and perception and led to a positive attitude and improved practice in nurses in the ICUs.\n\n▪ All participants (100%) had used PRs before, and 20 of them (66.7%) had experienced complications caused by PRs.\n\n\n\n▪ Investigating influencing factors of PR use in China ICU: A prospective, cross-sectional, observational study.\n\n○ Characterized the use of PRs in three ICU (ICUs) in a general hospital in Nantong, China.\n\n○ Explored risk factors potentially related to PR use.\n\n\n\n• Prospective, cross-sectional, observational study\n\n○ 312 patients from three ICUs at a general hospital\n\n\n\n▪ 61.2% of the patients were restrained. 56.5% of the patient’s bilateral upper limb restraints were used, and 22.3% of four-point restraints.\n\n▪ The median length of PR use was 20 shifts (8hrs shift). 42.9% of patients were continuously restrained for more than 24 hours. In 75.9% of the cases, PR was used only once, and for the remaining, it was reapplied during the ICU stay.\n\n▪ For 51.3% of patients, observational data was recorded in nurses' notes. There is no data for removal time, patient responses, or complications. Less than 1/3 of patients gave informed consent for PR.\n\n▪ Mostly restraint aimed to prevent the accidental removal of the medical devices to decrease any threat to the airway.\n\n▪ Use of analgesics as an independent protective factor for PR use. The nurse’s record reflects a need for standard guidelines and policies for PR use in hospital ICUs in China. Age, delirium, mechanical ventilation, and analgesic use are risk factors related to PR use.\n\n\n\n• Nurses’ perceptions and practice of PR in China.\n\n○ Identify the perceptions and practice of PR in China.\n\n\n\n▪ Mixed methods Descriptive study Qualitative interviews A quantitative cross-sectional survey\n\n○ 18 nurses were interviewed. Of 330 nurses surveyed,\n\n\n\n▪ Quantitative findings: PR is commonly used for patient safety. It is more often used in ICUs than in medical-surgical wards. more often used on the night shift.\n\n▪ Qualitative findings: staff shortages and heavy workload were the most common reasons for PR. In-service/education is needed to minimize PR use in China.\n\n\n\n• The prevalence and incidence of restraint use in a Canadian adult ICU: A prospective cohort study.\n\n○ Determine the extent of PR use in an urban teaching ICU.\n\n○ To identify patient-specific factors that may contribute to the application of PRs.\n\n○ Explore nurses’ rationale for use.\n\n\n\n▪ Mixed-methods study. A prospective cohort design was used to collect patient data, and semi-structured interviews were used to collect nurse data.\n\n○ In total, 30 permanent ICU staff nurses and 72 patients were admitted during the study period in the mixed medical-surgical ICU.\n\n\n\n▪ Quantitative Data: Gender is not a contributing factor to the use of PRs. 75% of patients are restrained during their hospitalization. The prevalence rate was 358 restraint days per 1,000 ICU days.\n\n▪ Four self-extubations were documented during the study (3 patients without restraint and one documented as a fear of being restrained). The presence of an endotracheal tube increased the odds of PR application eight-fold. Low nurse-to-patient ratios increased the odds of restraint use. All opioids (95%) or midazolam administration (95%) increased the odds of restraint use.\n\n▪ Qualitative data: nurses’ interviews\n\n▪ According to 57% of nurses, patients are restrained prior to interference with medical equipment. They did not consult with the physician before they restrained the patient. They had no alternative but to use PR to prevent extubation.\n\n▪ Many of them expressed negative feelings about using PRs. Most nurses had empathy for tied patients and employed creative strategies to reduce their use or minimize the impact on the patient’s freedom.\n\n▪ Deciding to remove restraints is dependent on patient behavior.\n\n▪ The decision to remove the restraint was made when the patient demonstrated “cooperation with the nurse, was awake and aware of the surroundings,” and did not try to touch the tube, or when the patient was ready to have the endotracheal tube removed.\n\n\n\n• Use of PRs in Dutch ICU: A Prospective Multicenter Study.\n\n○ Characterize the use of PR in ICU.\n\n○ Prevalence, adherence to protocols, and correlates of the use of PR was determined.\n\n○ For comparisons between ICUs, adjustments were made for differences in patients’ characteristics.\n\n\n\n▪ A prospective, cross-sectional, observational multicenter study with two visits to each ICU\n\n○ The sample included 379 patients and 346 nurses from 25 different Dutch ICUs.\n\n\n\n▪ 23% were physically restrained during the researcher's visit. In 11 units (44%), the use of PR was more frequent, although this finding was not significant. 31% of nurses reported the use of a protocol for PR.\n\n▪ The risk of PR is increased in patients with delirium or coma who cannot communicate verbally and are receiving psychoactive or sedative medications. There is no independent relationship between PR use and gender, illness severity, or nurse-to-patient ratio.\n\n\n\n• Predictors of PR use in Canadian ICUs.\n\n○ Describe patterns of PR use in mechanically ventilated patients (prevalence, number of days of use, number of episodes of use).\n\n○ Identify patient, treatment, and ICU/hospital characteristics associated with PR use and number of days of use.\n\n\n\n▪ A secondary analysis of a prospective observational study\n\n○ A sample of mechanically ventilated patients was admitted to 51 Canadian ICUs.\n\n\n\n▪ PR was used with 374/711 patients. The average use of PR is 4.1 (SD 4.0) days (1 to 26 days). 83% applied only once, while the remaining reapplied multiple times during their ICU stay.\n\n▪ Restrained patients experienced more adverse events and received higher daily doses of sedatives, analgesics, and antipsychotics. Use of sedative, analgesic, and antipsychotic drugs, agitation, heavy sedation, and the occurrence of an adverse event predicted PR use or the number of days used.\n\n\n\n• PRs practice in adult ICU in Egypt.\n\n○ Investigate the practices of PRs among CCNs in El-Mansoura City, Egypt.\n\n\n\n▪ A descriptive cross-sectional design with repeated observations\n\n○ A convenience sample of two groups Group 1 consists of 275 physically restrained ICU patients. Group 2: 153 ICU nurses with at least one year of experience in one of the ICUs\n\n\n\n▪ Restrained sites assessment is not documented in patients' records. Nurses’ self-report: PR is commonly (68%) used in ICUs.\n\n▪ Individuals responsible for the decision to apply PR are nurses (58.2%), followed by physicians and nurses (41.1%).\n\n▪ The most common PR behavior is an attempt to remove medical equipment (79.1%). 64.7% for resisting treatment or care and 46.4% for the attempt to get out of bed. Ensuring patient safety (96.1%) is the most important rationale for applying PR.\n\n▪ Upper and lower limb restraints (37.9%) are the most common PR. Nurse-patient ratios and nurse workloads strongly contribute to the use of PR.\n\n▪ Documentation of PR and assessment of restrained body parts is maintained by experienced nurses rather than novice nurses.\n\n\n\n• Examination of Ethical Dilemmas Experienced by Adult ICU Nurses in PR Practices.\n\n○ Determine perceptions of ethical dilemmas by nurses in the application of PR.\n\n\n\n▪ A descriptive and cross-sectional study\n\n○ There are 55 intensive care nurses working in two hospitals' adult ICUs.\n\n\n\n▪ 92.7% of nurses experienced the application of PR. 85.5% received training on ethics; 78.2% did not participate in training regarding ethical dilemmas. 94.5% of nurses reported that PR must be applied in ICUs.\n\n▪ According to 70.9% of nurses, the decision of PR was jointly by the nurse and the physician and 25.5% by the physician alone. According to 65.5% of nurses, no family consent was taken for PR. 63.6% did not hesitate over PR.\n\n▪ The reasons for PR are to prevent falls (25.4%), harming themselves (25.4%), removing the tubes (18.5%), maintaining the posture of the patient (3.8%), applying medical treatment (13.0%), and calm down the patient (13.9%).\n\n▪ 36.4% of nurses felt difficulty in deciding PR use and experienced ethical dilemmas.\n\n\n\n• Restraints in ICU-A mixed method study.\n\n○ Provide a detailed description of the use of restraints in three ICU.\n\n\n\n▪ Mixed methods—quantitative observational data and qualitative in-depth individual interviews\n\n○ 5 medical practitioners and 15 registered nurses from 3 ICUs. There were 219 patients observed.\n\n\n\n▪ Quantitative results: 1:1 was the nurse-patient ratio. 48.4% of the patients were restrained. 21.46% of patients were on analgesics and/or sedatives. 21.46% were restrained but not sedated. Patients were restrained for an average of 9 days (between 1 and 53). Ineffectively tied to nine patients\n\n▪ Qualitative findings: restraint, a balancing act: all agreed that there is a place for the use of restraints in the ICU. Patients’ agitation needs to be assessed before PR.\n\n▪ Proper PR use is described as a “balancing act” between its benefits and disadvantages. More than half of them stated that PR is primarily used to allow clinical staff to leave the patient unattended.\n\n▪ Mostly, nurses are the decision-makers for PR. Not required Doctor’s prescription & they reluctant for that. Communication between the doctor, the patient, and their families is critical.\n\n\n\n• CCNs’ decisions regarding physical restraints in two Canadian ICUs: A prospective observational study.\n\n○ Describe reasons for physical restraint application, alternative measures attempted, if any, prior to PR application, and reasons for restraint discontinuation.\n\n\n\n▪ A prospective, observational study\n\n○ Medical records of 141 patients from two medical-surgical ICUs\n\n\n\n▪ Patients were mostly restrained using wrist restraints (91%). Four-point (all four limbs) restraints (.4%) and unilateral wrist-ankle and wrist-mitten restraint combinations are used infrequently (.2%). 83% of restraints were applied on the preceding night shift.\n\n▪ Agitation 43%, restlessness 17%, and restraining as a precautionary measure to prevent accidents. In 33%, alternative measures were considered before PR. Device removal and maintaining patient safety 17% are the common reasons for PR. In 21% of patients, chemical restraint was used as an alternative.\n\n▪ Restraint discontinuation was recorded for 57% patients, with the most common being a calm and cooperative patient for more than two hours.\n\n\n\n• PR Use in Turkish ICU.\n\n○ Determine intensive care nurses’ reasons for the application and removal of PR.\n\n○ Determine PR patterns used in Turkey ICUs.\n\n\n\n▪ Descriptive and cross-sectional research designs.\n\n○ 190 nurses work in the ICUs of 7 hospitals.\n\n\n\n▪ There is no set policy or guidelines for restraint application practice. 84.7% PR without a physician’s order. 59.5% are not documented in nursing notes. Wrist and ankle ties are often (59.5%) used for PR. There was no difference in the frequency of restraint use between day and night shifts.\n\n▪ 36.8% of complications were reported, and the most common one was skin breakdown. Maintenance of the placement of medical devices is the main (86.8%) reason for PR.\n\n▪ Improved mental status is an important reason for the removal of restraints (68.9%).\n\n\n\n• PR use in ICU across Europe: The PRICE study.\n\n○ Examine PR practices across European ICUs.\n\n\n\n▪ Point prevalence survey conducted prospectively\n\n○ In 9 countries, 34 general (adult) ICUs were observed and examined for charts or medical records by registered nurses and doctors. Out of 669 patients, physical and chemical restraints were used on 566 patients.\n\n\n\n▪ The extent of PR varied across units. use of PR not related to the time of the week. PR is more likely in ventilated and sedated patients in the unit with a lower daytime nurse-patient ratio.\n\n▪ Restlessness and delirium are the most common reasons for PR. Commercial wrist restraints are the most common. Patient safety is the dominant rationale for PR.\n\n\n\n• PRs in ICU: a national questionnaire survey of PR use for critically ill patients undergoing invasive mechanical ventilation in Japan.\n\n○ Describe the frequency of PR use among Japanese patients undergoing mechanical ventilation.\n\n○ To verify the hypothesis that insufficient human resources have increased the frequency of PRs.\n\n\n\n▪ Cross-sectional online open-anonymous survey\n\n○ Nurses in the ICU with a patient-to-nurse ratio of no more than 2.\n\n\n\n▪ PR is commonly used among mechanically ventilated patients in Japan. PR use varies among ICUs, irrespective of human resources and the proportion of beds in private rooms.\n\n▪ A systematic approach is needed to reduce PR use in mechanically ventilated patients.\n\n\n\n• The effect of PR on neurovascular complications in ICU.\n\n○ Investigate the effect of PR on the occurrence of neurovascular complications and their rate.\n\n\n\n▪ A prospective observational cohort study\n\n○ 90 patients from anaesthesia and the internal ICU.\n\n\n\n▪ PR was used in the first 24 hours of hospitalization for 85.6% of patients.71.1% of patients had restraints on both wrists, with 17.8% having restraints on the right wrist and 11.1% having restraints on the left wrist. 71.6% was a roll of gauze, 17.6% was tough cuff material, and 10.8% was a green foam tie.\n\n▪ After the first 24 hours, complications increased. A roll of gauze was used most commonly on the wrist. The roll of gauze and tough cuff material types led to an increase in redness.\n\n▪ The duration of PR increases the risk of neurovascular complications. Nurses did not regularly check the restrained wrist and did not focus on the peripheral circulation.\n\n\n\n• Psychotropic drug use in physically restrained, critically ill adults receiving mechanical ventilation.\n\n○ Characterize psychotropic drug interventions before and after the use of PRs in critically ill adults receiving mechanical ventilation.\n\n\n\n▪ A single-centre, prospective, observational study.\n\n○ 93 patients who were admitted to the ICU\n\n\n\n▪ All patients have 2-point Posey soft wrist restraints. Two patients started with the use of 4-point restraints and subsequently transitioned to 2-point restraints.\n\n▪ The indication for PR was documented for 91 patients, and 2 patients were not documented. The most common documented indication was the prevention of treatment interference.\n\n▪ The median duration of restraint was 21 hours (interquartile range, 9–70 hours); 43 patients (48%) were restrained for more than 24 hours. More patients received psychotropic drugs after PRs than before.\n\n▪ Administration of opioids was more common after the use of PRs and accounted for more drug interventions.\n\n▪ More patients received a psychotropic drug intervention after physical restraints were applied than before (86% vs. 56%). Administration of opioids was more common after the use of physical restraints (54% vs 20%) and accounted for more drug interventions (45% vs 29%).\n\n▪ 16% remained over sedated and remained agitated before and after physical restraint. However, after the application of physical restraint, 20% of patients became over sedated and 6% less sedated.\n\n▪ 10% of the patients become more agitated, compared to 8% less agitated.\n\n\n\n• Determinants of nurses’ use of PRs in surgical ICU patients.\n\n○ Describe nurses’ determinants of initiation and discontinuation of restraints in surgical ICU patients.\n\n\n\n▪ Qualitative descriptive design.\n\n○ 13 nurses working in the Surgical ICU.\n\n\n\n▪ The initiation or discontinuation of PR is determined by the threat to patient safety (interruption or removal of monitoring and therapeutic devices). Surgical ICU experiences variable degrees of altered mental status. Restraints are used as an intervention to reduce self-extubation. Restraints are occasionally used to prevent injury to the staff because of patient behavior.\n\n▪ Nurses identify patient-specific behaviors, including orientation and functional capacity, that determine restraint use. Nurses describe patient behaviors that predict the successful discontinuation of restraints without perceived negative effects. Thoughtful consideration is given to delirium patients due to the inconsistent responses to restraint use experienced by this patient population.\n\n▪ The nurse’s ability to be vigilant in-patient care provides an atmosphere of security. Targeted nurse-driven interventions help in reducing restraint use, especially in delirious patients.\n\n\n\n• Using a decision wheel to reduce use of restraints in a medical-surgical ICU.\n\n○ Decrease use of restraints in a medical-surgical ICU.\n\n○ To determine if a decision support tool is useful in helping bedside nurses determine whether or not to restrain a patient\n\n\n\n▪ A pilot study with a quasi-experimental design was conducted.\n\n○ Bedside nurses from the medical-surgical ICU\n\n\n\n▪ In month one, 64 device dislodges occurred and 38% of the patients were restrained. During months 2 to 4, 51 devices were dislodged, and 12% of the patients were restrained.\n\n▪ During the study, the use of restraints was reduced by 32%. There is a significant difference in restraint incidence before and after the use of the RDW, and there are no appreciable differences between the day shift and the night shift. For months 2 to 4, the RDW was used for 28.6%.\n\n▪ 81% strongly agreed that the RDW was easily accessible. 62% slightly agreed that the RDW was useful in making decisions about the use of restraints.\n\n▪ According to 85% of participants, the primary rationale for restraints is to prevent people from pulling out ET tubes. 77% felt comfortable removing restraints without a physician's order.\n\n▪ 84% responded to using RDW on a regular basis. Many explained that an additional resource would also be beneficial and wanted to rely on their own clinical judgment on restraints.\n\n\n\n• Factors behind ethical dilemmas regarding PR for CCNs.\n\n○ Explore factors behind ethical dilemmas for CCNs overusing PR for patients.\n\n\n\n▪ Qualitative study using conventional content analysis approach.\n\n○ The 17 CCNs were purposefully recruited from the 4 ICUs.\n\n\n\n▪ The outcome of using PR is the factor behind ethical dilemmas for CCNs.\n\n▪ PR is used to ensure patient safety and prevent damage to patients and others. They were compelled to ignore patient rights and autonomy and use PR because of heavy workload and ward crowdedness.\n\n▪ Other than PR, there is no choice but to use it to ensure patient safety.\n\n▪ PR mentally damages patients and causes them problems such as fear of the ICU, depression, anger, aggression, restlessness, agitation, and anxiety.\n\n▪ The risks of not using PR are delays in treatments, long hospital stays, falls, tissue trauma, pulling or removal of connections, heavy treatment costs, and even death.\n\n▪ Nurses are not authorized to use PR without a medical order, but restraints are used without a physician’s order. Nurses perceive low support from physicians if a patient experiences a fall.\n\n▪ Nurses felt conflicted due to the violation of patient rights and experience. Some of them felt uncertainty even after leaving the hospital.\n\n\n\n• Nurses' Information, Attitude and Practices towards use of PR in ICU.\n\n○ Determine the knowledge, attitude and application levels of nurses working in critical care units about PR applied on patients.\n\n\n\n▪ Descriptive and correlation studies\n\n○ 158 nurses who work in medical-surgical intensive ICUs in hospitals and graduated from the faculty of health sciences\n\n\n\n▪ Nurses deciding on the use of PR have higher scores than physicians. Nurses' attitude scores were found to be higher than those of physicians. Physicians' practice scores were found to be higher than those of nurses.\n\n▪ Nurses have a sufficient level of information but negative attitudes and are insufficient in practice.\n\n\n\n• Reducing Use of Restraints in ICU: A Quality Improvement Project.\n\n○ Reduce and sustain the restraint rates to less than the national database means rates for all 5 ICU\n\n\n\n▪ A quality improvement process Quantitative observational data from five ICUs with nine non-validated survey tools\n\n○ 119 ICU nurses and ICU data from five ICUs\n\n\n\n▪ The Restraint collaborative lowered the restraint rate. Bedside nurses engaged in evidence-based practice using the latest evidence-share willingly with colleagues. The restraint culture shifted from most patients to minimal use of restraints.\n\n▪ The use of restraints was added to the daily-goals checklist and the need for restraints was assessed during daily inter-professional rounds.\n\n▪ There is a lack of alternatives as a barrier to the removal of PRs. PRs may increase moral distress for nurses who care for these patients.\n\n\n\n• Impact of a Restraint Management Bundle on Restraint Use in an ICU.\n\n○ Explored the impact of a restraint management bundle on restraint use, quality, and safety outcomes.\n\n\n\n▪ Secondary data analysis of the pre and post cohort groups\n\n○ Data was extracted for 2701 patients from a 24-bed general ICU. There are 65 clinical RNs and 12 nursing care partners. Data from the EMR is used. In the pre-cohort group of 1339 patients and the post-cohort group of 1362 patients,\n\n\n\n▪ There were 24.3% of patients restrained in the pre-cohort group compared to the post-cohort group (20.9%). The number of restrained patients per patient-day averaged 0.075 for the pre-cohort group compared with 0.059 for the post-cohort group. The number of restraint episodes per patient day averaged 0.191 for the pre-cohort group, compared with 0.133 for the post-cohort group.\n\n▪ The average ICU length of stay was 3.64 days in the pre-cohort group compared with 3.60 days in the post-cohort group.\n\n▪ The result shows a significant reduction in restraint use and duration, although ICU length of stay remained stable over time.\n\n\nResults\n\nTwenty-one articles were found to be suitable for this review (Table 2). The studies were conducted in China, Japan, Turkey, Egypt, Iran, Canada, South Africa, the United States of America, the Netherland, and Europe. The quantitative data was gathered from various sources via observation and survey, while the qualitative data was gathered through face-to-face interviews. Each study has a different sample size.\n\nThe following are some of the themes that developed from the literature: i) high prevalence of PR application in adult critical care units; ii) determinants of PR applications; iii) types of PR in adult critical care units; iv) decision maker of PR; v) moral and ethical dilemma in PR application; vi) awareness and guidelines for PR applications; vii) common complications and use of sedation, analgesics, antipsychotic drugs in PR application.\n\nThe fact that PRs are most commonly employed in the adult critical care unit was obvious. Descriptive research in China found that ICUs used PRs more frequently than medical-surgical wards.16 In this review, we found that 23% to 75% of the patients were restrained during their stay in the critical care unit.4,17–19 Critical care nurses (CCNs) (68%) reported that PRs were most commonly used in ICUs.20 According to 94.5% of CCNs physical restraint must be applied in ICU.21 Most nurses working in critical care units experienced (68% to 100%) the use of PRs.1,21 According to Langley et al.,22 all of the participants in their study agreed that PRs have a place in the ICU. And they stated that, before using PR the patient’s agitation must be assessed.\n\nAccording to a study conducted in Canada by Luk et al.,23 83% of restraints were employed on the night shift and Jiang et al.16 support that PR is more commonly used on the night shift. Turgay et al.24 on the other hand, found no variations in the frequency of PR use between night and day shifts. PRs were utilized by 57% of nurses prior to the patient’s interference with medical equipment.17\n\nFive studies looked into nurse-to-patient ratios. According to Kandeel & Attia,20 nurse workloads play a significant effect on the use of PR. Benbenbishty et al.25 found that PRs are frequently utilized for sedated and mechanically ventilated patients in units with a lower daytime nurse-to-patient ratio. And according to Hamilton et al.17 restraint use was more likely with low nurse-to-patient ratios. The nurse-to-patient ratio was mentioned in the other two studies, but there was no discussion of the relationship between the ratio and PR applications.18,22 Regardless of personnel resources or the number of beds in private rooms, PR usage varied among ICUs in a cross-sectional online survey conducted in Japan.26\n\nAccording to Ertuğrul & Özden,27 out of total restrained patients, 85.6% were initiated in the first 24 hours of their hospitalization. The duration of PRs varied from hours to days. An article from Canada explored the median duration of restraint as 21 hours28 while a study from China found that patients stayed restrained for up to 20 shifts (8 hrs shift).4 According to Langley et al.22 and Luk et al.19 the patients were restrained for an average of 9 and 4.1 days respectively. In a study, Hamilton et al.17 found a prevalence rate of 358 restraint days per 1,000 ICU days. From two observational studies, out of total restrained patients, 42.9% to 48% were restrained for more than 24 hours.4,28 Repeated application of PRs highlighted in some studies however, in most of the cases (75.9% - 83%) the PR was applied only once during ICU stay.4,19\n\nDocumentation is vital when a nurse takes care of a patient. It will protect them from legal consequences arising from the outcome or lack of restraint. In a study, patients’ observational data were recorded in 51.3% of nursing notes and no data for removal time, patient responses, or complications were accurately recorded.4 The indication for PR was reported for 91 patients and two individuals were not documented, according to Guenette et al.28 More than 59% had no documentation of PR as per Turgay et al.24 According to Kandeel & Attia,20 patient records do not contain information about the assessment of restraint sites. According to them, experienced nurses maintained better documentation regarding PR application and assessment than novice nurses.\n\nMany studies support the lack of documentation of PR applications among patients.4,20,24,28 Hence, the prevalence rate of PR applications can be more than the available data suggests. The high prevalence rate of PRs shows its importance in the adult critical care unit, making it inevitable in the care of patients.\n\nThe primary justification for restraints is patient safety. PRs are designed to prevent the unintentional removal of medical or therapeutic devices, hence reducing the threat to life.4,16,17,20,21,23,24,29–31 The presence of an endotracheal tube raised the probabilities of PR application eight-fold, according to Hamilton et al.17 who also emphasized the incidence of self-extubation in patients who were not restrained. Restraints were utilized as a preventative measure to prevent self-extubation.29 The most prevalent documented indication in a observational study was the prevention of treatment interference.28 Other indications for PR include prevention of falls or attempts to get out of bed, maintenance of posture & calming down the patient, and managing treatment resistance or care.20,21\n\nIn this review, two studies show heavy workload and ward overflow with staff shortages as common reasons for PR.16,31 According to the response of more than half of the samples in qualitative data collected by Langley et al.,22 PRs were used primarily for the benefit of the clinical staff and to leave the patient unattended. Nurses face difficulties to identify an alternative as a barrier to the removal of PRs to ensure patient safety.17,30,31 However, in a study, for 33% of patients, alternative measures were considered prior to PR, and in 21% of cases chemical restraints were used instead.23\n\nRestraints are sometimes employed to prevent injury to personnel or to oneself as a result of patient behavior such as agitation, delirium, restlessness, and varying degrees of impaired mental status.17,23,25,29 Patients with delirium or coma, who are taking psychoactive or sedative drugs, and who are unable to speak vocally, are at a higher risk of receiving PR.18 Establishing an alternative measure for reducing the use of PRs while ensuring patient safety remains a predominant challenge for nurses.\n\nPatient’s requirements and desires must be addressed when applying for PR. Due to the variable responses to restraint treatment in this patient population, special consideration is given to delirium patients. The nurse’s capacity to maintain vigilance in patient care creates a safe environment.29\n\nThe decision to release restraints is based on the patient’s behavior. Improved mental status (68.9%) is a vital indicator of the removal of restraint.24 Restraints were removed from 57% patients who were generally calm and cooperative for more than two hours.23 The nurses described that successful withdrawal of restraints without perceived negative effects is predicted according to patient behaviors.29 According to the CCNs, the decision to remove the restraint was made when the patient cooperated with the nurse, was awake and aware of their surroundings, and did not attempt to touch the tube, or when the patient was ready to have the endotracheal tube removed.17 Before stopping PR, however, it should be determined if there is a risk to the patient’s safety. Falls, tissue injuries, pulling or removing connections, delays in therapies, extended hospital stays, high treatment costs, and even death are all risks of not utilizing PR.31\n\nIn critical care units, bilateral upper limb restraints were most commonly used.27,28 ICU patients are also restrained using four-point restraints.4,20,24 Among 141 patients in Canada, most were restrained using wrist restraints (91%). All-four-limb restraints were used on a few patients (4%) and combinations of unilateral wrist-ankle and wrist-mitten restraints were rarely employed (2%).23\n\nBenbenbishty et al.25 explored the common use of commercial wrist restraints. In a study in Turkey, PR was used with tough cuff material, green foam tie, and a roll of gauze at a rate of 17.6%, 10.8%, and 71%, respectively. The roll of gauze was used most commonly on the wrist.27 Hence, it can be articulated that the type of PR depends on the need of the patient and the material available in the unit.\n\nThe majority of the research in this review supports the nurse’s role as the principal decision-maker in the application and removal of PRs. In Egypt, nurses were responsible for 58.2% of the choice to use PR, while 41.1% was decided by both physicians and nurses.20 According to Turgay et al.,24 84.7% of PR were applied without a physician’s order in Turkey and according to Balcı & Arslan,32 nurses deciding on the use of PR have higher scores than physicians. However, Yönt et al.21 stated that 70.9% were decided jointly by the nurse and the physician and 25.5% by the physician alone. Before restricting a patient in Canada, nurses did not confer with the physician.17 Nurses are the primary decision-makers in PR, according to Langley et al.22 from South Africa. Nurses in Iran are not allowed to use PR without a medical order; however, restraints are used without a physician’s order since nurses believe physicians are unsupportive if further complications arise from not using PR (e.g. if a patient falls).31 In California, 77% of nurses felt confident releasing restraints without a doctor’s order. Nurses wanted to rely on their own clinical judgment when determining whether or not to restrain a patient.30\n\nThe literature shows that nurses play a significant involvement in the decision to use restraints on patients. In this review, no studies mention the role of patients or their families. Inconsistencies in the role should be addressed with a standard guideline that specifies each individual’s role (physician, nurse, patient, or family), and it should be very clear about a physician’s written order for PRs.\n\nMoral distress may increase among the nurses who care for patients under PR.33 Many nurses voiced dissatisfaction with the use of PRs. Most of them empathized with restrained patients and established innovative ways to diminish PR use or lessen the impact on the patient’s freedom.17 The ethical issues for CCNs are caused by the outcomes of utilizing PR. Because of the overwhelming workload and nursing unit overflow, they felt obligated to disregard patient rights and autonomy in favor of PR. Due to the breach of patient rights and experience, nurses were conflicted. Even after leaving their shift, some of them felt uncertain.31 Nurses encounter ethical issues due to harm and benefit principles, according to Yönt et al.21 In their study, according to 65.5 % of nurses, no family consent was obtained for PR, and 63.6 % of nurses have no reservations about PR.\n\nIn a Chinese study, only about a third of restrained patients gave informed consent for PR.4 Communication between physicians, patients, and families is paramount. The proper application of PR should be a balancing act between its benefits and drawbacks.22 These studies show the moral and ethical dilemmas facing nurses in the application of PR. Appropriate organizational policies will help nurses to overcome moral and ethical dilemmas. In addition, adequate training and education may be needed to prevent the psychological impact on the nurses.\n\nA quality improvement project conducted in the US33 shows a reduction in restraint rate after restraint collaboration and the restraint culture shifted from heavy to minimal use. The use of restraints was included in the daily-goals checklist, and the need for restraint was assessed daily during the multidisciplinary rounds. Furthermore the researcher added that, nurses who engage in evidence-based practice use the most up-to-date evidence and gladly share it with their colleagues. The impact of a restraint management bundle in an ICU on restraint utilization was studied by Hall et al.34 When compared to the pre-cohort group, there was a reduction in the total number of restraint patients in the ICU in the post-cohort group (24.3% vs 20.9%). The average number of restrained patients per patient day decreased among the group (0.075 vs 0.059), and the average of restraint events per patient day also decreased (0.191 vs 0.133). According to the data, restraint use, and duration were reduced dramatically. The length of stay in the ICU, on the other hand, remained consistent over time (3.64 vs 3.6 days).\n\nTargeted nurse-led interventions can help reduce the usage of restraints, especially in delirious patients.29 Hevener et al.30 conducted a quasi-experimental study in an ICU with the implementation of a restraint decision wheel (RDW) to reduce the usage of restraints, and the results demonstrate that restraints are gradually reduced in critical care units. In the first month, 64 devices were dislodged, and 38% of the patients were restrained; in the second to fourth months, only 51 devices were dislodged and 13% were restrained. During the research, the restraint used decreased to 32%. This study suggested 81% of nurses strongly agreed that the RDW was easy to use, and 62% thought that it was helpful in deciding whether or not to employ restraints, and 84% of nurses supported using the RDW on a regular basis. Many of them, however, stated that having another resource would be good.\n\nIn a descriptive and correlational study regarding PR, physician’s practice scores were found to be higher than those of nurses. Nurses have a sufficient level of information regarding restraint but have negative attitudes towards it. However, nurses’ attitude scores were found to be higher than those of physicians. And in practice, nurses’ skillset is lacking/insufficient.32 This opened a floor for the training need of nurses about PRs. Ahmadi et al.1 conducted Interventional Educational Program for ICU nurses to modify negative attitudes regarding the use of PRs. It leads to a positive attitude and improved the level of knowledge, perception, and practice among them.\n\nIn the descriptive and cross-sectional study, Yönt et al.21 concluded that 36.4% of nurses felt difficulty in deciding on PR use and ethical dilemmas. The majority of them (78.2%) did not participate in training regarding ethical dilemmas. They recommended providing training for the nurses regarding ethical principles related to PR and PR application. In addition, they suggested having established policies for the use of PR in the ICU.\n\nIn a prospective multicenter study at Dutch ICUs, only 31% of nurses reported the use of a protocol for PR.18 In this review, two studies highlighted the need for a set policy or guideline for the restraint practice4,16 and Unoki et al.26 suggested in-service education and the establishment of a systematic approach to reducing PR use in mechanically ventilated patients. However, the effectiveness and possibility of de-escalation in critically ill patients were not tested in any of the studies in this review.\n\nThe overall analysis of the data in this theme shows the high need for training for nurses regarding PR application. The establishment of a protocol or guidance will be more beneficial in the management of a patient with restraint. Implementation of Restraint Management Bundle, restraint decision wheel, and Targeted nurse-driven interventions can improve restraint application in ICU.\n\nStudies in this review show the negative outcomes of PRs like neuromuscular complications, increasing the need for sedation, analgesics, and antipsychotics. Turgay et al.24 reported 36.8% complications and the most common one was skin breakdown. In Iran, 66.7% of the nurse had experienced complications caused by PRs.1 According to prospective observational cohort research, most issues increased after the first 24 hours. An increase in redness was generated by the roll of gauze and tough cuff material. The length of PR raises the risk of neurovascular problems. Nurses failed to pay attention to peripheral circulation and failed to check the restrained wrist on a frequent basis.27 Observational data from South Africa shows that 21.46% of patients with analgesics and/or sedatives. There were patients managed with restraint (21.46%) and no sedation.22\n\nMore patients obtained psychiatric medicines after PRs were applied, according to a single-center, prospective, observational study done in Canada. According to that study, following the adoption of PRs, opioid administration became more widespread, accounting for more pharmacological interventions. Prior to PR, fewer people were treated with psychiatric drugs than subsequently (56% vs 86%). The administration of opioids was more common after the use of PRs (20 % vs 54%) and accounted for more pharmacological interventions (29% vs 45%). Before and after PR, 16% of 50 patients remained oversedated and disturbed. However, 20% of individuals got overly sedated after receiving PR, whereas 6% became less sedated. Furthermore, 10% of patients become more agitated, compared to eight percent who become less agitated.28 According to Hamilton et al.,17 all opioid or midazolam administration (95 %) increased the likelihood of restraint use. Analgesic, sedative, and antipsychotic medication use, excessive sedation, agitation, and the incidence of an adverse event all predicted PR use or days utilized.19 However, according to Gu et al.,4 analgesic use can be an independent protective factor for PR use.\n\nPRs have a psychological effect on patients, causing issues including fear of the ICU, depression, anger, aggression, restlessness, agitation, and anxiety.19 The impact of PR on the outcome of the physical and psychological elements was disclosed in this overview of studies on this topic. Restraint complications may have an impact on the patient’s long-term and short-term outcomes. Those issues can be avoided by assessing the restraints on a frequent basis.\n\n\nDiscussion and implications\n\nThe magnitude of restraint utilization in adult critical care units is shown through a study of the current literature. PR is a common procedure in ICUs, according to this review. The review’s goal was driven by five questions, which were addressed and discussed under seven themes. Restraint is a technique for preventing the unintentional removal of medical or therapeutic equipment in order to reduce the risk of death.31 It is frequently used to prevent treatment interference.28 PR was extensively used to maintain medical devices among intensive care patients, and the type of PR was easily constructed by nurses.24 The most prevalent reason for restraint removal noted by nurses in a study was the recovery of mental status.1 CCNs will continue to utilize restraints until other ways have been scientifically proven to be effective in ICUs.24\n\nRestraints may be used as a result of a heavy workload and a shortage of staff nurses.16,31 A systematic approach is needed to reduce PR use among mechanically ventilated patients26 and implementation of the ABCDEF bundle can help avoid the use of restraints, prevent delirium and improve the management of delirium.33\n\nNurses encounter practical, legal, and ethical challenges when administering PR to patients. In-service training on the use of PRs and ethical principles should be given to nurses to ensure that they make the best option possible on ethical issues. Furthermore, it is suggested that an evidence-based institutional policy governing the use of PR in ICUs be established. Create awareness among ICU nurses about the detrimental effects of PR on patients.21\n\nThe importance of nurses as decision-makers in PR is highlighted in this literature. To improve patient safety, critical-care nurses should undergo in-service training on the use of PRs.20 To ensure a patient’s safety, the least restrictive technique with the least risk and the most benefit to the patient should be used. It is necessary to analyze and resolve any unmet care needs or concerns. Restraints should not be used for the prevention of falls or the management of patient behavior as a routine. Consider a medical condition or symptom that suggests the necessity for immediate protective intervention to avoid violent behavior or getting out of bed. Bring the patient closer to the nurse’s station so that he or she can closely observe. Adequate staffing is required to monitor the patients closely. Non-self-destructive behavior should be described to the patient in simple terms, and the patient should be able to articulate his or her understanding. People who are agitated as a result of pain or an adverse reaction to a current drug or medication require intervention instead of applying restraints.35 Evidence-based guidelines and educational interventions should be developed to support restraining practices.17 This review underlines the lack of research on patients’ experiences with restraint throughout their ICU admission. There are variations in the way restraint is prescribed and documented. Furthermore, a restraint protocol and guidelines have the ability to improve the critical care unit’s restraint culture and practice.\n\n\nConclusion\n\nThe use of PRs in the adult critical care unit is important for the treatment of life-threatening behavior. The number of days of PR usage is linked to the occurrence of an adverse event. As a result, long-term physical restrictions on patients should be avoided, and patients who are physically restrained should have a neuromuscular, circulatory, and skin assessment. The necessity for clear norms and policies for PR use is reflected in this review. Evidence-based guidelines will assist and support CCNs in making the best judgments possible about the use of restraints. To standardize nursing practice linked to the use of restraints for the protection of patient rights, and handling of ethical, legal, and emotional difficulties associated with PR, intensive care nurses require further education on the principles of restraint application. Furthermore, more study is needed to determine appropriate restraint alternatives.", "appendix": "Data availability\n\nNo data is associated with this article.\n\nFigshare: Quality assessment checklist for publications to be considered for review - Adapted from JBI and CASP, https://doi.org/10.6084/m9.figshare.21378213.v4. 36\n\nThis project contains the following extended data:\n\n- Table 1. doc (Example of quality assessment checklist).\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\nRepository name: PRISMA checklist used for integrative review, https://doi.org/10.6084/m9.figshare.21780632.v1. 37\n\nData are available under the terms of the Creative Commons Zero “No rights reserved” data waiver (CC0 1.0 Public domain dedication).\n\n\nReference\n\nAhmadi M, Bagheri-Saweh MI, Nouri B, et al.: Effect of Interventional Educational Programs on Intensive Care Nurses’ Perception, Knowledge, Attitude, and Practice About Physical Restraints: A Pre-/Postclinical Trial. Crit. Care Nurs. Q. 2019 Jan/Mar; 42(1): 106–116. PubMed Abstract \| Publisher Full Text\n\nReade MC, Eastwood GM, Bellomo R, et al.: Effect of Dexmedetomidine Added to Standard Care on Ventilator-Free Time in Patients With Agitated Delirium: A Randomized Clinical Trial. JAMA. 2016 Apr 12; 315(14): 1460–1468. PubMed Abstract \| Publisher Full Text\n\nHofsø K, Coyer FM: Part 1. Chemical and physical restraints in the management of mechanically ventilated patients in the ICU: contributing factors. Intensive Crit. Care Nurs. 2007 Oct; 23(5): 249–255. PubMed Abstract \| Publisher Full Text\n\nGu T, Wang X, Deng N, et al.: Investigating influencing factors of physical restraint use in China intensive care units: A prospective, cross-sectional, observational study. Aust. Crit. Care. 2019 May; 32(3): 193–198. PubMed Abstract \| Publisher Full Text\n\nMartin B: Restraint use in acute and critical care settings: changing practice. AACN Clin. Issues. 2002 May; 13(2): 294–306. PubMed Abstract \| Publisher Full Text\n\nTeece A, Baker J, Smith H: Identifying determinants for the application of physical or chemical restraint in the management of psychomotor agitation on the critical care unit. J. Clin. Nurs. 2020 Jan; 29(1-2): 5–19. Publisher Full Text\n\nZiaei M, Massoudifar A, Rajabpour-Sanati A, et al.: Management of Violence and Aggression in Emergency Environment; a Narrative Review of 200 Related Articles. Adv. J. Emerg. Med. 2018 Nov 29; 3(1): e7. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMantovani C, Migon MN, Alheira FV, et al.: Manejo de paciente agitado ou agressivo [Management of the violent or agitated patient]. Braz. J. Psychiatry. 2010 Oct; 32 Suppl 2: S96–S103. Portuguese. PubMed Abstract \| Publisher Full Text\n\nCrutchfield P, Gibb TS, Redinger MJ, et al.: The Conditions for Ethical Application of Restraints. Chest. 2019 Mar; 155(3): 617–625. PubMed Abstract \| Publisher Full Text\n\nMehrok S, Belsiyal CX, Kamboj P, et al.: The use of physical restraints- knowledge and attitude of nurses of a tertiary care institute, Uttarakhand, India. J. Educ. Health Promot. 2020 Mar 31; 9: 77. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCritical appraisal tools. JBI.[cited 2020Jul26].Reference Source\n\nCASP checklists - CASP - critical appraisal skills programme. CASP.[cited 2020 Jul 26].Reference Source\n\nHigginbottom GM, Richter MS, Mogale RS, et al.: Identification of nursing assessment models/tools validated in clinical practice for use with diverse ethno-cultural groups: an integrative review of the literature. BMC Nurs. 2011 Aug 3; 10: 16. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nWhittemore R, Knafl K: The integrative review: updated methodology. J. Adv. Nurs. 2005 Dec; 52(5): 546–553. Publisher Full Text\n\nCooper HM: Synthesizing research: A guide for literature reviews. Thousand Oaks, CA:Sage;2006.\n\nJiang H, Li C, Gu Y, et al.: Nurses’ perceptions and practice of physical restraint in China. Nurs. Ethics. 2015 Sep; 22(6): 652–660. PubMed Abstract \| Publisher Full Text\n\nHamilton D, Griesdale D, Mion LC: The prevalence and incidence of restraint use in a Canadian adult intensive care unit: A prospective cohort study. Can. J. Crit. Care Nurs. 2017; 28(3): 25–33.Reference Source\n\nvan der Kooi AW , Peelen LM, Raijmakers RJ, et al.: Use of physical restraints in Dutch intensive care units: a prospective multicenter study. Am. J. Crit. Care. 2015 Nov; 24(6): 488–495. PubMed Abstract \| Publisher Full Text\n\nLuk E, Sneyers B, Rose L, et al.: Predictors of physical restraint use in Canadian intensive care units. Crit. Care. 2014 Mar 24; 18(2): R46. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKandeel NA, Attia AK: Physical restraints practice in adult intensive care units in Egypt. Nurs. Health Sci. 2013 Mar; 15(1): 79–85. PubMed Abstract \| Publisher Full Text\n\nYönt GH, Korhan EA, Dizer B, et al.: Examination of ethical dilemmas experienced by adult intensive care unit nurses in physical restraint practices. Holist. Nurs. Pract. 2014 Mar-Apr; 28(2): 85–90. PubMed Abstract \| Publisher Full Text\n\nLangley G, Schmollgruber S, Egan A: Restraints in intensive care units--a mixed method study. Intensive Crit. Care Nurs. 2011 Apr; 27(2): 67–75. PubMed Abstract \| Publisher Full Text\n\nLuk E, Burry L, Rezaie S, et al.: Critical care nurses’ decisions regarding physical restraints in two Canadian ICUs: A prospective observational study. Can. J. Crit. Care Nurs. 2015 Winter; 26(4): 16–22. PubMed Abstract\n\nTurgay AS, Sari D, Genc RE: Physical restraint use in Turkish intensive care units. Clin. Nurse Spec. 2009 Mar-Apr; 23(2): 68–72. PubMed Abstract \| Publisher Full Text\n\nBenbenbishty J, Adam S, Endacott R: Physical restraint use in intensive care units across Europe: the PRICE study. Intensive Crit. Care Nurs. 2010 Oct; 26(5): 241–245. PubMed Abstract \| Publisher Full Text\n\nUnoki T, Sakuramoto H, Ouchi A, et al.: Physical restraints in intensive care units: a national questionnaire survey of physical restraint use for critically ill patients undergoing invasive mechanical ventilation in Japan. Acute Med. Surg. 2018 Dec 6; 6(1): 68–72. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nErtuğrul B, Özden D: The effect of physical restraint on neurovascular complications in intensive care units. Aust. Crit. Care. 2020 Jan; 33(1): 30–38. PubMed Abstract \| Publisher Full Text\n\nGuenette M, Burry L, Cheung A, et al.: Psychotropic Drug Use in Physically Restrained, Critically Ill Adults Receiving Mechanical Ventilation. Am. J. Crit. Care. 2017 Sep; 26(5): 380–387. PubMed Abstract \| Publisher Full Text\n\nDolan J, Dolan Looby SE: Determinants of Nurses’ Use of Physical Restraints in Surgical Intensive Care Unit Patients. Am. J. Crit. Care. 2017 Sep; 26(5): 373–379. Publisher Full Text\n\nHevener S, Rickabaugh B, Marsh T: Using a Decision Wheel to Reduce Use of Restraints in a Medical-Surgical Intensive Care Unit. Am. J. Crit. Care. 2016 Nov; 25(6): 479–486. PubMed Abstract \| Publisher Full Text\n\nSalehi Z, Najafi Ghezeljeh T, Hajibabaee F, et al.: Factors behind ethical dilemmas regarding physical restraint for critical care nurses. Nurs. Ethics. 2020 Mar; 27(2): 598–608. Publisher Full Text\n\nBalci H, Arslan S: Nurses’ Information, Attıtude and Practices towards Use of Physical Restraint in Intensive Care Units. J. Caring Sci. 2018 Jun 1; 7(2): 75–81. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nMitchell DA, Panchisin T, Seckel MA: Reducing Use of Restraints in Intensive Care Units: A Quality Improvement Project. Crit. Care Nurse. 2018 Aug; 38(4): e8–e16. PubMed Abstract \| Publisher Full Text\n\nHall DK, Zimbro KS, Maduro RS, et al.: Impact of a Restraint Management Bundle on Restraint Use in an Intensive Care Unit. J. Nurs. Care Qual. 2018 Apr/Jun; 33(2): 143–148. PubMed Abstract \| Publisher Full Text\n\nState Operations Manual Appendix A-Survey Protocol, Regulations and Interpretive Guidelines for Hospitals Transmittals for Appendix A.Cms.gov.2020. [cited 2021Dec18].Reference Source\n\nKavumpurath J, Mani KKC, Devaraj NK, et al.:Quality assessment checklist for publications to be considered for review - Adapted from JBI and CASP. [Dataset]. figshare. 2022.Publisher Full Text\n\nKavumpurath J, Mani KKC, Ahmed FR, et al.:Prisma checklist used for an integrative review. Dataset. figshare. 2022. Publisher Full Text" }	[ { "id": "161973", "date": "22 Feb 2023", "name": "Pei Boon Ooi", "expertise": [ "Reviewer Expertise As I work as a counsellor", "my area of expertise may not be directly involved with critical care which may serve as a limitation if this is a clinical study. However", "I have published a few systematic review papers." ], "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 listed a few aspects of physical restraints, which is a common procedure, in adult critical care units. The authors performed an integrative review which included comprehensively all research designs -i.e., quantitative, qualitative, mixed methodologies, and quality improvement projects. Twenty-one published articles were scrutinized according to the PRISMA protocols and the findings were evaluated and summarized into seven key topics which are insightful for future researchers to consider when it comes to adult critical care. These themes, especially the high prevalence of PR application in the adult critical care unit and the determinants of PR applications will be useful for consideration when it comes to the use of PRs in the adult critical care units. Additionally, the other important but often times silent aspects such as the moral and ethical dilemma, awareness and guidelines for PR applications were also identified and discussed. Most importantly, this integrative review underlined the lack of research on patients’ experiences with restraint throughout their ICU admission.\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": "247584", "date": "06 Mar 2024", "name": "Ziad Alostaz", "expertise": [ "Reviewer Expertise Physical restraint use in ICUs." ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.\n\nNot approved Fundamental flaws in the paper seriously undermine the findings and conclusions\n\nThank you for the opportunity to review this manuscript. The aim of this integrative review was to examine recent evidence on the use of physical restraints (PR) in adult critical care. This is an important topic, and while I appreciate the work conducted, I wonder about the novelty of the study, i.e., what does this review add to the literature? Are the methods/findings of this study novel? How do the findings of this review differ, expand, or complement the findings of the following reviews: Perez D, et. al. 2019 (ref 1), Alostaz Z, et. al. 2022 (ref 2). The rationale for and objective of the review is stated, but I would recommend more consistency. For example, while the abstract states the aim is to \"examine the recent evidence on the use of PR in adult critical care,\" the body of the manuscript states that \"with the use of the following questions, this review will look into the best available evidence on the use of PR in adult critical care in regard to: 1) prevalence of PR; 2) factors that influence PR; 3) the role the nurse plays in the implementation of PR; 4) the nurse’s experience caring for the patient with PR; and 5) the complications of applying PR.\" Furthermore, under the search methods, it was stated that \"the goal of this study is to conduct a thorough assessment of the available evidence on PR in the adult critical care unit.\" Please note that there were no questions reported to support the sentence \"with the use of the following questions.\" More details are needed to allow the replication of this review. For example, it would be helpful to provide the full search strategy for one of the databases (e.g., Medline). In the section discussing exclusion criteria, it appears that researchers primarily outlined how they limited the search rather than explicit criteria for excluding studies from the review. To enhance the reproducibility of this review, I recommend explicitly stating the predetermined criteria for exclusion. For example, exclusion of chemical restraints studies, studies conducted in any other setting outside ICUs, previous literature reviews, editorials, and conference abstracts, etc. Finally, I would recommend a review of the grammar used in the article as there was a mix-up of tenses (present, past, future). For example, under the aim it says \"this review will look into...\". Past tense should be used here, and there are many instances throughout.\n\nAre the rationale for, and objectives of, the Systematic Review clearly stated? Partly\n\nAre sufficient details of the methods and analysis provided to allow replication by others? Partly\n\nIs the statistical analysis and its interpretation appropriate? Not applicable\n\nAre the conclusions drawn adequately supported by the results presented in the review? Yes", "responses": [] } ]	1	https://f1000research.com/articles/12-114
https://f1000research.com/articles/12-918/v1	01 Aug 23	{ "type": "Brief Report", "title": "Mutational profile of primary clear cell renal cell carcinoma predicts recurrence and potential candidacy for adjuvant immune checkpoint inhibition", "authors": [ "Panagiotis J. Vlachostergios", "Maria Papathanassiou", "Maria Anagnostou", "Eleni Thodou", "Ioannis Tamposis", "Lampros Mitrakas", "Ioannis Zachos", "Maria Ioannou", "George K. Koukoulis", "Maria Samara", "Vassilios Tzortzis", "Maria Papathanassiou", "Maria Anagnostou", "Eleni Thodou", "Ioannis Tamposis", "Lampros Mitrakas", "Ioannis Zachos", "Maria Ioannou", "George K. Koukoulis", "Maria Samara", "Vassilios Tzortzis" ], "abstract": "Background: The risk of recurrence after nephrectomy for primary clear cell renal cell carcinoma (ccRCC) is estimated in daily practice solely based on clinical criteria. The aim of this study was to assess the prognostic relevance of common somatic mutations with respect to tumor aggressiveness and outcomes of ccRCC patients after definitive treatment. Methods: Primary tumors from 37 patients with ccRCC who underwent radical nephrectomy were analyzed for presence of somatic mutations using a 15-gene targeted next-generation sequencing (NGS) panel. Associations to histopathologic characteristics and outcomes were investigated in the study cohort (n=37) and validated in The Cancer Genome Atlas (TCGA) ccRCC cohort (n=451). Results: VHL was the most frequently mutated gene (51%), followed by PBRM1 (27%), BAP1 (13%), SETD2 (13%), KDM5C (5%), ATM (5%), MTOR (5%), and PTEN (3%). One-third of patients did not have any somatic mutations within the 15-gene panel. The vast majority of tumors harboring no mutations at all or VHL-only mutations (51%) were more frequently of smaller size (pT1-2) and earlier stage (I/II), whereas presence of any other gene mutations in various combinations with or without VHL was enriched in larger (pT3) and higher stage tumors (III) (p=0.02). No recurrences were noted in patients with unmutated tumors or VHL-only mutations as opposed to three relapses in patients with non-VHL somatic mutations (p=0.06). Presence of somatic mutations in PBRM1, BAP1, SETD2, KDM5C, ATM, MTOR, or PTEN genes in 451 TCGA ccRCC patients was associated with a significantly shorter disease-free survival (DFS) compared to those with unaltered tumors (q=0.01). Conclusions: Preliminary findings from this ongoing study support the prognostic value of non-VHL mutations including PBRM1, BAP1, SETD2, KDM5C, ATM, MTOR, and PTEN in primary ccRCC tumors as surrogates of earlier recurrence and potential selection for adjuvant immune checkpoint inhibition.", "keywords": [ "clear cell", "kidney cancer", "renal cell carcinoma", "recurrence", "immune checkpoint inhibition", "genomics", "mutational profile", "next generation sequencing" ], "content": "Introduction\n\nRenal cell carcinoma (RCC) is a heterogenous group of kidney cancers originating from the nephron.1 Renal cell carcinoma ranks among the ten most frequently diagnosed malignancies worldwide, with an estimated 400.000 new diagnoses and more than 170.000 deaths annually.2,3 Clear cell RCC (ccRCC) is the most common RCC subtype, accounting for about 70-75% of cases and has a distinct molecular profile.1,4\n\nLocalized ccRCC is treated with surgical resection, either partial or radical nephrectomy. Nevertheless, one-third of these patients experience recurrence.5 So far, ccRCC recurrence, disease progression and mortality are being predicted using clinicopathological criteria.6 While various recurrence models have been proposed, they only marginally outperformed standard staging.7 Further, they demonstrate statistically significant variability in their predictive ability over time, rendering implementation into clinical practice and clinical trial design challenging.7\n\nImmune checkpoint inhibition with the use of pembrolizumab, a monoclonal antibody against programmed death-1 (PD-1), is approved as adjuvant therapy for patients with resected ccRCC who have a high risk of recurrence.8 This was based on results of a phase III randomized double-blind study comparing pembrolizumab with placebo, which demonstrated a significant improvement in disease-free survival (DFS).9 Patient selection criteria for a high risk of recurrence included tumor stage II with nuclear grade 4 or sarcomatoid differentiation, tumor stage III or higher, regional lymph-node metastasis, or stage M1 without evidence of disease after combined nephrectomy and metastasectomy either concurrently or within a year from primary tumor resection.9\n\nWhat currently remains an unmet need is the ability to predict which patients with ccRCC will relapse using a single or composite molecular biomarker that would be more directly related with tumor biology.\n\nIn this ongoing prospective study, we examined the mutational profile of patients with non-metastatic ccRCC who underwent nephrectomy, followed by observation or adjuvant immunotherapy with pembrolizumab depending on established clinical and histopathological criteria. We studied associations of mutated genes with high-risk features and assessed the prognostic relevance of somatic mutations with regard to DFS after nephrectomy with or without adjuvant immunotherapy.\n\n\nMethods\n\nThe study was conducted in accordance with the Declaration of Helsinki and approved by the Institutional Review Board and Ethics Committee of Faculty of Medicine, University of Thessaly (3214/29.07.2016) on 29 July 2016.\n\nThis was a prospective single-center cohort study of patients with a diagnosis of ccRCC who underwent radical nephrectomy followed by observation or adjuvant immune checkpoint inhibition with pembrolizumab at the University Hospital of Larissa between December 2020 and February 2023. Eligible subjects included patients of ≥18 years of age, with histologically confirmed non-metastatic ccRCC, without prior systemic therapy for RCC. Patients were eligible if they had an intermediate-to-high or high risk of recurrence based on histopathological features including pT2 with grade 4 or sarcomatoid differentiation, pT3 or pT4 with any grade, or any pT and grade with presence of positive lymph nodes (N+). Subjects unable to provide consent, those with low risk of recurrence or subjects receiving steroids at a daily dose above 10mg of prednisone for an active autoimmune or other condition were excluded from the study. The primary endpoint of the study was the percentage of patients without disease recurrence.\n\nFresh frozen tissue samples were acquired from patients. Tumor tissue was acquired after surgical resection, cut in 5 mg cubes and stored in stabilization solution (RNA later, Thermo Fisher Scientific) at -80oC freezer, after written informed consent was obtained. DNA extraction and quantification was performed from 5 mg of fresh-frozen tissue. Library preparation was conducted with the use of DNA AmpliSeq for Ion Torrent, with an input of 40 ng DNA per sample. Sample libraries were quantified with the use of Qubit (Thermo-Fisher Scientific) and real-time polymerase chain reaction (PCR), then sequenced on Ion Torrent S5 sequencer, using the Oncomine Kidney panel (Thermo-Fisher Scientific). Library amplification was conducted using the Library PLUS for Ion Torrent kit (Thermo Fisher). Library amplification included enzyme activation at 99oC for 2 minutes, 16 cycles of denaturation at 99oC for 15 seconds and annealing and extension steps at 60oC for 4 minutes and a final hold step at 10oC. The commercially available OncomineTM Kidney Panel (Thermo Fisher Scientific) provided the primer pairs used for library preparation. qPCR was conducted using the Ion Universal Library Quantitation Kit (Thermo Fisher Scientific). qPCR steps include an initial step of incubation at 50oC for 2 minutes, a polymerase activation step at 95oC for 2 minutes, 40 cycles of 95oC for 15 seconds and 60oC for 1 minute and a final hold step at 10oC.10\n\nClinicopathological characteristics recorded for the analysis included patient age, sex, ISUP grade, tumor diameter, T-stage, presence of vascular invasion, presence of sarcomatoid differentiation, presence of necrosis, AJCC stage, and emergence of recurrent disease during follow up. Nephrectomy surgical specimens were reviewed by two independent pathologists from our institution.\n\nA publicly available database, cBioportal for Cancer Genomics (accessed on 24 May 2023), was used to query DNA sequencing data for mutations in a prospective multicenter cohort from The Cancer Genome Atlas (TCGA) including 451 patients with ccRCC (accessed on 24 May 2023).\n\nThe following genes were analyzed for presence of somatic mutations: ATM, BAP1, KDM5C, MET, MTOR, NF2, PBRM1, PIK3CA, PTEN, SETD2, SMARCB1, TP53, TSC1, TSC2, and VHL. Variant calling was performed using the Ion Reporter Software (Thermo-Fisher Scientific). The Pearson’s Chi squared test was used to determine whether there was a statistically significant difference in clinicopathological characteristics and emergence of recurrence between subgroups of patients with distinct mutational profiles (unmutated or VHL-only mutated versus other gene mutations). Time-to-event outcomes (DFS) were estimated using the Kaplan-Meier method. Multiple hypothesis test correction was applied using the Benjamini–Hochberg method. All tests were two-sided, and p and q values ≤0.05 were considered statistically significant. The IBM SPSS v.22 software was used for the analysis.\n\n\nResults\n\nWe first assessed the frequency of mutations in primary ccRCC tumors. In the discovery cohort (n=37), patients’ clinical and histopathological characteristics are described in Table 1. VHL was the most frequently mutated gene (n=19; 51%), followed by PBRM1 (n=10; 27%), BAP1 (n=5; 13%), SETD2 (n=5; 13%), KDM5C (n=2, 5%), ATM (n=2, 5%), MTOR (n=2, 5%), and PTEN (n=1, 3%) (Table 2). Variant types per gene are listed in the data file.23 11 patients (30%) did not have any somatic mutations within the 15-gene targeted panel.\n\nTumors harboring no mutations at all or only VHL mutations (n=19, 51%) were associated with smaller size (pT1-2 n=17, 89%) and earlier stage (I/II n=17; 89%), whereas presence of any other gene mutations in various combinations with or without VHL was enriched in larger (pT3, n=8; 44%; p=0.02) and more advanced tumors (III, n=8; 44%; p=0.02) (Table 3). There was also a trend towards higher frequency of ISUP grade, vascular invasion, and necrosis in these tumors (Table 3).\n\nIn the validation TCGA cohort (n=451), similar mutations frequencies were noted, including VHL in 50% of patients/samples, PBRRM1 in 29%, SETD2 in 11%, BAP1 in 9%, MTOR in 7%, KDM5C in 6%, PTEN in 4%, and ATM in 2.7%, respectively (Figure 1). Larger and higher stage tumors, particularly T3a, T3b, and stage III tended to have a higher frequency of non-VHL mutations (p=0.282; q=0.437) (Figure 2).\n\nNo recurrences were noted in patients with unmutated tumors or VHL-only mutations whereas three patients (17%) with other somatic mutations relapsed (p=0.06) (Table 4). Another three patients received and completed adjuvant PD-1 inhibition with pembrolizumab until present, none of whom recurred despite the presence of PBRM1 and SETD2 mutations in 2/3 and 1/3, respectively. Presence of somatic mutations in PBRM1, BAP1, SETD2, KDM5C, ATM, MTOR, or PTEN genes in 451 TCGA ccRCC patients was associated with a significantly shorter DFS compared to those with unaltered tumors (p<0.001; q=0.01) (Figure 3).\n\n\nDiscussion\n\nThis ongoing prospective study examined the mutational profile of patients with ccRCC on primary tumors after nephrectomy followed by observation or adjuvant immunotherapy with pembrolizumab and assessed for associations of mutated genes with high-risk features and DFS. In this preliminary analysis of the first 37 patients, non-VHL mutations, including mutations in PBRM1, SETD2, BAP1, KDM5C, MTOR, PTEN, or ATM genes in a targeted 15-gene NGS panel were significantly associated with more aggressive histopathological characteristics including larger size, and higher stage. Presence of mutations in any of those genes as opposed to completely unmutated or VHL-only mutated tumors was also associated with higher ISUP grade, necrosis, sarcomatoid differentiation, vascular invasion and predicted recurrence. In ccRCC tumors from TCGA, non-VHL mutations in the same genes were also associated with high-risk features and predicted a significantly shorter DFS compared to VHL-only mutations or complete absence thereof.\n\nThe tumor suppressor VHL is the most frequently mutated gene in ccRCC and is a major player in renal cell carcinogenesis. However, VHL mutations alone are insufficient to drive disease progression.11 Mounting evidence has revealed an emerging role of other genes, heavily involved in chromatin rearrangement and epigenetic DNA modifications, including PBRM1, SETD2, BAP1, and KDM5C in ccRCC progression.12,13 Inactivating mutations or/and low expression of these genes in primary renal tumors have been associated with poor outcomes.14–20\n\nDue to the retrospective nature of these studies and lack of reproducibility, particularly across immunohistochemical assessments21,22 in an era when observation was the only available modality post-operatively even in high-risk patients, there has been a paucity of data to support testing of these genes as a molecular tool to assist in selection of patients who might benefit from adjuvant therapy.\n\nOur ongoing prospective study addresses this gap by demonstrating that patients who had either no mutation or mutations in the most frequently altered gene, VHL, were more likely to have smaller tumors and experienced a more benign course without relapse, compared to those patients with tumors that harbored mutations in other genes, including PBRM1, BAP1, SETD2, KDM5C, ATM, MTOR, or PTEN. Thus, this study suggests that patients with mutations in these high-risk genes might be more suitable candidates and should be prioritized for post-operative immunotherapy.\n\nOur study was limited by small size and relatively short follow-up of patients. Nevertheless, presence of an early “signal” of high-risk genes in this preliminary report will be further studied in additional patients being accrued as part of this ongoing prospective study.", "appendix": "Data availability\n\nfigshare: F1000Res_Vlachostergios et al_raw data (subm).xlsx. https://doi.org/10.6084/m9.figshare.23697252.v1. 23\n\nData are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).\n\nData from the validation TCGA cohort analyzed in this study are available from cbioportal.org, http://www.cbioportal.org/study/summary?id=kirc_tcga.\n\n\nReferences\n\nShuch B, Amin A, Armstrong AJ, et al.: Under-standing pathologic variants of renal cell carcinoma: distilling therapeutic opportunities from biologic complexity. Eur. Urol. 2015; 67: 85–97. PubMed Abstract \| Publisher Full Text\n\nHsieh JJ, Purdue MP, Signoretti S, et al.: Renal cell carcinoma. Nat. Rev. Dis. Primers. 2017; 3: 17009. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nBray F, Ferlay J, Soerjomataram I, et al.: Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J. Clin. 2018; 68: 394–424. PubMed Abstract \| Publisher Full Text\n\nCancer Genome Atlas Research Network: Comprehensive molecular characterization of clear cell renal cell carcinoma. Nature. 2013; 499: 43–49. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLi Y, Lih TM, Dhanasekaran SM, et al.: Clinical Proteomic Tumor Analysis Consor-tium. Histopathologic and proteogenomic heterogeneity reveals features of clear cell renal cell carcinoma aggressiveness. Cancer Cell. 2023; 41: 139–163.e17. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLeibovich BC, Blute ML, Cheville JC, et al.: Prediction of progression after radical nephrectomy for patients with clear cell renal cell carcinoma: a stratification tool for prospective clinical trials. Cancer. 2003; 97: 1663–1671. Publisher Full Text\n\nCorrea AF, Jegede O, Haas NB, et al.: Predicting Renal Cancer Recurrence: Defining Limitations of Existing Prognostic Models With Prospective Trial-Based Validation. J. Clin. Oncol. 2019; 37: 2062–2071. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nCosso F, Roviello G, Nesi G, et al.: Adjuvant Therapy for Renal Cell Carcinoma: Hype or Hope? Int. J. Mol. Sci. 2023; 24: 4243. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nChoueiri TK, Tomczak P, Park SH, et al.: Adjuvant Pembrolizumab after Nephrectomy in Renal-Cell Carcinoma. N. Engl. J. Med. 2021; 385: 683–694. Publisher Full Text\n\nPapathanassiou M, Vlachostergios P: DNA library preparation for Ion Torrent S5 sequencing.Publisher Full Text\n\nRicketts CJ, De Cubas AA, Fan H, et al.: The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma. Cell Rep. 2018; 23: 313–326.e5. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nde Cubas AA , Rathmell WK: Epigenetic modifiers: activities in renal cell carcinoma. Nat. Rev. Urol. 2018; 15: 599–614. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nPeña-Llopis S, Vega-Rubín-de-Celis S, Liao A, et al.: BAP1 loss defines a new class of renal cell carcinoma. Nat. Genet. 2012; 44: 751–759. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nHakimi AA, Ostrovnaya I, Reva B, et al.: Adverse outcomes in clear cell renal cell carcinoma with mutations of 3p21 epigenetic regulators BAP1 and SETD2: a report by MSKCC and the KIRC TCGA research network. Clin. Cancer Res. 2013; 19: 3259–3267. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nJoseph RW, Kapur P, Serie DJ, et al.: Clear Cell Renal Cell Carcinoma Subtypes Identified by BAP1 and PBRM1 Expression. J. Urol. 2016; 195: 180–187. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nKapur P, Peña-Llopis S, Christie A, et al.: Effects on survival of BAP1 and PBRM1 mutations in sporadic clear-cell renal-cell carcinoma: a retrospective analysis with independent validation. Lancet Oncol. 2013; 14: 159–167. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nLiu W, Fu Q, An H, et al.: Decreased Expression of SETD2 Predicts Unfavorable Prognosis in Patients With Nonmetastatic Clear-Cell Renal Cell Carcinoma. Medicine (Baltimore). 2015; 94: e2004. Publisher Full Text\n\nOhsugi H, Yoshida T, Ohe C, et al.: The SSPN Score, a Novel Scoring System Incorporating PBRM1 Expression, Predicts Postoperative Recurrence for Patients with Non-metastatic Clear Cell Renal Cell Carcinoma. Ann. Surg. Oncol. 2021; 28: 2359–2366. PubMed Abstract \| Publisher Full Text\n\nda Costa WH , Rezende M, Carneiro FC, et al.: Polybromo-1 (PBRM1), a SWI/SNF complex subunit is a prognostic marker in clear cell renal cell carcinoma. BJU Int. 2014; 113: E157–E163. PubMed Abstract \| Publisher Full Text\n\nSantos VE, da Costa WH , Bezerra SM, et al.: Prognostic Impact of Loss of SETD2 in Clear Cell Renal Cell Carcinoma. Clin. Genitourin. Cancer. 2021; 19: 339–345. PubMed Abstract \| Publisher Full Text\n\nKim SH, Park WS, Park EY, et al.: The prognostic value of BAP1, PBRM1, pS6, PTEN, TGase2, PD-L1, CA9, PSMA, and Ki-67 tissue markers in localized renal cell carcinoma: A retrospective study of tissue microarrays using immunohistochemistry. PLoS One. 2017; 12: e0179610. PubMed Abstract \| Publisher Full Text \| Free Full Text\n\nNishikawa M, Miyake H, Harada K, et al.: Expression of molecular markers associated with the mammalian target of rapamycin pathway in nonmetastatic renal cell carcinoma: Effect on prognostic outcomes following radical nephrectomy. Urol. Oncol. 2014; 32(49): 49.e15–49.e21. PubMed Abstract \| Publisher Full Text\n\nVlachostergios PJ: F1000Res_Vlachostergios et al_raw data (subm).xlsx. figshare. Figure. 2023. Publisher Full Text" }	[ { "id": "192983", "date": "22 Aug 2023", "name": "Konstantinos Kamposioras", "expertise": [ "Reviewer Expertise Medical Oncology", "Clinical biomarkers" ], "suggestion": "Approved With Reservations", "report": "Approved With Reservations\n\ninfo_outline\nAlongside their report, reviewers assign a status to the article:\n\nApproved The paper is scientifically sound in its current form and only minor, if any, improvements are suggested\n\nApproved with reservations\nA number of small changes, sometimes more significant revisions are required to 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 to congratulate the authors on their excellent work. However, there are a few points that need further explanation.\nThe authors evaluated a number of genes in relation to clinical outcomes in a small number of cases.\nI would like to see the authors explain the biological rationale behind the two different molecular signatures and how this might relate to immunotherapy response, as suggested in the Discussion section.\n\nI would also like to know how this study compares with previously published reports and if there is any consistency in the literature with regard to their findings.\nHow do the authors see these findings changing or guiding clinical practice?\n\nIs the work clearly and accurately presented and does it cite the current literature? Yes\n\nIs the study design appropriate and is the work technically sound? Yes\n\nAre sufficient details of methods and analysis provided to allow replication by others? Yes\n\nIf applicable, is the statistical analysis and its interpretation appropriate? Yes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "11248", "date": "14 Jun 2024", "name": "Panagiotis J. Vlachostergios", "role": "Author Response", "response": "Reviewer 1 I would like to congratulate the authors on their excellent work. However, there are a few points that need further explanation. The authors evaluated a number of genes in relation to clinical outcomes in a small number of cases. 1. I would like to see the authors explain the biological rationale behind the two different molecular signatures and how this might relate to immunotherapy response, as suggested in the Discussion section. Response: We appreciate the Reviewer’s comment. We have added a detailed discussion on the biological rationale of our study and how the selected genes may relate to response to immune checkpoint inhibition, as follows: “Cancer is a disease caused by the accumulation of genomic alterations.11 This is a multistep process during which certain somatic mutations confer a survival advantage by activating signaling pathways that are associated with several hallmarks of cancer, including proliferative signaling, evasion of growth suppression, resistance to cell death, replicative immortality, angiogenesis, invasion and metastasis, reprogramming of energy metabolism and evasion of immune recognition and destruction.12 Since these biological principles apply to the majority of solid tumors, including RCCs, we hypothesized that the higher the number of pathogenic mutations within a primary renal tumor, the more aggressive clinical behavior could be observed. The tumor suppressor VHL is the most frequently mutated gene in ccRCC and is a major player in renal cell carcinogenesis. However, VHL mutations alone are insufficient to drive disease progression, and have no prognostic or predictive value. 13,14 Mounting evidence has revealed an emerging role of other genes, heavily involved in chromatin rearrangement and epigenetic DNA modifications, including PBRM1, SETD2, BAP1, and KDM5C in ccRCC progression. 15 , 16 Inactivating mutations or/and low expression of these genes in primary renal tumors have been associated with poor outcomes. 17 – 23 Interestingly, many of these frequently non-VHL genes, including PBRM1, BAP1, SETD2, have been investigated in the metastatic setting as potential predictors of response or resistance to immune checkpoint inhibitors (ICIs). For example, mutated PBRM1 was included in a composite biomarker together with tumor infiltrating lymphocytes (TILs) and absence of necrosis predicting a favorable response to ICIs.24,25 Likewise, SETD2 loss results in greater vulnerability to immune checkpoint blockade compared to SETD2-proficient tumors, in vitro and in vivo.26 BAP1-mutated tumors, while they portend a worse prognosis, they are more likely to be PD-L1 positive and demonstrate a more inflamed immune microenvironment suggesting that immune-targeting approaches could benefit these patients.27 Another DNA damage response and repair gene, ATM, was the second most frequently altered gene in ICI-responders with advanced RCC.28 Pancancer analyses of tumors from ICI-treated patients suggested that those with KDM5C alterations have a substantially higher tumor mutational burden (TMB) level and a significantly higher level of CD8+ T cell infiltration and T effector signature which were associated with prolonged OS compared to the wild-type group.29 Expression of PTEN/PI3K/mTOR pathway genes was significantly associated with numerous immune cells and immune-evasive mediators such as CD274/PD-L1, TGFBR1, CSF1R and PDCD1 in patients with ccRCC,30 suggesting that alterations in this pathway could also play a role in shaping these patients’ outcomes after treatment with ICIs. Our ongoing prospective study examined the mutational profile of patients with ccRCC on primary tumors after nephrectomy followed by observation or adjuvant immunotherapy with pembrolizumab and assessed for associations of mutated genes with high-risk features and DFS. We hypothesized that primary RCC tumors either umutated or harboring VHL mutations might be associated with a more benign clinical course after nephrectomy compared to those with a burden of mutations in other, non-VHL genes.“ References (new): 11. Meyerson M, Gabriel S, Getz G: Advances in understanding cancer genomes through second-generation sequencing. Nat Rev Genet. 2010;11:685-696. 10.1038/nrg2841 12. Hanahan D, Weinberg RA: Hallmarks of cancer: the next generation. Cell. 2011; 144:646-674. 10.1016/j.cell.2011.02.013. 14. Kim BJ, Kim JH, Kim HS, Zang DY: Prognostic and predictive value of VHL gene alteration in renal cell carcinoma: a meta-analysis and review. Oncotarget. 2017;8:13979-13985. 10.18632/oncotarget.14704. PMC5355155. 24. Deutsch JS, Lipson EJ, Danilova L, et al: Combinatorial biomarker for predicting outcomes to anti-PD-1 therapy in patients with metastatic clear cell renal cell carcinoma. Cell Rep Med. 2023; 4:100947. 10.1016/j.xcrm.2023.100947. PMC9975323. 25. Wang N, Qin Y, Du F, Wang X, Song C: Prevalence of SWI/SNF genomic alterations in cancer and association with the response to immune checkpoint inhibitors: A systematic review and meta-analysis. Gene. 2022; 834:146638. 10.1016/j.gene.2022.146638. 26. Liu XD, Zhang YT, McGrail DJ, et al: SETD2 Loss and ATR Inhibition Synergize to Promote cGAS Signaling and Immunotherapy Response in Renal Cell Carcinoma. Clin Cancer Res. 2023; 29:4002-4015. 10.1158/1078-0432.CCR-23-1003. PMC10592192. 27. Kapur P, Rajaram S, Brugarolas J. The expanding role of BAP1 in clear cell renal cell carcinoma. Hum Pathol. 2023; 133:22-31. 10.1016/j.humpath.2022.07.022. PMC9898467. 28. Ged Y, Chaim JL, DiNatale RG, et al: DNA damage repair pathway alterations in metastatic clear cell renal cell carcinoma and implications on systemic therapy. J Immunother Cancer. 2020;8:e000230. 10.1136/jitc-2019-000230. PMC7311069. 29. Chen XJ, Ren AQ, Zheng L, Zheng ED: Predictive Value of KDM5C Alterations for Immune Checkpoint Inhibitors Treatment Outcomes in Patients With Cancer. Front Immunol. 2021;12:664847. 10.3389/fimmu.2021.664847. PMC8089485. 30. Li N, Chen J, Liu Q, et al: Prognostic significance and tumor-immune infiltration of mTOR in clear cell renal cell carcinoma. PeerJ. 2021;9:e11901. 10.7717/peerj.11901. PMC8378334. 2. I would also like to know how this study compares with previously published reports and if there is any consistency in the literature with regard to their findings. Response: We have added relevant literature that is in concordance with our study findings, as follows: “Our findings are in line with a previous work with slightly different design, whereby primary RCC tumors were segregated into VHL+0, VHL+1, VHL+2, and VHL+≥3 mutations.33 In both the discovery and validation cohorts of the study, those patients with a VHL+0 tumor had longer 5-year DFS and were proposed as candidates for surveillance. Conversely, patients with VHL+2 and VHL+≥3 tumors experienced shorter DFS rates of less than 50% and were deemed candidates for adjuvant therapy.33” Reference (new): 33. Vasudev NS, Scelo G, Glennon KI, et al: Application of Genomic Sequencing to Refine Patient Stratification for Adjuvant Therapy in Renal Cell Carcinoma. Clin Cancer Res. 2023;29:1220-1231. 10.1158/1078-0432.CCR-22-1936. PMC10068441. 3. How do the authors see these findings changing or guiding clinical practice? Response: We have now added a paragraph discussing the potential implications of our study for changing or guiding clinical practice, as follows: ”Collectively, our study combined with emerging evidence on the genomic landscape of RCC might open new avenues for both prognostication and better selection of a subgroup of patients with RCC that could benefit from adjuvant anti-PD1 immunotherapy.”" } ] }, { "id": "228073", "date": "09 Mar 2024", "name": "Athanasia Pavlopoulou", "expertise": [ "Reviewer Expertise Molecular Biology", "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 conducted a study of the molecular profile of RCC primary tumors in a small cohort of patients and examined whether particular gene mutations were associated with clinicopathological characteristics and outcomes of patients during a short follow up period. The following points need to be clarified:\n- how do the specific genes examined in this study relate to RCC prognosis in the literature? - the lack of transcriptional or epigenetic analyses should be discussed as a limitation 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? Yes\n\nAre all the source data underlying the results available to ensure full reproducibility? Yes\n\nAre the conclusions drawn adequately supported by the results? Yes", "responses": [ { "c_id": "11249", "date": "14 Jun 2024", "name": "Panagiotis J. Vlachostergios", "role": "Author Response", "response": "Reviewer 2 The authors conducted a study of the molecular profile of RCC primary tumors in a small cohort of patients and examined whether particular gene mutations were associated with clinicopathological characteristics and outcomes of patients during a short follow up period. The following points need to be clarified: 1. How do the specific genes examined in this study relate to RCC prognosis in the literature? Response: We appreciate the Reviewer’s comment. We have indicated in the Discussion section that: ”Inactivating mutations or/and low expression of these genes in primary renal tumors have been associated with poor outcomes. 14 – 20” 2. The lack of transcriptional or epigenetic analyses should be discussed as a limitation of the study. Response: We appreciate the Reviewer’s comment. We have now discussed the lack of transcriptional or/and epigenetic analyses as a limitation of our study, in the Discussion section. All edits in the revised manuscript are highlighted with ”Track changes” tool of MS Word." } ] } ]	1	https://f1000research.com/articles/12-918

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